Attempt to improve JBrowseTest stability (#125)

* Attempt to improve JBrowseTest stability

Author: bbimber

.github/workflows/build.yml

@@ -45,7 +45,7 @@ jobs:
           GENERATE_DIST: ${{ steps.default-branch.branch == steps.extract-branch.branch && '1' || '0' }}
 
       - name: Publish Release
-        if: github.ref == '/refs/heads/${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}' && github.event_name == 'push'
+        if: github.ref == '/refs/heads/${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}' && github.event_name == 'push' && github.base_ref == ''
         uses: "marvinpinto/action-automatic-releases@latest"
         with:
           repo_token: "${{ secrets.PAT }}"

cluster/src/org/labkey/cluster/ClusterController.java

@@ -21,6 +21,10 @@
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.action.ConfirmAction;
 import org.labkey.api.action.SpringActionController;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
@@ -43,7 +47,9 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 public class ClusterController extends SpringActionController
 {
@@ -162,6 +168,95 @@ public void setJobIds(String jobIds)
         }
     }
 
+
+    public static class ResetPipelineJobLogFileForm
+    {
+        private int _jobId;
+        private String _filePath;
+
+        public int getJobId()
+        {
+            return _jobId;
+        }
+
+        public void setJobId(int jobId)
+        {
+            _jobId = jobId;
+        }
+
+        public String getFilePath()
+        {
+            return _filePath;
+        }
+
+        public void setFilePath(String filePath)
+        {
+            _filePath = filePath;
+        }
+    }
+
+    @RequiresSiteAdmin
+    public class ResetPipelineJobLogFileAction extends ConfirmAction<ResetPipelineJobLogFileForm>
+    {
+        public void validateCommand(ResetPipelineJobLogFileForm form, Errors errors)
+        {
+
+        }
+
+        public URLHelper getSuccessURL(ResetPipelineJobLogFileForm form)
+        {
+            return PageFlowUtil.urlProvider(PipelineStatusUrls.class).urlBegin(getContainer());
+        }
+
+        public ModelAndView getConfirmView(ResetPipelineJobLogFileForm form, BindException errors) throws Exception
+        {
+            return new HtmlView(HtmlString.unsafe("This will change the PipelineJob log file path for the selected job to the path below." +
+                    "<br><br>" +
+                    "<label>Enter Job ID(s): </label><input name=\"jobId\"><br>" +
+                    "<label>New Filepath: </label><input name=\"filePath\"><br>"));
+        }
+
+        @Override
+        public boolean handlePost(ResetPipelineJobLogFileForm form, BindException errors) throws Exception
+        {
+            if (form.getJobId() == 0)
+            {
+                errors.reject(ERROR_MSG, "No JobId provided");
+                return false;
+            }
+
+            PipelineStatusFile sf = PipelineService.get().getStatusFile(form.getJobId());
+            if (sf == null)
+            {
+                errors.reject(ERROR_MSG, "Unable to find job: " + form.getJobId());
+                return false;
+            }
+
+            String path = StringUtils.trimToNull(form.getFilePath());
+            if (path == null)
+            {
+                errors.reject(ERROR_MSG, "Missing filepath: " + form.getFilePath());
+                return false;
+            }
+
+            File logFile = new File(path);
+            if (!logFile.exists())
+            {
+                errors.reject(ERROR_MSG, "File doesnt exist: " + form.getFilePath());
+                return false;
+            }
+
+            Map<String, Object> toUpdate = new HashMap<>();
+            toUpdate.put("RowId", form.getJobId());
+            toUpdate.put("FilePath", path);
+
+            TableInfo ti = DbSchema.get("pipeline", DbSchemaType.Module).getTable("StatusFiles");
+            Table.update(getUser(), ti, toUpdate, form.getJobId());
+
+            return false;
+        }
+    }
+
     @RequiresSiteAdmin
     public class RecoverCompletedJobsAction extends ConfirmAction<JobIdsForm>
     {
@@ -212,7 +307,6 @@ public boolean handlePost(JobIdsForm form, BindException errors) throws Exceptio
             }
 
             sfs.forEach(sf -> {
-
                 File log = new File(sf.getFilePath());
                 File json = AbstractClusterExecutionEngine.getSerializedJobFile(log);
                 if (!json.exists())

jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java

@@ -309,6 +309,9 @@ private void testSampleFiltersFromUrl()
         beginAt("/home/jbrowse-jbrowse.view?session=mgap&sampleFilters=mgap:m00010");
         waitForJBrowseToLoad();
 
+        // NOTE: this should be replaced with something more specific
+        sleep(5000);
+
         // Wait for variants to load:
         getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV A -> T"));
 
@@ -346,11 +349,6 @@ private By getVariantWithinTrack(String trackId, String variantText)
         l = l.append(Locator.xpath("//*[name()='text' and contains(text(), '" + variantText + "')]/..")).notHidden();
 
         waitForElementToDisappear(Locator.tagWithText("p", "Loading"));
-        sleep(250);
-        waitForElement(l);
-
-        waitForElementToDisappear(Locator.tagWithText("p", "Loading"));
-        sleep(250);
         waitForElement(l);
 
         return By.xpath(l.toXpath());