first attempt to represent duo as json-schema

services/workers/src/test/java/org/sagebionetworks/schema/worker/JsonSchemaWorkerIntegrationTest.java

@@ -209,7 +209,7 @@ public String loadStringFromClasspath(String name) throws Exception {
 
 	@Test
 	public void testMainUseCase() throws Exception {
-		bootstrapAndCreateOrganization();
+		bootstrapAndCreateOrganization("my.organization");
 		String[] schemasToRegister = { "pets/PetType.json", "pets/Pet.json", "pets/CatBreed.json", "pets/DogBreed.json",
 				"pets/Cat.json", "pets/Dog.json", "pets/PetPhoto.json" };
 		for (String fileName : schemasToRegister) {
@@ -252,11 +252,11 @@ public void testMainUseCase() throws Exception {
 		printJson(result);
 	}
 
-	void bootstrapAndCreateOrganization() throws RecoverableMessageException, InterruptedException {
+	void bootstrapAndCreateOrganization(String organizationName) throws RecoverableMessageException, InterruptedException {
 		jsonSchemaManager.truncateAll();
 		schemaBootstrap.bootstrapSynapseSchemas();
 		CreateOrganizationRequest createOrgRequest = new CreateOrganizationRequest();
-		createOrgRequest.setOrganizationName("my.organization");
+		createOrgRequest.setOrganizationName(organizationName);
 		organization = jsonSchemaManager.createOrganziation(adminUserInfo, createOrgRequest);
 	}
 
@@ -288,7 +288,7 @@ public void testGetValidationSchemaWorker() throws AssertionError, AsynchJobFail
 
 	@Test
 	public void testEntitySchemaValidation() throws Exception {
-		bootstrapAndCreateOrganization();
+		bootstrapAndCreateOrganization("my.organization");
 		String projectId = entityManager.createEntity(adminUserInfo, new Project(), null);
 		Project project = entityManager.getEntity(adminUserInfo, projectId, Project.class);
 
@@ -352,7 +352,7 @@ public void testCreateWithDryRun() throws Exception {
 
 	@Test
 	public void testEntitySchemaValidationWithBoolean() throws Exception {
-		bootstrapAndCreateOrganization();
+		bootstrapAndCreateOrganization("my.organization");
 		String projectId = entityManager.createEntity(adminUserInfo, new Project(), null);
 		Project project = entityManager.getEntity(adminUserInfo, projectId, Project.class);
 
@@ -397,7 +397,7 @@ public void testEntitySchemaValidationWithBoolean() throws Exception {
 	@Test
 	public void testNoSemanticVersionSchemaRevalidationWithSchemaChange() throws Exception {
 		// PLFM-6757
-		bootstrapAndCreateOrganization();
+		bootstrapAndCreateOrganization("my.organization");
 		String projectId = entityManager.createEntity(adminUserInfo, new Project(), null);
 		Project project = entityManager.getEntity(adminUserInfo, projectId, Project.class);
 
@@ -683,6 +683,91 @@ public void testValidationSchemaIndexWithReindexingAndRevalidation() throws Exce
 		waitForValidationResultsToBeNotFound(adminUserInfo, folderId);
 	}
 
+	@Test
+	public void testDuoSchema() throws Exception {
+		bootstrapAndCreateOrganization("ebispot.duo");
+		String[] schemasToRegister = { "schema/DUO/hmb.json", "schema/DUO/irb.json", "schema/DUO/duo.json"};
+		for (String fileName : schemasToRegister) {
+			JsonSchema schema = getSchemaFromClasspath(fileName);
+			registerSchema(schema);
+		}
+
+		JsonSchema validationSchema = jsonSchemaManager.getValidationSchema("ebispot.duo-duo");
+		assertNotNull(schemaBootstrap);
+		printJson(validationSchema);
+		assertNotNull(validationSchema.getDefinitions());
+		assertTrue(validationSchema.getDefinitions().containsKey("ebispot.duo-D0000006"));
+		assertTrue(validationSchema.getDefinitions().containsKey("ebispot.duo-D0000021"));
+
+
+		String validJsonFile = loadStringFromClasspath("schema/DUO/ValidDuoFile.json");
+		JSONObject validJson = new JSONObject(validJsonFile);
+		JsonSubject mockSubject = Mockito.mock(JsonSubject.class);
+		when(mockSubject.toJson()).thenReturn(validJson);
+		// this schema should be valid
+		ValidationResults result = jsonSchemaValidationManager.validate(validationSchema, mockSubject);
+		assertNotNull(result);
+		assertTrue(result.getIsValid());
+	}
+
+	@Test
+	public void testDuoSchemaAppliedAgainstValidFileJson() throws Exception {
+		bootstrapAndCreateOrganization("ebispot.duo");
+		jsonSchemaManager.createOrganziation(adminUserInfo, new CreateOrganizationRequest().setOrganizationName("some.project"));
+		String[] schemasToRegister = { 
+				"schema/DUO/D0000001.json",
+				"schema/DUO/D0000004.json",
+				"schema/DUO/D0000006.json",
+				"schema/DUO/D0000007.json",
+				"schema/DUO/D0000011.json",
+				"schema/DUO/D0000012.json",
+				"schema/DUO/D0000015.json",
+				"schema/DUO/D0000016.json",
+				"schema/DUO/D0000018.json",
+				"schema/DUO/D0000019.json",
+				"schema/DUO/D0000020.json",
+				"schema/DUO/D0000021.json",
+				"schema/DUO/D0000022.json",
+				"schema/DUO/D0000024.json",
+				"schema/DUO/D0000025.json",
+				"schema/DUO/D0000026.json",
+				"schema/DUO/D0000027.json",
+				"schema/DUO/D0000028.json",
+				"schema/DUO/D0000029.json",
+				"schema/DUO/D0000042.json",
+				"schema/DUO/D0000043.json",
+				"schema/DUO/D0000044.json",
+				"schema/DUO/D0000045.json",
+				"schema/DUO/D0000046.json",
+				"schema/DUO/duo.json",
+				"schema/DUO/DuoMainStory.json",
+		};
+		for (String fileName : schemasToRegister) {
+			JsonSchema schema = getSchemaFromClasspath(fileName);
+			registerSchema(schema);
+		}
+
+		JsonSchema duoMain = jsonSchemaManager.getValidationSchema("ebispot.duo-duo");
+		assertNotNull(duoMain);
+		printJson(duoMain);
+
+		JsonSchema validationSchema = jsonSchemaManager.getValidationSchema("some.project-main");
+		assertNotNull(validationSchema);
+		printJson(validationSchema);
+
+		String[] validJsonFiles = { "schema/DUO/ValidSyn1.json", "schema/DUO/ValidSyn4.json" };
+		for (String schemaFile : validJsonFiles) {
+			String validJsonFile = loadStringFromClasspath(schemaFile);
+			JSONObject validJson = new JSONObject(validJsonFile);
+			JsonSubject mockSubject = Mockito.mock(JsonSubject.class);
+			when(mockSubject.toJson()).thenReturn(validJson);
+			// this schema should be valid
+			ValidationResults result = jsonSchemaValidationManager.validate(validationSchema, mockSubject);
+			assertNotNull(result);
+			assertTrue(result.getIsValid());
+		}
+	}
+
 	/**
 	 * Wait for the validation results
 	 * 

services/workers/src/test/resources/schema/DUO/D0000001.json

@@ -0,0 +1,6 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000001",
+	"title": "data use permission",
+	"description":"A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used."
+}

services/workers/src/test/resources/schema/DUO/D0000004.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000004",
+	"title": "no restriction",
+	"properties": {
+		"NRES": {
+			"type": "boolean",
+			"description": "This data use permission indicates there is no restriction on use.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000006.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000006",
+	"title": "health or medical or biomedical research",
+	"properties": {
+		"HMB": {
+			"type": "boolean",
+			"description": "This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000007.json

@@ -0,0 +1,33 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000007",
+	"title": "disease specific research",
+	"properties": {
+		"DS": {
+			"type": "boolean",
+			"description": "This data use permission indicates that use is allowed provided it is related to the specified disease.",
+			"default": "false"
+		}
+	},
+	"if": {
+		"properties": {
+			"DS": {
+				"const": true
+			}
+		}
+	},
+	"then": {
+		"properties": {
+			"DS_disease": {
+				"type": "string",
+				"description": "DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md",
+				"enum": [
+					"cancer",
+					"alzheimer",
+					"amnesia",
+					"..."
+				]
+			}
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000011.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000011",
+	"title": "population origins or ancestry research only",
+	"properties": {
+		"POA": {
+			"type": "boolean",
+			"description": "This data use permission indicates that use of the data is limited to the study of population origins or ancestry.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000012.json

@@ -0,0 +1,31 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000012",
+	"title": "research specific restrictions",
+	"properties": {
+		"RS": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that use is limited to studies of a certain research type.",
+			"default": "false"
+		}
+	},
+	"if": {
+		"properties": {
+			"RS": {
+				"const": true
+			}
+		}
+	},
+	"then": {
+		"properties": {
+			"RS_research_type": {
+				"type": "string",
+				"description": "...",
+				"enum": [
+					"cancer",
+					"..."
+				]
+			}
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000015.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000015",
+	"title": "no general methods research",
+	"properties": {
+		"NMDS": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000016.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000016",
+	"title": "genetic studies only",
+	"properties": {
+		"GSO": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000018.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000018",
+	"title": "not for profit, non commercial use only",
+	"properties": {
+		"NPUNCU": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000019.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000019",
+	"title": "publication required",
+	"properties": {
+		"PUB": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000020.json

@@ -0,0 +1,27 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000020",
+	"title": "collaboration required",
+	"properties": {
+		"COL": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).",
+			"default": "false"
+		}
+	},
+	"if": {
+		"properties": {
+			"COL": {
+				"const": true
+			}
+		}
+	},
+	"then": {
+		"properties": {
+			"COL_PI": {
+				"type": "string",
+				"description": "This could be coupled with a string describing the primary study investigator(s)."
+			}
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000021.json

@@ -0,0 +1,12 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000021",
+	"title": "ethics approval required",
+	"properties": {
+		"IRB": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.",
+			"default": "false"
+		}
+	}
+}

services/workers/src/test/resources/schema/DUO/D0000022.json

@@ -0,0 +1,27 @@
+{
+	"$schema": "http://json-schema.org/draft-07/schema",
+	"$id": "ebispot.duo-D0000022",
+	"title": "geographical restriction",
+	"properties": {
+		"GS": {
+			"type": "boolean",
+			"description": "This data use modifier indicates that use is limited to within a specific geographic region.",
+			"default": "false"
+		}
+	},
+	"if": {
+		"properties": {
+			"GS": {
+				"const": true
+			}
+		}
+	},
+	"then": {
+		"properties": {
+			"GS_location": {
+				"type": "string",
+				"description": "This should be coupled with an ontology term describing the geographical location the restriction applies to."
+			}
+		}
+	}
+}