Merge pull request #289 from ncihtan/288-fds-890-htan-schema-error-wh…

…en-calling-visualizeattributes-endpoint

[FDS-890] Fixes for scheama visualisation

HTAN.model.csv

@@ -77,7 +77,7 @@ Imaging Level 3 Image,Quality controlled imaging data,,"Component, Filename, Fil
 10x Visium Spatial Transcriptomics - RNA-seq Level 2,Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.,,"Component, Filename, File Format, Checksum, HTAN Data File ID, HTAN Parent Data File ID, UMI Tag, Whitelist Spatial Barcode File Link, Spatial Barcode Tag, Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, HTAN Parent Biospecimen ID, Run ID, Capture Area",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 1,,
 10x Visium Spatial Transcriptomics - Auxiliary Files,"Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Visium File Type, Slide ID, Capture Area, Workflow Version, Workflow Link",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 1, 10x Visium Spatial Transcriptomics - RNA-seq Level 2",,
 10x Visium Spatial Transcriptomics - RNA-seq Level 3,Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Visium File Type, Workflow Version, Workflow Link, Capture Area, Spots under tissue, Mean Reads per Spatial Spot, Median Number Genes per Spatial Spot, Sequencing Saturation, Proportion Reads Mapped, Proportion Reads Mapped to Transcriptome, Median UMI Counts per Spot",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 2, 10x Visium Spatial Transcriptomics - Auxiliary Files",,
-10x Visium Spatial Transcriptomics - RNA-seq Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 3",,
+10x Visium Spatial Transcriptomics - RNA-seq Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 3,,
 Visium File Type,The file type generated for the visium experiment.,"reference png, reference jpg, json scale factors, probe dataset csv, qc result html, filtered mex, unfiltered mex, tissue_positions, barcodes, features, fiducial image png, fiducial image jpg, detected image png, detected jpg, high res image, low res image, json scale factors, probe dataset csv",,,TRUE,Spatial Transcriptomics,,,
 Run ID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,,,,TRUE,Spatial Transcriptomics,,,
 Capture Area,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.","A, B, C, D, A1, B1, C1, D1",,,FALSE,Spatial Transcriptomics,,,
@@ -167,7 +167,7 @@ Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomi
 Mass Spectrometry Level 2,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 1,,
 Mass Spectrometry Level 3,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 2,,
 Mass Spectrometry Level 4,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 3,,
-Mass Spectrometry Auxiliary File,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID",,FALSE,Assay,File,,
+Mass Spectrometry Auxiliary File,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID",,FALSE,Assay,,,
 Imaging Level 3 Channels,Channel-level Metadata Attributes,,"HTAN Channel Metadata ID, Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub Cycle Number, Antibody Role, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope Element, Metal Isotope Mass, Oligo Barcode Upper Strand, Oligo Barcode Lower Strand, Dilution, Concentration",,FALSE,Assay,,,
 HTAN Channel Metadata ID,HTAN ID for this channel metadata table (same for all rows),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
 Channel ID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
@@ -879,7 +879,7 @@ Antibody Notes,Notes on antibodies replacements and antibody recognition observa
 Pre-processing Completed,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
 Pre-processing Required,Pre-processing steps required to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
 Publication,"An empty parent attribute for publications",,,,FALSE,,,,
-Publication Manifest,Publication specific attributes.,,"Publication-associated HTAN Parent Data File ID, HTAN Grant ID, HTAN Center ID, Publication Content Type, DOI, Title, Authors, Corresponding Author, Corresponding Author ORCID, Year of Publication, Location of Publication, Publication Abstract, License, PMID, Publication contains HTAN ID, Data Type, Tool, Supporting Link, Supporting Link Description",,FALSE,Publication,Publication,,
+Publication Manifest,Publication specific attributes.,,"Component,Publication-associated HTAN Parent Data File ID, HTAN Grant ID, HTAN Center ID, Publication Content Type, DOI, Title, Authors, Corresponding Author, Corresponding Author ORCID, Year of Publication, Location of Publication, Publication Abstract, License, PMID, Publication contains HTAN ID, Data Type, Tool, Supporting Link, Supporting Link Description",,FALSE,Publication,Publication,,
 Publication-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the content presented/published. Should be comma-separated lists.,,,,TRUE,Publication,,,list like
 HTAN Grant ID,HTAN grant number(s) (i.e. CA------ format) associated with the content presented/published.,,,,TRUE,Publication,,,list like
 HTAN Center ID,List of HTAN Center ID(s) associated with the content presented/published.,"HTA1, HTA2, HTA3, HTA4, HTA5, HTA6, HTA7, HTA8, HTA9, HTA10, HTA11, HTA12, HTA13, HTA14",,,TRUE,Publication,,,list like

HTAN.model.jsonld

@@ -10901,11 +10901,6 @@
             },
             "sms:displayName": "Mass Spectrometry Auxiliary File",
             "sms:required": "sms:false",
-            "sms:requiresComponent": [
-                {
-                    "@id": "bts:File"
-                }
-            ],
             "sms:requiresDependency": [
                 {
                     "@id": "bts:Component"
@@ -46494,6 +46489,9 @@
                 }
             ],
             "sms:requiresDependency": [
+                {
+                    "@id": "bts:Component"
+                },
                 {
                     "@id": "bts:Publication-associatedHTANParentDataFileID"
                 },