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Merge pull request #381 from LabKey/fb_long_is_the_new_int
2 parents 34811c3 + 59f010c commit 4883710

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81 files changed

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

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -61,8 +61,8 @@ public class RefNtSequenceModel implements Serializable
6161
private String _name;
6262
//deprecated
6363
private String _sequence;
64-
private Integer _sequenceFile;
65-
private Integer _jobId;
64+
private Long _sequenceFile;
65+
private Long _jobId;
6666
private String _category;
6767
private String _subset;
6868
private String _locus;
@@ -171,12 +171,12 @@ public void setSequence(String sequence)
171171
_sequence = sequence;
172172
}
173173

174-
public Integer getSequenceFile()
174+
public Long getSequenceFile()
175175
{
176176
return _sequenceFile;
177177
}
178178

179-
public void setSequenceFile(Integer sequenceFile)
179+
public void setSequenceFile(Long sequenceFile)
180180
{
181181
_sequenceFile = sequenceFile;
182182
}
@@ -361,12 +361,12 @@ public void setModified(Date modified)
361361
_modified = modified;
362362
}
363363

364-
public Integer getJobId()
364+
public Long getJobId()
365365
{
366366
return _jobId;
367367
}
368368

369-
public void setJobId(Integer jobId)
369+
public void setJobId(Long jobId)
370370
{
371371
_jobId = jobId;
372372
}

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ static public void setInstance(SequenceAnalysisService instance)
6969

7070
abstract public ReadData getReadData(int rowId, User u);
7171

72-
abstract public Readset getReadset(int readsetId, User u);
72+
abstract public Readset getReadset(long readsetId, User u);
7373

7474
abstract public ReferenceGenome getReferenceGenome(int rowId, User u) throws PipelineJobException;
7575

@@ -87,7 +87,7 @@ static public void setInstance(SequenceAnalysisService instance)
8787

8888
abstract public String getUnzippedBaseName(String filename);
8989

90-
abstract public Integer getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
90+
abstract public Long getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
9191

9292
abstract public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u, DemographicsProvider d);
9393

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

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -37,11 +37,11 @@ public class SequenceOutputFile implements Serializable
3737
private Integer _rowid;
3838
private String _name;
3939
private String _description;
40-
private Integer _dataId;
40+
private Long _dataId;
4141
private Integer _library_id;
42-
private Integer _readset;
43-
private Integer _analysis_id;
44-
private Integer _runid;
42+
private Long _readset;
43+
private Long _analysis_id;
44+
private Long _runid;
4545
private String _category;
4646
private Boolean _intermediate;
4747
private String _container;
@@ -86,12 +86,12 @@ public void setDescription(String description)
8686
_description = description;
8787
}
8888

89-
public Integer getDataId()
89+
public Long getDataId()
9090
{
9191
return _dataId;
9292
}
9393

94-
public void setDataId(Integer dataId)
94+
public void setDataId(Long dataId)
9595
{
9696
_dataId = dataId;
9797
}
@@ -106,32 +106,32 @@ public void setLibrary_id(Integer library_id)
106106
_library_id = library_id;
107107
}
108108

109-
public Integer getReadset()
109+
public Long getReadset()
110110
{
111111
return _readset;
112112
}
113113

114-
public void setReadset(Integer readset)
114+
public void setReadset(Long readset)
115115
{
116116
_readset = readset;
117117
}
118118

119-
public Integer getAnalysis_id()
119+
public Long getAnalysis_id()
120120
{
121121
return _analysis_id;
122122
}
123123

124-
public void setAnalysis_id(Integer analysis_id)
124+
public void setAnalysis_id(Long analysis_id)
125125
{
126126
_analysis_id = analysis_id;
127127
}
128128

129-
public Integer getRunId()
129+
public Long getRunId()
130130
{
131131
return _runid;
132132
}
133133

134-
public void setRunId(Integer runid)
134+
public void setRunId(Long runid)
135135
{
136136
_runid = runid;
137137
}

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

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -31,24 +31,24 @@
3131
*/
3232
public interface AnalysisModel extends Serializable
3333
{
34-
Integer getAnalysisId();
34+
Long getAnalysisId();
3535

36-
Integer getRunId();
36+
Long getRunId();
3737

3838
String getContainer();
3939

40-
Integer getReadset();
40+
Long getReadset();
4141

42-
Integer getAlignmentFile();
42+
Long getAlignmentFile();
4343

4444
File getAlignmentFileObject();
4545

4646
ExpData getAlignmentData();
4747

4848
@Deprecated
49-
Integer getReferenceLibrary();
49+
Long getReferenceLibrary();
5050

51-
void setReferenceLibrary(Integer libraryId);
51+
void setReferenceLibrary(Long libraryId);
5252

5353
ExpData getReferenceLibraryData(User u) throws PipelineJobException;
5454

@@ -64,7 +64,7 @@ public interface AnalysisModel extends Serializable
6464

6565
Integer getCreatedby();
6666

67-
Integer getRowId();
67+
Long getRowId();
6868

6969
String getDescription();
7070

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

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -24,27 +24,27 @@
2424
*/
2525
public interface ReadData extends Serializable
2626
{
27-
Integer getRowid();
27+
Long getRowid();
2828

29-
Integer getReadset();
29+
Long getReadset();
3030

3131
String getPlatformUnit();
3232

3333
String getCenterName();
3434

3535
Date getDate();
3636

37-
Integer getFileId1();
37+
Long getFileId1();
3838

39-
Integer getFileId2();
39+
Long getFileId2();
4040

4141
File getFile1();
4242

4343
File getFile2();
4444

4545
String getDescription();
4646

47-
Integer getRunId();
47+
Long getRunId();
4848

4949
String getContainer();
5050

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

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ public interface Readset extends Serializable
4646

4747
Integer getInstrumentRunId();
4848

49-
Integer getReadsetId();
49+
Long getReadsetId();
5050

5151
String getBarcode5();
5252

@@ -56,7 +56,7 @@ public interface Readset extends Serializable
5656

5757
Double getConcentration();
5858

59-
int getRowId();
59+
long getRowId();
6060

6161
String getContainer();
6262

@@ -72,7 +72,7 @@ public interface Readset extends Serializable
7272

7373
String getStatus();
7474

75-
Integer getRunId();
75+
Long getRunId();
7676

7777
boolean hasPairedData();
7878

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,7 @@ public List<SequenceOutput> getSequenceOutputs()
103103
}
104104

105105
@Override
106-
public void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
106+
public void addSequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description)
107107
{
108108
_intermediateFiles.remove(file);
109109

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ public interface PipelineOutputTracker
1717
/**
1818
* Add a SequenceOutputFile for this job. These files are tracked and displayed through the browser UI.
1919
*/
20-
void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description);
20+
void addSequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description);
2121

2222
/**
2323
* Remove a previously added intermediate file

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

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -92,12 +92,12 @@ class SequenceOutput
9292
private final File _file;
9393
private final String _label;
9494
private final String _category;
95-
private final Integer _readsetId;
96-
private final Integer _analysisId;
95+
private final Long _readsetId;
96+
private final Long _analysisId;
9797
private final Integer _genomeId;
9898
private final String _description;
9999

100-
public SequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
100+
public SequenceOutput(File file, String label, String category, @Nullable Long readsetId, @Nullable Long analysisId, @Nullable Integer genomeId, @Nullable String description)
101101
{
102102
_file = file;
103103
_label = label;
@@ -123,12 +123,12 @@ public String getCategory()
123123
return _category;
124124
}
125125

126-
public Integer getReadsetId()
126+
public Long getReadsetId()
127127
{
128128
return _readsetId;
129129
}
130130

131-
public Integer getAnalysisId()
131+
public Long getAnalysisId()
132132
{
133133
return _analysisId;
134134
}
@@ -148,7 +148,7 @@ class PicardMetricsOutput
148148
{
149149
File _metricFile;
150150
File _inputFile;
151-
Integer _readsetId;
151+
Long _readsetId;
152152
TYPE _type;
153153

154154
public enum TYPE
@@ -157,7 +157,7 @@ public enum TYPE
157157
reads()
158158
}
159159

160-
public PicardMetricsOutput(File metricFile, File inputFile, Integer readsetId)
160+
public PicardMetricsOutput(File metricFile, File inputFile, Long readsetId)
161161
{
162162
_metricFile = metricFile;
163163
_inputFile = inputFile;
@@ -170,7 +170,7 @@ public PicardMetricsOutput(File metricFile, File inputFile, Integer readsetId)
170170
* 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
171171
* metrics to a specific file.
172172
*/
173-
public PicardMetricsOutput(File metricFile, TYPE type, Integer readsetId)
173+
public PicardMetricsOutput(File metricFile, TYPE type, Long readsetId)
174174
{
175175
_metricFile = metricFile;
176176
_type = type;
@@ -187,7 +187,7 @@ public File getInputFile()
187187
return _inputFile;
188188
}
189189

190-
public Integer getReadsetId()
190+
public Long getReadsetId()
191191
{
192192
return _readsetId;
193193
}

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@ public interface ReferenceGenome extends Serializable
7575
* this will correspond to the permanent FASTA, as opposed to the copy used in this job. If this FASTA was created specifically for
7676
* this job then the FASTA will be in the analysis directory.
7777
*/
78-
Integer getFastaExpDataId();
78+
Long getFastaExpDataId();
7979

8080
/**
8181
* @param name The name used by the aligner to identify its cached directory

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