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GlobalPathogenAnalysisService
/
gpas-cli
The CLI client for GPAS SC2
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duplicate path in fastq1 and fastq2 does not trigger validation failure
#65
bede
closed
2 years ago
1
Replace calls to requests.get() with httpx.get()
#64
bede
closed
2 years ago
1
Optionally mask dates to week and month level according to user details
#63
bede
closed
2 years ago
1
Test paired bam sorting
#62
bede
closed
2 years ago
1
Test runless and batchless sample metadata
#61
bede
closed
2 years ago
1
Run number discrepencies in submission payload between 0.2.1 and EC 1.0.8
#60
bede
closed
2 years ago
1
Batches submission payload not encoded as UTF-8
#59
bede
closed
2 years ago
1
add functionality to specify GUIDs in a plaintext file for gpas download
#58
philipwfowler
opened
2 years ago
1
Validate primer scheme enums
#57
bede
opened
2 years ago
0
Add user agent string to cli-upload interface
#56
bede
closed
2 years ago
2
SubmissionError with country code CYM
#55
bede
closed
2 years ago
2
collection_date error in tip of main
#54
bede
closed
2 years ago
1
Test coverage for negative controls
#53
bede
closed
2 years ago
1
HCELEC-413 error message is not implicit when sample name is null or empty
#52
KuzminaAnna
closed
2 years ago
1
HCELEC-411 Error not thrown when there is special character in the metadata file name
#51
KuzminaAnna
closed
2 years ago
5
HCELEC-412 Exception while uploading illumina sample possibly since tag validation did not cover empty tag at subfield level
#50
KuzminaAnna
closed
2 years ago
5
Automatically delete fastqs from temp dir after successful upload.
#49
bede
closed
2 years ago
4
Ubuntu 18 support
#48
bede
closed
2 years ago
4
CI for PyInstaller executables
#47
bede
closed
2 years ago
1
Date validation is broken
#46
bede
closed
2 years ago
1
Windows support
#45
bede
closed
2 years ago
4
Make use of multiprocessing depend on --processes >= 1, not --json-messages
#44
bede
closed
2 years ago
3
HCELEC-399 user can not run gpas-cli on Linux 16 or 18 OS
#43
KuzminaAnna
closed
2 years ago
3
HCELEC-395 metadata district does not allow null value
#42
KuzminaAnna
closed
2 years ago
8
HCELEC-396 Only 1 Error is returned although there are Multiple Errors which show up in Electron Client for the same file
#41
KuzminaAnna
closed
2 years ago
3
Notify of newer release on execution
#40
bede
closed
2 years ago
2
Faster uploads for users with high TCP RTTs to London datacentre
#39
bede
closed
2 years ago
1
Increase resilience when using poor connections
#38
bede
closed
2 years ago
1
Optional debug to file
#37
bede
opened
2 years ago
0
Reorganise long validation if-else block
#36
bede
opened
2 years ago
0
Pyinstaller version of cli-upload does not correctly detect binary deps in same directory
#35
bede
closed
2 years ago
1
Problems with Nuitka, Pyinstaller and tqdm progress bars
#34
bede
closed
2 years ago
2
Test samples with insufficient reads after decontamination
#33
bede
closed
2 years ago
1
Document upload CSV field specifications
#32
bede
closed
1 year ago
0
Allow specification of mapping csv path
#31
bede
closed
2 years ago
1
Allow alternative reasonable fastq suffixes
#30
bede
closed
2 years ago
1
Make upload_csv batch field nullable
#29
bede
closed
2 years ago
1
Tidy up instance variables
#28
bede
closed
2 years ago
0
Honour and test working dir, output dir for both downloaded files and mapping CSV
#27
bede
closed
2 years ago
1
Put batch name inside mapping csv filename
#26
bede
closed
2 years ago
1
Plumb parse_decontamination_stats() back into parallelised decontamination flow
#25
bede
closed
2 years ago
1
High level Python API mimicking CLI
#24
bede
closed
2 years ago
1
Standardise use of sample and sample_name, especially in EC interface
#23
bede
closed
2 years ago
0
Friendlier token error
#22
bede
closed
2 years ago
1
Increase test coverage
#21
bede
closed
1 year ago
0
Basic documentation
#20
bede
opened
2 years ago
0
Pin all deps
#19
bede
closed
2 years ago
1
Pytest coverage
#18
bede
closed
2 years ago
1
Module reorganisation
#17
bede
opened
2 years ago
0
Automatic token refresh
#16
bede
closed
2 years ago
1
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