fix: add null guard in duration format helper + test (#324)

seqeralabs · Aug 28, 2023 · 86cdf4d · 86cdf4d
1 parent a93504e
commit 86cdf4d
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Showing 4 changed files with 133 additions and 10 deletions.
diff --git a/src/main/java/io/seqera/tower/cli/utils/FormatHelper.java b/src/main/java/io/seqera/tower/cli/utils/FormatHelper.java
@@ -11,16 +11,7 @@
 
 package io.seqera.tower.cli.utils;
 
-import io.seqera.tower.model.ActionResponseDto;
-import io.seqera.tower.model.ActionStatus;
-import io.seqera.tower.model.ComputeEnvStatus;
-import io.seqera.tower.model.ListActionsResponseActionInfo;
-import io.seqera.tower.model.OrgRole;
-import io.seqera.tower.model.ParticipantType;
-import io.seqera.tower.model.PipelineDbDto;
-import io.seqera.tower.model.WorkflowStatus;
-import io.seqera.tower.model.ListLabelsResponse;
-import io.seqera.tower.model.ListWorkflowsResponseListWorkflowsElement;
+import io.seqera.tower.model.*;
 import picocli.CommandLine;
 
 import java.time.Duration;
@@ -39,6 +30,10 @@ public static String formatDate(OffsetDateTime date) {
     }
 
     public static String formatDurationMillis(Long duration) {
+        if (duration == null) {
+            return "";
+        }
+
         Duration d = Duration.ofMillis(duration);
         long days = d.toDaysPart();
         long hours = d.toHoursPart();

diff --git a/src/test/java/io/seqera/tower/cli/runs/TaskCmdTest.java b/src/test/java/io/seqera/tower/cli/runs/TaskCmdTest.java
@@ -54,4 +54,28 @@ void testTaskDetail(MockServerClient mock) throws JsonProcessingException {
         assertEquals(StringUtils.chop(new TaskView(general, command, environment, times, resources, usage).toString()), out.stdOut);
         assertEquals(0, out.exitCode);
     }
+
+    @Test
+    void testTaskDetailWithNullValues(MockServerClient mock) throws JsonProcessingException {
+        mock.when(
+                request().withMethod("GET").withPath("/workflow/5J9pBnWd6uoC3w/task/1"), exactly(1)
+        ).respond(
+                response().withStatusCode(200).withBody(loadResource("runs/task_detail_null_values")).withContentType(MediaType.APPLICATION_JSON)
+        );
+
+        ExecOut out = exec(mock,"runs", "view", "-i", "5J9pBnWd6uoC3w", "task", "-t", "1", "--execution-time", "--resources-requested", "--resources-usage");
+
+        Task task = parseJson(new String(loadResource("runs/task_object_null_values")), Task.class);
+
+        Map<String, Object> general = TaskCmd.parseGeneralData(task);
+        String command = task.getScript() != null ? task.getScript() : null;
+        String environment = task.getEnv() != null ? task.getEnv() : null;
+        Map<String, Object> times = TaskCmd.parseExecutionTimeData(task);
+        Map<String, Object> resources = TaskCmd.parseResourcesRequestedData(task);
+        Map<String, Object> usage = TaskCmd.parseResourcesUsageData(task);
+
+        assertEquals("", out.stdErr);
+        assertEquals(StringUtils.chop(new TaskView(general, command, environment, times, resources, usage).toString()), out.stdOut);
+        assertEquals(0, out.exitCode);
+    }
 }
diff --git a/src/test/resources/runcmd/runs/task_detail_null_values.json b/src/test/resources/runcmd/runs/task_detail_null_values.json
@@ -0,0 +1,53 @@
+{
+  "task": {
+    "id": 232916258,
+    "taskId": 1,
+    "status": "COMPLETED",
+    "dateCreated": "2021-11-15T14:59:36Z",
+    "lastUpdated": "2021-11-15T15:06:58Z",
+    "submit": "2021-11-15T14:59:36Z",
+    "start": "2021-11-15T15:06:38Z",
+    "complete": "2021-11-15T15:06:58Z",
+    "attempt": 1,
+    "scratch": null,
+    "workdir": "s3://nextflow-ci/scratch/5J9pBnWd6uoC3w/38/2d0f03566d485112b53f082c477338",
+    "env": "PYTHONNOUSERSITE=1\nR_PROFILE_USER=/.Rprofile\nR_ENVIRON_USER=/.Renviron\n",
+    "cloudZone": "eu-west-1a",
+    "priceModel": "spot",
+    "cost": null,
+    "errorAction": null,
+    "exitStatus": 0,
+    "realtime": 0,
+    "nativeId": "ca1878f1-169c-4013-b30d-c5807ea1a3dd",
+    "pcpu": 63.6,
+    "pmem": 0,
+    "rss": 10067968,
+    "vmem": null,
+    "peakRss": 10067968,
+    "peakVmem": 33243136,
+    "rchar": 673556,
+    "wchar": 1428,
+    "syscr": 242,
+    "syscw": 17,
+    "readBytes": 7213056,
+    "writeBytes": 12288,
+    "volCtxt": 15,
+    "invCtxt": 4,
+    "process": "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK",
+    "disk": null,
+    "container": "quay.io/biocontainers/python:3.8.3",
+    "queue": "TowerForge-1voNN3Mve8r49Ek6hFCN5v-work",
+    "cpus": 1,
+    "memory": 6442450944,
+    "machineType": "r4.large",
+    "executor": "awsbatch",
+    "tag": "samplesheet_test.csv",
+    "time": null,
+    "duration": null,
+    "script": "\ncheck_samplesheet.py \\\n    samplesheet_test.csv \\\n    samplesheet.valid.csv\n\ncat <<-END_VERSIONS > versions.yml\nSAMPLESHEET_CHECK:\n    python: $(python --version | sed 's/Python //g')\nEND_VERSIONS\n",
+    "module": [],
+    "hash": "38/2d0f03",
+    "exit": "0",
+    "name": "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)"
+  }
+}
diff --git a/src/test/resources/runcmd/runs/task_object_null_values.json b/src/test/resources/runcmd/runs/task_object_null_values.json
@@ -0,0 +1,51 @@
+{
+  "id": 232916258,
+  "taskId": 1,
+  "status": "COMPLETED",
+  "dateCreated": "2021-11-15T14:59:36Z",
+  "lastUpdated": null,
+  "submit": "2021-11-15T14:59:36Z",
+  "start": "2021-11-15T15:06:38Z",
+  "complete": "2021-11-15T15:06:58Z",
+  "attempt": 1,
+  "scratch": null,
+  "workdir": "s3://nextflow-ci/scratch/5J9pBnWd6uoC3w/38/2d0f03566d485112b53f082c477338",
+  "env": "PYTHONNOUSERSITE=1\nR_PROFILE_USER=/.Rprofile\nR_ENVIRON_USER=/.Renviron\n",
+  "cloudZone": "eu-west-1a",
+  "priceModel": "spot",
+  "cost": null,
+  "errorAction": null,
+  "exitStatus": 0,
+  "realtime": 0,
+  "nativeId": "ca1878f1-169c-4013-b30d-c5807ea1a3dd",
+  "pcpu": 63.6,
+  "pmem": 0,
+  "rss": 10067968,
+  "vmem": null,
+  "peakRss": 10067968,
+  "peakVmem": 33243136,
+  "rchar": 673556,
+  "wchar": 1428,
+  "syscr": 242,
+  "syscw": 17,
+  "readBytes": 7213056,
+  "writeBytes": 12288,
+  "volCtxt": 15,
+  "invCtxt": 4,
+  "process": "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK",
+  "container": "quay.io/biocontainers/python:3.8.3",
+  "queue": "TowerForge-1voNN3Mve8r49Ek6hFCN5v-work",
+  "cpus": 1,
+  "memory": 6442450944,
+  "machineType": "r4.large",
+  "executor": "awsbatch",
+  "tag": "samplesheet_test.csv",
+  "disk": null,
+  "time": null,
+  "duration": null,
+  "script": "\ncheck_samplesheet.py \\\n    samplesheet_test.csv \\\n    samplesheet.valid.csv\n\ncat <<-END_VERSIONS > versions.yml\nSAMPLESHEET_CHECK:\n    python: $(python --version | sed 's/Python //g')\nEND_VERSIONS\n",
+  "module": [],
+  "hash": "38/2d0f03",
+  "exit": "0",
+  "name": "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)"
+}