From 53ecbbfc698407167144f6e8173d1b1788fc0a30 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Sun, 8 Jun 2025 15:00:39 -0700 Subject: [PATCH] Minor auto-refactor code cleanup on a massive scale --- .../OConnorExperimentsController.java | 25 +++++------ .../OConnorExperimentsModule.java | 4 +- .../query/ExperimentsTable.java | 2 +- .../test/tests/OConnorExperimentTest.java | 4 +- .../labkey/test/tests/OConnorListTest.java | 2 +- .../genotyping/GenotypingController.java | 44 +++++++++---------- .../labkey/genotyping/GenotypingManager.java | 2 +- .../genotyping/GenotypingQuerySchema.java | 16 +++---- .../genotyping/HaplotypeAssayProvider.java | 2 +- .../genotyping/HaplotypeDataCollector.java | 4 +- .../genotyping/HaplotypeDataHandler.java | 12 ++--- .../genotyping/HaplotypeProtocolSchema.java | 6 +-- .../genotyping/IlluminaFastqParser.java | 14 +++--- .../labkey/genotyping/Import454ReadsJob.java | 2 +- .../genotyping/ImportIlluminaReadsJob.java | 4 +- .../genotyping/ImportPacBioReadsJob.java | 8 ++-- .../genotyping/ReadsPipelineProvider.java | 2 +- .../src/org/labkey/genotyping/Status.java | 4 +- .../labkey/genotyping/SubmitAnalysisJob.java | 1 - .../genotyping/galaxy/GalaxyServer.java | 2 +- .../sequences/AlleleFastaLoader.java | 3 +- .../genotyping/sequences/SequenceManager.java | 1 - .../view/editHaplotypeAssignment.jsp | 2 +- .../view/haplotypeAssignmentReport.jsp | 2 +- .../view/importHaplotypeAssignments.jsp | 4 +- .../labkey/test/tests/GenotypingBaseTest.java | 2 +- .../org/labkey/test/tests/GenotypingTest.java | 2 +- .../labkey/test/tests/HaplotypeAssayTest.java | 2 +- .../org/labkey/test/tests/IlluminaTest.java | 10 ++--- .../src/org/labkey/test/tests/PacBioTest.java | 20 ++++----- 30 files changed, 103 insertions(+), 105 deletions(-) diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java index 417de1a7..fd6b148c 100644 --- a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java +++ b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java @@ -17,7 +17,6 @@ package org.labkey.oconnorexperiments; import org.apache.commons.io.FileUtils; -import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.LogManager; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; @@ -93,7 +92,7 @@ public OConnorExperimentsController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) @@ -108,7 +107,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(AdminPermission.class) - public class MigrateDataAction extends FormViewAction + public static class MigrateDataAction extends FormViewAction { @Override public void validateCommand(UserForm target, Errors errors) @@ -234,7 +233,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception // Move files File sourceFile = new File(fileContentService.getFileRoot(sourceContainer).getPath() + File.separator + "@files", databaseMap.get("expnumber").toString()); File targetDir = new File(fileContentService.getFileRoot(targetContainer).getPath() + File.separator + databaseMap.get("expnumber").toString() + File.separator + "@files"); - LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile.toString() + "' to directory '" + targetDir.toString() +"'" ); + LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile + "' to directory '" + targetDir +"'" ); if (sourceFile.exists()) { FileUtils.copyDirectory(sourceFile, targetDir); @@ -258,7 +257,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception Map map = new CaseInsensitiveHashMap<>(); map.put("container", databaseMap.get("ContainerStr")); - String[] parents = new String[0]; + String[] parents; ArrayList parentsEntityId = new ArrayList<>(); if (databaseMap.get("expParent") != null) { @@ -280,9 +279,9 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception } } } - if (parentsEntityId.size() > 0) + if (!parentsEntityId.isEmpty()) { - map.put("ParentExperiments", parentsEntityId.toArray(new String[parentsEntityId.size()])); + map.put("ParentExperiments", parentsEntityId.toArray(new String[0])); // workaround, pass user, container - databaseMap.get("Container"), singleton list LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber")); @@ -423,7 +422,7 @@ public void setFinalMigration(boolean finalMigration) */ @RequiresLogin @RequiresPermission(InsertPermission.class) - public class InsertExperimentAction extends FormHandlerAction + public static class InsertExperimentAction extends FormHandlerAction { private Container newExperiment; @@ -465,7 +464,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception @RequiresLogin @RequiresPermission(ReadPermission.class) - public class GetExperimentAction extends ReadOnlyApiAction + public static class GetExperimentAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Object o, BindException errors) throws Exception @@ -474,7 +473,7 @@ public ApiResponse execute(Object o, BindException errors) throws Exception TableInfo table = schema.getTable(OConnorExperimentsUserSchema.Table.Experiments.name()); QueryUpdateService qus = table.getUpdateService(); - List> pks = Collections.singletonList(Collections.singletonMap("Container", (Object)getContainer().getId())); + List> pks = Collections.singletonList(Collections.singletonMap("Container", getContainer().getId())); List> result = qus.getRows(getUser(), getContainer(), pks); ApiSimpleResponse resp = new ApiSimpleResponse(); @@ -495,14 +494,14 @@ public ApiResponse execute(Object o, BindException errors) throws Exception } @RequiresPermission(UpdatePermission.class) - public class HistoryAction extends SimpleViewAction + public static class HistoryAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) { getPageConfig().setNoIndex(); getPageConfig().setNoFollow(); - return new JspView("/org/labkey/oconnorexperiments/view/history.jsp", null, errors); + return new JspView<>("/org/labkey/oconnorexperiments/view/history.jsp", null, errors); } @Override @@ -528,7 +527,7 @@ public void setId(String id) } @RequiresPermission(ReadPermission.class) - public class LookupWorkbookAction extends SimpleViewAction + public static class LookupWorkbookAction extends SimpleViewAction { @Override public ModelAndView getView(LookupWorkbookForm form, BindException errors) diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsModule.java b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsModule.java index bed7f363..de30762c 100644 --- a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsModule.java +++ b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsModule.java @@ -128,7 +128,7 @@ public Set getSchemaNames() } // Listener that just updates the experiment changed date when a wiki is modified. - private class OConnorWikiChangeListener implements WikiChangeListener + private static class OConnorWikiChangeListener implements WikiChangeListener { @Override public void wikiCreated(User user, Container c, String name) @@ -150,7 +150,7 @@ public void wikiDeleted(User user, Container c, String name) } // Listener that just updates the experiment changed date when a file is uploaded/renamed. - private class OConnorFileChangeListener implements FileListener + private static class OConnorFileChangeListener implements FileListener { @Override public void fileCreated(@NotNull File created, @Nullable User user, @Nullable Container container) diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java b/OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java index 9c16c91a..c48094aa 100644 --- a/OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java +++ b/OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java @@ -505,7 +505,7 @@ public boolean next() throws BatchValidationException } Collection parentExperiments = (Collection)o; - if (parentExperiments.size() == 0) + if (parentExperiments.isEmpty()) return true; // Validate each ParentExperiment is a workbook and create list of maps for insertion diff --git a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java index f4f2b472..559a5877 100644 --- a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java +++ b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java @@ -64,7 +64,7 @@ public class OConnorExperimentTest extends BaseWebDriverTest implements Postgres private static final String TABLE_NAME = "Experiments"; private static final String EXPERIMENT_TYPE_TABLE_NAME = "ExperimentType"; private static final String EXPERIMENT_SAVE_SIGNAL = "experimentDataSave"; // See experimentField.html - private ArrayList pkeys = new ArrayList<>(); + private final ArrayList pkeys = new ArrayList<>(); @Nullable @Override @@ -327,7 +327,7 @@ protected void deleteViaJavaApi() DeleteRowsCommand cmd = new DeleteRowsCommand(SCHEMA_NAME, TABLE_NAME); Connection cn = WebTestHelper.getRemoteApiConnection(); for (String pk : pkeys) - cmd.addRow(Collections.singletonMap("container", (Object) pk)); + cmd.addRow(Collections.singletonMap("container", pk)); SaveRowsResponse resp = cmd.execute(cn, getProjectName()); assertEquals("Expected to delete " + pkeys.size() + " rows", pkeys.size(), resp.getRowsAffected().intValue()); diff --git a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java index a422b5c0..7be23da7 100644 --- a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java +++ b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java @@ -70,7 +70,7 @@ public List getAssociatedModules() @LogMethod public static void setup() { - OConnorListTest initTest = (OConnorListTest)getCurrentTest(); + OConnorListTest initTest = getCurrentTest(); initTest.setupOConnorProject(); } diff --git a/genotyping/src/org/labkey/genotyping/GenotypingController.java b/genotyping/src/org/labkey/genotyping/GenotypingController.java index 924762ae..f215fab6 100644 --- a/genotyping/src/org/labkey/genotyping/GenotypingController.java +++ b/genotyping/src/org/labkey/genotyping/GenotypingController.java @@ -154,7 +154,7 @@ public GenotypingController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleRedirectAction + public static class BeginAction extends SimpleRedirectAction { @Override public ActionURL getRedirectURL(Object o) @@ -222,7 +222,7 @@ public void setError(String error) @RequiresPermission(ReadPermission.class) - public class AnalysisAction extends QueryViewAction + public static class AnalysisAction extends QueryViewAction { private GenotypingAnalysis _analysis = null; @@ -316,7 +316,7 @@ private ActionURL getDeleteMatchesURL(int analysisId) // TODO: Delete this action? No longer used? @RequiresPermission(DeletePermission.class) - public class DeleteMatchesAction extends FormHandlerAction + public static class DeleteMatchesAction extends FormHandlerAction { private int _count = 0; private String _error = null; @@ -363,7 +363,7 @@ public boolean handlePost(MatchesForm form, BindException errors) @RequiresPermission(AdminPermission.class) - public class LoadSequencesAction extends FormHandlerAction + public static class LoadSequencesAction extends FormHandlerAction { @Override public void validateCommand(ReturnUrlForm target, Errors errors) @@ -581,7 +581,7 @@ public void addNavTrail(NavTree root) @RequiresPermission(ReadPermission.class) @IgnoresTermsOfUse - public class MergeFastqFilesAction extends ExportAction + public static class MergeFastqFilesAction extends ExportAction { @Override public void export(MergeFastqFilesForm form, HttpServletResponse response, BindException errors) throws Exception @@ -698,7 +698,7 @@ public static ActionURL getMySettingsURL(Container c, ActionURL returnUrl) @RequiresPermission(ReadPermission.class) - public class MySettingsAction extends FormViewAction + public static class MySettingsAction extends FormViewAction { @Override public void validateCommand(MySettingsForm form, Errors errors) @@ -890,10 +890,10 @@ public void setPrefix(String prefix) public static class ImportReadsBean { - private List _runs; - private SEQUENCE_PLATFORMS _platform; - private String _readsPath; - private String _path; + private final List _runs; + private final SEQUENCE_PLATFORMS _platform; + private final String _readsPath; + private final String _path; private String _prefix; private ImportReadsBean(List runs, String readsPath, String path, @Nullable String platform, @Nullable String prefix) @@ -1124,7 +1124,7 @@ private ActionURL getAnalyzeURL(int runId, ActionURL cancelURL) @RequiresPermission(InsertPermission.class) - public class AnalyzeAction extends FormViewAction + public static class AnalyzeAction extends FormViewAction { @Override public void validateCommand(AnalyzeForm target, Errors errors) @@ -1501,7 +1501,7 @@ public static ActionURL getSequencesURL(Container c, @Nullable Integer dictionar @RequiresPermission(ReadPermission.class) - public class SequencesAction extends QueryViewAction + public static class SequencesAction extends QueryViewAction { public SequencesAction() { @@ -1563,7 +1563,7 @@ public void setAnalysis(Integer analysis) @SuppressWarnings({"UnusedDeclaration"}) // URL defined on sequences.rowId column in genotyping.xml @RequiresPermission(ReadPermission.class) - public class SequenceAction extends SimpleViewAction + public static class SequenceAction extends SimpleViewAction { @Override public ModelAndView getView(SequenceForm form, BindException errors) @@ -1607,7 +1607,7 @@ public static ActionURL getRunsURL(Container c) @RequiresPermission(ReadPermission.class) - public class RunsAction extends QueryViewAction + public static class RunsAction extends QueryViewAction { public RunsAction() { @@ -1636,7 +1636,7 @@ public static ActionURL getAnalysesURL(Container c) @RequiresPermission(ReadPermission.class) - public class AnalysesAction extends QueryViewAction + public static class AnalysesAction extends QueryViewAction { public AnalysesAction() { @@ -1727,7 +1727,7 @@ public static ActionURL getRunURL(Container c, GenotypingRun run) public static final String FASTQ_FILE_FORMAT = "FASTQ_FILE"; public static final String FASTQ_FORMAT = "FASTQ"; - private abstract class ReadsAction
extends QueryViewAction + private abstract static class ReadsAction extends QueryViewAction { private static final String DATA_REGION_NAME = "Reads"; @@ -1905,7 +1905,7 @@ protected void handleSettings(QuerySettings settings) @RequiresPermission(AdminPermission.class) - public class DeleteRunsAction extends FormHandlerAction + public static class DeleteRunsAction extends FormHandlerAction { @Override public void validateCommand(Object target, Errors errors) @@ -1936,7 +1936,7 @@ public ActionURL getSuccessURL(Object o) @RequiresPermission(DeletePermission.class) - public class DeleteAnalysesAction extends FormHandlerAction + public static class DeleteAnalysesAction extends FormHandlerAction { @Override public void validateCommand(Object target, Errors errors) @@ -2036,7 +2036,7 @@ protected void handleSettings(QuerySettings settings) } } - public class AssignmentReportBean + public static class AssignmentReportBean { private final Collection _ids; private final String _assayName; @@ -2101,7 +2101,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(ReadPermission.class) - public class DuplicateAssignmentReportAction extends BaseAssayAction + public static class DuplicateAssignmentReportAction extends BaseAssayAction { private ExpProtocol _protocol; @@ -2128,7 +2128,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(ReadPermission.class) - public class STRDiscrepanciesAssignmentReportAction extends SimpleViewAction + public static class STRDiscrepanciesAssignmentReportAction extends SimpleViewAction { private ExpProtocol _protocol; private static final String DELIM = "[;,/]"; @@ -2355,7 +2355,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(UpdatePermission.class) - public class EditHaplotypeAssignmentAction extends SimpleViewAction + public static class EditHaplotypeAssignmentAction extends SimpleViewAction { @Override public ModelAndView getView(AssignmentForm form, BindException errors) diff --git a/genotyping/src/org/labkey/genotyping/GenotypingManager.java b/genotyping/src/org/labkey/genotyping/GenotypingManager.java index 8f8e2bc6..3daa2c53 100644 --- a/genotyping/src/org/labkey/genotyping/GenotypingManager.java +++ b/genotyping/src/org/labkey/genotyping/GenotypingManager.java @@ -443,7 +443,7 @@ public int deleteMatches(Container c, User user, int analysisId, List m GenotypingAnalysis analysis = GenotypingManager.get().getAnalysis(c, analysisId); // Verify that matches were posted - if (matchIds.size() < 1) + if (matchIds.isEmpty()) throw new IllegalStateException("No matches were selected"); // Count the corresponding matches in the database, making sure they belong to this analysis diff --git a/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java b/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java index f7405454..5341d948 100644 --- a/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java +++ b/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java @@ -151,7 +151,7 @@ FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) @Override FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) { - FilteredTable table = new FilteredTable(GS.getReadsTable(), schema, cf) + FilteredTable table = new FilteredTable<>(GS.getReadsTable(), schema, cf) { @Override protected void applyContainerFilter(ContainerFilter filter) @@ -253,7 +253,7 @@ public TableInfo getLookupTableInfo() @Override FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) { - FilteredTable table = new FilteredTable(GS.getAnalysesTable(), schema, cf) + FilteredTable table = new FilteredTable<>(GS.getAnalysesTable(), schema, cf) { @Override protected void applyContainerFilter(ContainerFilter filter) @@ -375,7 +375,7 @@ public TableInfo getLookupTableInfo() @Override FilteredTable createTable(final GenotypingQuerySchema schema, ContainerFilter cf) { - FilteredTable table = new FilteredTable(GS.getSequenceFilesTable(), schema, cf) + FilteredTable table = new FilteredTable<>(GS.getSequenceFilesTable(), schema, cf) { @Override protected void applyContainerFilter(ContainerFilter filter) @@ -528,14 +528,14 @@ boolean isAvailable(GenotypingQuerySchema schema) @Override FilteredTable createTable(final GenotypingQuerySchema schema, ContainerFilter cf) { - FilteredTable table = new FilteredTable(GS.getIlluminaTemplatesTable(), schema, cf) + FilteredTable table = new FilteredTable<>(GS.getIlluminaTemplatesTable(), schema, cf) { @Override public QueryUpdateService getUpdateService() { TableInfo table = getRealTable(); return (table != null && table.getTableType() == DatabaseTableType.TABLE ? - new DefaultQueryUpdateService(this, table): + new DefaultQueryUpdateService(this, table) : null); } @@ -595,7 +595,7 @@ FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) @Override FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) { - SimpleUserSchema.SimpleTable table = new SimpleUserSchema.SimpleTable(schema, GS.getAnimalAnalysisTable(), cf) + SimpleUserSchema.SimpleTable table = new SimpleUserSchema.SimpleTable<>(schema, GS.getAnimalAnalysisTable(), cf) { @Override protected void applyContainerFilter(ContainerFilter filter) @@ -645,7 +645,7 @@ protected void applyContainerFilter(ContainerFilter filter) @Override FilteredTable createTable(GenotypingQuerySchema schema, ContainerFilter cf) { - SimpleUserSchema.SimpleTable table = new SimpleUserSchema.SimpleTable(schema, GS.getAnimalHaplotypeAssignmentTable(), cf) + SimpleUserSchema.SimpleTable table = new SimpleUserSchema.SimpleTable<>(schema, GS.getAnimalHaplotypeAssignmentTable(), cf) { @Override protected void applyContainerFilter(ContainerFilter filter) @@ -805,7 +805,7 @@ private ExprColumn createConcatenatedHaplotypeColumn(SimpleUserSchema.SimpleTabl // We need to strip out the unassigned, empty markers // Example concatenated values, pre-replacement, are '~, A001, ~, B004, B023, ~'; '~, ~, ~, ~, ~, ~' SQLFragment concatSQL = new SQLFragment("REPLACE(REPLACE(REPLACE("); - concatSQL.append(table.getSqlDialect().concatenate(haplotypeSQLs.toArray(new SQLFragment[haplotypeSQLs.size()]))); + concatSQL.append(table.getSqlDialect().concatenate(haplotypeSQLs.toArray(new SQLFragment[0]))); concatSQL.append(", '" + NULL_HAPLOTYPE_MARKER + ", ', ''), ', " + NULL_HAPLOTYPE_MARKER + "', ''), '" + NULL_HAPLOTYPE_MARKER + "', '')"); ExprColumn result = new ExprColumn(table, "ConcatenatedHaplotypes", concatSQL, JdbcType.VARCHAR); diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java b/genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java index 13844db9..793e29e3 100644 --- a/genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java +++ b/genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java @@ -133,7 +133,7 @@ public String getName() } @Override - public HttpView getDataDescriptionView(AssayRunUploadForm form) + public HttpView getDataDescriptionView(AssayRunUploadForm form) { return new HtmlView(""); } diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java b/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java index df1b661c..ead2db07 100644 --- a/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java +++ b/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java @@ -86,10 +86,10 @@ public Map createData(ContextType context) throws IOException, for (Map.Entry property : HaplotypeAssayProvider.getColumnMappingProperties(protocol).entrySet()) { String value = context.getRequest().getParameter(property.getKey()); - if (property.getValue().isRequired() && (value == null || value.equals(""))) + if (property.getValue().isRequired() && (value == null || value.isEmpty())) errorColHeaders.add(property.getValue().getLabel()); } - if (errorColHeaders.size() > 0) + if (!errorColHeaders.isEmpty()) { throw new ExperimentException("Column header mapping missing for: " + StringUtils.join(errorColHeaders, ", ")); } diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java index 69b13836..c9f29e7c 100644 --- a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java +++ b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java @@ -218,7 +218,7 @@ private Map ensureAnimalIds(Map ids, Map> insertedRow = updateService.insertRows(user, container, Collections.singletonList(row), errors, null, new HashMap()); + List> insertedRow = updateService.insertRows(user, container, Collections.singletonList(row), errors, null, new HashMap<>()); throwFirstError(errors); if (insertedRow.size() != 1) { @@ -291,7 +291,7 @@ private Map ensureHaplotypeNames(List> insertedRow = updateService.insertRows(user, container, Collections.singletonList(row), errors, null, new HashMap()); + List> insertedRow = updateService.insertRows(user, container, Collections.singletonList(row), errors, null, new HashMap<>()); throwFirstError(errors); if (insertedRow.size() != 1) { @@ -352,7 +352,7 @@ private Map insertAnimalAnalysis(ExpRun run, List> insertedRows = updateService.insertRows(user, container, rows, errors, null, new HashMap()); + List> insertedRows = updateService.insertRows(user, container, rows, errors, null, new HashMap<>()); throwFirstError(errors); // return a mapping from the AnimalId to the AnimalAnalysis RowId @@ -452,7 +452,7 @@ private void insertHaplotypeAssignments(ExpProtocol protocol, List> insertedRows = updateService.insertRows(user, container, rows, errors, null, new HashMap()); + List> insertedRows = updateService.insertRows(user, container, rows, errors, null, new HashMap<>()); throwFirstError(errors); } @@ -522,9 +522,9 @@ private void deleteDatas(ExpData data) } /** Correponds to a single animal's row in the incoming TSV */ - public class HaplotypeAssignmentDataRow + public static class HaplotypeAssignmentDataRow { - private Map _dataMap = new HashMap<>(); + private final Map _dataMap = new HashMap<>(); public void addToDataMap(String key, String value) { diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeProtocolSchema.java b/genotyping/src/org/labkey/genotyping/HaplotypeProtocolSchema.java index afc7f4a8..1fa7d852 100644 --- a/genotyping/src/org/labkey/genotyping/HaplotypeProtocolSchema.java +++ b/genotyping/src/org/labkey/genotyping/HaplotypeProtocolSchema.java @@ -102,7 +102,7 @@ public TableInfo getTable(String name, @Nullable ContainerFilter cf, boolean inc @Override public @Nullable TableInfo createDataTable(ContainerFilter cf, boolean includeCopiedToStudyColumns) { - FilteredTable table = (FilteredTable)new GenotypingQuerySchema(getUser(), getContainer()).getTable(GenotypingQuerySchema.TableType.AnimalAnalysis.name(), cf,true, true); + FilteredTable table = (FilteredTable)new GenotypingQuerySchema(getUser(), getContainer()).getTable(GenotypingQuerySchema.TableType.AnimalAnalysis.name(), cf,true, true); List keys = new ArrayList<>(table.getDefaultVisibleColumns()); HashSet defaults = HaplotypeAssayProvider.getDefaultColumns(); List props = HaplotypeAssayProvider.getDomainProps(getProtocol()); @@ -132,7 +132,7 @@ public TableInfo getTable(String name, @Nullable ContainerFilter cf, boolean inc table.setDefaultVisibleColumns(keys); - table.getMutableColumn("RunId").setFk(new LookupForeignKey() + table.getMutableColumnOrThrow("RunId").setFk(new LookupForeignKey() { @Override public TableInfo getLookupTableInfo() @@ -143,7 +143,7 @@ public TableInfo getLookupTableInfo() return table; } - private ExprColumn makeColumnFromRunField(DomainProperty prop, boolean max, SQLFragment selectStatement, FilteredTable table){ + private ExprColumn makeColumnFromRunField(DomainProperty prop, boolean max, SQLFragment selectStatement, FilteredTable table){ String field = prop.getName(); String label = prop.getLabel() != null ? prop.getLabel() : ColumnInfo.labelFromName(prop.getName()); diff --git a/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java b/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java index 210c8ec4..29c2bc84 100644 --- a/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java +++ b/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java @@ -64,13 +64,13 @@ */ public class IlluminaFastqParser { - private String _outputPrefix; - private Map _sampleIndexToIdMap; - private Map _sampleIdToIndexMap; - private Map _sampleNameToIdMap; - private List _files; - private Map, FileInfo> _fileInfo = new HashMap<>(); - private Logger _logger; + private final String _outputPrefix; + private final Map _sampleIndexToIdMap; + private final Map _sampleIdToIndexMap; + private final Map _sampleNameToIdMap; + private final List _files; + private final Map, FileInfo> _fileInfo = new HashMap<>(); + private final Logger _logger; public IlluminaFastqParser(@Nullable String outputPrefix, Map sampleIndexToIdMap, Map sampleIdToIndexMap, Map sampleNameToIdMap, Logger logger, List files) { diff --git a/genotyping/src/org/labkey/genotyping/Import454ReadsJob.java b/genotyping/src/org/labkey/genotyping/Import454ReadsJob.java index c138a120..7a068b2e 100644 --- a/genotyping/src/org/labkey/genotyping/Import454ReadsJob.java +++ b/genotyping/src/org/labkey/genotyping/Import454ReadsJob.java @@ -151,7 +151,7 @@ private void importReads() throws IOException, SQLException, PipelineJobExceptio columns.add(new ColumnDescriptor("run", Integer.class, _run.getRowId())); columns.add(new ColumnDescriptor("sampleid", Integer.class)); - loader.setColumns(columns.toArray(new ColumnDescriptor[columns.size()])); + loader.setColumns(columns.toArray(new ColumnDescriptor[0])); SampleManager.SampleIdFinder finder = new SampleManager.SampleIdFinder(_run, getUser(), sampleKeyColumns, "importing reads"); diff --git a/genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java b/genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java index b4b5b1ea..11e43d17 100644 --- a/genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java +++ b/genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java @@ -144,7 +144,7 @@ private void importReads() throws PipelineJobException, SQLException Map sampleNameToIdMap = new HashMap<>(); sampleIndexToIdMap.put(0, 0); //placeholder for control and unmapped reads sampleIdToIndexMap.put(0, 0); - Boolean inSamples = false; + boolean inSamples = false; int sampleIdx = 0; while ((nextLine = reader.readNext()) != null) @@ -206,7 +206,7 @@ private void importReads() throws PipelineJobException, SQLException _fastqFiles = IlluminaFastqParser.inferIlluminaInputsFromPath(_sampleFile.getParent(), _fastqPrefix); } - if (_fastqFiles.size() == 0) + if (_fastqFiles.isEmpty()) { throw new PipelineJobException("No FASTQ files" + (_fastqPrefix == null ? "" : " matching the prefix '" + _fastqPrefix) + "' were found"); } diff --git a/genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java b/genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java index 18b2507e..7c14ff82 100644 --- a/genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java +++ b/genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java @@ -60,9 +60,9 @@ public class ImportPacBioReadsJob extends ReadsJob { private File _sampleFile; private String _fastqPrefix; - private List _pools = new LinkedList<>(); - private String _dirSubstring = "pool"; - private String[] _extensions = {"fastq.gz", "fastq"}; + private final List _pools = new LinkedList<>(); + private final String _dirSubstring = "pool"; + private final String[] _extensions = {"fastq.gz", "fastq"}; // For serialization protected ImportPacBioReadsJob() {} @@ -332,7 +332,7 @@ public Integer getNumReads(File fastqFile, int fileNum, int poolNum) return totalReads; } - class PacBioPool + static class PacBioPool { int poolNum; List fastqFiles = new ArrayList<>(); diff --git a/genotyping/src/org/labkey/genotyping/ReadsPipelineProvider.java b/genotyping/src/org/labkey/genotyping/ReadsPipelineProvider.java index 09df662e..3042e4ae 100644 --- a/genotyping/src/org/labkey/genotyping/ReadsPipelineProvider.java +++ b/genotyping/src/org/labkey/genotyping/ReadsPipelineProvider.java @@ -30,7 +30,7 @@ public class ReadsPipelineProvider extends PipelineProvider { String _platform; - FileFilter _readsFilter = null; + FileFilter _readsFilter; public ReadsPipelineProvider(String name, Module owningModule, String platform) { diff --git a/genotyping/src/org/labkey/genotyping/Status.java b/genotyping/src/org/labkey/genotyping/Status.java index 1e718942..72558945 100644 --- a/genotyping/src/org/labkey/genotyping/Status.java +++ b/genotyping/src/org/labkey/genotyping/Status.java @@ -40,9 +40,9 @@ public static Status getStatus(int statusId) return _map.get(statusId); } - private int _statusId; + private final int _statusId; - private Status(int statusId) + Status(int statusId) { _statusId = statusId; } diff --git a/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java b/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java index 39988a45..f0102063 100644 --- a/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java +++ b/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java @@ -43,7 +43,6 @@ import java.io.File; import java.io.IOException; -import java.io.OutputStream; import java.net.URISyntaxException; import java.sql.SQLException; import java.util.HashMap; diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java index 2d9b57ea..deac1c3f 100644 --- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java +++ b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java @@ -167,7 +167,7 @@ private String post(String relativeUrl, String body) throws IOException } - public class Item + public static class Item { private final ItemType _type; private final String _apiUrl; diff --git a/genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java b/genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java index 4e72a7fd..cca9b965 100644 --- a/genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java +++ b/genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java @@ -28,7 +28,8 @@ public class AlleleFastaLoader extends FastaLoader { protected AlleleFastaLoader(File fastaFile) { - super(fastaFile, new FastaIteratorElementFactory() { + super(fastaFile, new FastaIteratorElementFactory<>() + { @Override public Allele createNext(String header, byte[] body) { diff --git a/genotyping/src/org/labkey/genotyping/sequences/SequenceManager.java b/genotyping/src/org/labkey/genotyping/sequences/SequenceManager.java index a406ec33..1ea6f278 100644 --- a/genotyping/src/org/labkey/genotyping/sequences/SequenceManager.java +++ b/genotyping/src/org/labkey/genotyping/sequences/SequenceManager.java @@ -30,7 +30,6 @@ import org.labkey.api.query.QueryHelper; import org.labkey.api.security.User; import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.util.ResultSetUtil; import org.labkey.api.view.NotFoundException; import org.labkey.api.writer.FastaEntry; import org.labkey.api.writer.FastaWriter; diff --git a/genotyping/src/org/labkey/genotyping/view/editHaplotypeAssignment.jsp b/genotyping/src/org/labkey/genotyping/view/editHaplotypeAssignment.jsp index 131e306f..0228f1c9 100644 --- a/genotyping/src/org/labkey/genotyping/view/editHaplotypeAssignment.jsp +++ b/genotyping/src/org/labkey/genotyping/view/editHaplotypeAssignment.jsp @@ -30,7 +30,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); GenotypingController.AssignmentForm bean = me.getModelBean(); final String formDivId = "form" + getRequestScopedUID(); diff --git a/genotyping/src/org/labkey/genotyping/view/haplotypeAssignmentReport.jsp b/genotyping/src/org/labkey/genotyping/view/haplotypeAssignmentReport.jsp index 43107ca3..d7e0eeaa 100644 --- a/genotyping/src/org/labkey/genotyping/view/haplotypeAssignmentReport.jsp +++ b/genotyping/src/org/labkey/genotyping/view/haplotypeAssignmentReport.jsp @@ -30,7 +30,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); GenotypingController.AssignmentReportBean bean = me.getModelBean(); final String idEntryFormDivId = "idEntryForm" + getRequestScopedUID(); final String queryWebPartDivId = "queryWebPart" + getRequestScopedUID(); diff --git a/genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp b/genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp index 9772bfa3..ae2cd3a2 100644 --- a/genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp +++ b/genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp @@ -26,11 +26,11 @@ <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); HaplotypeProtocolBean bean = me.getModelBean(); HaplotypeDataCollector dataCollector = bean.getDataCollector(); String[] reshowData = {}; - if (dataCollector.getReshowValue("data") != null && !dataCollector.getReshowValue("data").equals("")) + if (dataCollector.getReshowValue("data") != null && !dataCollector.getReshowValue("data").isEmpty()) { reshowData = dataCollector.getReshowValue("data").split("\\r?\\n"); } diff --git a/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java b/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java index 78c22b81..61e065b4 100644 --- a/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java +++ b/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java @@ -134,7 +134,7 @@ private void deleteTemplateRow(boolean failOnError) { Connection cn = WebTestHelper.getRemoteApiConnection(); DeleteRowsCommand cmd = new DeleteRowsCommand("genotyping", "IlluminaTemplates"); - cmd.addRow(Collections.singletonMap("Name", (Object) TEMPLATE_NAME)); + cmd.addRow(Collections.singletonMap("Name", TEMPLATE_NAME)); SaveRowsResponse resp; try { diff --git a/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java b/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java index f270d793..32d6c074 100644 --- a/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java +++ b/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java @@ -45,7 +45,7 @@ protected String getProjectName() @BeforeClass public static void setupProject() { - GenotypingTest init = (GenotypingTest)getCurrentTest(); + GenotypingTest init = getCurrentTest(); init.doSetup(); } diff --git a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java index 5a5c7325..4fe84922 100644 --- a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java +++ b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java @@ -65,7 +65,7 @@ protected String getProjectName() @BeforeClass public static void setupProject() { - HaplotypeAssayTest init = (HaplotypeAssayTest)getCurrentTest(); + HaplotypeAssayTest init = getCurrentTest(); init.doSetup(); } diff --git a/genotyping/test/src/org/labkey/test/tests/IlluminaTest.java b/genotyping/test/src/org/labkey/test/tests/IlluminaTest.java index 9b3273a4..9a56aedd 100644 --- a/genotyping/test/src/org/labkey/test/tests/IlluminaTest.java +++ b/genotyping/test/src/org/labkey/test/tests/IlluminaTest.java @@ -60,7 +60,7 @@ protected String getProjectName() @BeforeClass public static void setupProject() { - IlluminaTest init = (IlluminaTest)getCurrentTest(); + IlluminaTest init = getCurrentTest(); init.doSetup(); } @@ -213,8 +213,8 @@ private enum ExportType ZIP("ZIP Archive of Individual Files", ".zip"), FASTQ("Merge into Single FASTQ File", ".fastq.gz"); - private String _radioLabel; - private String _fileSuffix; + private final String _radioLabel; + private final String _fileSuffix; ExportType(String radioLabel, String fileSuffix) { @@ -415,7 +415,7 @@ private void assertExportButtonPresent() } - private class OutputFilter implements FilenameFilter + private static class OutputFilter implements FilenameFilter { @Override public boolean accept(File dir, String name) @@ -431,7 +431,7 @@ private void verifyIlluminaSamples() assertEquals(30, files.length); DataRegionTable d = new DataRegionTable("Reads", this); - assertEquals(d.getDataRowCount(), 30); + assertEquals(30, d.getDataRowCount()); assertTextPresent("Read Count"); assertEquals("9", d.getDataAsText(d.getIndexWhereDataAppears("IlluminaSamples-R1-4947.fastq.gz", "Filename") + 1, "Read Count")); } diff --git a/genotyping/test/src/org/labkey/test/tests/PacBioTest.java b/genotyping/test/src/org/labkey/test/tests/PacBioTest.java index 3e16f3b2..eb3203ff 100644 --- a/genotyping/test/src/org/labkey/test/tests/PacBioTest.java +++ b/genotyping/test/src/org/labkey/test/tests/PacBioTest.java @@ -47,23 +47,23 @@ public class PacBioTest extends GenotypingBaseTest private static final String PAC_BIO_RUN = "2"; private static final Map> POOL1_DATA = - Collections.unmodifiableMap(new HashMap>() + Collections.unmodifiableMap(new HashMap<>() {{ - put(0, Arrays.asList("lbc1--lbc1.fastq", "1858", "5", "1")); - put(1, Arrays.asList("lbc2--lbc2.fastq", "1859", "12", "1")); - }}); + put(0, Arrays.asList("lbc1--lbc1.fastq", "1858", "5", "1")); + put(1, Arrays.asList("lbc2--lbc2.fastq", "1859", "12", "1")); + }}); private static final Map> POOL2_DATA = - Collections.unmodifiableMap(new HashMap>() + Collections.unmodifiableMap(new HashMap<>() {{ - put(0, Arrays.asList("lbc14--lbc14.fastq.gz", "1871", "7", "2")); - put(1, Arrays.asList("lbc15--lbc15.fastq.gz", "1872", "6", "2")); - put(2, Arrays.asList("lbc16--lbc16.fastq.gz", "1873", "0", "2")); - }}); + put(0, Arrays.asList("lbc14--lbc14.fastq.gz", "1871", "7", "2")); + put(1, Arrays.asList("lbc15--lbc15.fastq.gz", "1872", "6", "2")); + put(2, Arrays.asList("lbc16--lbc16.fastq.gz", "1873", "0", "2")); + }}); @BeforeClass public static void setupProject() { - PacBioTest init = (PacBioTest)getCurrentTest(); + PacBioTest init = getCurrentTest(); init.doSetup(); }