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GlobalPathogenAnalysisService
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gpas-cli
The CLI client for GPAS SC2
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gpas auth subcommand to allow windowed IDCS login and token retrieval without accessing GPAS portal
#115
bede
opened
1 year ago
0
PyInstaller builds failing with PyInstaller >= 5.6.2
#114
bede
opened
1 year ago
1
PyInstaller executable built on 22.04 LTS complains about glibc on 20.04 LTS
#113
bede
closed
1 year ago
1
cli 0.8.4 - "cannot pickle '_thread.RLock' object" error when uploading samples with 10 parallel connections
#112
KuzminaAnna
opened
1 year ago
3
Download: --rename and --out-dir are mutually exclusive
#111
bede
closed
1 year ago
1
Add relatedness subcommand
#110
bede
opened
1 year ago
0
Tests: properly clear up lingering mapping CSVs created during testing
#109
bede
opened
1 year ago
0
dot/period char in sample_name causes crash
#108
bede
closed
1 year ago
1
0.8.0 allows submission of mixed empty & populated run numbers, which fail server side validation
#107
bede
closed
1 year ago
1
Version subcommand broken in PyInstaller distribution?
#106
bede
closed
1 year ago
1
Validation edge cases opened up by arbitrary metadata passthrough feature
#105
bede
closed
1 year ago
1
Friendly error message when user lacks API permissions
#104
bede
closed
1 year ago
1
Add (and maintain) a latest tag in Dockerhub
#103
JezSw
closed
1 year ago
1
Test decontamination using synthetic human reads
#102
bede
closed
1 year ago
1
EC 1.1.4 with gpas-cli 0.6.0 - Error message "unauthorised for this user" appears for invalid tags
#101
KuzminaAnna
opened
1 year ago
1
gpas-cli 0.6.0 - phrasing was changed for some of the error messages
#100
KuzminaAnna
closed
1 year ago
3
EC 1.1.4 : User is only able to upload samples if tags assigned to user has access flag set to yes
#99
KuzminaAnna
opened
1 year ago
1
Make mapping CSV creation more testable
#98
bede
opened
1 year ago
0
Pass through arbitrary fields in upload CSV to the mapping CSV
#97
bede
closed
1 year ago
1
Eelectron Client : "fastq file does not exist" error message appears, even if fastq exists
#96
KuzminaAnna
opened
1 year ago
2
EC 1.1.4: "sample_name must be unique" error message is not returned to the user if metadata contains invalid platform
#95
KuzminaAnna
closed
1 year ago
1
EC 1.1.4: Error message is wrong if sample names are empty
#94
KuzminaAnna
closed
1 year ago
2
Uploading empty sample names produce errors containing "NaN"
#93
bede
closed
1 year ago
2
Exception telemetry
#92
bede
closed
1 year ago
1
Migrate to latest Pandera
#91
bede
opened
1 year ago
1
Retry failed async downloads, verify downloaded file integrity
#90
bede
closed
1 year ago
1
Add new file types available from revised get_output API
#89
bede
opened
1 year ago
0
Enable parallelisation in PyInstaller distribution
#88
bede
closed
1 year ago
1
KeyError given upload csv with mixture of populated and unpopulated run_numbers
#87
bede
closed
1 year ago
1
Integer sample names trigger ValidationError
#86
bede
closed
1 year ago
1
Tags are validated at organisation- rather than user-level
#85
bede
closed
1 year ago
2
Move Docker images to GHCR
#84
bede
opened
1 year ago
0
Log a warning when an httpx.RequestError is raised, caught and retried
#83
bede
closed
1 year ago
1
gpas-cli v0.5.1 - it is no longer possible to perform bulk upload of identical samples (batch upload testing)
#82
KuzminaAnna
closed
1 year ago
4
Support *.fq.gz suffix
#81
bede
opened
1 year ago
1
Docker support
#80
bede
closed
1 year ago
3
Configurable rate limit for status and download calls
#79
bede
closed
1 year ago
1
Change batches API payload `uploader` key names
#78
bede
closed
1 year ago
1
Gracefully handle users with no tags
#77
bede
closed
1 year ago
1
Sensible handling of empty FASTQs
#76
bede
opened
1 year ago
9
Return forthcoming information about tag-associated sharing as JSON message for EC
#75
bede
opened
1 year ago
0
Unify package and PyInstaller CLI
#74
bede
closed
1 year ago
1
When multiple garbage sample names are provided, ValidationError returns auto incremented fictitious sample names
#73
bede
closed
1 year ago
3
Bundle PyInstaller assets with release
#72
bede
opened
2 years ago
1
"Instrument Platform of Nanopore is not being rejected for Illumina Fastq File"
#71
bede
closed
2 years ago
1
Added instruction of how to build ReadItAndKeep and Samtools under Windows.
#70
Oleksandr-Boochnew
closed
2 years ago
0
Implemented Windows binaries build job.
#69
Oleksandr-Boochnew
closed
2 years ago
2
run numbers are not generated in ascending order
#68
bede
closed
2 years ago
1
Collapse duplicate errors per sample
#67
bede
closed
2 years ago
1
Normalise sorting of ValidationErrors by sample name and error
#66
bede
closed
2 years ago
1
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