checkpoint - migrate to using long/Long to represent any integer ID value (rowId, objectId, etc).

labkey-matthewb · labkey-matthewb · commit 7a5ea523f0a3 · 2025-07-29T09:49:54.000-07:00
diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/view/SkylineToolsStoreWebPart.jsp b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/view/SkylineToolsStoreWebPart.jsp
@@ -20,6 +20,7 @@
 <%@ page import="java.util.Iterator" %>
 <%@ page import="java.util.List" %>
 <%@ page import="java.util.Map" %>
+<%@ page import="org.labkey.api.collections.IntHashMap" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%!
@@ -237,7 +238,7 @@
 
 <div id="all-tools" style="clear: both; padding-top: 2px;">
 <%
-    HashMap<Integer, String> toolOwners = new HashMap<>();
+    HashMap<Integer, String> toolOwners = new IntHashMap<>();
     for (SkylineTool tool : tools)
     {
         final String tableId = "table-" + tool.getName().replaceAll("[^A-Za-z0-9]", "");
diff --git a/lincs/src/org/labkey/lincs/DocImportListener.java b/lincs/src/org/labkey/lincs/DocImportListener.java
@@ -137,7 +137,7 @@ public void onDocumentImport(Container container, User user, ITargetedMSRun skyl
             return;
         }
 
-        int jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());
+        long jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());
         _log.info("LINCS: Queued job Id " + jobId +" for creating GCT files for " + skylineRun.getFileName() + ". Container: " + container.getPath());
 
         pspJob.setPipelineJobId(jobId);
diff --git a/lincs/src/org/labkey/lincs/LincsController.java b/lincs/src/org/labkey/lincs/LincsController.java
@@ -1556,7 +1556,7 @@ public boolean handlePost(LincsPspJobForm form, BindException errors)
                 return false;
             }
 
-            int jobId = PipelineService.get().getJobId(getUser(), container, job.getJobGUID());
+            long jobId = PipelineService.get().getJobId(getUser(), container, job.getJobGUID());
             newPspJob.setPipelineJobId(jobId);
             lincsManager.updatePipelineJobId(newPspJob);
             return true;
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspJob.java b/lincs/src/org/labkey/lincs/psp/LincsPspJob.java
@@ -9,7 +9,7 @@ public class LincsPspJob
     private int id;
     private long _runId;
     private Container _container;
-    private Integer _pipelineJobId;
+    private Long _pipelineJobId;
 
     private String _pspJobId;
     private String pspJobName;
@@ -59,12 +59,12 @@ public void setContainer(Container container)
         _container = container;
     }
 
-    public Integer getPipelineJobId()
+    public Long getPipelineJobId()
     {
         return _pipelineJobId;
     }
 
-    public void setPipelineJobId(Integer pipelineJobId)
+    public void setPipelineJobId(Long pipelineJobId)
     {
         _pipelineJobId = pipelineJobId;
     }
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspTask.java b/lincs/src/org/labkey/lincs/psp/LincsPspTask.java
@@ -81,7 +81,7 @@ private void postToPsp(LincsPspJobSupport jobSupport, User user, Logger log) thr
 
             if(pspJob.getPipelineJobId() == null)
             {
-                Integer pipelineJobId = (PipelineService.get().getJobId(getJob().getUser(), getJob().getContainer(), getJob().getJobGUID()));
+                Long pipelineJobId = (PipelineService.get().getJobId(getJob().getUser(), getJob().getContainer(), getJob().getJobGUID()));
                 pspJob.setPipelineJobId(pipelineJobId);
             }
 
diff --git a/nextflow/src/org/labkey/nextflow/NextFlowManager.java b/nextflow/src/org/labkey/nextflow/NextFlowManager.java
@@ -174,7 +174,7 @@ private DbSchema getDbSchema()
         return DbSchema.get(SCHEMA_NAME, DbSchemaType.Module);
     }
 
-    private Integer getJobId(NextFlowPipelineJob job)
+    private Long getJobId(NextFlowPipelineJob job)
     {
         PipelineStatusFile file = PipelineService.get().getStatusFile(job.getJobGUID());
         return file == null ? null : file.getRowId();
@@ -185,15 +185,15 @@ public int getInvocationCount(NextFlowPipelineJob job)
         return getInvocationCount(getJobId(job));
     }
 
-    private int getInvocationCount(int jobId)
+    private int getInvocationCount(long jobId)
     {
         Integer result = new SqlSelector(getDbSchema(), new SQLFragment("SELECT InvocationCount FROM nextflow.Job WHERE JobId = ?", jobId)).getObject(Integer.class);
         return result != null ? result.intValue() : 0;
     }
 
     public int incrementInvocationCount(NextFlowPipelineJob job)
     {
-        int jobId = getJobId(job);
+        long jobId = getJobId(job);
         int current = getInvocationCount(jobId);
         current++;
         if (current == 1)
diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
@@ -3416,7 +3416,7 @@ private DataValidation submitValidationJob(@NotNull ExperimentAnnotations experi
                     validation = DataValidationManager.saveDataValidation(validation, user);
                     PxDataValidationPipelineJob job = new PxDataValidationPipelineJob(info, root, experimentAnnotations, validation.getId());
                     PipelineService.get().queueJob(job);
-                    Integer jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());
+                    Long jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());
                     if (jobId == null)
                     {
                         errors.reject(ERROR_MSG, "Data validation job was not submitted for experiment Id: " + experimentAnnotations.getId());
@@ -3487,7 +3487,7 @@ public ModelAndView getView(PxDataValidationForm form, BindException errors)
                 return new SimpleErrorView(errors, false);
             }
 
-            int jobId = validation.getJobId();
+            long jobId = validation.getJobId();
             PipelineStatusFile pipelineJobStatus = PipelineService.get().getStatusFile(jobId);
             JournalSubmission js = SubmissionManager.getNewestJournalSubmission(_experimentAnnotations);
             JspView view;
@@ -3585,7 +3585,7 @@ public Object execute(PxDataValidationForm form, BindException errors) throws Ex
             DataValidation validation = DataValidationManager.getValidation(form.getValidationId(), getContainer());
             if (validation != null)
             {
-                int jobId = validation.getJobId();
+                long jobId = validation.getJobId();
                 PipelineStatusFile status = PipelineService.get().getStatusFile(jobId);
                 if (status != null)
                 {
@@ -5804,7 +5804,7 @@ public boolean handlePost(NewExperimentAnnotationsForm form, BindException error
 
                     // Add all runs in the folder
                     List<? extends ExpRun> runsInFolder = ExperimentService.get().getExpRuns(getContainer(), null, null);
-                    int[] runIds = new int[runsInFolder.size()];
+                    long[] runIds = new long[runsInFolder.size()];
                     int i = 0;
                     for(ExpRun run: runsInFolder)
                     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java
@@ -1,5 +1,6 @@
 package org.labkey.panoramapublic;
 
+import org.apache.commons.lang3.ArrayUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.admin.AbstractFolderImportFactory;
@@ -98,7 +99,7 @@ else if (experiments.size() > 1)
                 ExperimentAnnotations targetExperiment = createNewExperimentAnnotations(experiment, sourceExperiment, user, log);
 
                 // Get a list of all the ExpRuns imported to subfolders of this folder.
-                int[] runRowIdsInSubfolders = getAllExpRunRowIdsInSubfolders(container);
+                long[] runRowIdsInSubfolders = getAllExpRunRowIdsInSubfolders(container);
                 if (runRowIdsInSubfolders.length > 0)
                 {
                     // The folder export and import process, creates a new experiment in exp.experiment.
@@ -119,11 +120,11 @@ else if (experiments.size() > 1)
         }
     }
 
-    private static int[] getAllExpRunRowIdsInSubfolders(Container container)
+    private static long[] getAllExpRunRowIdsInSubfolders(Container container)
     {
         Set<Container> children = ContainerManager.getAllChildren(container);
         ExperimentService expService = ExperimentService.get();
-        List<Integer> expRunRowIds = new ArrayList<>();
+        List<Long> expRunRowIds = new ArrayList<>();
         for(Container child: children)
         {
             if(container.equals(child))
@@ -136,7 +137,7 @@ private static int[] getAllExpRunRowIdsInSubfolders(Container container)
                 expRunRowIds.add(run.getRowId());
             }
         }
-        int[] intIds = new int[expRunRowIds.size()];
+        long[] intIds = new long[expRunRowIds.size()];
         for(int i = 0; i < expRunRowIds.size(); i++)
         {
             intIds[i] = expRunRowIds.get(i);
diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/ExperimentAnnotations.java b/panoramapublic/src/org/labkey/panoramapublic/model/ExperimentAnnotations.java
@@ -49,7 +49,7 @@
  */
 public class ExperimentAnnotations extends DbEntity
 {
-    private int _experimentId;
+    private long _experimentId;
     private Container _container;
     private String _title;
     private String _experimentDescription;
@@ -83,12 +83,12 @@ public class ExperimentAnnotations extends DbEntity
 
     public ExperimentAnnotations() {}
 
-    public int getExperimentId()
+    public long getExperimentId()
     {
         return _experimentId;
     }
 
-    public void setExperimentId(int experimentId)
+    public void setExperimentId(long experimentId)
     {
         _experimentId = experimentId;
     }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java
@@ -15,7 +15,7 @@ public class DataValidation extends DbEntity
     private static final SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("yyyy-MM-d HH:mm");
 
     private int _experimentAnnotationsId;
-    private int _jobId;
+    private long _jobId;
     private PxStatus _status;
 
     public DataValidation() {}
@@ -35,12 +35,12 @@ public void setExperimentAnnotationsId(int experimentAnnotationsId)
         _experimentAnnotationsId = experimentAnnotationsId;
     }
 
-    public int getJobId()
+    public long getJobId()
     {
         return _jobId;
     }
 
-    public void setJobId(int jobId)
+    public void setJobId(long jobId)
     {
         _jobId = jobId;
     }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationTask.java
@@ -50,7 +50,7 @@ public void doValidation(PipelineJob job, PxDataValidationJobSupport jobSupport)
                         jobSupport.getValidationId(), exptAnnotations.getContainer().getPath()));
             }
             log.info(String.format("Validating data for experiment Id: %d, validation Id: %d", exptAnnotations.getId(), validation.getId()));
-            Integer pipelineJobId = (PipelineService.get().getJobId(job.getUser(), job.getContainer(), job.getJobGUID()));
+            Long pipelineJobId = (PipelineService.get().getJobId(job.getUser(), job.getContainer(), job.getJobGUID()));
             if (pipelineJobId != null && pipelineJobId != validation.getJobId())
             {
                 throw new PipelineJobException(String.format("Unexpected pipeline job Id %d.  Job Id saved in the validation row (Id: %d) is %d.",
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java
@@ -19,6 +19,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.junit.Assert;
 import org.junit.Test;
+import org.labkey.api.collections.LongHashMap;
 import org.labkey.api.targetedms.IModification;
 import org.labkey.api.targetedms.ITargetedMSRun;
 import org.labkey.api.targetedms.TargetedMSService;
@@ -47,8 +48,8 @@ public static List<PxModification> getModifications(ExperimentAnnotations expAnn
     {
         List<ITargetedMSRun> runs = ExperimentAnnotationsManager.getTargetedMSRuns(expAnnot);
 
-        Map<Long, PxModification> strModMap = new HashMap<>();
-        Map<Long, PxModification> isoModMap = new HashMap<>();
+        Map<Long, PxModification> strModMap = new LongHashMap<>();
+        Map<Long, PxModification> isoModMap = new LongHashMap<>();
 
         UnimodModifications uMods = UnimodUtil.getUnimod(); // Read the UNIMOD modifications
 
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
@@ -20,6 +20,7 @@
 import org.apache.logging.log4j.Logger;
 import org.json.JSONException;
 import org.json.JSONObject;
+import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.logging.LogHelper;
@@ -120,7 +121,7 @@ public static Map<Integer, String> getScientificNames(List<Integer> taxIds) thro
     {
         String queryUrl = eutilsUrl + "&id=" + StringUtils.join(taxIds, ",");
 
-        Map<Integer, String> sciNameMap = new HashMap<>();
+        Map<Integer, String> sciNameMap = new IntHashMap<>();
 
         HttpURLConnection conn = null;
         try
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java
@@ -17,6 +17,7 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
+import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.security.User;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.logging.LogHelper;
@@ -181,7 +182,7 @@ void writeSpeciesList(ExperimentAnnotations experimentAnnotations)
         }
 
         boolean ncbiLookupError = false;
-        Map<Integer, String> sciNameMap = new HashMap<>();
+        Map<Integer, String> sciNameMap = new IntHashMap<>();
         try
         {
             sciNameMap = getScientificNames(taxIds);
diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java
@@ -147,7 +147,7 @@ public static boolean isPipelineJobRunning(DataValidation validation)
 
     public static PipelineStatusFile getPipelineJobStatus(@NotNull DataValidation validation)
     {
-        int jobId = validation.getJobId();
+        long jobId = validation.getJobId();
         return PipelineService.get().getStatusFile(jobId);
     }
 
diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java
@@ -85,7 +85,7 @@ public static ExperimentAnnotations get(int experimentAnnotationsId, Container c
      * @param experimentId FK -> exp.experiment.rowId
      * @return ExperimentAnnotations object with the given experimentId
      */
-    public static ExperimentAnnotations getForExperimentId(int experimentId)
+    public static ExperimentAnnotations getForExperimentId(long experimentId)
     {
         return new TableSelector(PanoramaPublicManager.getTableInfoExperimentAnnotations(),
                 new SimpleFilter(FieldKey.fromParts("ExperimentId"), experimentId), null).getObject(ExperimentAnnotations.class);
@@ -123,7 +123,7 @@ public static void excludeSubfoldersFromExperiment(ExperimentAnnotations expAnno
 
         // Get all the runs in the experiment.
         List<? extends ExpRun> runs = experiment.getRuns();
-        List<Integer> rowIdsToRemove = new ArrayList<>();
+        List<Long> rowIdsToRemove = new ArrayList<>();
         Container expContainer = experiment.getContainer();
         // Get a list of runs that are not in the folder where the experiment is defined.
         for(ExpRun run: runs)
@@ -134,9 +134,9 @@ public static void excludeSubfoldersFromExperiment(ExperimentAnnotations expAnno
             }
         }
 
-        int[] rowIds = new int[rowIdsToRemove.size()];
+        long[] rowIds = new long[rowIdsToRemove.size()];
         int i = 0;
-        for(Integer rowId: rowIdsToRemove)
+        for(Long rowId: rowIdsToRemove)
         {
             rowIds[i++] = rowId;
         }
@@ -152,11 +152,11 @@ public static void excludeSubfoldersFromExperiment(ExperimentAnnotations expAnno
         }
     }
 
-    private static void removeRunIds(ExpExperiment experiment, int[] rowIds, User user)
+    private static void removeRunIds(ExpExperiment experiment, long[] rowIds, User user)
     {
         ExperimentService expService = ExperimentService.get();
 
-        for(int rowId: rowIds)
+        for (long rowId: rowIds)
         {
             ExpRun run = expService.getExpRun(rowId);
             if(run != null)
@@ -187,15 +187,15 @@ public static void includeSubfoldersInExperiment(ExperimentAnnotations expAnnota
 
         // Get a list of runs that already belong to the experiment.
         List<? extends ExpRun> existingRuns = experiment.getRuns();
-        Set<Integer> existingRunRowIds = new HashSet<>();
+        Set<Long> existingRunRowIds = new HashSet<>();
         for(ExpRun run: existingRuns)
         {
             existingRunRowIds.add(run.getRowId());
         }
 
         // Keep runs that do not already belong to the experiment.
         runs.removeIf(run -> existingRunRowIds.contains(run.getRowId()));
-        int[] rowIds = new int[runs.size()];
+        long[] rowIds = new long[runs.size()];
         int i = 0;
         for(ExpRun run: runs)
         {
@@ -213,10 +213,10 @@ public static void includeSubfoldersInExperiment(ExperimentAnnotations expAnnota
         }
     }
 
-    public static void addSelectedRunsToExperiment(ExpExperiment experiment, int[] rowIds, User user)
+    public static void addSelectedRunsToExperiment(ExpExperiment experiment, long[] rowIds, User user)
     {
         List<ExpRun> runs = new ArrayList<>();
-        for (int rowId : rowIds)
+        for (long rowId : rowIds)
         {
             ExpRun run = ExperimentService.get().getExpRun(rowId);
             if (run != null)
diff --git a/panoramapublic/src/org/labkey/panoramapublic/speclib/BlibReader.java b/panoramapublic/src/org/labkey/panoramapublic/speclib/BlibReader.java
@@ -1,6 +1,8 @@
 package org.labkey.panoramapublic.speclib;
 
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.collections.IntHashMap;
+
 import java.sql.Connection;
 import java.sql.ResultSet;
 import java.sql.ResultSetMetaData;
@@ -27,7 +29,7 @@ public class BlibReader extends SpecLibReader
 
             List<LibSourceFile> sourceFiles = new ArrayList<>();
 
-            Map<Integer, Set<String>> scoreTypes = new HashMap<>(); // file id -> score types
+            Map<Integer, Set<String>> scoreTypes = new IntHashMap<>(); // file id -> score types
             if(hasTable(conn, "ScoreTypes")) // Older .blib files do not have a ScoreTypes table
             {
                 try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("SELECT DISTINCT r.fileID, s.scoreType FROM RefSpectra as r JOIN ScoreTypes s ON r.scoreType = s.id"))
diff --git a/panoramapublic/src/org/labkey/panoramapublic/view/publish/pxValidationRunning.jsp b/panoramapublic/src/org/labkey/panoramapublic/view/publish/pxValidationRunning.jsp
@@ -20,7 +20,7 @@
 <%
     JspView<PxValidationStatusBean> view = HttpView.currentView();
     var bean = view.getModelBean();
-    int jobId = bean.getDataValidation().getJobId();
+    long jobId = bean.getDataValidation().getJobId();
     var jobStatus = bean.getPipelineJobStatus();
     var onPageLoadMsg = jobStatus != null ? (String.format("Data validation job is %s. This page will automatically refresh with the validation progress.",
             jobStatus.isActive() ? (PipelineJob.TaskStatus.waiting.matches(jobStatus.getStatus()) ? "in the queue" : "running") : "complete"))
diff --git a/panoramapublic/src/org/labkey/panoramapublic/view/publish/pxValidationStatus.jsp b/panoramapublic/src/org/labkey/panoramapublic/view/publish/pxValidationStatus.jsp
@@ -28,7 +28,7 @@
     ExperimentAnnotations experimentAnnotations = bean.getExpAnnotations();
     int experimentAnnotationsId = experimentAnnotations.getId();
     boolean includeSubfolders = experimentAnnotations.isIncludeSubfolders();
-    int jobId = bean.getDataValidation().getJobId();
+    long jobId = bean.getDataValidation().getJobId();
     Integer journalId = bean.getJournalId();
     var submitAction = SpringActionController.getActionName(PanoramaPublicController.PublishExperimentAction.class);
     Submission submission = bean.getSubmission();
diff --git a/testresults/src/org/labkey/testresults/TestResultsController.java b/testresults/src/org/labkey/testresults/TestResultsController.java
diff --git a/testresults/src/org/labkey/testresults/view/RunDownBean.java b/testresults/src/org/labkey/testresults/view/RunDownBean.java

Original file line number	Diff line number	Diff line change
`@@ -137,7 +137,7 @@ public void onDocumentImport(Container container, User user, ITargetedMSRun skyl`
`137`	`137`	`return;`
`138`	`138`	`}`
`139`	`139`
`140`		`- int jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());`
	`140`	`+ long jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());`
`141`	`141`	`_log.info("LINCS: Queued job Id " + jobId +" for creating GCT files for " + skylineRun.getFileName() + ". Container: " + container.getPath());`
`142`	`142`
`143`	`143`	`pspJob.setPipelineJobId(jobId);`
Original file line number	Diff line number	Diff line change
`@@ -1556,7 +1556,7 @@ public boolean handlePost(LincsPspJobForm form, BindException errors)`
`1556`	`1556`	`return false;`
`1557`	`1557`	`}`
`1558`	`1558`
`1559`		`- int jobId = PipelineService.get().getJobId(getUser(), container, job.getJobGUID());`
	`1559`	`+ long jobId = PipelineService.get().getJobId(getUser(), container, job.getJobGUID());`
`1560`	`1560`	`newPspJob.setPipelineJobId(jobId);`
`1561`	`1561`	`lincsManager.updatePipelineJobId(newPspJob);`
`1562`	`1562`	`return true;`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,7 @@ public class LincsPspJob`
`9`	`9`	`private int id;`
`10`	`10`	`private long _runId;`
`11`	`11`	`private Container _container;`
`12`		`- private Integer _pipelineJobId;`
	`12`	`+ private Long _pipelineJobId;`
`13`	`13`
`14`	`14`	`private String _pspJobId;`
`15`	`15`	`private String pspJobName;`
`@@ -59,12 +59,12 @@ public void setContainer(Container container)`
`59`	`59`	`_container = container;`
`60`	`60`	`}`
`61`	`61`
`62`		`- public Integer getPipelineJobId()`
	`62`	`+ public Long getPipelineJobId()`
`63`	`63`	`{`
`64`	`64`	`return _pipelineJobId;`
`65`	`65`	`}`
`66`	`66`
`67`		`- public void setPipelineJobId(Integer pipelineJobId)`
	`67`	`+ public void setPipelineJobId(Long pipelineJobId)`
`68`	`68`	`{`
`69`	`69`	`_pipelineJobId = pipelineJobId;`
`70`	`70`	`}`
Original file line number	Diff line number	Diff line change
`@@ -81,7 +81,7 @@ private void postToPsp(LincsPspJobSupport jobSupport, User user, Logger log) thr`
`81`	`81`
`82`	`82`	`if(pspJob.getPipelineJobId() == null)`
`83`	`83`	`{`
`84`		`- Integer pipelineJobId = (PipelineService.get().getJobId(getJob().getUser(), getJob().getContainer(), getJob().getJobGUID()));`
	`84`	`+ Long pipelineJobId = (PipelineService.get().getJobId(getJob().getUser(), getJob().getContainer(), getJob().getJobGUID()));`
`85`	`85`	`pspJob.setPipelineJobId(pipelineJobId);`
`86`	`86`	`}`
`87`	`87`
Original file line number	Diff line number	Diff line change
`@@ -174,7 +174,7 @@ private DbSchema getDbSchema()`
`174`	`174`	`return DbSchema.get(SCHEMA_NAME, DbSchemaType.Module);`
`175`	`175`	`}`
`176`	`176`
`177`		`- private Integer getJobId(NextFlowPipelineJob job)`
	`177`	`+ private Long getJobId(NextFlowPipelineJob job)`
`178`	`178`	`{`
`179`	`179`	`PipelineStatusFile file = PipelineService.get().getStatusFile(job.getJobGUID());`
`180`	`180`	`return file == null ? null : file.getRowId();`
`@@ -185,15 +185,15 @@ public int getInvocationCount(NextFlowPipelineJob job)`
`185`	`185`	`return getInvocationCount(getJobId(job));`
`186`	`186`	`}`
`187`	`187`
`188`		`- private int getInvocationCount(int jobId)`
	`188`	`+ private int getInvocationCount(long jobId)`
`189`	`189`	`{`
`190`	`190`	`Integer result = new SqlSelector(getDbSchema(), new SQLFragment("SELECT InvocationCount FROM nextflow.Job WHERE JobId = ?", jobId)).getObject(Integer.class);`
`191`	`191`	`return result != null ? result.intValue() : 0;`
`192`	`192`	`}`
`193`	`193`
`194`	`194`	`public int incrementInvocationCount(NextFlowPipelineJob job)`
`195`	`195`	`{`
`196`		`- int jobId = getJobId(job);`
	`196`	`+ long jobId = getJobId(job);`
`197`	`197`	`int current = getInvocationCount(jobId);`
`198`	`198`	`current++;`
`199`	`199`	`if (current == 1)`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,6 @@`
`1`	`1`	`package org.labkey.panoramapublic;`
`2`	`2`
	`3`	`+import org.apache.commons.lang3.ArrayUtils;`
`3`	`4`	`import org.apache.logging.log4j.Logger;`
`4`	`5`	`import org.jetbrains.annotations.Nullable;`
`5`	`6`	`import org.labkey.api.admin.AbstractFolderImportFactory;`
`@@ -98,7 +99,7 @@ else if (experiments.size() > 1)`
`98`	`99`	`ExperimentAnnotations targetExperiment = createNewExperimentAnnotations(experiment, sourceExperiment, user, log);`
`99`	`100`
`100`	`101`	`// Get a list of all the ExpRuns imported to subfolders of this folder.`
`101`		`- int[] runRowIdsInSubfolders = getAllExpRunRowIdsInSubfolders(container);`
	`102`	`+ long[] runRowIdsInSubfolders = getAllExpRunRowIdsInSubfolders(container);`
`102`	`103`	`if (runRowIdsInSubfolders.length > 0)`
`103`	`104`	`{`
`104`	`105`	`// The folder export and import process, creates a new experiment in exp.experiment.`
`@@ -119,11 +120,11 @@ else if (experiments.size() > 1)`
`119`	`120`	`}`
`120`	`121`	`}`
`121`	`122`
`122`		`- private static int[] getAllExpRunRowIdsInSubfolders(Container container)`
	`123`	`+ private static long[] getAllExpRunRowIdsInSubfolders(Container container)`
`123`	`124`	`{`
`124`	`125`	`Set<Container> children = ContainerManager.getAllChildren(container);`
`125`	`126`	`ExperimentService expService = ExperimentService.get();`
`126`		`- List<Integer> expRunRowIds = new ArrayList<>();`
	`127`	`+ List<Long> expRunRowIds = new ArrayList<>();`
`127`	`128`	`for(Container child: children)`
`128`	`129`	`{`
`129`	`130`	`if(container.equals(child))`
`@@ -136,7 +137,7 @@ private static int[] getAllExpRunRowIdsInSubfolders(Container container)`
`136`	`137`	`expRunRowIds.add(run.getRowId());`
`137`	`138`	`}`
`138`	`139`	`}`
`139`		`- int[] intIds = new int[expRunRowIds.size()];`
	`140`	`+ long[] intIds = new long[expRunRowIds.size()];`
`140`	`141`	`for(int i = 0; i < expRunRowIds.size(); i++)`
`141`	`142`	`{`
`142`	`143`	`intIds[i] = expRunRowIds.get(i);`
Original file line number	Diff line number	Diff line change
`@@ -49,7 +49,7 @@`
`49`	`49`	`*/`
`50`	`50`	`public class ExperimentAnnotations extends DbEntity`
`51`	`51`	`{`
`52`		`- private int _experimentId;`
	`52`	`+ private long _experimentId;`
`53`	`53`	`private Container _container;`
`54`	`54`	`private String _title;`
`55`	`55`	`private String _experimentDescription;`
`@@ -83,12 +83,12 @@ public class ExperimentAnnotations extends DbEntity`
`83`	`83`
`84`	`84`	`public ExperimentAnnotations() {}`
`85`	`85`
`86`		`- public int getExperimentId()`
	`86`	`+ public long getExperimentId()`
`87`	`87`	`{`
`88`	`88`	`return _experimentId;`
`89`	`89`	`}`
`90`	`90`
`91`		`- public void setExperimentId(int experimentId)`
	`91`	`+ public void setExperimentId(long experimentId)`
`92`	`92`	`{`
`93`	`93`	`_experimentId = experimentId;`
`94`	`94`	`}`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@ public class DataValidation extends DbEntity`
`15`	`15`	`private static final SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("yyyy-MM-d HH:mm");`
`16`	`16`
`17`	`17`	`private int _experimentAnnotationsId;`
`18`		`- private int _jobId;`
	`18`	`+ private long _jobId;`
`19`	`19`	`private PxStatus _status;`
`20`	`20`
`21`	`21`	`public DataValidation() {}`
`@@ -35,12 +35,12 @@ public void setExperimentAnnotationsId(int experimentAnnotationsId)`
`35`	`35`	`_experimentAnnotationsId = experimentAnnotationsId;`
`36`	`36`	`}`
`37`	`37`
`38`		`- public int getJobId()`
	`38`	`+ public long getJobId()`
`39`	`39`	`{`
`40`	`40`	`return _jobId;`
`41`	`41`	`}`
`42`	`42`
`43`		`- public void setJobId(int jobId)`
	`43`	`+ public void setJobId(long jobId)`
`44`	`44`	`{`
`45`	`45`	`_jobId = jobId;`
`46`	`46`	`}`