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Merge branch 'discvr-25.11' into 25.11_fb_25.7_merge
2 parents 13e70fd + 2b26ae1 commit ed34b1a

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‎.github/dependabot.yml‎

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@@ -4,4 +4,4 @@ updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "daily"
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interval: "weekly"

‎.github/workflows/branch_release.yml‎

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tags:
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- '*'
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permissions:
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pull-requests: write
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contents: write
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jobs:
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branch_release:
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if: github.event.created && github.event.sender.login == 'labkey-teamcity'

‎.github/workflows/merge_release.yml‎

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types:
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- submitted
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permissions:
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pull-requests: write
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contents: write
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jobs:
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merge_release:
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if: >

‎.github/workflows/validate_pr.yml‎

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- reopened
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- ready_for_review
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permissions:
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pull-requests: write
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jobs:
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validate_pr:
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if: github.event.pull_request.head.repo.owner.login == 'LabKey'

‎OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncModule.java‎

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Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
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import org.labkey.api.data.DbSchemaType;
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import org.labkey.api.module.Module;
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import org.labkey.api.module.ModuleContext;
26+
import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.module.SpringModule;
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import org.labkey.api.query.DefaultSchema;
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import org.labkey.api.query.DetailsURL;
@@ -100,7 +101,8 @@ public boolean isAvailable(DefaultSchema schema, Module module)
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{
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modules = new HashSet<>(modules);
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modules.add(this);
103-
ContainerManager.getSharedContainer().setActiveModules(modules);
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if (ModuleLoader.getInstance().shouldInsertData())
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ContainerManager.getSharedContainer().setActiveModules(modules);
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}
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}
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@@ -117,7 +119,7 @@ public boolean isAvailable(DefaultSchema schema, Module module)
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}
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@Override
120-
public @NotNull Set<Class> getIntegrationTests()
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public @NotNull Set<Class<?>> getIntegrationTests()
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{
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return PageFlowUtil.set(LdapSyncRunner.TestCase.class);
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}

‎OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncAuditProvider.java‎

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Original file line numberDiff line numberDiff line change
@@ -36,8 +36,8 @@ public class LdapSyncAuditProvider extends AbstractAuditTypeProvider implements
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static final List<FieldKey> defaultVisibleColumns = new ArrayList<>();
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static {
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static
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{
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defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_CREATED));
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defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_CREATED_BY));
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defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_IMPERSONATED_BY));
@@ -47,6 +47,11 @@ public class LdapSyncAuditProvider extends AbstractAuditTypeProvider implements
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defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_COMMENT));
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}
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public LdapSyncAuditProvider()
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{
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super(new LdapSyncAuditDomainKind());
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}
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@Override
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public String getEventName()
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{
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@Override
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public TableInfo createTableInfo(UserSchema userSchema, ContainerFilter cf)
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{
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DefaultAuditTypeTable table = new DefaultAuditTypeTable(this, createStorageTableInfo(), userSchema, cf, defaultVisibleColumns)
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return new DefaultAuditTypeTable(LdapSyncAuditProvider.this, createStorageTableInfo(), userSchema, cf, defaultVisibleColumns)
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{
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@Override
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protected void initColumn(MutableColumnInfo col)
@@ -87,7 +92,6 @@ else if (COLUMN_NAME_MEMBERSHIPS_CHANGED.equalsIgnoreCase(col.getName()))
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}
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}
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};
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return table;
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}
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@Override
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return defaultVisibleColumns;
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}
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99-
@Override
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protected AbstractAuditDomainKind getDomainKind()
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{
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return new LdapSyncAuditDomainKind();
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}
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@Override
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public Map<FieldKey, String> legacyNameMap()
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{

‎QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java‎

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@@ -40,7 +40,7 @@ public String getName()
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@Override
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public @Nullable Double getSchemaVersion()
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{
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return 23.000;
43+
return 25.000;
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}
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@Override
@@ -81,4 +81,4 @@ public Set<String> getSchemaNames()
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{
8282
return Collections.singleton(QueryExtensionsSchema.NAME);
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}
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}
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}

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

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@@ -61,8 +61,8 @@ public class RefNtSequenceModel implements Serializable
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private String _name;
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//deprecated
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private String _sequence;
64-
private Integer _sequenceFile;
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private Integer _jobId;
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private Long _sequenceFile;
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private Long _jobId;
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private String _category;
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private String _subset;
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private String _locus;
@@ -171,12 +171,12 @@ public void setSequence(String sequence)
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_sequence = sequence;
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}
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174-
public Integer getSequenceFile()
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public Long getSequenceFile()
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{
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return _sequenceFile;
177177
}
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179-
public void setSequenceFile(Integer sequenceFile)
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public void setSequenceFile(Long sequenceFile)
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{
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_sequenceFile = sequenceFile;
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}
@@ -361,12 +361,12 @@ public void setModified(Date modified)
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_modified = modified;
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}
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364-
public Integer getJobId()
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public Long getJobId()
365365
{
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return _jobId;
367367
}
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369-
public void setJobId(Integer jobId)
369+
public void setJobId(Long jobId)
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{
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_jobId = jobId;
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}

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

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@@ -69,7 +69,7 @@ static public void setInstance(SequenceAnalysisService instance)
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abstract public ReadData getReadData(int rowId, User u);
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72-
abstract public Readset getReadset(int readsetId, User u);
72+
abstract public Readset getReadset(long readsetId, User u);
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7474
abstract public ReferenceGenome getReferenceGenome(int rowId, User u) throws PipelineJobException;
7575

@@ -87,7 +87,7 @@ static public void setInstance(SequenceAnalysisService instance)
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abstract public String getUnzippedBaseName(String filename);
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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

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@@ -37,11 +37,11 @@ public class SequenceOutputFile implements Serializable
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private Integer _rowid;
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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;
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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
}

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