diff --git a/.github/workflows/schematic-ci.yml b/.github/workflows/schematic-ci.yml index 00017b9e..819dd0a8 100644 --- a/.github/workflows/schematic-ci.yml +++ b/.github/workflows/schematic-ci.yml @@ -16,7 +16,7 @@ jobs: if: ${{ !contains(github.event.head_commit.message, '[skip schematic]') }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.pull_request.head.ref }} persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. @@ -45,27 +45,33 @@ jobs: # Additionally test PRs test: name: Test with schematic - if: "!contains( github.event.pull_request.labels.*.name, 'skip tests')" needs: [build] - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest env: SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} permissions: pull-requests: write strategy: matrix: - schematic-version: [23.9.1] + schematic-version: [24.1.1] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.pull_request.head.ref }} fetch-depth: 1 + - uses: actions/setup-python@v5 + with: + python-version: '3.10.12' + - name: Setup schematic id: setup-schematic - run: pip3 install schematicpy==${{ matrix.schematic-version }} + run: pip install schematicpy==${{ matrix.schematic-version }} + - name: Sanity-check successful installation and version + run: pip show schematicpy + - name: Test generate working-directory: tests/generate continue-on-error: true diff --git a/NF.jsonld b/NF.jsonld index 8d800c29..afd7fdf3 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -16,7 +16,13 @@ }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { + "@id" : "bts:EutropicsPharmaceuticals" + }, { "@id" : "bts:CincinnatiChildren'sHospitalMedicalCenter" + }, { + "@id" : "bts:MemorialSloaneKetteringCancerCenter" + }, { + "@id" : "bts:Dana-FarberCancerInstitute" }, { "@id" : "bts:MassachusettsGeneralHospital" }, { @@ -109,6 +115,8 @@ "@id" : "bts:VanAndelResearchInstitute" }, { "@id" : "bts:UniversityofCalifornia,Irvine" + }, { + "@id" : "bts:UniversityofCambridge" }, { "@id" : "bts:UniversityofNorthCarolina,Greensboro" }, { @@ -11950,6 +11958,17 @@ }, "sms:displayName" : "CRISPR", "sms:required" : "sms:false" + }, { + "@id" : "bts:Dana-FarberCancerInstitute", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Dana-FarberCancerInstitute", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Dana-Farber Cancer Institute", + "sms:required" : "sms:false" }, { "@id" : "bts:AlbertEinsteinCollegeofMedicine", "@type" : "rdfs:Class", @@ -13776,6 +13795,17 @@ }, "sms:displayName" : "calcium retention capacity assay", "sms:required" : "sms:false" + }, { + "@id" : "bts:MemorialSloaneKetteringCancerCenter", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MemorialSloaneKetteringCancerCenter", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Memorial Sloane Kettering Cancer Center", + "sms:required" : "sms:false" }, { "@id" : "bts:HS-PSS", "@type" : "rdfs:Class", @@ -13985,6 +14015,17 @@ }, "sms:displayName" : "Rockefeller University", "sms:required" : "sms:false" + }, { + "@id" : "bts:UniversityofCambridge", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "UniversityofCambridge", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "University of Cambridge", + "sms:required" : "sms:false" }, { "@id" : "bts:braingrowthmeasurement", "@type" : "rdfs:Class", @@ -21861,6 +21902,17 @@ }, "sms:displayName" : "FLIPR high-throughput cellular screening", "sms:required" : "sms:false" + }, { + "@id" : "bts:EutropicsPharmaceuticals", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EutropicsPharmaceuticals", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Eutropics Pharmaceuticals", + "sms:required" : "sms:false" }, { "@id" : "bts:Nf1-OPG", "@type" : "rdfs:Class", diff --git a/modules/Other/Organization.yaml b/modules/Other/Organization.yaml index eb6203e5..7a471d7f 100644 --- a/modules/Other/Organization.yaml +++ b/modules/Other/Organization.yaml @@ -1,8 +1,11 @@ enums: Institution: permissible_values: + Eutropics Pharmaceuticals: Cincinnati Children's Hospital Medical Center: meaning: https://ror.org/01hcyya48 + Memorial Sloane Kettering Cancer Center: + Dana-Farber Cancer Institute: Massachusetts General Hospital: description: '' University of Tennessee, Health Science Center: @@ -95,6 +98,7 @@ enums: description: '' University of California, Irvine: description: '' + University of Cambridge: University of North Carolina, Greensboro: description: '' University of Toledo: diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh index 1176f650..5785a96a 100755 --- a/tests/generate/basic_templates.sh +++ b/tests/generate/basic_templates.sh @@ -37,8 +37,7 @@ mkdir -p $LOG_DIR for i in ${!TEMPLATES[@]} do echo ">>>>>>> Generating ${TEMPLATES[$i]}" - schematic manifest --config config.yml \ - get -dt ${TEMPLATES[$i]} --title ${TEMPLATES[$i]} -s | tee $LOG_DIR/${TEMPLATES[$i]%.*}_log.txt + schematic manifest --config ./config.yml get -dt "${TEMPLATES[$i]}" --title "${TEMPLATES[$i]}" -s | tee $LOG_DIR/${TEMPLATES[$i]%.*}_log sleep $SLEEP_THROTTLE done diff --git a/tests/test-suite-report.Rmd b/tests/test-suite-report.Rmd index 46c1140a..19a35af9 100644 --- a/tests/test-suite-report.Rmd +++ b/tests/test-suite-report.Rmd @@ -27,7 +27,7 @@ md_link <- function (url) { ```{r parse-generation-logs, echo=FALSE} gen_logs <- list.files("generate/logs", full.names = TRUE) -templates <- gsub("_.*", "", basename(gen_logs)) +templates <- gsub("_log", "", basename(gen_logs)) gen_test_results <- lapply(gen_logs, readLines) gen_test_links <- sapply(gen_test_results, md_link) gen_test_reaction <- sapply(lengths(gen_test_results), test_reaction)