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Add HTAN ID validation rules #304

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merged 6 commits into from
Nov 29, 2023
Merged

Add HTAN ID validation rules #304

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756760d
Add HTAN ID validation rules
adamjtaylor Sep 28, 2023
1b514c0
GitHub Action: convert *.model.csv to *.model.jsonld
adamjtaylor Sep 28, 2023
ba9a6bc
Merge branch 'main' into 268-improve-validation-for-htan-ids
adamjtaylor Oct 27, 2023
76e8704
Merge branch 'main' into 268-improve-validation-for-htan-ids
adamjtaylor Nov 14, 2023
1515c5d
Enable HTA16 to be valid
adamjtaylor Nov 29, 2023
9601fee
GitHub Action: convert *.model.csv to *.model.jsonld
adamjtaylor Nov 29, 2023
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6 changes: 3 additions & 3 deletions HTAN.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ File,A type of Information Content Entity specific to OS,,,,FALSE,Information Co
Filename,Name of a file,,,,TRUE,,,,regex search ^(([a-zA-Z0-9\_\-\.\+\(\'\)\ ]+\/)+[a-zA-Z0-9\_\-\.\+\(\'\)]+)$
File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc",,,TRUE,,,,
Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,,
HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning
HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
HTAN Parent ID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Parent Biospecimen ID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,,,
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12 changes: 9 additions & 3 deletions HTAN.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -2800,7 +2800,9 @@
},
"sms:displayName": "HTAN Data File ID",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning"
]
},
{
"@id": "bts:HTANParticipantID",
Expand All @@ -2817,7 +2819,9 @@
},
"sms:displayName": "HTAN Participant ID",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))$ warning"
]
},
{
"@id": "bts:HTANBiospecimenID",
Expand All @@ -2834,7 +2838,9 @@
},
"sms:displayName": "HTAN Biospecimen ID",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning"
]
},
{
"@id": "bts:HTANParentID",
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