Integer -> Long

Author: labkey-matthewb

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;
 

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

@@ -39,8 +39,8 @@ public class SequenceOutputFile implements Serializable
     private String _description;
     private Long _dataId;
     private Integer _library_id;
-    private Integer _readset;
-    private Integer _analysis_id;
+    private Long _readset;
+    private Long _analysis_id;
     private Long _runid;
     private String _category;
     private Boolean _intermediate;
@@ -106,22 +106,22 @@ 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;
     }

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

@@ -31,13 +31,13 @@
  */
 public interface AnalysisModel extends Serializable
 {
-    Integer getAnalysisId();
+    Long getAnalysisId();
 
     Long getRunId();
 
     String getContainer();
 
-    Integer getReadset();
+    Long getReadset();
 
     Long getAlignmentFile();
 
@@ -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

@@ -24,9 +24,9 @@
  */
 public interface ReadData extends Serializable
 {
-    Integer getRowid();
+    Long getRowid();
 
-    Integer getReadset();
+    Long getReadset();
 
     String getPlatformUnit();
 

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();
 

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/SequenceAnalysisJobSupport.java

@@ -39,15 +39,15 @@ public interface SequenceAnalysisJobSupport extends Serializable
 
     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

@@ -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, Long 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;