xszheng2020/the_stack_dedup_python_hits_6 · Datasets at Hugging Face

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Python

app/h5/views/__init__.py

by46/coffee

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[ "MIT" ]

null

app/h5/views/__init__.py

by46/coffee

f12e1e95f12da7e322a432a6386a1147c5549c3b

[ "MIT" ]

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app/h5/views/__init__.py

by46/coffee

f12e1e95f12da7e322a432a6386a1147c5549c3b

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from . import editor

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Python

shhh/views/__init__.py

olaoladapo/shhh

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[ "MIT" ]

243

2019-09-17T23:29:38.000Z

2022-03-29T07:29:36.000Z

shhh/views/__init__.py

olaoladapo/shhh

f02fb875559342a118963c22d28dd867e3be282d

[ "MIT" ]

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2019-09-18T12:52:18.000Z

2022-03-31T16:07:15.000Z

shhh/views/__init__.py

shiitakepl/shhh

54fc69ae741a7309d8ba996200fe6fd40b0345eb

[ "MIT" ]

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2019-09-18T12:59:01.000Z

2022-03-25T16:42:09.000Z

from .views import views

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Python

csrank/dataset_reader/__init__.py

helegraf/cs-ranking

a635d59a254e7d4cad06c3e04f7593392e0b9cec

[ "Apache-2.0" ]

null

csrank/dataset_reader/__init__.py

helegraf/cs-ranking

a635d59a254e7d4cad06c3e04f7593392e0b9cec

[ "Apache-2.0" ]

null

csrank/dataset_reader/__init__.py

helegraf/cs-ranking

a635d59a254e7d4cad06c3e04f7593392e0b9cec

[ "Apache-2.0" ]

null

from .choicefunctions import * from .discretechoice import * from .dyadranking import * from .expedia_dataset_reader import ExpediaDatasetReader from .labelranking import * from .objectranking import * from .synthetic_dataset_generator import SyntheticIterator

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Python

tests/test_group_resource.py

akebrissman/gateway

84f8093af854418f64175dd499c021b6d71f85d2

[ "MIT" ]

null

tests/test_group_resource.py

akebrissman/gateway

84f8093af854418f64175dd499c021b6d71f85d2

[ "MIT" ]

2

2019-10-25T18:58:18.000Z

2019-11-16T13:10:38.000Z

tests/test_group_resource.py

akebrissman/gateway

84f8093af854418f64175dd499c021b6d71f85d2

[ "MIT" ]

2

2019-10-17T09:06:09.000Z

2019-10-18T10:09:13.000Z

def test_get_group_no_match(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.get(api, headers=headers) assert response.status_code == 404 assert response.is_json is True def test_put_new_group(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} body = '{ "url": "URL New", "name": "123456789012345" }' response = test_client.put(api, headers=headers, data=body) assert response.status_code == 200 assert response.is_json is True def test_put_same_group(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} body = '{ "url": "URL Update", "name": "123456789012345" }' response = test_client.put(api, headers=headers, data=body) assert response.status_code == 200 assert response.is_json is True def test_get_group(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.get(api, headers=headers) assert response.status_code == 200 assert response.is_json is True def test_post_group(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} body = '{ "url": "URL 30", "name": "123456789012346" }' response = test_client.post(api, headers=headers, data=body) assert response.status_code == 201 assert response.is_json is True def test_post_same_group(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} body = '{ "url": "URL 30", "name": "123456789012346" }' response = test_client.post(api, headers=headers, data=body) assert response.status_code == 409 assert response.is_json is True def test_get_all_groups(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.get(api, headers=headers) assert response.status_code == 200 assert response.is_json is True def test_delete_group(test_client): api = 'api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.delete(api, headers=headers) assert response.status_code == 200 assert response.is_json is True def test_delete_same_group(test_client): api = 'api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.delete(api, headers=headers) assert response.status_code == 200 assert response.is_json is True def test_get_groups_no_match_(test_client): api = 'api/group/123456789012345' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.get(api, headers=headers) assert response.status_code == 404 assert response.is_json is True def test_get_all_group_no_bearer(test_client): api = '/api/group' headers = {'content-type': 'application/json'} response = test_client.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header is expected" def test_get_group_no_bearer(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json'} response = test_client.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header is expected" def test_put_group_no_bearer(test_client): api = '/api/group/123456789012345' headers = {'content-type': 'application/json'} body = '{ "name": "123456789012345", "group": "Group New" }' response = test_client.put(api, headers=headers, data=body) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header is expected" def test_post_group_no_bearer(test_client): api = '/api/group' headers = {'content-type': 'application/json'} body = '{ "url": "URL 30", "name": "123456789012346" }' response = test_client.post(api, headers=headers, data=body) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header is expected" def test_delete_group_no_bearer(test_client): api = 'api/group/123456789012345' headers = {'content-type': 'application/json'} response = test_client.delete(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header is expected" def test_get_all_group_invalid_bearer_name(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': 'NoBearer 123'} response = test_client.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header must be a Bearer token" def test_get_all_group_invalid_bearer_one_part(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': 'Bearer'} response = test_client.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Token not found" def test_get_all_group_invalid_bearer_three_parts(test_client): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': 'Bearer 123 Bearer'} response = test_client.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Authorization header must be a valid Bearer token" def test_get_all_group_invalid_pub_key_in_token(test_client): import os pub_key = os.getenv("AUTH_PUBLIC_KEY") os.environ["AUTH_PUBLIC_KEY"] = "ABC" api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client.application.bearer} response = test_client.get(api, headers=headers) os.environ["AUTH_PUBLIC_KEY"] = pub_key assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Unable to parse authentication token" def test_get_all_group_expired_token(test_client_expired_token): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client_expired_token.application.bearer} response = test_client_expired_token.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Token is expired" def test_get_all_group_missing_kid_in_token(test_client_missing_kid_in_token): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client_missing_kid_in_token.application.bearer} response = test_client_missing_kid_in_token.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "No kid found in token" def test_get_all_group_invalid_aud_in_token(test_client_invalid_aud_in_token): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client_invalid_aud_in_token.application.bearer} response = test_client_invalid_aud_in_token.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "Incorrect claims, please check the audience and issuer" def test_get_all_group_invalid_signature_in_token(test_client_invalid_signature_in_token): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client_invalid_signature_in_token.application.bearer} response = test_client_invalid_signature_in_token.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "The signature is not valid" def test_get_all_group_missing_scope_in_token(test_client_missing_scope_in_token): api = '/api/group' headers = {'content-type': 'application/json', 'Authorization': test_client_missing_scope_in_token.application.bearer} response = test_client_missing_scope_in_token.get(api, headers=headers) assert response.status_code == 401 assert response.is_json is True assert response.json['description'] == "No matching scope found in token"

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Python

core/src/zeit/zett/browser/article.py

rickdg/vivi

16134ac954bf8425646d4ad47bdd1f372e089355

[ "BSD-3-Clause" ]

5

2019-05-16T09:51:29.000Z

2021-05-31T09:30:03.000Z

core/src/zeit/zett/browser/article.py

rickdg/vivi

16134ac954bf8425646d4ad47bdd1f372e089355

[ "BSD-3-Clause" ]

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2022-03-23T15:05:56.000Z

core/src/zeit/zett/browser/article.py

rickdg/vivi

16134ac954bf8425646d4ad47bdd1f372e089355

[ "BSD-3-Clause" ]

3

2020-08-14T11:01:17.000Z

2022-01-08T17:32:19.000Z

import zeit.zett.browser.social import zeit.cms.browser.interfaces import zeit.content.article.edit.browser.push class Social(zeit.content.article.edit.browser.push.Social, zeit.zett.browser.social.SocialBase): pass

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Python

testPackage/myPackage/modTwo.py

stevejryan/PythonPackagingTemplate

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[ "MIT" ]

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2020-10-01T03:07:40.000Z

testPackage/myPackage/modTwo.py

stevejryan/PythonPackagingTemplate

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[ "MIT" ]

null

testPackage/myPackage/modTwo.py

stevejryan/PythonPackagingTemplate

82e2715a150f8a018b03fee9f2c6238f2680d9f6

[ "MIT" ]

null

def funcTwo(): print("can you add stuff?")

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Python

tests/test_settings.py

neuroio/neuroio-python

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[ "MIT" ]

null

tests/test_settings.py

neuroio/neuroio-python

160f96515877e5e2ee0e888b7424c77cb2d7496a

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2021-09-06T08:23:09.000Z

2021-11-10T16:19:20.000Z

tests/test_settings.py

neuroio/neuroio-python

160f96515877e5e2ee0e888b7424c77cb2d7496a

[ "MIT" ]

null

import pytest import respx from neuroio.constants import API_BASE_URL @respx.mock def test_get_200(client): request = respx.get(f"{API_BASE_URL}/v1/settings/thresholds/").respond( status_code=200, json={"exact": 1, "ha": 1, "junk": 1}, ) response = client.settings.get() assert request.called assert response.status_code == 200 assert response.json() == {"exact": 1, "ha": 1, "junk": 1} @respx.mock @pytest.mark.asyncio async def test_async_get_200(async_client): request = respx.get(f"{API_BASE_URL}/v1/settings/thresholds/").respond( status_code=200, json={"exact": 1, "ha": 1, "junk": 1}, ) response = await async_client.settings.get() assert request.called assert response.status_code == 200 assert response.json() == {"exact": 1, "ha": 1, "junk": 1} @respx.mock def test_update_200(client): request = respx.patch(f"{API_BASE_URL}/v1/settings/thresholds/").respond( status_code=200, json={"exact": 2, "ha": 2, "junk": 2}, ) response = client.settings.update(2, 2, 2) assert request.called assert response.status_code == 200 assert response.json() == {"exact": 2, "ha": 2, "junk": 2} @respx.mock @pytest.mark.asyncio async def test_async_update_200(async_client): request = respx.patch(f"{API_BASE_URL}/v1/settings/thresholds/").respond( status_code=200, json={"exact": 2, "ha": 2, "junk": 2}, ) response = await async_client.settings.update(2, 2, 2) assert request.called assert response.status_code == 200 assert response.json() == {"exact": 2, "ha": 2, "junk": 2} @respx.mock def test_reset_200(client): request = respx.post( f"{API_BASE_URL}/v1/settings/thresholds/reset/" ).respond(status_code=200) response = client.settings.reset() assert request.called assert response.status_code == 200 @respx.mock @pytest.mark.asyncio async def test_async_reset_200(async_client): request = respx.post( f"{API_BASE_URL}/v1/settings/thresholds/reset/" ).respond(status_code=200) response = await async_client.settings.reset() assert request.called assert response.status_code == 200

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py

Python

nightingale/regression/__init__.py

idin/nightingale

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[ "MIT" ]

null

nightingale/regression/__init__.py

idin/nightingale

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[ "MIT" ]

null

nightingale/regression/__init__.py

idin/nightingale

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[ "MIT" ]

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from .LogisticRegression import LogisticRegression from .OLS import OLS from .GEE import GEE, LogisticGEE from .Regression import Regression from .get_regression_model import get_regression_model

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cassiopeia/dto/spectator.py

artemigkh/cassiopeia

fa78cb8f86ea21857916a707d04de6a05498033e

[ "MIT" ]

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2016-02-15T17:33:40.000Z

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cassiopeia/dto/spectator.py

artemigkh/cassiopeia

fa78cb8f86ea21857916a707d04de6a05498033e

[ "MIT" ]

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2016-02-13T00:04:15.000Z

2022-03-24T18:56:36.000Z

cassiopeia/dto/spectator.py

artemigkh/cassiopeia

fa78cb8f86ea21857916a707d04de6a05498033e

[ "MIT" ]

174

2016-02-21T16:34:30.000Z

2022-03-21T20:46:50.000Z

from .common import DtoObject class CurrentGameInfoDto(DtoObject): pass class FeaturedGamesDto(DtoObject): pass

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pymapd/dtypes.py

vishalbelsare/pymapd

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2018-09-27T14:58:46.000Z

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pymapd/dtypes.py

heavyai/pymapd

36f971f8b49a33287ccc341a30f8c43a36d379a3

[ "Apache-2.0" ]

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2018-10-13T12:57:17.000Z

2021-10-20T23:45:24.000Z

pymapd/dtypes.py

heavyai/pymapd

36f971f8b49a33287ccc341a30f8c43a36d379a3

[ "Apache-2.0" ]

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2018-10-10T11:04:06.000Z

2021-04-23T20:08:08.000Z

from omnisci.dtypes import *

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Python

nevermore/data/datamodule/__init__.py

mmmmmddddd/nevermore

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2021-09-25T16:07:04.000Z

nevermore/data/datamodule/__init__.py

mmmmmddddd/nevermore

8ee8904e5bb84184dcb543cec4ca04dc26c6efea

[ "Apache-2.0" ]

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2021-08-30T08:47:04.000Z

2021-08-31T11:25:26.000Z

nevermore/data/datamodule/__init__.py

mmmmmddddd/nevermore

8ee8904e5bb84184dcb543cec4ca04dc26c6efea

[ "Apache-2.0" ]

null

from .nyuv2 import NYUv2DataModule

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home/migrations/0005_auto_20180823_0920.py

higab85/drugsandme

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[ "MIT" ]

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2016-10-10T10:07:39.000Z

2018-10-29T19:57:52.000Z

home/migrations/0005_auto_20180823_0920.py

higab85/drugsandme

7db66d9687ac9a04132de94edda364f191d497d7

[ "MIT" ]

12

2016-11-04T18:59:17.000Z

2022-03-11T23:32:52.000Z

home/migrations/0005_auto_20180823_0920.py

higab85/drugsandme

7db66d9687ac9a04132de94edda364f191d497d7

[ "MIT" ]

2

2016-09-29T22:48:26.000Z

2019-10-01T19:55:14.000Z

# Generated by Django 2.0.7 on 2018-08-23 09:20 from django.db import migrations, models import django.db.models.deletion import modelcluster.fields import wagtail.core.blocks import wagtail.core.fields import wagtail.images.blocks class Migration(migrations.Migration): dependencies = [ ('home', '0004_auto_20180807_0902'), ] operations = [ migrations.CreateModel( name='IndexBlurbEN', fields=[ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), ('sort_order', models.IntegerField(blank=True, editable=False, null=True)), ('section_name', models.CharField(blank=True, max_length=50)), ('section_content', wagtail.core.fields.StreamField([('text', wagtail.core.blocks.RichTextBlock()), ('partners', wagtail.core.blocks.ListBlock(wagtail.core.blocks.StructBlock([('name', wagtail.core.blocks.CharBlock(blank=True, max_length=25)), ('link', wagtail.core.blocks.CharBlock(blank=True, max_length=255)), ('logo', wagtail.images.blocks.ImageChooserBlock())])))], blank=True)), ], options={ 'ordering': ['sort_order'], 'abstract': False, }, ), migrations.CreateModel( name='IndexBlurbES', fields=[ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), ('sort_order', models.IntegerField(blank=True, editable=False, null=True)), ('section_name', models.CharField(blank=True, max_length=50)), ('section_content', wagtail.core.fields.StreamField([('text', wagtail.core.blocks.RichTextBlock()), ('partners', wagtail.core.blocks.ListBlock(wagtail.core.blocks.StructBlock([('name', wagtail.core.blocks.CharBlock(blank=True, max_length=25)), ('link', wagtail.core.blocks.CharBlock(blank=True, max_length=255)), ('logo', wagtail.images.blocks.ImageChooserBlock())])))], blank=True)), ], options={ 'ordering': ['sort_order'], 'abstract': False, }, ), migrations.RemoveField( model_name='indexblurb', name='article', ), migrations.RenameField( model_name='homepage', old_name='title_tip_drugs', new_name='title_lead_en', ), migrations.RenameField( model_name='homepage', old_name='title_tip_me', new_name='title_lead_es', ), migrations.AddField( model_name='homepage', name='title_tip_drugs_en', field=models.CharField(blank=True, max_length=255), ), migrations.AddField( model_name='homepage', name='title_tip_drugs_es', field=models.CharField(blank=True, max_length=255), ), migrations.AddField( model_name='homepage', name='title_tip_me_en', field=models.CharField(blank=True, max_length=255), ), migrations.AddField( model_name='homepage', name='title_tip_me_es', field=models.CharField(blank=True, max_length=255), ), migrations.DeleteModel( name='IndexBlurb', ), migrations.AddField( model_name='indexblurbes', name='article', field=modelcluster.fields.ParentalKey(on_delete=django.db.models.deletion.CASCADE, related_name='index_sections_es', to='home.HomePage'), ), migrations.AddField( model_name='indexblurben', name='article', field=modelcluster.fields.ParentalKey(on_delete=django.db.models.deletion.CASCADE, related_name='index_sections_en', to='home.HomePage'), ), ]

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0

null

0

6

e7c976d4f2a066a6a8d1ba80dfb73b2421211f0b

27

py

Python

database/__init__.py

markmelnic/Carsen-Logic

7a43f465e61f2e8713d04395877dfaf00a0f663e

[ "MIT" ]

1

2021-09-05T10:50:42.000Z

database/__init__.py

markmelnic/Carsen-Crawler

6f5a7b7b7ba7cdad04c0dd30a53d17239dda6965

[ "MIT" ]

null

database/__init__.py

markmelnic/Carsen-Crawler

6f5a7b7b7ba7cdad04c0dd30a53d17239dda6965

[ "MIT" ]

4

2020-10-31T14:09:01.000Z

2022-01-13T20:48:37.000Z

from database.db import DB

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6

99dd7ad7b483482fcd178a90958f624794511bd0

44

py

Python

models/contextuals/__init__.py

datactivist/dataoutai

a1db230a31e78d17cd1c79daa8c13a508d493f9f

[ "MIT" ]

1

2022-01-19T19:06:18.000Z

models/contextuals/__init__.py

datactivist/dataoutai

a1db230a31e78d17cd1c79daa8c13a508d493f9f

[ "MIT" ]

4

2021-12-01T19:44:54.000Z

2022-01-12T15:48:53.000Z

models/contextuals/__init__.py

datactivist/dataoutai

a1db230a31e78d17cd1c79daa8c13a508d493f9f

[ "MIT" ]

null

from .sbert import ContextualEmbeddingModel

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43

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1

0

1

0

6

821736f98cf14f5ce1e5196c206fb3028207846c

90

py

Python

samples/sample_enum_names.py

NobuyukiInoue/Example_dnspython

550bce804315862a0050ef9b1cae304ca45481c0

[ "MIT" ]

1

2019-07-08T11:32:03.000Z

samples/sample_enum_names.py

NobuyukiInoue/Example_dnspython

550bce804315862a0050ef9b1cae304ca45481c0

[ "MIT" ]

null

samples/sample_enum_names.py

NobuyukiInoue/Example_dnspython

550bce804315862a0050ef9b1cae304ca45481c0

[ "MIT" ]

null

import dns.e164 n = dns.e164.from_e164("+1 555 1212") print(n) print(dns.e164.to_e164(n))

18

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19

90

3.263158

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0

1

0

1

0

null

0

1

0

6

416f853bde5380a07f5b880a51657938dcb3bce4

390

py

Python

python/6_kyu/data_reverse.py

CommonLouis/CodeWars_Solutions

f325c12effbd361905027864848e06ce07ec941e

[ "MIT" ]

null

python/6_kyu/data_reverse.py

CommonLouis/CodeWars_Solutions

f325c12effbd361905027864848e06ce07ec941e

[ "MIT" ]

null

python/6_kyu/data_reverse.py

CommonLouis/CodeWars_Solutions

f325c12effbd361905027864848e06ce07ec941e

[ "MIT" ]

null

""" Michael Persico Oct.09, 2021 Data Reverse https://www.codewars.com/kata/569d488d61b812a0f7000015 """ def data_reverse(data): return sum([data[i:i + 8] for i in range(0,len(data), 8)][::-1], []) if __name__ == "__main__": print(data_reverse([1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,0,1,0,1,0,1,0])) # [1,0,1,0,1,0,1,0,0,0,0,0,1,1,1,1,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1]

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390

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0.097436

390

12

159

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false

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0.25

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null

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0

1

0

null

0

1

0

1

0

6

41704865996d49e48cc2b6df3d95c21449a8431d

26

py

Python

graphgallery/functional/edge_level/__init__.py

dongzizhu/GraphGallery

c65eab42daeb52de5019609fe7b368e30863b4ae

[ "MIT" ]

1

2020-07-29T08:00:32.000Z

graphgallery/functional/edge_level/__init__.py

dongzizhu/GraphGallery

c65eab42daeb52de5019609fe7b368e30863b4ae

[ "MIT" ]

null

graphgallery/functional/edge_level/__init__.py

dongzizhu/GraphGallery

c65eab42daeb52de5019609fe7b368e30863b4ae

[ "MIT" ]

null

from .transform import *

13

25

0.730769

3

26

6.333333

1

0

0.192308

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1

26

0.904762

0

1

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1

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1

0

null

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0

null

0

1

0

1

0

1

0

6

68c0c7bebfb8165c02b9c3567ba1f0baaf50e693

113

py

Python

cvpl-xml/xml/exceptions.py

robinsax/canvas-plugin-multirepo

20fd6a3cc42af5f2cde73e3b100d3edeb4e50c01

[ "Apache-2.0" ]

null

cvpl-xml/xml/exceptions.py

robinsax/canvas-plugin-multirepo

20fd6a3cc42af5f2cde73e3b100d3edeb4e50c01

[ "Apache-2.0" ]

null

cvpl-xml/xml/exceptions.py

robinsax/canvas-plugin-multirepo

20fd6a3cc42af5f2cde73e3b100d3edeb4e50c01

[ "Apache-2.0" ]

null

# coding utf-8 ''' Exceptions. ''' class XMLSyntaxError(Exception): pass class ConversionError(Exception): pass

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113

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0

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true

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1

0

null

0

1

0

1

0

6

6bc85338b7ea5c26c66d401329c612c7d5219cff

696

py

Python

octicons16px/file_diff.py

andrewp-as-is/octicons16px.py

1272dc9f290619d83bd881e87dbd723b0c48844c

[ "Unlicense" ]

1

2021-01-28T06:47:39.000Z

octicons16px/file_diff.py

andrewp-as-is/octicons16px.py

1272dc9f290619d83bd881e87dbd723b0c48844c

[ "Unlicense" ]

null

octicons16px/file_diff.py

andrewp-as-is/octicons16px.py

1272dc9f290619d83bd881e87dbd723b0c48844c

[ "Unlicense" ]

null

OCTICON_FILE_DIFF = """ <svg class="octicon octicon-file-diff" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" width="16" height="16"><path fill-rule="evenodd" d="M2.75 1.5a.25.25 0 00-.25.25v12.5c0 .138.112.25.25.25h10.5a.25.25 0 00.25-.25V4.664a.25.25 0 00-.073-.177l-2.914-2.914a.25.25 0 00-.177-.073H2.75zM1 1.75C1 .784 1.784 0 2.75 0h7.586c.464 0 .909.184 1.237.513l2.914 2.914c.329.328.513.773.513 1.237v9.586A1.75 1.75 0 0113.25 16H2.75A1.75 1.75 0 011 14.25V1.75zm7 1.5a.75.75 0 01.75.75v1.5h1.5a.75.75 0 010 1.5h-1.5v1.5a.75.75 0 01-1.5 0V7h-1.5a.75.75 0 010-1.5h1.5V4A.75.75 0 018 3.25zm-3 8a.75.75 0 01.75-.75h4.5a.75.75 0 010 1.5h-4.5a.75.75 0 01-.75-.75z"></path></svg> """

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696

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0

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1

0

null

0

6

6bcac64f89c55cdecb4c0c5c5a004a3278b7a9d2

27

py

Python

config/__init__.py

AlexanderFengler/LAN_scripts

2f79f0c85c6301bba9858536376a36ba01e558a0

[ "MIT" ]

1

2021-07-22T01:19:41.000Z

config/__init__.py

AlexanderFengler/LAN_scripts

2f79f0c85c6301bba9858536376a36ba01e558a0

[ "MIT" ]

null

config/__init__.py

AlexanderFengler/LAN_scripts

2f79f0c85c6301bba9858536376a36ba01e558a0

[ "MIT" ]

null

from .config_utils import *

27

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true

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null

0

1

0

1

0

1

0

6

6bffc2408603e9afd2d388e619e914416ec56b66

168

py

Python

queen.py

omerihtizaz/chess-AI

97a18f30b64ac502117c1424861f997e078737ff

[ "MIT" ]

null

queen.py

omerihtizaz/chess-AI

97a18f30b64ac502117c1424861f997e078737ff

[ "MIT" ]

null

queen.py

omerihtizaz/chess-AI

97a18f30b64ac502117c1424861f997e078737ff

[ "MIT" ]

null

from bishop import * from rook import * def getQueenMovements(board, player): return joinList(getBishopMovements(board, player), getRookMovements(board, player))

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168

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6

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0

1

0.25

false

0

0.5

0.25

1

0

1

0

null

1

0

1

0

null

0

1

0

1

0

6

d411a7aee4a973de451dbd7f702376ad7056ea8c

73

py

Python

src/po/GithubPO.py

d9nchik/selenium

a4363a4a4ae0c58a9b1ae94923bf3e25ec65ced4

[ "MIT" ]

null

src/po/GithubPO.py

d9nchik/selenium

a4363a4a4ae0c58a9b1ae94923bf3e25ec65ced4

[ "MIT" ]

null

src/po/GithubPO.py

d9nchik/selenium

a4363a4a4ae0c58a9b1ae94923bf3e25ec65ced4

[ "MIT" ]

1

2021-05-26T15:10:50.000Z

import src.po.DefaultPO as dpo class GithubPO(dpo.DefaultPO): pass

12.166667

30

0.739726

11

73

4.909091

0.818182

0

0.178082

73

5

31

14.6

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0

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0

true

0.333333

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0.666667

0

1

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null

0

1

0

null

0

1

0

1

0

6

d422938e811ee5f3aafa6ce77665e43c85c8ba06

167

py

Python

tensorcv/__init__.py

Hourout/tensorcv

620559ee90921e036c8a84877d806a5c21010511

[ "Apache-2.0" ]

8

2018-12-06T05:02:29.000Z

2021-08-25T07:09:29.000Z

tensorcv/__init__.py

Hourout/keras-cv

620559ee90921e036c8a84877d806a5c21010511

[ "Apache-2.0" ]

null

tensorcv/__init__.py

Hourout/keras-cv

620559ee90921e036c8a84877d806a5c21010511

[ "Apache-2.0" ]

4

2018-12-06T05:02:32.000Z

2019-06-04T11:15:39.000Z

from tensorcv import Classification from tensorcv import image from tensorcv import data from tensorcv import losses __version__ = '0.2.0' __author__ = 'JinQing Lee'

20.875

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167

5.521739

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0

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0

1

0

1

0

6

d453c9afec5b861ee835938e9120505c34a04ac5

10,064

py

Python

paloma/tests/mail.py

piquadrat/paloma

7c621e81e48b38099f71cdff02b621efb0f499d1

[ "Apache-2.0" ]

null

paloma/tests/mail.py

piquadrat/paloma

7c621e81e48b38099f71cdff02b621efb0f499d1

[ "Apache-2.0" ]

null

paloma/tests/mail.py

piquadrat/paloma

7c621e81e48b38099f71cdff02b621efb0f499d1

[ "Apache-2.0" ]

null

import os from paloma import Mail, TemplateMail from django.core import mail from django.test.utils import override_settings from .testcase import TestCase TEMPLATE_DIRS = (os.path.join(os.path.abspath(os.path.dirname(__file__)), 'templates'), ) @override_settings(DEFAULT_FROM_EMAIL='default@example.com', DEFAULT_FROM_NAME='Default sender') class MailTestCase(TestCase): """Test case for :class:`Mail`. """ def assertSimple(self, sent, **kwargs): self.assertEqual(sent.subject, kwargs.pop('subject', 'Subject of the e-mail')) self.assertEqual(sent.body, kwargs.pop('body', 'Body of the e-mail')) from_email = kwargs.pop('from_email', 'default@example.com') from_name = kwargs.pop('from_name', 'Default sender') if from_name: self.assertEqual(sent.from_email, '%s <%s>' % (from_name, from_email)) else: self.assertEqual(sent.from_email, from_email) self.assertEqual(len(sent.to), 1) self.assertEqual(sent.to[0], kwargs.pop('to', 'test@example.com')) html_alternatives = filter(lambda a: a[1] == 'text/html', sent.alternatives) self.assertEqual(any(html_alternatives), 'html_body' in kwargs) if 'html_body' in kwargs: html_body = kwargs.pop('html_body') actual_html_body, mime_type = html_alternatives[0] self.assertEqual(html_body, actual_html_body) def test_init__defaults_to_setting_for_from_email_and_from_name(self): """Mail().__init__(from_name=None, from_email=None) uses defaults """ class TestMail(Mail): subject = 'Subject of the e-mail' # Test with global. with override_settings(DEFAULT_FROM_EMAIL='someone@example.com', DEFAULT_FROM_NAME='Someone'): m = TestMail() self.assertEqual(m.from_email, 'someone@example.com') self.assertEqual(m.from_name, 'Someone') with self.assertMailsSent(1): m.send('test@example.com', 'Body of the e-mail') self.assertSimple(mail.outbox[-1], from_email='someone@example.com', from_name='Someone') def test_send__respects_from_email_ivar_from_sent(self): """Mail().send(..) respects from_email instance variable """ class TestMail(Mail): subject = 'Subject of the e-mail' from_email = 'from@example.com' # Test without global. with override_settings(DEFAULT_FROM_EMAIL=None): with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail') self.assertSimple(mail.outbox[-1], from_email='from@example.com') # Test with global. with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail') self.assertSimple(mail.outbox[-1], from_email='from@example.com') def test_send__respects_from_name_ivar_from_sent(self): """Mail().send(..) respects from_name instance variable """ class TestMail(Mail): subject = 'Subject of the e-mail' from_name = 'Overridden' # Test without global. with override_settings(DEFAULT_FROM_NAME=None): with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail') self.assertSimple(mail.outbox[-1], from_name='Overridden') # Test with global. with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail') self.assertSimple(mail.outbox[-1], from_name='Overridden') def test_send__respects_subject(self): """Mail().send(..) respects subject argument """ class TestMail(Mail): subject = 'Not this subject of the e-mail' with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail', subject='This is the subject') self.assertSimple(mail.outbox[-1], subject='This is the subject') def test_send__with_html_body(self): """Mail().send(..) with HTML body sends both plain text and HTML body """ class TestMail(Mail): subject = 'Subject of the e-mail' html_body = '<h1>HTML body of the e-mail</h1>' with self.assertMailsSent(1): TestMail().send('test@example.com', 'Body of the e-mail', html_body) self.assertSimple(mail.outbox[-1], html_body=html_body) @override_settings(DEFAULT_FROM_EMAIL='default@example.com', DEFAULT_FROM_NAME='Default sender', TEMPLATE_DIRS=TEMPLATE_DIRS) class TemplateMailTestCase(TestCase): """Test case for :class:`TemplateMail`. """ def assertSimple(self, sent, body, **kwargs): self.assertEqual(sent.subject, kwargs.pop('subject', 'Subject of the e-mail')) self.assertEqual(sent.body, body) from_email = kwargs.pop('from_email', 'default@example.com') from_name = kwargs.pop('from_name', 'Default sender') if from_name: self.assertEqual(sent.from_email, '%s <%s>' % (from_name, from_email)) else: self.assertEqual(sent.from_email, from_email) self.assertEqual(len(sent.to), 1) self.assertEqual(sent.to[0], kwargs.pop('to', 'test@example.com')) html_alternatives = filter(lambda a: a[1] == 'text/html', sent.alternatives) self.assertEqual(any(html_alternatives), 'html_body' in kwargs) if 'html_body' in kwargs: html_body = kwargs.pop('html_body') actual_html_body, mime_type = html_alternatives[0] self.assertEqual(html_body, actual_html_body) def test_send__only_text_template(self): """TemplateMail(<only text template>).send(..) sends expected e-mail """ # Local context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' text_template_name = 'test_mail.txt' with self.assertMailsSent(1): TestMail().send('test@example.com', {'a': 'in local context'}) self.assertSimple(mail.outbox[-1], body=u'Test body.\n\nHas variable in local context.') # Class context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' text_template_name = 'test_mail.txt' with self.assertMailsSent(1): TestMail(context={'a': 'in class context'}) \ .send('test@example.com') self.assertSimple(mail.outbox[-1], body=u'Test body.\n\nHas variable in class context.') # Class and local context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' text_template_name = 'test_mail.txt' with self.assertMailsSent(1): TestMail(context={'a': 'in class context'}) \ .send('test@example.com', {'a': 'in local context'}) self.assertSimple(mail.outbox[-1], body=u'Test body.\n\nHas variable in local context.') def test_send__templated(self): """TemplateMail(<templated>).send(..) sends expected e-mail """ # Local context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' subject_template_name = 'test_mail_subject.txt' text_template_name = 'test_mail.txt' html_template_name = 'test_mail.html' with self.assertMailsSent(1): TestMail().send('test@example.com', {'a': 'in local context'}) body_format = u'Test body.\n\nHas variable %s.' html_body_format = u'''<html> <body> <p>Test body.</p> <p>Has variable %s.</p> </body> </html>''' self.assertSimple( mail.outbox[-1], subject=u'Test subject with variable in local context', body=body_format % ('in local context'), html_body=html_body_format % ('in local context') ) # Class context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' subject_template_name = 'test_mail_subject.txt' text_template_name = 'test_mail.txt' html_template_name = 'test_mail.html' with self.assertMailsSent(1): TestMail(context={'a': 'in class context'}) \ .send('test@example.com') self.assertSimple( mail.outbox[-1], subject=u'Test subject with variable in class context', body=body_format % ('in class context'), html_body=html_body_format % ('in class context') ) # Class and local context variable. class TestMail(TemplateMail): subject = 'Subject of the e-mail' subject_template_name = 'test_mail_subject.txt' text_template_name = 'test_mail.txt' html_template_name = 'test_mail.html' with self.assertMailsSent(1): TestMail(context={'a': 'in class context'}) \ .send('test@example.com', {'a': 'in local context'}) self.assertSimple( mail.outbox[-1], subject=u'Test subject with variable in local context', body=body_format % ('in local context'), html_body=html_body_format % ('in local context') ) __all__ = ( 'MailTestCase', 'TemplateMailTestCase', )

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null

0

1

0

null

0

6

2e19441bbe0130f7ead2d8dac701870d2d48b983

2,381

py

Python

CJIC.py

LeandroPOliveira/SAP-Scripting

8a0f50a1e14a9e1040300bbdefb671c917cc32e9

[ "MIT" ]

null

CJIC.py

LeandroPOliveira/SAP-Scripting

8a0f50a1e14a9e1040300bbdefb671c917cc32e9

[ "MIT" ]

null

CJIC.py

LeandroPOliveira/SAP-Scripting

8a0f50a1e14a9e1040300bbdefb671c917cc32e9

[ "MIT" ]

null

# Importar o pacote pandas para trabalhar com arquivos excel import pandas as pd # Abrir arquivo de script gerado pelo SAP arquivo = open('CJIC.vbs', 'a') # modo 'a' de append, insere novos dados no arquivo sem excluir os que estavam # Abrir arquivo com os dados a serem lançados dados = pd.read_excel('CJIC.xlsx', dtype=str) # iterar sobre as linhas do arquivo excel e buscar os dados necessários para o script for index, row in dados.iterrows(): # Adicionar os dados ao script arquivo.write(f''' session.findById("wnd[0]").maximize session.findById("wnd[0]/tbar[0]/okcd").text = "CJIC" session.findById("wnd[0]").sendVKey 0 session.findById("wnd[0]/usr/ctxtCN_PSPNR-LOW").text = "RSG.22.001.022.1.01.1" session.findById("wnd[0]/usr/ctxtCN_ACTVT-LOW").text = "" session.findById("wnd[0]/usr/ctxtP_DISVAR").text = "/IMOB_OBJETO" session.findById("wnd[0]/usr/ctxtP_DISVAR").setFocus session.findById("wnd[0]/usr/ctxtP_DISVAR").caretPosition = 12 session.findById("wnd[0]/tbar[1]/btn[8]").press session.findById("wnd[0]/usr/cntlGRID1/shellcont/shell/shellcont[1]/shell").setCurrentCell -1,"POBID" session.findById("wnd[0]/usr/cntlGRID1/shellcont/shell/shellcont[1]/shell").selectColumn "POBID" session.findById("wnd[0]/tbar[1]/btn[29]").press session.findById("wnd[1]/usr/ssub%_SUBSCREEN_FREESEL:SAPLSSEL:1105/ctxt%%DYN001-LOW").text = "7010083 0010" session.findById("wnd[1]/usr/ssub%_SUBSCREEN_FREESEL:SAPLSSEL:1105/ctxt%%DYN001-LOW").caretPosition = 12 session.findById("wnd[1]/tbar[0]/btn[0]").press session.findById("wnd[0]/usr/cntlGRID1/shellcont/shell/shellcont[1]/shell").setCurrentCell -1,"" session.findById("wnd[0]/usr/cntlGRID1/shellcont/shell/shellcont[1]/shell").selectAll session.findById("wnd[0]/tbar[1]/btn[13]").press session.findById("wnd[0]/usr/tblSAPLKOBSTC_RULES/ctxtDKOBR-EMPGE[1,0]").text = "601201-0" session.findById("wnd[0]/usr/tblSAPLKOBSTC_RULES/ctxtCOBRB-URZUO[7,0]").text = "4" session.findById("wnd[0]/usr/tblSAPLKOBSTC_RULES/txtCOBRB-AQZIF[4,0]").setFocus session.findById("wnd[0]/usr/tblSAPLKOBSTC_RULES/txtCOBRB-AQZIF[4,0]").caretPosition = 0 session.findById("wnd[0]").sendVKey 3 session.findById("wnd[0]/tbar[0]/btn[11]").press session.findById("wnd[0]/tbar[0]/btn[3]").press session.findById("wnd[1]/usr/btnSPOP-OPTION1").press session.findById("wnd[0]/tbar[0]/btn[3]").press ''') # Fechar o arquivo de script arquivo.close()

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0.029412

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null

1

0

1

null

0

6

2e53327fbf97bdf472b8d359d31b74e90f338b78

96

py

Python

venv/lib/python3.8/site-packages/poetry/core/version/requirements.py

Retraces/UkraineBot

3d5d7f8aaa58fa0cb8b98733b8808e5dfbdb8b71

[ "MIT" ]

2

2022-03-13T01:58:52.000Z

2022-03-31T06:07:54.000Z

venv/lib/python3.8/site-packages/poetry/core/version/requirements.py

DesmoSearch/Desmobot

b70b45df3485351f471080deb5c785c4bc5c4beb

[ "MIT" ]

19

2021-11-20T04:09:18.000Z

2022-03-23T15:05:55.000Z

venv/lib/python3.8/site-packages/poetry/core/version/requirements.py

DesmoSearch/Desmobot

b70b45df3485351f471080deb5c785c4bc5c4beb

[ "MIT" ]

null

/home/runner/.cache/pip/pool/d2/11/dd/e3884139b17b0a08a7b9a047150bd735a59c2e947b2451d690b1dd9f43

96

0.895833

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96

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null

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0

1

0

1

0

null

1

0

1

0

6

2e56bd51ebd3408db2e560a6e4739824d955551e

495

py

Python

terrascript/triton/r.py

vutsalsinghal/python-terrascript

3b9fb5ad77453d330fb0cd03524154a342c5d5dc

[ "BSD-2-Clause" ]

null

terrascript/triton/r.py

vutsalsinghal/python-terrascript

3b9fb5ad77453d330fb0cd03524154a342c5d5dc

[ "BSD-2-Clause" ]

null

terrascript/triton/r.py

vutsalsinghal/python-terrascript

3b9fb5ad77453d330fb0cd03524154a342c5d5dc

[ "BSD-2-Clause" ]

null

# terrascript/triton/r.py import terrascript class triton_fabric(terrascript.Resource): pass class triton_firewall_rule(terrascript.Resource): pass class triton_instance_template(terrascript.Resource): pass class triton_key(terrascript.Resource): pass class triton_machine(terrascript.Resource): pass class triton_service_group(terrascript.Resource): pass class triton_snapshot(terrascript.Resource): pass class triton_vlan(terrascript.Resource): pass

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null

1

0

null

0

1

0

1

0

6

2e716ff5a715c9fdbc64b7e22f805d208d3e274d

40

py

Python

dliplib/utils/__init__.py

oterobaguer/ct-dip-benchmark

0539c284c94089ed86421ea0892cd68aa1d0575a

[ "Apache-2.0" ]

null

dliplib/utils/__init__.py

oterobaguer/ct-dip-benchmark

0539c284c94089ed86421ea0892cd68aa1d0575a

[ "Apache-2.0" ]

null

dliplib/utils/__init__.py

oterobaguer/ct-dip-benchmark

0539c284c94089ed86421ea0892cd68aa1d0575a

[ "Apache-2.0" ]

null

from dliplib.utils.params import Params

20

39

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0

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0

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0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

2e8074ebb56b9a2484ee303e95d1563da249c5e6

24

py

Python

dask-gateway-server/dask_gateway_server/proxy/__init__.py

AndreaGiardini/dask-gateway

c2583548df19359d24031e1dd9161c616d3bed50

[ "BSD-3-Clause" ]

69

2019-09-19T06:19:48.000Z

2022-02-04T23:01:15.000Z

dask-gateway-server/dask_gateway_server/proxy/__init__.py

AndreaGiardini/dask-gateway

c2583548df19359d24031e1dd9161c616d3bed50

[ "BSD-3-Clause" ]

318

2019-09-18T18:42:57.000Z

2022-03-31T11:05:38.000Z

dask-gateway-server/dask_gateway_server/proxy/__init__.py

AndreaGiardini/dask-gateway

c2583548df19359d24031e1dd9161c616d3bed50

[ "BSD-3-Clause" ]

61

2019-09-18T18:09:56.000Z

2022-03-25T20:35:11.000Z

from .core import Proxy

12

23

0.791667

4

24

4.75

1

0

0.166667

24

1

24

0.95

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null

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1

0

null

0

1

0

1

0

1

0

6

2e91f726ea14b6aa0e88fa8cc530ae1b9074db18

295

py

Python

scripts/helper/__init__.py

lovaulonze/nice_pub_figure

311c04f6bc97f5a22c3bdf75ef1d192dfa8475a7

[ "MIT" ]

null

scripts/helper/__init__.py

lovaulonze/nice_pub_figure

311c04f6bc97f5a22c3bdf75ef1d192dfa8475a7

[ "MIT" ]

null

scripts/helper/__init__.py

lovaulonze/nice_pub_figure

311c04f6bc97f5a22c3bdf75ef1d192dfa8475a7

[ "MIT" ]

null

from . import mpl_helper # Load mpl setting as well from .mpl_helper import gridplots, grid_labels from .mpl_helper import savepgf, add_img_ax from .path_helper import root_path, script_path from .path_helper import img_path, tex_path, build_path from .tex_helper import clean_width_cache

42.142857

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0.168142

0

0.138983

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6

58

49.166667

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1

0

null

0

1

0

1

0

1

0

6

cf31e82b8625c47027d51f603032bd7c49c9ad5c

487

py

Python

gnn_agglomeration/pyg_datasets/__init__.py

bentaculum/gnn_agglomeration

e5b8a693ba78433b8a3721ac3102630c2a79a1e4

[ "MIT" ]

2

2021-05-19T01:56:52.000Z

2021-07-08T20:50:38.000Z

gnn_agglomeration/pyg_datasets/__init__.py

benjamin9555/gnn_agglomeration

e5b8a693ba78433b8a3721ac3102630c2a79a1e4

[ "MIT" ]

14

2019-07-17T19:23:09.000Z

2021-02-02T22:01:49.000Z

gnn_agglomeration/pyg_datasets/__init__.py

benjamin9555/gnn_agglomeration

e5b8a693ba78433b8a3721ac3102630c2a79a1e4

[ "MIT" ]

2

2019-07-17T20:14:03.000Z

2019-07-27T16:20:52.000Z

from .hemibrain_dataset_blockwise import HemibrainDatasetBlockwise # noqa from .hemibrain_dataset_blockwise_in_memory import HemibrainDatasetBlockwiseInMemory # noqa from .hemibrain_dataset_random import HemibrainDatasetRandom # noqa from .hemibrain_dataset_random_in_memory import HemibrainDatasetRandomInMemory # noqa from .hemibrain_graph_unmasked import HemibrainGraphUnmasked # noqa from .hemibrain_graph_masked import HemibrainGraphMasked # noqa from . import toy_datasets

48.7

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9

93

54.111111

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true

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null

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0

null

0

1

0

1

0

1

0

6

cf3e220ab7b8edf0ba28250a48d14c4835a3e650

1,385

py

Python

app/improving_agent/models/__init__.py

brettasmi/EvidARA

319bbe80ddb4d7d6aa4f1db005ad5461e015a8bc

[ "MIT" ]

null

app/improving_agent/models/__init__.py

brettasmi/EvidARA

319bbe80ddb4d7d6aa4f1db005ad5461e015a8bc

[ "MIT" ]

5

2020-06-25T21:47:50.000Z

2020-07-15T01:22:51.000Z

app/improving_agent/models/__init__.py

suihuanglab/evidARA

cf5b8bbdb9f90136c66b58c694acf2efc18ffc22

[ "MIT" ]

1

2020-03-23T10:39:59.000Z

# coding: utf-8 # flake8: noqa from __future__ import absolute_import # import models into model package from improving_agent.models.async_query import AsyncQuery from improving_agent.models.attribute import Attribute from improving_agent.models.edge import Edge from improving_agent.models.edge_binding import EdgeBinding from improving_agent.models.knowledge_graph import KnowledgeGraph from improving_agent.models.log_entry import LogEntry from improving_agent.models.log_level import LogLevel from improving_agent.models.message import Message from improving_agent.models.meta_attribute import MetaAttribute from improving_agent.models.meta_edge import MetaEdge from improving_agent.models.meta_knowledge_graph import MetaKnowledgeGraph from improving_agent.models.meta_node import MetaNode from improving_agent.models.node import Node from improving_agent.models.node_binding import NodeBinding from improving_agent.models.q_edge import QEdge from improving_agent.models.q_node import QNode from improving_agent.models.query import Query from improving_agent.models.query_constraint import QueryConstraint from improving_agent.models.query_graph import QueryGraph from improving_agent.models.response import Response from improving_agent.models.result import Result from improving_agent.models.schema2 import Schema2 from improving_agent.models.sub_attribute import SubAttribute

47.758621

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null

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1

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1

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6

cf795254af783d664b11ec5ae045c27293b9b117

3,875

py

Python

tests/client/schedules_test.py

jozefbonnar/pydactyl

b45ce82ac0e20c786ffd3a65bab959c9bb3226ba

[ "MIT" ]

null

tests/client/schedules_test.py

jozefbonnar/pydactyl

b45ce82ac0e20c786ffd3a65bab959c9bb3226ba

[ "MIT" ]

null

tests/client/schedules_test.py

jozefbonnar/pydactyl

b45ce82ac0e20c786ffd3a65bab959c9bb3226ba

[ "MIT" ]

null

import unittest from unittest import mock from pydactyl import PterodactylClient class SchedulesTests(unittest.TestCase): def setUp(self): self.api = PterodactylClient(url='dummy', api_key='dummy') @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_list_schedules(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules', } self.api.client.servers.schedules.list_schedules('srv123') mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_create_schedule(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules', 'mode': 'POST', 'data': {'name': 'test', 'minute': '*', 'hour': '1', 'day_of_week': 'pants', 'day_of_month': 'doggo', 'is_active': True}, } self.api.client.servers.schedules.create_schedule( 'srv123', 'test', '*', '1', 'pants', 'doggo') mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_get_schedule_details(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/3', } self.api.client.servers.schedules.get_schedule_details('srv123', 3) mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_update_schedule(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/4', 'mode': 'POST', 'data': {'name': 'test', 'minute': '*', 'hour': '1', 'day_of_week': 'pants', 'day_of_month': 'doggo', 'is_active': True}, } self.api.client.servers.schedules.update_schedule( 'srv123', 4, 'test', '*', '1', 'pants', 'doggo') mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_delete_schedule(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/5', 'mode': 'DELETE', } self.api.client.servers.schedules.delete_schedule('srv123', 5) mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_create_task(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/5/tasks', 'mode': 'POST', 'data': {'action': 'command', 'payload': 'say Hello World', 'time_offset': '6'} } self.api.client.servers.schedules.create_task('srv123', 5, 'command', 'say Hello World', '6') mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_update_task(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/5/tasks/4', 'mode': 'POST', 'data': {'action': 'command', 'payload': 'say Hello World', 'time_offset': '6'} } self.api.client.servers.schedules.update_task('srv123', 5, 4, 'command', 'say Hello World', '6') mock_api.assert_called_with(**expected) @mock.patch('pydactyl.api.base.PterodactylAPI._api_request') def test_delete_task(self, mock_api): expected = { 'endpoint': 'client/servers/srv123/schedules/5/tasks/4', 'mode': 'DELETE', } self.api.client.servers.schedules.delete_task('srv123', 5, 4) mock_api.assert_called_with(**expected) if __name__ == '__main__': unittest.main()

39.141414

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81

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0

null

0

1

0

null

0

6

cf7c22dd318039cc4f2e3a5eff77c87bfeaf63d3

141

py

Python

modular_sphere/__init__.py

mcaniot/modular_sphere

dcced596fa79f924b361c5f8384e612778e9b360

[ "Apache-2.0" ]

1

2021-03-24T14:56:58.000Z

modular_sphere/__init__.py

mcaniot/modular_sphere

dcced596fa79f924b361c5f8384e612778e9b360

[ "Apache-2.0" ]

null

modular_sphere/__init__.py

mcaniot/modular_sphere

dcced596fa79f924b361c5f8384e612778e9b360

[ "Apache-2.0" ]

null

from modular_sphere.robot_sphere import RobotSphere from modular_sphere.simulation_manager import SimulationManager name = 'modular_sphere'

28.2

63

0.879433

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0.285714

0

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141

4

64

35.25

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1

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0

null

0

1

0

1

0

6

d8488dc29ae80241bee30ee1357375ddb9d76078

3,888

py

Python

tests/http_future/unmarshall_response_test.py

sjaensch/aiobravado

d3f1eb71883b1f24c4b592917890160eb3d3cbcc

[ "BSD-3-Clause" ]

19

2017-11-20T22:47:12.000Z

2021-12-23T15:56:41.000Z

tests/http_future/unmarshall_response_test.py

sjaensch/aiobravado

d3f1eb71883b1f24c4b592917890160eb3d3cbcc

[ "BSD-3-Clause" ]

10

2018-01-11T12:53:01.000Z

2020-01-27T20:05:51.000Z

tests/http_future/unmarshall_response_test.py

sjaensch/aiobravado

d3f1eb71883b1f24c4b592917890160eb3d3cbcc

[ "BSD-3-Clause" ]

4

2017-11-18T12:37:14.000Z

2021-03-19T14:48:13.000Z

# -*- coding: utf-8 -*- from functools import partial import pytest from bravado_core.exception import MatchingResponseNotFound from bravado_core.operation import Operation from bravado_core.response import IncomingResponse from mock import Mock from mock import patch from aiobravado.exception import HTTPError from aiobravado.http_future import unmarshal_response def unmarshal_response_inner_factory(result): async def mock_umi(*args, **kwargs): return result return mock_umi def test_5XX(event_loop): incoming_response = Mock(spec=IncomingResponse, status_code=500) operation = Mock(spec=Operation) with pytest.raises(HTTPError) as excinfo: event_loop.run_until_complete(unmarshal_response(incoming_response, operation)) assert excinfo.value.response.status_code == 500 @patch('aiobravado.http_future.unmarshal_response_inner', new_callable=partial(unmarshal_response_inner_factory, 99)) def test_2XX(_1, event_loop): incoming_response = Mock(spec=IncomingResponse) incoming_response.status_code = 200 operation = Mock(spec=Operation) event_loop.run_until_complete(unmarshal_response(incoming_response, operation)) assert incoming_response.swagger_result == 99 @patch('aiobravado.http_future.unmarshal_response_inner', side_effect=MatchingResponseNotFound('boo')) def test_2XX_matching_response_not_found_in_spec(_1, event_loop): incoming_response = Mock(spec=IncomingResponse, status_code=200) operation = Mock(spec=Operation) with pytest.raises(HTTPError) as excinfo: event_loop.run_until_complete(unmarshal_response(incoming_response, operation)) assert excinfo.value.response.status_code == 200 assert excinfo.value.message == 'boo' @patch('aiobravado.http_future.unmarshal_response_inner', side_effect=MatchingResponseNotFound) def test_4XX_matching_response_not_found_in_spec(_1, event_loop): incoming_response = Mock(spec=IncomingResponse, status_code=404) operation = Mock(spec=Operation) with pytest.raises(HTTPError) as excinfo: event_loop.run_until_complete(unmarshal_response(incoming_response, operation)) assert excinfo.value.response.status_code == 404 @patch( 'aiobravado.http_future.unmarshal_response_inner', new_callable=partial(unmarshal_response_inner_factory, {'msg': 'Not found'}) ) def test_4XX(_1, event_loop): incoming_response = Mock(spec=IncomingResponse, status_code=404) operation = Mock(spec=Operation) with pytest.raises(HTTPError) as excinfo: event_loop.run_until_complete(unmarshal_response(incoming_response, operation)) assert excinfo.value.response.status_code == 404 assert excinfo.value.swagger_result == {'msg': 'Not found'} @patch('aiobravado.http_future.unmarshal_response_inner', new_callable=partial(unmarshal_response_inner_factory, 99)) def test_response_callbacks_executed_on_happy_path(_1, event_loop): incoming_response = Mock(spec=IncomingResponse) incoming_response.status_code = 200 operation = Mock(spec=Operation) callback = Mock() event_loop.run_until_complete( unmarshal_response(incoming_response, operation, response_callbacks=[callback]) ) assert incoming_response.swagger_result == 99 assert callback.call_count == 1 @patch('aiobravado.http_future.unmarshal_response_inner', new_callable=partial(unmarshal_response_inner_factory, 99)) def test_response_callbacks_executed_on_failure(_1, event_loop): incoming_response = Mock(spec=IncomingResponse, status_code=404) operation = Mock(spec=Operation) callback = Mock() with pytest.raises(HTTPError) as excinfo: event_loop.run_until_complete( unmarshal_response(incoming_response, operation, response_callbacks=[callback]) ) assert excinfo.value.response.status_code == 404 assert callback.call_count == 1

40.5

117

0.785494

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3,888

6.083857

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0.060303

0.813232

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3,888

95

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0

null

0

1

0

null

0

6

d8bd96fc0109a56ed7c9c977bd1aaab9a48a08e8

1,076

py

Python

tests/fake/fallbacks/circuit_breaker/rules.py

rafaelgotts/django-toolkit

10b68cbb326bdbc8c2d9efda5edbfc7768476a72

[ "MIT" ]

14

2016-07-25T19:29:05.000Z

2021-12-10T19:12:37.000Z

tests/fake/fallbacks/circuit_breaker/rules.py

rafaelgotts/django-toolkit

10b68cbb326bdbc8c2d9efda5edbfc7768476a72

[ "MIT" ]

37

2016-07-22T12:28:02.000Z

2021-03-19T21:52:39.000Z

tests/fake/fallbacks/circuit_breaker/rules.py

rafaelgotts/django-toolkit

10b68cbb326bdbc8c2d9efda5edbfc7768476a72

[ "MIT" ]

8

2016-10-05T13:02:32.000Z

2020-08-02T12:59:08.000Z

# -*- coding: utf-8 -*- from django_toolkit.fallbacks.circuit_breaker.rules import Rule class FakeRuleShouldOpen(Rule): def should_open_circuit(self, total_failures, total_requests): return True def log_increase_failures(self, total_failures, total_requests): pass class FakeRuleShouldNotOpen(Rule): def should_open_circuit(self, total_failures, total_requests): return False def log_increase_failures(self, total_failures, total_requests): pass class FakeRuleShouldNotIncreaseFailure(Rule): def should_increase_failure_count(self): return False def should_open_circuit(self, total_failures, total_requests): return False def log_increase_failures(self, total_failures, total_requests): pass class FakeRuleShouldNotIncreaseRequest(Rule): def should_increase_request_count(self): return False def should_open_circuit(self, total_failures, total_requests): return False def log_increase_failures(self, total_failures, total_requests): pass

23.911111

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0.742565

124

1,076

6.120968

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0.094862

0.179183

0.231884

0.693017

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0.192379

1,076

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null

0

1

0

1

0

1

0

6

2b4a70b0fbf208abe80c129e59068241a5c0dbb7

2,289

py

Python

pymatflow/elk/base/math.py

DeqiTang/pymatflow

bd8776feb40ecef0e6704ee898d9f42ded3b0186

[ "MIT" ]

6

2020-03-06T16:13:08.000Z

2022-03-09T07:53:34.000Z

pymatflow/elk/base/math.py

DeqiTang/pymatflow

bd8776feb40ecef0e6704ee898d9f42ded3b0186

[ "MIT" ]

1

2021-10-02T02:23:08.000Z

2021-11-08T13:29:37.000Z

pymatflow/elk/base/math.py

DeqiTang/pymatflow

bd8776feb40ecef0e6704ee898d9f42ded3b0186

[ "MIT" ]

1

2021-07-10T16:28:14.000Z

class rootsolver: """ """ def __init__(self): self.params = {} def to_string(self): out = "" for item in self.params: if self.params[item] == None: continue out += "%s = %s\n" % (item, self.params[item]) out += "\n" return out def set_params(self, params): """ """ for item in params: if len(item.split("/")) == 3: self.params[item.split("/")[-1]] = params[item] continue class sparskit: """ """ def __init__(self): self.params = {} def to_string(self): out = "" for item in self.params: if self.params[item] == None: continue out += "%s = %s\n" % (item, self.params[item]) out += "\n" return out def set_params(self, params): """ """ for item in params: if len(item.split("/")) == 3: self.params[item.split("/")[-1]] = params[item] continue class math: """ """ def __init__(self): self.params = {} self.rootsolver = rootsolver() self.sparskit = sparskit() def to_string(self): out = "" for item in self.params: if self.params[item] == None: continue out += "%s = %s\n" % (item, self.params[item]) out += "\n" out += self.rootsolver.to_string() out += self.sparskit.to_string() return out def set_params(self, params): """ """ for item in params: if len(item.split("/")) == 2: self.params[item.split("/")[-1]] = params[item] continue if item.split("/")[1] == "RootSolver": self.rootsolver.set_params({item: params[item]}) elif item.split("/")[1] == "SPARSKIT": self.sparskit.set_params({item: params[item]}) else: pass

27.578313

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4.187793

0.13615

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0

1

0

1

0

1

0

null

0

6

995f24d84ef6642c4bd25a93d39921feb91b1bcd

84

py

Python

exercises/rail-fence-cipher/rail_fence_cipher.py

kishankj/python

82042de746128127502e109111e6c4e8ab002af6

[ "MIT" ]

1,177

2017-06-21T20:24:06.000Z

2022-03-29T02:30:55.000Z

exercises/rail-fence-cipher/rail_fence_cipher.py

kishankj/python

82042de746128127502e109111e6c4e8ab002af6

[ "MIT" ]

1,890

2017-06-18T20:06:10.000Z

2022-03-31T18:35:51.000Z

exercises/rail-fence-cipher/rail_fence_cipher.py

kishankj/python

82042de746128127502e109111e6c4e8ab002af6

[ "MIT" ]

1,095

2017-06-26T23:06:19.000Z

2022-03-29T03:25:38.000Z

def encode(message, rails): pass def decode(encoded_message, rails): pass

12

35

0.690476

11

84

5.181818

0.636364

0.421053

0.561404

0

0.214286

84

6

36

14

0.863636

0

0.5

0

1

0.5

false

0.5

0

0.5

0

1

0

null

1

0

1

0

null

0

1

0

1

0

6

998dc126363b109b7d1a5f04e481dd5f751d2f0a

74

py

Python

app/forms.py

leni1/points-accrual

5f93ab86cc824d7c8e99eb9d87ce2d528f03c075

[ "BSD-3-Clause" ]

null

app/forms.py

leni1/points-accrual

5f93ab86cc824d7c8e99eb9d87ce2d528f03c075

[ "BSD-3-Clause" ]

null

app/forms.py

leni1/points-accrual

5f93ab86cc824d7c8e99eb9d87ce2d528f03c075

[ "BSD-3-Clause" ]

null

from django import forms class ExpenseRequestForm(forms.Form): pass

12.333333

37

0.77027

9

74

6.333333

0.888889

0

0.175676

74

5

38

14.8

0.934426

0

1

0

true

0.333333

0

0.666667

0

1

0

null

0

1

0

null

0

1

0

1

0

6

511381d36b9c87e015b8ba801a8ccaf99655f3ce

39

py

Python

fhir_kindling/serde/__init__.py

migraf/fhir-kindling

2a3c00ba261a629f58b2408bbff18080ec08b069

[ "MIT" ]

3

2021-12-19T03:17:54.000Z

2022-02-24T10:29:25.000Z

fhir_kindling/serde/__init__.py

migraf/fhir-kindling

2a3c00ba261a629f58b2408bbff18080ec08b069

[ "MIT" ]

60

2021-10-30T12:12:39.000Z

2022-03-28T07:24:38.000Z

fhir_kindling/serde/__init__.py

migraf/fhir-kindling

2a3c00ba261a629f58b2408bbff18080ec08b069

[ "MIT" ]

1

2022-02-24T11:06:48.000Z

from .csv_parser import flatten_bundle

19.5

38

0.871795

6

39

5.333333

1

0

0.102564

39

1

39

0.914286

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

51366f09604e2ff0a0c804a53075e5200092b1da

70

py

Python

tests/expectations/mr-x-mr-explicit-order.py

Crunch-io/crunch-cube

80986d5b2106c774f05176fb6c6a5ea0d840f09d

[ "MIT" ]

3

2021-01-22T20:42:31.000Z

2021-06-02T17:53:19.000Z

tests/expectations/mr-x-mr-explicit-order.py

Crunch-io/crunch-cube

80986d5b2106c774f05176fb6c6a5ea0d840f09d

[ "MIT" ]

331

2017-11-13T22:41:56.000Z

2021-12-02T21:59:43.000Z

tests/expectations/mr-x-mr-explicit-order.py

Crunch-io/crunch-cube

80986d5b2106c774f05176fb6c6a5ea0d840f09d

[ "MIT" ]

1

2021-02-19T02:49:00.000Z

[[3, 22, 8, 22], [45, 3, 12, 45], [12, 8, 86, 86], [45, 22, 86, 130]]

35

69

0.414286

16

70

1.8125

0.4375

0

0.537037

0.228571

70

1

70

0

1

0

true

0

1

0

1

null

0

1

0

1

0

1

0

null

0

1

0

6

5a8d304bb0e580cfcad7bb586d37b65a2381fbdf

7,310

py

Python

crawler/crawler/treewalk/scheduler/responses.py

amosproj/amos-ss2020-metadata-hub

f8434b27b306332c117a8dd20a8a55a3104d0f89

[ "MIT" ]

9

2020-04-23T14:22:48.000Z

2022-02-25T21:35:05.000Z

crawler/crawler/treewalk/scheduler/responses.py

amosproj/amos-ss2020-metadata-hub

f8434b27b306332c117a8dd20a8a55a3104d0f89

[ "MIT" ]

42

2020-04-24T17:59:33.000Z

2022-02-16T01:09:23.000Z

crawler/crawler/treewalk/scheduler/responses.py

amosproj/amos-ss2020-metadata-hub

f8434b27b306332c117a8dd20a8a55a3104d0f89

[ "MIT" ]

2

2020-08-17T11:19:44.000Z

2021-04-30T08:32:05.000Z

"""This module contains the responses coming from the scheduler.""" # Local imports import crawler.communication as communication def respond_config_already_present(identifier: str) -> None: """Respond that the config is already present in the schedule. This function creates a corresponding response object and inserts it in the scheduler output queue. Args: identifier (str): identifier of the configuration """ response = communication.Response( success=False, message=( f'Configuration with identifier {identifier} ' f'is already present in the schedule, thus it was not added.' ), command=communication.SCHEDULER_ADD_CONFIG ) communication.scheduler_queue_output.put(response) def respond_config_inserted(identifier: str, success: bool) -> None: """Respond that the config was inserted in the database. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the insertion succeeded or failed. Args: identifier (str): identifier of the configuration success (bool): insertion succeeded/failed """ if success: response = communication.Response( success=True, message=( f'Configuration with identifier {identifier} ' f'was successfully added to the schedule.' ), command=communication.SCHEDULER_ADD_CONFIG ) else: response = communication.Response( success=False, message=( f'Configuration with identifier {identifier} ' f'wasn\'t added to the schedule due to an internal error.' ), command=communication.SCHEDULER_ADD_CONFIG ) communication.scheduler_queue_output.put(response) def respond_config_deleted(identifier: str, success: bool) -> None: """Respond that the config was deleted from the database. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the deletion succeeded or failed. Args: identifier (str): identifier of the configuration success (bool): insertion succeeded/failed """ if success: response = communication.Response( success=True, message=( f'Configuration with identifier {identifier} ' f'was successfully deleted from the schedule.' ), command=communication.SCHEDULER_REMOVE_CONFIG ) else: response = communication.Response( success=False, message=( f'Configuration with identifier {identifier} ' f'wasn\'t deleted from the schedule (not present).' ), command=communication.SCHEDULER_REMOVE_CONFIG ) communication.scheduler_queue_output.put(response) def respond_schedule(schedule: dict) -> None: """Respond the TreeWalk schedule. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the insertion succeeded or failed. Args: schedule (dict): schedule """ if schedule is None: response = communication.Response( success=False, message='Unable to read schedule.', command=communication.SCHEDULER_GET_SCHEDULE ) else: response = communication.Response( success=True, message=schedule, command=communication.SCHEDULER_GET_SCHEDULE ) communication.scheduler_queue_output.put(response) def respond_interval_overlaps(identifier: str) -> None: """Respond that the interval overlaps with a already existing one. This function creates a corresponding response object and inserts it in the scheduler output queue. Args: identifier (str): identifier of the interval """ response = communication.Response( success=False, message=(f'Interval with identifier {identifier} is overlapping.'), command=communication.SCHEDULER_ADD_INTERVAL ) communication.scheduler_queue_output.put(response) def respond_interval_inserted(identifier: str, success: bool) -> None: """Respond that the interval was inserted in the database. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the insertion succeeded or failed. Args: identifier (str): identifier of the interval success (bool): insertion succeeded/failed """ if success: response = communication.Response( success=True, message=( f'Interval with identifier {identifier} ' f'was successfully added.' ), command=communication.SCHEDULER_ADD_INTERVAL ) else: response = communication.Response( success=False, message=( f'Interval with identifier {identifier} ' f'wasn\'t added to the database due to an internal error.' ), command=communication.SCHEDULER_ADD_INTERVAL ) communication.scheduler_queue_output.put(response) def respond_interval_deleted(identifier: str, success: bool) -> None: """Respond that the interval was deleted from the database. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the insertion succeeded or failed. Args: identifier (str): identifier of the interval success (bool): insertion succeeded/failed """ if success: response = communication.Response( success=True, message=( f'Interval with identifier {identifier} ' f'was successfully deleted from the database.' ), command=communication.SCHEDULER_REMOVE_INTERVAL ) else: response = communication.Response( success=False, message=( f'Interval with identifier {identifier} ' f'wasn\'t deleted from the database because it wasn\' present.' ), command=communication.SCHEDULER_REMOVE_INTERVAL ) communication.scheduler_queue_output.put(response) def respond_intervals(intervals: dict) -> None: """Respond the intervals. This function creates a corresponding response object and inserts it in the scheduler output queue. The response depends if the insertion succeeded or failed. Args: intervals (dict): intervals """ if intervals is None: response = communication.Response( success=False, message='Unable to read intervals.', command=communication.SCHEDULER_GET_INTERVALS ) else: response = communication.Response( success=True, message=intervals, command=communication.SCHEDULER_GET_INTERVALS ) communication.scheduler_queue_output.put(response)

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null

0

1

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null

0

6

5ad422ecaa5acdaa32cd265aee26a9d83bb32465

2,502

py

Python

tests/test_async_finder.py

alialdakheel/splinter

b4c48dc0af9ef98d7d9268f42f4d31a51e65fd68

[ "BSD-3-Clause" ]

null

tests/test_async_finder.py

alialdakheel/splinter

b4c48dc0af9ef98d7d9268f42f4d31a51e65fd68

[ "BSD-3-Clause" ]

null

tests/test_async_finder.py

alialdakheel/splinter

b4c48dc0af9ef98d7d9268f42f4d31a51e65fd68

[ "BSD-3-Clause" ]

null

# -*- coding: utf-8 -*- # Copyright 2012 splinter authors. All rights reserved. # Use of this source code is governed by a BSD-style # license that can be found in the LICENSE file. from .base import supported_browsers from .fake_webapp import EXAMPLE_APP import pytest @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_css_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_css(".async-element", wait_time=10) assert 1 == len(elements) @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_xpath_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_xpath("//h4", wait_time=10) assert 1 == len(elements) @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_tag_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_tag("h4", wait_time=10) assert 1 == len(elements) @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_id_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_id("async-header", wait_time=10) assert 1 == len(elements) @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_name_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_name("async-input", wait_time=10) assert 1 == len(elements) @pytest.mark.parametrize('browser_name', supported_browsers) def test_find_by_value_should_found_an_async_element(get_new_browser, browser_name): browser = get_new_browser(browser_name) browser.visit(EXAMPLE_APP) browser.find_by_css(".add-async-element").click() elements = browser.find_by_value("async-header-value", wait_time=10) assert 1 == len(elements)

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null

0

1

0

null

0

6

51f4cdeb23017006192cd46d4b798aee037c8bd8

25

py

Python

chadlib/collection/__init__.py

cjreynol/chadlib

e417a6c5b100b7124a7d9b61d0120b3caa897bb8

[ "MIT" ]

1

2021-08-06T21:56:52.000Z

chadlib/collection/__init__.py

cjreynol/chadlib

e417a6c5b100b7124a7d9b61d0120b3caa897bb8

[ "MIT" ]

null

chadlib/collection/__init__.py

cjreynol/chadlib

e417a6c5b100b7124a7d9b61d0120b3caa897bb8

[ "MIT" ]

null

from .stack import Stack

12.5

24

0.8

4

25

5

0.75

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1

25

0.952381

0

1

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0

null

0

1

0

1

0

1

0

6

cfcfebd134e39a6d1f7d24e787d043e219d5b351

133

py

Python

communicode/__init__.py

thomashancock/CommuniCode-old-for-presentation

a21746ba70ead268ff31f03016f4889b765bf4af

[ "MIT" ]

null

communicode/__init__.py

thomashancock/CommuniCode-old-for-presentation

a21746ba70ead268ff31f03016f4889b765bf4af

[ "MIT" ]

1

2015-08-03T08:56:02.000Z

2015-08-24T17:25:56.000Z

communicode/__init__.py

FrejaThoresen/CommuniCode

509f7062238a53ff96d137f5b07111de2c61639d

[ "MIT" ]

null

import gitlab from django.conf import settings git = gitlab.Gitlab(settings.SECRET_GITLAB_HOST, token=settings.SECRET_GITLAB_TOKEN)

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null

0

1

0

1

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6

3200d2b5bcd54c5dee257a42a44850c248d1f0dc

102

py

Python

chessdotcom/__init__.py

Phalanthus/chess.com

9d5b722035c502146354a51d6ab7735cdc88ccfa

[ "MIT" ]

28

2020-12-13T23:37:11.000Z

2022-03-31T02:01:34.000Z

chessdotcom/__init__.py

Phalanthus/chess.com

9d5b722035c502146354a51d6ab7735cdc88ccfa

[ "MIT" ]

7

2021-03-01T15:24:15.000Z

2022-02-27T03:38:54.000Z

chessdotcom/__init__.py

Phalanthus/chess.com

9d5b722035c502146354a51d6ab7735cdc88ccfa

[ "MIT" ]

2

2020-06-25T13:16:18.000Z

2020-06-25T21:42:50.000Z

from chessdotcom.types import ChessDotComError, ChessDotComResponse from chessdotcom.client import *

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true

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1

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6

5c6a52e623a3fc0381f14de5394f9e21d84ede20

76

py

Python

schpf/__init__.py

mag1pie/scHPF

926f8831b4167ad877572a5e34d1e7d2f729b1c4

[ "BSD-2-Clause" ]

null

schpf/__init__.py

mag1pie/scHPF

926f8831b4167ad877572a5e34d1e7d2f729b1c4

[ "BSD-2-Clause" ]

null

schpf/__init__.py

mag1pie/scHPF

926f8831b4167ad877572a5e34d1e7d2f729b1c4

[ "BSD-2-Clause" ]

null

from .scHPF_ import * from .util import * from ._version import __version__

19

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5.3

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1

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null

0

1

0

1

0

1

0

6

5cb339014726b852be63e5d06b521682896434e3

220

py

Python

src/chemspace/__init__.py

sunoru/VisChemSpace

d30e8e3568ade91a68e6fa299dd67d7fd9166bc4

[ "MIT" ]

1

2019-01-03T06:09:19.000Z

src/chemspace/__init__.py

sunoru/VisChemSpace

d30e8e3568ade91a68e6fa299dd67d7fd9166bc4

[ "MIT" ]

null

src/chemspace/__init__.py

sunoru/VisChemSpace

d30e8e3568ade91a68e6fa299dd67d7fd9166bc4

[ "MIT" ]

null

from chemspace.load_data import load_data, load_nmr, load_ir from chemspace.types import NMRVector, IRVector, SpectrumVector from chemspace.fingerprints import Fingerprints from chemspace.graph import ChemicalSpaceGraph

44

63

0.872727

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220

6.714286

0.5

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0

0.090909

220

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0

true

0

1

0

1

0.25

1

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0

1

0

null

0

1

0

1

0

1

0

6

7a46224293f69ae5223617bb536ce4e3e195bd31

31

py

Python

bumblebee/bees/weibo/__init__.py

nosoyyo/bumblebee

60452b03b2cd255ae4582a830b463fe7183e209e

[ "Apache-2.0" ]

null

bumblebee/bees/weibo/__init__.py

nosoyyo/bumblebee

60452b03b2cd255ae4582a830b463fe7183e209e

[ "Apache-2.0" ]

null

bumblebee/bees/weibo/__init__.py

nosoyyo/bumblebee

60452b03b2cd255ae4582a830b463fe7183e209e

[ "Apache-2.0" ]

null

from .weibobee import WeiboBee

15.5

30

0.83871

4

31

6.5

0.75

0

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31

1

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0.962963

0

1

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true

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1

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1

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1

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null

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1

0

null

0

1

0

1

0

1

0

6

7aa3e9a5096c5ddc3c9ace004c03500d96bcecca

408

py

Python

tests/transformer/operators/test_comparison_operators.py

rahulbahal7/restricted-python

c39cffe71dfc30630e946977735303d3a65b0383

[ "ZPL-2.1" ]

236

2015-01-03T17:14:53.000Z

2022-03-01T15:52:46.000Z

tests/transformer/operators/test_comparison_operators.py

rahulbahal7/restricted-python

c39cffe71dfc30630e946977735303d3a65b0383

[ "ZPL-2.1" ]

149

2016-10-24T06:56:44.000Z

2022-02-24T08:09:10.000Z

tests/transformer/operators/test_comparison_operators.py

rahulbahal7/restricted-python

c39cffe71dfc30630e946977735303d3a65b0383

[ "ZPL-2.1" ]

30

2015-04-03T05:38:13.000Z

2021-11-10T05:13:38.000Z

from tests.helper import restricted_eval def test_Eq(): assert restricted_eval('1 == 1') is True def test_NotEq(): assert restricted_eval('1 != 2') is True def test_Gt(): assert restricted_eval('2 > 1') is True def test_Lt(): assert restricted_eval('1 < 2') def test_GtE(): assert restricted_eval('2 >= 2') is True def test_LtE(): assert restricted_eval('1 <= 2') is True

15.692308

44

0.659314

64

408

4

0.296875

0.382813

0.46875

0.328125

0.496094

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0

0.037267

0.210784

408

25

45

16.32

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0

0.083333

0

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1

0.461538

true

0

0.076923

0

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0

null

1

0

null

0

1

0

1

0

6

7aad8df958d81efe593a9b784e5a22aa229d8e5d

28

py

Python

rlib/algorithms/vpg/__init__.py

MarcioPorto/rlib

5919f2dc52105000a23a25c31bbac260ca63565f

[ "MIT" ]

1

2019-09-08T08:33:13.000Z

rlib/algorithms/vpg/__init__.py

MarcioPorto/rlib

5919f2dc52105000a23a25c31bbac260ca63565f

[ "MIT" ]

26

2019-03-15T03:11:21.000Z

2022-03-11T23:42:46.000Z

rlib/algorithms/vpg/__init__.py

MarcioPorto/rlib

5919f2dc52105000a23a25c31bbac260ca63565f

[ "MIT" ]

null

from .agent import VPGAgent

14

27

0.821429

4

28

5.75

1

0

0.142857

28

1

28

0.958333

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

8fbb8025465b4a97be202eba2279336ee52264bd

133

py

Python

Dataset/Leetcode/train/104/581.py

kkcookies99/UAST

fff81885aa07901786141a71e5600a08d7cb4868

[ "MIT" ]

null

Dataset/Leetcode/train/104/581.py

kkcookies99/UAST

fff81885aa07901786141a71e5600a08d7cb4868

[ "MIT" ]

null

Dataset/Leetcode/train/104/581.py

kkcookies99/UAST

fff81885aa07901786141a71e5600a08d7cb4868

[ "MIT" ]

null

class Solution(object): def XXX(self, root): return 0 if not root else max(self.XXX(root.left),self.XXX(root.right))+1

26.6

82

0.661654

23

133

3.826087

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0.25

0

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133

4

83

33.25

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0

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false

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null

0

1

0

1

0

6

8fd1f45836e437c9643d4ba819ed0b645f0c743e

99

py

Python

tests/conftest.py

upymake/pypan

a0bc128780d59a1dfccad82b592a4f31f5d35386

[ "MIT" ]

3

2020-06-23T21:24:20.000Z

2020-09-03T02:09:31.000Z

tests/conftest.py

upymake/pypan

a0bc128780d59a1dfccad82b592a4f31f5d35386

[ "MIT" ]

18

2020-04-26T09:55:14.000Z

2022-01-19T10:05:00.000Z

tests/conftest.py

vyahello/pypan

a0bc128780d59a1dfccad82b592a4f31f5d35386

[ "MIT" ]

null

from _pytest.config.argparsing import Parser from _pytest.fixtures import SubRequest import pytest

24.75

44

0.868687

13

99

6.461538

0.615385

0.238095

0

0.10101

99

3

45

33

0.94382

0

1

0

true

0

1

0

1

0

1

0

null

1

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1

0

null

0

1

0

1

0

1

0

6

8fd2db782e2435e85d39fe95558b66e3169ac206

2,303

py

Python

tests/sentry/api/endpoints/test_project_search_details.py

vperron/sentry

4ea0c8cb120a3165f0e0b185c64213b69ab621ea

[ "BSD-3-Clause" ]

20

2016-10-01T04:29:24.000Z

2020-10-09T07:23:34.000Z

tests/sentry/api/endpoints/test_project_search_details.py

tobetterman/sentry

fe85d3aee19dcdbfdd27921c4fb04529fc995a79

[ "BSD-3-Clause" ]

null

tests/sentry/api/endpoints/test_project_search_details.py

tobetterman/sentry

fe85d3aee19dcdbfdd27921c4fb04529fc995a79

[ "BSD-3-Clause" ]

7

2016-10-27T05:12:45.000Z

2021-05-01T14:29:53.000Z

from __future__ import absolute_import from django.core.urlresolvers import reverse from sentry.models import SavedSearch from sentry.testutils import APITestCase class ProjectSearchDetailsTest(APITestCase): def test_simple(self): self.login_as(user=self.user) project = self.create_project(name='foo') search = SavedSearch.objects.create( project=project, name='foo', query='', ) url = reverse('sentry-api-0-project-search-details', kwargs={ 'organization_slug': project.organization.slug, 'project_slug': project.slug, 'search_id': search.id, }) response = self.client.get(url) assert response.status_code == 200, response.content assert response.data['id'] == str(search.id) class UpdateProjectSearchDetailsTest(APITestCase): def test_simple(self): self.login_as(user=self.user) project = self.create_project(name='foo') search = SavedSearch.objects.create( project=project, name='foo', query='', ) url = reverse('sentry-api-0-project-search-details', kwargs={ 'organization_slug': project.organization.slug, 'project_slug': project.slug, 'search_id': search.id, }) response = self.client.put(url, {'name': 'bar'}) assert response.status_code == 200, response.content assert response.data['id'] == str(search.id) search = SavedSearch.objects.get(id=search.id) assert search.name == 'bar' class DeleteProjectSearchTest(APITestCase): def test_simple(self): self.login_as(user=self.user) project = self.create_project(name='foo') search = SavedSearch.objects.create( project=project, name='foo', query='', ) url = reverse('sentry-api-0-project-search-details', kwargs={ 'organization_slug': project.organization.slug, 'project_slug': project.slug, 'search_id': search.id, }) response = self.client.delete(url) assert response.status_code == 204, response.content assert not SavedSearch.objects.filter(id=search.id).exists()

29.909091

69

0.613982

243

2,303

5.711934

0.230453

0.057637

0.060519

0.051873

0.729827

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0

0.007117

0.267911

2,303

76

70

30.302632

0.816133

0

0.701754

0

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0

0.122807

1

0.052632

false

0

0.070175

0

0.175439

0

null

0

1

0

1

0

null

0

6

89003c26224155d30406f5cb927c49bc462a46ef

142

py

Python

PyVuka/svd.py

NobregaIPI/pyvuka

62b0540af8fc0a556fa9f5b2338f81b74dac1902

[ "Unlicense" ]

null

PyVuka/svd.py

NobregaIPI/pyvuka

62b0540af8fc0a556fa9f5b2338f81b74dac1902

[ "Unlicense" ]

null

PyVuka/svd.py

NobregaIPI/pyvuka

62b0540af8fc0a556fa9f5b2338f81b74dac1902

[ "Unlicense" ]

2

2020-02-07T18:51:42.000Z

2021-07-07T15:51:21.000Z

from numpy.linalg.linalg import svd as npsvd def svd(): """Perform a singular value decomposition.""" print("SVD not implemented")

17.75

49

0.697183

19

142

5.210526

0.842105

0

0.190141

142

7

50

20.285714

0.86087

0.274648

0

0.197917

0

1

0.333333

true

0

0.333333

0

0.666667

0.333333

1

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0

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0

null

0

1

0

1

0

1

0

6

890a2edb0b1a27198f200280cf2922c2c606e2a7

22,049

py

Python

tests/test_bitey_cpu_addressing_mode.py

jgerrish/bitey

a393a83c19338d94116f3405f4b8a0f03ea84d79

[ "MIT" ]

null

tests/test_bitey_cpu_addressing_mode.py

jgerrish/bitey

a393a83c19338d94116f3405f4b8a0f03ea84d79

[ "MIT" ]

null

tests/test_bitey_cpu_addressing_mode.py

jgerrish/bitey

a393a83c19338d94116f3405f4b8a0f03ea84d79

[ "MIT" ]

null

import pytest from bitey.cpu.addressing_mode import ( AbsoluteAddressingMode, AbsoluteIndirectAddressingMode, AbsoluteIndirectPageBoundaryBugAddressingMode, AbsoluteXAddressingMode, AbsoluteYAddressingMode, AccumulatorAddressingMode, ImpliedAddressingMode, IndexedIndirectAddressingMode, IndirectIndexedAddressingMode, ZeroPageAddressingMode, ZeroPageXAddressingMode, ZeroPageYAddressingMode, RelativeAddressingMode, ) from bitey.computer.computer import Computer def build_computer(): with open("chip/6502.json") as f: chip_data = f.read() computer = Computer.build_from_json(chip_data) assert len(computer.memory.memory) == 65536 return computer return None # module scope means run once per test module @pytest.fixture(scope="module") def setup(): computer = build_computer() yield computer def test_cpu_addressing_mode_implied_get_value(): iam = ImpliedAddressingMode() assert type(iam) == ImpliedAddressingMode assert iam.get_value(None, None, None) == (None, None) def test_cpu_addressing_mode_absolute_get_value(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) computer.memory.write(0x2010, 0x33) computer.cpu.registers["PC"].set(0x0B) aam = AbsoluteAddressingMode() assert type(aam) == AbsoluteAddressingMode value = aam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert aam.adl == 0x10 assert aam.adh == 0x20 assert value == (0x2010, 0x33) assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_indirect_get_value(setup): computer = setup computer.reset() # Pointer to the pointer to the effective address computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) # Pointer to the effective address computer.memory.write(0x2010, 0x33) computer.memory.write(0x2011, 0x55) computer.memory.write(0x5533, 0x11) computer.cpu.registers["PC"].set(0x0B) aam = AbsoluteIndirectAddressingMode() assert type(aam) == AbsoluteIndirectAddressingMode value = aam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) # adl and adh are the effective address low and high bytes # not the original address (PC + 1, PC + 2) assert aam.adl == 0x33 assert aam.adh == 0x55 assert value == (0x5533, 0x11) assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_immediate_get_value(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.cpu.registers["PC"].set(0x0B) zpam = ZeroPageAddressingMode() assert type(zpam) == ZeroPageAddressingMode value = zpam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert value == (0x10, 0x33) assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_zeropagex_get_value(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0x51, 0xC1) computer.cpu.registers["PC"].set(0x0B) # set the X register computer.cpu.registers["X"].set(0x41) zpxam = ZeroPageXAddressingMode() assert type(zpxam) == ZeroPageXAddressingMode (address, value) = zpxam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0x51 assert value == 0xC1 assert computer.cpu.registers["PC"].get() == 0x0C def test_cpu_addressing_mode_zeropagex_get_value_wrap(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0x05, 0xC1) computer.cpu.registers["PC"].set(0x0B) # set the X register computer.cpu.registers["X"].set(0xF5) zpxam = ZeroPageXAddressingMode() assert type(zpxam) == ZeroPageXAddressingMode (address, value) = zpxam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0x05 assert value == 0xC1 assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_zeropagex_get_value_wrap_on_255(setup): "Test wrapping exactly on a value of 0xFF" computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0x06, 0xC1) computer.memory.write(0xFF, 0xFD) computer.cpu.registers["PC"].set(0x0B) # set the X register computer.cpu.registers["X"].set(0xEF) # The sum should be 0xFF zpxam = ZeroPageXAddressingMode() assert type(zpxam) == ZeroPageXAddressingMode (address, value) = zpxam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0xFF assert value == 0xFD assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_zeropagey_get_value(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0x51, 0xC1) computer.cpu.registers["PC"].set(0x0B) # set the Y register computer.cpu.registers["Y"].set(0x41) zpyam = ZeroPageYAddressingMode() assert type(zpyam) == ZeroPageYAddressingMode (address, value) = zpyam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0x51 assert value == 0xC1 assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_zeropagey_get_value_wrap(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0x05, 0xC1) computer.cpu.registers["PC"].set(0x0B) # set the Y register computer.cpu.registers["Y"].set(0xF5) zpyam = ZeroPageYAddressingMode() assert type(zpyam) == ZeroPageYAddressingMode (address, value) = zpyam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0x05 assert value == 0xC1 assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_zeropagey_get_value_nowrap_ff(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x10, 0x33) computer.memory.write(0xFF, 0xC1) computer.cpu.registers["PC"].set(0x0B) # set the Y register computer.cpu.registers["Y"].set(0xEF) zpyam = ZeroPageYAddressingMode() assert type(zpyam) == ZeroPageYAddressingMode (address, value) = zpyam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0xFF assert value == 0xC1 assert computer.cpu.registers["PC"].value == 0x0C def test_cpu_addressing_mode_relative_get_value(setup): computer = setup computer.reset() computer.memory.write(0xA0, 0x10) computer.memory.write(0x00B1, 0x12) computer.cpu.registers["PC"].set(0xA0) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0x00B1 assert value == 0x12 def test_cpu_addressing_mode_relative_get_value_negative(setup): computer = setup computer.reset() computer.memory.write(0x0070, 0xB0) computer.memory.write(0x0021, 0x1A) computer.cpu.registers["PC"].set(0x70) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0x0021 assert value == 0x1A def test_cpu_addressing_mode_relative_get_value_negative_lt_zero(setup): computer = setup computer.reset() computer.memory.write(0x0020, 0xB0) computer.memory.write(0xFFD1, 0x15) computer.cpu.registers["PC"].set(0x20) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0xFFD1 assert value == 0x15 def test_cpu_addressing_mode_relative_get_value_negative_page_crossing(setup): computer = setup computer.reset() computer.memory.write(0x70, 0xB0) computer.memory.write(0x0021, 0x08) computer.cpu.registers["PC"].set(0x70) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0x0021 assert value == 0x08 def test_cpu_addressing_mode_relative_get_value_page_crossing(setup): computer = setup computer.reset() computer.memory.write(0xA0, 0x60) computer.memory.write(0x0101, 0xD1) computer.cpu.registers["PC"].set(0xA0) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0x0101 assert value == 0xD1 def test_cpu_addressing_mode_relative_get_value_gt_16_bit(setup): computer = setup computer.reset() computer.memory.write(0xFFC0, 0x60) computer.memory.write(0x0021, 0x10) computer.cpu.registers["PC"].set(0xFFC0) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0x0021 assert value == 0x0010 def test_cpu_addressing_mode_relative_get_value_lt_zero(setup): computer = setup computer.reset() computer.memory.write(0x0003, 0x80) computer.memory.write(0xFF84, 0xF3) computer.cpu.registers["PC"].set(0x0003) rel = RelativeAddressingMode() assert type(rel) == RelativeAddressingMode (addr, value) = rel.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert addr == 0xFF84 assert value == 0xF3 def test_cpu_addressing_mode_indirect_indexed(setup): computer = setup computer.reset() # Zero Page ADL computer.memory.write(0x10, 0x70) # Zero Page ADH computer.memory.write(0x11, 0x0B) # Final address computer.memory.write(0x0B75, 0x73) computer.cpu.registers["PC"].set(0x10) computer.cpu.registers["Y"].set(0x05) am = IndirectIndexedAddressingMode() assert type(am) == IndirectIndexedAddressingMode value = am.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert value == (0xB75, 0x73) def test_cpu_addressing_mode_indirect_indexed_page_rollover(setup): computer = setup computer.reset() # Zero Page ADL computer.memory.write(0x10, 0x70) # Zero Page ADH computer.memory.write(0x11, 0xFF) # Final address computer.memory.write(0x0009, 0x73) computer.cpu.registers["PC"].set(0x10) computer.cpu.registers["Y"].set(0x99) am = IndirectIndexedAddressingMode() assert type(am) == IndirectIndexedAddressingMode (address, value) = am.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0x09 assert value == 0x73 def test_cpu_addressing_mode_indirect_indexed_page_norollover_ffff(setup): computer = setup computer.reset() # Zero Page ADL computer.memory.write(0x10, 0x70) # Zero Page ADH computer.memory.write(0x11, 0xFF) # Final address computer.memory.write(0xFFFF, 0x73) computer.cpu.registers["PC"].set(0x10) computer.cpu.registers["Y"].set(0x8F) am = IndirectIndexedAddressingMode() assert type(am) == IndirectIndexedAddressingMode (address, value) = am.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address == 0xFFFF assert value == 0x73 def test_cpu_addressing_mode_indexed_indirect(setup): computer = setup computer.reset() # Zero Page ADL computer.memory.write(0x14, 0x70) # Zero Page ADH computer.memory.write(0x15, 0x0B) # Final address computer.memory.write(0x0B70, 0x73) computer.cpu.registers["PC"].set(0x10) computer.cpu.registers["X"].set(0x04) am = IndexedIndirectAddressingMode() assert type(am) == IndexedIndirectAddressingMode value = am.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert value == (0x0B70, 0x73) def test_cpu_addressing_mode_indexed_indirect_incorrect_wrap(setup): "Test for bug with incorrect wrap case" computer = setup computer.reset() # Zero Page ADL computer.memory.write(0xFF, 0x70) # Zero Page ADH computer.memory.write(0x00, 0x0B) # Final address computer.memory.write(0x0B70, 0x73) computer.cpu.registers["PC"].set(0xFB) computer.cpu.registers["X"].set(0x04) am = IndexedIndirectAddressingMode() assert type(am) == IndexedIndirectAddressingMode value = am.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert value == (0x0B70, 0x73) def test_cpu_addressing_mode_absolute_x(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) computer.memory.write(0x2015, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["X"].set(0x05) axam = AbsoluteXAddressingMode() assert type(axam) == AbsoluteXAddressingMode value = axam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert axam.adl == 0x10 assert axam.adh == 0x20 assert value == (0x2015, 0x33) assert computer.cpu.registers["PC"].value == 13 def test_cpu_addressing_mode_absolute_x_page_crossing(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) computer.memory.write(0x2105, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["X"].set(0xF5) axam = AbsoluteXAddressingMode() assert type(axam) == AbsoluteXAddressingMode value = axam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) assert axam.adl == 0x10 assert axam.adh == 0x20 assert value == (0x2105, 0x33) assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_x_eom_wrap(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0xFF) computer.memory.write(0x0005, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["X"].set(0xF5) axam = AbsoluteXAddressingMode() assert type(axam) == AbsoluteXAddressingMode (address, value) = axam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert axam.adl == 0x10 assert axam.adh == 0xFF assert address == 0x05 assert value == 0x33 assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_x_eom_nowrap_ffff(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0xFF) computer.memory.write(0x0006, 0x33) computer.memory.write(0xFFFF, 0xC4) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["X"].set(0xEF) axam = AbsoluteXAddressingMode() assert type(axam) == AbsoluteXAddressingMode (address, value) = axam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert axam.adl == 0x10 assert axam.adh == 0xFF assert address == 0xFFFF assert value == 0xC4 assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_y(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) computer.memory.write(0x2023, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["Y"].set(0x13) ayam = AbsoluteYAddressingMode() assert type(ayam) == AbsoluteYAddressingMode (address, value) = ayam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert ayam.adl == 0x10 assert ayam.adh == 0x20 assert value == 0x33 assert address == 0x2023 assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_y_page_crossing(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) computer.memory.write(0x2105, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["Y"].set(0xF5) ayam = AbsoluteYAddressingMode() assert type(ayam) == AbsoluteYAddressingMode (address, value) = ayam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert ayam.adl == 0x10 assert ayam.adh == 0x20 assert address == 0x2105 assert value == 0x33 assert computer.cpu.registers["PC"].value == 0x0D def test_cpu_addressing_mode_absolute_y_eom_wrap(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0xFF) computer.memory.write(0x0005, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["Y"].set(0xF5) ayam = AbsoluteYAddressingMode() assert type(ayam) == AbsoluteYAddressingMode (address, value) = ayam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert ayam.adl == 0x10 assert ayam.adh == 0xFF assert address == 0x0005 assert value == 0x33 assert computer.cpu.registers["PC"].value == 0x0D def test_cpu_addressing_mode_absolute_y_eom_nowrap_ffff(setup): computer = setup computer.reset() computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0xFF) computer.memory.write(0xFFFF, 0x33) computer.cpu.registers["PC"].set(0x0B) computer.cpu.registers["Y"].set(0xEF) ayam = AbsoluteYAddressingMode() assert type(ayam) == AbsoluteYAddressingMode (address, value) = ayam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert ayam.adl == 0x10 assert ayam.adh == 0xFF assert value == 0x33 assert address == 0xFFFF assert computer.cpu.registers["PC"].value == 0x0D def test_cpu_addressing_mode_absolute_indirect_get_instr_str(setup): computer = setup computer.reset() # Pointer to the address containing the effective address computer.memory.write(0x01, 0xA0) computer.memory.write(0x02, 0x00) # The pointer to the effective address computer.memory.write(0xA0, 0x05) computer.memory.write(0xA1, 0x00) computer.cpu.registers["PC"].set(0x01) aiam = AbsoluteIndirectAddressingMode() inst_str = aiam.get_inst_str( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert inst_str == "($0005)" def test_cpu_addressing_mode_accumulator(setup): "Test accumulator addressing mode" computer = setup computer.reset() computer.cpu.registers["PC"].set(0x00) computer.cpu.registers["A"].set(0x13) aam = AccumulatorAddressingMode() inst_str = aam.get_inst_str( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert type(aam) == AccumulatorAddressingMode (address, value) = aam.get_value( computer.cpu.flags, computer.cpu.registers, computer.memory ) assert address is None assert value == 0x13 assert computer.cpu.registers["PC"].get() == 0x00 assert inst_str == "" def test_cpu_addressing_mode_absolute_indirect_page_boundary_bug_get_value(setup): computer = setup computer.reset() # Pointer to the pointer to the effective address computer.memory.write(0x0B, 0x10) computer.memory.write(0x0C, 0x20) # Pointer to the effective address computer.memory.write(0x2010, 0x33) computer.memory.write(0x2011, 0x55) computer.memory.write(0x5533, 0x11) computer.cpu.registers["PC"].set(0x0B) aam = AbsoluteIndirectPageBoundaryBugAddressingMode(3) assert type(aam) == AbsoluteIndirectPageBoundaryBugAddressingMode value = aam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) # adl and adh are the effective address low and high bytes # not the original address (PC + 1, PC + 2) assert aam.adl == 0x33 assert aam.adh == 0x55 assert value == (0x5533, 0x11) assert computer.cpu.registers["PC"].get() == 0x0D def test_cpu_addressing_mode_absolute_indirect_page_boundary_bug_wrap_get_value(setup): computer = setup computer.reset() # Pointer to the pointer to the effective address computer.memory.write(0x00FF, 0x10) computer.memory.write(0x0000, 0x20) # Pointer to the effective address computer.memory.write(0x2010, 0x33) computer.memory.write(0x2011, 0x55) computer.memory.write(0x5533, 0x11) computer.cpu.registers["PC"].set(0x00FF) aam = AbsoluteIndirectPageBoundaryBugAddressingMode(3) assert type(aam) == AbsoluteIndirectPageBoundaryBugAddressingMode value = aam.get_value(computer.cpu.flags, computer.cpu.registers, computer.memory) # adl and adh are the effective address low and high bytes # not the original address (PC + 1, PC + 2) assert aam.adl == 0x33 assert aam.adh == 0x55 assert value == (0x5533, 0x11) # Technically, the JMP instruction is the only instruction that uses this "buggy" # mode, so this shouldn't matter assert computer.cpu.registers["PC"].get() == 0x101

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6

64eb79e696a787f6f3ea5d4a6fd3eb52dbdc5d8b

122

py

Python

modules/msa/msa/utils/misc.py

haoyutan/MSA-Framework

7c5553b244347f26029729161e15e60b0cc805f5

[ "MIT" ]

2

2016-11-22T11:44:52.000Z

2017-08-29T02:38:01.000Z

modules/msa/msa/utils/misc.py

haoyutan/MSA-Framework

7c5553b244347f26029729161e15e60b0cc805f5

[ "MIT" ]

null

modules/msa/msa/utils/misc.py

haoyutan/MSA-Framework

7c5553b244347f26029729161e15e60b0cc805f5

[ "MIT" ]

null

import binascii, os def random_hex_string(length=40): return binascii.hexlify(os.urandom(int(length / 2))).decode()

20.333333

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77

py

Python

pages/matched_page.py

cgonzalez21/Test_Results

d7ce78f873a985742e00c7ce5d3d6c65447df537

[ "MIT" ]

null

pages/matched_page.py

cgonzalez21/Test_Results

d7ce78f873a985742e00c7ce5d3d6c65447df537

[ "MIT" ]

null

pages/matched_page.py

cgonzalez21/Test_Results

d7ce78f873a985742e00c7ce5d3d6c65447df537

[ "MIT" ]

null

from pages.base_page import BasePage class MatchedPage(BasePage): pass

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py

Python

scout/commands/export/__init__.py

szilvajuhos/scout

2f4a03fb3192a57c99fd62be626e8c22051e81af

[ "BSD-3-Clause" ]

1

2019-08-17T21:20:04.000Z

scout/commands/export/__init__.py

szilvajuhos/scout

2f4a03fb3192a57c99fd62be626e8c22051e81af

[ "BSD-3-Clause" ]

null

scout/commands/export/__init__.py

szilvajuhos/scout

2f4a03fb3192a57c99fd62be626e8c22051e81af

[ "BSD-3-Clause" ]

null

from .export_command import export

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py

Python

qiita_db/test/test_metadata_template.py

JWDebelius/qiita

3378e0fabe40a846691600e5de4fb72a3db70dd1

[ "BSD-3-Clause" ]

null

qiita_db/test/test_metadata_template.py

JWDebelius/qiita

3378e0fabe40a846691600e5de4fb72a3db70dd1

[ "BSD-3-Clause" ]

null

qiita_db/test/test_metadata_template.py

JWDebelius/qiita

3378e0fabe40a846691600e5de4fb72a3db70dd1

[ "BSD-3-Clause" ]

null

# ----------------------------------------------------------------------------- # Copyright (c) 2014--, The Qiita Development Team. # # Distributed under the terms of the BSD 3-clause License. # # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- from future.builtins import zip from six import StringIO from unittest import TestCase, main from datetime import datetime from tempfile import mkstemp from time import strftime from os import close, remove from os.path import join, basename from collections import Iterable import numpy.testing as npt import pandas as pd from pandas.util.testing import assert_frame_equal from qiita_core.util import qiita_test_checker from qiita_core.exceptions import IncompetentQiitaDeveloperError from qiita_db.exceptions import (QiitaDBDuplicateError, QiitaDBUnknownIDError, QiitaDBNotImplementedError, QiitaDBDuplicateHeaderError, QiitaDBExecutionError, QiitaDBColumnError, QiitaDBError, QiitaDBWarning) from qiita_db.study import Study, StudyPerson from qiita_db.user import User from qiita_db.data import RawData from qiita_db.util import (exists_table, get_db_files_base_dir, get_mountpoint, get_count, get_table_cols) from qiita_db.metadata_template import ( _get_datatypes, _as_python_types, MetadataTemplate, SampleTemplate, PrepTemplate, BaseSample, PrepSample, Sample, _prefix_sample_names_with_id, load_template_to_dataframe, get_invalid_sample_names) class TestUtilMetadataMap(TestCase): """Tests some utility functions on the metadata_template module""" def setUp(self): metadata_dict = { 'Sample1': {'int_col': 1, 'float_col': 2.1, 'str_col': 'str1'}, 'Sample2': {'int_col': 2, 'float_col': 3.1, 'str_col': '200'}, 'Sample3': {'int_col': 3, 'float_col': 3, 'str_col': 'string30'}, } self.metadata_map = pd.DataFrame.from_dict(metadata_dict, orient='index') self.headers = ['float_col', 'str_col', 'int_col'] def test_get_datatypes(self): """Correctly returns the data types of each column""" obs = _get_datatypes(self.metadata_map.ix[:, self.headers]) exp = ['float8', 'varchar', 'integer'] self.assertEqual(obs, exp) def test_as_python_types(self): """Correctly returns the columns as python types""" obs = _as_python_types(self.metadata_map, self.headers) exp = [[2.1, 3.1, 3], ['str1', '200', 'string30'], [1, 2, 3]] self.assertEqual(obs, exp) def test_prefix_sample_names_with_id(self): exp_metadata_dict = { '1.Sample1': {'int_col': 1, 'float_col': 2.1, 'str_col': 'str1'}, '1.Sample2': {'int_col': 2, 'float_col': 3.1, 'str_col': '200'}, '1.Sample3': {'int_col': 3, 'float_col': 3, 'str_col': 'string30'}, } exp_df = pd.DataFrame.from_dict(exp_metadata_dict, orient='index') _prefix_sample_names_with_id(self.metadata_map, 1) self.metadata_map.sort_index(inplace=True) exp_df.sort_index(inplace=True) assert_frame_equal(self.metadata_map, exp_df) @qiita_test_checker() class TestBaseSample(TestCase): """Tests the BaseSample class""" def test_init(self): """BaseSample init should raise an error (it's a base class)""" with self.assertRaises(IncompetentQiitaDeveloperError): BaseSample('SKM7.640188', SampleTemplate(1)) def test_exists(self): """exists should raise an error if called from the base class""" with self.assertRaises(IncompetentQiitaDeveloperError): BaseSample.exists('SKM7.640188', SampleTemplate(1)) @qiita_test_checker() class TestSample(TestCase): """Tests the Sample class""" def setUp(self): self.sample_template = SampleTemplate(1) self.sample_id = '1.SKB8.640193' self.tester = Sample(self.sample_id, self.sample_template) self.exp_categories = {'physical_location', 'has_physical_specimen', 'has_extracted_data', 'sample_type', 'required_sample_info_status', 'collection_timestamp', 'host_subject_id', 'description', 'season_environment', 'assigned_from_geo', 'texture', 'taxon_id', 'depth', 'host_taxid', 'common_name', 'water_content_soil', 'elevation', 'temp', 'tot_nitro', 'samp_salinity', 'altitude', 'env_biome', 'country', 'ph', 'anonymized_name', 'tot_org_carb', 'description_duplicate', 'env_feature', 'latitude', 'longitude'} def test_init_unknown_error(self): """Init raises an error if the sample id is not found in the template """ with self.assertRaises(QiitaDBUnknownIDError): Sample('Not_a_Sample', self.sample_template) def test_init_wrong_template(self): """Raises an error if using a PrepTemplate instead of SampleTemplate""" with self.assertRaises(IncompetentQiitaDeveloperError): Sample('SKB8.640193', PrepTemplate(1)) def test_init(self): """Init correctly initializes the sample object""" sample = Sample(self.sample_id, self.sample_template) # Check that the internal id have been correctly set self.assertEqual(sample._id, '1.SKB8.640193') # Check that the internal template have been correctly set self.assertEqual(sample._md_template, self.sample_template) # Check that the internal dynamic table name have been correctly set self.assertEqual(sample._dynamic_table, "sample_1") def test_eq_true(self): """Equality correctly returns true""" other = Sample(self.sample_id, self.sample_template) self.assertTrue(self.tester == other) def test_eq_false_type(self): """Equality returns false if types are not equal""" other = PrepSample(self.sample_id, PrepTemplate(1)) self.assertFalse(self.tester == other) def test_eq_false_id(self): """Equality returns false if ids are different""" other = Sample('1.SKD8.640184', self.sample_template) self.assertFalse(self.tester == other) def test_exists_true(self): """Exists returns true if the sample exists""" self.assertTrue(Sample.exists(self.sample_id, self.sample_template)) def test_exists_false(self): """Exists returns false if the sample does not exists""" self.assertFalse(Sample.exists('Not_a_Sample', self.sample_template)) def test_get_categories(self): """Correctly returns the set of category headers""" obs = self.tester._get_categories(self.conn_handler) self.assertEqual(obs, self.exp_categories) def test_len(self): """Len returns the correct number of categories""" self.assertEqual(len(self.tester), 30) def test_getitem_required(self): """Get item returns the correct metadata value from the required table """ self.assertEqual(self.tester['physical_location'], 'ANL') self.assertEqual(self.tester['collection_timestamp'], datetime(2011, 11, 11, 13, 00, 00)) self.assertTrue(self.tester['has_physical_specimen']) def test_getitem_dynamic(self): """Get item returns the correct metadata value from the dynamic table """ self.assertEqual(self.tester['SEASON_ENVIRONMENT'], 'winter') self.assertEqual(self.tester['depth'], 0.15) def test_getitem_id_column(self): """Get item returns the correct metadata value from the changed column """ self.assertEqual(self.tester['required_sample_info_status'], 'completed') def test_getitem_error(self): """Get item raises an error if category does not exists""" with self.assertRaises(KeyError): self.tester['Not_a_Category'] def test_setitem(self): with self.assertRaises(QiitaDBColumnError): self.tester['column that does not exist'] = 0.30 self.assertEqual(self.tester['tot_nitro'], 1.41) self.tester['tot_nitro'] = '1234.5' self.assertEqual(self.tester['tot_nitro'], 1234.5) def test_delitem(self): """delitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBNotImplementedError): del self.tester['DEPTH'] def test_iter(self): """iter returns an iterator over the category headers""" obs = self.tester.__iter__() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_categories) def test_contains_true(self): """contains returns true if the category header exists""" self.assertTrue('DEPTH' in self.tester) self.assertTrue('depth' in self.tester) def test_contains_false(self): """contains returns false if the category header does not exists""" self.assertFalse('Not_a_Category' in self.tester) def test_keys(self): """keys returns an iterator over the metadata headers""" obs = self.tester.keys() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_categories) def test_values(self): """values returns an iterator over the values""" obs = self.tester.values() self.assertTrue(isinstance(obs, Iterable)) exp = {'ANL', True, True, 'ENVO:soil', 'completed', datetime(2011, 11, 11, 13, 00, 00), '1001:M7', 'Cannabis Soil Microbiome', 'winter', 'n', '64.6 sand, 17.6 silt, 17.8 clay', '1118232', 0.15, '3483', 'root metagenome', 0.164, 114, 15, 1.41, 7.15, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.94, 'SKB8', 5, 'Burmese root', 'ENVO:plant-associated habitat', 74.0894932572, 65.3283470202} self.assertEqual(set(obs), exp) def test_items(self): """items returns an iterator over the (key, value) tuples""" obs = self.tester.items() self.assertTrue(isinstance(obs, Iterable)) exp = {('physical_location', 'ANL'), ('has_physical_specimen', True), ('has_extracted_data', True), ('sample_type', 'ENVO:soil'), ('required_sample_info_status', 'completed'), ('collection_timestamp', datetime(2011, 11, 11, 13, 00, 00)), ('host_subject_id', '1001:M7'), ('description', 'Cannabis Soil Microbiome'), ('season_environment', 'winter'), ('assigned_from_geo', 'n'), ('texture', '64.6 sand, 17.6 silt, 17.8 clay'), ('taxon_id', '1118232'), ('depth', 0.15), ('host_taxid', '3483'), ('common_name', 'root metagenome'), ('water_content_soil', 0.164), ('elevation', 114), ('temp', 15), ('tot_nitro', 1.41), ('samp_salinity', 7.15), ('altitude', 0), ('env_biome', 'ENVO:Temperate grasslands, savannas, and shrubland biome'), ('country', 'GAZ:United States of America'), ('ph', 6.94), ('anonymized_name', 'SKB8'), ('tot_org_carb', 5), ('description_duplicate', 'Burmese root'), ('env_feature', 'ENVO:plant-associated habitat'), ('latitude', 74.0894932572), ('longitude', 65.3283470202)} self.assertEqual(set(obs), exp) def test_get(self): """get returns the correct sample object""" self.assertEqual(self.tester.get('SEASON_ENVIRONMENT'), 'winter') self.assertEqual(self.tester.get('depth'), 0.15) def test_get_none(self): """get returns none if the sample id is not present""" self.assertTrue(self.tester.get('Not_a_Category') is None) @qiita_test_checker() class TestPrepSample(TestCase): """Tests the PrepSample class""" def setUp(self): self.prep_template = PrepTemplate(1) self.sample_id = '1.SKB8.640193' self.tester = PrepSample(self.sample_id, self.prep_template) self.exp_categories = {'center_name', 'center_project_name', 'emp_status', 'barcodesequence', 'library_construction_protocol', 'linkerprimersequence', 'target_subfragment', 'target_gene', 'run_center', 'run_prefix', 'run_date', 'experiment_center', 'experiment_design_description', 'experiment_title', 'platform', 'samp_size', 'sequencing_meth', 'illumina_technology', 'sample_center', 'pcr_primers', 'study_center'} def test_init_unknown_error(self): """Init errors if the PrepSample id is not found in the template""" with self.assertRaises(QiitaDBUnknownIDError): PrepSample('Not_a_Sample', self.prep_template) def test_init_wrong_template(self): """Raises an error if using a SampleTemplate instead of PrepTemplate""" with self.assertRaises(IncompetentQiitaDeveloperError): PrepSample('1.SKB8.640193', SampleTemplate(1)) def test_init(self): """Init correctly initializes the PrepSample object""" sample = PrepSample(self.sample_id, self.prep_template) # Check that the internal id have been correctly set self.assertEqual(sample._id, '1.SKB8.640193') # Check that the internal template have been correctly set self.assertEqual(sample._md_template, self.prep_template) # Check that the internal dynamic table name have been correctly set self.assertEqual(sample._dynamic_table, "prep_1") def test_eq_true(self): """Equality correctly returns true""" other = PrepSample(self.sample_id, self.prep_template) self.assertTrue(self.tester == other) def test_eq_false_type(self): """Equality returns false if types are not equal""" other = Sample(self.sample_id, SampleTemplate(1)) self.assertFalse(self.tester == other) def test_eq_false_id(self): """Equality returns false if ids are different""" other = PrepSample('1.SKD8.640184', self.prep_template) self.assertFalse(self.tester == other) def test_exists_true(self): """Exists returns true if the PrepSample exists""" self.assertTrue(PrepSample.exists(self.sample_id, self.prep_template)) def test_exists_false(self): """Exists returns false if the PrepSample does not exists""" self.assertFalse(PrepSample.exists('Not_a_Sample', self.prep_template)) def test_get_categories(self): """Correctly returns the set of category headers""" obs = self.tester._get_categories(self.conn_handler) self.assertEqual(obs, self.exp_categories) def test_len(self): """Len returns the correct number of categories""" self.assertEqual(len(self.tester), 21) def test_getitem_required(self): """Get item returns the correct metadata value from the required table """ self.assertEqual(self.tester['center_name'], 'ANL') self.assertTrue(self.tester['center_project_name'] is None) def test_getitem_dynamic(self): """Get item returns the correct metadata value from the dynamic table """ self.assertEqual(self.tester['pcr_primers'], 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT') self.assertEqual(self.tester['barcodesequence'], 'AGCGCTCACATC') def test_getitem_id_column(self): """Get item returns the correct metadata value from the changed column """ self.assertEqual(self.tester['emp_status'], 'EMP') def test_getitem_error(self): """Get item raises an error if category does not exists""" with self.assertRaises(KeyError): self.tester['Not_a_Category'] def test_setitem(self): """setitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBNotImplementedError): self.tester['barcodesequence'] = 'GTCCGCAAGTTA' def test_delitem(self): """delitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBNotImplementedError): del self.tester['pcr_primers'] def test_iter(self): """iter returns an iterator over the category headers""" obs = self.tester.__iter__() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_categories) def test_contains_true(self): """contains returns true if the category header exists""" self.assertTrue('BarcodeSequence' in self.tester) self.assertTrue('barcodesequence' in self.tester) def test_contains_false(self): """contains returns false if the category header does not exists""" self.assertFalse('Not_a_Category' in self.tester) def test_keys(self): """keys returns an iterator over the metadata headers""" obs = self.tester.keys() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_categories) def test_values(self): """values returns an iterator over the values""" obs = self.tester.values() self.assertTrue(isinstance(obs, Iterable)) exp = {'ANL', None, None, None, 'EMP', 'AGCGCTCACATC', 'This analysis was done as in Caporaso et al 2011 Genome ' 'research. The PCR primers (F515/R806) were developed against ' 'the V4 region of the 16S rRNA (both bacteria and archaea), ' 'which we determined would yield optimal community clustering ' 'with reads of this length using a procedure similar to that of' ' ref. 15. [For reference, this primer pair amplifies the ' 'region 533_786 in the Escherichia coli strain 83972 sequence ' '(greengenes accession no. prokMSA_id:470367).] The reverse PCR' ' primer is barcoded with a 12-base error-correcting Golay code' ' to facilitate multiplexing of up to 1,500 samples per lane, ' 'and both PCR primers contain sequencer adapter regions.', 'GTGCCAGCMGCCGCGGTAA', 'V4', '16S rRNA', 'ANL', 's_G1_L001_sequences', '8/1/12', 'ANL', 'micro biome of soil and rhizosphere of cannabis plants from ' 'CA', 'Cannabis Soil Microbiome', 'Illumina', '.25,g', 'Sequencing by synthesis', 'MiSeq', 'ANL', 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT', 'CCME'} self.assertEqual(set(obs), exp) def test_items(self): """items returns an iterator over the (key, value) tuples""" obs = self.tester.items() self.assertTrue(isinstance(obs, Iterable)) exp = {('center_name', 'ANL'), ('center_project_name', None), ('emp_status', 'EMP'), ('barcodesequence', 'AGCGCTCACATC'), ('library_construction_protocol', 'This analysis was done as in Caporaso et al 2011 Genome ' 'research. The PCR primers (F515/R806) were developed against ' 'the V4 region of the 16S rRNA (both bacteria and archaea), ' 'which we determined would yield optimal community clustering ' 'with reads of this length using a procedure similar to that ' 'of ref. 15. [For reference, this primer pair amplifies the ' 'region 533_786 in the Escherichia coli strain 83972 sequence ' '(greengenes accession no. prokMSA_id:470367).] The reverse ' 'PCR primer is barcoded with a 12-base error-correcting Golay ' 'code to facilitate multiplexing of up to 1,500 samples per ' 'lane, and both PCR primers contain sequencer adapter ' 'regions.'), ('linkerprimersequence', 'GTGCCAGCMGCCGCGGTAA'), ('target_subfragment', 'V4'), ('target_gene', '16S rRNA'), ('run_center', 'ANL'), ('run_prefix', 's_G1_L001_sequences'), ('run_date', '8/1/12'), ('experiment_center', 'ANL'), ('experiment_design_description', 'micro biome of soil and rhizosphere of cannabis plants ' 'from CA'), ('experiment_title', 'Cannabis Soil Microbiome'), ('platform', 'Illumina'), ('samp_size', '.25,g'), ('sequencing_meth', 'Sequencing by synthesis'), ('illumina_technology', 'MiSeq'), ('sample_center', 'ANL'), ('pcr_primers', 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT'), ('study_center', 'CCME')} self.assertEqual(set(obs), exp) def test_get(self): """get returns the correct sample object""" self.assertEqual(self.tester.get('barcodesequence'), 'AGCGCTCACATC') def test_get_none(self): """get returns none if the sample id is not present""" self.assertTrue(self.tester.get('Not_a_Category') is None) @qiita_test_checker() class TestMetadataTemplate(TestCase): """Tests the MetadataTemplate base class""" def setUp(self): self.study = Study(1) def test_init(self): """Init raises an error because it's not called from a subclass""" with self.assertRaises(IncompetentQiitaDeveloperError): MetadataTemplate(1) def test_create(self): """Create raises an error because it's not called from a subclass""" with self.assertRaises(QiitaDBNotImplementedError): MetadataTemplate.create() def test_exist(self): """Exists raises an error because it's not called from a subclass""" with self.assertRaises(IncompetentQiitaDeveloperError): MetadataTemplate.exists(self.study) def test_table_name(self): """table name raises an error because it's not called from a subclass """ with self.assertRaises(IncompetentQiitaDeveloperError): MetadataTemplate._table_name(self.study) @qiita_test_checker() class TestSampleTemplate(TestCase): """Tests the SampleTemplate class""" def setUp(self): self.metadata_dict = { 'Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'int_column': 1, 'latitude': 42.42, 'longitude': 41.41}, 'Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'int_column': 2, 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'latitude': 4.2, 'longitude': 1.1}, 'Sample3': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'int_column': 3, 'latitude': 4.8, 'longitude': 4.41}, } self.metadata = pd.DataFrame.from_dict(self.metadata_dict, orient='index') metadata_str_prefix_dict = { 'foo.Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'latitude': 42.42, 'longitude': 41.41}, 'bar.Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'latitude': 4.2, 'longitude': 1.1}, 'foo.Sample3': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'latitude': 4.8, 'longitude': 4.41}, } self.metadata_str_prefix = pd.DataFrame.from_dict( metadata_str_prefix_dict, orient='index') metadata_int_prefix_dict = { '12.Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'latitude': 42.42, 'longitude': 41.41}, '12.Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'latitude': 4.2, 'longitude': 1.1}, '12.Sample3': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'latitude': 4.8, 'longitude': 4.41}, } self.metadata_int_pref = pd.DataFrame.from_dict( metadata_int_prefix_dict, orient='index') metadata_prefixed_dict = { '2.Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'latitude': 42.42, 'longitude': 41.41}, '2.Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'latitude': 4.2, 'longitude': 1.1}, '2.Sample3': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'latitude': 4.8, 'longitude': 4.41}, } self.metadata_prefixed = pd.DataFrame.from_dict( metadata_prefixed_dict, orient='index') self.test_study = Study(1) info = { "timeseries_type_id": 1, "metadata_complete": True, "mixs_compliant": True, "number_samples_collected": 25, "number_samples_promised": 28, "portal_type_id": 3, "study_alias": "FCM", "study_description": "Microbiome of people who eat nothing but " "fried chicken", "study_abstract": "Exploring how a high fat diet changes the " "gut microbiome", "emp_person_id": StudyPerson(2), "principal_investigator_id": StudyPerson(3), "lab_person_id": StudyPerson(1) } self.new_study = Study.create(User('test@foo.bar'), "Fried Chicken Microbiome", [1], info) self.tester = SampleTemplate(1) self.exp_sample_ids = { '1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200', '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198', '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190', '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182', '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197', '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187', '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'} self._clean_up_files = [] self.metadata_dict_updated_dict = { 'Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '6', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'int_column': 1, 'latitude': 42.42, 'longitude': 41.41}, 'Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '5', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'the only one', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'int_column': 2, 'latitude': 4.2, 'longitude': 1.1}, 'Sample3': {'physical_location': 'new location', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '10', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'int_column': 3, 'latitude': 4.8, 'longitude': 4.41}, } self.metadata_dict_updated = pd.DataFrame.from_dict( self.metadata_dict_updated_dict, orient='index') metadata_dict_updated_sample_error = { 'Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '6', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'int_column': 1, 'latitude': 42.42, 'longitude': 41.41}, 'Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '5', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'the only one', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'int_column': 2, 'latitude': 4.2, 'longitude': 1.1}, 'Sample3': {'physical_location': 'new location', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '10', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'int_column': 3, 'latitude': 4.8, 'longitude': 4.41}, 'Sample4': {'physical_location': 'new location', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '10', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 4', 'str_column': 'Value for sample 4', 'int_column': 4, 'latitude': 4.8, 'longitude': 4.41} } self.metadata_dict_updated_sample_error = pd.DataFrame.from_dict( metadata_dict_updated_sample_error, orient='index') metadata_dict_updated_column_error = { 'Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '6', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'str_column': 'Value for sample 1', 'int_column': 1, 'latitude': 42.42, 'longitude': 41.41, 'extra_col': True}, 'Sample2': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '5', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'the only one', 'Description': 'Test Sample 2', 'str_column': 'Value for sample 2', 'int_column': 2, 'latitude': 4.2, 'longitude': 1.1, 'extra_col': True}, 'Sample3': {'physical_location': 'new location', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': '10', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 3', 'str_column': 'Value for sample 3', 'int_column': 3, 'latitude': 4.8, 'longitude': 4.41, 'extra_col': True}, } self.metadata_dict_updated_column_error = pd.DataFrame.from_dict( metadata_dict_updated_column_error, orient='index') def tearDown(self): for f in self._clean_up_files: remove(f) def test_study_id(self): """Ensure that the correct study ID is returned""" self.assertEqual(self.tester.study_id, 1) def test_init_unknown_error(self): """Init raises an error if the id is not known""" with self.assertRaises(QiitaDBUnknownIDError): SampleTemplate(2) def test_init(self): """Init successfully instantiates the object""" st = SampleTemplate(1) self.assertTrue(st.id, 1) def test_table_name(self): """Table name return the correct string""" obs = SampleTemplate._table_name(self.test_study.id) self.assertEqual(obs, "sample_1") def test_create_duplicate(self): """Create raises an error when creating a duplicated SampleTemplate""" with self.assertRaises(QiitaDBDuplicateError): SampleTemplate.create(self.metadata, self.test_study) def test_create_duplicate_header(self): """Create raises an error when duplicate headers are present""" self.metadata['STR_COLUMN'] = pd.Series(['', '', ''], index=self.metadata.index) with self.assertRaises(QiitaDBDuplicateHeaderError): SampleTemplate.create(self.metadata, self.new_study) def test_create_bad_sample_names(self): """Create raises an error when duplicate headers are present""" # set a horrible list of sample names self.metadata.index = ['o()xxxx[{::::::::>', 'sample.1', 'sample.3'] with self.assertRaises(QiitaDBColumnError): SampleTemplate.create(self.metadata, self.new_study) def test_create_error_cleanup(self): """Create does not modify the database if an error happens""" metadata_dict = { 'Sample1': {'physical_location': 'location1', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type1', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 1', 'group': 'Forcing the creation to fail', 'latitude': 42.42, 'longitude': 41.41} } metadata = pd.DataFrame.from_dict(metadata_dict, orient='index') with self.assertRaises(QiitaDBExecutionError): SampleTemplate.create(metadata, self.new_study) sql = """SELECT EXISTS( SELECT * FROM qiita.required_sample_info WHERE sample_id=%s)""" sample_id = "%d.Sample1" % self.new_study.id self.assertFalse( self.conn_handler.execute_fetchone(sql, (sample_id,))[0]) sql = """SELECT EXISTS( SELECT * FROM qiita.study_sample_columns WHERE study_id=%s)""" self.assertFalse( self.conn_handler.execute_fetchone(sql, (self.new_study.id,))[0]) self.assertFalse( exists_table("sample_%d" % self.new_study.id, self.conn_handler)) def test_create(self): """Creates a new SampleTemplate""" st = SampleTemplate.create(self.metadata, self.new_study) # The returned object has the correct id self.assertEqual(st.id, 2) # The relevant rows to required_sample_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.required_sample_info WHERE study_id=2") # sample_id study_id physical_location has_physical_specimen # has_extracted_data sample_type required_sample_info_status_id # collection_timestamp host_subject_id description exp = [["2.Sample1", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 1", 42.42, 41.41], ["2.Sample2", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 2", 4.2, 1.1], ["2.Sample3", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 3", 4.8, 4.41]] self.assertEqual(obs, exp) # The relevant rows have been added to the study_sample_columns obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.study_sample_columns WHERE study_id=2") # study_id, column_name, column_type exp = [[2, "str_column", "varchar"], [2L, 'int_column', 'integer']] self.assertEqual(obs, exp) # The new table exists self.assertTrue(exists_table("sample_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.sample_2") # sample_id, str_column exp = [['2.Sample1', 1, "Value for sample 1"], ['2.Sample2', 2, "Value for sample 2"], ['2.Sample3', 3, "Value for sample 3"]] self.assertEqual(obs, exp) def test_create_int_prefix(self): """Creates a new SampleTemplate""" st = SampleTemplate.create(self.metadata_int_pref, self.new_study) # The returned object has the correct id self.assertEqual(st.id, 2) # The relevant rows to required_sample_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.required_sample_info WHERE study_id=2") # sample_id study_id physical_location has_physical_specimen # has_extracted_data sample_type required_sample_info_status_id # collection_timestamp host_subject_id description exp = [["2.12.Sample1", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 1", 42.42, 41.41], ["2.12.Sample2", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 2", 4.2, 1.1], ["2.12.Sample3", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 3", 4.8, 4.41]] self.assertEqual(obs, exp) # The relevant rows have been added to the study_sample_columns obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.study_sample_columns WHERE study_id=2") # study_id, column_name, column_type exp = [[2, "str_column", "varchar"]] self.assertEqual(obs, exp) # The new table exists self.assertTrue(exists_table("sample_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.sample_2") # sample_id, str_column exp = [['2.12.Sample1', "Value for sample 1"], ['2.12.Sample2', "Value for sample 2"], ['2.12.Sample3', "Value for sample 3"]] self.assertEqual(obs, exp) def test_create_str_prefixes(self): """Creates a new SampleTemplate""" st = SampleTemplate.create(self.metadata_str_prefix, self.new_study) # The returned object has the correct id self.assertEqual(st.id, 2) # The relevant rows to required_sample_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.required_sample_info WHERE study_id=2") # sample_id study_id physical_location has_physical_specimen # has_extracted_data sample_type required_sample_info_status_id # collection_timestamp host_subject_id description exp = [["2.foo.Sample1", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 1", 42.42, 41.41], ["2.bar.Sample2", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 2", 4.2, 1.1], ["2.foo.Sample3", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 3", 4.8, 4.41]] self.assertEqual(sorted(obs), sorted(exp)) # The relevant rows have been added to the study_sample_columns obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.study_sample_columns WHERE study_id=2") # study_id, column_name, column_type exp = [[2, "str_column", "varchar"]] self.assertEqual(obs, exp) # The new table exists self.assertTrue(exists_table("sample_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.sample_2") # sample_id, str_column exp = [['2.foo.Sample1', "Value for sample 1"], ['2.bar.Sample2', "Value for sample 2"], ['2.foo.Sample3', "Value for sample 3"]] self.assertEqual(sorted(obs), sorted(exp)) def test_create_already_prefixed_samples(self): """Creates a new SampleTemplate with the samples already prefixed""" st = npt.assert_warns(QiitaDBWarning, SampleTemplate.create, self.metadata_prefixed, self.new_study) # The returned object has the correct id self.assertEqual(st.id, 2) # The relevant rows to required_sample_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.required_sample_info WHERE study_id=2") # sample_id study_id physical_location has_physical_specimen # has_extracted_data sample_type required_sample_info_status_id # collection_timestamp host_subject_id description exp = [["2.Sample1", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 1", 42.42, 41.41], ["2.Sample2", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 2", 4.2, 1.1], ["2.Sample3", 2, "location1", True, True, "type1", 1, datetime(2014, 5, 29, 12, 24, 51), "NotIdentified", "Test Sample 3", 4.8, 4.41]] self.assertEqual(obs, exp) # The relevant rows have been added to the study_sample_columns obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.study_sample_columns WHERE study_id=2") # study_id, column_name, column_type exp = [[2, "str_column", "varchar"]] self.assertEqual(obs, exp) # The new table exists self.assertTrue(exists_table("sample_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.sample_2") # sample_id, str_column exp = [['2.Sample1', "Value for sample 1"], ['2.Sample2', "Value for sample 2"], ['2.Sample3', "Value for sample 3"]] self.assertEqual(obs, exp) def test_delete(self): """Deletes Sample template 1""" SampleTemplate.create(self.metadata, self.new_study) SampleTemplate.delete(2) obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.required_sample_info WHERE study_id=2") exp = [] self.assertEqual(obs, exp) obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.study_sample_columns WHERE study_id=2") exp = [] self.assertEqual(obs, exp) with self.assertRaises(QiitaDBExecutionError): self.conn_handler.execute_fetchall( "SELECT * FROM qiita.sample_2") def test_delete_unkonwn_id_error(self): """Try to delete a non existent prep template""" with self.assertRaises(QiitaDBUnknownIDError): SampleTemplate.delete(5) def test_exists_true(self): """Exists returns true when the SampleTemplate already exists""" self.assertTrue(SampleTemplate.exists(self.test_study.id)) def test_exists_false(self): """Exists returns false when the SampleTemplate does not exists""" self.assertFalse(SampleTemplate.exists(self.new_study.id)) def test_get_sample_ids(self): """get_sample_ids returns the correct set of sample ids""" obs = self.tester._get_sample_ids(self.conn_handler) self.assertEqual(obs, self.exp_sample_ids) def test_len(self): """Len returns the correct number of sample ids""" self.assertEqual(len(self.tester), 27) def test_getitem(self): """Get item returns the correct sample object""" obs = self.tester['1.SKM7.640188'] exp = Sample('1.SKM7.640188', self.tester) self.assertEqual(obs, exp) def test_getitem_error(self): """Get item raises an error if key does not exists""" with self.assertRaises(KeyError): self.tester['Not_a_Sample'] def test_update_category(self): """setitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBUnknownIDError): self.tester.update_category('country', {"foo": "bar"}) with self.assertRaises(QiitaDBColumnError): self.tester.update_category('missing column', {'1.SKM7.640188': 'stuff'}) negtest = self.tester['1.SKM7.640188']['country'] mapping = {'1.SKB1.640202': "1", '1.SKB5.640181': "2", '1.SKD6.640190': "3"} self.tester.update_category('country', mapping) self.assertEqual(self.tester['1.SKB1.640202']['country'], "1") self.assertEqual(self.tester['1.SKB5.640181']['country'], "2") self.assertEqual(self.tester['1.SKD6.640190']['country'], "3") self.assertEqual(self.tester['1.SKM7.640188']['country'], negtest) # test updating a required_sample_info mapping = {'1.SKB1.640202': "1", '1.SKB5.640181': "2", '1.SKD6.640190': "3"} self.tester.update_category('required_sample_info_status_id', mapping) self.assertEqual( self.tester['1.SKB1.640202']['required_sample_info_status'], "received") self.assertEqual( self.tester['1.SKB5.640181']['required_sample_info_status'], "in_preparation") self.assertEqual( self.tester['1.SKD6.640190']['required_sample_info_status'], "running") self.assertEqual( self.tester['1.SKM7.640188']['required_sample_info_status'], "completed") # testing that if fails when trying to change an int column value # to str st = SampleTemplate.create(self.metadata, self.new_study) mapping = {'2.Sample1': "no_value"} with self.assertRaises(ValueError): st.update_category('int_column', mapping) def test_update(self): """Updates values in existing mapping file""" # creating a new sample template st = SampleTemplate.create(self.metadata, self.new_study) # updating the sample template st.update(self.metadata_dict_updated) # validating values exp = self.metadata_dict_updated_dict['Sample1'].values() obs = st.get('2.Sample1').values() self.assertItemsEqual(obs, exp) exp = self.metadata_dict_updated_dict['Sample2'].values() obs = st.get('2.Sample2').values() self.assertItemsEqual(obs, exp) exp = self.metadata_dict_updated_dict['Sample3'].values() obs = st.get('2.Sample3').values() self.assertItemsEqual(obs, exp) # checking errors with self.assertRaises(QiitaDBError): st.update(self.metadata_dict_updated_sample_error) with self.assertRaises(QiitaDBError): st.update(self.metadata_dict_updated_column_error) def test_add_category(self): column = "new_column" dtype = "varchar" default = "stuff" mapping = {'1.SKB1.640202': "1", '1.SKB5.640181': "2", '1.SKD6.640190': "3"} exp = { '1.SKB1.640202': "1", '1.SKB2.640194': "stuff", '1.SKB3.640195': "stuff", '1.SKB4.640189': "stuff", '1.SKB5.640181': "2", '1.SKB6.640176': "stuff", '1.SKB7.640196': "stuff", '1.SKB8.640193': "stuff", '1.SKB9.640200': "stuff", '1.SKD1.640179': "stuff", '1.SKD2.640178': "stuff", '1.SKD3.640198': "stuff", '1.SKD4.640185': "stuff", '1.SKD5.640186': "stuff", '1.SKD6.640190': "3", '1.SKD7.640191': "stuff", '1.SKD8.640184': "stuff", '1.SKD9.640182': "stuff", '1.SKM1.640183': "stuff", '1.SKM2.640199': "stuff", '1.SKM3.640197': "stuff", '1.SKM4.640180': "stuff", '1.SKM5.640177': "stuff", '1.SKM6.640187': "stuff", '1.SKM7.640188': "stuff", '1.SKM8.640201': "stuff", '1.SKM9.640192': "stuff"} self.tester.add_category(column, mapping, dtype, default) obs = {k: v['new_column'] for k, v in self.tester.items()} self.assertEqual(obs, exp) def test_categories(self): exp = {'season_environment', 'assigned_from_geo', 'texture', 'taxon_id', 'depth', 'host_taxid', 'common_name', 'water_content_soil', 'elevation', 'temp', 'tot_nitro', 'samp_salinity', 'altitude', 'env_biome', 'country', 'ph', 'anonymized_name', 'tot_org_carb', 'description_duplicate', 'env_feature'} obs = self.tester.categories() self.assertEqual(obs, exp) def test_remove_category(self): with self.assertRaises(QiitaDBColumnError): self.tester.remove_category('does not exist') for v in self.tester.values(): self.assertIn('elevation', v) self.tester.remove_category('elevation') for v in self.tester.values(): self.assertNotIn('elevation', v) def test_iter(self): """iter returns an iterator over the sample ids""" obs = self.tester.__iter__() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_sample_ids) def test_contains_true(self): """contains returns true if the sample id exists""" self.assertTrue('1.SKM7.640188' in self.tester) def test_contains_false(self): """contains returns false if the sample id does not exists""" self.assertFalse('Not_a_Sample' in self.tester) def test_keys(self): """keys returns an iterator over the sample ids""" obs = self.tester.keys() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_sample_ids) def test_values(self): """values returns an iterator over the values""" obs = self.tester.values() self.assertTrue(isinstance(obs, Iterable)) exp = {Sample('1.SKB1.640202', self.tester), Sample('1.SKB2.640194', self.tester), Sample('1.SKB3.640195', self.tester), Sample('1.SKB4.640189', self.tester), Sample('1.SKB5.640181', self.tester), Sample('1.SKB6.640176', self.tester), Sample('1.SKB7.640196', self.tester), Sample('1.SKB8.640193', self.tester), Sample('1.SKB9.640200', self.tester), Sample('1.SKD1.640179', self.tester), Sample('1.SKD2.640178', self.tester), Sample('1.SKD3.640198', self.tester), Sample('1.SKD4.640185', self.tester), Sample('1.SKD5.640186', self.tester), Sample('1.SKD6.640190', self.tester), Sample('1.SKD7.640191', self.tester), Sample('1.SKD8.640184', self.tester), Sample('1.SKD9.640182', self.tester), Sample('1.SKM1.640183', self.tester), Sample('1.SKM2.640199', self.tester), Sample('1.SKM3.640197', self.tester), Sample('1.SKM4.640180', self.tester), Sample('1.SKM5.640177', self.tester), Sample('1.SKM6.640187', self.tester), Sample('1.SKM7.640188', self.tester), Sample('1.SKM8.640201', self.tester), Sample('1.SKM9.640192', self.tester)} # Creating a list and looping over it since unittest does not call # the __eq__ function on the objects for o, e in zip(sorted(list(obs), key=lambda x: x.id), sorted(exp, key=lambda x: x.id)): self.assertEqual(o, e) def test_items(self): """items returns an iterator over the (key, value) tuples""" obs = self.tester.items() self.assertTrue(isinstance(obs, Iterable)) exp = [('1.SKB1.640202', Sample('1.SKB1.640202', self.tester)), ('1.SKB2.640194', Sample('1.SKB2.640194', self.tester)), ('1.SKB3.640195', Sample('1.SKB3.640195', self.tester)), ('1.SKB4.640189', Sample('1.SKB4.640189', self.tester)), ('1.SKB5.640181', Sample('1.SKB5.640181', self.tester)), ('1.SKB6.640176', Sample('1.SKB6.640176', self.tester)), ('1.SKB7.640196', Sample('1.SKB7.640196', self.tester)), ('1.SKB8.640193', Sample('1.SKB8.640193', self.tester)), ('1.SKB9.640200', Sample('1.SKB9.640200', self.tester)), ('1.SKD1.640179', Sample('1.SKD1.640179', self.tester)), ('1.SKD2.640178', Sample('1.SKD2.640178', self.tester)), ('1.SKD3.640198', Sample('1.SKD3.640198', self.tester)), ('1.SKD4.640185', Sample('1.SKD4.640185', self.tester)), ('1.SKD5.640186', Sample('1.SKD5.640186', self.tester)), ('1.SKD6.640190', Sample('1.SKD6.640190', self.tester)), ('1.SKD7.640191', Sample('1.SKD7.640191', self.tester)), ('1.SKD8.640184', Sample('1.SKD8.640184', self.tester)), ('1.SKD9.640182', Sample('1.SKD9.640182', self.tester)), ('1.SKM1.640183', Sample('1.SKM1.640183', self.tester)), ('1.SKM2.640199', Sample('1.SKM2.640199', self.tester)), ('1.SKM3.640197', Sample('1.SKM3.640197', self.tester)), ('1.SKM4.640180', Sample('1.SKM4.640180', self.tester)), ('1.SKM5.640177', Sample('1.SKM5.640177', self.tester)), ('1.SKM6.640187', Sample('1.SKM6.640187', self.tester)), ('1.SKM7.640188', Sample('1.SKM7.640188', self.tester)), ('1.SKM8.640201', Sample('1.SKM8.640201', self.tester)), ('1.SKM9.640192', Sample('1.SKM9.640192', self.tester))] # Creating a list and looping over it since unittest does not call # the __eq__ function on the objects for o, e in zip(sorted(list(obs)), sorted(exp)): self.assertEqual(o, e) def test_get(self): """get returns the correct sample object""" obs = self.tester.get('1.SKM7.640188') exp = Sample('1.SKM7.640188', self.tester) self.assertEqual(obs, exp) def test_get_none(self): """get returns none if the sample id is not present""" self.assertTrue(self.tester.get('Not_a_Sample') is None) def test_to_file(self): """to file writes a tab delimited file with all the metadata""" fd, fp = mkstemp() close(fd) st = SampleTemplate.create(self.metadata, self.new_study) st.to_file(fp) self._clean_up_files.append(fp) with open(fp, 'U') as f: obs = f.read() self.assertEqual(obs, EXP_SAMPLE_TEMPLATE) fd, fp = mkstemp() close(fd) st.to_file(fp, {'2.Sample1', '2.Sample3'}) self._clean_up_files.append(fp) with open(fp, 'U') as f: obs = f.read() self.assertEqual(obs, EXP_SAMPLE_TEMPLATE_FEWER_SAMPLES) def test_get_filepath(self): # we will check that there is a new id only because the path will # change based on time and the same functionality is being tested # in data.py exp_id = self.conn_handler.execute_fetchone( "SELECT count(1) FROM qiita.filepath")[0] + 1 st = SampleTemplate.create(self.metadata, self.new_study) self.assertEqual(st.get_filepaths()[0][0], exp_id) # testing current functionaly, to add a new sample template # you need to erase it first SampleTemplate.delete(st.id) exp_id += 1 st = SampleTemplate.create(self.metadata, self.new_study) self.assertEqual(st.get_filepaths()[0][0], exp_id) def test_extend(self): # add new column and delete one that exists self.metadata['NEWCOL'] = pd.Series(['val1', 'val2', 'val3'], index=self.metadata.index) self.tester.extend(self.metadata) # test samples were appended successfully sql = ("SELECT sample_id FROM qiita.required_sample_info WHERE " "study_id = 1") obs = self.conn_handler.execute_fetchall(sql) exp = [['1.SKB8.640193'], ['1.SKD8.640184'], ['1.SKB7.640196'], ['1.SKM9.640192'], ['1.SKM4.640180'], ['1.SKM5.640177'], ['1.SKB5.640181'], ['1.SKD6.640190'], ['1.SKB2.640194'], ['1.SKD2.640178'], ['1.SKM7.640188'], ['1.SKB1.640202'], ['1.SKD1.640179'], ['1.SKD3.640198'], ['1.SKM8.640201'], ['1.SKM2.640199'], ['1.SKB9.640200'], ['1.SKD5.640186'], ['1.SKM3.640197'], ['1.SKD9.640182'], ['1.SKB4.640189'], ['1.SKD7.640191'], ['1.SKM6.640187'], ['1.SKD4.640185'], ['1.SKB3.640195'], ['1.SKB6.640176'], ['1.SKM1.640183'], ['1.Sample1'], ['1.Sample2'], ['1.Sample3']] self.assertEqual(obs, exp) sql = "SELECT sample_id FROM qiita.sample_1" obs = self.conn_handler.execute_fetchall(sql) exp = [['1.SKM7.640188'], ['1.SKD9.640182'], ['1.SKM8.640201'], ['1.SKB8.640193'], ['1.SKD2.640178'], ['1.SKM3.640197'], ['1.SKM4.640180'], ['1.SKB9.640200'], ['1.SKB4.640189'], ['1.SKB5.640181'], ['1.SKB6.640176'], ['1.SKM2.640199'], ['1.SKM5.640177'], ['1.SKB1.640202'], ['1.SKD8.640184'], ['1.SKD4.640185'], ['1.SKB3.640195'], ['1.SKM1.640183'], ['1.SKB7.640196'], ['1.SKD3.640198'], ['1.SKD7.640191'], ['1.SKD6.640190'], ['1.SKB2.640194'], ['1.SKM9.640192'], ['1.SKM6.640187'], ['1.SKD5.640186'], ['1.SKD1.640179'], ['1.Sample1'], ['1.Sample2'], ['1.Sample3']] self.assertEqual(obs, exp) # test new columns were added to *_cols table and dynamic table obs = get_table_cols('sample_1', self.conn_handler) exp = ['sample_id', 'season_environment', 'assigned_from_geo', 'texture', 'taxon_id', 'depth', 'host_taxid', 'common_name', 'water_content_soil', 'elevation', 'temp', 'tot_nitro', 'samp_salinity', 'altitude', 'env_biome', 'country', 'ph', 'anonymized_name', 'tot_org_carb', 'description_duplicate', 'env_feature', 'newcol', 'str_column', 'int_column'] self.assertItemsEqual(obs, exp) sql = "SELECT * FROM qiita.study_sample_columns WHERE study_id = 1" obs = self.conn_handler.execute_fetchall(sql) exp = [[1, 'str_column', 'varchar'], [1, 'newcol', 'varchar'], [1, 'ENV_FEATURE', 'varchar'], [1, 'Description_duplicate', 'varchar'], [1, 'TOT_ORG_CARB', 'float8'], [1, 'ANONYMIZED_NAME', 'varchar'], [1, 'PH', 'float8'], [1, 'COUNTRY', 'varchar'], [1, 'ENV_BIOME', 'varchar'], [1, 'ALTITUDE', 'float8'], [1, 'SAMP_SALINITY', 'float8'], [1, 'TOT_NITRO', 'float8'], [1, 'TEMP', 'float8'], [1, 'ELEVATION', 'float8'], [1, 'WATER_CONTENT_SOIL', 'float8'], [1, 'COMMON_NAME', 'varchar'], [1, 'HOST_TAXID', 'varchar'], [1, 'DEPTH', 'float8'], [1, 'TAXON_ID', 'varchar'], [1, 'TEXTURE', 'varchar'], [1, 'ASSIGNED_FROM_GEO', 'varchar'], [1, 'SEASON_ENVIRONMENT', 'varchar'], [1, 'sample_id', 'varchar'], [1L, 'int_column', 'integer']] self.assertItemsEqual(obs, exp) def test_extend_duplicated_samples(self): # First add new samples to template self.tester.extend(self.metadata) self.metadata_dict['Sample5'] = { 'physical_location': 'location5', 'has_physical_specimen': True, 'has_extracted_data': True, 'sample_type': 'type5', 'required_sample_info_status': 'received', 'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51), 'host_subject_id': 'NotIdentified', 'Description': 'Test Sample 5', 'str_column': 'Value for sample 5', 'int_column': 5, 'latitude': 45.45, 'longitude': 44.44} new_metadata = pd.DataFrame.from_dict(self.metadata_dict, orient='index') # Make sure adding duplicate samples raises warning npt.assert_warns(QiitaDBWarning, self.tester.extend, new_metadata) # Make sure unknown sample still added to the study sql = "SELECT sample_id FROM qiita.sample_1" obs = self.conn_handler.execute_fetchall(sql) exp = [['1.SKM7.640188'], ['1.SKD9.640182'], ['1.SKM8.640201'], ['1.SKB8.640193'], ['1.SKD2.640178'], ['1.SKM3.640197'], ['1.SKM4.640180'], ['1.SKB9.640200'], ['1.SKB4.640189'], ['1.SKB5.640181'], ['1.SKB6.640176'], ['1.SKM2.640199'], ['1.SKM5.640177'], ['1.SKB1.640202'], ['1.SKD8.640184'], ['1.SKD4.640185'], ['1.SKB3.640195'], ['1.SKM1.640183'], ['1.SKB7.640196'], ['1.SKD3.640198'], ['1.SKD7.640191'], ['1.SKD6.640190'], ['1.SKB2.640194'], ['1.SKM9.640192'], ['1.SKM6.640187'], ['1.SKD5.640186'], ['1.SKD1.640179'], ['1.Sample1'], ['1.Sample2'], ['1.Sample3'], ['1.Sample5']] self.assertEqual(obs, exp) @qiita_test_checker() class TestPrepTemplate(TestCase): """Tests the PrepTemplate class""" def setUp(self): self.metadata_dict = { 'SKB8.640193': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 1', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'GTCCGCAAGTTA', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, 'SKD8.640184': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 2', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CGTAGAGCTCTC', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, 'SKB7.640196': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 3', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CCTCTGAGAGCT', 'run_prefix': "s_G1_L002_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'} } self.metadata = pd.DataFrame.from_dict(self.metadata_dict, orient='index') metadata_prefixed_dict = { '1.SKB8.640193': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 1', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'GTCCGCAAGTTA', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, '1.SKD8.640184': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 2', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CGTAGAGCTCTC', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, '1.SKB7.640196': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 3', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CCTCTGAGAGCT', 'run_prefix': "s_G1_L002_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'} } self.metadata_prefixed = pd.DataFrame.from_dict(metadata_prefixed_dict, orient='index') self.test_raw_data = RawData(1) self.test_study = Study(1) self.data_type = "18S" self.data_type_id = 2 fd, seqs_fp = mkstemp(suffix='_seqs.fastq') close(fd) fd, barcodes_fp = mkstemp(suffix='_barcodes.fastq') close(fd) filepaths = [(seqs_fp, 1), (barcodes_fp, 2)] with open(seqs_fp, "w") as f: f.write("\n") with open(barcodes_fp, "w") as f: f.write("\n") self.new_raw_data = RawData.create(2, [Study(1)], filepaths=filepaths) db_test_raw_dir = join(get_db_files_base_dir(), 'raw_data') db_seqs_fp = join(db_test_raw_dir, "5_%s" % basename(seqs_fp)) db_barcodes_fp = join(db_test_raw_dir, "5_%s" % basename(barcodes_fp)) self._clean_up_files = [db_seqs_fp, db_barcodes_fp] self.tester = PrepTemplate(1) self.exp_sample_ids = { '1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200', '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198', '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190', '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182', '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197', '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187', '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'} def tearDown(self): for f in self._clean_up_files: remove(f) def test_study_id(self): """Ensure that the correct study ID is returned""" self.assertEqual(self.tester.study_id, 1) def test_init_unknown_error(self): """Init raises an error if the id is not known""" with self.assertRaises(QiitaDBUnknownIDError): PrepTemplate(2) def test_init(self): """Init successfully instantiates the object""" st = PrepTemplate(1) self.assertTrue(st.id, 1) def test_table_name(self): """Table name return the correct string""" obs = PrepTemplate._table_name(1) self.assertEqual(obs, "prep_1") def test_create_duplicate_header(self): """Create raises an error when duplicate headers are present""" self.metadata['STR_COLUMN'] = pd.Series(['', '', ''], index=self.metadata.index) with self.assertRaises(QiitaDBDuplicateHeaderError): PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) def test_create_bad_sample_names(self): # set a horrible list of sample names self.metadata.index = ['o()xxxx[{::::::::>', 'sample.1', 'sample.3'] with self.assertRaises(QiitaDBColumnError): PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) def test_create_unknown_sample_names(self): # set two real and one fake sample name self.metadata_dict['NOTREAL'] = self.metadata_dict['SKB7.640196'] del self.metadata_dict['SKB7.640196'] self.metadata = pd.DataFrame.from_dict(self.metadata_dict, orient='index') # Test error raised and correct error given with self.assertRaises(QiitaDBExecutionError) as err: PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) self.assertEqual( str(err.exception), 'Samples found in prep template but not sample' ' template: 1.NOTREAL') def test_create_shorter_prep_template(self): # remove one sample so not all samples in the prep template del self.metadata_dict['SKB7.640196'] self.metadata = pd.DataFrame.from_dict(self.metadata_dict, orient='index') pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) # make sure the two samples were added correctly self.assertEqual(pt.id, 2) obs = self.conn_handler.execute_fetchall( "SELECT sample_id FROM qiita.prep_2") exp = [['1.SKB8.640193'], ['1.SKD8.640184']] self.assertEqual(obs, exp) def test_create_error_cleanup(self): """Create does not modify the database if an error happens""" metadata_dict = { 'SKB8.640193': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'group': 2, 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'GTCCGCAAGTTA', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, 'SKD8.640184': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'group': 1, 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CGTAGAGCTCTC', 'run_prefix': "s_G1_L001_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'}, 'SKB7.640196': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'group': 'Value for sample 3', 'linkerprimersequence': 'GTGCCAGCMGCCGCGGTAA', 'barcodesequence': 'CCTCTGAGAGCT', 'run_prefix': "s_G1_L002_sequences", 'platform': 'ILLUMINA', 'library_construction_protocol': 'AAAA', 'experiment_design_description': 'BBBB'} } metadata = pd.DataFrame.from_dict(metadata_dict, orient='index') exp_id = get_count("qiita.prep_template") + 1 with self.assertRaises(QiitaDBExecutionError): PrepTemplate.create(metadata, self.new_raw_data, self.test_study, self.data_type) sql = """SELECT EXISTS( SELECT * FROM qiita.prep_template WHERE prep_template_id=%s)""" self.assertFalse(self.conn_handler.execute_fetchone(sql, (exp_id,))[0]) sql = """SELECT EXISTS( SELECT * FROM qiita.common_prep_info WHERE prep_template_id=%s)""" self.assertFalse(self.conn_handler.execute_fetchone(sql, (exp_id,))[0]) sql = """SELECT EXISTS( SELECT * FROM qiita.prep_columns WHERE prep_template_id=%s)""" self.assertFalse(self.conn_handler.execute_fetchone(sql, (exp_id,))[0]) self.assertFalse(exists_table("prep_%d" % exp_id, self.conn_handler)) def test_create(self): """Creates a new PrepTemplate""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) # The returned object has the correct id self.assertEqual(pt.id, 2) # The row in the prep template table has been created obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_template WHERE prep_template_id=2") # prep_template_id, data_type_id, raw_data_id, preprocessing_status, # investigation_type self.assertEqual(obs, [[2, 2, 5, 'not_preprocessed', None]]) # The relevant rows to common_prep_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.common_prep_info WHERE prep_template_id=2") # prep_template_id, sample_id, study_id, center_name, # center_project_name, emp_status_id exp = [[2, '1.SKB8.640193', 'ANL', 'Test Project', 1], [2, '1.SKD8.640184', 'ANL', 'Test Project', 1], [2, '1.SKB7.640196', 'ANL', 'Test Project', 1]] self.assertEqual(sorted(obs), sorted(exp)) # The relevant rows have been added to the prep_columns table obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_columns WHERE prep_template_id=2") # prep_template_id, column_name, column_type exp = [[2, 'str_column', 'varchar'], [2, 'ebi_submission_accession', 'varchar'], [2, 'run_prefix', 'varchar'], [2, 'barcodesequence', 'varchar'], [2, 'linkerprimersequence', 'varchar'], [2, 'platform', 'varchar'], [2, 'experiment_design_description', 'varchar'], [2, 'library_construction_protocol', 'varchar']] self.assertEqual(sorted(obs), sorted(exp)) # The new table exists self.assertTrue(exists_table("prep_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_2") # sample_id, study_id, str_column, ebi_submission_accession, # run_prefix, barcodesequence, linkerprimersequence exp = [['1.SKB7.640196', 'Value for sample 3', 'ILLUMINA', 's_G1_L002_sequences', 'CCTCTGAGAGCT', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKB8.640193', 'Value for sample 1', 'ILLUMINA', 's_G1_L001_sequences', 'GTCCGCAAGTTA', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKD8.640184', 'Value for sample 2', 'ILLUMINA', 's_G1_L001_sequences', 'CGTAGAGCTCTC', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA']] self.assertEqual(sorted(obs), sorted(exp)) # prep and qiime files have been created filepaths = pt.get_filepaths() self.assertEqual(len(filepaths), 2) self.assertEqual(filepaths[0][0], 22) self.assertEqual(filepaths[1][0], 21) def test_create_already_prefixed_samples(self): """Creates a new PrepTemplate""" pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, self.metadata_prefixed, self.new_raw_data, self.test_study, self.data_type) # The returned object has the correct id self.assertEqual(pt.id, 2) # The row in the prep template table has been created obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_template WHERE prep_template_id=2") # prep_template_id, data_type_id, raw_data_id, preprocessing_status, # investigation_type self.assertEqual(obs, [[2, 2, 5, 'not_preprocessed', None]]) # The relevant rows to common_prep_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.common_prep_info WHERE prep_template_id=2") # prep_template_id, sample_id, study_id, center_name, # center_project_name, emp_status_id exp = [[2, '1.SKB8.640193', 'ANL', 'Test Project', 1], [2, '1.SKD8.640184', 'ANL', 'Test Project', 1], [2, '1.SKB7.640196', 'ANL', 'Test Project', 1]] self.assertEqual(sorted(obs), sorted(exp)) # The relevant rows have been added to the prep_columns table obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_columns WHERE prep_template_id=2") # prep_template_id, column_name, column_type exp = [[2, 'str_column', 'varchar'], [2, 'ebi_submission_accession', 'varchar'], [2, 'run_prefix', 'varchar'], [2, 'barcodesequence', 'varchar'], [2, 'linkerprimersequence', 'varchar'], [2, 'platform', 'varchar'], [2, 'experiment_design_description', 'varchar'], [2, 'library_construction_protocol', 'varchar']] self.assertEqual(sorted(obs), sorted(exp)) # The new table exists self.assertTrue(exists_table("prep_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_2") # sample_id, study_id, str_column, ebi_submission_accession, # run_prefix, barcodesequence, linkerprimersequence exp = [['1.SKB7.640196', 'Value for sample 3', 'ILLUMINA', 's_G1_L002_sequences', 'CCTCTGAGAGCT', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKB8.640193', 'Value for sample 1', 'ILLUMINA', 's_G1_L001_sequences', 'GTCCGCAAGTTA', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKD8.640184', 'Value for sample 2', 'ILLUMINA', 's_G1_L001_sequences', 'CGTAGAGCTCTC', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA']] self.assertEqual(sorted(obs), sorted(exp)) # prep and qiime files have been created filepaths = pt.get_filepaths() self.assertEqual(len(filepaths), 2) self.assertEqual(filepaths[0][0], 22) self.assertEqual(filepaths[1][0], 21) def test_create_qiime_mapping_file(self): pt = PrepTemplate(1) # creating prep template file _id, fp = get_mountpoint('templates')[0] fpp = join(fp, '%d_prep_%d_%s.txt' % (pt.study_id, pt.id, strftime("%Y%m%d-%H%M%S"))) pt.to_file(fpp) pt.add_filepath(fpp) _, filepath = pt.get_filepaths()[0] obs_fp = pt.create_qiime_mapping_file(filepath) exp_fp = join(fp, '1_prep_1_qiime_19700101-000000.txt') obs = pd.read_csv(obs_fp, sep='\t', infer_datetime_format=True, parse_dates=True, index_col=False, comment='\t') exp = pd.read_csv(exp_fp, sep='\t', infer_datetime_format=True, parse_dates=True, index_col=False, comment='\t') assert_frame_equal(obs, exp) # testing failure, first lest remove some lines of the prep template with open(filepath, 'r') as filepath_fh: data = filepath_fh.read().splitlines() with open(filepath, 'w') as filepath_fh: for i, d in enumerate(data): if i == 4: # adding fake sample line = d.split('\t') line[0] = 'fake_sample' line = '\t'.join(line) filepath_fh.write(line + '\n') break filepath_fh.write(d + '\n') with self.assertRaises(ValueError): pt.create_qiime_mapping_file(filepath) def test_create_data_type_id(self): """Creates a new PrepTemplate passing the data_type_id""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) # The returned object has the correct id self.assertEqual(pt.id, 2) # The row in the prep template table have been created obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_template WHERE prep_template_id=2") # prep_template_id, data_type_id, raw_data_id, preprocessing_status, # investigation_type self.assertEqual(obs, [[2, 2, 5, 'not_preprocessed', None]]) # The relevant rows to common_prep_info have been added. obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.common_prep_info WHERE prep_template_id=2") # prep_template_id, sample_id, center_name, # center_project_name, emp_status_id exp = [[2, '1.SKB8.640193', 'ANL', 'Test Project', 1], [2, '1.SKD8.640184', 'ANL', 'Test Project', 1], [2, '1.SKB7.640196', 'ANL', 'Test Project', 1]] self.assertEqual(sorted(obs), sorted(exp)) # The relevant rows have been added to the prep_columns table obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_columns WHERE prep_template_id=2") # prep_template_id, column_name, column_type exp = [[2, 'str_column', 'varchar'], [2, 'ebi_submission_accession', 'varchar'], [2, 'run_prefix', 'varchar'], [2, 'barcodesequence', 'varchar'], [2, 'linkerprimersequence', 'varchar'], [2, 'platform', 'varchar'], [2, 'experiment_design_description', 'varchar'], [2, 'library_construction_protocol', 'varchar']] self.assertEqual(sorted(obs), sorted(exp)) # The new table exists self.assertTrue(exists_table("prep_2", self.conn_handler)) # The new table hosts the correct values obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_2") # sample_id, str_column, ebi_submission_accession, # run_prefix, barcodesequence, linkerprimersequence exp = [['1.SKB7.640196', 'Value for sample 3', 'ILLUMINA', 's_G1_L002_sequences', 'CCTCTGAGAGCT', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKB8.640193', 'Value for sample 1', 'ILLUMINA', 's_G1_L001_sequences', 'GTCCGCAAGTTA', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA'], ['1.SKD8.640184', 'Value for sample 2', 'ILLUMINA', 's_G1_L001_sequences', 'CGTAGAGCTCTC', None, 'GTGCCAGCMGCCGCGGTAA', 'BBBB', 'AAAA']] self.assertEqual(sorted(obs), sorted(exp)) def test_create_error(self): """Create raises an error if any required columns are missing """ metadata_dict = { '1.SKB8.640193': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status_id': 1, 'str_column': 'Value for sample 1'}, '1.SKD8.640184': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status_id': 1, 'str_column': 'Value for sample 2'}, '1.SKB7.640196': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status_id': 1, 'str_column': 'Value for sample 3'} } metadata = pd.DataFrame.from_dict(metadata_dict, orient='index') with self.assertRaises(QiitaDBColumnError): PrepTemplate.create(metadata, self.new_raw_data, self.test_study, self.data_type) def test_create_error_template_special(self): """Create raises an error if not all columns are on the template""" metadata_dict = { '1.SKB8.640193': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 1', 'barcodesequence': 'GTCCGCAAGTTA'}, '1.SKD8.640184': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 2', 'barcodesequence': 'CGTAGAGCTCTC'}, '1.SKB7.640196': {'center_name': 'ANL', 'center_project_name': 'Test Project', 'ebi_submission_accession': None, 'EMP_status': 'EMP', 'str_column': 'Value for sample 3', 'barcodesequence': 'CCTCTGAGAGCT'} } metadata = pd.DataFrame.from_dict(metadata_dict, orient='index') with self.assertRaises(QiitaDBColumnError): PrepTemplate.create(metadata, self.new_raw_data, self.test_study, self.data_type) def test_create_investigation_type_error(self): """Create raises an error if the investigation_type does not exists""" with self.assertRaises(QiitaDBColumnError): PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id, 'Not a term') def test_delete_error(self): """Try to delete a prep template that already has preprocessed data""" with self.assertRaises(QiitaDBExecutionError): PrepTemplate.delete(1) def test_delete_unkonwn_id_error(self): """Try to delete a non existent prep template""" with self.assertRaises(QiitaDBUnknownIDError): PrepTemplate.delete(5) def test_delete(self): """Deletes prep template 2""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) PrepTemplate.delete(pt.id) obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_template WHERE prep_template_id=2") exp = [] self.assertEqual(obs, exp) obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.common_prep_info WHERE prep_template_id=2") exp = [] self.assertEqual(obs, exp) obs = self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_columns WHERE prep_template_id=2") exp = [] self.assertEqual(obs, exp) with self.assertRaises(QiitaDBExecutionError): self.conn_handler.execute_fetchall( "SELECT * FROM qiita.prep_2") def test_exists_true(self): """Exists returns true when the PrepTemplate already exists""" self.assertTrue(PrepTemplate.exists(1)) def test_exists_false(self): """Exists returns false when the PrepTemplate does not exists""" self.assertFalse(PrepTemplate.exists(2)) def test_get_sample_ids(self): """get_sample_ids returns the correct set of sample ids""" obs = self.tester._get_sample_ids(self.conn_handler) self.assertEqual(obs, self.exp_sample_ids) def test_len(self): """Len returns the correct number of sample ids""" self.assertEqual(len(self.tester), 27) def test_getitem(self): """Get item returns the correct sample object""" obs = self.tester['1.SKM7.640188'] exp = PrepSample('1.SKM7.640188', self.tester) self.assertEqual(obs, exp) def test_getitem_error(self): """Get item raises an error if key does not exists""" with self.assertRaises(KeyError): self.tester['Not_a_Sample'] def test_setitem(self): """setitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBNotImplementedError): self.tester['1.SKM7.640188'] = PrepSample('1.SKM7.640188', self.tester) def test_delitem(self): """delitem raises an error (currently not allowed)""" with self.assertRaises(QiitaDBNotImplementedError): del self.tester['1.SKM7.640188'] def test_iter(self): """iter returns an iterator over the sample ids""" obs = self.tester.__iter__() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_sample_ids) def test_contains_true(self): """contains returns true if the sample id exists""" self.assertTrue('1.SKM7.640188' in self.tester) def test_contains_false(self): """contains returns false if the sample id does not exists""" self.assertFalse('Not_a_Sample' in self.tester) def test_keys(self): """keys returns an iterator over the sample ids""" obs = self.tester.keys() self.assertTrue(isinstance(obs, Iterable)) self.assertEqual(set(obs), self.exp_sample_ids) def test_values(self): """values returns an iterator over the values""" obs = self.tester.values() self.assertTrue(isinstance(obs, Iterable)) exp = {PrepSample('1.SKB1.640202', self.tester), PrepSample('1.SKB2.640194', self.tester), PrepSample('1.SKB3.640195', self.tester), PrepSample('1.SKB4.640189', self.tester), PrepSample('1.SKB5.640181', self.tester), PrepSample('1.SKB6.640176', self.tester), PrepSample('1.SKB7.640196', self.tester), PrepSample('1.SKB8.640193', self.tester), PrepSample('1.SKB9.640200', self.tester), PrepSample('1.SKD1.640179', self.tester), PrepSample('1.SKD2.640178', self.tester), PrepSample('1.SKD3.640198', self.tester), PrepSample('1.SKD4.640185', self.tester), PrepSample('1.SKD5.640186', self.tester), PrepSample('1.SKD6.640190', self.tester), PrepSample('1.SKD7.640191', self.tester), PrepSample('1.SKD8.640184', self.tester), PrepSample('1.SKD9.640182', self.tester), PrepSample('1.SKM1.640183', self.tester), PrepSample('1.SKM2.640199', self.tester), PrepSample('1.SKM3.640197', self.tester), PrepSample('1.SKM4.640180', self.tester), PrepSample('1.SKM5.640177', self.tester), PrepSample('1.SKM6.640187', self.tester), PrepSample('1.SKM7.640188', self.tester), PrepSample('1.SKM8.640201', self.tester), PrepSample('1.SKM9.640192', self.tester)} # Creating a list and looping over it since unittest does not call # the __eq__ function on the objects for o, e in zip(sorted(list(obs), key=lambda x: x.id), sorted(exp, key=lambda x: x.id)): self.assertEqual(o, e) def test_items(self): """items returns an iterator over the (key, value) tuples""" obs = self.tester.items() self.assertTrue(isinstance(obs, Iterable)) exp = [('1.SKB1.640202', PrepSample('1.SKB1.640202', self.tester)), ('1.SKB2.640194', PrepSample('1.SKB2.640194', self.tester)), ('1.SKB3.640195', PrepSample('1.SKB3.640195', self.tester)), ('1.SKB4.640189', PrepSample('1.SKB4.640189', self.tester)), ('1.SKB5.640181', PrepSample('1.SKB5.640181', self.tester)), ('1.SKB6.640176', PrepSample('1.SKB6.640176', self.tester)), ('1.SKB7.640196', PrepSample('1.SKB7.640196', self.tester)), ('1.SKB8.640193', PrepSample('1.SKB8.640193', self.tester)), ('1.SKB9.640200', PrepSample('1.SKB9.640200', self.tester)), ('1.SKD1.640179', PrepSample('1.SKD1.640179', self.tester)), ('1.SKD2.640178', PrepSample('1.SKD2.640178', self.tester)), ('1.SKD3.640198', PrepSample('1.SKD3.640198', self.tester)), ('1.SKD4.640185', PrepSample('1.SKD4.640185', self.tester)), ('1.SKD5.640186', PrepSample('1.SKD5.640186', self.tester)), ('1.SKD6.640190', PrepSample('1.SKD6.640190', self.tester)), ('1.SKD7.640191', PrepSample('1.SKD7.640191', self.tester)), ('1.SKD8.640184', PrepSample('1.SKD8.640184', self.tester)), ('1.SKD9.640182', PrepSample('1.SKD9.640182', self.tester)), ('1.SKM1.640183', PrepSample('1.SKM1.640183', self.tester)), ('1.SKM2.640199', PrepSample('1.SKM2.640199', self.tester)), ('1.SKM3.640197', PrepSample('1.SKM3.640197', self.tester)), ('1.SKM4.640180', PrepSample('1.SKM4.640180', self.tester)), ('1.SKM5.640177', PrepSample('1.SKM5.640177', self.tester)), ('1.SKM6.640187', PrepSample('1.SKM6.640187', self.tester)), ('1.SKM7.640188', PrepSample('1.SKM7.640188', self.tester)), ('1.SKM8.640201', PrepSample('1.SKM8.640201', self.tester)), ('1.SKM9.640192', PrepSample('1.SKM9.640192', self.tester))] # Creating a list and looping over it since unittest does not call # the __eq__ function on the objects for o, e in zip(sorted(list(obs)), sorted(exp)): self.assertEqual(o, e) def test_get(self): """get returns the correct PrepSample object""" obs = self.tester.get('1.SKM7.640188') exp = PrepSample('1.SKM7.640188', self.tester) self.assertEqual(obs, exp) def test_get_none(self): """get returns none if the sample id is not present""" self.assertTrue(self.tester.get('Not_a_Sample') is None) def test_to_file(self): """to file writes a tab delimited file with all the metadata""" fd, fp = mkstemp() close(fd) pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type) pt.to_file(fp) self._clean_up_files.append(fp) with open(fp, 'U') as f: obs = f.read() self.assertEqual(obs, EXP_PREP_TEMPLATE) def test_data_type(self): """data_type returns the string with the data_type""" self.assertTrue(self.tester.data_type(), "18S") def test_data_type_id(self): """data_type returns the int with the data_type_id""" self.assertTrue(self.tester.data_type(ret_id=True), 2) def test_raw_data(self): """Returns the raw_data associated with the prep template""" self.assertEqual(self.tester.raw_data, 1) def test_preprocessed_data(self): """Returns the preprocessed data list generated from this template""" self.assertEqual(self.tester.preprocessed_data, [1, 2]) def test_preprocessing_status(self): """preprocessing_status works correctly""" # Success case pt = PrepTemplate(1) self.assertEqual(pt.preprocessing_status, 'success') # not preprocessed case pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) self.assertEqual(pt.preprocessing_status, 'not_preprocessed') def test_preprocessing_status_setter(self): """Able to update the preprocessing status""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) self.assertEqual(pt.preprocessing_status, 'not_preprocessed') pt.preprocessing_status = 'preprocessing' self.assertEqual(pt.preprocessing_status, 'preprocessing') pt.preprocessing_status = 'success' self.assertEqual(pt.preprocessing_status, 'success') def test_preprocessing_status_setter_failed(self): """Able to update preprocessing_status with a failure message""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) state = 'failed: some error message' self.assertEqual(pt.preprocessing_status, 'not_preprocessed') pt.preprocessing_status = state self.assertEqual(pt.preprocessing_status, state) def test_preprocessing_status_setter_valueerror(self): """Raises an error if the status is not recognized""" with self.assertRaises(ValueError): self.tester.preprocessing_status = 'not a valid state' def test_investigation_type(self): """investigation_type works correctly""" self.assertEqual(self.tester.investigation_type, "Metagenomics") def test_investigation_type_setter(self): """Able to update the investigation type""" pt = PrepTemplate.create(self.metadata, self.new_raw_data, self.test_study, self.data_type_id) self.assertEqual(pt.investigation_type, None) pt.investigation_type = "Other" self.assertEqual(pt.investigation_type, 'Other') with self.assertRaises(QiitaDBColumnError): pt.investigation_type = "should fail" def test_investigation_type_instance_setter(self): pt = PrepTemplate(1) pt.investigation_type = 'RNASeq' self.assertEqual(pt.investigation_type, 'RNASeq') class TestUtilities(TestCase): def test_load_template_to_dataframe(self): obs = load_template_to_dataframe(StringIO(EXP_SAMPLE_TEMPLATE)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_duplicate_cols(self): obs = load_template_to_dataframe( StringIO(EXP_SAMPLE_TEMPLATE_DUPE_COLS)) obs = list(obs.columns) exp = ['collection_timestamp', 'description', 'has_extracted_data', 'has_physical_specimen', 'host_subject_id', 'latitude', 'longitude', 'physical_location', 'required_sample_info_status', 'sample_type', 'str_column', 'str_column'] self.assertEqual(obs, exp) def test_load_template_to_dataframe_scrubbing(self): obs = load_template_to_dataframe(StringIO(EXP_SAMPLE_TEMPLATE_SPACES)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_empty_columns(self): obs = npt.assert_warns(QiitaDBWarning, load_template_to_dataframe, StringIO(EXP_ST_SPACES_EMPTY_COLUMN)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_empty_rows(self): obs = load_template_to_dataframe( StringIO(EXP_SAMPLE_TEMPLATE_SPACES_EMPTY_ROW)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_no_sample_name_cast(self): obs = load_template_to_dataframe( StringIO(EXP_SAMPLE_TEMPLATE_NUMBER_SAMPLE_NAMES)) exp = pd.DataFrame.from_dict( SAMPLE_TEMPLATE_NUMBER_SAMPLE_NAMES_DICT_FORM) exp.index.name = 'sample_name' obs.sort_index(inplace=True) exp.sort_index(inplace=True) assert_frame_equal(obs, exp) def test_load_template_to_dataframe_empty_sample_names(self): obs = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_NO_SAMPLE_NAMES)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) obs = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_NO_SAMPLE_NAMES_SOME_SPACES)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_empty_column(self): obs = npt.assert_warns(QiitaDBWarning, load_template_to_dataframe, StringIO(SAMPLE_TEMPLATE_EMPTY_COLUMN)) exp = pd.DataFrame.from_dict(ST_EMPTY_COLUMN_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_column_with_nas(self): obs = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_COLUMN_WITH_NAS)) exp = pd.DataFrame.from_dict(ST_COLUMN_WITH_NAS_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_load_template_to_dataframe_exception(self): with self.assertRaises(QiitaDBColumnError): x = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_NO_SAMPLE_NAME)) # prevent flake8 from complaining x.strip() def test_load_template_to_dataframe_whitespace(self): obs = load_template_to_dataframe( StringIO(EXP_SAMPLE_TEMPLATE_WHITESPACE)) exp = pd.DataFrame.from_dict(SAMPLE_TEMPLATE_DICT_FORM) exp.index.name = 'sample_name' assert_frame_equal(obs, exp) def test_get_invalid_sample_names(self): all_valid = ['2.sample.1', 'foo.bar.baz', 'roses', 'are', 'red', 'v10l3t5', '4r3', '81u3'] obs = get_invalid_sample_names(all_valid) self.assertEqual(obs, []) all_valid = ['sample.1', 'sample.2', 'SAMPLE.1', 'BOOOM'] obs = get_invalid_sample_names(all_valid) self.assertEqual(obs, []) def test_get_invalid_sample_names_str(self): one_invalid = ['2.sample.1', 'foo.bar.baz', 'roses', 'are', 'red', 'I am the chosen one', 'v10l3t5', '4r3', '81u3'] obs = get_invalid_sample_names(one_invalid) self.assertItemsEqual(obs, ['I am the chosen one']) one_invalid = ['2.sample.1', 'foo.bar.baz', 'roses', 'are', 'red', ':L{=<', ':L}=<', '4r3', '81u3'] obs = get_invalid_sample_names(one_invalid) self.assertItemsEqual(obs, [':L{=<', ':L}=<']) def test_get_get_invalid_sample_names_mixed(self): one_invalid = ['.', '1', '2'] obs = get_invalid_sample_names(one_invalid) self.assertItemsEqual(obs, []) one_invalid = [' ', ' ', ' '] obs = get_invalid_sample_names(one_invalid) self.assertItemsEqual(obs, [' ', ' ', ' ']) def test_invalid_lat_long(self): with self.assertRaises(QiitaDBColumnError): obs = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_INVALID_LATITUDE_COLUMNS)) # prevent flake8 from complaining str(obs) with self.assertRaises(QiitaDBColumnError): obs = load_template_to_dataframe( StringIO(SAMPLE_TEMPLATE_INVALID_LONGITUDE_COLUMNS)) # prevent flake8 from complaining str(obs) EXP_SAMPLE_TEMPLATE = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\tstr_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\tNotIdentified" "\t1\t42.42\t41.41\tlocation1\treceived\ttype1\tValue for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\tTest Sample 2\tTrue\tTrue\tNotIdentified" "\t2\t4.2\t1.1\tlocation1\treceived\ttype1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\tTrue\tNotIdentified" "\t3\t4.8\t4.41\tlocation1\treceived\ttype1\tValue for sample 3\n") EXP_SAMPLE_TEMPLATE_DUPE_COLS = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\tstr_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\tValue for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t4.2\t1.1\tlocation1\treceived\t" "type1\tValue for sample 2\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\tValue for sample 3\n") EXP_SAMPLE_TEMPLATE_FEWER_SAMPLES = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\t" "longitude\tphysical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\tNotIdentified" "\t1\t42.42\t41.41\tlocation1\treceived\ttype1\tValue for sample 1\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\tTrue\tNotIdentified" "\t3\t4.8\t4.41\tlocation1\treceived\ttype1\tValue for sample 3\n") EXP_SAMPLE_TEMPLATE_SPACES = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1 \t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2 \t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n") EXP_SAMPLE_TEMPLATE_WHITESPACE = ( "sample_name \tcollection_timestamp\t description \thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2\t 2014-05-29 12:24:51 \t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\t Value for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\t Test Sample 3 \tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n") EXP_SAMPLE_TEMPLATE_SPACES_EMPTY_ROW = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1 \t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2 \t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n" "\t\t\t\t\t\t\t\t\t\t\t\t\n" "\t\t\t\t\t\t\t\t\t\t\t\t\n") EXP_ST_SPACES_EMPTY_COLUMN = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\t\n" "2.Sample1 \t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\t\n" "2.Sample2 \t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\tValue for sample 2\t\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\t\n") EXP_SAMPLE_TEMPLATE_NUMBER_SAMPLE_NAMES = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "002.000\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "1.11111\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t4.2\t1.1\tlocation1\treceived\t" "type1\tValue for sample 2\n" "0.12121\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n") SAMPLE_TEMPLATE_NO_SAMPLE_NAMES = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n" "\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n" "\t\t\t\t\t\t\t\t\t\t\t\n" ) SAMPLE_TEMPLATE_NO_SAMPLE_NAMES_SOME_SPACES = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tint_column\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t1\t42.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t2\t4.2\t1.1\tlocation1\t" "received\ttype1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t3\t4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n" "\t\t\t\t\t \t\t\t\t\t \t\t\n" ) SAMPLE_TEMPLATE_EMPTY_COLUMN = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t42.42\t41.41\tlocation1\treceived\ttype1\t" "\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t4.2\t1.1\tlocation1\treceived\t" "type1\t\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "\n") SAMPLE_TEMPLATE_COLUMN_WITH_NAS = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t42.42\t41.41\tlocation1\treceived\ttype1\t" "NA\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t4.2\t1.1\tlocation1\treceived\t" "type1\tNA\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "NA\n") SAMPLE_TEMPLATE_NO_SAMPLE_NAME = ( ":L}={\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "NotIdentified\t42.42\t41.41\tlocation1\treceived\ttype1\t" "NA\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\tNotIdentified\t4.2\t1.1\tlocation1\treceived\t" "type1\tNA\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\tNotIdentified\t4.8\t4.41\tlocation1\treceived\ttype1\t" "NA\n") SAMPLE_TEMPLATE_INVALID_LATITUDE_COLUMNS = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "1\t42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\1\t4.2\t1.1\tlocation1\treceived\t" "type1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\1\tXXXXX4.8\t4.41\tlocation1\treceived\ttype1\t" "Value for sample 3\n") SAMPLE_TEMPLATE_INVALID_LONGITUDE_COLUMNS = ( "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t" "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t" "physical_location\trequired_sample_info_status\tsample_type\t" "str_column\n" "2.Sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\t" "1\t11.42\t41.41\tlocation1\treceived\ttype1\t" "Value for sample 1\n" "2.Sample2\t2014-05-29 12:24:51\t" "Test Sample 2\tTrue\tTrue\1\t4.2\tXXX\tlocation1\treceived\t" "type1\tValue for sample 2\n" "2.Sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\t" "True\1\t4.8\t4.XXXXX41\tlocation1\treceived\ttype1\t" "Value for sample 3\n") SAMPLE_TEMPLATE_DICT_FORM = { 'collection_timestamp': {'2.Sample1': '2014-05-29 12:24:51', '2.Sample2': '2014-05-29 12:24:51', '2.Sample3': '2014-05-29 12:24:51'}, 'description': {'2.Sample1': 'Test Sample 1', '2.Sample2': 'Test Sample 2', '2.Sample3': 'Test Sample 3'}, 'has_extracted_data': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'has_physical_specimen': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'host_subject_id': {'2.Sample1': 'NotIdentified', '2.Sample2': 'NotIdentified', '2.Sample3': 'NotIdentified'}, 'latitude': {'2.Sample1': 42.420000000000002, '2.Sample2': 4.2000000000000002, '2.Sample3': 4.7999999999999998}, 'longitude': {'2.Sample1': 41.409999999999997, '2.Sample2': 1.1000000000000001, '2.Sample3': 4.4100000000000001}, 'physical_location': {'2.Sample1': 'location1', '2.Sample2': 'location1', '2.Sample3': 'location1'}, 'required_sample_info_status': {'2.Sample1': 'received', '2.Sample2': 'received', '2.Sample3': 'received'}, 'sample_type': {'2.Sample1': 'type1', '2.Sample2': 'type1', '2.Sample3': 'type1'}, 'str_column': {'2.Sample1': 'Value for sample 1', '2.Sample2': 'Value for sample 2', '2.Sample3': 'Value for sample 3'}, 'int_column': {'2.Sample1': 1, '2.Sample2': 2, '2.Sample3': 3} } SAMPLE_TEMPLATE_NUMBER_SAMPLE_NAMES_DICT_FORM = { 'collection_timestamp': {'002.000': '2014-05-29 12:24:51', '1.11111': '2014-05-29 12:24:51', '0.12121': '2014-05-29 12:24:51'}, 'description': {'002.000': 'Test Sample 1', '1.11111': 'Test Sample 2', '0.12121': 'Test Sample 3'}, 'has_extracted_data': {'002.000': True, '1.11111': True, '0.12121': True}, 'has_physical_specimen': {'002.000': True, '1.11111': True, '0.12121': True}, 'host_subject_id': {'002.000': 'NotIdentified', '1.11111': 'NotIdentified', '0.12121': 'NotIdentified'}, 'latitude': {'002.000': 42.420000000000002, '1.11111': 4.2000000000000002, '0.12121': 4.7999999999999998}, 'longitude': {'002.000': 41.409999999999997, '1.11111': 1.1000000000000001, '0.12121': 4.4100000000000001}, 'physical_location': {'002.000': 'location1', '1.11111': 'location1', '0.12121': 'location1'}, 'required_sample_info_status': {'002.000': 'received', '1.11111': 'received', '0.12121': 'received'}, 'sample_type': {'002.000': 'type1', '1.11111': 'type1', '0.12121': 'type1'}, 'str_column': {'002.000': 'Value for sample 1', '1.11111': 'Value for sample 2', '0.12121': 'Value for sample 3'}} ST_EMPTY_COLUMN_DICT_FORM = \ {'collection_timestamp': {'2.Sample1': '2014-05-29 12:24:51', '2.Sample2': '2014-05-29 12:24:51', '2.Sample3': '2014-05-29 12:24:51'}, 'description': {'2.Sample1': 'Test Sample 1', '2.Sample2': 'Test Sample 2', '2.Sample3': 'Test Sample 3'}, 'has_extracted_data': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'has_physical_specimen': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'host_subject_id': {'2.Sample1': 'NotIdentified', '2.Sample2': 'NotIdentified', '2.Sample3': 'NotIdentified'}, 'latitude': {'2.Sample1': 42.420000000000002, '2.Sample2': 4.2000000000000002, '2.Sample3': 4.7999999999999998}, 'longitude': {'2.Sample1': 41.409999999999997, '2.Sample2': 1.1000000000000001, '2.Sample3': 4.4100000000000001}, 'physical_location': {'2.Sample1': 'location1', '2.Sample2': 'location1', '2.Sample3': 'location1'}, 'required_sample_info_status': {'2.Sample1': 'received', '2.Sample2': 'received', '2.Sample3': 'received'}, 'sample_type': {'2.Sample1': 'type1', '2.Sample2': 'type1', '2.Sample3': 'type1'}} ST_COLUMN_WITH_NAS_DICT_FORM = \ {'collection_timestamp': {'2.Sample1': '2014-05-29 12:24:51', '2.Sample2': '2014-05-29 12:24:51', '2.Sample3': '2014-05-29 12:24:51'}, 'description': {'2.Sample1': 'Test Sample 1', '2.Sample2': 'Test Sample 2', '2.Sample3': 'Test Sample 3'}, 'has_extracted_data': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'has_physical_specimen': {'2.Sample1': True, '2.Sample2': True, '2.Sample3': True}, 'host_subject_id': {'2.Sample1': 'NotIdentified', '2.Sample2': 'NotIdentified', '2.Sample3': 'NotIdentified'}, 'latitude': {'2.Sample1': 42.420000000000002, '2.Sample2': 4.2000000000000002, '2.Sample3': 4.7999999999999998}, 'longitude': {'2.Sample1': 41.409999999999997, '2.Sample2': 1.1000000000000001, '2.Sample3': 4.4100000000000001}, 'physical_location': {'2.Sample1': 'location1', '2.Sample2': 'location1', '2.Sample3': 'location1'}, 'required_sample_info_status': {'2.Sample1': 'received', '2.Sample2': 'received', '2.Sample3': 'received'}, 'sample_type': {'2.Sample1': 'type1', '2.Sample2': 'type1', '2.Sample3': 'type1'}, 'str_column': {'2.Sample1': 'NA', '2.Sample2': 'NA', '2.Sample3': 'NA'}} EXP_PREP_TEMPLATE = ( 'sample_name\tbarcodesequence\tcenter_name\tcenter_project_name\t' 'ebi_submission_accession\temp_status\texperiment_design_description\t' 'library_construction_protocol\tlinkerprimersequence\tplatform\t' 'run_prefix\tstr_column\n' '1.SKB7.640196\tCCTCTGAGAGCT\tANL\tTest Project\tNone\tEMP\tBBBB\tAAAA\t' 'GTGCCAGCMGCCGCGGTAA\tILLUMINA\ts_G1_L002_sequences\tValue for sample 3\n' '1.SKB8.640193\tGTCCGCAAGTTA\tANL\tTest Project\tNone\tEMP\tBBBB\tAAAA\t' 'GTGCCAGCMGCCGCGGTAA\tILLUMINA\ts_G1_L001_sequences\tValue for sample 1\n' '1.SKD8.640184\tCGTAGAGCTCTC\tANL\tTest Project\tNone\tEMP\tBBBB\tAAAA\t' 'GTGCCAGCMGCCGCGGTAA\tILLUMINA\ts_G1_L001_sequences\tValue for sample 2\n') if __name__ == '__main__': main()

47.896772

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0

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135,021

2,818

80

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56b5f82d84bd7f6563e6493350c8151edca3261f

38

py

Python

lemmiwinks/extractor/__init__.py

nesfit/WPD

543afd5c60862db4aff91b1d3a89b77e690f9383

[ "MIT" ]

4

2018-01-08T22:46:03.000Z

2018-04-08T09:02:22.000Z

lemmiwinks/extractor/__init__.py

nesfit/WPD

543afd5c60862db4aff91b1d3a89b77e690f9383

[ "MIT" ]

1

2018-08-07T18:25:18.000Z

lemmiwinks/extractor/__init__.py

nesfit/WPD

543afd5c60862db4aff91b1d3a89b77e690f9383

[ "MIT" ]

1

2018-01-08T21:13:41.000Z

from .extractor import RegexExtractor

19

37

0.868421

4

38

8.25

1

0

0.105263

38

1

38

0.970588

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

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1

0

1

0

1

0

6

85857e316dd7c1f25ad43a0b6a8d1dd3411670c6

710

py

Python

cvplus/__init__.py

AndyTsangChun/cvutil

3f53e794a990eefe1573d3df05b2cc62f26da0a6

[ "Apache-2.0" ]

null

cvplus/__init__.py

AndyTsangChun/cvutil

3f53e794a990eefe1573d3df05b2cc62f26da0a6

[ "Apache-2.0" ]

null

cvplus/__init__.py

AndyTsangChun/cvutil

3f53e794a990eefe1573d3df05b2cc62f26da0a6

[ "Apache-2.0" ]

null

from .py_logger import PyLogger from .color_util import genColors from .color_util import hsv2rgb from .color_util import rgb2hex from .cv_util import getTextBoxRatio from .cv_util import drawDashedLine from .cv_util import location2bbox from .cv_util import bbox2location from .cv_util import bbox_iou from .cv_util import interval_overlap from .img_util import normalize from .img_util import getDownSampleImage from .img_util import getCroppedImage from .img_util import npa2base64 from .img_util import base642npa from .img_util import saveImgRGB from .img_util import PIL2CV from .img_util import CV2PIL from .img_util import getCenterPoint from .img_util import distanceOfpoints from .model import *

27.307692

40

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105

710

5.504762

0.295238

0.32872

0.190311

0.294118

0

0.019293

0.123944

710

25

41

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0.909968

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1

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true

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1

0

null

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null

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0

1

0

6

a4567015ffddbf733a1264a3934fe052e78c7e8f

36,705

py

Python

docs/quick_references/qr_helper.py

lingruiluo/jp_doodle

b3935208821898f22ab504c2b26dd4d37f08f0e4

[ "BSD-2-Clause" ]

43

2018-10-10T08:38:07.000Z

2022-03-19T22:44:42.000Z

docs/quick_references/qr_helper.py

firmfrol19/jp_doodle

cb34938edaedbe15590ebe8024060dd97bb69fa9

[ "BSD-2-Clause" ]

8

2018-09-17T19:49:45.000Z

2020-08-24T15:51:16.000Z

docs/quick_references/qr_helper.py

firmfrol19/jp_doodle

cb34938edaedbe15590ebe8024060dd97bb69fa9

[ "BSD-2-Clause" ]

5

2019-06-13T15:53:55.000Z

2020-11-13T01:22:56.000Z

from jp_doodle.dual_canvas import swatch from jp_doodle.auto_capture import embed_hidden, PythonExample, JavascriptExample import inspect # widen the notebook from jp_doodle import data_tables data_tables.widen_notebook() DO_EMBEDDINGS = False def show(frame, file_prefix=None, do_display=True): if DO_EMBEDDINGS: if file_prefix is None: file_prefix = inspect.stack()[1][3] filename = file_prefix + ".png" canvas_widget = frame.get_canvas() with embed_hidden(canvas_widget, filename): if do_display: frame.show() else: if do_display: frame.show() def python_example(markdown, code, width=320, height=120, embeddable=True): file_prefix = inspect.stack()[1][3] filename = file_prefix + ".png" EG = PythonExample(markdown, code, filename, width, height, embeddable=embeddable) EG.embed_prologue() EG.embed_code() EG.embed_widget(DO_EMBEDDINGS) def js_example(markdown, code, width=320, height=120, axes=True, embeddable=True): file_prefix = inspect.stack()[1][3] filename = file_prefix + ".png" EG = JavascriptExample(markdown, code, filename, width, height, axes=axes, embeddable=embeddable) EG.embed_prologue() EG.embed_code() EG.embed_widget(DO_EMBEDDINGS) def js_frame_example(): return js_example( """ ### Create a reference frame inside a dual canvas Pixel coordinates are rarely the most convenient coordinate systems to use for scientific visualizations. Reference frames allow drawing using transformed coordinates. The `frame_region` method creates a frame by mapping reference points in the pixel space to reference points in the reference frame coordinate space. Objects can then be drawn on the reference frame and the underlying coordinates will be converted automatically. The following Javascript creates a reference `frame` from the canvas `element` and draws some reference marks on the frame. Reference axes in canvas coordinates are also shown in grey. """, """ // Map pixel coords (10,10) and (400,100) // to frame coords (-1, 0) and (1, 2) var frame = element.frame_region( 10, 10, 400, 100, -1, 0, 1, 2); // draw some reference marks on the frame: frame.text({x:-1, y:0, text:"-1,0", color:"red", background:"yellow"} ); frame.text({x:1, y:2, text:"1,2", align:"right", color:"red", background:"yellow"} ); frame.lower_left_axes({min_x:-1, min_y:0, max_x:1, max_y:2, x_anchor:0, y_anchor:1, max_tick_count:5, color:"blue"}) """ ) def js_lasso_example(): return js_example( """ ### Selecting named objects by surrounding them with a lasso The ``` element.do_lasso(callback, config, delete_after) ``` method allows the user to select named objects by surrounding them with a graphical loop. After the loop is complete the callback receives a dictionary mapping the names of the selected objects to their descriptions. The optional argument `config` is provides configuration parameters and the optional boolean argument `delete_after` deletes the lasso polygon after selection if `true`. """, """ // draw some named objects on the canvas for (var i=10; i<300; i+=40) { for (var j=10; j<100; j+=15) { var ijtext = i+","+j element.text({x:i, y:j, text:ijtext, name:ijtext, color:"red", background:"yellow"} ); } } // Add a text area to display the result of the lasso operation: var info = $("<div/>").appendTo(element); info.html("Mouse down and encircle elements to select them with the lasso."); var lasso_callback = function(mapping) { var txt = "Lasso circled: "; for (var name in mapping) { txt += " (" + name + "),"; } info.html(txt); } element.do_lasso(lasso_callback, {}, true); """ ) def js_mouse_tracking_example(): return js_example( """ ### Mouse tracking The following code tracks mouse moves over the whole canvas and moves an external HTML DIV and a canvas circle in coordination with the pointer position. """, """ // Mouse tracking DIV let tooltip = $("<div>Move the mouse over the canvas.</div>").appendTo(element); tooltip.css({background: "yellow", width:120}); // Mouse tracking circle let circle = element.circle({name:true, x:10, y:10, r:13, color: "red"}); var event_handler = function(event) { var element_offset = element.visible_canvas.offset(); var canvas_location = element.event_model_location(event); var pixel_offset = element.event_pixel_location(event); // move the tooltip near the mouse tooltip.offset({ left: pixel_offset.x + element_offset.left + 5, top: pixel_offset.y + element_offset.top + 5, }); // move the circle under the mouse. circle.change({x:canvas_location.x, y:canvas_location.y}); // Report canvas position in the tooltip tooltip.html("x=" + Math.floor(canvas_location.x) + "<br> y=" + Math.floor(canvas_location.y)); }; element.on_canvas_event("mousemove", event_handler); """ ) def js_event_callback(): return js_example( """ ### Displaying mouse move coordinates The following widget contains a `rectangle` drawn on a `frame`. The `model_location` coordinates for a `mousemove` over the rectangle are reported in an appended `info_div` text area. The `model_location` gives coordinates for the reference frame associated with the object. """, """ // Map pixel coords (10,10) and (400,100) // to frame coords (-1, 0) and (1, 2) var frame = element.frame_region( 10, 10, 400, 100, -1, 0, 1, 2); // Create a named rectangle to receive events. var rectangle = frame.frame_rect({x:-0.8, y:0.1, w:1.3, h:1.9, color:"cyan", name:true}); frame.lower_left_axes({min_x:-1, min_y:0, max_x:1, max_y:2, x_anchor:0, y_anchor:1, max_tick_count:5, color:"blue"}); var info_div = $("<div/>").appendTo(element); info_div.html("Please mouse over the cyan rectangle"); var mouse_over_handler = function(event) { var x = event.model_location.x; var y = event.model_location.y; info_div.html("x=" + x + "; y=" + y); }; // Attach the event handler to the rectangle. rectangle.on("mousemove", mouse_over_handler); """ ) def js_2_frame_example(): return js_example( """ ### Create two reference frames inside a dual canvas It is possible to create many reference frames inside a dual canvas each with a different coordinate transform. The following Javascript places two canvases side-by-side and annotates them similarly using the same frame coordinates. """, """ // Map pixel coords (10,10) and (190,100) to frame coords (-1, 0) and (1, 2) in frame1 var frame1 = element.frame_region( 10, 10, 190, 100, -1, 0, 1, 2); // draw some reference marks on the frame1: frame1.text({x:-1, y:0, text:"-1,0", color:"red", background:"yellow"} ); frame1.text({x:1, y:2, text:"1,2", align:"right", color:"red", background:"yellow"} ); frame1.lower_left_axes({min_x:-1, min_y:0, max_x:1, max_y:2, x_anchor:0, y_anchor:1, max_tick_count:5, color:"blue"}) // Map pixel coords (210,10) and (400,100) to frame coords (-1, 0) and (1, 2) in frame2 var frame2 = element.frame_region( 210, 10, 400, 100, -1, 0, 1, 2); // draw some reference marks on the frame1: frame2.text({x:-1, y:0, text:"-1,0", color:"red", background:"cyan"} ); frame2.text({x:1, y:2, text:"1,2", align:"right", color:"red", background:"cyan"} ); frame2.lower_left_axes({min_x:-1, min_y:0, max_x:1, max_y:2, x_anchor:0, y_anchor:1, max_tick_count:5, color:"green"}) """ ) def py_arrow_example(): return python_example( """ ### Drawing arrows The `arrow` method draws an arrow between a head position and a tail position. """, ''' widget.arrow( head_length=30, x1=50, y1=10, # The tail end point of the line x2=320, y2=70, # The head end point of the line color="red", # Optional color (default: "black") lineWidth=4, # Optional line width lineDash=[2,2], # Optional line dash pattern head_angle=45, # Optional head segment angle in degrees (default 45) head_offset=10, # Optional offset of head from endpoint symmetric=True, # If true draw two arrow head segments (default False) ) ''') def js_arrow_example(): return js_example( """ ### Drawing arrows The `arrow` method draws an arrow between a head position and a tail position. """, ''' element.arrow({ head_length:30, x1:50, y1:10, // The tail end point of the line x2:320, y2:70, // The head end point of the line color:"red", // Optional color (default: "black") lineWidth:4, // Optional line width lineDash:[2,2], // Optional line dash pattern head_angle:45, // Optional head segment angle in degrees (default 45) head_offset:10, // Optional offset of head from endpoint symmetric:true, // If true draw two arrow head segments (default False) }); ''') def py_double_arrow_example(): return python_example( """ ### Drawing double arrows The `double_arrow` method draws an arrow between a head position and a tail position with head marks at both ends. """, ''' widget.double_arrow( head_length=30, x1=50, y1=10, # The tail end point of the line x2=320, y2=70, # The head end point of the line color="red", # Optional color (default: "black") back_color="blue", # Optional color of back arrow lineWidth=4, # Optional line width lineDash=[2,2], # Optional line dash pattern head_angle=45, # Optional head segment angle in degrees (default 45) back_angle=90, # Optional back head segment angle head_offset=10, # Optional offset of head from endpoint back_offset=0, # Optional, offset of back pointing head mark symmetric=False, # If true draw two arrow head segments (default False) line_offset=5, # offset of back arrow from forward arros ) ''') def js_double_arrow_example(): return js_example( """ ### Drawing double arrows The `double_arrow` method draws an arrow between a head position and a tail position with head marks at both ends. """, ''' element.double_arrow({ head_length:30, x1:50, y1:10, // The tail end point of the line x2:320, y2:70, // The head end point of the line color:"red", // Optional color (default: "black") back_color:"blue", // Optional color of back arrow lineWidth:4, // Optional line width lineDash:[2,2], // Optional line dash pattern head_angle:45, // Optional head segment angle in degrees (default 45) back_angle:90, // Optional back head segment angle head_offset:10, // Optional offset of head from endpoint back_offset:0, // Optional, offset of back pointing head mark symmetric:false, // If true draw two arrow head segments (default False) line_offset:5, // offset of back arrow from forward arros }); ''') def py_event_example(): return python_example( """ ### Attaching event callbacks The `object.on(etype, callback)` attaches a `callback` to be called when the object recieves an event of type `etype`. """, ''' # this circle cannot be mutated and does not respond to events because it is not named. widget.circle(x=0, y=0, r=100, color="#e99") # this text is named and can be mutated and can respond to events txt1 = widget.text(x=0, y=0, text="Hello World", degrees=45, name=True, font= "40pt Arial", color="#ee3", background="#9e9", align="center", valign="center") # add a click event bound to the txt which transitions the text rotation def on_click(*ignored): txt1.transition(text="That tickles", degrees=720, color="#f90", background="#009", seconds_duration=5) txt1.on("click", on_click) ''') def py_line_example(): return python_example( """ ### Drawing lines The `line` method draws a line segment between two end points. """, ''' widget.line( x1=50, y1=10, # One end point of the line x2=320, y2=30, # The other end point of the line color="cyan", # Optional color (default: "black") lineWidth=4, # Optional line width lineDash=[5,2,1], # Optional line dash pattern ) ''') def js_line_example(): return js_example( """ ### Drawing lines The `line` method draws a line segment between two end points. """, ''' element.line({ x1:50, y1:10, // One end point of the line x2:320, y2:100, // The other end point of the line color:"cyan", // Optional color (default: "black") lineWidth:4, // Optional line width lineDash:[5,2,1], // Optional line dash pattern }) ''') def py_polyline_example(): return python_example( """ ### Drawing polylines The `polyline` method draws sequence of connected line segments. """, ''' points = [(50,20), (40, 60), (140, 111), (300,4), (100,70)] widget.polyline( points=points, # The vertices of the polyline path color="green", # Optional color (default: "black") lineWidth=3, # Optional line width lineDash=[5,5], # Optional line dash pattern ) ''') def js_polyline_example(): return js_example( """ ### Drawing polylines The `polygon` method with `fill:false` and `close:false` draws sequence of connected line segments. """, ''' var points = [[50,20], [40, 60], [140, 111], [300,4], [100,70]]; element.polygon({ points:points, // The vertices of the polyline path color:"green", // Optional color (default: "black") lineWidth:3, // Optional line width lineDash:[5,5], // Optional line dash pattern fill:false, close:false, }); ''') def py_polygon_example(): return python_example( """ ### Drawing polygons The `polygon` method draws closed sequence of connected line segments. """, ''' points = [(50,20), (40, 60), (140, 111), (300,4), (100,70)] widget.polygon( points=points, # The vertices of the polyline path color="green", # Optional color (default: "black") lineWidth=3, # Optional line width lineDash=[5,5], # Optional line dash pattern fill=False, # Optional, if True (default) fill interior ) ''') def js_polygon_example(): return js_example( """ ### Drawing polygons The `polygon` method (with the default of `close:true`) draws closed sequence of connected line segments. """, ''' var points = [[50,20], [40, 60], [140, 111], [300,4], [100,70]]; element.polygon({ points:points, // The vertices of the polyline path color:"green", // Optional color (default: "black") lineWidth:3, // Optional line width lineDash:[5,5], // Optional line dash pattern fill:false, // close:true, // default value }); ''') def js_circle_example(): return js_example( """ ### Drawing circles with canvas relative radius The `circle` method draws a circle sized relative to the canvas coordinate system. Circles on two frames with the same radius will have the same size. """, ''' // map (10,10), (100,100) to (-3,0),(3,6) in the frame frame = element.frame_region( 10, 10, 100, 100, -3, 0, 3, 6, ) // Draw a circle positioned relative to the frame and sized relative to the canvas. frame.circle({ x:4, y:2.5, r:20, // radius "r" is in canvas coordinates, not frame coordinates color:"blue", fill:false, lineWidth:5, lineDash:[5,5], }) frame.lower_left_axes({max_tick_count:5, color:"green"}); ''') def py_circle_example(): return python_example( """ ### Drawing circles with canvas relative radius The `circle` method draws a circle sized relative to the canvas coordinate system. Circles on two frames with the same radius will have the same size. """, ''' frame = widget.frame_region( minx=10, miny=10, maxx=100, maxy=100, frame_minx=-3, frame_miny=0, frame_maxx=3, frame_maxy=6, ) # Draw a circle positioned relative to the frame and sized relative to the canvas. frame.circle( x=4, y=2.5, r=20, # radius "r" is in canvas coordinates, not frame coordinates color="blue", fill=False, lineWidth=5, lineDash=[5,5], ) ''') def js_frame_circle_example(): return js_example( """ ### Drawing circles with frame relative radius The `frame_circle` method draws a circle sized relative to the current reference frame coordinate system. Frame circles on two frames with the same radius may have different sizes if the scaling differs between the frames. """, ''' frame = element.frame_region( 10, 10, 100, 100, -3, 0, 3, 6, ) // Draw a circle positioned and sized relative to the frame. frame.frame_circle({ x:4, y:2.5, r:3, // radius "r" is in frame coordinates color:"blue", fill:true, }); frame.lower_left_axes({max_tick_count:5, color:"green"}); ''') def py_frame_circle_example(): return python_example( """ ### Drawing circles with frame relative radius The `frame_circle` method draws a circle sized relative to the current reference frame coordinate system. Frame circles on two frames with the same radius may have different sizes if the scaling differs between the frames. """, ''' frame = widget.frame_region( minx=10, miny=10, maxx=100, maxy=100, frame_minx=-3, frame_miny=0, frame_maxx=3, frame_maxy=6, ) # Draw a circle positioned and sized relative to the frame. frame.frame_circle( x=4, y=2.5, r=3, # radius "r" is in frame coordinates color="blue", fill=True, ) ''') def py_star_example(): return python_example( """ ### Drawing stars The `star` method draws a star on the canvas. """, ''' # Draw a star (always positioned and sized relative to the frame) widget.star( x=40, y=25, radius=30, points=5, # optional number of points point_factor=2.1, # optional scale factor for outer radius color="magenta", fill=False, lineWidth=5, lineDash=[5,5], ) ''') def js_star_example(): return js_example( """ ### Drawing stars The `star` method draws a star on the canvas. """, ''' // Draw a star (always positioned and sized relative to the frame) element.star({ x:40, y:25, radius:30, points:5, // optional number of points point_factor:2.1, // optional scale factor for outer radius color:"magenta", fill:false, lineWidth:5, lineDash:[5,5], }) ''') def py_rect_example(): return python_example( """ ### Drawing rectangles with canvas relative size The `rect` method draws a rectangle sized relative to the canvas coordinate system. `rect`s on two frames with the same width and height will have the same size. """, ''' frame = widget.frame_region( minx=10, miny=10, maxx=100, maxy=100, frame_minx=-3, frame_miny=0, frame_maxx=3, frame_maxy=6, ) # Draw a rectangle positioned and sized relative to the frame. (x,y) = (4, 2.5) frame.rect( x=x, y=y, # rectangle position relative to the frame w=50, h=40, # width and height relative to the canvas dx=-10, dy=-10, # offset of lower left corner from (x,y) relative to the canvas color="green", degrees=10, # optional rotation in degrees fill=False, lineWidth=5, lineDash=[5,5], ) # Draw a reference point at (x, y) frame.circle(x, y, 5, "red") frame.lower_left_axes(color="pink") ''') def js_rect_example(): return js_example( """ ### Drawing rectangles with canvas relative size The `rect` method draws a rectangle sized relative to the canvas coordinate system. `rect`s on two frames with the same width and height will have the same size. """, ''' frame = element.frame_region( 10, 10, 100, 100, -3, 0, 3, 6, ); // Draw a rectangle positioned and sized relative to the frame. var x = 4; var y = 2.5; frame.rect({ x:x, y:y, // rectangle position relative to the frame w:50, h:40, // width and height relative to the canvas dx:-10, dy:-10, // offset of lower left corner from (x,y) relative to the canvas color:"green", degrees:10, // optional rotation in degrees fill:false, lineWidth:5, lineDash:[5,5], }); // Draw a reference point at (x, y) frame.circle({x:x, y:y, r:5, color:"red"}); frame.lower_left_axes({color:"pink", max_tick_count:5}) ''') def py_canvas_rect_example(): return python_example( """ ### Drawing rectangles with frame relative size The `frame_rect` method draws a rectangle sized relative to the current reference frame coordinate system. `frame_rect`s on two frames with the same width and height may have the different sizes. """, ''' frame = widget.frame_region( minx=10, miny=10, maxx=100, maxy=100, frame_minx=-3, frame_miny=0, frame_maxx=3, frame_maxy=6, ) # Draw a rectangle positioned and sized relative to the frame. (x,y) = (4, 2.5) frame.frame_rect( x=x, y=y, # rectangle position w=5, h=4, # width and height relative to frame dx=-1, dy=-1, # offset of lower left corner from (x,y) relative to frame color="green", fill=False, degrees=10, # optional rotation in degrees lineWidth=5, lineDash=[5,5], ) # Draw a reference point at (x, y) frame.circle(x, y, 5, "red") frame.lower_left_axes(color="pink") ''') def js_canvas_rect_example(): return js_example( """ ### Drawing rectangles with frame relative size The `frame_rect` method draws a rectangle sized relative to the current reference frame coordinate system. `frame_rect`s on two frames with the same width and height may have the different sizes. """, ''' frame = element.frame_region( 10, 10, 100, 100, -3, 0, 3, 6, ); // Draw a rectangle positioned and sized relative to the frame. var x = 4; var y = 2.5; frame.frame_rect({ x:x, y:y, // rectangle position w:5, h:4, // width and height relative to frame dx:-1, dy:-1, // offset of lower left corner from (x,y) relative to frame color:"green", fill:false, degrees:10, // optional rotation in degrees lineWidth:5, lineDash:[5,5], }) // Draw a reference point at (x, y) frame.circle({x:x, y:y, r:5, color:"red"}); frame.lower_left_axes({color:"pink", max_tick_count:5}) ''') def py_text_example(): return python_example( """ ### Drawing text The `text` method draws a text screen on the canvas. The position of the text is determined by the current reference frame but the text font parameters are relative to the shared canvas coordinate space. """, ''' (x, y) = (50,20) widget.text( x=x, y=y, text="We the people", color="white", # Optional color (default: "black") font="italic 52px Courier", # optional background="#a00", # optional degrees=-15, # optional rotation in degrees align="center", # or "left" or "right", optional valign="center", # or "bottom", optional ) # Draw a reference point at (x, y) widget.circle(x, y, 5, "magenta") ''') def js_text_example(): return js_example( """ ### Drawing text The `text` method draws a text screen on the canvas. The position of the text is determined by the current reference frame but the text font parameters are relative to the shared canvas coordinate space. """, ''' var x = 240; var y = 30; element.text({ x:x, y:y, text:"We the people", color:"white", // Optional color (default: "black") font:"italic 52px Courier", // optional background:"#a00", // optional degrees:-15, // optional rotation in degrees align:"center", // or "left" or "right", optional valign:"center", // or "bottom", optional }) // Draw a reference point at (x, y) element.circle({x:x, y:y, r:5, color:"red"}); ''') def js_event_example(): return js_example( """ ### Attaching event callbacks The `object.on(etype, callback)` attaches a `callback` to be called when the object recieves an event of type `etype`. """, ''' // this circle cannot be mutated and does not respond to events because it is not named. element.circle({x:0, y:0, r:100, color:"#e99"}); // this text is named and can be mutated and can respond to events var txt1 = element.text({x:0, y:0, text:"Click me please", degrees:45, name:true, font:"40pt Arial", color:"#e3e", background:"#9e9", align:"center", valign:"center"}); // add a click event bound to the txt which transitions the text rotation var on_click = function() { var seconds_duration = 5; txt1.transition({text:"That tickles", degrees:720, color:"#f90", background:"#009"}, seconds_duration); }; txt1.on("click", on_click) ''') def js_no_name_no_event_example(): return js_example( """ ### Unnamed objects are invisible to events If an object is not named it will not respond to events but a named object drawn undernieth the unnamed object may receive the event. A named object may also disable events by setting `events=False` -- the resulting object can be changed or deleted but it will not respond to events. ```Javascript widget.circle({x:0, y:0, r:100, color:"#e99", name:True, events:False}); ``` Below the circle obscures the text but clicks in the center of the circle are recieved by the text. """, ''' // this text is named and can be mutated and can respond to events var txt1 = element.text({x:0, y:0, text:"CLICK THE CENTER OF THE CIRCLE", degrees:25, name:true, font:"40pt Arial", color:"#e3e", background:"#9e9", align:"center", valign:"center"}); // This circle cannot be mutated and does not respond to events because it is not named. // The txt1 undernieth the circle may respond to clicks on the circle. element.circle({x:0, y:0, r:70, color:"#e99"}); // add a click event bound to the txt which transitions the text rotation var on_click = function() { var seconds_duration = 5; txt1.transition({text:"That tickles", degrees:720, color:"#f90", background:"#009"}, seconds_duration); }; txt1.on("click", on_click) ''') def js_event_top_only_example(): return js_example( """ ### Only the top named object responds to events Only the top named object under an event receives the event even if it is drawn using a transparent color. Any object underneith the top object will not receive the event. """, ''' // this text is named and can be mutated and can respond to events var txt1 = element.text({x:0, y:0, text:"TRY TO CLICK THE CENTER OF THE CIRCLE", degrees:15, name:true, font:"40pt Arial", color:"#e3e", background:"#9e9", align:"center", valign:"center"}); // This circle CAN be mutated and MAY respond to events because it is named. // The txt1 undernieth the circle will not respond to clicks on the circle. element.circle({x:0, y:0, r:70, color:"#e99", name:true}); // add a click event bound to the txt which transitions the text rotation var on_click = function() { var seconds_duration = 5; txt1.transition({text:"That tickles", degrees:720, color:"#f90", background:"#009"}, seconds_duration); }; txt1.on("click", on_click) ''') def js_axes_example(): return js_example( """ ### Drawing axes The `left_axis`, `right_axis`, `bottom_axis`, `top_axis`, and `lower_left_axis` methods draw axes on the canvas. """, ''' element.left_axis({ min_value:10, max_value:80, axis_origin:{x:40, y:0}, max_tick_count:3, color:"green", add_end_points:true }) element.right_axis({ min_value:10, max_value:80, axis_origin:{x:240, y:0}, max_tick_count:7, color:"red" }) element.bottom_axis({ min_value:60, max_value:110, axis_origin:{x:0, y:0}, max_tick_count:5, color:"blue" }) element.top_axis({ min_value:130, max_value:180, axis_origin:{x:0, y:0}, max_tick_count:5, color:"orange" }) element.lower_left_axes({ min_x:50, min_y:30, max_x:210, max_y:90, x_anchor:130, y_anchor:66, max_tick_count:4, color:"brown" }); ''', axes=False) def py_full_image_example(): return python_example( """ ### Drawing whole images Before an image can be drawn on a canvas the image must be loaded. The `name_imagea_url` methodß loads an image from a file or a remote resource. After the image has been loaded and named the `named_image` draws the loaded image. If no subimage is specified the whole image is drawn into the rectangular region. A loaded image may be drawn any number of times. """, ''' # load the image from a remote resource mandrill_url = "http://sipi.usc.edu/database/preview/misc/4.2.03.png" widget.name_image_url( image_name="mandrill", url=mandrill_url, ) # draw the named image (any number of times) (x, y) = (50,20) widget.named_image( # Draw the *whole* image (don't specify the s* parameters) image_name="mandrill", x=x, y=y, # rectangle position relative to the canvas w=150, h=140, # width and height relative to the frame dx=-30, dy=-50, # optional offset of lower left corner from (x,y) relative to the canvas degrees=10, # optional rotation in degrees ) # Draw a reference point at (x, y) widget.circle(x, y, 5, "magenta") ''', embeddable=False) def js_full_image_example(): return js_example( """ ### Drawing whole images Before an image can be drawn on a canvas the image must be loaded. The `name_imagea_url` methodß loads an image from a file or a remote resource. After the image has been loaded and named the `named_image` draws the loaded image. If no subimage is specified the whole image is drawn into the rectangular region. A loaded image may be drawn any number of times. """, ''' // load the image from a remote resource var mandrill_url = "http://sipi.usc.edu/database/preview/misc/4.2.03.png"; element.name_image_url("mandrill", mandrill_url); // draw the named image (any number of times) var x = 50; var y = 20; element.named_image({ // Draw the *whole* image (don't specify the s* parameters) image_name:"mandrill", x:x, y:y, // rectangle position relative to the canvas w:150, h:140, // width and height relative to the frame dx:-30, dy:-50, // optional offset of lower left corner from (x,y) relative to the canvas degrees:10, // optional rotation in degrees }); // Draw a reference point at (x, y) element.circle({x:x, y:y, r:5, color:"magenta"}); ''', embeddable=False) def py_part_image_example(): return python_example( """ ### Drawing parts of images The `named_image` draws part of a loaded image if the subimage parameters sx, sy, sWidth, and sHeight are specified. """, ''' # load the image from a remote resource mandrill_url = "http://sipi.usc.edu/database/preview/misc/4.2.03.png" widget.name_image_url( image_name="mandrill", url=mandrill_url, ) # draw the named image (any number of times) (x, y) = (50,20) widget.named_image( # Draw just the eyes (by specifying the subimage) image_name="mandrill", x=x, y=y, # rectangle position relative to the canvas w=150, h=40, # width and height relative to the frame dx=-30, dy=-10, # optional offset of lower left corner from (x,y) relative to the canvas degrees=10, # optional rotation in degrees sx=30, sy=15, # subimage upper left corner in image coordinates sWidth=140, sHeight=20, # subimage extent in image coordinates ) # Draw a reference point at (x, y) widget.circle(x, y, 5, "magenta") ''', embeddable=False) def js_part_image_example(): return js_example( """ ### Drawing parts of images The `named_image` draws part of a loaded image if the subimage parameters sx, sy, sWidth, and sHeight are specified. """, ''' // load the image from a remote resource var mandrill_url = "http://sipi.usc.edu/database/preview/misc/4.2.03.png"; element.name_image_url("mandrill", mandrill_url); // draw the named image (any number of times) var x = 50; var y = 20; // draw the named image (any number of times) element.named_image({ // Draw the *whole* image (don't specify the s* parameters) image_name:"mandrill", x:x, y:y, // rectangle position relative to the canvas w:150, h:140, // width and height relative to the frame dx:-30, dy:-50, // optional offset of lower left corner from (x,y) relative to the canvas degrees:10, // optional rotation in degrees sx:30, sy:15, // subimage upper left corner in image coordinates sWidth:140, sHeight:20, // subimage extent in image coordinates }); // Draw a reference point at (x, y) element.circle({x:x, y:y, r:5, color:"magenta"}); ''', embeddable=False) def py_bw_image_example(): return python_example( """ ### Drawing black and white images from arrays The `name_image_array` can load a black and white image from a 2 dimensional `numpy` array. The numeric values in the array should be in the range from 0 to 255. """, ''' # Make a "black and white" array. import numpy as np checkerboard = np.zeros((8,8)) for i in range(8): for j in range(8): if (i + j) % 2 == 0: checkerboard[i,j] = 64 + 3*i*j # Load the image from the array. widget.name_image_array( image_name="checkerboard", np_array=checkerboard, ) # draw the named image (any number of times) (x, y) = (50,20) widget.named_image( # Draw just the eyes (by specifying the subimage) image_name="checkerboard", x=x, y=y, # rectangle position relative to the canvas w=150, h=140, # width and height relative to the frame dx=-30, dy=-10, # offset of lower left corner from (x,y) relative to the canvas degrees=10, # optional rotation in degrees ) # Draw a reference point at (x, y) widget.circle(x, y, 5, "magenta") ''') def py_color_image_example(): return python_example( """ ### Drawing color images from arrays The `name_image_array` can load a color image from a 3 dimensional `numpy` array of shape "width by height by 3" or "width by height by 4". The values at `array[:,:,1:3]` represent the red, green, and blue color values for the pixel and should be in the range 0 to 255. If provided the values at `array[:,:,3]` represent the opacity of the pixel and should be in the range 0 (transparent) to 1.0 (fully opaque). """, ''' # Make a "color" numpy array import numpy as np checkerboard = np.zeros((8,8,3)) R = G = B = 255 for i in range(8): for j in range(8): if (i + j) % 2 == 0: checkerboard[i,j] = (R, G, B) R = (G + 123) % 256 else: checkerboard[i,j] = (G, R, R) G = (R + 201) % 256 # Load the image from the array widget.name_image_array( image_name="checkerboard", np_array=checkerboard, ) # draw the named image (any number of times) (x, y) = (50,20) widget.named_image( # Draw just the eyes (by specifying the subimage) image_name="checkerboard", x=x, y=y, # rectangle position relative to the canvas w=150, h=140, # width and height relative to the frame dx=-30, dy=-10, # offset of lower left corner from (x,y) relative to the canvas degrees=-50, # optional rotation in degrees ) # Draw a reference point at (x, y) widget.circle(x, y, 10, "yellow") ''') def html_hello_world(): from IPython.display import display, Markdown txt = open("minimal.html").read() L = ["```HTML", txt, "```"] md = "\n".join(L) display(Markdown(md))

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0

1

0

null

0

1

0

1

0

6

a47f34da66634483663c102d2f6ac0337c109f62

42

py

Python

modules/__init__.py

autonomousvision/data_aggregation

76777156a465cbb77d6d5ab88da8f1812e7ff043

[ "MIT" ]

29

2020-03-19T14:11:15.000Z

2022-02-01T14:51:40.000Z

modules/__init__.py

autonomousvision/data_aggregation

76777156a465cbb77d6d5ab88da8f1812e7ff043

[ "MIT" ]

4

2020-06-24T18:49:27.000Z

2020-11-18T12:31:26.000Z

modules/__init__.py

autonomousvision/data_aggregation

76777156a465cbb77d6d5ab88da8f1812e7ff043

[ "MIT" ]

5

2020-06-24T02:00:13.000Z

2021-06-05T08:54:34.000Z

from .screen_manager import ScreenManager

21

41

0.880952

5

42

7.2

1

0

0.095238

42

1

42

0.947368

0

1

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true

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0

null

0

1

0

1

0

1

0

6

f14e7e682d2f946602e52d6a24b48c8f876442b8

164

py

Python

transactions/views.py

Hesiod-Labs/Luca-Python

4fc33449126ce94862ecd3f427c2902bebfcc74a

[ "MIT" ]

1

2019-04-05T01:50:04.000Z

transactions/views.py

Hesiod-Labs/Luca-Python

4fc33449126ce94862ecd3f427c2902bebfcc74a

[ "MIT" ]

null

transactions/views.py

Hesiod-Labs/Luca-Python

4fc33449126ce94862ecd3f427c2902bebfcc74a

[ "MIT" ]

null

from django.shortcuts import render from django.http import HttpResponse # Create your views here. def home(request): return HttpResponse("Work in Progress")

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43

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null

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null

0

1

0

1

0

6

74b522b2c558e2df5ad030725797d5752ec9ed13

38

py

Python

src/parse_audits/__main__.py

harmony5/parse_audits

7f2ecc2ff0848759b4a602a3f8f83b7f698fc64a

[ "MIT" ]

1

2021-05-01T09:10:41.000Z

src/parse_audits/__main__.py

harmony5/parse_audits

7f2ecc2ff0848759b4a602a3f8f83b7f698fc64a

[ "MIT" ]

null

src/parse_audits/__main__.py

harmony5/parse_audits

7f2ecc2ff0848759b4a602a3f8f83b7f698fc64a

[ "MIT" ]

null

from parser_cli.cli import cli cli()

9.5

30

0.763158

7

38

4

0.571429

0.428571

0

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3

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0

1

0

null

0

1

0

1

0

6

74c73ad458e5600d401017748986b822006ba05d

37,077

py

Python

SplitSpikein.py

PavriLab/IgH_VDJ_PROcapseq

c8435a0cd651f81352ecdfa77a136b8d18301482

[ "MIT" ]

null

SplitSpikein.py

PavriLab/IgH_VDJ_PROcapseq

c8435a0cd651f81352ecdfa77a136b8d18301482

[ "MIT" ]

2

2019-03-22T17:30:11.000Z

2019-05-15T12:32:54.000Z

SplitSpikein.py

PavriLab/IgH_VDJ_PROcapseq

c8435a0cd651f81352ecdfa77a136b8d18301482

[ "MIT" ]

null

#!/usr/bin/env python3 import re, os, sys from argparse import ArgumentParser, RawDescriptionHelpFormatter # from collections import Counter import pysam ############# ## Read Me ## ############# # Based on the revised/cleaned version of DiscardNonIghReads.py # # Created: 07/jan/2020 by: kimon.froussios@imp.ac.at # # The major assumption of this script is that alignment was done with bowtie --best --strata -a # This means that only equally-best alignments are reported as multimappers (by number of mismatches). ################# ## Parameters ## ################ usage = "Split mouse reads from drosophila spike-in reads" version = "0.1.0" # Main Parsers parser = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter) parser.add_argument("-a", "--allSamFile", type=str, required=True, help="BAM file with all the mapped reads") parser.add_argument("-o", "--outDir", type=str, required=True, dest="outDir", help="Destination directory.") args = parser.parse_args() ################# ## Pre-defined Settings ################ # Flybase r6.27 - all chromosomes and scaffolds spikeChroms = ["2L","2R","3L","3R","4","X","Y","mitochondrion_genome", "rDNA","2Cen_mapped_Scaffold_10_D1684","2Cen_mapped_Scaffold_43_D1668","2R2_mapped_Scaffold_56_D1828","3Cen_mapped_Scaffold_1_D1896_D1895","3Cen_mapped_Scaffold_27_D1777","3Cen_mapped_Scaffold_31_D1643_D1653_D1791","3Cen_mapped_Scaffold_36_D1605","3Cen_mapped_Scaffold_41_D1641","3Cen_mapped_Scaffold_50_D1686","X3X4_mapped_Scaffold_6_D1712","X3X4_mapped_Scaffold_14_D1732","XY_mapped_Scaffold_42_D1648","Y_mapped_Scaffold_5_D1748_D1610","Y_mapped_Scaffold_9_D1573","Y_mapped_Scaffold_12_D1771","Y_mapped_Scaffold_15_D1727","Y_mapped_Scaffold_18_D1698","Y_mapped_Scaffold_20_D1762_D1719","Y_mapped_Scaffold_21_D1683_D1693","Y_mapped_Scaffold_23_D1638","Y_mapped_Scaffold_26_D1717","Y_mapped_Scaffold_30_D1720","Y_mapped_Scaffold_34_D1584","Y_mapped_Scaffold_53_D1765", 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########## # Categorize read names ########## mouse = set() fly = set() both = set() inSam = pysam.AlignmentFile(args.allSamFile, "rb") # Multiple alignments of a read are reported individually. for read in inSam: if not read.is_unmapped: if read.reference_name in spikeChroms: # Mapped to spike-in reference (fly). fly.add(read.query_name) else: # Mapped to reference of interest (mouse). mouse.add(read.query_name) inSam.close() # Distinguish multimappers. both = mouse & fly # It's mapped to both mouse and fly mouse = mouse - both # Only to mouse fly = fly - both # Only to fly ########## # Categorize reads ########## prefix = re.sub(".sam|.bam", "", os.path.basename(args.allSamFile)) prefix = re.sub(".deduped|.aln", "", prefix) # Re-open input from the start. inSam = pysam.AlignmentFile(args.allSamFile, "rb") # Mapped only to target locus. outMouse = pysam.AlignmentFile(os.path.join(args.outDir, prefix + "_subject.bam"), "wb", template=inSam) # Mapped to target locus but equally well mapped to native IgH region. outFly = pysam.AlignmentFile(os.path.join(args.outDir, prefix + "_spikein.bam"), "wb", template=inSam) # Unique and non-unique mapped to locus (ie. the above two together). outBoth = pysam.AlignmentFile(os.path.join(args.outDir, prefix + "_ambiguous.bam"), "wb", template=inSam) for read in inSam: # Discard unmapped reads. if not read.is_unmapped: if read.query_name in mouse: outMouse.write(read) elif read.query_name in fly: outFly.write(read) elif read.query_name in both: outBoth.write(read) inSam.close() outMouse.close() outFly.close() outBoth.close()

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6

2d0e785722a643a0751d95a2dc1fc6715ab01384

35

py

Python

CodeWars/Python/030-Sum_of_angles.py

IsFilimonov/Interviews

261b59cd80e1451804c37b03b4cce7c1b63f609d

[ "MIT" ]

2

2021-05-09T22:39:49.000Z

2021-09-16T12:44:09.000Z

CodeWars/Python/030-Sum_of_angles.py

IsFilimonov/Interviews

261b59cd80e1451804c37b03b4cce7c1b63f609d

[ "MIT" ]

null

CodeWars/Python/030-Sum_of_angles.py

IsFilimonov/Interviews

261b59cd80e1451804c37b03b4cce7c1b63f609d

[ "MIT" ]

null

def angle(n): return (n-2)*180

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7487994641381887e98fd23f0957f62499e652eb

11,298

py

Python

trainingsetai/__init__.py

trainingset-ai/trainingsetai-python-sdk

b5c412044cc649f0527a9ae82e0641132d901b04

[ "MIT" ]

1

2021-01-19T08:22:56.000Z

trainingsetai/__init__.py

trainingset-ai/trainingsetai-python-sdk

b5c412044cc649f0527a9ae82e0641132d901b04

[ "MIT" ]

null

trainingsetai/__init__.py

trainingset-ai/trainingsetai-python-sdk

b5c412044cc649f0527a9ae82e0641132d901b04

[ "MIT" ]

null

import requests BASE_URL = "https://api.trainingset.ai/api" class TrainingsetException(Exception): def __init__(self, message, status_code): super(TrainingsetException, self).__init__( '<Response [{}]> {}'.format(status_code, message)) self.code = status_code class TrainingsetInvalidRequest(TrainingsetException, ValueError): pass class TrainingsetClient: def __init__(self, api_key): self.session = requests.Session() self.session.headers.update({'user_key': api_key}) def _get_request(self, endpoint, params={}): r = self.session.get(BASE_URL + endpoint, params=params) if r.status_code == 200: return r.json() else: try: error = r.json() except ValueError: error = r.text if r.status_code == 400: raise TrainingsetInvalidRequest( error["message"], r.status_code) else: raise TrainingsetException(error, r.status_code) def _post_request(self, endpoint, data): r = self.session.post(BASE_URL + endpoint, json=data) if r.status_code == 200: return r.json() else: try: error = r.json() except ValueError: error = r.text if r.status_code == 400: raise TrainingsetInvalidRequest( error["message"], r.status_code) else: raise TrainingsetException(error, r.status_code) def get_tasks(self, parameters={}): """ Returns a list of tasks. parameters object: `sort`: [["attribute_name",1 or -1]], example: [["_id",1]], 1 is ascending, -1 is descending `rangeStart`: YYYY-MM-DD, example: "2020-01-31" `rangeEnd`: YYYY-MM-DD, example: "2020-12-31" `type`: "annotation-box" | "annotation-line" | "annotation-polygon" | "annotation-box" | "annotation-pcd" | "categorization-image" | "segmentation" `status`: "pending" | "completed" | "cancelled" | "error" | "ready" | "working" `project`: string, projectID, example: "5f6359d0838a1d868f54cac4" `limit`: integer `skip`: integer `id`: string, ID of the task `qa_status`: "accepted" | "pending" | "rejected" Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._get_request("/task/by-custom-filter", parameters) def delete_task(self, task_id): """ Deletes a task. """ response = self.session.delete(BASE_URL + "/task/" + task_id) return response.json() def create_box_annotation_task(self, task): """ Creates a box type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `min_height`: Minimum height of each box drawn in the task (Optional) (Number) `min_width`: Minimum width of each box drawn in the task (Optional) (Number) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `automatic_prelabel`: Automatically prelabel the picture (Optional) (Boolean) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/box", task) def create_line_annotation_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `min_vertices`: Minimum number of vertices that a polygon drawn in the task must have (Optional)(Number) `max_vertices`: Maximum number of vertices that a polygon drawn in the task must have (Optional)(Number) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `automatic_prelabel`: Automatically prelabel the picture (Optional) (Boolean) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/line", task) def create_polygon_annotation_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `min_vertices`: Minimum number of vertices that a polygon drawn in the task must have (Optional)(Number) `max_vertices`: Maximum number of vertices that a polygon drawn in the task must have (Optional)(Number) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `automatic_prelabel`: Automatically prelabel the picture (Optional) (Boolean) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/polygon", task) def create_point_annotation_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `automatic_prelabel`: Automatically prelabel the picture (Optional) (Boolean) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/point", task) def create_point_cloud_annotation_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `cameras`: Camera parameters, each camera is an object (Optional) (CameraObject Array) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/pcd", task) def create_segmentation_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `with_labels`: Define if the task has tags (Optional) (Boolean) `objects_to_annotate`: List of objects to be annotated (Optional) (AnnotationObject Array) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) `automatic_prelabel`: Automatically prelabel the picture (Optional) (Boolean) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/annotation/segmentation", task) def create_image_categorization_task(self, task): """ Creates a line type annotation task. task object: `instructions`: Instructions for drawing the task (Required) (String) `categories`: Categories into which an image can be categorized (Required) (String Array) `attachment_url`: HTTP/HTTPS Image address where the drawing of the task is carried out (Required) (String) `allow_multiple`: Allow multiple categories to be selected (Optional) (Boolean) `with_labels`: Define if the task has tags (Optional) (Boolean) `project`: Name of the project that belongs to the task (Optional) (String) `callback_url`: URL to which you will get task results delivered (Optional) (String) Check the documentation for more info: https://documenter.getpostman.com/view/10426338/Szf9V75M?version=latest#783c6a4f-373a-4559-a68a-30cd98808d73 """ return self._post_request("/task/categorization/image", task) def create_project(self, project_name, summary, instructions, automatic_prelabel, automatic_label): """ Creates a new project. """ return self._post_request("/project", { "name": project_name, "summary": summary, "instructions": instructions, "automatic_prelabel": automatic_prelabel, "automatic_label": automatic_label, }) def get_projects(self): """ Fetches a list of projects. """ return self._get_request("/project") def delete_project(self, project_id): """ Deletes a project by it's identifier. """ response = self.session.delete(BASE_URL + "/project/" + project_id) return response.json()

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null

0

1

0

6

77879300dbcba02b4e42942f60db7bbf45785e2e

590

py

Python

sm_widgets/models/ontology.py

binh-vu/sm-gui

dd5faa09b7570762aa63bf9f2ff88081cf132db4

[ "MIT" ]

null

sm_widgets/models/ontology.py

binh-vu/sm-gui

dd5faa09b7570762aa63bf9f2ff88081cf132db4

[ "MIT" ]

null

sm_widgets/models/ontology.py

binh-vu/sm-gui

dd5faa09b7570762aa63bf9f2ff88081cf132db4

[ "MIT" ]

null

from dataclasses import dataclass, field from typing import List, Set, Optional @dataclass class OntClass: uri: str label: str aliases: List[str] description: str parents: List[str] parents_closure: Set[str] = field(default_factory=set) @property def readable_label(self): return self.label @dataclass class OntProperty: uri: str label: str aliases: List[str] description: str parents: List[str] parents_closure: Set[str] = field(default_factory=set) @property def readable_label(self): return self.label

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1

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null

0

6

7ae2cf1ccad8cecbf0a0bc8a3d2be40943a04509

34

py

Python

runtest.py

tzakrajs/yaiges

046e376dc7a03466cf2860cf29509d251ed667e3

[ "Apache-2.0" ]

null

runtest.py

tzakrajs/yaiges

046e376dc7a03466cf2860cf29509d251ed667e3

[ "Apache-2.0" ]

null

runtest.py

tzakrajs/yaiges

046e376dc7a03466cf2860cf29509d251ed667e3

[ "Apache-2.0" ]

null

#!/usr/bin/python3 import asyncio

11.333333

18

0.764706

5

34

5.2

1

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0.088235

34

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0

1

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1

0

6

7aefb3899ee49c492294932181e2bb7dbac73100

14,571

py

Python

tests/syntax/simple_expression/test_assignment_ops.py

PowerOlive/mindspore

bda20724a94113cedd12c3ed9083141012da1f15

[ "Apache-2.0" ]

3,200

2020-02-17T12:45:41.000Z

2022-03-31T20:21:16.000Z

tests/syntax/simple_expression/test_assignment_ops.py

zimo-geek/mindspore

665ec683d4af85c71b2a1f0d6829356f2bc0e1ff

[ "Apache-2.0" ]

176

2020-02-12T02:52:11.000Z

2022-03-28T22:15:55.000Z

tests/syntax/simple_expression/test_assignment_ops.py

zimo-geek/mindspore

665ec683d4af85c71b2a1f0d6829356f2bc0e1ff

[ "Apache-2.0" ]

621

2020-03-09T01:31:41.000Z

2022-03-30T03:43:19.000Z

# Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # ============================================================================ import numpy as np import mindspore.context as context import mindspore.nn as nn from mindspore import Tensor, Parameter from mindspore.common.initializer import initializer from mindspore.ops import operations as P context.set_context(mode=context.GRAPH_MODE) class Assign(nn.Cell): def __init__(self, x, y): super(Assign, self).__init__() self.x = Parameter(initializer(x, x.shape), name="x") self.y = Parameter(initializer(y, y.shape), name="y") self.assign = P.Assign() def construct(self): self.assign(self.y, self.x) return self.y def test_assign_bool(): x = Tensor(np.ones([3, 3]).astype(np.bool_)) y = Tensor(np.zeros([3, 3]).astype(np.bool_)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.bool_) print(output) assert np.all(output == output_expect) def test_assign_int8(): x = Tensor(np.ones([3, 3]).astype(np.int8)) y = Tensor(np.zeros([3, 3]).astype(np.int8)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.int8) print(output) assert np.all(output == output_expect) def test_assign_uint8(): x = Tensor(np.ones([3, 3]).astype(np.uint8)) y = Tensor(np.zeros([3, 3]).astype(np.uint8)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.uint8) print(output) assert np.all(output == output_expect) def test_assign_int16(): x = Tensor(np.ones([3, 3]).astype(np.int16)) y = Tensor(np.zeros([3, 3]).astype(np.int16)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.int16) print(output) assert np.all(output == output_expect) def test_assign_uint16(): x = Tensor(np.ones([3, 3]).astype(np.uint16)) y = Tensor(np.zeros([3, 3]).astype(np.uint16)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.uint16) print(output) assert np.all(output == output_expect) def test_assign_int32(): x = Tensor(np.ones([3, 3]).astype(np.int32)) y = Tensor(np.zeros([3, 3]).astype(np.int32)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.int32) print(output) assert np.all(output == output_expect) def test_assign_uint32(): x = Tensor(np.ones([3, 3]).astype(np.uint32)) y = Tensor(np.zeros([3, 3]).astype(np.uint32)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.uint32) print(output) assert np.all(output == output_expect) def test_assign_int64(): x = Tensor(np.ones([3, 3]).astype(np.int64)) y = Tensor(np.zeros([3, 3]).astype(np.int64)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.int64) print(output) assert np.all(output == output_expect) def test_assign_uint64(): x = Tensor(np.ones([3, 3]).astype(np.uint64)) y = Tensor(np.zeros([3, 3]).astype(np.uint64)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.ones([3, 3]).astype(np.uint64) print(output) assert np.all(output == output_expect) def test_assign_float16(): x = Tensor(np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float16)) y = Tensor(np.array([[0.4, 0.5, 0.5], [0.6, 0.7, 0.8], [0.1, 0.2, 0.3]]).astype(np.float16)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float16) print(output) assert np.all(output - output_expect < 1e-6) def test_assign_float32(): x = Tensor(np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float32)) y = Tensor(np.array([[0.4, 0.5, 0.5], [0.6, 0.7, 0.8], [0.1, 0.2, 0.3]]).astype(np.float32)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float32) print(output) assert np.all(output - output_expect < 1e-6) def test_assign_float64(): x = Tensor(np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float64)) y = Tensor(np.array([[0.4, 0.5, 0.5], [0.6, 0.7, 0.8], [0.1, 0.2, 0.3]]).astype(np.float64)) assign = Assign(x, y) output = assign() output = output.asnumpy() output_expect = np.array([[0.1, 0.2, 0.3], [0.4, 0.5, 0.5], [0.6, 0.7, 0.8]]).astype(np.float64) print(output) assert np.all(output - output_expect < 1e-6) class AssignAdd(nn.Cell): def __init__(self, x, y): super(AssignAdd, self).__init__() self.x = Parameter(initializer(x, x.shape), name="x") self.y = Parameter(initializer(y, y.shape), name="y") self.assignadd = P.AssignAdd() def construct(self): self.assignadd(self.y, self.x) return self.y def test_number_assignadd_number(): input_x = 2 result1 = 5 result2 = 5 result1 += input_x assignadd = AssignAdd(result2, input_x) result2 = assignadd() expect = 7 assert np.all(result1 == expect) assert np.all(result2 == expect) def test_tensor_assignadd_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result1 = Tensor(np.array([[4, -2], [2, 17]])) result2 = Tensor(np.array([[4, -2], [2, 17]])) result1 += input_x result2 = AssignAdd(result2, input_x)() expect = Tensor(np.array([[6, 0], [5, 20]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_tensor_assignadd_number(): input_x = 3 result1 = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result2 = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result1 += input_x result2 = AssignAdd(result2, input_x)() expect = Tensor(np.array([[7, 1], [5, 20]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_number_assignadd_tensor(): result1 = 3 result2 = 3 input_x = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result1 += input_x result2 = AssignAdd(result2, input_x)() expect = Tensor(np.array([[7, 1], [5, 20]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_tuple_assignadd_tuple(): result1 = (1, 2, 3, 4) result2 = (1, 2, 3, 4) input_x = (2, 3, 4, 5, 6) result1 += input_x result2 = AssignAdd(result2, input_x)() expect = (1, 2, 3, 4, 2, 3, 4, 5, 6) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_string_assignadd_string(): result1 = "string111" result2 = "string111" input_x = "string222" result1 += input_x result2 = AssignAdd(result2, input_x)() expect = "string111string222" assert result1 == expect assert result2 == expect class AssignSub(nn.Cell): def __init__(self, x, y): super(AssignSub, self).__init__() self.x = Parameter(initializer(x, x.shape), name="x") self.y = Parameter(initializer(y, y.shape), name="y") self.assignsub = P.AssignSub() def construct(self): self.assignsub(self.y, self.x) return self.y def test_number_assignsub_number(): input_x = 2 result1 = 5 result2 = 5 result1 -= input_x result2 = AssignSub(result2, input_x)() expect = 3 assert np.all(result1 == expect) assert np.all(result2 == expect) def test_tensor_assignsub_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result1 = Tensor(np.array([[4, -2], [2, 17]])) result2 = Tensor(np.array([[4, -2], [2, 17]])) result1 -= input_x result2 = AssignSub(result2, input_x)() expect = Tensor(np.array([[2, -4], [-1, 14]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_tensor_assignsub_number(): input_x = 3 result1 = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result2 = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result1 -= input_x result2 = AssignSub(result2, input_x)() expect = Tensor(np.array([[1, -5], [-1, 14]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_number_assignsub_tensor(): result1 = 3 result2 = 3 input_x = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result1 -= input_x result2 = AssignSub(result2, input_x)() expect = Tensor(np.array([[-1, 5], [1, -14]])) assert np.all(result1.asnumpy() == expect) assert np.all(result2.asnumpy() == expect) def test_number_assignmul_number(): input_x = 2 result = 5 result *= input_x expect = 10 assert np.all(result == expect) def test_tensor_assignmul_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result = Tensor(np.array([[4, -2], [2, 17]])) result *= input_x expect = Tensor(np.array([[8, -4], [6, 51]])) assert np.all(result.asnumpy() == expect) def test_tensor_assignmul_number(): input_x = 3 result = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result *= input_x expect = Tensor(np.array([[12, -6], [6, 51]])) assert np.all(result.asnumpy() == expect) def test_number_assignmul_tensor(): result = 3 input_x = Tensor(np.array([[4, -2], [2, 17]])).astype(np.float16) result *= input_x expect = Tensor(np.array([[12, -6], [6, 51]])) assert np.all(result.asnumpy() == expect) def test_number_assigndiv_number(): input_x = 2 result = 5 result /= input_x expect = 2.5 assert np.all(result == expect) def test_tensor_assigndiv_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result = Tensor(np.array([[4, -2], [6, 15]])) result /= input_x expect = Tensor(np.array([[2, -1], [2, 5]])) assert np.all(result.asnumpy() == expect) def test_tensor_assigndiv_number(): input_x = 3 result = Tensor(np.array([[9, -3], [6, 15]])).astype(np.float16) result /= input_x expect = Tensor(np.array([[3, -1], [2, 5]])) assert np.all(result.asnumpy() == expect) def test_number_assigndiv_tensor(): result = 3 input_x = Tensor(np.array([[2, -2], [2, -2]])).astype(np.float16) result /= input_x expect = Tensor(np.array([[1.5, -1.5], [1.5, -1.5]])) assert np.all(result.asnumpy() == expect) def test_number_assignmod_number(): input_x = 2 result = 5 result %= input_x expect = 1 assert np.all(result == expect) def test_tensor_assignmod_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result = Tensor(np.array([[4, -2], [6, 15]])) result %= input_x expect = Tensor(np.array([[0, 0], [0, 0]])) assert np.all(result.asnumpy() == expect) def test_tensor_assignmod_number(): input_x = 3 result = Tensor(np.array([[9, -3], [7, 15]])).astype(np.float16) result %= input_x expect = Tensor(np.array([[0, 0], [1, 0]])) assert np.all(result.asnumpy() == expect) def test_number_assignmod_tensor(): result = 3 input_x = Tensor(np.array([[2, -2], [2, -2]])).astype(np.float16) result %= input_x expect = Tensor(np.array([[1, -1], [1, -1]])) assert np.all(result.asnumpy() == expect) def test_number_assignmulmul_number(): input_x = 2 result = 5 result **= input_x expect = 25 assert np.all(result == expect) def test_tensor_assignmulmul_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result = Tensor(np.array([[4, -2], [6, 5]])) result **= input_x expect = Tensor(np.array([[16, 4], [216, 125]])) assert np.all(result.asnumpy() == expect) def test_tensor_assignmulmul_number(): input_x = 3 result = Tensor(np.array([[9, -3], [7, 5]])).astype(np.float16) result **= input_x expect = Tensor(np.array([[729, -27], [343, 125]])) assert np.all(result.asnumpy() == expect) def test_number_assignmulmul_tensor(): result = 3 input_x = Tensor(np.array([[2, 2], [2, 2]])).astype(np.float16) result **= input_x expect = Tensor(np.array([[9, 9], [9, 9]])) assert np.all(result.asnumpy() == expect) def test_number_assigndivdiv_number(): input_x = 2 result = 5 result //= input_x expect = 2 assert np.all(result == expect) def test_tensor_assigndivdiv_tensor(): input_x = Tensor(np.array([[2, 2], [3, 3]])) result = Tensor(np.array([[4, -2], [6, 6]])) result //= input_x expect = Tensor(np.array([[2, -1], [2, 2]])) assert np.all(result.asnumpy() == expect) def test_tensor_assigndivdiv_number(): input_x = 3 result = Tensor(np.array([[9, -3], [15, 9]])).astype(np.float16) result //= input_x expect = Tensor(np.array([[3, -1], [5, 3]])) assert np.all(result.asnumpy() == expect) def test_number_assigndivdiv_tensor(): result = 3 input_x = Tensor(np.array([[1, 2], [2, 2]])).astype(np.float16) result //= input_x expect = Tensor(np.array([[3, 1], [1, 1]])) assert np.all(result.asnumpy() == expect)

30.293139

78

0.589596

2,134

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3.914714

0.074039

0.073737

0.091812

0.03232

0.848216

0.824635

0.821882

0.803328

0.715825

0.672851

0

0.0664

0.226889

14,571

480

79

30.35625

0.675189

0.043786

0

0.614555

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0.003664

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0.140162

1

0.12938

false

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0.032345

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null

0

1

0

null

0

6

24cca90261604a465cd68c565c39e57d7d5b47ed

49

py

Python

pypureclient/flasharray/__init__.py

tlewis-ps/py-pure-client

589b2c0dc0a5e890eb74902a8056e43723400d50

[ "BSD-2-Clause" ]

null

pypureclient/flasharray/__init__.py

tlewis-ps/py-pure-client

589b2c0dc0a5e890eb74902a8056e43723400d50

[ "BSD-2-Clause" ]

1

2021-11-17T18:59:56.000Z

pypureclient/flasharray/__init__.py

tlewis-ps/py-pure-client

589b2c0dc0a5e890eb74902a8056e43723400d50

[ "BSD-2-Clause" ]

1

2021-11-02T21:47:34.000Z

from .FA_2_4 import * from .client import Client

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26

0.77551

9

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4

0.666667

0

0.04878

0.163265

49

2

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true

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null

0

1

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1

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1

0

6

700b58cb81b44a35238b337b16fdc6042fccf45b

18,187

py

Python

build/bdist.macosx-10.9-x86_64/wininst/PURELIB/data_xray/report/core.py

amplifilo/data-xray

c68c9b352efde0776189210794aeef84ae2cf6c2

[ "Apache-2.0" ]

null

build/bdist.macosx-10.9-x86_64/wininst/PURELIB/data_xray/report/core.py

amplifilo/data-xray

c68c9b352efde0776189210794aeef84ae2cf6c2

[ "Apache-2.0" ]

null

build/bdist.macosx-10.9-x86_64/wininst/PURELIB/data_xray/report/core.py

amplifilo/data-xray

c68c9b352efde0776189210794aeef84ae2cf6c2

[ "Apache-2.0" ]

null

from ..scan import PlotImage from ..grid import * import numpy as np from pptx import Presentation from pptx.util import Inches from matplotlib import pyplot as plt import pandas as pd #some utilies to work with powerpoint meanstd = lambda arr: np.std(np.ravel(arr)/np.mean(np.ravel(arr))) class SummaryPPT(object): def __init__(self, pname="image_summary", new=False, fdict=None, maximages=50, chanselect = {'scan':'Z', 'grid':'cf'}, **kwargs): if fdict is None: print('please specify data to summarize') return else: fdicts = [fdict[i:i + maximages] for i in range(0, len(fdict), maximages)] self.topdir = os.path.commonpath([j.fname for j in fdict]) + '/' self.chanselect = chanselect for j,f in enumerate(fdicts): self.presentation_name = pname + '_' + str(j) self.pptx_file_name = self.topdir + self.presentation_name + '.pptx' self.fdict = f #self.new = new self.init_ppt(self.presentation_name) #self.insert_images() self.insert_data() #try: self.pres.save(self.pptx_file_name) print('batch ' + str(j) +' stored in : ' + self.pptx_file_name ) #except: # print('something wrong with saving the presentation file ' + self.pptx_file_name) def init_ppt(self, presentation_name): pres = Presentation() pres.notes_master.name = self.presentation_name self.pres = pres def insert_data(self): for fj in self.fdict: if re.findall('sxm', fj.fname): try: if self.chanselect == "Automatic": # attempt to recognize good data plotsignals = [] for c in fj.signals.keys(): sig = fj.signals[c]['forward'] sig = sig[~np.isnan(sig)] if meanstd(sig) > 2: plotsignals.append(c) plotsignals.append('Z') plotsignals = list(set(plotsignals)) # no dobule Z else: plotsignals = self.chanselect['scan'] nrows = 2 if len(plotsignals) > 2 else 1 ncols = int(np.ceil(len(plotsignals) / nrows)) f3, a3 = plt.subplots(nrows, ncols); if a3 is not list: a3 = [a3] for c, a in zip(plotsignals, np.ravel(a3)): PlotImage(fj, chan=c, ax=a, high_pass=None); [a.axis('off') for a in np.ravel(a3)] xy = ['X', 'Y'] offset = fj.header['scan_offset'] / 1e-9 xyoffsets = [xy[j] + '=' + str(np.round(offset[j], 2)) + ' nm ' for j in [0, 1]] titleString = [fj.fname] titleString.append('Bias: ' + str(fj.header['bias']) + 'V') titleString.append('Control: ' + fj.header['z-controller']['Name'][0]) titleString.append('Offsets: ' + xyoffsets[0] + xyoffsets[1]) titleString.append('Resolution: ' + str(fj.header['scan_pixels'])) self.fig_to_ppt([f3], leftop=[1, 2], txt=titleString) print(os.path.basename(fj.ds.fname) + ' imported') f3.clf(); # close figure so that it doesn't clog up in the end except: print(os.path.basename(fj.fname) + ' failed') elif re.findall('3ds', fj.fname): try: fig, ax = plt.subplots(1, 2) ChanHistogramDS(fj.ds, xy=['bias', self.chanselect['grid']], xymod=[lambda x: x, lambda x: x / np.mean(np.ravel(x))], ax=ax[0], label=['bias', self.chanselect['grid'], '']) # plop in a clustered map km = ChanPcaKmeansDS(fj.ds, xvec='bias', chan=self.chanselect['grid'], mod=lambda x: x / np.mean(np.ravel(x)), comps=6, nclust=4, fig=None) ax[1].imshow(km) #plt.colorbar() titleString = [fj.fname] except: print(os.path.basename(fj.fname) + ' failed. Import skipped') continue # titleString.append('Bias: ' + str(fj.header['bias']) + 'V') # titleString.append('Control: ' + fj.header['z-controller']['Name'][0]) # titleString.append('Offsets: ' + xyoffsets[0] + xyoffsets[1]) # titleString.append('Resolution: ' + str(fj.header['scan_pixels'])) try: self.fig_to_ppt([fig], leftop=[1, 2], txt=titleString) print(os.path.basename(fj.fname) + ' imported') fig.clf(); # close figure so that it doesn't clog up in the end except: print(os.path.basename(fj.fname) + ' import into ppt failed') def insert_maps(self, mapchan=['cf']): #plop in a histogram of the map channel across the whole thing for fj in self.fdict: fig,ax=plt.subplots(2,1, figsize=(8,5)) ChanHistogramDS(fj.ds, xy=['bias',mapchan[0]], xymod=[lambda x:x,lambda x:x/np.mean(np.ravel(x))], ax=ax[0], label=['bias',mapchan[0][:-1],'']) #plop in a clustered map km = ChanPcaKmeansDS(fj.ds, xvec='bias', chan=mapchan[0], mod = lambda x: x/np.mean(np.ravel(x)), comps=6, nclust=4, fig=None) ax[1].imshow(km) plt.colorbar() #fig.savefig("pca_3d.png",bbox_inches='tight') ###need to add name attribute to grids titleString = [fj.fname] # titleString.append('Bias: ' + str(fj.header['bias']) + 'V') # titleString.append('Control: ' + fj.header['z-controller']['Name'][0]) # titleString.append('Offsets: ' + xyoffsets[0] + xyoffsets[1]) # titleString.append('Resolution: ' + str(fj.header['scan_pixels'])) try: self.fig_to_ppt([f3], leftop=[1, 2], txt=titleString) print(os.path.basename(fj.ds.fname) + ' imported') f3.clf(); #close figure so that it doesn't clog up in the end except: print(os.path.basename(fj.ds.fname) + ' failed') #self.fig_to_ppt([f3], leftop=[1, 2], txt=titleString) return def insert_images(self): """ Dumpt a batch of images into a powerpoint :param chanselect: :param fdict: :param topdir: :return: """ #for folder in (self.fdict.keys()): # self.text_to_slide(folder) # newpres = Presentation() # newpres.notes_master.name = 'sum1.pptx' # newpres.save(newpres.notes_master.name) for fj in self.fdict: # TextToSlide(fj.fname,pres=pres) try: # scf = {1:(12,6), 2:(12,9), 3:(12,10)} if self.chanselect == "Automatic": #attempt to recognize good data plotsignals = [] for c in fj.signals.keys(): sig = fj.signals[c]['forward'] sig = sig[~np.isnan(sig)] if meanstd(sig) > 2: plotsignals.append(c) plotsignals.append('Z') plotsignals = list(set(plotsignals)) #no dobule Z else: plotsignals = self.chanselect nrows = 2 if len(plotsignals) > 2 else 1 ncols = int(np.ceil(len(plotsignals)/nrows)) f3, a3 = plt.subplots(nrows,ncols); if a3 is not list: a3 = [a3] for c,a in zip(plotsignals,np.ravel(a3)): PlotImage(fj, chan=c, ax=a, high_pass=None); [a.axis('off') for a in np.ravel(a3)] xy = ['X','Y'] offset = fj.header['scan_offset']/1e-9 xyoffsets = [xy[j] + '=' + str(np.round(offset[j],2)) + ' nm ' for j in [0,1]] titleString = [fj.fname] titleString.append('Bias: ' + str(fj.header['bias']) + 'V') titleString.append('Control: ' + fj.header['z-controller']['Name'][0]) titleString.append('Offsets: ' + xyoffsets[0] + xyoffsets[1]) titleString.append('Resolution: ' + str(fj.header['scan_pixels'])) self.fig_to_ppt([f3], leftop=[1, 2], txt=titleString) print(os.path.basename(fj.ds.fname) + ' imported') f3.clf(); #close figure so that it doesn't clog up in the end except: print(os.path.basename(fj.ds.fname) + ' failed') def png_to_ppt(self, pngfile, ttl = []): """ Plop a PNG file into powerpoint slide :param pngfile: :param pres: :param ttl: :return: """ #blank_slide_layout = pres.slide_layouts[6] title_slide_layout = self.pres.slide_layouts[9] left = top = Inches(1) slide = self.pres.slides.add_slide(title_slide_layout) slide.shapes.add_picture(pngfile, left, top) subtitle = slide.placeholders[1] title = slide.shapes.title if len(ttl): subtitle.text = ttl def fig_to_ppt(self, figs, leftop=[0,1.5], txt=None): """ Plop figures into powerpoint :param figs: :param pres: :param leftop: :param txt: :return: """ #savepptx needs to be a full path. If None is provided the default presentation #will be created with a name sum1.pptx in the current folder from pptx.util import Inches blank_slide_layout = self.pres.slide_layouts[5] left = Inches(leftop[0]) top = Inches(leftop[1]) tmp_path = 't1.png' for figp in figs: plt.savefig(tmp_path, transparent=1, format='png', dpi=300, bbox_inches = 'tight') slide = self.pres.slides.add_slide(blank_slide_layout) slide.shapes.add_picture(tmp_path, left, top) if txt is not None: self.text_to_slide(txt, slide=slide) def text_to_slide(self, txt, slide=None): #lets make txt a list of strings """ convert text to slide :param txt: list of strings :param pres: :param slide: :return: """ from pptx.util import Pt #title = slide.shapes.title #subtitle = slide.placeholders[1] # title.text = "Hello, World!" #subtitle.text = "python-pptx was here!" # prs.save('test.pptx') from pptx.util import Inches if self.pres == None: print('please init presentation') else: if slide is None: bullet_slide_layout = self.pres.slide_layouts[5] slide = self.pres.slides.add_slide(bullet_slide_layout) shapes = slide.shapes countshapes = 0 #just catch the first shape object with a frame in it for shape in slide.shapes: if not shape.has_text_frame: continue elif countshapes > 0: tframe = shape.text_frame tframe.clear() #print('caught one') else: text_frame = shape.text_frame text_frame.clear() countshapes = 1 text_frame.clear() p = text_frame.paragraphs[0] for t in txt: run = p.add_run() run.text = t font = run.font font.name = 'Calibri' font.size = Pt(12) # p.text = t p = text_frame.add_paragraph() # class SummaryPPT2(object): # def __init__(self, pname='summary', new=False, fdict=None, topdir=None, **kwargs): # if fdict is None: # print('please specify data to summarize') # return # else: # self.fdict = fdict # self.pname = pname # self.new = new # if topdir==None: # topdir = os.getcwd() # def crawl_and_save(self): # for ind, (folder, files) in enumerate(zip(fdict.keys(), fdict.items())): # #self.topdir = os.path.commonpath([j.ds.fname for j in fdict]) + '/' # self.presentation_name = pname # self.pptx_file_name = folder + self.presentation_name + '.pptx' # self.new = new # self.init_ppt() # self.insert_images() # try: # self.pres.save(self.pptx.file_name) # print('images stored in : ' + self.pptx_file_name ) # except: # print('something wrong with saving the presentation file') # def init_ppt(self): # """ # Initialize powerpoint presentation # :param pname: # :param new: # :return: # """ # if self.presentation_name is None: # newpres = Presentation() # newpres.notes_master.name = 'sum1.pptx' # newpres.save(newpres.notes_master.name) # self.pres = newpres # elif self.new: # newpres = Presentation() # newpres.notes_master.name = self.presentation_name # newpres.save(newpres.notes_master.name) # self.pres = newpres # else: # pres = Presentation(self.presentation_name) # pres.notes_master.name = self.presentation_name # self.pres = pres # def insert_images(self, chanselect='Z'): # """ # Dumpt a batch of images into a powerpoint # :param chanselect: # :param fdict: # :param topdir: # :return: # """ # #for folder in (self.fdict.keys()): # # self.text_to_slide(folder) # for fj in self.fdict: # # TextToSlide(fj.fname,pres=pres) # try: # f3, a3 = plt.subplots(1, 1) # d2 = PlotImage(fj, chan=chanselect, ax=a3, high_pass=None) # self.fig_to_ppt([f3], leftop=[3, 2], txt=fj.fname) # print(os.path.basename(fj.ds.fname) + ' imported') # except: # print(os.path.basename(fj.ds.fname) + ' failed') # def png_to_ppt(self, pngfile, ttl = []): # """ # Plop a PNG file into powerpoint slide # :param pngfile: # :param pres: # :param ttl: # :return: # """ # #blank_slide_layout = pres.slide_layouts[6] # title_slide_layout = self.pres.slide_layouts[9] # left = top = Inches(1) # slide = self.pres.slides.add_slide(title_slide_layout) # slide.shapes.add_picture(pngfile, left, top) # subtitle = slide.placeholders[1] # title = slide.shapes.title # if len(ttl): # subtitle.text = ttl # def fig_to_ppt(self, figs, leftop=[0,1.5], txt=None): # """ # Plop figures into powerpoint # :param figs: # :param pres: # :param leftop: # :param txt: # :return: # """ # #savepptx needs to be a full path. If None is provided the default presentation # #will be created with a name sum1.pptx in the current folder # from pptx.util import Inches # blank_slide_layout = self.pres.slide_layouts[5] # left = Inches(leftop[0]) # top = Inches(leftop[1]) # tmp_path = 't1.png' # for figp in figs: # plt.savefig(tmp_path, transparent=1, format='png', dpi=300, bbox_inches = 'tight') # slide = self.pres.slides.add_slide(blank_slide_layout) # slide.shapes.add_picture(tmp_path, left, top) # if txt is not None: # self.text_to_slide(txt, slide=slide) # def text_to_slide(self, txt, slide=None): # """ # convert text to slide # :param txt: # :param pres: # :param slide: # :return: # """ # from pptx.util import Pt # #title = slide.shapes.title # #subtitle = slide.placeholders[1] # # title.text = "Hello, World!" # #subtitle.text = "python-pptx was here!" # # prs.save('test.pptx') # from pptx.util import Inches # if self.pres == None: # print('please init presentation') # else: # if slide is None: # bullet_slide_layout = self.pres.slide_layouts[5] # slide = self.pres.slides.add_slide(bullet_slide_layout) # shapes = slide.shapes # countshapes = 0 # #just catch the first shape object with a frame in it # for shape in slide.shapes: # if not shape.has_text_frame: # continue # elif countshapes > 0: # tframe = shape.text_frame # tframe.clear() # #print('caught one') # else: # text_frame = shape.text_frame # text_frame.clear() # countshapes = 1 # text_frame.clear() # p = text_frame.paragraphs[0] # run = p.add_run() # run.text = txt # font = run.font # font.name = 'Calibri' # font.size = Pt(12)

36.013861

157

0.500027

2,044

18,187

4.364971

0.141389

0.017933

0.024658

0.023425

0.836023

0.803183

0.773369

0.767765

0.758798

0.743667

0

0.013923

0.379997

18,187

504

158

36.085317

0.777315

0.4214

0

0.5

0

0.048563

0

1

0.043478

false

0.01087

0.086957

0

0.146739

0.065217

0

null

0

1

0

null

0

6

702edac88458909cbf9bb408ff36f4f7c52574a5

84

py

Python

nptel_modules/module3/payload_generator_with_exit.py

ByteHackr/SecureSystemEngineering_IITM

94319e9111a42ed9de837c78f14271d9cf65b5e5

[ "MIT" ]

null

nptel_modules/module3/payload_generator_with_exit.py

ByteHackr/SecureSystemEngineering_IITM

94319e9111a42ed9de837c78f14271d9cf65b5e5

[ "MIT" ]

null

nptel_modules/module3/payload_generator_with_exit.py

ByteHackr/SecureSystemEngineering_IITM

94319e9111a42ed9de837c78f14271d9cf65b5e5

[ "MIT" ]

null

y = "A"*76 + "\x40\x29\xe4\xf7" + "\xb0\x67\xe3\xf7" + "\x2b\x10\xf6\xf7" print y

21

74

0.547619

17

84

2.705882

0.823529

0

0.253521

0.154762

84

3

75

28

0.394366

0

0.590361

0

0.5

0

null

0

null

0.5

1

0

null

0

1

0

1

0

1

0

null

0

1

0

1

0

6

565d1e5e1c141c954054353557aeaf84f7666c49

140

py

Python

webapp/main/views.py

eude313/pitch

fc7dec88ff6c3dbe7d08287dead6fd9d4eb7f785

[ "MIT" ]

null

webapp/main/views.py

eude313/pitch

fc7dec88ff6c3dbe7d08287dead6fd9d4eb7f785

[ "MIT" ]

null

webapp/main/views.py

eude313/pitch

fc7dec88ff6c3dbe7d08287dead6fd9d4eb7f785

[ "MIT" ]

null

from . import main from flask import render_template # landing page @main.route('/') def home(): return render_template('index.html')

15.555556

40

0.721429

19

140

5.210526

0.736842

0.282828

0

0.157143

140

8

41

17.5

0.838983

0.085714

0

0.088

0

1

0.2

true

0

0.4

0.2

0.8

0

1

0

null

1

0

1

0

null

0

1

0

1

0

6

5676d89039606acc19eab955a5740e6bbdd4e532

265

py

Python

reward/batcher/__init__.py

lgvaz/torchrl

cfff8acaf70d1fec72169162b95ab5ad3547d17a

[ "MIT" ]

5

2018-06-21T14:33:40.000Z

2018-08-18T02:26:03.000Z

reward/batcher/__init__.py

lgvaz/reward

cfff8acaf70d1fec72169162b95ab5ad3547d17a

[ "MIT" ]

null

reward/batcher/__init__.py

lgvaz/reward

cfff8acaf70d1fec72169162b95ab5ad3547d17a

[ "MIT" ]

2

2018-05-08T03:34:49.000Z

2018-06-22T15:04:17.000Z

from .base_batcher import BaseBatcher from .rollout_batcher import RolloutBatcher from .replay_batcher import ReplayBatcher from .prioritized_replay_batcher import PrReplayBatcher from .demo_replay_batcher import DemoReplayBatcher import reward.batcher.transforms

33.125

55

0.886792

31

265

7.354839

0.483871

0.285088

0.25

0

0.086792

265

7

56

37.857143

0.942149

0

1

0

true

0

1

0

1

0

null

1

0

1

0

null

0

1

0

1

0

1

0

6

3b24dd51019898c02180822ff9f623866d5b207e

25

py

Python

Camera-Node/main.py

thearyadev/Security-System

f9fa48196eef4dc83a9059e10e3c97e2f0842b8d

[ "MIT" ]

1

2022-02-26T21:43:19.000Z

Camera-Node/main.py

thearyadev/Security-System

f9fa48196eef4dc83a9059e10e3c97e2f0842b8d

[ "MIT" ]

null

Camera-Node/main.py

thearyadev/Security-System

f9fa48196eef4dc83a9059e10e3c97e2f0842b8d

[ "MIT" ]

null

from utils import Camera

12.5

24

0.84

4

25

5.25

1

0

0.16

25

1

25

1

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

3b5771f237adc11d33dc88f220736794c9c4b286

319

py

Python

tests/test_get_stats.py

jeremiahfallin/roleML

47539f2be594347e64339a0fcc42fececc9db298

[ "MIT" ]

55

2019-03-19T03:57:06.000Z

2021-11-21T01:40:24.000Z

tests/test_get_stats.py

jeremiahfallin/roleML

47539f2be594347e64339a0fcc42fececc9db298

[ "MIT" ]

19

2019-03-12T03:49:19.000Z

2021-10-04T18:48:57.000Z

tests/test_get_stats.py

RiftNemesis/roleML

78fcda9459339d764c92c584fb59e61e09c3c5a9

[ "MIT" ]

19

2019-03-13T04:40:08.000Z

2021-09-27T13:16:52.000Z

from roleml.features import _get_stats_at_10 def test_get_stats_na(clean_game_na): assert clean_game_na["stats_at_10"] == _get_stats_at_10(clean_game_na["game"]["timeline"]) def test_get_stats_euw(clean_game_euw): assert clean_game_euw["stats_at_10"] == _get_stats_at_10(clean_game_euw["game"]["timeline"])

31.9

96

0.789969

56

319

3.892857

0.285714

0.247706

0.206422

0.165138

0.275229

0

0.034364

0.087774

319

9

97

35.444444

0.714777

0

0.144201

0

0.4

1

0.4

false

0

0.2

0

0.6

0

null

1

0

1

0

null

0

1

0

1

0

6

8e7212814b34289385934136e01fb6f2e85cd068

60

py

Python

interface/ui/__init__.py

hoefkensj/portal

90682fc90172d215f0ac3213124dfecacc099581

[ "Unlicense" ]

null

interface/ui/__init__.py

hoefkensj/portal

90682fc90172d215f0ac3213124dfecacc099581

[ "Unlicense" ]

null

interface/ui/__init__.py

hoefkensj/portal

90682fc90172d215f0ac3213124dfecacc099581

[ "Unlicense" ]

null

#!/usr/bin/env python from . import cli from . import cpy

10

21

0.683333

10

60

4.1

0.8

0.487805

0

0.2

60

5

22

12

0.854167

0.333333

0

1

0

true

0

1

0

1

0

1

0

null

1

0

1

0

null

0

1

0

1

0

1

0

6

8e933e821dc734be6253b25e92b64001ba026e77

2,551

py

Python

epytope/Data/pssms/smmpmbec/mat/B_53_01_10.py

christopher-mohr/epytope

8ac9fe52c0b263bdb03235a5a6dffcb72012a4fd

[ "BSD-3-Clause" ]

7

2021-02-01T18:11:28.000Z

2022-01-31T19:14:07.000Z

epytope/Data/pssms/smmpmbec/mat/B_53_01_10.py

christopher-mohr/epytope

8ac9fe52c0b263bdb03235a5a6dffcb72012a4fd

[ "BSD-3-Clause" ]

22

2021-01-02T15:25:23.000Z

2022-03-14T11:32:53.000Z

epytope/Data/pssms/smmpmbec/mat/B_53_01_10.py

christopher-mohr/epytope

8ac9fe52c0b263bdb03235a5a6dffcb72012a4fd

[ "BSD-3-Clause" ]

4

2021-05-28T08:50:38.000Z

2022-03-14T11:45:32.000Z

B_53_01_10 = {0: {'A': 0.264, 'C': -0.444, 'E': 0.109, 'D': 0.329, 'G': 0.102, 'F': -0.991, 'I': -0.163, 'H': -0.304, 'K': 0.557, 'M': -0.463, 'L': -0.322, 'N': 0.117, 'Q': 0.481, 'P': 1.036, 'S': 0.256, 'R': 0.223, 'T': 0.208, 'W': -0.2, 'V': 0.044, 'Y': -0.838}, 1: {'A': -0.327, 'C': 0.032, 'E': 0.43, 'D': 0.13, 'G': 0.002, 'F': 0.024, 'I': -0.168, 'H': 0.052, 'K': 0.37, 'M': -0.245, 'L': 0.058, 'N': 0.254, 'Q': 0.294, 'P': -1.203, 'S': -0.021, 'R': 0.206, 'T': 0.134, 'W': 0.049, 'V': -0.43, 'Y': 0.36}, 2: {'A': -0.007, 'C': -0.005, 'E': -0.035, 'D': 0.02, 'G': 0.013, 'F': -0.055, 'I': -0.174, 'H': 0.088, 'K': 0.187, 'M': -0.161, 'L': -0.087, 'N': 0.066, 'Q': -0.002, 'P': 0.053, 'S': 0.098, 'R': 0.133, 'T': 0.052, 'W': -0.049, 'V': -0.111, 'Y': -0.023}, 3: {'A': 0.042, 'C': -0.053, 'E': -0.039, 'D': -0.035, 'G': -0.043, 'F': -0.056, 'I': -0.015, 'H': 0.045, 'K': 0.116, 'M': -0.023, 'L': 0.0, 'N': -0.01, 'Q': 0.004, 'P': 0.015, 'S': 0.01, 'R': 0.12, 'T': 0.005, 'W': -0.059, 'V': 0.004, 'Y': -0.028}, 4: {'A': 0.123, 'C': 0.004, 'E': 0.001, 'D': -0.104, 'G': 0.084, 'F': -0.219, 'I': -0.164, 'H': 0.012, 'K': 0.198, 'M': -0.153, 'L': -0.093, 'N': 0.047, 'Q': 0.139, 'P': 0.139, 'S': 0.076, 'R': 0.255, 'T': 0.002, 'W': -0.166, 'V': -0.02, 'Y': -0.162}, 5: {'A': 0.108, 'C': 0.083, 'E': 0.047, 'D': 0.031, 'G': 0.035, 'F': -0.065, 'I': -0.103, 'H': 0.046, 'K': 0.122, 'M': -0.062, 'L': -0.13, 'N': 0.022, 'Q': -0.032, 'P': -0.102, 'S': 0.054, 'R': 0.14, 'T': -0.059, 'W': -0.002, 'V': -0.06, 'Y': -0.073}, 6: {'A': 0.079, 'C': -0.061, 'E': -0.057, 'D': -0.087, 'G': -0.011, 'F': -0.04, 'I': 0.043, 'H': 0.071, 'K': 0.217, 'M': -0.023, 'L': -0.024, 'N': -0.03, 'Q': -0.016, 'P': 0.052, 'S': 0.001, 'R': 0.211, 'T': -0.074, 'W': -0.131, 'V': -0.008, 'Y': -0.116}, 7: {'A': -0.056, 'C': -0.086, 'E': -0.063, 'D': 0.018, 'G': 0.17, 'F': 0.033, 'I': -0.046, 'H': 0.065, 'K': 0.292, 'M': -0.148, 'L': -0.183, 'N': 0.07, 'Q': 0.002, 'P': 0.16, 'S': 0.081, 'R': 0.11, 'T': -0.077, 'W': -0.17, 'V': -0.041, 'Y': -0.133}, 8: {'A': 0.207, 'C': -0.009, 'E': -0.004, 'D': 0.101, 'G': 0.067, 'F': -0.08, 'I': -0.101, 'H': -0.02, 'K': 0.201, 'M': -0.092, 'L': -0.177, 'N': -0.148, 'Q': -0.087, 'P': 0.03, 'S': 0.069, 'R': 0.231, 'T': 0.023, 'W': -0.102, 'V': -0.018, 'Y': -0.091}, 9: {'A': 0.587, 'C': -0.484, 'E': 0.356, 'D': 0.471, 'G': 0.078, 'F': -0.861, 'I': -0.424, 'H': -0.112, 'K': 0.227, 'M': -0.246, 'L': -0.135, 'N': 0.043, 'Q': 0.124, 'P': 0.923, 'S': 0.266, 'R': 0.38, 'T': 0.282, 'W': -1.46, 'V': 0.383, 'Y': -0.399}, -1: {'con': 4.5361}}

2,551

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null

0

1

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1

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null

0

6

8ef2068fe56c6948a0b65c3b7863738bba790c30

16,910

py

Python

seshat/seshat/functools.py

XecusM/SESHAT

34cf989e99e11f645339ce7190d92ff816062243

[ "MIT" ]

null

seshat/seshat/functools.py

XecusM/SESHAT

34cf989e99e11f645339ce7190d92ff816062243

[ "MIT" ]

null

seshat/seshat/functools.py

XecusM/SESHAT

34cf989e99e11f645339ce7190d92ff816062243

[ "MIT" ]

null

from django.conf import settings from django.apps import apps import numpy as np import pandas as pd import os import json # Help Functions def export_module(model_data): ''' Function to export data ''' if not os.path.exists(settings.EXPORT_DIR): if not os.path.exists(settings.VAR_DIR): os.makedirs(settings.VAR_DIR) os.makedirs(settings.EXPORT_DIR) model = apps.get_model(model_data['app_name'], model_data['model_name']) if model_data['app_name'] == 'stock' and model_data['model_name'] == 'Item': file_name = 'items.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.filter( is_assembly=False).values_list( 'code', 'desciption', 'barcode', 'stock_limit', 'category__name', 'price', 'location__location__name', 'location__name', 'note', 'is_active',), columns=( 'code', 'desciption', 'barcode', 'stock_limit', 'category', 'price', 'location', 'sub_location', 'note', 'is_active') ) data = data.set_index('code') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': 'items', 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'stock' and model_data['model_name'] == 'Category': file_name = 'categories.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list('id', 'name'), columns=('id', 'name') ) data = data.set_index('id') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': 'categories', 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'stock' and model_data['model_name'] == 'SubLocation': file_name = 'locations.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list( 'id', 'location__name', 'name'), columns=( 'id', 'location', 'sub_location') ) data = data.set_index('id') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': 'locations', 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'customer' and model_data['model_name'] == 'Customer': file_name = 'customers.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list( 'id', 'company__name', 'first_name', 'last_name', 'email', 'phone', 'department', 'job', 'note'), columns=( 'id', 'company', 'barcode', 'first_name', 'last_name', 'email', 'phone', 'department', 'job', 'note') ) data = data.set_index('id') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': 'customers', 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'customer' and model_data['model_name'] == 'CustomerCompany': file_name = 'customers_companies.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list( 'name', 'desciption', 'phone', 'website', 'taxs_code', 'note'), columns=( 'name', 'desciption', 'phone', 'website', 'taxs_code', 'note') ) data = data.set_index('name') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': "customers' companies", 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'vendor' and model_data['model_name'] == 'Vendor': file_name = 'vendors.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list( 'id', 'company__name', 'first_name', 'last_name', 'email', 'phone', 'department', 'job', 'note'), columns=( 'id', 'company', 'barcode', 'first_name', 'last_name', 'email', 'phone', 'department', 'job', 'note') ) data = data.set_index('id') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': 'vendors', 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } elif model_data['app_name'] == 'vendor' and model_data['model_name'] == 'VendorCompany': file_name = 'vendors_companies.csv' if os.path.isfile(os.path.join(settings.RESTORE_DIR, file_name)): os.remove(os.path.join(settings.RESTORE_DIR, file_name)) data = pd.DataFrame.from_records( model.objects.all( ).values_list( 'name', 'desciption', 'phone', 'website', 'taxs_code', 'note'), columns=( 'name', 'desciption', 'phone', 'website', 'taxs_code', 'note') ) data = data.set_index('name') data.to_csv( os.path.join(settings.EXPORT_DIR, file_name), encoding='utf-8') return { 'message': "vendors' companies", 'path' :os.path.join(settings.EXPORT_DIR, file_name), 'file_name': file_name } else: return 'error' def import_module(model_data, file_name, request_user): ''' Function to import data ''' if not os.path.exists(settings.IMPORT_DIR): if not os.path.exists(settings.VAR_DIR): os.makedirs(settings.VAR_DIR) os.makedirs(settings.IMPORT_DIR) model = apps.get_model(model_data['app_name'], model_data['model_name']) objects = list() data = pd.read_csv(os.path.join(settings.IMPORT_DIR, file_name)) if model_data['app_name'] == 'stock' and model_data['model_name'] == 'Item': for i in list(data.index.values): if not model.objects.filter(code=pd_handeler(data.loc[i, 'code'])).exists(): category_model = apps.get_model( model_data['app_name'], 'Category') category = category_model.objects.get_or_create( name=data.loc[i, 'category']) location_model = apps.get_model( model_data['app_name'], 'Location') location = location_model.objects.get_or_create( name=data.loc[i, 'location']) sub_location_model = apps.get_model( model_data['app_name'], 'SubLocation') sub_location = sub_location_model.objects.get_or_create( location=location[0], name=data.loc[i, 'sub_location']) object = model( code=pd_handeler(data.loc[i, 'code']), desciption=pd_handeler(data.loc[i, 'desciption']), barcode=pd_handeler(data.loc[i, 'barcode']), stock_limit=pd_handeler(data.loc[i, 'stock_limit']), category=category[0], price=pd_handeler(data.loc[i, 'price']), location=sub_location[0], note=pd_handeler(data.loc[i, 'note']), is_active=pd_handeler(data.loc[i, 'is_active']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) items" elif model_data['app_name'] == 'stock' and model_data['model_name'] == 'Category': for i in list(data.index.values): if not model.objects.filter(name=pd_handeler(data.loc[i, 'name'])).exists(): object = model( name=pd_handeler(data.loc[i, 'name']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) categories" elif model_data['app_name'] == 'stock' and model_data['model_name'] == 'SubLocation': for i in list(data.index.values): if not model.objects.filter(name=pd_handeler(data.loc[i, 'sub_location'])).exists(): location_model = apps.get_model( model_data['app_name'], 'Location') location = location_model.objects.get_or_create( name=pd_handeler(data.loc[i, 'location'])) object = model( location=location[0], name=pd_handeler(data.loc[i, 'sub_location']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) locations" elif model_data['app_name'] == 'customer' and model_data['model_name'] == 'Customer': for i in list(data.index.values): company_model = apps.get_model( model_data['app_name'], 'CustomerCompany') company = company_model.objects.get_or_create( name=pd_handeler(data.loc[i, 'company'])) object = model( company=company[0], first_name=pd_handeler(data.loc[i, 'first_name']), last_name=pd_handeler(data.loc[i, 'last_name']), email=pd_handeler(data.loc[i, 'email']), department=pd_handeler(data.loc[i, 'department']), job=pd_handeler(data.loc[i, 'job']), note=pd_handeler(data.loc[i, 'note']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) customers" elif model_data['app_name'] == 'customer' and model_data['model_name'] == 'CustomerCompany': for i in list(data.index.values): if not model.objects.filter(name=pd_handeler(data.loc[i, 'name'])).exists(): object = model( name=pd_handeler(data.loc[i, 'name']), desciption=pd_handeler(data.loc[i, 'desciption']), phone=pd_handeler(data.loc[i, 'phone']), website=pd_handeler(data.loc[i, 'website']), taxs_code=pd_handeler(data.loc[i, 'taxs_code']), note=pd_handeler(data.loc[i, 'note']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) customers' companies" elif model_data['app_name'] == 'vendor' and model_data['model_name'] == 'Vendor': for i in list(data.index.values): company_model = apps.get_model( model_data['app_name'], 'VendorCompany') company = company_model.objects.get_or_create( name=pd_handeler(data.loc[i, 'company'])) object = model( company=company[0], first_name=pd_handeler(data.loc[i, 'first_name']), last_name=pd_handeler(data.loc[i, 'last_name']), email=pd_handeler(data.loc[i, 'email']), department=pd_handeler(data.loc[i, 'department']), job=pd_handeler(data.loc[i, 'job']), note=pd_handeler(data.loc[i, 'note']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) vendors" elif model_data['app_name'] == 'vendor' and model_data['model_name'] == 'VendorCompany': for i in list(data.index.values): if not model.objects.filter(name=pd_handeler(data.loc[i, 'name'])).exists(): object = model( name=pd_handeler(data.loc[i, 'name']), desciption=pd_handeler(data.loc[i, 'desciption']), phone=pd_handeler(data.loc[i, 'phone']), website=pd_handeler(data.loc[i, 'website']), taxs_code=pd_handeler(data.loc[i, 'taxs_code']), note=pd_handeler(data.loc[i, 'note']), created_by=request_user ) objects.append(object) message = f"({len(objects)}) vendors' companies" else: return 'error' try: model.objects.bulk_create(objects) return { 'message': message, 'file_name': file_name } except Exception as error_type: print(error_type) return 'error' def pd_handeler(value): ''' Handele the dataframe values before save it to database ''' if str(value) == str(np.nan): return None else: return value

47.903683

97

0.457895

1,609

16,910

4.595401

0.07831

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0.047606

0.094266

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0.823235

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null

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null

0

6

d92460c17622d3c81fed9ffb78649c9a05c2ac38

36

py

Python

compare_date_range/__init__.py

mattwalshdev/compare_date_range

57c78f4362e7b5f07e6708dd4d39c144bb9447a8

[ "MIT" ]

null

compare_date_range/__init__.py

mattwalshdev/compare_date_range

57c78f4362e7b5f07e6708dd4d39c144bb9447a8

[ "MIT" ]

null

compare_date_range/__init__.py

mattwalshdev/compare_date_range

57c78f4362e7b5f07e6708dd4d39c144bb9447a8

[ "MIT" ]

null

from .main import compare_date_range

36

0.888889

6

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36

1

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0.909091

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null

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0

1

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1

0

6

d961c7f21582181bd9aef789900aa2f3314dcf3f

87

py

Python

app/config/context.py

Zadigo/startup_nation

109d5dbc44422468d3931725e72f4bf7db0c4c49

[ "MIT" ]

null

app/config/context.py

Zadigo/startup_nation

109d5dbc44422468d3931725e72f4bf7db0c4c49

[ "MIT" ]

null

app/config/context.py

Zadigo/startup_nation

109d5dbc44422468d3931725e72f4bf7db0c4c49

[ "MIT" ]

null

def context_processor(func): def context(request): pass return context

17.4

28

0.666667

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5.7

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0

0.264368

87

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false

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null

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1

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1

0

6

d964bc6505f66488c8ce182adad8624fd86a898a

185

py

Python

src/django-nonrel/tests/regressiontests/formwizard/urls.py

adamjmcgrath/glancydesign

826ede7c639879d5b79ee730eb5e91422768cb02

[ "BSD-3-Clause" ]

790

2015-01-03T02:13:39.000Z

2020-05-10T19:53:57.000Z

tests/regressiontests/formwizard/urls.py

mradziej/django

5d38965743a369981c9a738a298f467f854a2919

[ "BSD-3-Clause" ]

1,361

2015-01-08T23:09:40.000Z

2020-04-14T00:03:04.000Z

tests/regressiontests/formwizard/urls.py

mradziej/django

5d38965743a369981c9a738a298f467f854a2919

[ "BSD-3-Clause" ]

155

2015-01-08T22:59:31.000Z

2020-04-08T08:01:53.000Z

from django.conf.urls.defaults import * from forms import ContactWizard, Page1, Page2, Page3 urlpatterns = patterns('', url(r'^wiz/$', ContactWizard([Page1, Page2, Page3])), )

26.428571

57

0.697297

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185

5.863636

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0.356589

0.434109

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0.038217

0.151351

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6

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30.833333

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null

0

1

0

6

d999932c0cb5d5f44969e6c0f4efde644db35bd1

107

py

Python

monorun/__init__.py

minghanz/MonoRUn

3a575ec7826d2b95e05bc87099b152434743f104

[ "MIT" ]

86

2021-03-24T02:10:17.000Z

2022-03-30T03:35:41.000Z

monorun/__init__.py

minghanz/MonoRUn

3a575ec7826d2b95e05bc87099b152434743f104

[ "MIT" ]

5

2021-06-03T09:23:30.000Z

2022-03-30T09:13:26.000Z

monorun/__init__.py

minghanz/MonoRUn

3a575ec7826d2b95e05bc87099b152434743f104

[ "MIT" ]

10

2021-05-18T04:15:39.000Z

2021-11-25T09:32:05.000Z

from .core import * from .datasets import * from .models import * from .ops import * from .runner import *

17.833333

23

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0.519481

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21.4

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1

0

1

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6

795eef20281b050104b8307eb723e72711efa115

153

py

Python

example/blueprints/testblueprint.py

MaayanLab/jupyter-template

dd05bfcb95c9eafb1a9df845b5d8fecae1d6b9d5

[ "Apache-2.0" ]

null

example/blueprints/testblueprint.py

MaayanLab/jupyter-template

dd05bfcb95c9eafb1a9df845b5d8fecae1d6b9d5

[ "Apache-2.0" ]

24

2020-04-07T17:04:47.000Z

2020-05-27T00:51:25.000Z

example/blueprints/testblueprint.py

MaayanLab/jupyter-template

dd05bfcb95c9eafb1a9df845b5d8fecae1d6b9d5

[ "Apache-2.0" ]

null

from flask import Blueprint testblueprint = Blueprint('testblueprint', __name__) @testblueprint.route('/') def testroute(): return 'Test Blueprint!'

19.125

52

0.75817

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7.466667

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0.392857

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0.117647

153

7

53

21.857143

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0.189542

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false

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null

1

0

1

0

null

0

1

0

6

7983f56eea93961f9c0a70fd423f832389ff4cae

1,548

py

Python

dev/Gems/CloudGemMetric/v1/AWS/common-code/Lib/numba/tests/complex_usecases.py

jeikabu/lumberyard

07228c605ce16cbf5aaa209a94a3cb9d6c1a4115

[ "AML" ]

1,738

2017-09-21T10:59:12.000Z

2022-03-31T21:05:46.000Z

dev/Gems/CloudGemMetric/v1/AWS/common-code/Lib/numba/tests/complex_usecases.py

jeikabu/lumberyard

07228c605ce16cbf5aaa209a94a3cb9d6c1a4115

[ "AML" ]

427

2017-09-29T22:54:36.000Z

2022-02-15T19:26:50.000Z

dev/Gems/CloudGemMetric/v1/AWS/common-code/Lib/numba/tests/complex_usecases.py

jeikabu/lumberyard

07228c605ce16cbf5aaa209a94a3cb9d6c1a4115

[ "AML" ]

671

2017-09-21T08:04:01.000Z

2022-03-29T14:30:07.000Z

from __future__ import division import cmath def div_usecase(x, y): return x / y def real_usecase(x): return x.real def imag_usecase(x): return x.imag def conjugate_usecase(x): return x.conjugate() def acos_usecase(x): return cmath.acos(x) def cos_usecase(x): return cmath.cos(x) def asin_usecase(x): return cmath.asin(x) def sin_usecase(x): return cmath.sin(x) def atan_usecase(x): return cmath.atan(x) def tan_usecase(x): return cmath.tan(x) def acosh_usecase(x): return cmath.acosh(x) def cosh_usecase(x): return cmath.cosh(x) def asinh_usecase(x): return cmath.asinh(x) def sinh_usecase(x): return cmath.sinh(x) def atanh_usecase(x): return cmath.atanh(x) def tanh_usecase(x): return cmath.tanh(x) def exp_usecase(x): return cmath.exp(x) def isfinite_usecase(x): return cmath.isfinite(x) def isinf_usecase(x): return cmath.isinf(x) def isnan_usecase(x): return cmath.isnan(x) def log_usecase(x): return cmath.log(x) def log_base_usecase(x, base): return cmath.log(x, base) def log10_usecase(x): return cmath.log10(x) def phase_usecase(x): return cmath.phase(x) def polar_usecase(x): return cmath.polar(x) _two = 2.0 def polar_as_complex_usecase(x): # HACK: clear errno by invoking float.__pow__ # (workaround for http://bugs.python.org/issue24489) _two ** _two return complex(*cmath.polar(x)) def rect_usecase(r, phi): return cmath.rect(r, phi) def sqrt_usecase(x): return cmath.sqrt(x)

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6

798a25e1048ad9409d29b44bdfd6e8a7a4ae1be0

36

py

Python

test/test_series/__init__.py

clebsonpy/HydroComp

9d17fa533e8a15c760030df5246ff531ddb4cb22

[ "MIT" ]

4

2020-05-14T20:03:49.000Z

2020-05-22T19:56:43.000Z

test/test_series/__init__.py

clebsonpy/HydroComp

9d17fa533e8a15c760030df5246ff531ddb4cb22

[ "MIT" ]

19

2019-06-27T18:12:27.000Z

2020-04-28T13:28:03.000Z

test/test_series/__init__.py

clebsonpy/HydroComp

9d17fa533e8a15c760030df5246ff531ddb4cb22

[ "MIT" ]

null

from re import I from .flow import *

18

19

0.75

7

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null

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1

0

1

0

1

0

6

79b88b6871ed2dfa7793027f730e6f6e3d5e5fbd

252

py

Python

localhost/_core/controller.py

KnJbMfLAgdkwZL/discord_webm_2ch_bot

18ce95f9d4b92c30079a4dbb2144dddaace00d03

[ "MIT" ]

null

localhost/_core/controller.py

KnJbMfLAgdkwZL/discord_webm_2ch_bot

18ce95f9d4b92c30079a4dbb2144dddaace00d03

[ "MIT" ]

null

localhost/_core/controller.py

KnJbMfLAgdkwZL/discord_webm_2ch_bot

18ce95f9d4b92c30079a4dbb2144dddaace00d03

[ "MIT" ]

null

class controller: def __init__(self): # print(f'Constructor {self.getName()}') pass def __del__(self): # print(f'Destructor {self.getName()}') pass def getName(self): return self.__class__.__name__

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6

8db9aba9a9e7e116173a2557a47f23c1b9565fda

43

py

Python

sdk/exception/system_exception.py

CLG0125/elemesdk

344466398bad7cf026e082e47c77d3ca98621ef3

[ "MIT" ]

1

2021-04-03T05:11:29.000Z

sdk/exception/system_exception.py

CLG0125/elemesdk

344466398bad7cf026e082e47c77d3ca98621ef3

[ "MIT" ]

null

sdk/exception/system_exception.py

CLG0125/elemesdk

344466398bad7cf026e082e47c77d3ca98621ef3

[ "MIT" ]

null

class SystemException(Exception):pass

14.333333

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1

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6

30e20a7de1623a9f749b570f10aebdd46b14170b

101

py

Python

pyhiveodbc/__init__.py

bi4group/PyHiveODBC

5cc42912cc90f817eeb2a75efa277d330cc9710d

[ "Apache-2.0" ]

2

2018-05-04T18:13:47.000Z

2018-12-05T08:46:29.000Z

pyhiveodbc/__init__.py

bi4group/PyHiveODBC

5cc42912cc90f817eeb2a75efa277d330cc9710d

[ "Apache-2.0" ]

null

pyhiveodbc/__init__.py

bi4group/PyHiveODBC

5cc42912cc90f817eeb2a75efa277d330cc9710d

[ "Apache-2.0" ]

2

2020-01-29T05:26:02.000Z

2020-10-13T14:30:42.000Z

from __future__ import absolute_import from __future__ import unicode_literals __version__ = '0.5.1'

25.25

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0.841584

14

101

5.071429

0.714286

0.28169

0.450704

0

0.033333

0.108911

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3

40

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null

0

1

0

1

0

6

30e9bff121a5294a667a70eb6c935a86eecb9cfe

134

py

Python

tests/test_index.py

kmbn/zeit-now-filter-feeds

a138b5d5f4b5113ad0f64dea9db1f1fd0d2cf687

[ "MIT" ]

null

tests/test_index.py

kmbn/zeit-now-filter-feeds

a138b5d5f4b5113ad0f64dea9db1f1fd0d2cf687

[ "MIT" ]

null

tests/test_index.py

kmbn/zeit-now-filter-feeds

a138b5d5f4b5113ad0f64dea9db1f1fd0d2cf687

[ "MIT" ]

null

"""Tests for index.py.""" def test_filter_feed(): # TODO: Add data directory with sample feeds and complete this test. pass

19.142857

72

0.686567

20

134

4.5

0.95

0

0.208955

134

6

73

22.333333

0.849057

0.649254

0

0.166667

0

1

0.5

true

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0

0.5

0

1

0

null

0

1

0

null

0

1

0

1

0

6

eb6368aa32bedbdee8322667625a0f39a8190a4e

46

py

Python

onadata/libs/utils/nose_plugins/__init__.py

gushil/kobocat

5ce27ed5fbf969b2ce68e8a59dd97ced74686711

[ "BSD-2-Clause" ]

38

2017-02-28T05:39:40.000Z

2019-01-16T04:39:04.000Z

onadata/libs/utils/nose_plugins/__init__.py

gushil/kobocat

5ce27ed5fbf969b2ce68e8a59dd97ced74686711

[ "BSD-2-Clause" ]

48

2019-03-18T09:26:31.000Z

2019-05-27T08:12:03.000Z

onadata/libs/utils/nose_plugins/__init__.py

gushil/kobocat

5ce27ed5fbf969b2ce68e8a59dd97ced74686711

[ "BSD-2-Clause" ]

5

2017-02-22T12:25:19.000Z

2019-01-15T11:16:40.000Z

from SilenceSouth import SilenceSouth # noqa

23

45

0.826087

5

46

7.6

0.8

0

0.152174

46

1

46

0.974359

0.086957

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

eb7ffc2878894c014a972376cffbef7ca2acedde

35

py

Python

catkin_ws/simulation/rviz_tools_py-master/src/rviz_tools_py/__init__.py

fontysrobotics/Blackboard_based_distributed_fleet_manager

a6b44738fe67f4948a69f8d45da58d981c6724e0

[ "BSD-3-Clause" ]

79

2020-04-23T04:39:00.000Z

2022-03-08T09:50:09.000Z

catkin_ws/simulation/rviz_tools_py-master/src/rviz_tools_py/__init__.py

fontysrobotics/Blackboard_based_distributed_fleet_manager

a6b44738fe67f4948a69f8d45da58d981c6724e0

[ "BSD-3-Clause" ]

1

2020-04-23T10:18:50.000Z

catkin_ws/simulation/rviz_tools_py-master/src/rviz_tools_py/__init__.py

fontysrobotics/Blackboard_based_distributed_fleet_manager

a6b44738fe67f4948a69f8d45da58d981c6724e0

[ "BSD-3-Clause" ]

29

2020-04-23T07:49:15.000Z

2022-03-26T11:48:53.000Z

from rviz_tools import RvizMarkers

17.5

34

0.885714

5

35

6

1

0

0.114286

35

1

35

0.967742

0

1

0

true

0

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1

0

1

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null

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null

0

1

0

1

0

1

0

6

eb9be2534c341f91e66f0f6ca6ff0226c416347b

114

py

Python

dpaste/contribute.py

mozafrank/dpaste

3be4bd13075ace2b4b9530172162b1af35bbd0d2

[ "MIT" ]

null

dpaste/contribute.py

mozafrank/dpaste

3be4bd13075ace2b4b9530172162b1af35bbd0d2

[ "MIT" ]

null

dpaste/contribute.py

mozafrank/dpaste

3be4bd13075ace2b4b9530172162b1af35bbd0d2

[ "MIT" ]

null

from django.shortcuts import render def contrib_file(request): return render(request,'dpaste/contribute.html')

22.8

49

0.807018

15

114

6.066667

0.866667

0

0.096491

114

4

50

28.5

0.883495

0

0.192982

0

1

0.333333

false

0

0.333333

1

0

1

0

null

0

1

0

null

0

1

0

1

0

6

ebe4cbeb2f61cd4e37a6614ab91c5e19c2358f54

32

py

Python

pontoon/tags/tests/conftest.py

foss4/pontoon

0503cc78f00e1e9d23c1ca885fe74a627563fc82

[ "BSD-3-Clause" ]

1,145

2015-05-15T01:08:16.000Z

2022-03-31T14:23:45.000Z

pontoon/tags/tests/conftest.py

foss4/pontoon

0503cc78f00e1e9d23c1ca885fe74a627563fc82

[ "BSD-3-Clause" ]

1,365

2015-05-04T21:54:18.000Z

2022-03-30T16:53:49.000Z

pontoon/tags/tests/conftest.py

foss4/pontoon

0503cc78f00e1e9d23c1ca885fe74a627563fc82

[ "BSD-3-Clause" ]

667

2015-05-04T21:33:45.000Z

2022-03-30T10:25:33.000Z

from .fixtures import * # noqa

16

31

0.6875

4

32

5.5

1

0

0.21875

32

1

32

0.88

0.125

0

1

0

true

0

1

0

1

0

1

0

null

0

1

0

null

0

1

0

1

0

1

0

6

6905dd059134296c87151d3dce08e5a992d15fc7

50

py

Python

utils/__init__.py

SBU-BMI/deep_survival_analysis

1953155f329ffdb884133ab187046b312844d320

[ "BSD-3-Clause" ]

null

utils/__init__.py

SBU-BMI/deep_survival_analysis

1953155f329ffdb884133ab187046b312844d320

[ "BSD-3-Clause" ]

null

utils/__init__.py

SBU-BMI/deep_survival_analysis

1953155f329ffdb884133ab187046b312844d320

[ "BSD-3-Clause" ]

null

from .utils import * from .pytorch_utils import *

16.666667

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50

5.285714

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0

0.16

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1

0

true

0

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0

null

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1

0

null

0

1

0

1

0

1

0

6

69187928745023645c6634409ac303f8537488d7

3,904

py

Python

asyncwhois/__init__.py

pogzyb/asyncwhois

44c74184a3b713ec9bdc7322cb7b78d41ea24756

[ "MIT" ]

25

2020-06-09T00:39:25.000Z

2022-02-21T08:54:09.000Z

asyncwhois/__init__.py

pogzyb/asyncwhois

44c74184a3b713ec9bdc7322cb7b78d41ea24756

[ "MIT" ]

17

2020-04-27T09:35:00.000Z

2022-02-15T01:56:16.000Z

asyncwhois/__init__.py

pogzyb/asyncwhois

44c74184a3b713ec9bdc7322cb7b78d41ea24756

[ "MIT" ]

4

2020-07-10T23:06:46.000Z

2022-01-22T10:30:04.000Z

from typing import Any, Optional from .pywhois import PyWhoIs __all__ = [ 'lookup', 'aio_lookup', 'whois_cmd_shell', 'aio_whois_cmd_shell', 'rdap_domain_lookup', 'aio_rdap_domain_lookup' ] __version__ = '0.4.1' def lookup(url: str, timeout: int = 10) -> PyWhoIs: """ Module entry point for whois lookups. Opens a socket connection to the whois server, submits a query, and then parses the query output from the server into a dictionary. Uses "socket.create_connection()" for the socket. Raises "QueryError" if connection to a server times out or fails. Raises "NotFoundError" if domain record is "not found" on the server. :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param timeout: whois server connection timeout (default 10 seconds) :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = PyWhoIs._from_url(url, timeout) return whois def whois_cmd_shell(url: str, timeout: int = 10) -> PyWhoIs: """ Equivalent to running "whois <domain>" from the shell. Uses subprocess.Popen(). :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param timeout: whois server connection timeout (default 10 seconds) :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = PyWhoIs._from_whois_cmd(url, timeout) return whois async def aio_lookup(url: str, timeout: int = 10) -> PyWhoIs: """ Asynchronous module entry point for whois lookups. Opens a socket connection to the whois server, submits a query, and then parses the query output from the server into a dictionary. Uses "asyncio.open_connection()" for the socket. Raises "QueryError" if connection to a server times out or fails. Raises "NotFoundError" if domain record is "not found" on the server. :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param timeout: whois server connection timeout (default 10 seconds) :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = await PyWhoIs._aio_from_url(url, timeout) return whois def rdap_domain_lookup(url: str, http_client: Optional[Any] = None) -> PyWhoIs: """ Runs an RDAP query for the given url. :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param http_client: Optional HTTP Client such as `httpx.Client` or `requests.Session` :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = PyWhoIs._rdap_domain_from_url(url, http_client) return whois async def aio_rdap_domain_lookup(url: str, http_client: Optional[Any] = None) -> PyWhoIs: """ Runs an RDAP query for the given url. :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param http_client: Optional Async HTTP Client such as `httpx.AsyncClient` :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = await PyWhoIs._aio_rdap_domain_from_url(url, http_client) return whois async def aio_whois_cmd_shell(url: str, timeout: int = 10) -> PyWhoIs: """ Equivalent to running "whois <domain>" from the shell. Leverages "asyncio.subprocess". IMPORTANT: Raises "NotImplementedError" if running on Windows and the event loop is not set to be type "asyncio.ProactorEventLoop". Must set: loop = asyncio.ProactorEventLoop() :param url: Any correctly formatted URL (e.g. https://en.wikipedia.org/wiki/WHOIS) :param timeout: whois server connection timeout (default 10 seconds) :return: instance of PyWhoIs with "query_output" and "parser_output" attributes """ whois = await PyWhoIs._aio_from_whois_cmd(url, timeout) return whois

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0

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0

1

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null

0

6

694f0b480c0c41a25c9df778d7727b1719cb8c95

37

py

Python

fetcher/__init__.py

molkoback/Fab-Lab-Tokens

07e9e250931cf344610561108fe199eed257d9b8

[ "MIT" ]

null

fetcher/__init__.py

molkoback/Fab-Lab-Tokens

07e9e250931cf344610561108fe199eed257d9b8

[ "MIT" ]

null

fetcher/__init__.py

molkoback/Fab-Lab-Tokens

07e9e250931cf344610561108fe199eed257d9b8

[ "MIT" ]

1

2018-10-17T07:05:12.000Z

from .fetcher import DocumentFetcher

18.5

36

0.864865

4

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1

0

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1

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0.969697

0

1

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true

0

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1

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0

null

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