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catalog: add basic tests for workflows, #TASK-6445
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130
opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/WorkflowManagerTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| package org.opencb.opencga.catalog.managers; | ||
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| import org.junit.Before; | ||
| import org.junit.Test; | ||
| import org.junit.experimental.categories.Category; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.opencga.catalog.db.api.WorkflowDBAdaptor; | ||
| import org.opencb.opencga.catalog.exceptions.CatalogException; | ||
| import org.opencb.opencga.core.models.workflow.Workflow; | ||
| import org.opencb.opencga.core.models.workflow.WorkflowRepository; | ||
| import org.opencb.opencga.core.models.workflow.WorkflowScript; | ||
| import org.opencb.opencga.core.models.workflow.WorkflowUpdateParams; | ||
| import org.opencb.opencga.core.response.OpenCGAResult; | ||
| import org.opencb.opencga.core.testclassification.duration.MediumTests; | ||
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| import java.util.Arrays; | ||
| import java.util.Collections; | ||
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| import static org.junit.Assert.*; | ||
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| @Category(MediumTests.class) | ||
| public class WorkflowManagerTest extends AbstractManagerTest { | ||
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| private WorkflowManager workflowManager; | ||
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| @Before | ||
| public void setUp() throws Exception { | ||
| super.setUp(); | ||
| workflowManager = catalogManager.getWorkflowManager(); | ||
| } | ||
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| @Test | ||
| public void createWorkflowTest() throws CatalogException { | ||
| Workflow workflow = new Workflow() | ||
| .setId("workflow") | ||
| .setScripts(Collections.singletonList(new WorkflowScript("pipeline.nf", "echo 'Hello world!'", true))); | ||
| OpenCGAResult<Workflow> result = workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken); | ||
| assertEquals(1, result.getNumResults()); | ||
| assertNotNull(result.first()); | ||
| assertEquals(workflow.getId(), result.first().getId()); | ||
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| // Add repository to workflow | ||
| workflow.setId("workflow2"); | ||
| workflow.setRepository(new WorkflowRepository("blabla")); | ||
| CatalogException catalogException = assertThrows(CatalogException.class, | ||
| () -> workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken)); | ||
| assertTrue(catalogException.getMessage().contains("script") && catalogException.getMessage().contains("repository")); | ||
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| // Remove script from workflow | ||
| workflow.setScripts(Collections.emptyList()); | ||
| result = workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken); | ||
| assertEquals(1, result.getNumResults()); | ||
| assertNotNull(result.first()); | ||
| assertEquals(workflow.getId(), result.first().getId()); | ||
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| // Remove script and add two scripts with 2 mains | ||
| workflow.setId("workflow3"); | ||
| workflow.setRepository(null); | ||
| workflow.setScripts(Arrays.asList( | ||
| new WorkflowScript("script1", "echo 'Hello'", true), | ||
| new WorkflowScript("script2", "echo 'World'", true) | ||
| )); | ||
| catalogException = assertThrows(CatalogException.class, | ||
| () -> workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken)); | ||
| assertTrue(catalogException.getMessage().contains("script") && catalogException.getMessage().contains("main")); | ||
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| // Add one single script without main | ||
| workflow.setScripts(Collections.singletonList( | ||
| new WorkflowScript("script1", "echo 'Hello'", false) | ||
| )); | ||
| catalogException = assertThrows(CatalogException.class, | ||
| () -> workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken)); | ||
| assertTrue(catalogException.getMessage().contains("script") && catalogException.getMessage().contains("main")); | ||
| } | ||
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| @Test | ||
| public void workflowSearchTest() throws CatalogException { | ||
| Workflow workflow = new Workflow() | ||
| .setId("workflow") | ||
| .setScripts(Collections.singletonList(new WorkflowScript("pipeline.nf", "echo 'Hello world!'", true))); | ||
| workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken); | ||
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| workflow = new Workflow() | ||
| .setId("workflow2") | ||
| .setDraft(true) | ||
| .setScripts(Collections.singletonList(new WorkflowScript("pipeline.nf", "echo 'Hello world!'", true))); | ||
| workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken); | ||
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| OpenCGAResult<Workflow> search = workflowManager.search(studyFqn, new Query(), QueryOptions.empty(), ownerToken); | ||
| assertEquals(2, search.getNumResults()); | ||
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| Query query = new Query(WorkflowDBAdaptor.QueryParams.DRAFT.key(), true); | ||
| search = workflowManager.search(studyFqn, query, QueryOptions.empty(), ownerToken); | ||
| assertEquals(1, search.getNumResults()); | ||
| assertEquals("workflow2", search.first().getId()); | ||
| assertTrue(search.first().isDraft()); | ||
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| query = new Query(WorkflowDBAdaptor.QueryParams.DRAFT.key(), false); | ||
| search = workflowManager.search(studyFqn, query, QueryOptions.empty(), ownerToken); | ||
| assertEquals(1, search.getNumResults()); | ||
| assertEquals("workflow", search.first().getId()); | ||
| assertFalse(search.first().isDraft()); | ||
| } | ||
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| @Test | ||
| public void updateWorkflowTest() throws CatalogException { | ||
| Workflow workflow = new Workflow() | ||
| .setId("workflow") | ||
| .setScripts(Collections.singletonList(new WorkflowScript("pipeline.nf", "echo 'Hello world!'", true))); | ||
| workflowManager.create(studyFqn, workflow, INCLUDE_RESULT, ownerToken); | ||
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| WorkflowUpdateParams updateParams = new WorkflowUpdateParams() | ||
| .setName("newName") | ||
| .setDraft(true) | ||
| .setCreationDate("20240101000000") | ||
| .setModificationDate("20240201000000") | ||
| .setDescription("description"); | ||
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| OpenCGAResult<Workflow> update = workflowManager.update(studyFqn, workflow.getId(), updateParams, INCLUDE_RESULT, ownerToken); | ||
| assertEquals(1, update.getNumUpdated()); | ||
| Workflow updatedWorkflow = update.first(); | ||
| assertEquals(updateParams.getName(), updatedWorkflow.getName()); | ||
| assertEquals(updateParams.isDraft(), updatedWorkflow.isDraft()); | ||
| assertEquals(updateParams.getCreationDate(), updatedWorkflow.getCreationDate()); | ||
| assertEquals(updateParams.getModificationDate(), updatedWorkflow.getModificationDate()); | ||
| assertEquals(updateParams.getDescription(), updatedWorkflow.getDescription()); | ||
| } | ||
|
|
||
| } |
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