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Clinical-Genomics
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preClinVar
A ClinVar API submission helper written in FastAPI
MIT License
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Combine `Reference sequence` and `HGVS` fields from Variant file to create the hgvs field in json submission object
#83
northwestwitch
closed
1 year ago
3
Submission status is "error"...
#82
dnil
closed
1 year ago
17
Parse record status from request
#80
northwestwitch
opened
1 year ago
0
Prepare minor version 2.3
#79
northwestwitch
closed
1 year ago
1
Clinsig fixcase
#78
northwestwitch
closed
1 year ago
2
ClinVar validation doesn't pass for uppercase/lowercase problem
#77
northwestwitch
closed
1 year ago
1
Prepare version 2.2
#76
northwestwitch
closed
1 year ago
1
Do not parse dbSNP IDs as Accession key/values
#75
northwestwitch
closed
1 year ago
0
Wrong Accession submitted in ClinVar tests
#74
northwestwitch
closed
1 year ago
3
Replace stage URL with prod URL on README
#73
northwestwitch
closed
1 year ago
1
Minor release 2.1
#72
northwestwitch
closed
1 year ago
1
Link to CG demo service on readme page
#71
northwestwitch
closed
1 year ago
0
Fixed muliple pheno parsing
#70
northwestwitch
closed
1 year ago
1
Multiple phenotypes are not parsed correctly from file
#69
northwestwitch
closed
1 year ago
0
Parse variant coordinates, copy number and variant type
#68
northwestwitch
closed
1 year ago
1
Parse and add coordinates if HGVS is missing
#67
northwestwitch
closed
1 year ago
0
Prepare patch 2.0.1
#66
northwestwitch
closed
1 year ago
0
Fixed parsing of HP/HPO and HGVS fields
#65
northwestwitch
closed
1 year ago
1
Create major release v.2.0
#64
northwestwitch
closed
1 year ago
1
Update demo submission json file
#63
northwestwitch
closed
1 year ago
0
Add optional parameters to file conversion endpoints
#62
northwestwitch
closed
1 year ago
2
Add Actions badges on Readme
#61
northwestwitch
closed
1 year ago
1
Add 5 useful GitHub actions
#60
northwestwitch
closed
1 year ago
1
Created a new endpoint tsv_2_json
#59
northwestwitch
closed
1 year ago
2
Create an additional endpoint to parse TSVs separate from CSV_2_Json
#58
northwestwitch
closed
1 year ago
0
CSV_2_json endpoint should accept additional fields that don't find place in CSV files
#57
northwestwitch
closed
1 year ago
1
Upgrade to new API schema released after 2022-11-21
#56
northwestwitch
closed
1 year ago
1
Changed API - after 2022-11-21
#55
northwestwitch
closed
1 year ago
0
Old submission format with Assertion Criteria doesn't pass validation any more
#54
northwestwitch
closed
1 year ago
1
Add useful GitHub actions
#53
northwestwitch
closed
1 year ago
0
Simplify and fix CSV and TSV files parsing
#52
northwestwitch
closed
1 year ago
1
Generalize CSV conversion including fields not used by CG
#51
northwestwitch
opened
1 year ago
0
Prepare version 1.1
#50
northwestwitch
closed
1 year ago
2
Support for tab delimited CSV files
#49
northwestwitch
closed
1 year ago
1
Accept also tab separated CSV files
#48
northwestwitch
closed
1 year ago
0
Fix parsing of CSV files missing assertion criteria col
#47
northwestwitch
closed
1 year ago
2
TypeError: argument of type 'NoneType' is not iterable
#46
northwestwitch
closed
1 year ago
1
Prepare new patch 1.0.2
#45
northwestwitch
closed
1 year ago
1
Prevent StopIteration crash when parsing empty CSV files
#44
northwestwitch
closed
1 year ago
1
Do not crash when empty CSV files are provided
#43
northwestwitch
closed
1 year ago
1
Error in csv_2_json while reading csv files
#42
northwestwitch
closed
1 year ago
1
Add an interface that allows to load Variant and CaseData file to convert them to json
#41
northwestwitch
opened
1 year ago
0
Add instructions oh how preClinVar at CG can be used by anybody to convert their files to json
#40
northwestwitch
closed
1 year ago
0
Updates to ClinVar Submission API Schema - mid November
#39
northwestwitch
closed
1 year ago
1
Patch 1.0.1
#38
northwestwitch
closed
2 years ago
1
Fixed Dockerfile command that prevented image to be pushed to Docker Hub
#37
northwestwitch
closed
2 years ago
1
Publishing of a new release image on Docker Hub fails
#36
northwestwitch
closed
2 years ago
1
Prepare major version 1.0
#35
northwestwitch
closed
2 years ago
1
Pass api key as form field and not query arg
#34
northwestwitch
closed
2 years ago
2
Add tests for validate and dry-run endpoints
#33
northwestwitch
closed
2 years ago
1
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