Patch/workflow tests (#293)

* Update workflow and resolve #288 for test
* Build jsonld

.github/workflows/schematic-ci.yml

@@ -64,7 +64,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        schematic-version: [develop, v22.8.1, list-comma-patch]
+        schematic-version: [23.1.1]
 
     steps:
       - name: Checkout repository
@@ -74,16 +74,13 @@ jobs:
 
       - name: Setup schematic
         id: setup-schematic
-        uses: nf-osi/actions/setup-schematic@ab2581d5a9c169c2062f5cbef3d64c7020f55cfb
-        with:
-          schematic-version: ${{ matrix.schematic-version }}
+        run: pip3 install schematicpy==${{ matrix.schematic-version }}
 
       - name: Test validate
         working-directory: tests
         continue-on-error: true
         run: |
           cp ../NF.jsonld NF.jsonld
-          source ${{ env.SCHEMATIC_ENV }}
           ./test.sh
 
       - name: Upload test artifacts

.gitignore

@@ -8,6 +8,13 @@ publish/**
 *.schema.json
 *.manifest.csv
 *.test.xlsx
+tests/**_log.txt
+
+# IDE data and other data for code tools
+.idea
+.lsp
+.clj-kondo
+.Rhistory
 
 # Misc
 .Rhistory

NF.csv

@@ -127,6 +127,7 @@ quantitative PCR,"Quantitative PCR (Q-PCR) is used to measure the quantity of a
 clinical data,"Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,,
 photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay,"","","",""
 cAMP-Glo Max Assay,"The cAMP-Glo Max Assay from Promega is a bioluminescent assay used for the quantification of cyclic AMP (cAMP) in cell-based assays. It utilizes a luminescent luciferase-based detection system to detect the levels of cAMP in cell lysates, which can be used to study G protein-coupled receptor (GPCR) signaling and other intracellular signaling pathways.",,,FALSE,https://www.promega.com/products/cell-signaling/gpcr-signaling/camp_glo-max-assay/?catNum=V1681,assay,,,,cAMP_Glo_Max,Class,Assay,Assay,Assay,,,
+Von Frey test,Assay applying electrical stimulus to assess pain in rodents.,"","",FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592204/,assay,,"","",Von_Frey_Test,"",Assay,Assay,"","","",""
 channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","",""
 MRISequence,The scanning sequence/modality that is used for a conventional MRI scan.,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery","",FALSE,Sage Bionetworks,experimentalData,,"","",MRI_Sequence,Class,Assay,Assay_Parameter,"","","",""
 T1-weighted,"","","",FALSE,Sage Bionetworks,MRISequence,,"","",T1-weighted,Class,Assay,Assay_Parameter,MRI_Sequence,"","",""
@@ -238,7 +239,7 @@ LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, bo
 Promega GloMax Discover,"(From vendor) Microplate reader with high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities.",,,FALSE,https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000,platform,,,,Promega_GloMax_Discover,Class,Assay,Platform,Platform,,,
 BGISEQ-500,"(From vendor) BGISEQ-500 is an industry leading high-throughput sequencing solution, powered by combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB™) technology.",,,FALSE,https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf,platform,,,,BGISEQ_500,Class,Assay,Platform,Platform,,,
 drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,,
-assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph,cAMP-Glo Max Assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
+assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph,cAMP-Glo Max Assay,Von Frey test",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
 platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip v1.0 (850k),Illumina Infinium MethylationEPIC BeadChip v2.0 (935k), Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,TRUE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
 targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit."
 libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,,

NF.jsonld

@@ -4178,6 +4178,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:VonFreytest",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Assay applying electrical stimulus to assess pain in rodents.",
+            "rdfs:label": "VonFreytest",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Von Frey test",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Channel",
             "@type": "rdfs:Class",
@@ -6492,6 +6509,9 @@
                 },
                 {
                     "@id": "bts:CAMP-GloMaxAssay"
+                },
+                {
+                    "@id": "bts:VonFreytest"
                 }
             ],
             "sms:displayName": "assay",

modules/Assay/Assay.csv

@@ -127,3 +127,4 @@ quantitative PCR,"Quantitative PCR (Q-PCR) is used to measure the quantity of a
 clinical data,"Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,,
 photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay,"","","",""
 cAMP-Glo Max Assay,"The cAMP-Glo Max Assay from Promega is a bioluminescent assay used for the quantification of cyclic AMP (cAMP) in cell-based assays. It utilizes a luminescent luciferase-based detection system to detect the levels of cAMP in cell lysates, which can be used to study G protein-coupled receptor (GPCR) signaling and other intracellular signaling pathways.",,,FALSE,https://www.promega.com/products/cell-signaling/gpcr-signaling/camp_glo-max-assay/?catNum=V1681,assay,,,,cAMP_Glo_Max,Class,Assay,Assay,Assay,,,
+Von Frey test,Assay applying electrical stimulus to assess pain in rodents.,"","",FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592204/,assay,,"","",Von_Frey_Test,"",Assay,Assay,"","","",""