Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / GlobalPathogenAnalysisService/gpas-cli issues and pull requests

#114 - PyInstaller builds failing with PyInstaller >= 5.6.2

Issue - State: open - Opened by bede about 2 years ago - 1 comment

#113 - PyInstaller executable built on 22.04 LTS complains about glibc on 20.04 LTS

Issue - State: closed - Opened by bede about 2 years ago - 1 comment
Labels: bug

#111 - Download: --rename and --out-dir are mutually exclusive

Issue - State: closed - Opened by bede about 2 years ago - 1 comment
Labels: bug

#110 - Add relatedness subcommand

Issue - State: open - Opened by bede about 2 years ago
Labels: enhancement

#108 - dot/period char in sample_name causes crash

Issue - State: closed - Opened by bede about 2 years ago - 1 comment

#106 - Version subcommand broken in PyInstaller distribution?

Issue - State: closed - Opened by bede about 2 years ago - 1 comment

#105 - Validation edge cases opened up by arbitrary metadata passthrough feature

Issue - State: closed - Opened by bede about 2 years ago - 1 comment

#104 - Friendly error message when user lacks API permissions

Issue - State: closed - Opened by bede about 2 years ago - 1 comment

#103 - Add (and maintain) a latest tag in Dockerhub

Issue - State: closed - Opened by JezSw about 2 years ago - 1 comment

#102 - Test decontamination using synthetic human reads

Issue - State: closed - Opened by bede about 2 years ago - 1 comment

#101 - EC 1.1.4 with gpas-cli 0.6.0 - Error message "unauthorised for this user" appears for invalid tags

Issue - State: open - Opened by KuzminaAnna about 2 years ago - 1 comment
Labels: blocked

#100 - gpas-cli 0.6.0 - phrasing was changed for some of the error messages

Issue - State: closed - Opened by KuzminaAnna about 2 years ago - 3 comments

#99 - EC 1.1.4 : User is only able to upload samples if tags assigned to user has access flag set to yes

Issue - State: open - Opened by KuzminaAnna about 2 years ago - 1 comment
Labels: blocked

#98 - Make mapping CSV creation more testable

Issue - State: open - Opened by bede over 2 years ago

#97 - Pass through arbitrary fields in upload CSV to the mapping CSV

Issue - State: closed - Opened by bede over 2 years ago - 1 comment
Labels: enhancement

#96 - Eelectron Client : "fastq file does not exist" error message appears, even if fastq exists

Issue - State: open - Opened by KuzminaAnna over 2 years ago - 2 comments
Labels: blocked, cannot reproduce

#94 - EC 1.1.4: Error message is wrong if sample names are empty

Issue - State: closed - Opened by KuzminaAnna over 2 years ago - 2 comments

#93 - Uploading empty sample names produce errors containing "NaN"

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#92 - Exception telemetry

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#91 - Migrate to latest Pandera

Issue - State: open - Opened by bede over 2 years ago - 1 comment

#90 - Retry failed async downloads, verify downloaded file integrity

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#89 - Add new file types available from revised get_output API

Issue - State: open - Opened by bede over 2 years ago

#88 - Enable parallelisation in PyInstaller distribution

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#87 - KeyError given upload csv with mixture of populated and unpopulated run_numbers

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#86 - Integer sample names trigger ValidationError

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#85 - Tags are validated at organisation- rather than user-level

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#84 - Move Docker images to GHCR

Issue - State: open - Opened by bede over 2 years ago

#83 - Log a warning when an httpx.RequestError is raised, caught and retried

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#81 - Support *.fq.gz suffix

Issue - State: open - Opened by bede over 2 years ago - 1 comment

#80 - Docker support

Issue - State: closed - Opened by bede over 2 years ago - 3 comments
Labels: enhancement

#79 - Configurable rate limit for status and download calls

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#78 - Change batches API payload `uploader` key names

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#77 - Gracefully handle users with no tags

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#76 - Sensible handling of empty FASTQs

Issue - State: open - Opened by bede over 2 years ago - 9 comments

#74 - Unify package and PyInstaller CLI

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#73 - When multiple garbage sample names are provided, ValidationError returns auto incremented fictitious sample names

Issue - State: closed - Opened by bede over 2 years ago - 3 comments
Labels: wontfix, low-priority

#72 - Bundle PyInstaller assets with release

Issue - State: open - Opened by bede over 2 years ago - 1 comment

#71 - "Instrument Platform of Nanopore is not being rejected for Illumina Fastq File"

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#69 - Implemented Windows binaries build job.

Pull Request - State: closed - Opened by Oleksandr-Boochnew over 2 years ago - 2 comments

#68 - run numbers are not generated in ascending order

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#67 - Collapse duplicate errors per sample

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#66 - Normalise sorting of ValidationErrors by sample name and error

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#65 - duplicate path in fastq1 and fastq2 does not trigger validation failure

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#64 - Replace calls to requests.get() with httpx.get()

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#63 - Optionally mask dates to week and month level according to user details

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#62 - Test paired bam sorting

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#61 - Test runless and batchless sample metadata

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#60 - Run number discrepencies in submission payload between 0.2.1 and EC 1.0.8

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#59 - Batches submission payload not encoded as UTF-8

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#58 - add functionality to specify GUIDs in a plaintext file for gpas download

Issue - State: open - Opened by philipwfowler over 2 years ago - 1 comment
Labels: enhancement, low-priority

#57 - Validate primer scheme enums

Issue - State: open - Opened by bede over 2 years ago

#56 - Add user agent string to cli-upload interface

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#55 - SubmissionError with country code CYM

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#54 - collection_date error in tip of main

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#53 - Test coverage for negative controls

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#52 - HCELEC-413 error message is not implicit when sample name is null or empty

Issue - State: closed - Opened by KuzminaAnna over 2 years ago - 1 comment

#49 - Automatically delete fastqs from temp dir after successful upload.

Issue - State: closed - Opened by bede over 2 years ago - 4 comments

#48 - Ubuntu 18 support

Issue - State: closed - Opened by bede over 2 years ago - 4 comments

#47 - CI for PyInstaller executables

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#46 - Date validation is broken

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#45 - Windows support

Issue - State: closed - Opened by bede over 2 years ago - 4 comments

#44 - Make use of multiprocessing depend on --processes >= 1, not --json-messages

Issue - State: closed - Opened by bede over 2 years ago - 3 comments

#43 - HCELEC-399 user can not run gpas-cli on Linux 16 or 18 OS

Issue - State: closed - Opened by KuzminaAnna over 2 years ago - 3 comments

#42 - HCELEC-395 metadata district does not allow null value

Issue - State: closed - Opened by KuzminaAnna over 2 years ago - 8 comments

#40 - Notify of newer release on execution

Issue - State: closed - Opened by bede over 2 years ago - 2 comments
Labels: enhancement

#39 - Faster uploads for users with high TCP RTTs to London datacentre

Issue - State: closed - Opened by bede over 2 years ago - 1 comment
Labels: enhancement

#38 - Increase resilience when using poor connections

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#37 - Optional debug to file

Issue - State: open - Opened by bede over 2 years ago
Labels: enhancement

#36 - Reorganise long validation if-else block

Issue - State: open - Opened by bede over 2 years ago

#34 - Problems with Nuitka, Pyinstaller and tqdm progress bars

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#33 - Test samples with insufficient reads after decontamination

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#32 - Document upload CSV field specifications

Issue - State: closed - Opened by bede over 2 years ago

#31 - Allow specification of mapping csv path

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#30 - Allow alternative reasonable fastq suffixes

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#29 - Make upload_csv batch field nullable

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#28 - Tidy up instance variables

Issue - State: closed - Opened by bede over 2 years ago

#25 - Plumb parse_decontamination_stats() back into parallelised decontamination flow

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#24 - High level Python API mimicking CLI

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#22 - Friendlier token error

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#21 - Increase test coverage

Issue - State: closed - Opened by bede over 2 years ago

#15 - Pyinstaller builds

Issue - State: closed - Opened by bede over 2 years ago - 5 comments

#13 - Use dataclass for `Sample`

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#8 - Implement new JSON interface for Electron client

Issue - State: closed - Opened by bede over 2 years ago - 2 comments

#7 - Disable pandera coercion

Issue - State: closed - Opened by bede over 2 years ago - 1 comment
Labels: low-priority

#6 - Release checklist

Issue - State: closed - Opened by bede over 2 years ago - 1 comment

#5 - Record number of reads removed during decontamination

Issue - State: closed - Opened by bede over 2 years ago - 1 comment