Instruction stringlengths 13 145k | input_code stringlengths 35 390k | output_code stringlengths 35 390k |
|---|---|---|
Set `nomad_job_id` for compendia jobs
### Context
I was trying to look for a compendia processor job where I only had the `nomad_job_id`
### Problem or idea
Looks like we don't set the `nomad_job_id` for the compendia processor jobs
```sql
$ select * from processor_jobs where pipeline_applied='COMPENDIA' a... | common/data_refinery_common/utils.py
<|code_start|>import csv
import hashlib
import io
import os
import re
from functools import partial
from itertools import groupby
from typing import Dict, Set
from urllib.parse import urlparse
import nomad
import requests
from django.conf import settings
from django.core.exceptions ... | common/data_refinery_common/utils.py
<|code_start|>import csv
import hashlib
import io
import os
import re
from functools import partial
from itertools import groupby
from typing import Dict, Set
from urllib.parse import urlparse
import nomad
import requests
from django.conf import settings
from django.core.exceptions ... |
[HOTFIX] Prevent compendia jobs from getting cleaned up and fix QN jobs
## Issue Number
#1728
#1726
#1727
| foreman/data_refinery_foreman/foreman/management/commands/create_compendia.py
<|code_start|>import sys
from django.core.management.base import BaseCommand
from data_refinery_common.job_lookup import ProcessorPipeline
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_common.message_q... | foreman/data_refinery_foreman/foreman/management/commands/create_compendia.py
<|code_start|>import sys
from django.core.management.base import BaseCommand
from data_refinery_common.job_lookup import ProcessorPipeline
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_common.message_q... |
API Stats include timestamp of last broken cache
### Context
Our database has a 10 minute cache.
### Problem or idea
It'd be nifty to be able to look at the stats endpoint response and figure out when it was last busted.
### Solution or next step
Include that timestamp.
| api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... | api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... |
Improve docs and make deploy.sh easier to invoke correctly
## Issue Number
I don't think there's one that's quite specific to the types of documentation improvements this introduces.
## Purpose/Implementation Notes
Our README was getting behind. This brings it up to date and makes the deploy process easier to ... | api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... | api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... |
Create command to delete invalid compendias
### Context
https://github.com/AlexsLemonade/refinebio/pull/1734
Compendia need a QN target so they can be quantile normalized. We need 100 samples on the sample platform to create a QN target. Therefore any organisms without 100 samples on the same platform should be i... | common/data_refinery_common/models/models.py
<|code_start|>import hashlib
import io
import os
import shutil
import pytz
import uuid
import boto3
from botocore.client import Config
from datetime import datetime
from functools import partial
from typing import Dict, Set
from django.db.models import Count, Prefetch, Da... | common/data_refinery_common/models/models.py
<|code_start|>import hashlib
import io
import os
import shutil
import pytz
import uuid
import boto3
from botocore.client import Config
from datetime import datetime
from functools import partial
from typing import Dict, Set
from django.db.models import Count, Prefetch, Da... |
Quantpendia doesn't seem to run
### Context
Just triggered the quantpendia job for Danio
### Problem or idea
It doesn't seem to have started:
```
ubuntu@ip-10-0-80-121:~$ ./run_management_command.sh create_compendia --organisms=DANIO_RERIO --quant-sf-only=True --svd-algorithm=None
fd6293be1671e7c5ebf63a96... | common/data_refinery_common/message_queue.py
<|code_start|>"""Provides an interface to send messages to the Message Queue."""
from __future__ import absolute_import, unicode_literals
import nomad
from django.conf import settings
from enum import Enum
from nomad.api.exceptions import URLNotFoundNomadException
from da... | common/data_refinery_common/message_queue.py
<|code_start|>"""Provides an interface to send messages to the Message Queue."""
from __future__ import absolute_import, unicode_literals
import nomad
from django.conf import settings
from enum import Enum
from nomad.api.exceptions import URLNotFoundNomadException
from da... |
Quantpendia failed to upload to S3
### Context
We kicked off quantpendia jobs for all organisms but they weren't succeeding because they couldn't upload to S3.
### Problem or idea
This is probably just because the worker instances don't have access to the compendia S3 bucket. The smasher probably has those per... | workers/data_refinery_workers/processors/create_quantpendia.py
<|code_start|>import os
import logging
import shutil
import time
from django.utils import timezone
from typing import Dict, List, Tuple
import psutil
from data_refinery_common.job_lookup import PipelineEnum
from data_refinery_common.logging import get_and_... | workers/data_refinery_workers/processors/create_quantpendia.py
<|code_start|>import os
import logging
import shutil
import time
from django.utils import timezone
from django.conf import settings
from typing import Dict, List, Tuple
import psutil
from data_refinery_common.job_lookup import PipelineEnum
from data_refine... |
Extend processor exception classes to include additional arbitrary context
### Context
#1843 is dope. However right now those exceptions can only be used to log the job id. If we wanted to log a sample accession or what have you, we couldn't do it as it is.
### Problem or idea
We've created some new exception ... | workers/data_refinery_workers/processors/utils.py
<|code_start|>import os
import random
import shutil
import signal
import string
import subprocess
import sys
import yaml
from django.conf import settings
from django.utils import timezone
from typing import List, Dict, Callable
from data_refinery_common.job_lookup imp... | workers/data_refinery_workers/processors/utils.py
<|code_start|>import os
import random
import shutil
import signal
import string
import subprocess
import sys
import yaml
from django.conf import settings
from django.utils import timezone
from typing import List, Dict, Callable
from data_refinery_common.job_lookup imp... |
Quantpendia command timmed out for MUS_MUSCULUS
Error:
```
ubuntu@ip-10-0-127-71:~$ docker logs inspiring_goldberg
2019-11-11 22:18:45,252 i-04bb28b499152d24f [volume: -1] data_refinery_foreman.foreman.management.commands.create_quantpendia INFO [organism: HOMO_SAPIENS] [job_id: 29380081]: Sending compendia job fo... | foreman/data_refinery_foreman/foreman/management/commands/create_quantpendia.py
<|code_start|>import sys
from django.core.management.base import BaseCommand
from data_refinery_common.job_lookup import ProcessorPipeline
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_common.message... | foreman/data_refinery_foreman/foreman/management/commands/create_quantpendia.py
<|code_start|>import sys
import time
from django.core.management.base import BaseCommand
from data_refinery_common.job_lookup import ProcessorPipeline
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_co... |
Add the biggest `failure_reason` to the dashboard?
### Context
I have been debugging some sample processing errors.
### Problem or idea
I think it would be useful to have a list of the top failure reasons and the number of samples that they affect. I'm not sure if the dashboard is a good place for this.
```... | api/data_refinery_api/urls.py
<|code_start|>from rest_framework.routers import DefaultRouter
from django.conf.urls import url, include
from django.conf import settings
from django.contrib import admin
from django.urls import include, path
from rest_framework.views import APIView
from rest_framework.response import Resp... | api/data_refinery_api/urls.py
<|code_start|>from rest_framework.routers import DefaultRouter
from django.conf.urls import url, include
from django.conf import settings
from django.contrib import admin
from django.urls import include, path
from rest_framework.views import APIView
from rest_framework.response import Resp... |
Compendium Missing Generated File
### Context
`RATTUS_NORVEGICUS/rattus_norvegicus.tsv` is missing.
<img width="832" alt="Screen Shot 2019-11-27 at 10 29 50 PM" src="https://user-images.githubusercontent.com/1075609/69775087-ae306e00-1165-11ea-9a64-1035c56ea079.png">
### Problem or idea
This should be inclu... | workers/data_refinery_workers/processors/create_compendia.py
<|code_start|>import logging
import os
import shutil
import time
import itertools
from typing import Dict
from django.utils import timezone
from django.db.models import Q, Count
from fancyimpute import IterativeSVD
import numpy as np
import pandas as pd
impo... | workers/data_refinery_workers/processors/create_compendia.py
<|code_start|>import logging
import os
import shutil
import time
import itertools
from typing import Dict
from django.utils import timezone
from django.db.models import Q, Count
from fancyimpute import IterativeSVD
import numpy as np
import pandas as pd
impo... |
Record which samples end up making it into a compendia
### Context
As we build compendia we drop some samples that aren't suitable for various reasons. However the only record in our database that tracks what samples are in it is the dataset object which has every sample including those that get dropped.
### Prob... | workers/data_refinery_workers/processors/create_compendia.py
<|code_start|>import logging
import os
import shutil
import time
import itertools
from typing import Dict
from django.utils import timezone
from django.db.models import Q, Count
from fancyimpute import IterativeSVD
import numpy as np
import pandas as pd
impo... | workers/data_refinery_workers/processors/create_compendia.py
<|code_start|>import logging
import os
import shutil
import time
import itertools
from typing import Dict
from django.utils import timezone
from django.db.models import Q, Count
from fancyimpute import IterativeSVD
import numpy as np
import pandas as pd
impo... |
Smasher jobs don't mark datasets as failures when they fail
### Context
There's a couple places in the smasher code where we delay failing the job so that the job can make it to the `_notify()` function so it can let the user know that their dataset failed to process.
### Problem or idea
The job eventually get... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import boto3
import csv
import os
import rpy2
import rpy2.robjects as ro
import shutil
import simplejson as json
import string
import warnings
import requests
import psutil
import logging
import time
from botocore.exceptions imp... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import boto3
import csv
import os
import rpy2
import rpy2.robjects as ro
import shutil
import simplejson as json
import string
import warnings
import requests
import psutil
import logging
import time
from botocore.exceptions imp... |
Too many emails when dataset fails to smash
### Context
I tried to download a dataset from refine.bio which failed. (Nov 19, 20)
### Problem or idea
I received 5 emails that day and 4 of them in a span of 20 minutes, all with the same failure reason.
For another one, I tried to download I got 3 emails in a span... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import boto3
import csv
import os
import rpy2
import rpy2.robjects as ro
import shutil
import simplejson as json
import string
import warnings
import requests
import psutil
import logging
import time
from botocore.exceptions imp... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import boto3
import csv
import os
import rpy2
import rpy2.robjects as ro
import shutil
import simplejson as json
import string
import warnings
import requests
import psutil
import logging
import time
from botocore.exceptions imp... |
Transcriptome indices won't make both long and short versions
### Context
I'm pretty sure this is an issue that should affect prod. I saw it locally as part of #2035. While I did get transcriptome indices made successfully, I didn't look hard enough and it appears that only one of the two jobs succeeded because afte... | foreman/data_refinery_foreman/surveyor/transcriptome_index.py
<|code_start|>import re
import urllib
from abc import ABC
from django.utils import timezone
from typing import List, Dict
from data_refinery_common.job_lookup import ProcessorPipeline, Downloaders
from data_refinery_common.logging import get_and_configure_... | foreman/data_refinery_foreman/surveyor/transcriptome_index.py
<|code_start|>import csv
import re
import shutil
import urllib
from abc import ABC
from typing import List, Dict
from data_refinery_common.job_lookup import Downloaders
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_co... |
Engagement bot has gone away
### Problem or idea
Engagement bot hasn't been posting since 27th Dec
### Solution or next step
Fix the engagement bot
| api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... | api/data_refinery_api/views.py
<|code_start|>from datetime import timedelta, datetime
import requests
import nomad
from typing import Dict
from itertools import groupby
from re import match
from django.conf import settings
from django.views.decorators.cache import cache_page
from django.db.models import Count, Prefetch... |
Processing info: Sample is not available but only tximport is run on it
Ex:
https://www.refine.bio/experiments/SRP074593/gene-expression-profiling-of-drosophila-s2r-cells-following-rnai-mediated-knockdown-of-transcription-factors
:
""" We were associating tximport with all samples in an experiment
even though some of them were unprocessed.
Re... |
Engagement bot summary doesn't seem to be working
### Context
https://github.com/AlexsLemonade/refinebio/issues/2140
### Problem or idea
Tested today and reported no downloads in the last 7 days.
> **EngagementBot**
> There were no downloads in the last 7 days.
However there were a few that should have ... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... |
Engagement bot thinks every user is a returning user
### Context
https://alexslemonade.slack.com/archives/CRK42AL1Y/p1587988808265500
### Problem or idea
@dvenprasad says 6 of those are new users. There must be a bug in the queries it uses or something.
### Solution or next step
Fix the engagement bot so... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... |
Store locations from where our users download data
### Context
https://github.com/AlexsLemonade/refinebio/pull/2216#discussion_r401233850
### Problem or idea
Our engagement bot only stores IPs from the users, but we are also interested in their locations which can change over the years.
### Solution or next... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from django.conf import settings
from django.core.management.base import BaseCommand
from django.utils import timezone
import requests
from data_refinery_common.models import DatasetAnnotation
class Command(BaseComman... |
There are two Illumina HiSeq 2000 platforms
<img width="259" alt="Screen_Shot_2020-05-05_at_3_37_37_PM" src="https://user-images.githubusercontent.com/15315514/81108350-93b5aa00-8ee6-11ea-98b1-8c572d59cb4d.png">
Are they the same thing? It's confusing.
| common/data_refinery_common/migrations/0057_fix_platform_accessions_spaces.py
<|code_start|><|code_end|>
| common/data_refinery_common/migrations/0057_fix_platform_accessions_spaces.py
<|code_start|>from django.db import migrations
from django.utils import timezone
from data_refinery_common.utils import get_supported_rnaseq_platforms
def remove_spaces_from_platform_accessions(apps, schema_editor):
Sample = apps.get_m... |
We should be able to detect more than one p-value column in our Illumina pipeline
### Context
#2275
### Problem or idea
It looks like right now we only detect one p-value column for each Illumina sample (under certain conditions), which causes some samples to fail processing.
### Solution or next step
M... | foreman/data_refinery_foreman/foreman/main.py
<|code_start|>import datetime
import random
import socket
import sys
import time
import traceback
from typing import List
from django.conf import settings
from django.db.models.expressions import Q
from django.utils import timezone
import nomad
from nomad import Nomad
fro... | foreman/data_refinery_foreman/foreman/main.py
<|code_start|>import datetime
import random
import socket
import sys
import time
import traceback
from typing import List
from django.conf import settings
from django.db.models.expressions import Q
from django.utils import timezone
import nomad
from nomad import Nomad
fro... |
Validate that samples added to the dataset are downloadable
### Context
We allow datasets like [this](https://www.refine.bio/dataset/98e449b3-b485-4786-8529-79dc50e4cd5b) to be created.
### Problem or idea
This dataset has *at least one experiment* and it also has *at least one sample per experiment*, but it s... | api/data_refinery_api/serializers.py
<|code_start|>from collections import defaultdict
from django.db.models import Count, Q
from rest_framework import serializers
import boto3
from django_elasticsearch_dsl_drf.serializers import DocumentSerializer
from data_refinery_common.models import (
APIToken,
Compendi... | api/data_refinery_api/serializers.py
<|code_start|>from collections import defaultdict
from django.db.models import Count, Q
from rest_framework import serializers
import boto3
from django_elasticsearch_dsl_drf.serializers import DocumentSerializer
from data_refinery_common.models import (
APIToken,
Compendi... |
Make the dataset API simpler to use
### Context
Pairing with @kurtwheeler on the email validation code for the dataset endpoint this morning
### Problem or idea
@kurtwheeler pointed out that there is no good reason why we have to start the datset using a PUT request, except that is how we do it on the frontend... | api/data_refinery_api/urls.py
<|code_start|>from django.conf import settings
from django.conf.urls import url
from django.contrib import admin
from django.urls import include, path
from django.views.generic import RedirectView
from rest_framework import permissions
from drf_yasg import openapi
from drf_yasg.views impo... | api/data_refinery_api/urls.py
<|code_start|>from django.conf import settings
from django.conf.urls import url
from django.contrib import admin
from django.urls import include, path
from django.views.generic import RedirectView
from rest_framework import permissions
from drf_yasg import openapi
from drf_yasg.views impo... |
Make the response for non-downloadable samples more programmer-friendly
### Context
Right now the message is a string with an error message and accession codes inside of it.
### Problem or idea
We don't want users to have to parse the error message to get the accessions they need to remove from their dataset.
### S... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains CreateDatasetView and DatasetView
##
from collections import defaultdict
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import filters, generics, serializers
from drf_yasg impor... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains CreateDatasetView and DatasetView
##
from collections import defaultdict
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import filters, generics, serializers
from drf_yasg impor... |
Make the token endpoint more programmer-friendly
### Context
I was writing up an example of how to create a dataset using the API
### Problem or idea
Just like it should only take one request to create a dataset if you have everything ready, I don't see a good reason why we need two requests to create an API t... | api/data_refinery_api/urls.py
<|code_start|>from re import match
from django.conf import settings
from django.conf.urls import url
from django.contrib import admin
from django.http import JsonResponse
from django.urls import include, path
from django.views.generic import RedirectView
from rest_framework import permiss... | api/data_refinery_api/urls.py
<|code_start|>from re import match
from django.conf import settings
from django.conf.urls import url
from django.contrib import admin
from django.http import JsonResponse
from django.urls import include, path
from django.views.generic import RedirectView
from rest_framework import permiss... |
Dataset validation seems to be broken.
### Context
I saw a couple slackbot messages about no smashable files.1
### Problem or idea
Dataset ids:
* a71c681e-7dab-4d99-93c7-c43382ef0c72
* 1fd5bca4-c322-4433-ac65-d5d8f616d679
I only looked into 1fd5bca4-c322-4433-ac65-d5d8f616d679 but it had no email address ... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains DatasetView
##
from collections import defaultdict
from django.core.exceptions import ValidationError
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import mixins, serializers, v... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains DatasetView
##
from collections import defaultdict
from django.core.exceptions import ValidationError
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import filters, generics, mix... |
Find a way to assign volume IDs to instances without EBS
### Context
https://github.com/AlexsLemonade/refinebio/issues/2254
### Problem or idea
We stopped creating EBS volumes now that we do all of the processing on the SSDs, but now we can only run one instance at once because instances are always assigned vo... | common/data_refinery_common/migrations/0059_auto_20200803_1719.py
<|code_start|><|code_end|>
common/data_refinery_common/models/jobs/downloader_job.py
<|code_start|>from typing import Set
from django.db import models
from django.utils import timezone
from nomad import Nomad
from data_refinery_common.models.jobs.job_... | common/data_refinery_common/migrations/0059_auto_20200803_1719.py
<|code_start|># Generated by Django 2.2.13 on 2020-08-03 17:19
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("data_refinery_common", "0058_auto_20200625_1402"),
]
operations = [... |
Don't fail when detecting column header for illumina sample
### Context
We have `4287` samples that failed because we weren't able to find an id column in their headers. For example for sample [GSM2677584](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2677584) we failed with the error:
`Could not find any... | foreman/data_refinery_foreman/surveyor/geo.py
<|code_start|>import shutil
from re import sub
from typing import Dict, List
import dateutil.parser
import GEOparse
from data_refinery_common.enums import Downloaders
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_common.models import... | foreman/data_refinery_foreman/surveyor/geo.py
<|code_start|>import shutil
from re import sub
from typing import Dict, List
import dateutil.parser
import GEOparse
from data_refinery_common.enums import Downloaders
from data_refinery_common.logging import get_and_configure_logger
from data_refinery_common.models import... |
`/search/` responses contain incorrect information
### Context
I found what was causing https://github.com/AlexsLemonade/refinebio-frontend/issues/955
### Problem or idea
Sometimes results returned from `/search/` contain incorrect information, which causes incorrect information like `No Species` to be display... | api/data_refinery_api/views/experiment_document.py
<|code_start|>##
# Experiment document views
##
from django.http import QueryDict
from django.utils.decorators import method_decorator
from rest_framework import serializers
from rest_framework.renderers import BrowsableAPIRenderer, JSONRenderer
from django_elasticse... | api/data_refinery_api/views/experiment_document.py
<|code_start|>##
# Experiment document views
##
from django.http import QueryDict
from django.utils.decorators import method_decorator
from rest_framework import serializers
from rest_framework.renderers import BrowsableAPIRenderer, JSONRenderer
from django_elasticse... |
Intialize automatic_survey.py command
### Context
In the foreman as a sibling next to other accession surveying commands (ie feed_the_beast) we should add a new command called `automatic_survey.py`. This command will be run via cron job should be executed daily.
This management command should:
- Determine how many s... | foreman/data_refinery_foreman/foreman/management/commands/automatic_survey.py
<|code_start|><|code_end|>
foreman/data_refinery_foreman/gatherer/agents/base.py
<|code_start|>"""Abstract base class for accession gathering automation agents."""
from abc import ABC, abstractmethod
from datetime import datetime
from http.c... | foreman/data_refinery_foreman/foreman/management/commands/automatic_survey.py
<|code_start|>"""
Automatic survey command.
"""
from django.core.management.base import BaseCommand
from django.template.defaultfilters import pluralize
from django.utils import timezone
from dateutil.relativedelta import relativedelta
fro... |
Add indices to new models for automatic accession gathering
### Context
We want to start adding indices to new models that we create.
### Problem or idea
_The context should lead to something, an idea or a problem that you’re facing. Put that here._
### Solution or next step
_You can tag others or simply leave i... | common/data_refinery_common/migrations/0072_auto_20220927_2235.py
<|code_start|><|code_end|>
common/data_refinery_common/models/gathered_accession.py
<|code_start|>from datetime import datetime
from django.db import models
from django.utils import timezone
class GatheredAccession(models.Model):
"""Gathered acces... | common/data_refinery_common/migrations/0072_auto_20220927_2235.py
<|code_start|># Generated by Django 3.2.7 on 2022-09-27 22:35
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("data_refinery_common", "0071_gatheredaccession"),
]
operations = [
... |
Duplicate Sample Accessions Breaks Dataset State
### Context
@jashapiro was adding some samples to a dataset recently when he noticed on the client side he was no longer able to modify his dataset. After some investigation I noticed that the issue occurred when samples with the same accessions codes are present in m... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains DatasetView
##
from collections import defaultdict
from django.core.exceptions import ValidationError
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import mixins, serializers, v... | api/data_refinery_api/views/dataset.py
<|code_start|>##
# Contains DatasetView
##
from collections import defaultdict
from django.core.exceptions import ValidationError
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from rest_framework import mixins, serializers, v... |
Cache Docker Images by Branch
### Context
We want to be able to cache docker image layers that are created locally as testing artfacts locally to be used by github actions.
The current prepare_images.sh does this but there was an issue with the definition for branch_name.
We also don't want to remove support non-c... | common/setup.py
<|code_start|>import os
from setuptools import find_packages, setup
# allow setup.py to be run from any path
os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
VERSION_FILE = "version"
try:
with open(VERSION_FILE, "rt") as version_file:
version_string = version... | common/setup.py
<|code_start|>import os
import re
from datetime import datetime
from setuptools import find_packages, setup
# allow setup.py to be run from any path
os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
VERSION_FILE = "version"
try:
with open(VERSION_FILE, "rt") as versio... |
Rename 'Refine.bio Mail Robot' to something descriptive
### Context
'Refine.bio Mail Robot' isn't super descriptive of what we use that email for. We use it to provide information about the datasets - processed or failed and the name should reflect that.
Also am a little concerned of the word robot getting it fla... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import logging
import os
import shutil
import time
from datetime import timedelta
from pathlib import Path
from typing import Dict, List
from urllib.parse import quote
from django.conf import settings
from django.utils import ti... | workers/data_refinery_workers/processors/smasher.py
<|code_start|># -*- coding: utf-8 -*-
import logging
import os
import shutil
import time
from datetime import timedelta
from pathlib import Path
from typing import Dict, List
from urllib.parse import quote
from django.conf import settings
from django.utils import ti... |
Clean up AWS Batch job definition list
### Problem or idea
The Batch job definition section contains 100+ pages of jobs (~2500 items). They haven't been cleaned up properly during deploy process for a while.
### Solution or next step
Clean up stale items, make sure job deregistering script takes care of old ... | infrastructure/delete_batch_job_queue.py
<|code_start|>import os
from time import sleep
import boto3
AWS_REGION = os.environ["AWS_REGION"]
AWS_BATCH_QUEUE_ALL_NAMES = os.environ["REFINEBIO_JOB_QUEUE_ALL_NAMES"].split(",")
batch = boto3.client("batch", region_name=AWS_REGION)
# First disable each job queue.
for batc... | infrastructure/delete_batch_job_queue.py
<|code_start|>import os
from time import sleep
import boto3
from botocore.exceptions import ClientError
AWS_BATCH_QUEUE_ALL_NAMES = os.environ["REFINEBIO_JOB_QUEUE_ALL_NAMES"].split(",")
batch = boto3.client("batch", region_name=os.environ["AWS_REGION"])
# First disable each... |
Weekly stats shows 0 downloads for some users
### Context
A lot of changes has gone into prod recently. One of them is the EngagementBot weekly stats updates.
### Problem or idea
The most recent summary contains lines like "0 downloads from " indicating some (potential) stats inaccuracy.
### Solution or nex... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from collections import Counter
from django.conf import settings
from django.core.management.base import BaseCommand
from django.template.defaultfilters import pluralize
from django.utils import timezone
import requests
... | api/data_refinery_api/management/commands/post_downloads_summary.py
<|code_start|>import datetime
from collections import Counter
from django.conf import settings
from django.core.management.base import BaseCommand
from django.template.defaultfilters import pluralize
from django.utils import timezone
import requests
... |
Support filtering on status in EPR
couldnt really find a nice place in WMS metadata spec to document the supported values for custom query parameters so i crammed it into the wms abstract...
| gen_ziektenplagenexotengroen.py
<|code_start|><|code_end|>
| gen_ziektenplagenexotengroen.py
<|code_start|>#!/usr/bin/env python
# Generates the ziektenplagenexotengroen mapfile.
# TODO rewrite using mappyfile, generalize.
from contextlib import contextmanager
indent: int = 0
def p(*strs: list[str]):
print(" " * indent, end="")
print(strs[0], end="")
if len(str... |
SPF support could be confusing
I note that the SPF RR type was discontinued in RFC 7208 (see https://tools.ietf.org/html/rfc7208#section-3.1). I tried searching for my own SPF records with the SPF type, but of course they were not found (they do show up as TXT records, which they are). This could lead to confusion as t... | lexicon/__main__.py
<|code_start|>#!/usr/bin/env python
import argparse
import os
import importlib
import sys
from client import Client
import pkg_resources
#based off https://docs.python.org/2/howto/argparse.html
def BaseProviderParser():
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument("... | lexicon/__main__.py
<|code_start|>#!/usr/bin/env python
import argparse
import os
import importlib
import sys
from client import Client
import pkg_resources
#based off https://docs.python.org/2/howto/argparse.html
def BaseProviderParser():
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument("... |
DNSPod Provider
DNSPod is one of the biggest DNS provider in China.
Here I wrote a DNSPod adapter.
and, I found lexicon can't work now. I did some fix in parsing environment variables.
notice, there is a --auth-id that not "standardize".
DNSPod API auth with an id and Token. this id is given one per token, it's not l... | lexicon/providers/dnspod.py
<|code_start|><|code_end|>
| lexicon/providers/dnspod.py
<|code_start|># -*- coding: utf-8 -*-
from base import Provider as BaseProvider
import requests
import json
def ProviderParser(subparser):
subparser.add_argument("--auth-username", help="specify api id used to authenticate")
subparser.add_argument("--auth-token", help="specify token... |
Case should be ignored when filtering records from digitalocean API
I noticed that digitalocean's HTTP API always returns `data` field of TXT records in lowercase, see [example](https://gist.github.com/jokester/e1152fd90ace2f71d767af1d96d802dc).
This can cause [lexicon](https://github.com/AnalogJ/lexicon/blob/b278cebf... | lexicon/providers/digitalocean.py
<|code_start|>from base import Provider as BaseProvider
import requests
import json
def ProviderParser(subparser):
subparser.add_argument("--auth-token", help="specify token used authenticate to DNS provider")
class Provider(BaseProvider):
def __init__(self, options, provide... | lexicon/providers/digitalocean.py
<|code_start|>from base import Provider as BaseProvider
import requests
import json
def ProviderParser(subparser):
subparser.add_argument("--auth-token", help="specify token used authenticate to DNS provider")
class Provider(BaseProvider):
def __init__(self, options, provide... |
CloudXNS Support
yet another big DNS service in China.
| lexicon/providers/cloudxns.py
<|code_start|><|code_end|>
| lexicon/providers/cloudxns.py
<|code_start|># -*- coding: utf-8 -*-
from base import Provider as BaseProvider
import requests
import json
import time
import hashlib
import urllib
def ProviderParser(subparser):
subparser.add_argument("--auth-username", help="specify API-KEY used authenticate to DNS provider")
s... |
route53 provider and tests
AWS Route 53 provider for lexicon
Notes:
- haven't (yet?) added any command line args for auth - I always use env vars or credentials files, and the provider uses boto under the hood, so follows the same [credential lookup approach](http://boto3.readthedocs.io/en/latest/guide/configuration.h... | lexicon/providers/route53.py
<|code_start|><|code_end|>
setup.py
<|code_start|>"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a co... | lexicon/providers/route53.py
<|code_start|>"""Provide support to Lexicon for AWS Route 53 DNS changes."""
from base import Provider as BaseProvider
import boto3
import botocore
def ProviderParser(subparser):
"""Specify arguments for AWS Route 53 Lexicon Provider."""
subparser.add_argument("--auth-access-key",... |
Gandi Records not picking up TTL
I'm trying to renew Lets Encrypt Certs using dehydrated, using lexicon to handle DNS modifications on a Gandi domain. New challenge TXT records are being created with a TTL of 3 hours. I have tried setting --ttl manually but they're always created with the default 3 hour TTL:
`lexi... | lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi DNS changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
The Gandi API is different from typical DNS APIs in... | lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi DNS changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
The Gandi API is different from typical DNS APIs in... |
Gandi Records not picking up TTL
I'm trying to renew Lets Encrypt Certs using dehydrated, using lexicon to handle DNS modifications on a Gandi domain. New challenge TXT records are being created with a TTL of 3 hours. I have tried setting --ttl manually but they're always created with the default 3 hour TTL:
`lexi... | lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi DNS changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
The Gandi API is different from typical DNS APIs in... | lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi DNS changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
The Gandi API is different from typical DNS APIs in... |
Yandex PDD provider
Hi
I create support Yandex PDD as a DNS provider.
But, I skip test because I haven't ideas to implementation it.
@AnalogJ please merge if it possible.
| lexicon/providers/yandex.py
<|code_start|><|code_end|>
| lexicon/providers/yandex.py
<|code_start|>from __future__ import print_function
from __future__ import absolute_import
from .base import Provider as BaseProvider
import requests
import json
__author__ = 'Aliaksandr Kharkevich'
__license__ = 'MIT'
__contact__ = 'https://github.com/kharkevich'
def ProviderParser(subpars... |
change transip provider to use transip-api
I noticed the transip provider was gone, and that there was a [new project](https://github.com/benkonrath/transip-api) providing a transip api.
I'm not sure how to specify the dependency from github, might be useful to put transip-api on pypi. Otherwise, command line usage ... | lexicon/providers/transip.py
<|code_start|><|code_end|>
setup.py
<|code_start|>"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a co... | lexicon/providers/transip.py
<|code_start|>from __future__ import print_function
from __future__ import absolute_import
from .base import Provider as BaseProvider
try:
from transip.service.dns import DnsEntry
from transip.service.domain import DomainService
except ImportError:
pass
def ProviderParser(sub... |
function update_record() in namesilo.py has wrong query parameter
origin: data['rdata'] = content
modified: data['rrvalue'] = content
| lexicon/providers/namesilo.py
<|code_start|>from __future__ import print_function
from __future__ import absolute_import
from .base import Provider as BaseProvider
import requests
from xml.etree import ElementTree
def ProviderParser(subparser):
subparser.add_argument("--auth-token", help="specify key used authenti... | lexicon/providers/namesilo.py
<|code_start|>from __future__ import print_function
from __future__ import absolute_import
from .base import Provider as BaseProvider
import requests
from xml.etree import ElementTree
def ProviderParser(subparser):
subparser.add_argument("--auth-token", help="specify key used authenti... |
unable to install transip dependencies or use transip plugin
Output: pip install dns-lexicon[transip]
```
Requirement already satisfied: dns-lexicon[transip] in ./lib/python2.7/site-packages
Requirement already satisfied: requests in ./lib/python2.7/site-packages (from dns-lexicon[transip])
Requirement already sati... | setup.py
<|code_start|>"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import... | setup.py
<|code_start|>"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import... |
Fix logging TypeError (digitalocean.py)
[This same issue](https://github.com/AnalogJ/lexicon/pull/128/commits/903af58378ab9942d817c57e0330b5f7ac26b4e9) exists in `lexicon/providers/digitalocean.py` line 111. The same edit is needed to fix it.
The error generated is:
```
Traceback (most recent call last):
File ... | lexicon/providers/digitalocean.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import json
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
subparser.add_argument("--auth-... | lexicon/providers/digitalocean.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import json
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
subparser.add_argument("--auth-... |
Route53: Public and Private Zones can't be distinguished.
I've been testing out lexicon for updating DNS records via Route53, and I have a Public and Private Zone with the same domain name.
I noticed that lexicon is only searching for the domain name by name, so in my case, my internal zone was the first created and s... | lexicon/providers/route53.py
<|code_start|>"""Provide support to Lexicon for AWS Route 53 DNS changes."""
from __future__ import absolute_import
from __future__ import print_function
import logging
from .base import Provider as BaseProvider
try:
import boto3 #optional dep
import botocore #optional dep
except... | lexicon/providers/route53.py
<|code_start|>"""Provide support to Lexicon for AWS Route 53 DNS changes."""
from __future__ import absolute_import
from __future__ import print_function
import logging
from .base import Provider as BaseProvider
try:
import boto3 #optional dep
import botocore #optional dep
except... |
Namecheap support not optional
Unlike route53 or softlayer and unlike what setup.py suggests, the namecheap provider is not optional in 2.1.17.
| lexicon/providers/namecheap.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import logging
import namecheap
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
subparser.add_argument(
'--auth-token... | lexicon/providers/namecheap.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import logging
from .base import Provider as BaseProvider
try:
import namecheap #optional dep
except ImportError:
pass
logger = logging.getLogger(__name__)
def ProviderParser(subparse... |
Support multiple records of the same type on an identifier
In [certbot](https://github.com/certbot/certbot), we use lexicon to create TXT records for a domain to prove to a SSL/TLS certificate authority that the user has control over that domain so the CA will give you a certificate which you can use to set up HTTPS. D... | lexicon/providers/onapp.py
<|code_start|><|code_end|>
| lexicon/providers/onapp.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import json
import logging
import requests
from requests.auth import HTTPBasicAuth
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
... |
Return value for list?
I very well might be looking at this wrong, but it appears that out of the box the "executable" that gets installed for linux can't actually get the list results as a return variable, only as a stdout debug message?
| lexicon/__main__.py
<|code_start|>#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import print_function
import argparse
import importlib
import logging
import os
import sys
import pkg_resources
from .client import Client
#based off https://docs.python.org/2/howto/argparse.html
logger =... | lexicon/__main__.py
<|code_start|>#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import print_function
import argparse
import importlib
import logging
import os
import sys
import json
import pkg_resources
from .client import Client
#based off https://docs.python.org/2/howto/argparse.ht... |
[Regression on #PR-203] CloudNS authentication broken when `auth-id` supplied
Provider CloudNS fails to authenticate when using auth-id for authentication, rather than auth-subid or auth-subuser.
Line 146 in lexicon/providers/cloudns.py reads `if self.is_given_option(self.options['auth_id']):`. It should instead sh... | lexicon/providers/cloudns.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
identity_group = subparser.add_mutually_exclusive... | lexicon/providers/cloudns.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
identity_group = subparser.add_mutually_exclusive... |
api change of online.net broke lexicon plugin
Hi,
Blame them ! i'm working on it...
| lexicon/providers/online.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import json
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
subparser.add_argument("--auth-token"... | lexicon/providers/online.py
<|code_start|>from __future__ import absolute_import
from __future__ import print_function
import json
import logging
import requests
from .base import Provider as BaseProvider
logger = logging.getLogger(__name__)
def ProviderParser(subparser):
subparser.add_argument("--auth-token"... |
test_hetzner tests mostly fail (without internet access?)
When running builds of packages for openSUSE, we have all builds in the isolated environment without a network connection. Perhaps it is the reason, why most ``test_hetzner`` tests fail (all other pass).
```
[ 6s] + py.test3 tests -v -k test_hetzner
[ 6... | lexicon/providers/hetzner.py
<|code_start|>from __future__ import absolute_import
from __future__ import unicode_literals
from contextlib import contextmanager
import hashlib
import logging
import re
import time
import requests
from six import string_types
from urllib3.util.retry import Retry
# Due to optional requir... | lexicon/providers/hetzner.py
<|code_start|>from __future__ import absolute_import
from __future__ import unicode_literals
from contextlib import contextmanager
import hashlib
import logging
import re
import time
import requests
from six import string_types
from urllib3.util.retry import Retry
# Due to optional requir... |
Memset provider: TypeError: string indices must be integers
Hi,
When using the Memset provider with the default table formatting I get this error:
```bash
$ lexicon memset create example.com TXT --name _acme-challenge.example.com --content BLAH --ttl 300
Traceback (most recent call last):
File "/usr/local/bi... | lexicon/cli.py
<|code_start|>#!/usr/bin/env python
"""Module for Lexicon command-line interface"""
from __future__ import absolute_import, print_function
import json
import logging
import os
import sys
from lexicon.client import Client
from lexicon.config import ConfigResolver
from lexicon.parser import generate_cli_m... | lexicon/cli.py
<|code_start|>#!/usr/bin/env python
"""Module for Lexicon command-line interface"""
from __future__ import absolute_import, print_function
import json
import logging
import os
import sys
from lexicon.client import Client
from lexicon.config import ConfigResolver
from lexicon.parser import generate_cli_m... |
Add Hover Provider
Opening issue just to say I'm working on adding Hover to lexicon. I'm working on my fork here: https://github.com/bkanuka/lexicon
I'm working on the tests/recordings and then I'll open a PR
| lexicon/providers/hover.py
<|code_start|><|code_end|>
| lexicon/providers/hover.py
<|code_start|>"""Module provider for Hover"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['hover.com']
def provider_parser(subpars... |
Rackspace provider not getting token from the identity API
_Update: solved! See my comment below._
I'm just starting out with lexicon and trying to get it working with Rackspace Cloud DNS. Requests are failing with a `requests.exceptions.HTTPError: 401 Client Error: Resource not found for validate token request` err... | lexicon/providers/rackspace.py
<|code_start|>"""Rackspace provider implementation"""
from __future__ import absolute_import
import json
import logging
import time
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['rackspacecloud.co... | lexicon/providers/rackspace.py
<|code_start|>"""Rackspace provider implementation"""
from __future__ import absolute_import
import json
import logging
import time
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['rackspacecloud.co... |
DNSimple crash with team member that does not have a plan
Here's the error I get (I have redacted my account number, domain and auth token)
```sh
$ lexicon dnsimple --auth-token REDACTED list REDACTED A
Traceback (most recent call last):
File "/usr/local/bin/lexicon", line 11, in <module>
sys.exit(main())
... | lexicon/providers/dnsimple.py
<|code_start|>"""Module provider for DNS Simple"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['dnsimple.com']
def provider_par... | lexicon/providers/dnsimple.py
<|code_start|>"""Module provider for DNS Simple"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['dnsimple.com']
def provider_par... |
PowerDNS dot notation
From PowerDNS 4.2 onwards, undotted notation is not supported.
From PowerDNS >=4.0 but <=4.1 the dotted notation is _optional_.
I suggest we implement the dotted notation _by default_ since that will work with both dotted and undotted versions.
We could have a flag to turn this behavior fo... | lexicon/providers/powerdns.py
<|code_start|>"""
Lexicon PowerDNS Provider
Author: Will Hughes, 2017
API Docs: https://doc.powerdns.com/md/httpapi/api_spec/
Implementation notes:
* The PowerDNS API does not assign a unique identifier to each record in the way
that Lexicon expects. We work around this by creating an I... | lexicon/providers/powerdns.py
<|code_start|>"""
Lexicon PowerDNS Provider
Author: Will Hughes, 2017
API Docs: https://doc.powerdns.com/md/httpapi/api_spec/
Implementation notes:
* The PowerDNS API does not assign a unique identifier to each record in the way
that Lexicon expects. We work around this by creating an I... |
gandi: updating deletes all record of same rtype
When using Gandi provider, if you update a specific record with a specific type, all records with a matching name will be deleted.
The if-condition handling the case is not correct.
| lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi LiveDNS and Gandi XMLRPC changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
Gandi introduced the LiveDNS A... | lexicon/providers/gandi.py
<|code_start|>"""Provide support to Lexicon for Gandi LiveDNS and Gandi XMLRPC changes.
Lexicon provides a common interface for querying and managing DNS services
through those services' APIs. This module implements the Lexicon interface
against the Gandi API.
Gandi introduced the LiveDNS A... |
DNS Made Easy needs retry logic, to recover from rate limiting errors
Originally certbot/certbot#7411.
DNS Made Easy has [restrictive rate limits](https://api-docs.dnsmadeeasy.com/?version=latest#f6f3c489-422d-4cf0-bccb-1933e6d655ac):
>To prevent unwanted flooding of the API system, there is a maximum number of req... | lexicon/providers/dnsmadeeasy.py
<|code_start|>"""Module provider for DNSMadeEasy"""
from __future__ import absolute_import
import hmac
import json
import logging
from builtins import bytes
from email.utils import formatdate
from hashlib import sha1
import requests
from lexicon.providers.base import Provider as BasePr... | lexicon/providers/dnsmadeeasy.py
<|code_start|>"""Module provider for DNSMadeEasy"""
from __future__ import absolute_import
import hmac
import json
import logging
from builtins import bytes
from email.utils import formatdate
from hashlib import sha1
from urllib3.util.retry import Retry
import requests
from requests.ad... |
LuaDNS _list_records fails due to missing "id" in API response
I'm using certbot with the luadns plugin which in turn uses lexicon.
I've been experiencing the error reported here: https://community.letsencrypt.org/t/luadns-renew-error/89634
```
2019-08-29 06:32:43,517:DEBUG:urllib3.connectionpool:https://api.luadn... | lexicon/providers/luadns.py
<|code_start|>"""Module provider for luadns"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['luadns.com']
def provider_parser(subp... | lexicon/providers/luadns.py
<|code_start|>"""Module provider for luadns"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['luadns.com']
def provider_parser(subp... |
Easyname provider is broken
Currently, easyname support is not working as the easyname website changed. There is a pull request with a working fix though: #449
I am in the process of getting things to work so it can be merged, but in the meantime you can just apply the 2 linechanges so you can use lexicon with eas... | lexicon/providers/easyname.py
<|code_start|>"""Module provider for Easyname DNS"""
from __future__ import absolute_import, print_function
import logging
from requests import Response, Session
# Handling optional dependency for this provider
try:
from bs4 import BeautifulSoup, Tag
except ImportError:
pass
fro... | lexicon/providers/easyname.py
<|code_start|>"""Module provider for Easyname DNS"""
from __future__ import absolute_import, print_function
import logging
from requests import Response, Session
# Handling optional dependency for this provider
try:
from bs4 import BeautifulSoup, Tag
except ImportError:
pass
fro... |
TLDExtract Private Domains for Dynamic DNS Providers
Hello all,
I'm currently putting together the plugin for dynu.com (listed in NYI proiders).
As Dynu also acts as Dynamic DNS provider with several toplevel domains as base for the dynamic domain (`yourhost.dynu.net`, `yourhost.freeddns.org`..., also, wildcards), ... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
from __future__ import absolute_import
import importlib
import tldextract
from lexicon import discovery
from lexicon.config import (
ConfigResolver, DictConfigSource,
legacy_config_resolver, n... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
from __future__ import absolute_import
import importlib
import os
import tldextract
from lexicon import discovery
from lexicon.config import (
ConfigResolver, DictConfigSource,
legacy_config_r... |
GoDaddy provider should recognize domaincontrol.com as its nameserver
For the auto provider, it should recognize that domains managed by GoDaddy often have nameservers under the *.domaincontrol.com namespace. You can verify this is GoDaddy via whois; and I also tested this by adding 'domaincontrol.com' to the recogniz... | lexicon/providers/godaddy.py
<|code_start|>"""Module provider for Godaddy"""
from __future__ import absolute_import
import hashlib
import json
import logging
import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry
from lexicon.providers.base import Provider as BaseProvider
LOG... | lexicon/providers/godaddy.py
<|code_start|>"""Module provider for Godaddy"""
from __future__ import absolute_import
import hashlib
import json
import logging
import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry
from lexicon.providers.base import Provider as BaseProvider
LOG... |
Provider Hetzner KonsoleH is broken
When using the latest version of lexicon, i.e.
```
$ lexicon --version
lexicon 3.3.11
```
there is a problem parsing the website:
```
$ lexicon hetzner create evk.services TXT --log_level DEBUG --name "_foo.foo2" --content "foo2"
Arguments: Namespace(action='create', au... | lexicon/providers/hetzner.py
<|code_start|>"""Module provider for Hetzner"""
from __future__ import absolute_import
from __future__ import unicode_literals
from contextlib import contextmanager
import hashlib
import logging
import re
import time
import requests
from six import string_types
from urllib3.util.retry impo... | lexicon/providers/hetzner.py
<|code_start|>"""Module provider for Hetzner"""
from __future__ import absolute_import
from __future__ import unicode_literals
from contextlib import contextmanager
import hashlib
import logging
import re
import time
import requests
from six import string_types
from urllib3.util.retry impo... |
Cloudflare provider only lists first DNS 100 entries for domain
How to reproduce:
* Have a CloudFlare domain with > 100 entries
* Create a new entry starting with a "high" letter, e.g. `zzzz.<domain>`
* List entries: only the first 100 entries will be returned, making it appear as though `zzzz` had not been create... | lexicon/providers/cloudflare.py
<|code_start|>"""Module provider for Cloudflare"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['cloudflare.com']
def provider... | lexicon/providers/cloudflare.py
<|code_start|>"""Module provider for Cloudflare"""
from __future__ import absolute_import
import json
import logging
import requests
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ['cloudflare.com']
def provider... |
Easyname not working anymore
Lexicon version: 3.3.27
I can't access anything on easyname right now:
```
Traceback (most recent call last):
File "/usr/local/bin/lexicon", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/dist-packages/lexicon/cli.py", line 117, in main
results = c... | lexicon/providers/easyname.py
<|code_start|>"""Module provider for Easyname DNS"""
from __future__ import absolute_import, print_function
import logging
from requests import Response, Session
# Handling optional dependency for this provider
try:
from bs4 import BeautifulSoup, Tag
except ImportError:
pass
fro... | lexicon/providers/easyname.py
<|code_start|>"""Module provider for Easyname DNS"""
from __future__ import absolute_import, print_function
import logging
from requests import Response, Session
# Handling optional dependency for this provider
try:
from bs4 import BeautifulSoup, Tag
except ImportError:
pass
fro... |
Route53 provider does not handle >100 hosted zones
Hello,
I ran into an interesting problem while setting up a system with certbot + lexicon. We have almost 200 hosted zones in AWS Route 53 and we were getting a "No domains found." error which I finally traced to the _authenticate method. I hacked together some chan... | lexicon/providers/route53.py
<|code_start|>"""Provide support to Lexicon for AWS Route 53 DNS changes."""
from __future__ import absolute_import
import hashlib
import logging
import re
from lexicon.providers.base import Provider as BaseProvider
try:
import boto3 # optional dep
import botocore # optional de... | lexicon/providers/route53.py
<|code_start|>"""Provide support to Lexicon for AWS Route 53 DNS changes."""
from __future__ import absolute_import
import hashlib
import logging
import re
from lexicon.providers.base import Provider as BaseProvider
try:
import boto3 # optional dep
import botocore # optional de... |
Plesk provider assumes `site_name` equals `domain` (which is not always true)
The plesk provider assumes that the `site_name` is always the same as the `domain`: https://github.com/AnalogJ/lexicon/blob/master/lexicon/providers/plesk.py#L52
That creates problems if one wants to create a record for a subdomain (e.g. `... | lexicon/providers/plesk.py
<|code_start|>"""
Lexicon Plesk Provider
Author: Jens Reimann, 2018
API Docs: https://docs.plesk.com/en-US/onyx/api-rpc
"""
import logging
from collections import defaultdict
from typing import Dict, List, Optional
from xml.etree import cElementTree
from xml.etree.ElementTree import Element... | lexicon/providers/plesk.py
<|code_start|>"""
Lexicon Plesk Provider
Author: Jens Reimann, 2018
API Docs: https://docs.plesk.com/en-US/onyx/api-rpc
"""
import logging
from collections import defaultdict
from typing import Dict, List, Optional
from xml.etree import cElementTree
from xml.etree.ElementTree import Element... |
Dreamhost integration will break November 2nd, 2021
It looks like Dreamhost is "retiring" some of it's API calls Nov 2nd, including `domain-list_domains` which Lexicon seems to use for validating the domain during initial auth:
https://help.dreamhost.com/hc/en-us/articles/217555767-Domain-API-commands
https://git... | lexicon/providers/dreamhost.py
<|code_start|>"""Module provider for Dreamhost"""
import base64
import json
import logging
import time
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS... | lexicon/providers/dreamhost.py
<|code_start|>"""Module provider for Dreamhost"""
import base64
import json
import logging
import time
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS... |
Plesk provider not working: invalid request (error code 1014)
The Plesk provider seems to be not working at all:
```
lexicon plesk --log_level DEBUG --auth-username apiuser --auth-password secret --plesk-server "https://plesk-api-host:8443" list mydomain.com A
```
leads to:
```
Arguments: Namespace(delegate... | lexicon/providers/plesk.py
<|code_start|>"""
Lexicon Plesk Provider
Author: Jens Reimann, 2018
API Docs: https://docs.plesk.com/en-US/onyx/api-rpc
"""
import logging
from collections import defaultdict
from typing import Dict, List, Optional
from xml.etree import cElementTree
from xml.etree.ElementTree import Element... | lexicon/providers/plesk.py
<|code_start|>"""
Lexicon Plesk Provider
Author: Jens Reimann, 2018
API Docs: https://docs.plesk.com/en-US/onyx/api-rpc
"""
import logging
from collections import defaultdict
from typing import Dict, List, Optional
from xml.etree import cElementTree
from xml.etree.ElementTree import Element... |
joker: HTTP 414 client error when adding a new record
Hi,
I get a "414 Client error" when trying to add a new record to one of my zones hosted at Joker. Is there an easy fix or is that a limitation of their API?
```
lexicon joker create example.com A --name a --content 127.0.0.1
Traceback (most recent call last... | lexicon/providers/joker.py
<|code_start|>"""Module provider for Joker.com"""
# The Joker.com API is well documented.
# Several specificities compared to classic REST API in other providers:
# - everything is done with GET requests: all parameters (including actual records data
# and authentication data) are passe... | lexicon/providers/joker.py
<|code_start|>"""Module provider for Joker.com"""
# The Joker.com API is well documented.
# Several specificities compared to classic REST API in other providers:
# - everything is done with GET requests: all parameters (including actual records data
# and authentication data) are passe... |
transip provider needs requests>=2.27.0 in dependency spec
The update of the transip provider from #1086 included in 3.9.2 uses `from requests.exceptions import JSONDecodeError` which was first included in requests 2.27.0 but the requirements spec only requires `>=2`:
https://github.com/AnalogJ/lexicon/blob/d8b26bcfff... | lexicon/providers/transip.py
<|code_start|>"""Module provider for TransIP"""
import binascii
import json
import logging
import uuid
from base64 import b64decode, b64encode
from typing import Any, Dict, List, Optional
import requests
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.prim... | lexicon/providers/transip.py
<|code_start|>"""Module provider for TransIP"""
import binascii
import json
import logging
import uuid
from base64 import b64decode, b64encode
from typing import Any, Dict, List, Optional
import requests
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.prim... |
RFE: Replace use of `pkg_resources` with `importlib.metadata`
See discussions:
[astropy/astropy#11091](https://github.com/astropy/astropy/pull/11091)
[pypa/pip#7413](https://github.com/pypa/pip/issues/7413)
```console
[tkloczko@devel-g2v lexicon-3.11.0]$ grep -r pkg_resources
lexicon/discovery.py:import pkg_reso... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
import importlib
import logging
import os
from typing import Dict, List, Optional, Type, Union, cast
import tldextract # type: ignore
from lexicon import config as helper_config
from lexicon import d... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
import importlib
import logging
import os
from typing import Dict, List, Optional, Type, Union, cast
import tldextract # type: ignore
from lexicon import config as helper_config
from lexicon import d... |
Add support for porkbun
https://porkbun.com/
Add support for porkbun
https://porkbun.com/
| lexicon/providers/porkbun.py
<|code_start|><|code_end|>
| lexicon/providers/porkbun.py
<|code_start|>import logging
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
import json
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ["porkbun.com"]
def provider_parser(subparser):
"""Return... |
Bug in create action for glesys provider
When creating an A record with the glesys provider, the full name is added instead of the host name.
```
lexicon_config = {
"provider_name" : "glesys",
"action": "create",
"domain": "somedomain.com",
"type": "A",
"name": "lexicon",
"content": "1... | lexicon/providers/glesys.py
<|code_start|>"""Module provider for Glesys"""
import json
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
NAMESERVER_DOMAINS = ["glesys.com"]
def provider_parser(subparser):
"""Generate a subparser for G... | lexicon/providers/glesys.py
<|code_start|>"""Module provider for Glesys"""
import json
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
NAMESERVER_DOMAINS = ["glesys.com"]
def provider_parser(subparser):
"""Generate a subparser for G... |
DuckDNS.org API support
The DuckDNS.org is a popular Dynamic DNS provider. And it supports the TXT records update which is used for issuing ACME certificates. Here is a sample https://github.com/acmesh-official/acme.sh/blob/master/dnsapi/dns_duckdns.sh
Could you please support it's API?
| lexicon/providers/duckdns.py
<|code_start|><|code_end|>
| lexicon/providers/duckdns.py
<|code_start|>"""\
Module provider for Duck DNS
The Duck DNS public API does not provide the whole set of features
supported by Lexicon: it only has one GET endpoint, "/update", authenticated by
the token which is given when you register with one of the supported
OAuth providers; the API o... |
Misleading error message: ProviderNotAvailableError - This provider (plesk) has required dependencies that are missing. Please install lexicon[plesk] first.
```
(venv) mypc:~/myprojects/dns-lexicon$ pip freeze
certifi==2019.9.11
cffi==1.13.2
chardet==3.0.4
cryptography==2.8
dns-lexicon==3.3.10
future==0.18.2
i... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
import importlib
import logging
import os
from typing import Dict, List, Optional, Type, Union, cast
import tldextract # type: ignore
from lexicon import config as helper_config
from lexicon import d... | lexicon/client.py
<|code_start|>"""Main module of Lexicon. Defines the Client class, that holds all Lexicon logic."""
import importlib
import logging
import os
from typing import Dict, List, Optional, Type, Union, cast
import tldextract # type: ignore
from lexicon import config as helper_config
from lexicon import d... |
Can't use lexicon with pending Cloudflare domains
I cannot use Lexicon with a domain that is `pending` (not `active`) in Cloudflare. It's useful to to be able to manipulate DNS records for `pending` domains before changing nameservers to minimize disruption.
## Context
1. Add a domain (e.g., `example.com`) in Clo... | lexicon/providers/cloudflare.py
<|code_start|>"""Module provider for Cloudflare"""
import json
import logging
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ["cloudflare.com"]
... | lexicon/providers/cloudflare.py
<|code_start|>"""Module provider for Cloudflare"""
import json
import logging
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.providers.base import Provider as BaseProvider
LOGGER = logging.getLogger(__name__)
NAMESERVER_DOMAINS = ["cloudflare.com"]
... |
Hover fails with "HTTPError: 400 Client Error: Bad Request for url"
Example command line with sensitive info replaced by "XXXXX":
lexicon hover --log_level DEBUG --auth-username "XXXXX" --auth-password "XXXXX" list XXXXX TXT
...outputs this:
Arguments: Namespace(delegated=None, config_dir='/root', provider_nam... | src/lexicon/_private/providers/hover.py
<|code_start|>"""Module provider for Hover"""
import json
import logging
from argparse import ArgumentParser
from typing import List
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.interfaces import Provider as BaseProvider
LOGGER = logging.getL... | src/lexicon/_private/providers/hover.py
<|code_start|>"""Module provider for Hover"""
import json
import logging
import re
from argparse import ArgumentParser
from typing import List
import pyotp
import requests
from lexicon.exceptions import AuthenticationError
from lexicon.interfaces import Provider as BaseProvider... |
[Feature]: Input Convert as cmd tool
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Feature
Converting input files from:
1. `json` → `toml` or `yaml`
2. `toml ` → `json ` or `yaml`
3. `yaml ` → `toml` or `toml `
### Possible Solution
_No r... | spectrafit/plugins/__init__.py
<|code_start|><|code_end|>
spectrafit/plugins/converter.py
<|code_start|><|code_end|>
spectrafit/tools.py
<|code_start|>"""Collection of essential tools for running SpectraFit."""
import json
import sys
from pathlib import Path
from typing import Any
from typing import Dict
from typing i... | spectrafit/plugins/__init__.py
<|code_start|>"""Plugins for SpectraFit."""
<|code_end|>
spectrafit/plugins/converter.py
<|code_start|>"""Convert the input and output files to the preferred file format."""
import argparse
import json
from pathlib import Path
from typing import Any
from typing import Dict
import toml
i... |
[Bug]: Correct Export of correlation as `*.csv`
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Behavior
```css
0,energy,energy,"[1.0, 0,...
```
### Expected Behavior
_No response_
### Steps To Reproduce
_No response_
### ⚙️ Environment
```markdown
- OS:
- Pyth... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.1"
<|code_end|>
spectrafit/models.py
<|code_start|>"""Minimization models for curve fitting."""
from collections import defaultdict
from dataclasses import dataclass
from typing import Any
from typing imp... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.2"
<|code_end|>
spectrafit/models.py
<|code_start|>"""Minimization models for curve fitting."""
from collections import defaultdict
from dataclasses import dataclass
from math import log
from math import ... |
[Docs]: Using builtin release drafter
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Information in the Docs
https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
### Anything else?
_No response_
### Code ... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.3"
<|code_end|>
spectrafit/api/models_model.py
<|code_start|>"""Reference model for the API of the models distributions."""
from typing import Callable
from typing import List
from typing import Optiona... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.4"
<|code_end|>
spectrafit/api/models_model.py
<|code_start|>"""Reference model for the API of the models distributions."""
from typing import Callable
from typing import List
from typing import Optiona... |
[Docs]: Using builtin release drafter
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Information in the Docs
https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
### Anything else?
_No response_
### Code ... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.4"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a0"
<|code_end|>
|
[Docs]: Update release drafter
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Information in the Docs
- Link to the complete changes of the latest release.
- Exclude auto commits in the contributor list
### Anything else?
_No response_
### Code of Conduct
... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a0"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a1"
<|code_end|>
|
[Docs]: Using mike for versioning docs
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Information in the Docs
https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/
### Anything else?
_No response_
### Code of Conduct
- [X] I agree to foll... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a2"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a3"
<|code_end|>
|
[Docs]: Update labeled criteria for CHANGELOG
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Information in the Docs
Update the labeler criteria for avoiding double labels in `CHANGELOG.md`
### Anything else?
_No response_
### Code of Conduct
- [X] I agree ... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a7"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0a8"
<|code_end|>
|
[Bug]: ASCII Char in creating branch
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Behavior
Is crashing
### Expected Behavior
Is realising a change in changeling
### Steps To Reproduce
_No response_
### ⚙️ Environment
```markdown
- OS:
- Python:
- spectrafit:
... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0b1"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "1.0.0b2"
<|code_end|>
|
[Feature]: Add python 3.11 support
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Current Missing Feature
Add python 3.11 support
### Possible Solution
_No response_
### Anything else?
_No response_
### Code of Conduct
- [X] I agree to follow this project's Code of Condu... | spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.6"
<|code_end|>
| spectrafit/__init__.py
<|code_start|>"""SpectraFit, fast command line tool for fitting data."""
__version__ = "0.16.7"
<|code_end|>
|
SSL: CERTIFICATE_VERIFY_FAILED
Hi,
I don't know if you got notified about my last comment in the closed issue #81 . I cannot reopen it, so ill try it this way:
Sorry, I hadn't had the time to test it.
I have tested it now with the newest version 3.0.0b5 and HASS 0.64.3
self.get_state() works now without any pr... | appdaemon/plugins/hass/hassapi.py
<|code_start|>import requests
import inspect
import appdaemon.appapi as appapi
import appdaemon.utils as utils
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
#
# Define an entities class as ... | appdaemon/plugins/hass/hassapi.py
<|code_start|>import requests
import inspect
import appdaemon.appapi as appapi
import appdaemon.utils as utils
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
#
# Define an entities class as ... |
Avoid copying states in get_state() if read-only access is needed only
Hi,
I think that deep-copying the whole HA state adds considerable overhead to ``get_state()``, especially when called for a whole domain or even complete HA state.
It turns out that in most cases, you just need read-only access to the states.... | appdaemon/adapi.py
<|code_start|>import datetime
import inspect
import iso8601
import re
from datetime import timedelta
import appdaemon.utils as utils
from appdaemon.appdaemon import AppDaemon
class ADAPI:
#
# Internal
#
def __init__(self, ad: AppDaemon, name, logging_obj, args, config, app_config,... | appdaemon/adapi.py
<|code_start|>import datetime
import inspect
import iso8601
import re
from datetime import timedelta
import appdaemon.utils as utils
from appdaemon.appdaemon import AppDaemon
class ADAPI:
#
# Internal
#
def __init__(self, ad: AppDaemon, name, logging_obj, args, config, app_config,... |
add oneshot to listen_event
I noticed that `listen_state` has `oneshot` which seems very useful. I think it makes sense to implement the same in `listen_event`. What do you guys think?
I might give this a shot if I have time soon.
| appdaemon/adapi.py
<|code_start|>import asyncio
import datetime
import inspect
import iso8601
import re
from datetime import timedelta
from copy import deepcopy
# needed for fake coro cb that looks like scheduler
import uuid
import appdaemon.utils as utils
from appdaemon.appdaemon import AppDaemon
class ADAPI:
... | appdaemon/adapi.py
<|code_start|>import asyncio
import datetime
import inspect
import iso8601
import re
from datetime import timedelta
from copy import deepcopy
# needed for fake coro cb that looks like scheduler
import uuid
import appdaemon.utils as utils
from appdaemon.appdaemon import AppDaemon
class ADAPI:
... |
turn_on service not working with async apps
## What did I do
I bumped into an [issue](https://community.home-assistant.io/t/need-help-with-appdaemon-4-and-async/163937) from the community forum that resulted to be the same problem I had recently. Consider the following simple application:
```python
import appdaemo... | appdaemon/__main__.py
<|code_start|>#!/usr/bin/python3
"""AppDaemon main() module.
AppDaemon module that contains main() along with argument parsing, instantiation of the AppDaemon and HTTP Objects,
also creates the loop and kicks everything off
"""
import sys
import argparse
import os
import os.path
import signal
... | appdaemon/__main__.py
<|code_start|>#!/usr/bin/python3
"""AppDaemon main() module.
AppDaemon module that contains main() along with argument parsing, instantiation of the AppDaemon and HTTP Objects,
also creates the loop and kicks everything off
"""
import argparse
import asyncio
import os
import os.path
import pla... |
TypeError: a bytes-like object is required, not 'str'
When I build and run (`docker build -t appdaemon:dev . && docker run appdaemon:dev`) the `dev` branch, the app exits with errors.
```
2021-02-21 10:25:51.952206 INFO AppDaemon: AppDaemon Version 4.0.6 starting
2021-02-21 10:25:51.953718 INFO AppDaemon: Python v... | appdaemon/http.py
<|code_start|>import asyncio
import json
import os
import re
import time
import traceback
import concurrent.futures
from urllib.parse import urlparse
import feedparser
from aiohttp import web
import ssl
import bcrypt
import uuid
from jinja2 import Environment, FileSystemLoader, select_autoescape
impo... | appdaemon/http.py
<|code_start|>import asyncio
import json
import os
import re
import time
import traceback
import concurrent.futures
from urllib.parse import urlparse
import feedparser
from aiohttp import web
import ssl
import bcrypt
import uuid
from jinja2 import Environment, FileSystemLoader, select_autoescape
impo... |
Rework AD's internal Service calls
Service calls within AD should no longer wait to return results by default
If results are needed, the user will have 2 options
1. Give the `call_service` api a callback to use
2. Set a flag, that it should wait for the result
This will help significantly speedup the core, as r... | appdaemon/adapi.py
<|code_start|>import asyncio
import datetime
import inspect
import iso8601
import re
from datetime import timedelta
from copy import deepcopy
from typing import Any, Optional, Callable
# needed for fake coro cb that looks like scheduler
import uuid
import appdaemon.utils as utils
from appdaemon.app... | appdaemon/adapi.py
<|code_start|>import asyncio
import datetime
import inspect
import iso8601
import re
from datetime import timedelta
from copy import deepcopy
from typing import Any, Optional, Callable
# needed for fake coro cb that looks like scheduler
import uuid
import appdaemon.utils as utils
from appdaemon.app... |
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