Improve tests

- Fix EMDataset-001.yaml so it validates - (Breaking) Replace `type` with `instrument_type` or `molecular_type`. Otherwise it breaks python tests. - (Breaking) Remove multivalued from institution - Fix datetime range Running `rm -r examples/output; make test-examples` still fails
osc-em · Aug 22, 2024 · 0b2ab23 · 0b2ab23
1 parent 3719334
commit 0b2ab23
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Showing 19 changed files with 1,173 additions and 1,068 deletions.
diff --git a/Makefile b/Makefile
@@ -133,7 +133,8 @@ ifneq ($(strip ${GEN_TS_ARGS}),)
 	$(RUN) gen-typescript ${GEN_TS_ARGS} $(SOURCE_SCHEMA_PATH) >${DEST}/typescript/${SCHEMA_NAME}.ts
 endif
 
-test: test-schema test-python test-examples
+test: test-validate test-examples test-python
+.PHONY: test test-validate test-examples test-python
 
 test-schema:
 	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)
@@ -151,6 +152,9 @@ else
 	$(info Ok)
 endif
 
+test-validate:
+	$(RUN) linkml-validate -s $(SOURCE_SCHEMA_PATH) src/data/examples/*.yaml
+
 convert-examples-to-%:
 	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml"))
 
@@ -169,7 +173,7 @@ examples/output: src/oscem_schemas/schema/oscem_schemas.yaml
 		--output-formats json \
 		--output-formats yaml \
 		--counter-example-input-directory src/data/examples/invalid \
-		--input-directory src/data/examples/valid \
+		--input-directory src/data/examples \
 		--output-directory $@ \
 		--schema $< > $@/README.md
 

diff --git a/README.md b/README.md
@@ -32,10 +32,16 @@ Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
 ## Developer Documentation
 
 <details>
-Use the `make` command to generate project artefacts:
+Use the `make` command to generate project artifacts:
 
+* `make setup`: one-time setup
 * `make all`: make everything
 * `make deploy`: deploys site
+* `make lint`: check syntax
+* `make test`: run tests
+* `make serve`: run docs locally on http://127.0.0.1:8000/oscem-schemas/
+* `make clean` : remove generated files
+
 </details>
 
 ## Credits

diff --git a/project/excel/oscem_schemas.xlsx b/project/excel/oscem_schemas.xlsx
diff --git a/project/graphql/oscem_schemas.graphql b/project/graphql/oscem_schemas.graphql
@@ -14,7 +14,7 @@ type Acquisition
     dosePerMovie: Float!
     energyFilter: EnergyFilter
     imageSize: ImageSize
-    datetime: Datetime!
+    datetime: Any!
     exposureTime: Float
     cryogen: String
     framesPerMovie: Integer
@@ -30,11 +30,15 @@ type Acquisition
     gainrefFlipRotate: String
   }
 
+type Any
+  {
+  }
+
 type Author
   {
     firstName: String
     workStatus: Boolean
-    institution: [Institution]!
+    institution: Institution!
     orcid: String!
     country: String!
     role: String
@@ -54,7 +58,7 @@ type BoundingBox2D
 type ChromaticAberrationCorrector
   {
     used: Boolean!
-    type: String!
+    instrumentType: String!
   }
 
 type EMDataset
@@ -131,7 +135,7 @@ type Ligand
 type Molecule
   {
     nameMol: String!
-    type: String!
+    molecularType: String!
     molecularClass: MoleculeClassEnum!
     sequence: String!
     naturalSource: String!
@@ -143,7 +147,7 @@ type Molecule
 
 type OverallMolecule
   {
-    type: String!
+    molecularType: String!
     nameSample: String!
     source: String!
     molecularWeight: Float
@@ -161,7 +165,7 @@ type Person
 type Phaseplate
   {
     used: Boolean!
-    type: String!
+    instrumentType: String!
   }
 
 type QuantityValue
@@ -216,7 +220,7 @@ type Specimen
 type SphericalAberrationCorrector
   {
     used: Boolean!
-    type: String!
+    instrumentType: String!
   }
 
 type TiltAngle

diff --git a/project/jsonld/oscem_schemas.context.jsonld b/project/jsonld/oscem_schemas.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-22T23:22:33",
+      "generation_date": "2024-08-23T00:59:03",
       "source": "oscem_schemas.yaml"
    },
    "@context": {
@@ -89,7 +89,7 @@
          "@id": "https://w3id.org/osc-em/instrument/cs"
       },
       "datetime": {
-         "@type": "xsd:dateTime",
+         "@type": "@id",
          "@id": "acquisition:datetime"
       },
       "detector": {
@@ -219,8 +219,8 @@
          "@type": "@id",
          "@id": "instrument"
       },
-      "type": {
-         "@id": "sample:/type"
+      "instrument_type": {
+         "@id": "acquisition:instrument_type"
       },
       "ligands": {
          "@type": "@id",
@@ -261,6 +261,9 @@
          },
          "@id": "sample:/molecular_class"
       },
+      "molecular_type": {
+         "@id": "sample:/molecular_type"
+      },
       "molecular_weight": {
          "@type": "xsd:float",
          "@id": "sample:/molecular_weight"
@@ -442,6 +445,9 @@
       "Acquisition": {
          "@id": "acquisition:Acquisition"
       },
+      "Any": {
+         "@id": "linkml:Any"
+      },
       "Author": {
          "@id": "https://w3id.org/osc-em/organizational/Author"
       },

diff --git a/project/jsonld/oscem_schemas.jsonld b/project/jsonld/oscem_schemas.jsonld
@@ -676,7 +676,18 @@
       "domain_of": [
         "Acquisition"
       ],
-      "range": "datetime",
+      "range": "Any",
+      "inlined": true,
+      "any_of": [
+        {
+          "range": "datetime",
+          "@type": "AnonymousSlotExpression"
+        },
+        {
+          "range": "date",
+          "@type": "AnonymousSlotExpression"
+        }
+      ],
       "@type": "SlotDefinition"
     },
     {
@@ -803,8 +814,7 @@
       "definition_uri": "https://w3id.org/osc-em/acquisitioninstrument_type",
       "description": "Details of a given specialist instrument",
       "from_schema": "https://w3id.org/osc-em/acquisition",
-      "slot_uri": "https://w3id.org/osc-em/acquisitiontype",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/acquisitioninstrument_type",
       "owner": "ChromaticAberrationCorrector",
       "domain_of": [
         "Phaseplate",
@@ -1093,7 +1103,7 @@
     {
       "name": "institution",
       "definition_uri": "https://w3id.org/osc-em/organizational/institution",
-      "description": "institution",
+      "description": "author's institution",
       "from_schema": "https://w3id.org/osc-em/organizational",
       "mappings": [
         "http://schema.org/Organization"
@@ -1104,7 +1114,6 @@
         "Author"
       ],
       "range": "Institution",
-      "multivalued": true,
       "inlined": true,
       "@type": "SlotDefinition"
     },
@@ -1285,8 +1294,7 @@
       "description": "Description of the overall supramolecular type, i.e., a complex",
       "title": "Type",
       "from_schema": "https://w3id.org/osc-em/sample",
-      "slot_uri": "https://w3id.org/osc-em/sample/type",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/sample/molecular_type",
       "owner": "Molecule",
       "domain_of": [
         "OverallMolecule",
@@ -2160,8 +2168,19 @@
       ],
       "is_usage_slot": true,
       "usage_slot_name": "datetime",
-      "range": "datetime",
+      "range": "Any",
       "required": true,
+      "inlined": true,
+      "any_of": [
+        {
+          "range": "datetime",
+          "@type": "AnonymousSlotExpression"
+        },
+        {
+          "range": "date",
+          "@type": "AnonymousSlotExpression"
+        }
+      ],
       "@type": "SlotDefinition"
     },
     {
@@ -2266,8 +2285,8 @@
       "from_schema": "https://w3id.org/osc-em/acquisition",
       "is_a": "instrument_type",
       "domain": "Phaseplate",
-      "slot_uri": "https://w3id.org/osc-em/acquisitiontype",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/acquisitioninstrument_type",
+      "alias": "instrument_type",
       "owner": "Phaseplate",
       "domain_of": [
         "Phaseplate"
@@ -2304,8 +2323,8 @@
       "from_schema": "https://w3id.org/osc-em/acquisition",
       "is_a": "instrument_type",
       "domain": "SphericalAberrationCorrector",
-      "slot_uri": "https://w3id.org/osc-em/acquisitiontype",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/acquisitioninstrument_type",
+      "alias": "instrument_type",
       "owner": "SphericalAberrationCorrector",
       "domain_of": [
         "SphericalAberrationCorrector"
@@ -2342,8 +2361,8 @@
       "from_schema": "https://w3id.org/osc-em/acquisition",
       "is_a": "instrument_type",
       "domain": "ChromaticAberrationCorrector",
-      "slot_uri": "https://w3id.org/osc-em/acquisitiontype",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/acquisitioninstrument_type",
+      "alias": "instrument_type",
       "owner": "ChromaticAberrationCorrector",
       "domain_of": [
         "ChromaticAberrationCorrector"
@@ -2558,7 +2577,7 @@
     {
       "name": "Author_institution",
       "definition_uri": "https://w3id.org/osc-em/organizational/institution",
-      "description": "institution",
+      "description": "author's institution",
       "from_schema": "https://w3id.org/osc-em/organizational",
       "mappings": [
         "http://schema.org/Organization"
@@ -2575,7 +2594,6 @@
       "usage_slot_name": "institution",
       "range": "Institution",
       "required": true,
-      "multivalued": true,
       "inlined": true,
       "@type": "SlotDefinition"
     },
@@ -2627,8 +2645,8 @@
       "from_schema": "https://w3id.org/osc-em/sample",
       "is_a": "molecular_type",
       "domain": "OverallMolecule",
-      "slot_uri": "https://w3id.org/osc-em/sample/type",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/sample/molecular_type",
+      "alias": "molecular_type",
       "owner": "OverallMolecule",
       "domain_of": [
         "OverallMolecule"
@@ -2726,8 +2744,8 @@
       "from_schema": "https://w3id.org/osc-em/sample",
       "is_a": "molecular_type",
       "domain": "Molecule",
-      "slot_uri": "https://w3id.org/osc-em/sample/type",
-      "alias": "type",
+      "slot_uri": "https://w3id.org/osc-em/sample/molecular_type",
+      "alias": "molecular_type",
       "owner": "Molecule",
       "domain_of": [
         "Molecule"
@@ -3761,6 +3779,18 @@
       "class_uri": "https://w3id.org/osc-em/tomography/TiltAngle",
       "@type": "ClassDefinition"
     },
+    {
+      "name": "Any",
+      "definition_uri": "https://w3id.org/osc-em/types/Any",
+      "description": "Any type, used as the base for type-narrowing.\n\nSee https://linkml.io/linkml/schemas/advanced.html",
+      "from_schema": "https://w3id.org/osc-em/types",
+      "mappings": [
+        "linkml:Any"
+      ],
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/linkml/Any",
+      "@type": "ClassDefinition"
+    },
     {
       "name": "Range",
       "definition_uri": "https://w3id.org/osc-em/types/Range",
@@ -3822,7 +3852,7 @@
   "source_file": "oscem_schemas.yaml",
   "source_file_date": "2024-08-22T23:20:17",
   "source_file_size": 1401,
-  "generation_date": "2024-08-22T23:22:33",
+  "generation_date": "2024-08-23T00:59:03",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/oscem_schemas.context.jsonld",