fix makefile to run withotu version flag

TranslatorSRI · Apr 25, 2024 · fa6a7f4 · fa6a7f4
2 parents fe17787 + ff0f67a
commit fa6a7f4
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Showing 35 changed files with 2,129 additions and 2,534 deletions.
diff --git a/Makefile b/Makefile
@@ -108,7 +108,7 @@ gen-examples:
 
 gen-project: $(PYMODEL)
 	$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
-	$(RUN) gen-pydantic --pydantic-version 2 src/translator_testing_model/schema/translator_testing_model.yaml > $(PYMODEL)/pydanticmodel.py
+	$(RUN) gen-pydantic src/translator_testing_model/schema/translator_testing_model.yaml > $(PYMODEL)/pydanticmodel.py
 
 
 test: test-schema test-python test-examples

diff --git a/examples/Bad-TestAsset-001.yaml b/examples/Bad-TestAsset-001.yaml
@@ -1,38 +1,15 @@
 # Example TestAsset data object
 ---
-# TODO: the TestAsset example data needs further elaboration
 
-#
-#   TestAsset:
-#    description: >-
-#      Represents a Test Asset, which is a single specific instance of
-#      TestCase-agnostic semantic parameters representing the
-#      specification of a Translator test target with inputs and (expected) outputs.
-#    is_a: TestEntity
-#    slots:
-#      - input_id
-#      - input_name
-#      - predicate
-#      - output_id
-#      - output_name
-#      - expected_output
-#      - test_issue
-#      - semantic_severity
-#      - in_v1
-#      - well_known
-#      - test_metadata
-#    slot_usage:
-#      id:
-#        aliases: ["AssetIdentifier"]
-#        range: uriorcurie
-#      tags:
-#        description: >-
-#          One or more 'tags' slot values (inherited from TestEntity) should generally
-#          be defined to specify TestAsset membership in a "Block List" collection
-#
 # Bad Query 1 - Missing required identifier?
 
 # id: example:TestAsset001
-name: foo bar
-description: This is a test asset
-test_meta_data: { "foo": "bar" }
+name: TestAsset001
+description: Fingolimod treats multiple sclerosis
+input_id: PUBCHEM.COMPOUND:107970
+predicate_name: treats
+output_id: MONDO:0005301
+expected_output: Acceptable
+test_runner_settings:
+  - "inferred"
+  - "test"
diff --git a/examples/Bad-TestCase-001.yaml b/examples/Bad-TestCase-001.yaml
diff --git a/examples/Bad-TestEntity-001.yaml b/examples/Bad-TestEntity-001.yaml
@@ -11,6 +11,8 @@
 #      - id
 #      - name
 #      - description
+#      - tags
+#      - test_runner_settings
 #
 # where the slots are:
 #

diff --git a/examples/Bad-TestEntity-002.yaml-uriorcurie_should_fail_but_does_not b/examples/Bad-TestEntity-002.yaml-uriorcurie_should_fail_but_does_not
@@ -11,6 +11,8 @@
 #      - id
 #      - name
 #      - description
+#      - tags
+#      - test_runner_settings
 #
 # where the slots are:
 #

diff --git a/examples/Good-AcceptanceTestAsset-001.yaml b/examples/Good-AcceptanceTestAsset-001.yaml
@@ -1,6 +1,7 @@
 # Example AcceptanceTestAsset data object
 ---
 # TODO: the AcceptanceTestAsset example data needs further elaboration
+#       (there don't seem to be any required: true AcceptanceTestAsset-specific fields)
 
 #
 #  AcceptanceTestAsset:
@@ -21,14 +22,16 @@
 #      - notes
 #
 id: example:AcceptanceTestAsset001
-name: foo bar
-description: This is a acceptance test case'
-runner_settings:
+name: AcceptanceTestAsset001
+description: Iron treats Aceruloplasminemia
+input_id: MONDO:0011426
+predicate_name: treats
+output_id: DRUGBANK:DB01592
+expected_output: NeverShow
+test_metadata:
+  id: "test:1"
+  test_source: SMURF
+test_runner_settings:
   - "inferred"
   - "test"
-test_metadata:
-  id: 1
-  test_source: SMURF,
-  test_reference: https://github.com/NCATSTranslator/Feedback/issues/506
-  test_objective: AcceptanceTest
 
diff --git a/examples/Good-AcceptanceTestCase-001.yaml b/examples/Good-AcceptanceTestCase-001.yaml
@@ -13,10 +13,20 @@
 id: example:AcceptanceTestCase001
 name: foo bar
 description: This is an acceptance test case
+test_runner_settings:
+  - "inferred"
+  - "test"
 test_assets:
-  - id: example:TestAsset001
-    name: foo bar
-    description: This is a test asset
-    runner_settings:
+  - id: example:AcceptanceTestAsset001
+    name: AcceptanceTestAsset001
+    description: Iron treats Aceruloplasminemia
+    input_id: MONDO:0011426
+    predicate_name: treats
+    output_id: DRUGBANK:DB01592
+    expected_output: NeverShow
+    test_runner_settings:
       - "inferred"
-      - "test"
+      - "test"
+    test_metadata:
+        id: "test:1"
+        test_source: SMURF
diff --git a/examples/Good-TestAsset-001.json b/examples/Good-TestAsset-001.json
@@ -1,16 +1,13 @@
 {
   "id": "example:TestAsset001",
-  "name": "foo bar",
-  "description": "This is a test asset",
-  "runner_settings": ["inferred", "test"],
+  "name": "TestAsset001",
+  "description": "Fingolimod treats multiple sclerosis",
+  "input_id": "PUBCHEM.COMPOUND:107970",
+  "predicate_name": "treats",
+  "output_id": "MONDO:0005301",
+  "expected_output": "Acceptable",
+  "test_runner_settings": ["inferred", "test"],
   "test_metadata": {
-        "id": "1",
-        "name": null,
-        "description": null,
-        "tags": [],
-        "test_source": "SMURF",
-        "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/506",
-        "test_objective": "AcceptanceTest",
-        "test_annotations": []
+    "id": "example:TestAsset001"
   }
 }
diff --git a/examples/Good-TestAsset-001.yaml b/examples/Good-TestAsset-001.yaml
@@ -1,7 +1,8 @@
 # Example TestAsset data object
 ---
-# TODO: the TestAsset example data needs further elaboration
+# TODO: the TestAsset example data may need further elaboration
 
+#
 #
 #   TestAsset:
 #    description: >-
@@ -12,15 +13,20 @@
 #    slots:
 #      - input_id
 #      - input_name
-#      - predicate
+#      - input_category
+#      - predicate_id
+#      - predicate_name
 #      - output_id
 #      - output_name
+#      - output_category
+#      - association
+#      - qualifiers
 #      - expected_output
 #      - test_issue
 #      - semantic_severity
 #      - in_v1
 #      - well_known
-#      - runner_settings
+#      - test_reference
 #    slot_usage:
 #      id:
 #        aliases: ["AssetIdentifier"]
@@ -29,7 +35,7 @@
 #        description: >-
 #          One or more 'tags' slot values (inherited from TestEntity) should generally
 #          be defined to specify TestAsset membership in a "Block List" collection
-#      runner_settings:
+#      test_runner_settings:
 #        description: >-
 #          Settings for the test harness, e.g. "inferred"
 #
@@ -38,19 +44,16 @@ name: TestAsset001
 description: Iron treats Aceruloplasminemia
 input_id: MONDO:0011426
 input_name: Aceruloplasminemia
-predicate: Treats
+predicate_name: treats
 output_id: DRUGBANK:DB01592
 output_name: Iron (PUBCHEM)
 expected_output: NeverShow
 test_reference: https://github.com/NCATSTranslator/Feedback/issues/506
 semantic_severity: NotApplicable
 in_v1: True
 well_known: False
-runner_settings:
-  - "inferred"
-  - "test"
 test_metadata:
-  id: 1
-  test_source: SMURF,
-  test_reference: https://github.com/NCATSTranslator/Feedback/issues/506
-  test_objective: AcceptanceTest
+  id: "example:TestAsset001"
+test_runner_settings:
+  - "inferred"
+  - "test"
diff --git a/examples/Good-TestCase-001.json b/examples/Good-TestCase-001.json
@@ -5,9 +5,17 @@
   "test_assets": [
     {
       "id": "example:TestAsset001",
-      "name": "foo bar",
-      "description": "This is a test asset",
-      "runner_settings": ["inferred","test_setting"]
+      "name": "TestAsset001",
+      "description": "Fingolimod treats multiple sclerosis",
+      "input_id": "PUBCHEM.COMPOUND:107970",
+      "predicate_name": "treats",
+      "output_id": "MONDO:0005301",
+      "expected_output": "Acceptable",
+      "test_runner_settings": ["inferred", "test"],
+      "test_metadata": {
+        "id": "example:TestMetadata001"
+      }
     }
-  ]
+  ],
+  "test_runner_settings": ["inferred", "test"]
 }
diff --git a/examples/Good-TestCase-001.yaml b/examples/Good-TestCase-001.yaml
@@ -2,6 +2,7 @@
 ---
 # TODO: the TestCase example data needs further elaboration
 #
+#
 #  TestCase:
 #    description: >-
 #      Represents a single enumerated instance of Test Case, derived from a
@@ -34,10 +35,20 @@
 id: example:TestCase001
 name: foo bar
 description: This is a test case
+# NOTE: we only provide the minimal set of TestAsset slots where required: true
 test_assets:
   - id: example:TestAsset001
-    name: foo bar
-    description: This is a test asset
-    runner_settings:
+    name: TestAsset001
+    input_id: MONDO:0011426
+    predicate_name: treats
+    output_id: DRUGBANK:DB01592
+    expected_output: NeverShow
+    test_runner_settings:
       - "inferred"
       - "test"
+    test_metadata:
+      id: test:1
+      test_source: SMURF
+test_runner_settings:
+  - "inferred"
+  - "test"
diff --git a/examples/Good-TestCaseSpecification-001.yaml b/examples/Good-TestCaseSpecification-001.yaml
@@ -11,3 +11,7 @@
 id: example:TestCaseSpecification001
 name: foo bar
 description: This is a test case specification
+test_case_specification_runner_settings:
+  - "inferred"
+  - "test"
+
diff --git a/examples/Good-TestEntity-Complete.yaml b/examples/Good-TestEntity-Complete.yaml
@@ -11,6 +11,8 @@
 #      - id
 #      - name
 #      - description
+#      - tags
+#      - test_runner_settings
 #
 # where the slots are:
 #

diff --git a/examples/Good-TestSuite-001.yaml b/examples/Good-TestSuite-001.yaml
@@ -18,3 +18,6 @@
 id: example:TestSuite001
 name: foo bar
 description: This is a test suite
+test_metadata:
+  id: test:1
+  test_source: SMURF
diff --git a/examples/SampleTestAssetList.json b/examples/SampleTestAssetList.json
@@ -1,20 +1,30 @@
 [
   {
     "id": "example:TestAsset001",
-    "name": "foo bar",
-    "description": "This is a test asset",
-    "runner_settings": ["inferred","test_setting"]
+    "name": "TestAsset001",
+    "description": "Fingolimod treats multiple sclerosis",
+    "input_id": "PUBCHEM.COMPOUND:107970",
+    "predicate_name": "treats",
+    "output_id": "MONDO:0005301",
+    "expected_output": "Acceptable",
+    "runner_settings": ["inferred", "test"],
+    "test_metadata": {
+      "id": "example:TestAsset001",
+      "source": "SMURF"
+    }
   },
   {
     "id": "example:TestAsset002",
-    "name": "tweedle dee",
-    "description": "This is another test asset",
-    "runner_settings": ["inferred","test_setting"]
-  },
-  {
-    "id": "example:TestAsset003",
-    "name": "tweedle dum",
-    "description": "This is yetanuder test asset",
-    "runner_settings": ["inferred","test_setting"]
+    "name": "TestAsset002",
+    "description": "Carbamazepine treats Cerebral palsy",
+    "input_id": "PUBCHEM.COMPOUND:2554",
+    "predicate_name": "treats",
+    "output_id": "MONDO:0006497",
+    "expected_output": "number_2_Acceptable",
+    "runner_settings": ["inferred", "test"],
+    "test_metadata": {
+      "id": "example:TestAsset001",
+      "source": "SMURF"
+    }
   }
 ]