Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update regex validation for Filename #314

Merged
merged 3 commits into from
Oct 26, 2023
Merged

Update regex validation for Filename #314

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4cd3a0b
Update filename regex
adamjtaylor Oct 24, 2023
5e5e7ab
Refine regex
adamjtaylor Oct 24, 2023
9fe1809
GitHub Action: convert *.model.csv to *.model.jsonld
adamjtaylor Oct 24, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion HTAN.model.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ Sequencing,Module for next generation sequencing assays,,,,FALSE,Assay,,,
Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",,,,TRUE,,,https://w3id.org/biolink/vocab/category,
Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test",,
File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile,
Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$
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,
Expand Down
2 changes: 1 addition & 1 deletion HTAN.model.jsonld
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2476,7 +2476,7 @@
"sms:displayName": "Filename",
"sms:required": "sms:true",
"sms:validationRules": [
"regex search ^.+\\/\\S*$"
"regex search ^(([a-zA-Z0-9\\_\\-\\.\\+\\(\\'\\)\\ ]+\\/)+[a-zA-Z0-9\\_\\-\\.\\+\\(\\'\\)]+)$"
]
},
{
Expand Down