Skip to content
This repository was archived by the owner on Jun 17, 2024. It is now read-only.

Releases: GlobalPathogenAnalysisService/gpas-cli

0.8.4

Choose a tag to compare

@bede bede released this 18 Jan 07:33
  • Fixes bug downloading fasta files when specifying both --out-dir and --rename
  • Changes to submission API timeouts and retry intervals
  • Suppress warning about chunksize for batches with >1000 samples

0.8.3

Choose a tag to compare

@bede bede released this 15 Dec 17:41

Fix for crash during decontamination of reads provided in BAM format when sample_name contains dot characters
Full Changelog: 0.8.2...0.8.3

0.8.2

Choose a tag to compare

@bede bede released this 13 Dec 15:41

Makes gpas --version work properly under PyInstaller

0.8.1

Choose a tag to compare

@bede bede released this 13 Dec 13:58
  • Fixes, tests regression where specifying run numbers for some samples in batch caused a submission error (reported by Deepak).
  • Fixes KeyError when validating certain missing mandatory fields, where a clear error message should be generated (reported by Deepak).
  • Use a longer timeout for batches API submission.
  • Allow user to choose number of connections used for parallel file upload (e.g. --connections 10)
  • Default number of upload connections reduced from 10 to 4 for better progress bar feedback on slow connections

Full Changelog: 0.8.0...0.8.1

0.8.0

Choose a tag to compare

@bede bede released this 30 Nov 17:58
  • Arbitrary metadata passthrough. The upload CSV may now contain additional arbitrary metadata columns which are copied into the mapping CSV generated at upload time. These data are never transmitted to GPAS.
  • Changes to backoff and retry strategies for increased resilience during various stages of the upload process.
  • Fixes and tests against a regression in 0.7.0 where JSON messages on stdout were contaminated by a stray print statement.
  • Eliminates autoincremented sample names from validation errors.
  • Fixes a ZeroDivisionError when handling empty FASTQs, accomodating perfect negative controls.
  • Better testing of decontamination.

0.7.1

Choose a tag to compare

@bede bede released this 15 Nov 16:02

Fixes issue where status and download subcommands would retry failed samples indefinitely

0.7.0

Choose a tag to compare

@bede bede released this 14 Nov 20:15
  • Automatic retries for status, download and upload finalisation requests
  • Parallel decontamination and upload now supported in all distribution methods including PyInstaller
  • Fixes various issues with run numbering and added edge case test coverage
  • Error reporting for fatal exceptions during upload
  • Fixes crash when uploading empty fastqs
  • Test improvements

0.6.0

Choose a tag to compare

@bede bede released this 27 Oct 14:12
  • Allow uploading of fastqs with identical checksums
  • Globally enable pandera type coercion, permitting integer sample names
  • Validate user-level tag permissions
  • Better MacOS arm64 instructions
  • Replace submission payload's upload_finish_time with upload_finish
  • Retry higher level RequestErrors for failed uploads
  • Version in PyInstaller artifact name
  • Unified PyInstaller-friendly CLI
  • Joint country-region validation as vectorised sample-level check
  • Update deps
  • Test empty country/region behaviour
  • Docker(Hub) support and detailed install instructions

0.6.0a

0.6.0a Pre-release
Pre-release

Choose a tag to compare

@bede bede released this 06 Oct 16:47
Retry higher level RequestErrors for failed uploads

0.5.1

Choose a tag to compare

@bede bede released this 14 Sep 18:28
  • Tolerate singleton reads in paired Illumina BAMs