add GE MRI

.github/workflows/main-ci.yml

@@ -10,10 +10,12 @@ on:
 
   workflow_dispatch:
 
+env:
+  SCHEMATIC_VERSION: 24.5.1
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
@@ -22,6 +24,10 @@ jobs:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
           fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository
 
+      - name: Get skip flags
+        id: check_skip_flags
+        run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s)" >> "$GITHUB_OUTPUT"
+
       - name: Setup custom build tools and make jsonld 
         shell: bash
         run: |
@@ -37,6 +43,18 @@ jobs:
           make Superdataset
           make PortalDataset
           make PortalStudy
+
+      # Set up supported python.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10.12' 
+
+      - name: Setup schematic and do another convert pass
+        id: schematic-convert
+        run: |
+          pip install schematicpy==${{ env.SCHEMATIC_VERSION }}  ipython==8.18.1
+          pip show schematicpy
+          schematic schema convert NF.jsonld
 
       - name: Commit files if there are changes
         run: |
@@ -56,6 +74,7 @@ jobs:
         with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ github.event.pull_request.head.ref }}
+
 
 
   # Additionally test PRs
@@ -67,9 +86,11 @@ jobs:
       SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}
     permissions:
       pull-requests: write
-    strategy:
-      matrix:
-        schematic-version: [24.4.1]  # cannot actually do parallel/concurrent testing and need to do sequential because of API rate limits
+    if: ${{ !contains(needs.check_skip_flags.outputs.HEAD_COMMIT_MESSAGE, '[skip tests]') }}
+    # strategy:
+    #  matrix:  
+    # cannot actually do parallel/concurrent testing because of API rate limits, 
+    # so we currently only test with one schematic version because it takes much too long with sequential
 
     steps:
       - uses: actions/checkout@v4
@@ -83,10 +104,9 @@ jobs:
 
       - name: Setup schematic
         id: setup-schematic
-        run: pip install schematicpy==${{ matrix.schematic-version }} ipython==8.18.1
-
-      - name: Sanity-check successful installation and version
-        run: pip show schematicpy
+        run: |
+          pip install schematicpy==${{ env.SCHEMATIC_VERSION }}  ipython==8.18.1
+          pip show schematicpy
 
       - name: Test generate
         working-directory: tests/generate
@@ -113,18 +133,18 @@ jobs:
       - name: Create test suite report
         working-directory: tests
         continue-on-error: true
-        run: docker run -v $(pwd):/tests -e SCHEMATIC=${{ matrix.schematic-version }} rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')"
+        run: docker run -v $(pwd):/tests -e SCHEMATIC=${{ env.SCHEMATIC_VERSION }} rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')"
 
       - name: Report on test suite as PR comment
         uses: mshick/add-pr-comment@v2
         with:
-          message-id: test-suite-report-${{ matrix.schematic-version }}
+          message-id: test-suite-report-${{ env.SCHEMATIC_VERSION }}
           message-path: |
             tests/test-suite-report.md
 
       - name: Upload test artifacts
         uses:  actions/upload-artifact@v4
         with:
-          name: test-logs-${{ matrix.schematic-version }}
+          name: test-logs-${{ env.SCHEMATIC_VERSION }}
           path: tests/**/logs
 

NF.jsonld

@@ -1093,6 +1093,8 @@
       "@id" : "bts:Schwannomatosis-NEC"
     }, {
       "@id" : "bts:SporadicSchwannoma"
+    }, {
+      "@id" : "bts:NoonanSyndrome"
     }, {
       "@id" : "bts:NotApplicable"
     } ],
@@ -6071,6 +6073,8 @@
       "@id" : "bts:LeicaS9Stereomicroscope"
     }, {
       "@id" : "bts:PhilipsAchieva3T"
+    }, {
+      "@id" : "bts:GEPremier3T"
     }, {
       "@id" : "bts:ZenoElectronicWalkway"
     }, {
@@ -10059,6 +10063,17 @@
     },
     "sms:displayName" : "icNF97.2b",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:NoonanSyndrome",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "NoonanSyndrome",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "Noonan Syndrome",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:plink",
     "@type" : "rdfs:Class",
@@ -14910,6 +14925,17 @@
     },
     "sms:displayName" : "University of Colorado Boulder",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:GEPremier3T",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "GEPremier3T",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "GE Premier 3T",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:UniversityofTexasSouthwesternMedicalCenter",
     "@type" : "rdfs:Class",

modules/Assay/Platform.yaml

@@ -190,6 +190,9 @@ enums:
       Philips Achieva 3T:
         description: Complete 3T MRI system, it offers an extremely broad clinical reach from routine head, spine and musculoskeletal imaging to the most advanced exams.
         source: https://clinicalimagingsystems.com/product/philips-achieva-3-0t-mri-scanner/
+      GE Premier 3T:
+        description: The GE Premier 3T is an advanced MRI scanner that offers high-resolution imaging capabilities and a 70 cm wide bore for patient comfort
+        source: ChatGPT (May 7 2024)
       Zeno Electronic Walkway:
         description: System for gait analysis.
         source: https://pubmed.ncbi.nlm.nih.gov/29286982/

modules/Sample/Diagnosis.yaml

@@ -12,7 +12,7 @@ enums:
       #  meaning: https://www.ebi.ac.uk/ols/ontologies/cco/terms?iri=http%3A%2F%2Fidentifiers.org%2Fomim%2F101000
       Schwannomatosis:
         description: A rare genetic disorder characterized by the presence of multiple schwannomas.
-        meaning: https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C6557
+        meaning: http://purl.obolibrary.org/obo/NCIT_C6557
       NF2-related schwannomatosis:
         description: Previously known as Neurofibromatosis type 2.
       SMARCB1-related schwannomatosis:
@@ -26,6 +26,9 @@ enums:
           Most schwannomas originate from the eighth cranial nerve, whereas neurofibromas more commonly arise along the spinal nerve roots.
         notes:
         - Not in NCIT as of 2023-06-07
+      Noonan Syndrome: 
+        description: A rare, highly variable, multisystemic disorder mainly characterized by short stature, distinctive facial features, congenital heart defects, cardiomyopathy and an increased risk to develop tumors in childhood.
+        meaning: http://www.orpha.net/ORDO/Orphanet_648
       Not Applicable:
 
   AgeGroupEnum: