index int64 | repo_name string | branch_name string | path string | content string | import_graph string |
|---|---|---|---|---|---|
82,924 | rgiessmann/abifpy | refs/heads/master | /setup.py | #!/usr/bin/env python
from setuptools import setup, find_packages
from abifpy import __version__
version = __version__
long_description = open("README.rst").read()
setup(
name = "abifpy",
version = version,
description = "abifpy is a module for reading ABI Sanger sequencing trace files.",
long_desc... | {"/setup.py": ["/abifpy.py"]} |
82,925 | rgiessmann/abifpy | refs/heads/master | /tests/test_abifpy.py | #!/usr/bin/env python
#
# test_abifpy.py
# python2 unit tests for abifpy
# http://github.com/bow/abifpy
import unittest
import datetime
import abifpy
class TestAbif(unittest.TestCase):
def __init__(self, filename):
unittest.TestCase.__init__(self, methodName='runTest')
self.filename = filename
... | {"/setup.py": ["/abifpy.py"]} |
82,926 | rgiessmann/abifpy | refs/heads/master | /abifpy.py | #!/usr/bin/env python
#
# abifpy.py
# python module for reading abi trace files
# http://github.com/bow/abifpy
"""Python module for reading .ab1 trace files."""
import datetime
import struct
from os.path import splitext, basename
from sys import version_info
RELEASE = False
__version_info__ = ('1', '0', )
__version... | {"/setup.py": ["/abifpy.py"]} |
82,973 | MaXooMa/NoyTwitter | refs/heads/master | /Dals/SqliteAdapter.py | import sqlite3
from Consts import Consts
from Objects.TwitterLogger import TwitterLogger
class SqliteAdapter():
def __init__(self):
self.connect()
def connect(self):
try:
self.conn = sqlite3.connect(Consts.TWITTER_DB_LOCATION)
except Exception as exc:
print exc
... | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,974 | MaXooMa/NoyTwitter | refs/heads/master | /Queries.py | import Consts
class Queries():
GET_POSTS_QUERY = """select * from Posts"""
INSERT_POSTS_QUERY = """INSERT INTO posts (id, creation_time, content) VALUES (NULL, '%s', '%s')""" | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,975 | MaXooMa/NoyTwitter | refs/heads/master | /Objects/TwitterPost.py | class TwitterPost():
def __init__(self, upload_time, post_content):
self.upload_time = upload_time
self.post_content = post_content
| {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,976 | MaXooMa/NoyTwitter | refs/heads/master | /Objects/TwitterLogger.py | import logging
class TwitterLogger:
def __init__(self):
self.logger = logging.getLogger('twitter_logger')
file_handler = logging.FileHandler(r'C:\Users\MainLaptop\Desktop\a.txt')
formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
file_handler.setFormatter(format... | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,977 | MaXooMa/NoyTwitter | refs/heads/master | /main.py | from Objects.TwitterLogger import TwitterLogger
from Objects.TwitterPost import TwitterPost
from Consts import Consts
from flask import Flask, request
from Dals.PostDAL import PostDAL
import os, datetime
app = Flask(__name__, static_url_path='/static')
"""def main():
logger = TwitterLogger().logger
logger.inf... | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,978 | MaXooMa/NoyTwitter | refs/heads/master | /Handlers.py | from main import app
@app.route('/')
def hello():
return "Twitter" | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,979 | MaXooMa/NoyTwitter | refs/heads/master | /Consts.py | class Consts(object):
'''TWITTER_DB_HOST = 'localhost'
TWITTER_DB_PORT = '3306'
TWITTER_DB_USER = 'noy'
TWITTER_DB_PASSWORD = '123'''
TWITTER_DB_LOCATION = 'noy_twitter_db.db'
POST_DB_TIME_INDEX = 1
POST_DB_CONTENT_INDEX = 2
FOLDER_NAME = 'Logger' | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,980 | MaXooMa/NoyTwitter | refs/heads/master | /Dals/PostDAL.py |
from datetime import datetime
from Consts import Consts
from Queries import Queries
from Objects.TwitterLogger import TwitterLogger
from Objects.TwitterPost import TwitterPost
from SqliteAdapter import SqliteAdapter
class PostDAL():
def __init__(self):
self.db_adapter = SqliteAdapter()
self.cur = ... | {"/Queries.py": ["/Consts.py"], "/main.py": ["/Objects/TwitterLogger.py", "/Objects/TwitterPost.py", "/Consts.py", "/Dals/PostDAL.py"], "/Handlers.py": ["/main.py"]} |
82,996 | prasadus92/nbx-assignment | refs/heads/master | /setup.py | import os
import re
from setuptools import setup
def read_version():
regexp = re.compile(r"^__version__\W*=\W*'([\d.abrc]+)'")
init_py = os.path.join(os.path.dirname(__file__),
'userservice', '__init__.py')
with open(init_py) as f:
for line in f:
match = reg... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
82,997 | prasadus92/nbx-assignment | refs/heads/master | /userservice/routes.py | from userservice.views import health, get_users, get_user, create_user, update_user, delete_user
def setup_routes(app):
app.router.add_get('/', health)
app.router.add_get('/users', get_users)
app.router.add_post('/users', create_user)
app.router.add_get('/users/{user_id:[0-9a-fA-F]+}', get_user)
a... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
82,998 | prasadus92/nbx-assignment | refs/heads/master | /init_db.py | from sqlalchemy import create_engine, MetaData
from userservice.db import user
from userservice.settings import BASE_DIR, get_config
DSN = "postgresql://{user}:{password}@{host}:{port}/{database}"
USER_CONFIG_PATH = BASE_DIR / 'config' / 'userservice.yaml'
USER_CONFIG = get_config(['-c', USER_CONFIG_PATH.as_posix()]... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
82,999 | prasadus92/nbx-assignment | refs/heads/master | /userservice/schema.py | CREATE_USER_REQUEST_SCHEMA = {
"type": "object",
"properties": {
"name": {"type": "string"},
"email": {"type": "string"}
},
"required": ["name", "email"],
"additionalProperties": False
}
CREATE_USER_RESPONSE_SCHEMA = {
"type": "object",
"properties": {
"id": {"type":... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,000 | prasadus92/nbx-assignment | refs/heads/master | /userservice/middlewares.py | import json
from aiohttp import web
from userservice.status import HTTP_500_INTERNAL_SERVER_ERROR, HTTP_404_NOT_FOUND, HTTP_400_BAD_REQUEST
def json_error(status_code: int, exception: Exception) -> web.Response:
return web.Response(
status=status_code,
body=json.dumps({
'error': str(... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,001 | prasadus92/nbx-assignment | refs/heads/master | /userservice/encoders.py | import datetime
import json
from uuid import UUID
class CustomEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, UUID):
return obj.hex
if isinstance(obj, datetime.datetime):
return obj.isoformat()
return json.JSONEncoder.default(self, obj)
| {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,002 | prasadus92/nbx-assignment | refs/heads/master | /userservice/db.py | import logging
import uuid
import aiopg.sa
from sqlalchemy import (
MetaData, Table, Column, String,
DateTime, func, select)
from sqlalchemy.dialects.postgresql import UUID
__all__ = ['init_pg', 'close_pg', 'user']
LOGGER = logging.getLogger(__name__)
USER_NOT_EXISTS_MSG = "User with id: {} does not exist"
... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,003 | prasadus92/nbx-assignment | refs/heads/master | /userservice/app.py | import logging
import sys
from aiohttp import web
from aiohttp_swagger import *
from userservice.db import close_pg, init_pg
from userservice.middlewares import setup_middlewares
from userservice.routes import setup_routes
from userservice.settings import get_config
LOGGER = logging.getLogger(__name__)
def init_ap... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,004 | prasadus92/nbx-assignment | refs/heads/master | /userservice/__main__.py | import sys
from userservice.app import main
main(sys.argv[1:])
| {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,005 | prasadus92/nbx-assignment | refs/heads/master | /userservice/views.py | import json
import logging
from aiohttp import web
from aiohttp_validate import validate
from userservice.encoders import CustomEncoder
from userservice.schema import CREATE_USER_REQUEST_SCHEMA, CREATE_USER_RESPONSE_SCHEMA, UPDATE_USER_REQUEST_SCHEMA, \
UPDATE_USER_RESPONSE_SCHEMA
from userservice.status import H... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,006 | prasadus92/nbx-assignment | refs/heads/master | /tests/test_integration.py | """Requires running Postgres"""
async def test_health(cli, tables_and_data):
response = await cli.get('/')
assert response.status == 200
assert 'user-service' in await response.text()
async def test_get_users(cli, tables_and_data):
response = await cli.get('/users')
assert response.status == 200... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,007 | prasadus92/nbx-assignment | refs/heads/master | /tests/configuration.py | import pytest
from init_db import (
setup_db,
teardown_db,
create_tables,
sample_data,
drop_tables
)
from userservice.app import main
from userservice.settings import get_config
@pytest.fixture
async def cli(loop, test_client, db):
app = await main()
return await test_client(app)
@pytes... | {"/userservice/routes.py": ["/userservice/views.py"], "/init_db.py": ["/userservice/db.py"], "/userservice/app.py": ["/userservice/db.py", "/userservice/middlewares.py", "/userservice/routes.py"], "/userservice/__main__.py": ["/userservice/app.py"], "/userservice/views.py": ["/userservice/encoders.py", "/userservice/sc... |
83,008 | juragi/python-web | refs/heads/master | /randomTest.py | import random
def printRandom():
print('random number: ', random.randrange(1,10)) | {"/web.py": ["/randomTest.py"]} |
83,009 | juragi/python-web | refs/heads/master | /web.py | from flask import Flask, render_template, request
import randomTest
app = Flask(__name__)
@app.route('/')
def index():
randomTest.printRandom()
return render_template('home.html')
@app.route('/about')
def about():
return render_template('about.html')
@app.route('/blog')
def blog():
return render_tem... | {"/web.py": ["/randomTest.py"]} |
83,046 | FredysMuriel4/HotelGirasol | refs/heads/main | /queries.py | import mysql.connector
class database:
def __init__(self):
super(database, self).__init__()
global hotelGirasolDB
hotelGirasolDB = mysql.connector.connect(
host='127.0.0.1',
user='root',
password='',
database='bdhotelgirasol'
)
######################################## RESERVAS #####################... | {"/views.py": ["/queries.py"], "/app.py": ["/views.py"]} |
83,047 | FredysMuriel4/HotelGirasol | refs/heads/main | /views.py | import tkinter as tk
from tkinter import StringVar
from tkinter import messagebox
from tkinter import ttk
from queries import database
db = database()
class Views:
def login(self):
def enter():
fun_empty = empty(user.get(), password.get())
if fun_empty != 0:
if user.get() == "Administrador" and passwor... | {"/views.py": ["/queries.py"], "/app.py": ["/views.py"]} |
83,048 | FredysMuriel4/HotelGirasol | refs/heads/main | /app.py | from views import Views
insView = Views()
class initialize():
def __init__(self):
super(initialize, self).__init__()
insView.login()
initialize() | {"/views.py": ["/queries.py"], "/app.py": ["/views.py"]} |
83,074 | ShikhaSaxena41/FakeNews12 | refs/heads/master | /headline.py | from bs4 import BeautifulSoup as bs
import requests
import numpy as np
import os
import pandas as pd
headers = {'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36'}
def news_list_request(news_list, news_table_tr, tag):
for news ... | {"/main.py": ["/prediction.py", "/headline.py"]} |
83,075 | ShikhaSaxena41/FakeNews12 | refs/heads/master | /main.py | from flask import Flask, render_template, request, url_for
from flask_paginate import Pagination, get_page_args
from flask_mysqldb import MySQL
import prediction as pred
app=Flask(__name__, static_folder='static', template_folder='templates')
import headline as hd
app.config['MYSQL_HOST'] = 'localhost'
app.config['MY... | {"/main.py": ["/prediction.py", "/headline.py"]} |
83,076 | ShikhaSaxena41/FakeNews12 | refs/heads/master | /prediction.py | import pickle
def detecting_fake_news(var):
load_model = pickle.load(open('final_model.sav', 'rb'))
prediction = load_model.predict([var])
prob = load_model.predict_proba([var])
return ("The given statement is "+str(prediction[0]),
"The truth probability score is "+str(prob[0][1]))
| {"/main.py": ["/prediction.py", "/headline.py"]} |
83,104 | bubo0/CSE256-Final-Project | refs/heads/master | /Classification_Web/input/forms.py | from django import forms
class NameForm(forms.Form):
input_text = forms.CharField(label='Input text', max_length=300,
widget=forms.TextInput(attrs={'style': 'width: 500px; height:30px; word-wrap:break-word; word-break:break-all'}))
| {"/Classification_Web/input/views.py": ["/Classification_Web/input/forms.py"]} |
83,105 | bubo0/CSE256-Final-Project | refs/heads/master | /Classification_Web/input/urls.py | from django.urls import path
from . import views
urlpatterns = [
path('', views.index, name='index'),
path('query', views.query, name='query'),
path('text', views.text, name='text'),
path('table', views.table, name='table'),
path('ajax/classify', views.classify, name='ajax/classify'),
] | {"/Classification_Web/input/views.py": ["/Classification_Web/input/forms.py"]} |
83,106 | bubo0/CSE256-Final-Project | refs/heads/master | /Classification_Web/input/views.py | from django.shortcuts import render
from django.http import HttpResponse
from django.http import JsonResponse
# from django.http import HttpResponseRedirect
from django.template import loader
import dill
from lime.lime_text import LimeTextExplainer
import pickle
from .forms import NameForm
import os
from django.conf im... | {"/Classification_Web/input/views.py": ["/Classification_Web/input/forms.py"]} |
83,117 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/expression_etl.py | """Expression ETL."""
import logging
import codecs
import uuid
import multiprocessing
import ijson
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
from transactors import CSVTransactor, Neo4jTransactor
class ExpressionETL(ETL):
"""Expression ETL."""
logger = logging.getLogger(__name__)
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,118 | alliance-genome/agr_loader | refs/heads/stage | /src/loader_common.py | """This is mainly used to create contextInfo"""
import logging
import os
import yaml
class Singleton(type):
"""Singleton"""
_instances = {}
def __call__(cls, *args, **kwargs):
if (cls, args, frozenset(kwargs.items())) not in cls._instances:
cls._instances[(cls, args, frozenset(kwarg... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,119 | alliance-genome/agr_loader | refs/heads/stage | /src/data_manager/sub_type_config.py | """Gets the subtypes config"""
import logging
from urllib.parse import urljoin
from files import Download
class SubTypeConfig():
"""SubType Configuration"""
logger = logging.getLogger(__name__)
def __init__(self, data_type, sub_data_type, file_url, local_file_location):
self.data_type = data_ty... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,120 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/stub_etl.py | """Stub ETL."""
import logging
import multiprocessing
from etl import ETL
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class StubETL(ETL):
"""Stub ETL."""
logger = logging.getLogger(__name__)
# Query templates which take params and will be processed later
query_te... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,121 | alliance-genome/agr_loader | refs/heads/stage | /src/files/comment_file.py | class CommentFile(object):
"""Comment File"""
def __init__(self, file_handle, commentstring="#"):
self.file_handle = file_handle
self.commentstring = commentstring
def next(self):
"""next"""
line = self.file_handle.next()
while line.startswith(self.commentstring):
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,122 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/go_annot_etl.py | """GO Anootation ETL."""
import logging
import csv
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from transactors import CSVTransactor, Neo4jTransactor
class GOAnnotETL(ETL):
"""GO Annotation ETL."""
logger = logging.getLogger(__name__)
# Query templates which take param... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,123 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/go_etl.py | """GO ETL."""
import logging
from ontobio import OntologyFactory
from etl import ETL
from etl.helpers import OBOHelper
from transactors import CSVTransactor, Neo4jTransactor
class GOETL(ETL):
"""GO ETL."""
logger = logging.getLogger(__name__)
# Query templates which take params and will be processed la... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,124 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/text_processing_helper.py | """Text Processing Helper"""
import re
class TextProcessingHelper():
"""Text Processing Helper"""
@staticmethod
def cleanhtml(raw_html):
"""Clean HTML"""
cleanr = re.compile('</.*?>')
cleantext = re.sub(cleanr, '>', raw_html)
cleanr = re.compile('<.*?>')
cleantext... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,125 | alliance-genome/agr_loader | refs/heads/stage | /src/files/csv_file.py | """CSV file"""
import logging
import codecs
import csv
from .comment_file import CommentFile
class CSVFile(object):
"""CSV file download"""
logger = logging.getLogger(__name__)
def __init__(self, filename):
self.filename = filename
def get_data(self):
"""Get Data"""
self.l... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,126 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/obo_helper.py | """OBO Helper."""
import logging
import json
from collections import defaultdict
from ontobio import OntologyFactory
from .etl_helper import ETLHelper
from .neo4j_helper import Neo4jHelper
class OBOHelper():
"""OBO Helper."""
logger = logging.getLogger(__name__)
etlh = ETLHelper()
@staticmethod
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,127 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/gene_disease_ortho_etl.py | """Gene Disease Orthology ETL."""
import logging
import multiprocessing
import uuid
from datetime import datetime
from etl import ETL
from transactors import CSVTransactor, Neo4jTransactor
from .helpers import Neo4jHelper
class GeneDiseaseOrthoETL(ETL):
"""Gene Disease Orthology ETL."""
logger = logging.ge... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,128 | alliance-genome/agr_loader | refs/heads/stage | /src/data_manager/__init__.py | from .data_file_manager import DataFileManager
from .data_type_config import DataTypeConfig
from .sub_type_config import SubTypeConfig | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,129 | alliance-genome/agr_loader | refs/heads/stage | /src/files/xml_file.py | """XML File"""
import logging
import xml.etree.ElementTree as ElementTree
class XMLFile():
"""XML File"""
logger = logging.getLogger(__name__)
def __init__(self, filename):
self.filename = filename
def get_data(self):
"""Get Data"""
self.logger.debug("Parsing XML data from... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,130 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/resource_descriptor_helper.py | """Resources Descriptor Helper"""
import logging
import uuid
import yaml
from files import Download
class ResourceDescriptorHelper():
"""Resource Descriptor Helper"""
logger = logging.getLogger(__name__)
list_of_descriptor_maps_to_load = []
@staticmethod
def get_data():
"""Get Data"""
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,131 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/genetic_interaction_etl.py | """Genetic Interaction ETL."""
import logging
import uuid
import csv
import re
import sys
import itertools
from etl import ETL
from transactors import CSVTransactor, Neo4jTransactor
from etl.helpers import Neo4jHelper, ETLHelper
# Test loading this requires:
# SPECIES: [Species]
# BGI: [FB, SGD, WB, ZFIN, RGD, MGI, ... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,132 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/molecular_interaction_etl.py | """Molecular Interaction ETL."""
import logging
import uuid
import csv
import re
import sys
import itertools
from etl import ETL
from transactors import CSVTransactor, Neo4jTransactor
from etl.helpers import Neo4jHelper, ETLHelper
# Test loading this requires:
# BGI: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN, SARS-CoV-2]
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,133 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/gene_descriptions_etl.py | """Gene Descriptions ETL."""
import copy
import json
import logging
import os
import datetime
import re
import requests
from collections import defaultdict
from etl import ETL
from etl.helpers import Neo4jHelper
from genedescriptions.config_parser import GenedescConfigParser
from genedescriptions.descriptions_writer ... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,134 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/__init__.py | from .etl import ETL
from .allele_etl import AlleleETL
from .disease_etl import DiseaseETL
from .expression_etl import ExpressionETL
from .bgi_etl import BGIETL
from .expression_atlas_etl import ExpressionAtlasETL
from .so_etl import SOETL
from .do_etl import DOETL
from .go_etl import GOETL
from .mi_etl import MIETL
fr... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,135 | alliance-genome/agr_loader | refs/heads/stage | /src/test/__init__.py | from .test_object import TestObject | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,136 | alliance-genome/agr_loader | refs/heads/stage | /src/test/schema_rel_tests.py | """Test Class"""
from etl import Neo4jHelper
def pytest_generate_tests(metafunc):
"""called once per each test function"""
funcarglist = metafunc.cls.params[metafunc.function.__name__]
argnames = sorted(funcarglist[0])
metafunc.parametrize(argnames, [[funcargs[name] for name in argnames] \
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,137 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/htp_metadatasample_etl.py | """HTP Meta Dataset Sample."""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from files import JSONFile
from transactors import CSVTransactor, Neo4jTransactor
import uuid
logger = logging.getLogger(__name__)
class HTPMetaDatasetSampleETL(ETL):
"""HTP Meta Data."""
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,138 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/do_etl.py | """DO ETL."""
import logging
import re
from ontobio import OntologyFactory
from etl import ETL
from etl.helpers import ETLHelper
from etl.helpers import OBOHelper
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class DOETL(ETL):
"""DO ETL."""
logger = logging.getLogger(__name_... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,139 | alliance-genome/agr_loader | refs/heads/stage | /src/transactors/file_transactor.py | """File Trnasactor"""
import logging
import multiprocessing
from time import sleep
from etl import ETL
class FileTransactor():
"""File Transactor"""
logger = logging.getLogger(__name__)
count = 0
queue = None
def __init__(self):
manager = multiprocessing.Manager()
FileTransact... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,140 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/etl_helper.py | """ETL Helper."""
import uuid
import logging
import json
import datetime
from .resource_descriptor_helper_2 import ResourceDescriptorHelper2
from .neo4j_helper import Neo4jHelper
class ETLHelper():
"""ETL Helper."""
logger = logging.getLogger(__name__)
rdh2 = ResourceDescriptorHelper2()
rdh2.get_dat... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,141 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/generic_ontology_etl.py |
"""Generic Ontology ETL."""
import logging
import multiprocessing
import re
from etl import ETL
from etl.helpers import OBOHelper
from files import TXTFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class GenericOntologyETL(ETL):
"""Generic Ontology ETL."""
logger = logg... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,142 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/experimental_condition_helper.py | """Experimental condition Helper"""
import logging
class ExperimentalConditionHelper():
"""Experimental condition Helper"""
logger = logging.getLogger(__name__)
def __init__(self, entity_join_label):
self.record_cond_relations = []
self.cond_relations = []
self.cond_nodes = dic... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,143 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/affected_genomic_model_etl.py | """Affected Genomic Model ETL."""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import TextProcessingHelper, ETLHelper
from files import JSONFile
from transactors import CSVTransactor, Neo4jTransactor
class AffectedGenomicModelETL(ETL):
"""ETL for adding Affected Genomic Model."""
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,144 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/orthology_etl.py | """Orthology ETL."""
from itertools import permutations
import logging
import uuid
import multiprocessing
import codecs
from random import shuffle
import ijson
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
# from files import JSONFile
from transactors import CSVTransactor, Neo4jTransactor
class... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,145 | alliance-genome/agr_loader | refs/heads/stage | /src/files/download.py | """Download."""
import logging
import os
import time
import urllib.request
from urllib.error import HTTPError, URLError
from .gzip_file import GZIPFile
from loader_common import ContextInfo
class Download(object):
"""Download"""
logger = logging.getLogger(__name__)
def __init__(self, savepath, url_to_re... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,146 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/geo_xref_etl.py | """GEO XREF ETL."""
import json
import logging
import urllib
import xmltodict
from pathlib import Path
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
from transactors import CSVTransactor, Neo4jTransactor
class GeoXrefETL(ETL):
"""GEO XREF ETL."""
logger = logging.getLogger(__name__)
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,147 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/gene_pheno_cross_reference_etl.py | """Gene Pheno XREF ETL."""
import logging
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
from transactors import CSVTransactor, Neo4jTransactor
class GenePhenoCrossReferenceETL(ETL):
"""Gene Pheno XREF ETL."""
logger = logging.getLogger(__name__)
pheno_xref_query_template = """
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,148 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/__init__.py | from .etl_helper import ETLHelper
from .neo4j_helper import Neo4jHelper
from .assembly_sequence_helper import AssemblySequenceHelper
from .obo_helper import OBOHelper
from .resource_descriptor_helper_2 import ResourceDescriptorHelper2
from .text_processing_helper import TextProcessingHelper
from .experimental_condition... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,149 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/biogrid_orcs_xref_etl.py | """BIOGRID ORCS XREF ETL."""
import logging
import glob
import csv
import os
import tarfile
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
from transactors import CSVTransactor, Neo4jTransactor
class BiogridOrcsXrefETL(ETL):
"""BIOGRID ORCS XREF ETL."""
logger = logging.getLogger(__name... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,150 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/bgi_etl.py | """BGI ETL."""
import logging
import sys
import uuid
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from transactors import CSVTransactor, Neo4jTransactor
from files import JSONFile
class BGIETL(ETL):
"""BGI ETL."""
logger = logging.getLogger(__name__)
# Query templates w... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,151 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/disease_etl.py | """Disease ETL."""
# TODO need to fix the difference between disaeseRecord and disease_record in original code
import logging
import multiprocessing
import uuid
from etl import ETL
from etl.helpers import ETLHelper
from etl.helpers import Neo4jHelper
from etl.helpers import ExperimentalConditionHelper
from files impo... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,152 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/closure_etl.py | """Closure ETL."""
import logging
import multiprocessing
from etl import ETL
from transactors import CSVTransactor
from transactors import Neo4jTransactor
from .helpers import Neo4jHelper
class ClosureETL(ETL):
"""Clojure ETL."""
logger = logging.getLogger(__name__)
insert_isa_partof_closure_query_tem... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,153 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/construct_etl.py | """Construct ETL."""
import logging
import multiprocessing
import uuid
from etl import ETL
from etl.helpers import ETLHelper
from etl.helpers import TextProcessingHelper
from files import JSONFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class ConstructETL(ETL):
"""Construct ... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,154 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/species_etl.py | """Species ETL."""
import logging
import yaml
from etl import ETL
from transactors import CSVTransactor
from transactors import Neo4jTransactor
from files import Download
class SpeciesETL(ETL):
"""Species ETL."""
logger = logging.getLogger(__name__)
# Query templates which take params and will be proce... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,155 | alliance-genome/agr_loader | refs/heads/stage | /src/transactors/__init__.py | from .transactor import Transactor
from .csv_transactor import CSVTransactor
from .neo4j_transactor import Neo4jTransactor
from .file_transactor import FileTransactor | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,156 | alliance-genome/agr_loader | refs/heads/stage | /src/files/tar_file.py | """TAR File"""
import logging
import os
import tarfile
import time
class TARFile(object):
"""TAR File"""
logger = logging.getLogger(__name__)
def __init__(self, path, tarfilename):
self.path = path
self.tarfilename = tarfilename
def extract_all(self):
"""Extract All"""
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,157 | alliance-genome/agr_loader | refs/heads/stage | /src/transactors/neo4j_transactor.py | """Neo4j Transacotr"""
import logging
import multiprocessing
import pickle
import time
from neo4j import GraphDatabase
from etl import ETL
from loader_common import ContextInfo
class Neo4jTransactor():
"""Neo4j Transactor"""
logger = logging.getLogger(__name__)
count = 0
queue = None
def __init... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,158 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/sequence_targeting_reagent_etl.py | """Sequence Targetting Reagent ETL."""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from files import JSONFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class SequenceTargetingReagentETL(ETL):
"""Sequence Targeting Reagent ETL.""... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,159 | alliance-genome/agr_loader | refs/heads/stage | /src/files/txt_file.py | """Text File"""
import logging
import codecs
class TXTFile(object):
"""Text File"""
logger = logging.getLogger(__name__)
def __init__(self, filename):
self.filename = filename
def get_data(self):
"""Get Data"""
self.logger.info("Loading txt data from %s...", self.filename)... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,160 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/node_count_etl.py | """Node Count ETL"""
import logging
import os
from etl import ETL
from files import TXTFile
from .helpers import Neo4jHelper
class NodeCountETL(ETL):
"""Node Count ETL"""
logger = logging.getLogger(__name__)
def __init__(self, config):
super().__init__()
self.data_type_config = config
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,161 | alliance-genome/agr_loader | refs/heads/stage | /src/files/__init__.py | from .csv_file import CSVFile
from .txt_file import TXTFile
from .json_file import JSONFile
from .tar_file import TARFile
from .download import Download
from .xml_file import XMLFile
from .zip_file import ZIPFile
from .comment_file import CommentFile
from .gzip_file import GZIPFile
| {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,162 | alliance-genome/agr_loader | refs/heads/stage | /src/test/specific_tests.py | from etl import Neo4jHelper
def test_fgf8a_exists():
"""Test fgf8a Exists"""
query = """MATCH (g:Gene)
WHERE g.symbol = 'fgf8a'
RETURN count(g) AS count"""
with Neo4jHelper.run_single_query(query) as result:
for record in result:
assert record["count"] > ... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,163 | alliance-genome/agr_loader | refs/heads/stage | /src/test/test_object.py | """Test Object"""
# Used for loading a test subset of data for AGR.
import logging
class TestObject():
"""Test Object"""
logger = logging.getLogger(__name__)
def __init__(self, use_test_object):
# TODO Separate gene ids from other forms of id?
self.use_test_object = use_test_object
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,164 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/neo4j_helper.py | """Neo4j Helper"""
import logging
from contextlib import contextmanager
from neo4j import GraphDatabase
from loader_common import ContextInfo
logger = logging.getLogger(__name__)
context_info = ContextInfo()
uri = "bolt://" + context_info.env["NEO4J_HOST"] + ":" + str(context_info.env["NEO4J_PORT"])
class Neo4jHelp... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,165 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/expression_atlas_etl.py | """Expression Atlas ETL."""
import logging
import multiprocessing
import xmltodict
from etl import ETL
from etl.helpers import ETLHelper, Neo4jHelper
from transactors import CSVTransactor, Neo4jTransactor
class ExpressionAtlasETL(ETL):
"""Expression Atlas ETL."""
logger = logging.getLogger(__name__)
#... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,166 | alliance-genome/agr_loader | refs/heads/stage | /src/transactors/csv_transactor.py | """CSV Transactor"""
from contextlib import ExitStack
import csv
import os
import logging
class CSVTransactor():
"""CSV Transactor"""
logger = logging.getLogger(__name__)
@staticmethod
def save_file_static(generator, generator_file_list):
"""Save File Static"""
with ExitStack() as s... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,167 | alliance-genome/agr_loader | refs/heads/stage | /src/files/gzip_file.py | import gzip
import shutil
import logging
import os
class GZIPFile(object):
def __init__(self, filename):
self.filename = filename
self.logger = logging.getLogger(__name__)
def extract(self):
"""Check whether the file is gzip encoded.
If so, attempt to extract the data."""
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,168 | alliance-genome/agr_loader | refs/heads/stage | /src/files/json_file.py | """JSON File"""
import logging
import codecs
import json
import os
import jsonschema as js
class JSONFile(object):
"""JSON File"""
logger = logging.getLogger(__name__)
def get_data(self, filename):
"""Get Data"""
self.logger.debug("Loading JSON data from %s ...", filename)
if ... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,169 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/mi_etl.py | """Molecular Interaction ETL."""
import logging
from etl import ETL
from etl.helpers import OBOHelper
from files import TXTFile
from transactors import CSVTransactor, Neo4jTransactor
class MIETL(ETL):
"""MI ETL."""
logger = logging.getLogger(__name__)
# Query templates which take params and will be pr... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,170 | alliance-genome/agr_loader | refs/heads/stage | /src/files/zip_file.py | """ZIP File"""
import logging
import os
import zipfile
class ZIPFile(object):
"""ZIP File"""
logger = logging.getLogger(__name__)
def __init__(self, path, zipfilename):
self.path = path
self.zipfilename = zipfilename
def extract_all(self):
"""Extract All"""
self.lo... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,171 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/transcript_etl.py | """Transcript ETL."""
import datetime
import re
import logging
import multiprocessing
import uuid
from etl import ETL
from etl.helpers import ETLHelper
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class TranscriptETL(ETL):
"""Transcript ETL."""
logger = logging.getLogger(__n... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,172 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/ecomap_etl.py | """ECOMAP ETL."""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import OBOHelper
from files import TXTFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class ECOMAPETL(ETL):
"""ECOMAP ETL."""
logger = logging.getLogger(__name__)
# Query tem... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,173 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/category_tag_etl.py | """CateogryTag ETL."""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from files import JSONFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class CategoryTagETL(ETL):
"""Category Tag ETL."""
logger = logging.getLogger(__name__)... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,174 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/mol_interactions_xref.py | """Molecular Interactions XREF ETL."""
import logging
from etl import ETL
from transactors import Neo4jTransactor
from .helpers import ETLHelper
class MolInteractionsXrefETL(ETL):
"""Molecular Interactions XREF ETL."""
logger = logging.getLogger(__name__)
# Query templates which take params and will b... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,175 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/so_etl.py | """SO ETL."""
import sys
import logging
from itertools import islice, chain, tee
from etl import ETL
from etl.helpers import OBOHelper
from files import TXTFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class SOETL(ETL):
"""SO ETL."""
logger = logging.getLogger(__name__)... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,176 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/vep_etl.py | """VEP ETL."""
import re
import logging
import multiprocessing
from etl import ETL
from etl.helpers import ETLHelper
from files import TXTFile
from transactors import CSVTransactor
from transactors import Neo4jTransactor
class VEPETL(ETL):
"""VEP ETL."""
logger = logging.getLogger(__name__)
# Query te... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,177 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/assembly_sequence_helper.py | """Assembly Sequence Helper"""
import logging
import os
import sys
import time
from pyfaidx import Fasta
class AssemblySequenceHelper():
"""Assembly Sequence Helper"""
logger = logging.getLogger(__name__)
def __init__(self, assembly, data_manager):
sub_type = assembly.replace('_', '')
... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,178 | alliance-genome/agr_loader | refs/heads/stage | /src/aggregate_loader.py | #!/usr/bin/env python
"""This is the main entry-point for running the ETL pipeline."""
import argparse
import logging
import multiprocessing
import os
import time
import coloredlogs
import json
from etl import (BGIETL, DOETL, ECOMAPETL, ETL, GOETL, MIETL, VEPETL,
AffectedGenomicModelETL, AlleleETL, B... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,179 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/helpers/resource_descriptor_helper_2.py | """Resource Descriptor Helper 2."""
import logging
import re
import yaml
from files import Download
class ResourceDescriptorHelper2():
"""Resource Descriptor Helper 2."""
logger = logging.getLogger(__name__)
resource_descriptor_dict = {}
#########################
# any local caching here.
##... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,180 | alliance-genome/agr_loader | refs/heads/stage | /src/test/schema_node_tests.py | """Schema Node Tests"""
from etl import Neo4jHelper
def pytest_generate_tests(metafunc):
"""PyTest Generate Tests"""
# called once per each test function
funcarglist = metafunc.cls.params[metafunc.function.__name__]
argnames = sorted(funcarglist[0])
metafunc.parametrize(argnames, [[funcargs[name... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,181 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/protein_sequence_etl.py | """Protein Sequence ETL"""
import logging
import multiprocessing
from etl import ETL
from etl.helpers import AssemblySequenceHelper
from etl.helpers import Neo4jHelper
from Bio.Seq import Seq
from transactors import CSVTransactor, Neo4jTransactor
from data_manager import DataFileManager
from loader_common import Conte... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
83,182 | alliance-genome/agr_loader | refs/heads/stage | /src/etl/expression_ribbon_other_etl.py | """Expression Ribbon Other ETL."""
import logging
from etl import ETL
from transactors import CSVTransactor, Neo4jTransactor
from .helpers import Neo4jHelper
class ExpressionRibbonOtherETL(ETL):
"""Expression Ribbon Other ETL."""
logger = logging.getLogger(__name__)
# Querys which do not take params a... | {"/src/files/csv_file.py": ["/src/files/comment_file.py"], "/src/etl/helpers/obo_helper.py": ["/src/etl/helpers/etl_helper.py", "/src/etl/helpers/neo4j_helper.py"], "/src/etl/gene_disease_ortho_etl.py": ["/src/etl/helpers/__init__.py"], "/src/data_manager/__init__.py": ["/src/data_manager/data_file_manager.py", "/src/d... |
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