Support BIGINT Primary Keys

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -61,8 +61,8 @@ public class RefNtSequenceModel implements Serializable
     private String _name;
     //deprecated
     private String _sequence;
-    private Integer _sequenceFile;
-    private Integer _jobId;
+    private Long _sequenceFile;
+    private Long _jobId;
     private String _category;
     private String _subset;
     private String _locus;
@@ -171,12 +171,12 @@ public void setSequence(String sequence)
         _sequence = sequence;
     }
 
-    public Integer getSequenceFile()
+    public Long getSequenceFile()
     {
         return _sequenceFile;
     }
 
-    public void setSequenceFile(Integer sequenceFile)
+    public void setSequenceFile(Long sequenceFile)
     {
         _sequenceFile = sequenceFile;
     }
@@ -361,12 +361,12 @@ public void setModified(Date modified)
         _modified = modified;
     }
 
-    public Integer getJobId()
+    public Long getJobId()
     {
         return _jobId;
     }
 
-    public void setJobId(Integer jobId)
+    public void setJobId(Long jobId)
     {
         _jobId = jobId;
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -69,7 +69,7 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public ReadData getReadData(int rowId, User u);
 
-    abstract public Readset getReadset(int readsetId, User u);
+    abstract public Readset getReadset(long readsetId, User u);
 
     abstract public ReferenceGenome getReferenceGenome(int rowId, User u) throws PipelineJobException;
 
@@ -87,7 +87,7 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public String getUnzippedBaseName(String filename);
 
-    abstract public Integer getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
+    abstract public Long getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
 
     abstract public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u, DemographicsProvider d);
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceOutputFile.java

@@ -37,11 +37,11 @@ public class SequenceOutputFile implements Serializable
     private Integer _rowid;
     private String _name;
     private String _description;
-    private Integer _dataId;
+    private Long _dataId;
     private Integer _library_id;
-    private Integer _readset;
-    private Integer _analysis_id;
-    private Integer _runid;
+    private Long _readset;
+    private Long _analysis_id;
+    private Long _runid;
     private String _category;
     private Boolean _intermediate;
     private String _container;
@@ -86,12 +86,12 @@ public void setDescription(String description)
         _description = description;
     }
 
-    public Integer getDataId()
+    public Long getDataId()
     {
         return _dataId;
     }
 
-    public void setDataId(Integer dataId)
+    public void setDataId(Long dataId)
     {
         _dataId = dataId;
     }
@@ -106,32 +106,32 @@ public void setLibrary_id(Integer library_id)
         _library_id = library_id;
     }
 
-    public Integer getReadset()
+    public Long getReadset()
     {
         return _readset;
     }
 
-    public void setReadset(Integer readset)
+    public void setReadset(Long readset)
     {
         _readset = readset;
     }
 
-    public Integer getAnalysis_id()
+    public Long getAnalysis_id()
     {
         return _analysis_id;
     }
 
-    public void setAnalysis_id(Integer analysis_id)
+    public void setAnalysis_id(Long analysis_id)
     {
         _analysis_id = analysis_id;
     }
 
-    public Integer getRunId()
+    public Long getRunId()
     {
         return _runid;
     }
 
-    public void setRunId(Integer runid)
+    public void setRunId(Long runid)
     {
         _runid = runid;
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/AnalysisModel.java

@@ -31,24 +31,24 @@
  */
 public interface AnalysisModel extends Serializable
 {
-    Integer getAnalysisId();
+    Long getAnalysisId();
 
-    Integer getRunId();
+    Long getRunId();
 
     String getContainer();
 
-    Integer getReadset();
+    Long getReadset();
 
-    Integer getAlignmentFile();
+    Long getAlignmentFile();
 
     File getAlignmentFileObject();
 
     ExpData getAlignmentData();
 
     @Deprecated
-    Integer getReferenceLibrary();
+    Long getReferenceLibrary();
 
-    void setReferenceLibrary(Integer libraryId);
+    void setReferenceLibrary(Long libraryId);
 
     ExpData getReferenceLibraryData(User u) throws PipelineJobException;
 
@@ -64,7 +64,7 @@ public interface AnalysisModel extends Serializable
 
     Integer getCreatedby();
 
-    Integer getRowId();
+    Long getRowId();
 
     String getDescription();
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/ReadData.java

@@ -24,27 +24,27 @@
  */
 public interface ReadData extends Serializable
 {
-    Integer getRowid();
+    Long getRowid();
 
-    Integer getReadset();
+    Long getReadset();
 
     String getPlatformUnit();
 
     String getCenterName();
 
     Date getDate();
 
-    Integer getFileId1();
+    Long getFileId1();
 
-    Integer getFileId2();
+    Long getFileId2();
 
     File getFile1();
 
     File getFile2();
 
     String getDescription();
 
-    Integer getRunId();
+    Long getRunId();
 
     String getContainer();
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/Readset.java

@@ -46,7 +46,7 @@ public interface Readset extends Serializable
 
     Integer getInstrumentRunId();
 
-    Integer getReadsetId();
+    Long getReadsetId();
 
     String getBarcode5();
 
@@ -56,7 +56,7 @@ public interface Readset extends Serializable
 
     Double getConcentration();
 
-    int getRowId();
+    long getRowId();
 
     String getContainer();
 
@@ -72,7 +72,7 @@ public interface Readset extends Serializable
 
     String getStatus();
 
-    Integer getRunId();
+    Long getRunId();
 
     boolean hasPairedData();
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/DefaultPipelineStepOutput.java

@@ -103,7 +103,7 @@ public List<SequenceOutput> getSequenceOutputs()
     }
 
     @Override
-    public void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
+    public void addSequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description)
     {
         _intermediateFiles.remove(file);
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineOutputTracker.java

@@ -17,7 +17,7 @@ public interface PipelineOutputTracker
     /**
      * Add a SequenceOutputFile for this job.  These files are tracked and displayed through the browser UI.
      */
-    void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description);
+    void addSequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description);
 
     /**
      * Remove a previously added intermediate file

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepOutput.java

@@ -92,12 +92,12 @@ class SequenceOutput
         private final File _file;
         private final String _label;
         private final String _category;
-        private final Integer _readsetId;
-        private final Integer _analysisId;
+        private final Long _readsetId;
+        private final Long _analysisId;
         private final Integer _genomeId;
         private final String _description;
 
-        public SequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
+        public SequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description)
         {
             _file = file;
             _label = label;
@@ -123,12 +123,12 @@ public String getCategory()
             return _category;
         }
 
-        public Integer getReadsetId()
+        public Long getReadsetId()
         {
             return _readsetId;
         }
 
-        public Integer getAnalysisId()
+        public Long getAnalysisId()
         {
             return _analysisId;
         }
@@ -148,7 +148,7 @@ class PicardMetricsOutput
     {
         File _metricFile;
         File _inputFile;
-        Integer _readsetId;
+        Long _readsetId;
         TYPE _type;
 
         public enum TYPE
@@ -157,7 +157,7 @@ public enum TYPE
             reads()
         }
 
-        public PicardMetricsOutput(File metricFile, File inputFile, Integer readsetId)
+        public PicardMetricsOutput(File metricFile, File inputFile, Long readsetId)
         {
             _metricFile = metricFile;
             _inputFile = inputFile;
@@ -170,7 +170,7 @@ public PicardMetricsOutput(File metricFile, File inputFile, Integer readsetId)
          * want to denote that these metrics will apply to the final file, but dont know its name yet.  This can be used instead of tying the
          * metrics to a specific file.
          */
-        public PicardMetricsOutput(File metricFile, TYPE type, Integer readsetId)
+        public PicardMetricsOutput(File metricFile, TYPE type, Long readsetId)
         {
             _metricFile = metricFile;
             _type = type;
@@ -187,7 +187,7 @@ public File getInputFile()
             return _inputFile;
         }
 
-        public Integer getReadsetId()
+        public Long getReadsetId()
         {
             return _readsetId;
         }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ReferenceGenome.java

@@ -75,7 +75,7 @@ public interface ReferenceGenome extends Serializable
      * this will correspond to the permanent FASTA, as opposed to the copy used in this job.  If this FASTA was created specifically for
      * this job then the FASTA will be in the analysis directory.
      */
-    Integer getFastaExpDataId();
+    Long getFastaExpDataId();
 
     /**
      * @param name The name used by the aligner to identify its cached directory

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceAnalysisJobSupport.java

@@ -35,19 +35,19 @@ public interface SequenceAnalysisJobSupport extends Serializable
 {
     void cacheExpData(ExpData data);
 
-    File getCachedData(int dataId);
+    File getCachedData(long dataId);
 
-    Map<Integer, File> getAllCachedData();
+    Map<Long, File> getAllCachedData();
 
-    Readset getCachedReadset(Integer rowId);
+    Readset getCachedReadset(Long rowId);
 
-    AnalysisModel getCachedAnalysis(int rowId);
+    AnalysisModel getCachedAnalysis(long rowId);
 
     List<Readset> getCachedReadsets();
 
-    void cacheReadset(int readsetId, User u);
+    void cacheReadset(long readsetId, User u);
 
-    void cacheReadset(int readsetId, User u, boolean allowReadsetsWithArchivedData);
+    void cacheReadset(long readsetId, User u, boolean allowReadsetsWithArchivedData);
 
     List<AnalysisModel> getCachedAnalyses();
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -115,7 +115,7 @@ static public void setInstance(SequencePipelineService instance)
     /**
      * Throws exception if no run is found
      */
-    abstract public Integer getExpRunIdForJob(PipelineJob job) throws PipelineJobException;
+    abstract public Long getExpRunIdForJob(PipelineJob job) throws PipelineJobException;
 
     abstract public long getLineCount(File f) throws PipelineJobException;
 
@@ -140,7 +140,7 @@ static public void setInstance(SequencePipelineService instance)
 
     abstract public boolean hasMinLineCount(File f, long minLines) throws PipelineJobException;
 
-    abstract public void updateOutputFile(SequenceOutputFile o, PipelineJob job, Integer runId, Integer analysisId);
+    abstract public void updateOutputFile(SequenceOutputFile o, PipelineJob job, Long runId, Long analysisId);
 
     abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java

@@ -62,11 +62,11 @@ public interface TaskFileManager extends PipelineOutputTracker
 
     void addPicardMetricsFiles(List<PipelineStepOutput.PicardMetricsOutput> files) throws PipelineJobException;
 
-    void writeMetricsToDb(Map<Integer, Integer> readsetMap, Map<Integer, Map<PipelineStepOutput.PicardMetricsOutput.TYPE, File>> typeMap) throws PipelineJobException;
+    void writeMetricsToDb(Map<Long, Long> readsetMap, Map<Long, Map<PipelineStepOutput.PicardMetricsOutput.TYPE, File>> typeMap) throws PipelineJobException;
 
     void deleteIntermediateFiles() throws PipelineJobException;
 
-    Set<SequenceOutputFile> createSequenceOutputRecords(@Nullable Integer analysisId)throws PipelineJobException;
+    Set<SequenceOutputFile> createSequenceOutputRecords(@Nullable Long analysisId)throws PipelineJobException;
 
     //should be used for remote jobs or local jobs running in a separate working directory
     void cleanup(Collection<RecordedAction> actions) throws PipelineJobException;

SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java

@@ -49,6 +49,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import static org.labkey.api.exp.api.ExperimentService.asInteger;
+
 /**
  * Created by bimber on 9/18/2016.
  */
@@ -235,7 +237,7 @@ private int createTestVcf(int genomeId, File vcf)
 
             params = Table.insert(TestContext.get().getUser(), SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES), params);
 
-            return (Integer)params.get("rowid");
+            return asInteger(params.get("rowid"));
         }
     }
 }