Geomx fixes (#88)

* Change "list" to "list like" for synId validations * Rebuild model csv and json
mc2-center · Mar 6, 2024 · c926e82 · c926e82
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commit c926e82
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Showing 3 changed files with 21 additions and 21 deletions.
diff --git a/mc2.model.csv b/mc2.model.csv
@@ -71,11 +71,11 @@ NanoStringGeoMxDSPLevel1_id,"Unique row identifier, used as a primary key for re
 Filename,Name of a file,,,TRUE,,,,HTAN,str
 File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","Alignment Format, Alignment Format (Pair Only), Alignment Format (Text), Annotated Text Format, Antimony, BAM, BCF, BED, BLAST Results, BNGL, Binary Format, Biological Model Format, Biological Pathway Or Network Format, CSV, Chemical Data Format, Cytoband Format, Cytoscape Input File Format, DCC, DCD, DSV, Database Hits (Sequence) Format , Docker Image Format, Document Format, Dot-Bracket Format, FASTA, FASTQ, FASTQ-Illumina, FCS, GCT/Res Format, GFF, GFF3, GIF, GML, GTF, Gene Annotation Format, Gene Cluster Format, Gene Expression Report Format, Genotype And Phenotype Annotation Format, Graph Format, H5AD, HDF, HDF5, HTML, Hidden Markov Model Format, Image Format, Individual Genetic Data Format, JPG, JSON, LSM, MAF, MAGE-ML, MAGE-TAB, MAT, MATLAB Script, MSF, Map Format, Mass Spectrometry Data Format, Matrix Format, NIFTI Format, Nexus Format, Not Applicable, NumPy Format, OME-TIFF, Ontology Format, PDF, PNG, PS, PSF, Phylip Format, Phylip Format Variant, Phylogenetic Tree Format, Phylogenetic Tree Format (Text), Protein Interaction Format, Python Script, R File Format, R Script, RDS, RNA Annotation Format, RNA Secondary Structure Format, RPKM, Raw Sequence Format, SAM, SBML, SQLite Format, SVG, Scores Format, Sequence Annotation Track Format, Sequence Cluster Format, Sequence Cluster Format (Protein), Sequence Feature Annotation Format, Sequence Feature Table Format, Sequence Feature Table Format (Text), Sequence Profile Format, Sequence Range Format, Sequence Record Format, Sequence Trace Format, Sequence Variation Annotation Format, TIFF, TSV, TXT, Tertiary Structure Format, Textual Format, Topology Format, Trajectory Format, VCF, Workflow Format, XML, YAML, bedgraph, bigWig, cel, imzML Metadata File, mzML, nii, pkl, sif, xls, xlsx, PDB, HED, MRC, Unspecified",,TRUE,,,,HTAN,str
 Parent Biospecimen ID,Biospecimen Identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,TRUE,,,,HTAN,list like
-Synapse ID of Data File,Synapse ID of file,,,TRUE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP Config File,Synapse ID of config.ini file generated by the GeoMx DSP workflow.,,,FALSE,,,,MC2/STE,list::regex match syn\d+
+Synapse ID of Data File,Synapse ID of file,,,TRUE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP Config File,Synapse ID of config.ini file generated by the GeoMx DSP workflow.,,,FALSE,,,,MC2/STE,list like::regex match syn\d+
 GeoMx DSP Assay Type,The assay type which was used for the GeoMx DSP pipeline.,"RNA nCounter, Protein nCounter, Protein NGS, RNA NGS",,FALSE,,,,HTAN,
 Target Depth,The targeted read depth prior to sequencing. Integer,,,TRUE,,,,HTAN,num
 Read Length,"The length of the sequencing reads. Can be integer, null",,,TRUE,,,,HTAN,num
@@ -89,11 +89,11 @@ GeoMx DSP Library Preparation Kit Vendor,Vendor of Library Preparation Kit. Stri
 GeoMx DSP Library Preparation Kit Version,Version of Library Preparation Kit. String,,,FALSE,,,,HTAN,str
 NanoString GeoMx DSP Level 2,Processed count conversion (DCC/RCC) files from GeoMX experiments,,"Component, NanoStringGeoMxDSPLevel2_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of Parent FASTQ File, Synapse ID of GeoMx Lab Worksheet File, Synapse ID of GeoMx DSP PKC File, Synapse ID of GeoMx DSP ROI Segment Annotation File, GeoMx DSP Assay Type, ROI Name, AOI Name, Software and Version, GeoMx DSP Genomic Reference, GeoMx DSP NGS Sequencing Platform, GeoMx DSP NGS Library Selection Method, GeoMx DSP NGS Library Preparation Kit Name, GeoMx DSP Library Preparation Kit Vendor, GeoMx DSP Library Preparation Kit Version",FALSE,,,,HTAN,
 NanoStringGeoMxDSPLevel2_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique
-Synapse ID of Parent FASTQ File,Synapse ID(s) indicating the FASTQ(s) associated with the file; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list::regex match syn\d+
+Synapse ID of Parent FASTQ File,Synapse ID(s) indicating the FASTQ(s) associated with the file; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list like::regex match syn\d+
 NanoString GeoMx DSP Imaging Level 2,,,"Component, NanoStringGeoMxDSPImagingLevel2_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of GeoMx ROI Segment Annotation File, ROI Name, AOI Name, Imaging Channel Names",FALSE,,,,HTAN,
 NanoStringGeoMxDSPImagingLevel2_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique
 GeoMx DSP Genomic Reference,Link or identifier for the reference genome associated with the files,,,FALSE,,,,HTAN,str
-Synapse ID of Parent Data File,Synapse ID indicating the file(s) from which the file was derived; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list::regex match syn\d+
+Synapse ID of Parent Data File,Synapse ID indicating the file(s) from which the file was derived; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list like::regex match syn\d+
 Imaging Channel Names,Name(s) of imaging channel(s) associated with the image; multiple values should be provided as a comma-separated list.,,,FALSE,,,,HTAN,list like
 NanoString GeoMx DSP Level 3,Files contain processed count data from the NanoString GeoMx DSP Pipeline.,,"Component, NanoStringGeoMxDSPLevel3_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of Parent Data File, Synapse ID GeoMx ROI Segment Annotation File, GeoMx DSP Unique Probe Count, GeoMx DSP Unique Target Count, Matrix Type, GeoMx DSP Workflow Type, GeoMx DSP Workflow Parameter Description, GeoMx DSP Workflow Link",FALSE,,,,HTAN,
 NanoStringGeoMxDSPLevel3_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique

diff --git a/mc2.model.jsonld b/mc2.model.jsonld
@@ -43694,7 +43694,7 @@
             "sms:displayName": "Synapse ID of Data File",
             "sms:required": "sms:true",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -43714,7 +43714,7 @@
             "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -43734,7 +43734,7 @@
             "sms:displayName": "Synapse ID of GeoMx DSP PKC File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -43754,7 +43754,7 @@
             "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -43774,7 +43774,7 @@
             "sms:displayName": "Synapse ID of GeoMx DSP Config File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -46251,7 +46251,7 @@
             "sms:displayName": "Synapse ID of Parent FASTQ File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },
@@ -46394,7 +46394,7 @@
             "sms:displayName": "Synapse ID of Parent Data File",
             "sms:required": "sms:false",
             "sms:validationRules": [
-                "list",
+                "list like",
                 "regex match syn\\d+"
             ]
         },

diff --git a/modules/geomx/annotationProperty.csv b/modules/geomx/annotationProperty.csv
@@ -4,11 +4,11 @@ NanoStringGeoMxDSPLevel1_id,"Unique row identifier, used as a primary key for re
 Filename,Name of a file,,,TRUE,,,,HTAN,str
 File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","Alignment Format, Alignment Format (Pair Only), Alignment Format (Text), Annotated Text Format, Antimony, BAM, BCF, BED, BLAST Results, BNGL, Binary Format, Biological Model Format, Biological Pathway Or Network Format, CSV, Chemical Data Format, Cytoband Format, Cytoscape Input File Format, DCC, DCD, DSV, Database Hits (Sequence) Format , Docker Image Format, Document Format, Dot-Bracket Format, FASTA, FASTQ, FASTQ-Illumina, FCS, GCT/Res Format, GFF, GFF3, GIF, GML, GTF, Gene Annotation Format, Gene Cluster Format, Gene Expression Report Format, Genotype And Phenotype Annotation Format, Graph Format, H5AD, HDF, HDF5, HTML, Hidden Markov Model Format, Image Format, Individual Genetic Data Format, JPG, JSON, LSM, MAF, MAGE-ML, MAGE-TAB, MAT, MATLAB Script, MSF, Map Format, Mass Spectrometry Data Format, Matrix Format, NIFTI Format, Nexus Format, Not Applicable, NumPy Format, OME-TIFF, Ontology Format, PDF, PNG, PS, PSF, Phylip Format, Phylip Format Variant, Phylogenetic Tree Format, Phylogenetic Tree Format (Text), Protein Interaction Format, Python Script, R File Format, R Script, RDS, RNA Annotation Format, RNA Secondary Structure Format, RPKM, Raw Sequence Format, SAM, SBML, SQLite Format, SVG, Scores Format, Sequence Annotation Track Format, Sequence Cluster Format, Sequence Cluster Format (Protein), Sequence Feature Annotation Format, Sequence Feature Table Format, Sequence Feature Table Format (Text), Sequence Profile Format, Sequence Range Format, Sequence Record Format, Sequence Trace Format, Sequence Variation Annotation Format, TIFF, TSV, TXT, Tertiary Structure Format, Textual Format, Topology Format, Trajectory Format, VCF, Workflow Format, XML, YAML, bedgraph, bigWig, cel, imzML Metadata File, mzML, nii, pkl, sif, xls, xlsx, PDB, HED, MRC, Unspecified",,TRUE,,,,HTAN,str
 Parent Biospecimen ID,Biospecimen Identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,TRUE,,,,HTAN,list like
-Synapse ID of Data File,Synapse ID of file,,,TRUE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment.,,,FALSE,,,,HTAN,list::regex match syn\d+
-Synapse ID of GeoMx DSP Config File,Synapse ID of config.ini file generated by the GeoMx DSP workflow.,,,FALSE,,,,MC2/STE,list::regex match syn\d+
+Synapse ID of Data File,Synapse ID of file,,,TRUE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment.,,,FALSE,,,,HTAN,list like::regex match syn\d+
+Synapse ID of GeoMx DSP Config File,Synapse ID of config.ini file generated by the GeoMx DSP workflow.,,,FALSE,,,,MC2/STE,list like::regex match syn\d+
 GeoMx DSP Assay Type,The assay type which was used for the GeoMx DSP pipeline.,"RNA nCounter, Protein nCounter, Protein NGS, RNA NGS",,FALSE,,,,HTAN,
 Target Depth,The targeted read depth prior to sequencing. Integer,,,TRUE,,,,HTAN,num
 Read Length,"The length of the sequencing reads. Can be integer, null",,,TRUE,,,,HTAN,num
@@ -22,11 +22,11 @@ GeoMx DSP Library Preparation Kit Vendor,Vendor of Library Preparation Kit. Stri
 GeoMx DSP Library Preparation Kit Version,Version of Library Preparation Kit. String,,,FALSE,,,,HTAN,str
 NanoString GeoMx DSP Level 2,Processed count conversion (DCC/RCC) files from GeoMX experiments,,"Component, NanoStringGeoMxDSPLevel2_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of Parent FASTQ File, Synapse ID of GeoMx Lab Worksheet File, Synapse ID of GeoMx DSP PKC File, Synapse ID of GeoMx DSP ROI Segment Annotation File, GeoMx DSP Assay Type, ROI Name, AOI Name, Software and Version, GeoMx DSP Genomic Reference, GeoMx DSP NGS Sequencing Platform, GeoMx DSP NGS Library Selection Method, GeoMx DSP NGS Library Preparation Kit Name, GeoMx DSP Library Preparation Kit Vendor, GeoMx DSP Library Preparation Kit Version",FALSE,,,,HTAN,
 NanoStringGeoMxDSPLevel2_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique
-Synapse ID of Parent FASTQ File,Synapse ID(s) indicating the FASTQ(s) associated with the file; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list::regex match syn\d+
+Synapse ID of Parent FASTQ File,Synapse ID(s) indicating the FASTQ(s) associated with the file; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list like::regex match syn\d+
 NanoString GeoMx DSP Imaging Level 2,,,"Component, NanoStringGeoMxDSPImagingLevel2_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of GeoMx ROI Segment Annotation File, ROI Name, AOI Name, Imaging Channel Names",FALSE,,,,HTAN,
 NanoStringGeoMxDSPImagingLevel2_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique
 GeoMx DSP Genomic Reference,Link or identifier for the reference genome associated with the files,,,FALSE,,,,HTAN,str
-Synapse ID of Parent Data File,Synapse ID indicating the file(s) from which the file was derived; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list::regex match syn\d+
+Synapse ID of Parent Data File,Synapse ID indicating the file(s) from which the file was derived; multiple parent files should be comma-separated,,,FALSE,,,,HTAN,list like::regex match syn\d+
 Imaging Channel Names,Name(s) of imaging channel(s) associated with the image; multiple values should be provided as a comma-separated list.,,,FALSE,,,,HTAN,list like
 NanoString GeoMx DSP Level 3,Files contain processed count data from the NanoString GeoMx DSP Pipeline.,,"Component, NanoStringGeoMxDSPLevel3_id, Filename, File Format, Parent Biospecimen ID, Synapse ID of Data File, Synapse ID of Parent Data File, Synapse ID GeoMx ROI Segment Annotation File, GeoMx DSP Unique Probe Count, GeoMx DSP Unique Target Count, Matrix Type, GeoMx DSP Workflow Type, GeoMx DSP Workflow Parameter Description, GeoMx DSP Workflow Link",FALSE,,,,HTAN,
 NanoStringGeoMxDSPLevel3_id,"Unique row identifier, used as a primary key for record updates",,,TRUE,,,,MC2,unique