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

Author: labkey-matthewb

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

@@ -62,7 +62,7 @@ public class RefNtSequenceModel implements Serializable
     //deprecated
     private String _sequence;
     private Long _sequenceFile;
-    private Integer _jobId;
+    private Long _jobId;
     private String _category;
     private String _subset;
     private String _locus;
@@ -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

@@ -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 _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;
     }
@@ -126,12 +126,12 @@ public void setAnalysis_id(Integer 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

@@ -33,22 +33,22 @@ public interface AnalysisModel extends Serializable
 {
     Integer getAnalysisId();
 
-    Integer getRunId();
+    Long getRunId();
 
     String getContainer();
 
     Integer 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;
 

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

@@ -34,17 +34,17 @@ public interface ReadData extends Serializable
 
     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

@@ -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/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

@@ -35,9 +35,9 @@ 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);
 

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, Integer analysisId);
 
     abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
 

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

@@ -28,15 +28,15 @@ public class ReadDataImpl implements ReadData
     private String _platformUnit;
     private String _centerName;
     private Date _date;
-    private Integer _fileId1;
-    private Integer _fileId2;
+    private Long _fileId1;
+    private Long _fileId2;
     private String _description;
     private String _container;
     private Date _created;
     private Integer _createdBy;
     private Date _modified;
     private Integer _modifiedBy;
-    private Integer _runId;
+    private Long _runId;
     private boolean _archived = false;
     private String sra_accession;
 
@@ -103,23 +103,23 @@ public void setDate(Date date)
     }
 
     @Override
-    public Integer getFileId1()
+    public Long getFileId1()
     {
         return _fileId1;
     }
 
-    public void setFileId1(Integer fileId1)
+    public void setFileId1(Long fileId1)
     {
         _fileId1 = fileId1;
     }
 
     @Override
-    public Integer getFileId2()
+    public Long getFileId2()
     {
         return _fileId2;
     }
 
-    public void setFileId2(Integer fileId2)
+    public void setFileId2(Long fileId2)
     {
         _fileId2 = fileId2;
     }
@@ -131,12 +131,12 @@ public String getDescription()
     }
 
     @Override
-    public Integer getRunId()
+    public Long getRunId()
     {
         return _runId;
     }
 
-    public void setRunId(Integer runId)
+    public void setRunId(Long runId)
     {
         _runId = runId;
     }
@@ -258,7 +258,7 @@ public Integer getTotalReads()
     }
 
     @Transient
-    private File getFile(int fileIdx, Integer fileId, boolean allowArchived)
+    private File getFile(int fileIdx, Long fileId, boolean allowArchived)
     {
         if (isArchived() && !allowArchived)
         {