feat: add submit unit test and refactor code for it

Signed-off-by: Justin Herr <[email protected]>
nextflow-io · Jun 22, 2023 · bc49aae · bc49aae
1 parent 0bdebed
commit bc49aae
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Showing 2 changed files with 47 additions and 3 deletions.
diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy
@@ -17,6 +17,7 @@
 package nextflow.ga4gh.tes.executor
 
 import nextflow.ga4gh.tes.client.model.TesFileType
+import nextflow.processor.TaskBean
 
 import static nextflow.processor.TaskStatus.COMPLETED
 import static nextflow.processor.TaskStatus.RUNNING
@@ -53,7 +54,7 @@ class TesTaskHandler extends TaskHandler {
 
     final List<TesState> STARTED_STATUSES = [TesState.INITIALIZING, TesState.RUNNING, TesState.PAUSED] + COMPLETE_STATUSES
 
-    final TesExecutor executor
+    private TesExecutor executor
 
     private final Path exitFile
 
@@ -75,6 +76,9 @@ class TesTaskHandler extends TaskHandler {
 
     private String requestId
 
+    /** only for testing purpose -- do not use */
+    protected TesTaskHandler() {}
+
     TesTaskHandler(TaskRun task, TesExecutor executor) {
         super(task)
         this.executor = executor
@@ -90,6 +94,8 @@ class TesTaskHandler extends TaskHandler {
         this.traceFile = task.workDir.resolve(TaskRun.CMD_TRACE)
     }
 
+    protected String getRequestId() { requestId }
+
     @Override
     boolean checkIfRunning() {
 
@@ -149,7 +155,7 @@ class TesTaskHandler extends TaskHandler {
 
         // create task wrapper
         String remoteBinDir = executor.getRemoteBinDir()
-        final bash = new TesBashBuilder(task, remoteBinDir)
+        final bash = newTesBashBuilder(task, remoteBinDir)
         bash.build()
 
         final body = newTesTask()
@@ -160,7 +166,11 @@ class TesTaskHandler extends TaskHandler {
         status = TaskStatus.SUBMITTED
     }
 
-    protected final TesTask newTesTask() {
+    protected TesBashBuilder newTesBashBuilder(TaskRun task, String remoteBinDir) {
+        return new TesBashBuilder(task, remoteBinDir)
+    }
+
+    protected TesTask newTesTask() {
         // the cmd list to launch it
         def job = new ArrayList(BashWrapperBuilder.BASH) << wrapperFile.getName()
         List cmd = ['/bin/bash','-c', job.join(' ') + " &> $TaskRun.CMD_LOG" ]

diff --git a/plugins/nf-ga4gh/src/test/nextflow/ga4gh/tes/executor/TesTaskHandlerTest.groovy b/plugins/nf-ga4gh/src/test/nextflow/ga4gh/tes/executor/TesTaskHandlerTest.groovy
@@ -16,6 +16,12 @@
 
 package nextflow.ga4gh.tes.executor
 
+import nextflow.ga4gh.tes.client.api.TaskServiceApi
+import nextflow.ga4gh.tes.client.model.TesCreateTaskResponse
+import nextflow.ga4gh.tes.client.model.TesTask
+import nextflow.processor.TaskStatus
+
+import java.nio.file.Path
 import java.nio.file.Paths
 
 import nextflow.processor.TaskConfig
@@ -49,5 +55,33 @@ class TesTaskHandlerTest extends Specification {
 
     }
 
+    def 'should submit job' () {
+
+        given:
+        def executor = Mock(TesExecutor)
+        def task = Mock(TaskRun)
+        def bashBuilder = Mock(TesBashBuilder)
+        def client = Mock(TaskServiceApi)
+        def handler = Spy(TesTaskHandler)
+        handler.@client = client
+        handler.@executor = executor
+        handler.task = task
+
+        def req = Mock(TesTask)
+        def resp = Mock(TesCreateTaskResponse)
+
+        when:
+        handler.submit()
+        then:
+        1 * executor.getRemoteBinDir() >> Path.of("/work/bin")
+        1 * handler.newTesBashBuilder(task, "/work/bin") >> bashBuilder
+        1 * bashBuilder.build() >> null
+        1 * handler.newTesTask() >> req
+        1 * client.createTask(req) >> resp
+        1 * resp.getId() >> '12345'
+
+        handler.status == TaskStatus.SUBMITTED
+        handler.requestId == '12345'
+    }
 
 }