Support BIGINT Primary Keys

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]", "");

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);

lincs/src/org/labkey/lincs/LincsController.java

@@ -1555,7 +1555,7 @@ 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;

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;
     }

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);
             }
 

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)

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java

@@ -3417,7 +3417,7 @@ 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());
@@ -3488,7 +3488,7 @@ 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;
@@ -3586,7 +3586,7 @@ 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)
                 {
@@ -5810,7 +5810,7 @@ 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)
                     {

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);

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;
     }

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;
     }

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.",

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
 

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

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);

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);
     }
 

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)

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"))

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"))

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();