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

Jump to bottom

add regex validation rule to filename attributes #145

Merged
merged 16 commits into from
May 8, 2023
Merged

add regex validation rule to filename attributes #145

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
16 commits
Select commit Hold shift + click to select a range
6081309
add regex validation rule to filename attributes
Jan 20, 2023
ec6af99
GitHub Action: convert *.model.csv to *.model.jsonld
brynnz22 Jan 20, 2023
55fcdb2
Update HTAN.model.csv
brynnz22 Jan 24, 2023
8edbf5b
GitHub Action: convert *.model.csv to *.model.jsonld
brynnz22 Jan 24, 2023
420c9f7
Update HTAN.model.csv
brynnz22 Jan 25, 2023
2269c25
Update HTAN.model.csv
brynnz22 Jan 25, 2023
e2dc7ba
Update HTAN.model.csv
brynnz22 Jan 25, 2023
d1dd12f
Update HTAN.model.csv
brynnz22 Jan 25, 2023
62d4e7b
GitHub Action: convert *.model.csv to *.model.jsonld
brynnz22 Jan 25, 2023
b539f6f
Merge branch 'main' into no-space-filenames
adamjtaylor Feb 20, 2023
f210882
Merge branch 'main' into no-space-filenames
adamjtaylor Mar 10, 2023
127bb7d
Merge branch 'main' into no-space-filenames
adamjtaylor Mar 10, 2023
dadb1f8
Merge branch 'main' into no-space-filenames
adamjtaylor Mar 20, 2023
2da70f3
Merge branch 'main' into no-space-filenames
adamjtaylor Mar 31, 2023
6fb6713
Merge branch 'main' into no-space-filenames
adamjtaylor May 5, 2023
053f9b5
Merge branch 'main' into no-space-filenames
adamjtaylor May 5, 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
4 changes: 2 additions & 2 deletions 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,,,"Filename, File Format",FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile,
Filename,Name of a file,,,,TRUE,,,,
Filename,Name of a file,,,,TRUE,,,,regex search ^\S*$
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",,,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 Expand Up @@ -149,7 +149,7 @@ Oligo Barcode Lower Strand,Oligo Barcode - Lower Strand,,,,FALSE,Imaging Level 3
Dilution,Dilution (eg 1:1000),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Concentration,Concentration (eg 10ug/mL),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, Not Applicable",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Channel Metadata Filename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,,,,TRUE,Imaging Level 2,,,
Channel Metadata Filename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,,,,TRUE,Imaging Level 2,,,regex search ^\S*$
adamjtaylor marked this conversation as resolved.
Show resolved Hide resolved
Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",,,,TRUE,Imaging,,http://purl.obolibrary.org/obo/OBI_0400169,
Objective,Objective,,,,FALSE,Imaging,,https://www.miti-consortium.org/,
NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),,,,TRUE,Imaging,,https://www.miti-consortium.org/,num
Expand Down
8 changes: 6 additions & 2 deletions HTAN.model.jsonld
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2473,7 +2473,9 @@
},
"sms:displayName": "Filename",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"regex search ^\\S*$"
]
},
{
"@id": "bts:fileFormat",
Expand Down Expand Up @@ -10640,7 +10642,9 @@
},
"sms:displayName": "Channel Metadata Filename",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"regex search ^\\S*$"
]
},
{
"@id": "bts:Microscope",
Expand Down