From a772e3216881cde2bbb04181ccabf358befbcbc5 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 --- .../skylinetoolsstore/RatingManager.java | 2 +- .../SkylineToolsStoreController.java | 33 +++-- .../SkylineToolsStoreModule.java | 25 ++-- .../SkylineToolsStoreSchema.java | 2 - .../skylinetoolsstore/model/Rating.java | 3 +- .../skylinetoolsstore/model/SkylineTool.java | 3 +- .../org/labkey/lincs/DocImportListener.java | 2 +- lincs/src/org/labkey/lincs/Gct.java | 18 +-- .../src/org/labkey/lincs/LincsController.java | 33 +++-- .../src/org/labkey/lincs/LincsDataTable.java | 20 +-- lincs/src/org/labkey/lincs/LincsManager.java | 2 +- lincs/src/org/labkey/lincs/LincsSchema.java | 2 +- .../lincs/cromwell/CromwellGctTask.java | 1 - .../labkey/lincs/psp/LincsPspPipelineJob.java | 8 +- .../PanoramaPublicController.java | 118 ++++++++++-------- .../PanoramaPublicListener.java | 2 +- .../PanoramaPublicMetadataImporter.java | 2 +- .../panoramapublic/PanoramaPublicModule.java | 6 +- .../PanoramaPublicSymlinkManager.java | 7 +- .../chromlib/ChromLibStateImporter.java | 7 +- .../model/JournalSubmission.java | 5 +- .../model/validation/DataValidation.java | 2 +- .../model/validation/Modification.java | 2 +- .../validation/SkylineDocSampleFile.java | 1 + .../model/validation/SpecLib.java | 2 +- .../model/validation/SpecLibSourceFile.java | 1 + .../model/validation/SpecLibValidation.java | 10 +- .../model/validation/Status.java | 2 +- .../pipeline/CopyExperimentFinalTask.java | 2 +- .../pipeline/CopyExperimentPipelineJob.java | 1 + .../pipeline/CopyLibraryStateTask.java | 2 +- .../pipeline/FilesMetadataImporter.java | 2 +- .../pipeline/FilesMetadataWriter.java | 2 +- .../pipeline/PxDataValidationPipelineJob.java | 1 - .../pipeline/ValidatorListener.java | 4 +- .../proteomexchange/ChemElement.java | 4 +- .../ExperimentModificationGetter.java | 8 +- .../proteomexchange/Formula.java | 4 +- .../proteomexchange/PxXmlWriter.java | 8 +- .../proteomexchange/UnimodModification.java | 10 +- .../proteomexchange/UnimodParser.java | 6 +- .../validator/DataValidator.java | 4 +- .../validator/ValidatorStatus.java | 1 - .../panoramapublic/query/ContainerJoin.java | 4 +- .../query/DataValidationManager.java | 26 ++-- .../query/ExperimentAnnotationsManager.java | 11 +- .../query/ExperimentAnnotationsTableInfo.java | 2 +- .../panoramapublic/query/JournalManager.java | 2 +- .../query/ModificationInfoManager.java | 4 +- .../panoramapublic/query/PxXmlManager.java | 1 - .../query/SubmissionManager.java | 4 +- .../query/SubmissionTableInfo.java | 1 - .../EditLibInfoDisplayColumnFactory.java | 1 - .../view/PanoramaPublicRunListView.java | 2 +- .../view/expannotations/experimentDetails.jsp | 2 +- .../panoramapublic/view/unimodMatchInfo.jsp | 4 +- .../PanoramaPublicSearchWebPart.java | 3 +- .../TargetedMsExperimentWebPart.java | 1 - .../panoramapublic/DataValidationPage.java | 10 +- .../PanoramaPublicBaseTest.java | 2 +- .../PanoramaPublicModificationsTest.java | 2 +- .../PanoramaPublicMyDataViewTest.java | 2 +- .../PanoramaWebPublicSearchTest.java | 6 +- .../pwebdashboard/ProjectAdminsTable.java | 2 +- signup/src/org/labkey/signup/SignUpAdmin.jsp | 2 +- .../org/labkey/signup/SignUpController.java | 16 +-- .../src/org/labkey/signup/SignUpModule.java | 2 +- .../testresults/SendTestResultsEmail.java | 4 +- .../testresults/TestResultsController.java | 76 +++++------ .../testresults/TestResultsWebPart.java | 6 +- .../testresults/model/GlobalSettings.java | 4 - .../labkey/testresults/model/RunDetail.java | 2 +- .../testresults/model/TestFailDetail.java | 2 +- .../org/labkey/testresults/model/User.java | 54 ++++---- .../labkey/testresults/view/RunDownBean.java | 4 +- .../testresults/view/TestsDataBean.java | 1 - .../testresults/view/multiFailureDetail.jsp | 8 +- .../org/labkey/testresults/view/rundown.jsp | 2 +- .../src/org/labkey/testresults/view/user.jsp | 2 +- 79 files changed, 316 insertions(+), 341 deletions(-) diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/RatingManager.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/RatingManager.java index b71a4965..800dde04 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/RatingManager.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/RatingManager.java @@ -87,7 +87,7 @@ public Rating[] getRatingsByToolAllVersions(String toolLsid) for (SkylineTool tool : tools) ratings.addAll(Arrays.asList(getRatingsByToolId(tool.getRowId()))); } - return ratings.toArray(new Rating[ratings.size()]); + return ratings.toArray(new Rating[0]); } public boolean userLeftRating(String toolLsid, User user) diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java index 3add115e..147a7205 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java @@ -129,7 +129,7 @@ public SkylineToolsStoreController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -460,7 +460,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, ArrayList toolOwnersUsers = parsedOwners.first; ArrayList toolOwnersInvalid = parsedOwners.second; - if (toolOwnersInvalid.size() > 0) + if (!toolOwnersInvalid.isEmpty()) { getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form", UNKNOWN_USERS + StringUtils.join(toolOwnersInvalid, ", ")); @@ -607,7 +607,7 @@ else if (!getContainer().hasPermission(getUser(), InsertPermission.class)) getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "sender", sender); getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "updatetarget", updateTargetString); getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "toolowners", toolOwners); - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolsStoreUpload.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolsStoreUpload.jsp", null); } @Override @@ -667,9 +667,9 @@ protected ModelAndView handleRequestInternal(HttpServletRequest httpServletReque final String ratingIdString = httpServletRequest.getParameter("ratingId"); int ratingId; try { - ratingId = (ratingIdString != null && !ratingIdString.isEmpty()) ? Integer.parseInt(ratingIdString) : -1;; + ratingId = (ratingIdString != null && !ratingIdString.isEmpty()) ? Integer.parseInt(ratingIdString) : -1; } catch(Exception e) { - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); } Rating rating = (ratingId < 0) ? null : RatingManager.get().getRatingById(ratingId); final SkylineTool tool = SkylineToolsStoreManager.get().getTool((toolId >= 0) ? toolId : rating.getToolId()); @@ -679,7 +679,7 @@ protected ModelAndView handleRequestInternal(HttpServletRequest httpServletReque try { ratingValue = Integer.parseInt(ratingValueString); } catch(Exception e) { - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); } final String ratingTitle = httpServletRequest.getParameter("title"); final String review = httpServletRequest.getParameter("review"); @@ -701,7 +701,7 @@ else if (ratingValue < 1 || ratingValue > 5) getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form", NO_RATING); } - else if (review == null || review.length() == 0) + else if (review == null || review.isEmpty()) { getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form", NO_REVIEW); @@ -748,7 +748,7 @@ else if (tool == null || (ratingId >= 0 && rating == null)) if (review != null) getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "formReview", review); - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null); } @Override @@ -813,7 +813,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, { httpServletRequest.setAttribute(BindingResult.MODEL_KEY_PREFIX + "form", INVALID_TOOL_ID + " " + suppTargetString); httpServletRequest.setAttribute(BindingResult.MODEL_KEY_PREFIX + "supptarget", suppTargetString); - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null); } SkylineTool tool = SkylineToolsStoreManager.get().getTool(suppTarget); @@ -846,7 +846,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, } getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "supptarget", suppTargetString); - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null); } @Override @@ -902,7 +902,7 @@ public void checkPermissions() throws UnauthorizedException } @RequiresLogin - public class DeleteAction extends FormHandlerAction + public static class DeleteAction extends FormHandlerAction { @Override public URLHelper getSuccessURL(IdForm idForm) @@ -1002,7 +1002,7 @@ public class DeleteLatestAction extends AbstractController implements Permission @Override public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception { - Integer id; + int id; try { id = Integer.parseInt(httpServletRequest.getParameter("id")); } @@ -1156,7 +1156,7 @@ public void checkPermissions() throws UnauthorizedException @RequiresNoPermission @ActionNames("downloadFile") - public class DownloadToolFileAction extends SimpleViewAction implements PermissionCheckable + public static class DownloadToolFileAction extends SimpleViewAction implements PermissionCheckable { @Override public ModelAndView getView(DownloadFileForm form, BindException errors) throws Exception @@ -1243,8 +1243,7 @@ public ModelAndView getView(ViewToolDetailsForm form, BindException errors) thro _tool = SkylineToolsStoreManager.get().getTool(toolId); if (_tool == null) { - StringBuilder msg = new StringBuilder("Could not find tool ").append(" by Id ").append(toolId); - errors.reject(SpringActionController.ERROR_MSG, msg.toString()); + errors.reject(SpringActionController.ERROR_MSG, "Could not find tool " + " by Id " + toolId); return new SimpleErrorView(errors); } } @@ -1396,7 +1395,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "toolowners", toolOwners); getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "sender", sender); getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "updatetarget", updateTargetString); - return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolManageOwners.jsp", null); + return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolManageOwners.jsp", null); } @Override @@ -1414,7 +1413,7 @@ public class UpdatePropertyAction extends AbstractController implements Permissi @Override public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception { - final Integer id = Integer.parseInt(httpServletRequest.getParameter("id")); + final int id = Integer.parseInt(httpServletRequest.getParameter("id")); final SkylineTool tool = SkylineToolsStoreManager.get().getTool(id); if(tool == null) diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java index 44604fd9..ef7813a9 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java @@ -32,7 +32,6 @@ import org.labkey.skylinetoolsstore.model.SkylineTool; import org.labkey.skylinetoolsstore.view.SkylineToolsStoreWebPart; -import java.lang.reflect.InvocationTargetException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -66,19 +65,21 @@ public boolean hasScripts() @NotNull protected Collection createWebPartFactories() { - return new ArrayList( - Arrays.asList( - new BaseWebPartFactory("Skyline Tool Store") { + return new ArrayList<>( + Arrays.asList( + new BaseWebPartFactory("Skyline Tool Store") { - addLegacyNames("Skyline Tools Store"); - } - @Override - public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) throws WebPartConfigurationException - { - return new SkylineToolsStoreWebPart(); + { + addLegacyNames("Skyline Tools Store"); + } + + @Override + public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) throws WebPartConfigurationException + { + return new SkylineToolsStoreWebPart(); + } } - } - )); + )); } @Override diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreSchema.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreSchema.java index f3a647e1..76552dd5 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreSchema.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreSchema.java @@ -20,8 +20,6 @@ import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.TableInfo; -import java.lang.String; - public class SkylineToolsStoreSchema { private static final SkylineToolsStoreSchema _instance = new SkylineToolsStoreSchema(); diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/Rating.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/Rating.java index b12ef358..c84cd1c5 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/Rating.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/Rating.java @@ -76,9 +76,8 @@ public void setRowId(Integer rowId) public boolean equals(Object obj) { - if (!(obj instanceof Rating)) + if (!(obj instanceof Rating p)) return false; - Rating p = (Rating)obj; return Objects.equals(_rating, p.getRating()) && Objects.equals(_toolId, p.getToolId()) && diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java index dce2a1ac..684f8397 100644 --- a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java +++ b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java @@ -177,9 +177,8 @@ public void setRowId(Integer rowId) public boolean equals(Object obj) { - if (!(obj instanceof SkylineTool)) + if (!(obj instanceof SkylineTool p)) return false; - SkylineTool p = (SkylineTool)obj; return Objects.equals(_name, p.getName()) && Objects.equals(_authors, p.getAuthors()) && diff --git a/lincs/src/org/labkey/lincs/DocImportListener.java b/lincs/src/org/labkey/lincs/DocImportListener.java index 0c2ae1c0..e9d5ce46 100644 --- a/lincs/src/org/labkey/lincs/DocImportListener.java +++ b/lincs/src/org/labkey/lincs/DocImportListener.java @@ -29,7 +29,7 @@ public class DocImportListener implements ExperimentListener, SkylineDocumentImportListener { - private static Logger _log = LogManager.getLogger(DocImportListener.class); + private static final Logger _log = LogManager.getLogger(DocImportListener.class); @Override public void beforeRunDelete(ExpProtocol protocol, ExpRun run, User user) diff --git a/lincs/src/org/labkey/lincs/Gct.java b/lincs/src/org/labkey/lincs/Gct.java index 971e1d97..ed04700a 100644 --- a/lincs/src/org/labkey/lincs/Gct.java +++ b/lincs/src/org/labkey/lincs/Gct.java @@ -32,11 +32,11 @@ */ public class Gct { - private List _probes; - private Map _probeIndexMap; - private List _replicates; - private Map _replicateIndexMap; - private GctTable _areaRatios; + private final List _probes; + private final Map _probeIndexMap; + private final List _replicates; + private final Map _replicateIndexMap; + private final GctTable _areaRatios; private List _probeAnnotationNames; private List _replicateAnnotationNames; @@ -164,7 +164,7 @@ public List getSortedReplicates() // Sort replicates by the value of the det_plate annotation, and then // by replicate name. For custom GCT, the replicate name is: // __ - List sortedReplicates = new ArrayList(_replicates.size()); + List sortedReplicates = new ArrayList<>(_replicates.size()); sortedReplicates.addAll(_replicates); sortedReplicates.sort((rep1, rep2) -> { @@ -262,7 +262,7 @@ public void setIgnoredProbeAnnotations(Set ignored) public static class GctEntity { private final String _name; - private Map _annotations; + private final Map _annotations; public GctEntity(String name) { @@ -418,7 +418,7 @@ public String toString() public interface GctKeyBuilder { - public T build(String key1, String key2); + T build(String key1, String key2); } public static class ProbePlateKeyBuilder implements GctKeyBuilder @@ -446,7 +446,7 @@ public GctFileException(String message, Throwable cause) public static class GctTable { - private Map _map; + private final Map _map; private List _sortedKey2; public GctTable() diff --git a/lincs/src/org/labkey/lincs/LincsController.java b/lincs/src/org/labkey/lincs/LincsController.java index 2179ba2f..2be090dc 100644 --- a/lincs/src/org/labkey/lincs/LincsController.java +++ b/lincs/src/org/labkey/lincs/LincsController.java @@ -130,12 +130,12 @@ public LincsController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) { - return new JspView("/org/labkey/lincs/view/hello.jsp"); + return new JspView<>("/org/labkey/lincs/view/hello.jsp"); } @Override @@ -216,7 +216,7 @@ public ApiResponse execute(GCTReportForm form, BindException errors) throws Exce throw new ApiUsageException("Could not find report with name " + form.getReportName()); } - if (!(report instanceof RReport)) + if (!(report instanceof RReport rreport)) { throw new ApiUsageException("The specified report is not based upon an R script and therefore cannot be executed."); } @@ -299,7 +299,6 @@ public ApiResponse execute(GCTReportForm form, BindException errors) throws Exce propertyValues.addPropertyValue("param.isotope", "medium"); } ctx.setBindPropertyValues(propertyValues); - RReport rreport = (RReport)report; try { // Execute the script @@ -388,7 +387,7 @@ public ModelAndView getView(CustomGCTForm customGCTForm, boolean reshow, BindExc { if(customGCTForm.getCustomGctBean() != null) { - JspView view = new JspView("/org/labkey/lincs/view/downloadCustomGCT.jsp", customGCTForm, errors); + JspView view = new JspView<>("/org/labkey/lincs/view/downloadCustomGCT.jsp", customGCTForm, errors); view.setFrame(WebPartView.FrameType.PORTAL); view.setTitle("Download Custom GCT"); return view; @@ -405,7 +404,7 @@ public ModelAndView getView(CustomGCTForm customGCTForm, boolean reshow, BindExc bean.setAnnotations(getReplicateAnnotationNameValues(getUser(), getContainer())); - JspView view = new JspView("/org/labkey/lincs/view/customGCTForm.jsp", bean, errors); + JspView view = new JspView<>("/org/labkey/lincs/view/customGCTForm.jsp", bean, errors); view.setFrame(WebPartView.FrameType.PORTAL); view.setTitle("Create Custom GCT"); return view; @@ -424,7 +423,7 @@ public boolean handlePost(CustomGCTForm customGCTForm, BindException errors) { return false; } - if(files.size() == 0) + if(files.isEmpty()) { errors.reject(ERROR_MSG, "No GCT files found in the folder for experiment type " + customGCTForm.getExperimentType()); return false; @@ -712,7 +711,7 @@ public void setReplicateAnnotationCount(int replicateAnnotationCount) } } @RequiresPermission(ReadPermission.class) - public class DownloadCustomGCTReportAction extends SimpleViewAction + public static class DownloadCustomGCTReportAction extends SimpleViewAction { @Override public ModelAndView getView(DownloadCustomGCTReportForm form, BindException errors) throws Exception @@ -762,7 +761,7 @@ public void setFileName(String fileName) _fileName = fileName; } } - public class CustomGCTBean + public static class CustomGCTBean { private List _annotations; private CustomGCTForm _form; @@ -836,8 +835,8 @@ else if (lAnnot.isIgnored()) public static class SelectedAnnotation { - private LincsAnnotation _lincsAnnotation; - private Set _values; + private final LincsAnnotation _lincsAnnotation; + private final Set _values; private SelectedAnnotation(LincsAnnotation lincsAnnotation) { @@ -891,7 +890,7 @@ static Path getGCTDir(Container container) private static final SimpleDateFormat dateFormat = new SimpleDateFormat("MM/dd/yyyy HH:mm:ss"); @RequiresPermission(ReadPermission.class) - public class GetLincsStatusAction extends ReadOnlyApiAction + public static class GetLincsStatusAction extends ReadOnlyApiAction { @Override public Object execute(Object o, BindException errors) @@ -1011,7 +1010,7 @@ private static boolean isOrHasAncestor(Container container, String name) @RequiresPermission(AdminPermission.class) @ActionNames("pspConfig") - public class ManageLincsClueCredentials extends FormViewAction + public static class ManageLincsClueCredentials extends FormViewAction { @Override public void validateCommand(ClueCredentialsForm target, Errors errors) {} @@ -1090,7 +1089,7 @@ public void setApiKey(String apiKey) } @RequiresPermission(AdminPermission.class) - public class CromwellConfigAction extends FormViewAction + public static class CromwellConfigAction extends FormViewAction { @Override public void validateCommand(CromwellConfigForm target, Errors errors) {} @@ -1307,7 +1306,7 @@ public Object getValue(RenderContext ctx) Integer progress = ctx.get(FieldKey.fromParts("Progress"), Integer.class); if(progress != null) { - String str = ""; + String str; int i = progress.intValue(); str = (i&1) == 1 ? "L2 done " : ""; str += (i&2) == 2 ? "L3 done " : ""; @@ -1329,7 +1328,7 @@ public Object getValue(RenderContext ctx) } @RequiresPermission(AdminPermission.class) - public class LincsPspJobStatusAction extends SimpleViewAction + public static class LincsPspJobStatusAction extends SimpleViewAction { @Override public ModelAndView getView(LincsPspJobForm form, BindException errors) @@ -1491,7 +1490,7 @@ public void setJobId(int jobId) } @RequiresSiteAdmin - public class SubmitPspJobAction extends FormHandlerAction + public static class SubmitPspJobAction extends FormHandlerAction { @Override public void validateCommand(LincsPspJobForm target, Errors errors) diff --git a/lincs/src/org/labkey/lincs/LincsDataTable.java b/lincs/src/org/labkey/lincs/LincsDataTable.java index 06d8a37c..8b07b65d 100644 --- a/lincs/src/org/labkey/lincs/LincsDataTable.java +++ b/lincs/src/org/labkey/lincs/LincsDataTable.java @@ -57,7 +57,7 @@ public class LincsDataTable extends FilteredTable public static final String PARENT_QUERY = "TargetedMSRunAndAnnotations"; public static final String NAME = "LincsDataTable"; public static final String PLATE_COL = "Plate"; - private static Pattern plateRegex = Pattern.compile("^LINCS.*_(Plate[a-zA-Z0-9]*)_.*\\.sky\\.zip$"); + private static final Pattern plateRegex = Pattern.compile("^LINCS.*_(Plate[a-zA-Z0-9]*)_.*\\.sky\\.zip$"); public LincsDataTable(@NotNull TableInfo table, @NotNull UserSchema userSchema) { @@ -122,19 +122,19 @@ public boolean isFilterable() var level2Col = wrapColumn("Level 2", getRealTable().getColumn(FieldKey.fromParts("FileName"))); addColumn(level2Col); - level2Col.setDisplayColumnFactory(colInfo -> new LincsDataTable.GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Two, gctDir, davUrl)); + level2Col.setDisplayColumnFactory(colInfo -> new GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Two, gctDir, davUrl)); var level3Col = wrapColumn("Level 3", getRealTable().getColumn(FieldKey.fromParts("FileName"))); addColumn(level3Col); - level3Col.setDisplayColumnFactory(colInfo -> new LincsDataTable.GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Three, gctDir, davUrl)); + level3Col.setDisplayColumnFactory(colInfo -> new GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Three, gctDir, davUrl)); var level4Col = wrapColumn("Level 4", getRealTable().getColumn(FieldKey.fromParts("FileName"))); addColumn(level4Col); - level4Col.setDisplayColumnFactory(colInfo -> new LincsDataTable.GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Four, gctDir, davUrl)); + level4Col.setDisplayColumnFactory(colInfo -> new GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Four, gctDir, davUrl)); var cfgCol = wrapColumn("Config", getRealTable().getColumn(FieldKey.fromParts("FileName"))); addColumn(cfgCol); - cfgCol.setDisplayColumnFactory(colInfo -> new LincsDataTable.GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Config, gctDir, davUrl)); + cfgCol.setDisplayColumnFactory(colInfo -> new GctColumnPSP(colInfo, assayType, LincsModule.LincsLevel.Config, gctDir, davUrl)); var pspJobCol = wrapColumn("PSP Job Status", getRealTable().getColumn(FieldKey.fromParts("FileName"))); addColumn(pspJobCol); @@ -223,12 +223,12 @@ public static String getBaseName(String fileName) return FileUtil.getBaseName(fileName, 1); } - public class GctColumnPSP extends DataColumn + public static class GctColumnPSP extends DataColumn { - private LincsModule.LincsAssay assayType; - private LincsModule.LincsLevel level; - private Path gctDir; - private String davUrl; + private final LincsModule.LincsAssay assayType; + private final LincsModule.LincsLevel level; + private final Path gctDir; + private final String davUrl; public GctColumnPSP(ColumnInfo col, LincsModule.LincsAssay assayType, LincsModule.LincsLevel level, Path gctDir, String davUrl) { diff --git a/lincs/src/org/labkey/lincs/LincsManager.java b/lincs/src/org/labkey/lincs/LincsManager.java index 9c608756..62926ccc 100644 --- a/lincs/src/org/labkey/lincs/LincsManager.java +++ b/lincs/src/org/labkey/lincs/LincsManager.java @@ -49,7 +49,7 @@ public class LincsManager { private static final LincsManager _instance = new LincsManager(); - private static Logger _log = LogManager.getLogger(LincsManager.class); + private static final Logger _log = LogManager.getLogger(LincsManager.class); private LincsManager() { diff --git a/lincs/src/org/labkey/lincs/LincsSchema.java b/lincs/src/org/labkey/lincs/LincsSchema.java index 338fd6c9..a2653f31 100644 --- a/lincs/src/org/labkey/lincs/LincsSchema.java +++ b/lincs/src/org/labkey/lincs/LincsSchema.java @@ -117,7 +117,7 @@ public void renderDetailsCellContents(RenderContext ctx, HtmlWriter out) } if (getTableNames().contains(name)) { - SimpleUserSchema.SimpleTable result = new SimpleUserSchema.SimpleTable(this, getSchema().getTable(name), cf) + SimpleUserSchema.SimpleTable result = new SimpleUserSchema.SimpleTable<>(this, getSchema().getTable(name), cf) { @Override public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class perm) diff --git a/lincs/src/org/labkey/lincs/cromwell/CromwellGctTask.java b/lincs/src/org/labkey/lincs/cromwell/CromwellGctTask.java index b6448e80..5d794010 100644 --- a/lincs/src/org/labkey/lincs/cromwell/CromwellGctTask.java +++ b/lincs/src/org/labkey/lincs/cromwell/CromwellGctTask.java @@ -19,7 +19,6 @@ import org.labkey.lincs.LincsModule; import org.labkey.lincs.psp.LincsPspJobSupport; -import java.io.IOException; import java.net.URI; import java.nio.file.Files; import java.nio.file.Path; diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java b/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java index 45f88a5d..46533c9b 100644 --- a/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java +++ b/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java @@ -16,10 +16,10 @@ public class LincsPspPipelineJob extends PipelineJob implements LincsPspJobSupport { - private ITargetedMSRun _run; - private String _description; - private LincsPspJob _pspJob; - private LincsPspJob _oldPspJob; + private final ITargetedMSRun _run; + private final String _description; + private final LincsPspJob _pspJob; + private final LincsPspJob _oldPspJob; @JsonCreator protected LincsPspPipelineJob(@JsonProperty("_run") ITargetedMSRun run, @JsonProperty("_pspJob") LincsPspJob pspJob, diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java index c54778be..9936aacd 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java @@ -421,7 +421,7 @@ public boolean handlePost(CreateJournalGroupForm form, BindException errors) errors.addError(new LabKeyError("Project name " + form.getProjectName() + " already exists.")); } } - else if(error.length() > 0) + else if(!error.isEmpty()) { errors.addError(new LabKeyError(error.toString())); } @@ -569,7 +569,7 @@ public boolean handlePost(JournalForm form, BindException errors) return false; } - if(JournalManager.getExperimentsForJournal(journal.getId()).size() > 0) + if(!JournalManager.getExperimentsForJournal(journal.getId()).isEmpty()) { // Do not delete the journal via the Admin console link if it contains any published data. // The journal project can still be deleted from the LabKey UI, however. @@ -1388,7 +1388,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(ReadPermission.class) - public class DownloadPanoramaLogoForBlueskyAction extends BaseDownloadAction + public static class DownloadPanoramaLogoForBlueskyAction extends BaseDownloadAction { @Nullable @Override @@ -1412,7 +1412,7 @@ public Pair getAttachment(AttachmentForm form) } @RequiresPermission(AdminOperationsPermission.class) - public class DeletePanoramaLogoForBlueskyAction extends FormHandlerAction + public static class DeletePanoramaLogoForBlueskyAction extends FormHandlerAction { @Override public void validateCommand(Object target, Errors errors) @@ -2213,12 +2213,12 @@ private ModelAndView getView(PublishExperimentForm form, BindException errors) { List allSubfolders = getAllSubfolders(_experimentAnnotations.getContainer()); List hiddenFolders = getHiddenFolders(allSubfolders, getUser()); - if(!_experimentAnnotations.isIncludeSubfolders() && allSubfolders.size() > 0) + if(!_experimentAnnotations.isIncludeSubfolders() && !allSubfolders.isEmpty()) { // Experiment is not configured to include subfolders but there are subfolders. ActionURL skipSubfolderCheckUrl = getViewContext().getActionURL().clone(); skipSubfolderCheckUrl.addParameter("doSubfolderCheck", "false"); - if(hiddenFolders.size() == 0) + if(hiddenFolders.isEmpty()) { // Return a view to make the user confirm their intention to include / exclude subfolders from the experiment. return getConfirmIncludeSubfoldersView(_experimentAnnotations, allSubfolders, skipSubfolderCheckUrl); @@ -2231,7 +2231,7 @@ private ModelAndView getView(PublishExperimentForm form, BindException errors) return getNoPermsInSubfoldersView(_experimentAnnotations, hiddenFolders, skipSubfolderCheckUrl); } } - else if(_experimentAnnotations.isIncludeSubfolders() && hiddenFolders.size() > 0) + else if(_experimentAnnotations.isIncludeSubfolders() && !hiddenFolders.isEmpty()) { // Experiment is already configured to include subfolders but there are subfolders where this user does // not have read permissions. @@ -2261,7 +2261,7 @@ else if(_experimentAnnotations.isIncludeSubfolders() && hiddenFolders.size() > 0 // This may be OK for template documents that do not have any imported chromatograms but they should be rare on Panorama. // Most documents should have chromatogram data (.skyd files in the .sky.zip archive) List notSkyZipRuns = getNotSkyZipRuns(_experimentAnnotations); - if (notSkyZipRuns.size() > 0) + if (!notSkyZipRuns.isEmpty()) { return new HtmlView(DIV("The following Skyline documents are incomplete. " + "Please upload the complete Skyline ZIP archive (.sky.zip file) by using the 'Upload to Panorama' button or menu in Skyline.", @@ -2536,7 +2536,7 @@ protected ModelAndView getMissingMetadataView(ExperimentAnnotations expAnnotatio @NotNull ModelAndView getMissingMetadataView(MissingMetadataBean missingMetadataBean, String viewTitle, BindException errors) { - JspView view = new JspView("/org/labkey/panoramapublic/view/publish/missingMetadata.jsp", missingMetadataBean, errors); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/publish/missingMetadata.jsp", missingMetadataBean, errors); view.setFrame(WebPartView.FrameType.PORTAL); view.setTitle(viewTitle); return view; @@ -2565,7 +2565,7 @@ void populateForm(PublishExperimentForm form, ExperimentAnnotations exptAnnotati form.setId(exptAnnotations.getId()); form.setShortAccessUrl(generateRandomUrl(RANDOM_URL_SIZE)); List journals = JournalManager.getJournals(); - if (journals.size() == 0) + if (journals.isEmpty()) { throw new NotFoundException("Could not find any journals."); } @@ -2606,7 +2606,7 @@ ModelAndView getConfirmView(PublishExperimentForm form, BindException errors) bean.setJournal(_journal); bean.setForm(form); - JspView confirmView = new JspView("/org/labkey/panoramapublic/view/publish/confirmSubmit.jsp", bean, errors); + JspView confirmView = new JspView<>("/org/labkey/panoramapublic/view/publish/confirmSubmit.jsp", bean, errors); confirmView.setTitle(getConfirmViewTitle()); return confirmView; } @@ -3007,7 +3007,7 @@ public PublishExperimentFormBean(PublishExperimentForm form, List journ _experimentAnnotations = experimentAnnotations; JournalSubmission js = SubmissionManager.getJournalSubmission(experimentAnnotations.getId(), form.getJournalId(), experimentAnnotations.getContainer()); // "Permanent Link" field in the form should not be editable if one or more copies of this experiment already exist in the journal project - _accessUrlEditable = js == null ? true : js.getCopiedSubmissions().size() == 0; + _accessUrlEditable = js == null ? true : js.getCopiedSubmissions().isEmpty(); } public PublishExperimentForm getForm() @@ -3188,6 +3188,7 @@ public void setShortCopyUrl(String shortCopyUrl) _shortCopyUrl = shortCopyUrl; } + @Override public ExperimentAnnotations lookupExperiment() { return ExperimentAnnotationsManager.get(getId()); @@ -3450,7 +3451,7 @@ public URLHelper getSuccessURL(PxDataValidationForm form) public void validateCommand(PxDataValidationForm form, Errors errors) { var validationJobs = PipelineService.get().getActivePipelineJobs(getUser(), getContainer(), PxValidationPipelineProvider.NAME); - if (validationJobs.size() > 0) + if (!validationJobs.isEmpty()) { var job = validationJobs.size() > 1 ? "jobs" : "job"; errors.reject(ERROR_MSG, String.format("%d data validation %s %s already running in this folder. Wait for the running %s to finish, or cancel the %s and try again.", @@ -3822,6 +3823,7 @@ void populateForm(PublishExperimentForm form, ExperimentAnnotations exptAnnotati form.setUpdate(true); } + @Override String getFormViewTitle(String journalName) { return "Update Submission Request to " + journalName; @@ -3889,6 +3891,7 @@ public abstract static class AbstractResubmitAction extends PublishExperimentAct abstract Submission getSubmission(); + @Override boolean validateGetRequest(PublishExperimentForm form, BindException errors) { return super.validateGetRequest(form, errors) && foundValidSubmissionRequest(form, errors); @@ -3912,6 +3915,7 @@ boolean foundValidSubmissionRequest(PublishExperimentForm form, Errors errors) return true; } + @Override protected void checkForValidation(ExperimentAnnotations experimentAnnotations, PublishExperimentForm form) { if (form.getValidationId() == null) @@ -3989,7 +3993,7 @@ void validateForm(PublishExperimentForm form, Errors errors) { if (foundValidSubmissionRequest(form, errors)) { - super.validateForm(form, errors);; + super.validateForm(form, errors); } } } @@ -4164,12 +4168,14 @@ private boolean canResubmit(PublishExperimentForm form, Errors errors) return true; } + @Override void populateForm(PublishExperimentForm form, ExperimentAnnotations exptAnnotations) { super.populateForm(form, exptAnnotations); form.setResubmit(true); } + @Override String getFormViewTitle(String journalName) { return "Resubmit Request to " + journalName; @@ -4396,7 +4402,7 @@ private static boolean hasSkylineDocs(@NotNull ExperimentAnnotations expAnnot) { Set expContainers = expAnnot.isIncludeSubfolders() ? ContainerManager.getAllChildren(expAnnot.getContainer()) : Collections.singleton(expAnnot.getContainer()); - return expContainers.stream().anyMatch(container -> service.getRuns(container).size() > 0); + return expContainers.stream().anyMatch(container -> !service.getRuns(container).isEmpty()); } return false; } @@ -5215,7 +5221,7 @@ public ModelAndView getFailView(DoiForm form, BindException errors) } @RequiresPermission(AdminOperationsPermission.class) - public class AssignDoiAction extends DoiAction + public static class AssignDoiAction extends DoiAction { private Doi _doi; @@ -5462,7 +5468,7 @@ public void setDoi(String doi) public static class PostToBlueskyOptionsAction extends SimpleViewAction { @Override - public ModelAndView getView(ExperimentIdForm form, BindException errors) throws Exception + public ModelAndView getView(ExperimentIdForm form, BindException errors) { return new HtmlView( DIV( @@ -5709,9 +5715,9 @@ public ModelAndView getView(NewExperimentAnnotationsForm form, BindException err view.setTitle(TargetedMSExperimentWebPart.WEB_PART_NAME); view.setInitialValue(SUBMITTER, getUser().getUserId()); List instruments = ExperimentAnnotationsManager.getContainerInstruments(getContainer(), getUser()); - if (instruments.size() > 0) + if (!instruments.isEmpty()) { - view.setInitialValue("instrument", StringUtils.join(instruments.stream().map(i -> i.getName()).collect(Collectors.toList()), ",")); + view.setInitialValue("instrument", StringUtils.join(instruments.stream().map(PsiInstrumentParser.PsiInstrument::getName).collect(Collectors.toList()), ",")); } return view; } @@ -5739,7 +5745,7 @@ public ModelAndView getView(NewExperimentAnnotationsForm form, boolean reshow, B // We are here either because handlePost failed or there were errors in the form (e.g. missing required values) ExperimentAnnotations expAnnot = form.getBean(); - if (expAnnot.getTitle() == null || expAnnot.getTitle().trim().length() == 0) + if (expAnnot.getTitle() == null || expAnnot.getTitle().trim().isEmpty()) { errors.reject(ERROR_MSG, "You must specify a title for the experiment"); } @@ -5986,7 +5992,7 @@ public ModelAndView getView(final ViewExperimentAnnotationsForm form, BindExcept HtmlView subfoldersView = null; if(exptAnnotations.isIncludeSubfolders()) { - if(children.size() == 0) + if(children.isEmpty()) { subfoldersView = new HtmlView(DIV(cl("labkey-error"),"Experiment is configured to include subfolders but no subfolders were found.", BR(), @@ -5999,7 +6005,7 @@ public ModelAndView getView(final ViewExperimentAnnotationsForm form, BindExcept getExcludeSubfoldersButton(exptAnnotations).build())); } } - else if(children.size() > 0) + else if(!children.isEmpty()) { subfoldersView = new HtmlView(DIV("This folder contains " + children.size() + " subfolders. " + "Data from the subfolders is not included in this experiment. Click the button below to include subfolders.", @@ -6020,7 +6026,7 @@ else if(children.size() > 0) // List of runs in the experiment. PanoramaPublicRunListView runListView = PanoramaPublicRunListView.createView(getViewContext(), exptAnnotations); TableInfo tinfo = runListView.getTable(); - if(tinfo instanceof FilteredTable) + if(tinfo instanceof FilteredTable filteredTable) { SQLFragment sql = new SQLFragment(); @@ -6029,19 +6035,19 @@ else if(children.size() > 0) sql.append(ExperimentService.get().getTinfoRunList(), "runlist").append(" "); sql.append("WHERE runlist.experimentId = ? AND runlist.experimentRunId = run.rowid) "); sql.add(experiment.getRowId()); - ((FilteredTable) tinfo).addCondition(sql); + filteredTable.addCondition(sql); } result.addView(runListView); // Add a table of spectral libraries, if there are any List runs = ExperimentAnnotationsManager.getTargetedMSRuns(exptAnnotations); TargetedMSService tmsSvc = TargetedMSService.get(); - if (runs.stream().anyMatch(run -> tmsSvc.getLibraries(run).size() > 0)) + if (runs.stream().anyMatch(run -> !tmsSvc.getLibraries(run).isEmpty())) { result.addView(new SpecLibView(getViewContext(), exptAnnotations)); } - if (runs.size() > 0) + if (!runs.isEmpty()) { // Structural modifications List runIds = runs.stream().map(ITargetedMSRun::getId).collect(Collectors.toList()); @@ -6287,16 +6293,15 @@ public void addNavTrail(NavTree root) } } - private @Nullable WebPartView getPublishedVersionsView(int sourceExperimentId) + private @Nullable WebPartView getPublishedVersionsView(int sourceExperimentId) { List publishedVersions = ExperimentAnnotationsManager.getPublishedVersionsOfExperiment(sourceExperimentId); - if (publishedVersions.size() > 0) + if (!publishedVersions.isEmpty()) { QuerySettings qSettings = new QuerySettings(getViewContext(), "PublishedVersions", "ExperimentAnnotations"); qSettings.setBaseFilter(new SimpleFilter(new SimpleFilter(FieldKey.fromParts("SourceExperimentId"), sourceExperimentId))); - List columns = new ArrayList<>(); - columns.addAll(List.of(FieldKey.fromParts("Version"), FieldKey.fromParts("Created"), FieldKey.fromParts("Link"), FieldKey.fromParts("Share"))); + List columns = new ArrayList<>(List.of(FieldKey.fromParts("Version"), FieldKey.fromParts("Created"), FieldKey.fromParts("Link"), FieldKey.fromParts("Share"))); if (publishedVersions.stream().anyMatch(ExperimentAnnotations::isPublished)) { columns.add(FieldKey.fromParts("Citation")); @@ -6443,7 +6448,7 @@ public boolean handlePost(ExperimentAnnotationsForm form, BindException errors) if (je != null && je.getLatestSubmission().isPxidRequested()) { List missingFields = DataValidationManager.getMissingExperimentMetadataFields(form.getBean()); - if(missingFields.size() > 0) + if(!missingFields.isEmpty()) { missingFields.stream().forEach(err -> errors.reject(ERROR_MSG, err)); return false; @@ -6468,7 +6473,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(DeletePermission.class) - public class DeleteSelectedExperimentAnnotationsAction extends ConfirmAction + public static class DeleteSelectedExperimentAnnotationsAction extends ConfirmAction { @Override public ModelAndView getConfirmView(SelectedIdsForm deleteForm, BindException errors) @@ -6546,9 +6551,9 @@ public void setDataRegionSelectionKey(String dataRegionSelectionKey) } } - public static interface SelectedExperimentIds + public interface SelectedExperimentIds { - public int[] getIds(); + int[] getIds(); } public static class DeleteExperimentAnnotationsForm extends ExperimentAnnotationsForm implements SelectedExperimentIds @@ -6561,7 +6566,7 @@ public int[] getIds() } @RequiresPermission(DeletePermission.class) - public class DeleteExperimentAnnotationsAction extends ConfirmAction + public static class DeleteExperimentAnnotationsAction extends ConfirmAction { private ExperimentAnnotations _expAnnotations; @@ -6609,6 +6614,7 @@ public static class IncludeSubFoldersInExperimentAction extends FormViewAction allSubfolders = getAllSubfolders(_expAnnot.getContainer()); - if (allSubfolders.size() == 0) + if (allSubfolders.isEmpty()) { errors.reject(ERROR_MSG, "No subfolders were found."); return; } List hiddenSubfolders = getHiddenFolders(allSubfolders, getUser()); - if (hiddenSubfolders.size() > 0) + if (!hiddenSubfolders.isEmpty()) { errors.reject(ERROR_MSG, "User needs read permissions in all the subfolders to be able to include them in the experiment."); return; @@ -6678,7 +6684,9 @@ public void validateCommand(ExperimentForm form, Errors errors) if(SpringActionController.getActionName(PublishExperimentAction.class).equals(action) || SpringActionController.getActionName(ResubmitExperimentAction.class).equals(action) || SpringActionController.getActionName(UpdateSubmissionAction.class).equals(action)) - _returnPublishExptUrl = returnUrl; + { + _returnPublishExptUrl = returnUrl; + } } } @@ -6924,7 +6932,7 @@ public ModelAndView getView(PublicationDetailsForm form, boolean reshow, BindExc private ModelAndView getPublicationDetailsView(PublicationDetailsForm form, BindException errors) { PublicationDetailsBean bean = new PublicationDetailsBean(form, _copiedExperiment); - JspView view = new JspView("/org/labkey/panoramapublic/view/publish/publicationDetails.jsp", bean, errors); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/publish/publicationDetails.jsp", bean, errors); view.setTitle("Publication Details"); return view; } @@ -6933,7 +6941,7 @@ private ModelAndView getPublicationDetailsView(PublicationDetailsForm form, Bind private ModelAndView getConfirmView(PublicationDetailsForm form, BindException errors) { PublicationDetailsBean bean = new PublicationDetailsBean(form, _copiedExperiment); - JspView view = new JspView("/org/labkey/panoramapublic/view/publish/confirmPublish.jsp", bean, errors); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/publish/confirmPublish.jsp", bean, errors); view.setTitle("Confirm Publication Details"); return view; } @@ -7092,7 +7100,7 @@ private void addDownloadDataWebpart(Container container) { String webpartName = PanoramaPublicModule.DOWNLOAD_DATA_INFO_WP; List parts = Portal.getParts(container, RAW_FILES_TAB); - if (parts.size() != 0) + if (!parts.isEmpty()) { if (!parts.stream().anyMatch(p -> webpartName.equals(p.getName()))) { @@ -7139,7 +7147,7 @@ private void postToBluesky() public ModelAndView getSuccessView(PublicationDetailsForm form) { PublishSuccessViewBean bean = new PublishSuccessViewBean(_expAnnot.getContainer(), _copiedExperiment, _madePublic, _addedPublication, _journal.getName()); - JspView view = new JspView("/org/labkey/panoramapublic/view/publish/publishSuccessView.jsp", bean); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/publish/publishSuccessView.jsp", bean); view.setTitle("Data Published"); view.setFrame(WebPartView.FrameType.PORTAL); return view; @@ -7898,7 +7906,7 @@ private ModelAndView getLibrarySummary(SpecLibForm form, SpectralLibrary library .filter(l -> l != 0 && library.getId() != l) .collect(Collectors.toSet()); List otherLibraries = SpecLibInfoManager.getLibraries(ids, getUser()); - if (otherLibraries.size() > 0) + if (!otherLibraries.isEmpty()) { List otherDocs = new ArrayList<>(); for (SpectralLibrary otherLib: otherLibraries) @@ -7960,7 +7968,7 @@ private ModelAndView getSourceFilesView(SpectralLibrary specLib, ITargetedMSRun try { List libSourceFiles = reader.readLibSourceFiles(run, specLib); - if (libSourceFiles == null || libSourceFiles.size() == 0) + if (libSourceFiles == null || libSourceFiles.isEmpty()) { view.addView(new HtmlView(DIV(cl("labkey-error"), "No library source file names were found."))); } @@ -7999,7 +8007,7 @@ private ModelAndView getSourceFilesView(SpectralLibrary specLib, ITargetedMSRun private DOM.Renderable createTable(String title, List fileNames) { - if (fileNames.size() > 0) + if (!fileNames.isEmpty()) { return TABLE(at(border, 1), THEAD(TR(TH(at(style, "padding:5px;"), STRONG(title)))), @@ -8872,7 +8880,7 @@ public void setModInfoId(int modInfoId) } @RequiresPermission(ReadPermission.class) - public class ViewExperimentModifications extends SimpleViewAction + public static class ViewExperimentModifications extends SimpleViewAction { @Override public ModelAndView getView(final ExperimentIdForm form, BindException errors) @@ -8895,7 +8903,7 @@ public ModelAndView getView(final ExperimentIdForm form, BindException errors) if (hasStructuralMods(svc, runs)) { result.addView(new HtmlView(H3(at(style, "margin-top:10px;"),"Structural Modifications"))); - if (ModificationInfoManager.getStructuralModInfosForExperiment(exptAnnotations.getId(), getContainer()).size() > 0) + if (!ModificationInfoManager.getStructuralModInfosForExperiment(exptAnnotations.getId(), getContainer()).isEmpty()) { result.addView(getAssignedUnimodMatchesMessage()); } @@ -8911,7 +8919,7 @@ public ModelAndView getView(final ExperimentIdForm form, BindException errors) if (hasIsotopeMods(svc, runs)) { result.addView(new HtmlView(H3(at(style, "margin-top:10px;"),"Isotope Modifications"))); - if (ModificationInfoManager.getIsotopeModInfosForExperiment(exptAnnotations.getId(), getContainer()).size() > 0) + if (!ModificationInfoManager.getIsotopeModInfosForExperiment(exptAnnotations.getId(), getContainer()).isEmpty()) { result.addView(getAssignedUnimodMatchesMessage()); } @@ -8935,12 +8943,12 @@ private HtmlView getAssignedUnimodMatchesMessage() } private boolean hasStructuralMods(TargetedMSService svc, List runs) { - return runs.stream().anyMatch(run -> svc.getStructuralModificationsUsedInRun(run.getId()).size() > 0); + return runs.stream().anyMatch(run -> !svc.getStructuralModificationsUsedInRun(run.getId()).isEmpty()); } private boolean hasIsotopeMods(TargetedMSService svc, List runs) { - return runs.stream().anyMatch(run -> svc.getIsotopeModificationsUsedInRun(run.getId()).size() > 0); + return runs.stream().anyMatch(run -> !svc.getIsotopeModificationsUsedInRun(run.getId()).isEmpty()); } @Override @@ -9028,7 +9036,7 @@ public static class UploadSampleFilesAction extends UploadMissingFilesAction @Nullable Status getValidationStatus(DataValidation validation, BindException errors) { Status validationStatus = DataValidationManager.getIncompleteSkyDocsInContainer(validation, getContainer(), getUser()); - if (validationStatus.getSkylineDocs().size() == 0) + if (validationStatus.getSkylineDocs().isEmpty()) { errors.reject(ERROR_MSG, "Could not find Skyline documents in the folder with missing sample files."); return null; @@ -9056,7 +9064,7 @@ public static class UploadSpecLibSourceFilesAction extends UploadMissingFilesAct @Nullable Status getValidationStatus(DataValidation validation, BindException errors) { Status validationStatus = DataValidationManager.getIncompleteSpecLibs(validation, getUser()); - if (validationStatus.getSpectralLibraries().size() == 0) + if (validationStatus.getSpectralLibraries().isEmpty()) { errors.reject(ERROR_MSG, "Could not find spectral libraries in the experiment with missing source files."); return null; @@ -9578,7 +9586,7 @@ public void setApprove(Boolean approved) } @RequiresPermission(ReadPermission.class) - public class CatalogImageDownloadAction extends BaseDownloadAction + public static class CatalogImageDownloadAction extends BaseDownloadAction { @Nullable @Override @@ -9701,7 +9709,7 @@ public ModelAndView getView(Object o, BindException errors) @RequiresPermission(ReadPermission.class) @RequiresLogin - public class MyDataViewAction extends SimpleViewAction + public static class MyDataViewAction extends SimpleViewAction { @Override public void addNavTrail(NavTree root) @@ -9728,7 +9736,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception } @RequiresSiteAdmin - public class CreatePanoramaPublicMessageAction extends SimpleViewAction + public static class CreatePanoramaPublicMessageAction extends SimpleViewAction { @Override public ModelAndView getView(PanoramaPublicMessageForm form, BindException errors) throws Exception diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicListener.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicListener.java index 8dfca87c..a0c4ba3f 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicListener.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicListener.java @@ -132,7 +132,7 @@ public List canDelete(ShortURLRecord shortUrl) // Check if the short URL is associated with a JournalExperiment, either as the shortAccessUrl or the shortCopyUrl. List journalExperiments = SubmissionManager.getJournalExperimentsWithShortUrl(shortUrl); - if (journalExperiments.size() > 0) + if (!journalExperiments.isEmpty()) { String url = shortUrl.getShortURL(); for (JournalExperiment je: journalExperiments) diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java index ac13766a..679b4384 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicMetadataImporter.java @@ -73,7 +73,7 @@ public void process(@Nullable PipelineJob job, FolderImportContext ctx, VirtualF // Get the experiment that was just created in the target folder as part of folder import. User user = job.getUser(); List experiments = ExperimentService.get().getExperiments(container, user, false, false); - if (experiments.size() == 0) + if (experiments.isEmpty()) { throw new PipelineJobException("No experiments found in the folder " + container.getPath()); } diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java index 06f4eae8..31cbe681 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java @@ -177,7 +177,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta @Override public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart) { - JspView view = new JspView("/org/labkey/panoramapublic/view/search/panoramaPublicProteinSearch.jsp", getDefaultProteinSearchForm()); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/search/panoramaPublicProteinSearch.jsp", getDefaultProteinSearchForm()); view.setTitle("Panorama Public Protein Search"); return view; } @@ -193,7 +193,7 @@ public boolean isAvailable(Container c, String scope, String location) @Override public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart) { - JspView view = new JspView("/org/labkey/panoramapublic/view/search/panoramaPublicPeptideSearch.jsp", getDefaultPeptideSearchForm()); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/search/panoramaPublicPeptideSearch.jsp", getDefaultPeptideSearchForm()); view.setTitle("Panorama Public Peptide Search"); return view; } @@ -218,7 +218,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta JournalManager.PublicDataUser publicDataUser = JournalManager.getPublicDataUser(journal); if (publicDataUser != null) { - JspView view = new JspView("/org/labkey/panoramapublic/view/publish/dataDownloadInfo.jsp", publicDataUser); + JspView view = new JspView<>("/org/labkey/panoramapublic/view/publish/dataDownloadInfo.jsp", publicDataUser); view.setTitle(DOWNLOAD_DATA_INFO_WP); return view; } diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicSymlinkManager.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicSymlinkManager.java index 43d9eada..da40e3de 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicSymlinkManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicSymlinkManager.java @@ -474,26 +474,25 @@ public boolean verifySymlinks() throws IOException } } - if(linkInvalidTarget.size() > 0) + if(!linkInvalidTarget.isEmpty()) { String linkInvalidTargets = linkInvalidTarget.entrySet().stream().map(String::valueOf).collect(Collectors.joining("\n")); _log.error(linkInvalidTarget.size() + " Symlinks with invalid targets: \n" + linkInvalidTargets); } - if(linkWithSymlinkTarget.size() > 0) + if(!linkWithSymlinkTarget.isEmpty()) { String linkWithSymlinkTargets = linkWithSymlinkTarget.entrySet().stream().map(String::valueOf).collect(Collectors.joining("\n")); _log.error(linkWithSymlinkTarget.size() + " Symlinks targeting symlinks: \n" + linkWithSymlinkTargets); } - return linkInvalidTarget.size() == 0 && linkWithSymlinkTarget.size() == 0; + return linkInvalidTarget.isEmpty() && linkWithSymlinkTarget.isEmpty(); } /** * Returns a set of containers that can have symlinks that target files in targetContainer. This includes the source container, * and containers with previous versions of the experiment. Only the container with the current version of the experiment * can have symlink targets. - * @param targetContainer * @return A set of containers that can have symlinks that target files in targetContainer */ private static Set getSymlinkContainers(Container targetContainer) diff --git a/panoramapublic/src/org/labkey/panoramapublic/chromlib/ChromLibStateImporter.java b/panoramapublic/src/org/labkey/panoramapublic/chromlib/ChromLibStateImporter.java index 74410117..45d7e7e7 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/chromlib/ChromLibStateImporter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/chromlib/ChromLibStateImporter.java @@ -29,9 +29,6 @@ import java.util.stream.Collectors; import static org.labkey.panoramapublic.chromlib.ChromLibStateManager.*; -import static org.labkey.panoramapublic.chromlib.ChromLibStateManager.getMoleculePrecursors; -import static org.labkey.panoramapublic.chromlib.ChromLibStateManager.getPeptideGroups; -import static org.labkey.panoramapublic.chromlib.ChromLibStateManager.getPrecursors; public abstract class ChromLibStateImporter @@ -172,7 +169,7 @@ LibPeptideGroup parsePeptideGroup(Map row, long runId) List getPeptideGroupDbMatches(LibPeptideGroup tsvPepGrp, String skyFile, Container container) throws ChromLibStateException { var dbIds = _pepGrpKeyMap.get(tsvPepGrp.getKey()); - if (dbIds == null || dbIds.size() == 0) + if (dbIds == null || dbIds.isEmpty()) { throw new ChromLibStateException(String.format("Expected a db row for peptide group '%s' in the Skyline document '%s'. Container '%s'.", tsvPepGrp.getLabel(), skyFile, container.getPath())); @@ -439,7 +436,7 @@ LibGeneralPrecursor getPrecursorDbMatch(LibGeneralPrecursor tsvPrecursor, String { var dbPepGrpMatches = _pepGrpPrecursorsList.stream().filter(p -> p.hasPrecursorDbMatch(tsvPrecursor)).collect(Collectors.toList()); - if (dbPepGrpMatches.size() == 0) + if (dbPepGrpMatches.isEmpty()) { throw new IllegalStateException(String.format("Expected a db row for precursor %s in the peptide group '%s'. Skyline document '%s'. Folder '%s'.", tsvPrecursor.getKey(), _pepGrpKey.toString(), skyFile, container.getPath())); diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java b/panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java index 231309d8..5760be33 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java @@ -104,7 +104,7 @@ private List submissions() */ public @Nullable Submission getLatestSubmission() { - return submissions().size() > 0 ? submissions().get(0) : null; + return !submissions().isEmpty() ? submissions().get(0) : null; } /** @@ -129,7 +129,7 @@ public boolean hasPendingSubmission() public @Nullable Submission getLatestCopiedSubmission() { List copiedSubmissions = getCopiedSubmissions(); - return copiedSubmissions.size() > 0 ? copiedSubmissions.get(0) : null; + return !copiedSubmissions.isEmpty() ? copiedSubmissions.get(0) : null; } /** @@ -170,7 +170,6 @@ public boolean isLatestSubmission(int submissionId) } /** - * @param copiedExperimentId * @return The lab head name entered in the submission request that was copied with the given copiedExperimentId. * Returns null if no lab head information was entered in the submission form. */ diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java index d3b3892f..fbdcd3c8 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/DataValidation.java @@ -57,7 +57,7 @@ public void setStatus(PxStatus status) public PxStatus getStatusIncludingExptMetadata(ExperimentAnnotations expAnnotations) { - if (isComplete() && DataValidationManager.getMissingExperimentMetadataFields(expAnnotations).size() > 0) + if (isComplete() && !DataValidationManager.getMissingExperimentMetadataFields(expAnnotations).isEmpty()) { return PxStatus.NotValid; } diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/Modification.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/Modification.java index 4411e550..c34cc8cb 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/Modification.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/Modification.java @@ -224,7 +224,7 @@ public JSONObject toJSON() if (_modInfo != null) { List unimodIdsAndNames = _modInfo.getUnimodInfos(); - if (unimodIdsAndNames.size() > 0) + if (!unimodIdsAndNames.isEmpty()) { jsonObject.put("unimodMatches", getUnimodMatchesJSON(unimodIdsAndNames)); jsonObject.put("modInfoId", _modInfo.getId()); diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SkylineDocSampleFile.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SkylineDocSampleFile.java index d1dafe2d..d2dfba1f 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SkylineDocSampleFile.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SkylineDocSampleFile.java @@ -48,6 +48,7 @@ public void setFilePathImported(String filePathImported) _filePathImported = filePathImported; } + @Override @NotNull public JSONObject toJSON(Container container) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLib.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLib.java index 0b83627c..09be78f8 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLib.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLib.java @@ -102,7 +102,7 @@ public JSONObject toJSON(Container expContainer) if (!isValid && getSpecLibInfo() == null) { List docLibraries = DataValidationManager.getSkylineDocSpecLibs(this); - if (docLibraries.size() > 0) + if (!docLibraries.isEmpty()) { // Add the database Id of a library used with one of the Skyline documents so that we can display a link to // add the "Add Library Information". The same library can be used with multiple documents. A new row is diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibSourceFile.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibSourceFile.java index e3201817..f1e46988 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibSourceFile.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibSourceFile.java @@ -84,6 +84,7 @@ public int hashCode() return Objects.hash(getSourceType(), getName()); } + @Override @NotNull public JSONObject toJSON(Container container) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java index f5e65cbd..c8682646 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java @@ -266,7 +266,7 @@ public String getStatusString() String missing = hasSpectrumFiles() ? "" : " spectrum file names"; if (isBibliospecLibrary() && !hasIdFiles()) { - missing += (missing.length() > 0 ? " and " : "") + " peptide ID file names"; + missing += (!missing.isEmpty() ? " and " : "") + " peptide ID file names"; } return "Library source files in the external repository cannot be verified since the library is missing " + missing + "."; } @@ -311,7 +311,7 @@ public boolean isPrositLibrary() // For example: Koina-Prosit_2020_intensity_HCD-Prosit_2019_irt where // Prosit_2020_intensity_HCD is the intensity model and Prosit_2019_irt is the retention time model. Skyline // supports multiple Koina models. - if(isBibliospecLibrary() && getSpectrumFiles().size() == 1 && getIdFiles().size() == 0) + if(isBibliospecLibrary() && getSpectrumFiles().size() == 1 && getIdFiles().isEmpty()) { String modelName = getSpectrumFiles().get(0).getName(); return "Prositintensity_prosit_publication_v1".equals(modelName) @@ -341,7 +341,7 @@ private boolean isAssayLibrary() if (isBibliospecLibrary()) { var spectrumFiles = getSpectrumFiles(); - return spectrumFiles.size() > 0 && spectrumFiles.stream().anyMatch(f -> f.getName().toLowerCase().endsWith(".csv")); + return !spectrumFiles.isEmpty() && spectrumFiles.stream().anyMatch(f -> f.getName().toLowerCase().endsWith(".csv")); } return false; } @@ -354,12 +354,12 @@ private boolean isIncompleteBlib() private boolean hasSpectrumFiles() { - return _spectrumFiles != null && _spectrumFiles.size() > 0; + return _spectrumFiles != null && !_spectrumFiles.isEmpty(); } private boolean hasIdFiles() { - return _idFiles != null && _idFiles.size() > 0; + return _idFiles != null && !_idFiles.isEmpty(); } private boolean foundSpectrumFiles() diff --git a/panoramapublic/src/org/labkey/panoramapublic/model/validation/Status.java b/panoramapublic/src/org/labkey/panoramapublic/model/validation/Status.java index e5d03a01..62a50e84 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/model/validation/Status.java +++ b/panoramapublic/src/org/labkey/panoramapublic/model/validation/Status.java @@ -185,7 +185,7 @@ public JSONArray toProgressSummaryJSON() json.put("Sample file validation completed for " + validatedCount + " / " + StringUtilsLabKey.pluralize(documentCount, "document") + "." + (missingFilesFound ? " Found missing sample files." : "")); } - if (getModifications().size() > 0) + if (!getModifications().isEmpty()) { boolean invalidModsFound = getModifications().stream().anyMatch(mod -> !mod.isValid()); json.put("Modifications validation complete." + (invalidModsFound ? " Found invalid modifications." : "")); diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java index 341f2a16..cb2c0138 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java @@ -793,7 +793,7 @@ private void hideDataPipelineTab(Container c) private void updateRawDataTab(Container c, FileContentService service, User user) { List rawDataTabParts = Portal.getEditableParts(c, TargetedMSService.RAW_FILES_TAB); - if(rawDataTabParts.size() == 0) + if(rawDataTabParts.isEmpty()) { return; // Nothing to do if there is no "Raw Data" tab. } diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java index 9c40977f..a6b3a594 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java @@ -242,6 +242,7 @@ public void setDeletePreviousCopy(boolean deletePreviousCopy) _deletePreviousCopy = deletePreviousCopy; } + @Override public String getPreviousVersionName() { return _previousVersionName; diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java index 80500c11..c87d0425 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java @@ -63,7 +63,7 @@ private void updateFolderType(PipelineJob job, CopyExperimentJobSupport jobSuppo var container = job.getContainer(); User user = job.getUser(); List experiments = ExperimentService.get().getExperiments(container, user, false, false); - if (experiments.size() == 0) + if (experiments.isEmpty()) { throw new PipelineJobException(String.format("No experiments found in the container '%s'.", container.getPath())); } diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java index 295b4993..c6f9fa74 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java @@ -42,7 +42,7 @@ private void doImport(Container container, boolean includeSubfolders, VirtualFil if (includeSubfolders) { List children = ContainerManager.getChildren(container); - if (children.size() > 0) + if (!children.isEmpty()) { var subfolders = vf.getDir("subfolders"); // TODO: Make SubfolderWriter.DIRECTORY_NAME public for (Container child : children) diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java index 3308a8bf..5ff51c40 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java @@ -62,7 +62,7 @@ private void writeFilesMetadata(VirtualFile vf, Container container, boolean inc if (includeSubfolders) { List children = ContainerManager.getChildren(container, user, FolderExportPermission.class); - if (children.size() > 0) + if (!children.isEmpty()) { var subfolders = vf.getDir("subfolders"); // TODO: Make SubfolderWriter.DIRECTORY_NAME public for (Container child : children) diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java index b8157ec1..e0c130bf 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java @@ -13,7 +13,6 @@ import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.panoramapublic.model.ExperimentAnnotations; -import org.labkey.panoramapublic.model.validation.DataValidation; import java.io.File; diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ValidatorListener.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ValidatorListener.java index 7ab9dbc5..4b0c0a31 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ValidatorListener.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ValidatorListener.java @@ -64,7 +64,7 @@ public void validatingModifications() public void modificationsValidated(ValidatorStatus status) { _log.info("Modifications validation:"); - if (status.getModifications().size() == 0) + if (status.getModifications().isEmpty()) { _log.info("No modifications were found in the submitted Skyline documents."); } @@ -132,7 +132,7 @@ public void spectralLibraryValidated(SpecLibValidator specLib) @Override public void spectralLibrariesValidated(ValidatorStatus status) { - if (status.getSpectralLibraries().size() == 0) + if (status.getSpectralLibraries().isEmpty()) { _log.info("Skyline documents in the experiment do not contain any spectral libraries."); } diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ChemElement.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ChemElement.java index e81dcf69..d2070e93 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ChemElement.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ChemElement.java @@ -50,8 +50,8 @@ public enum ChemElement private final String _symbol; private final double _avgMass; - private static Map titleMap = new HashMap<>(); - private static Map symbolMap = new HashMap<>(); + private static final Map titleMap = new HashMap<>(); + private static final Map symbolMap = new HashMap<>(); static { for (ChemElement el: ChemElement.values()) diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java index 160a501b..e8c307ad 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java @@ -305,7 +305,7 @@ public void addPossibleUnimod(UnimodModification uMod) public boolean hasPossibleUnimods() { - return _unimodModifications.size() > 0; + return !_unimodModifications.isEmpty(); } public @NotNull List getPossibleUnimodMatches() @@ -703,7 +703,7 @@ public void testStructuralMods() throws IOException printStructuralMod(mod, pxMod); List matches = unimodMatches.get(pxMod.getSkylineName()); - if (matches.size() == 0) + if (matches.isEmpty()) { assertFalse("Unexpected Unimod match for modification " + pxMod.getSkylineName(), pxMod.hasUnimodId()); assertEquals("Unexpected possible mods for modification " + pxMod.getSkylineName(), 0, pxMod.getPossibleUnimodMatches().size()); @@ -902,10 +902,10 @@ public void testIsotopicMods() throws IOException List expectedMatches = matches.get(pxMod.getSkylineName()); - if (expectedMatches.size() == 0) + if (expectedMatches.isEmpty()) { assertFalse("Unexpected Unimod match for isotopic modification " + pxMod.getSkylineName(), pxMod.hasUnimodId()); - assertTrue("Unexpected possible mods for isotopic modification " + pxMod.getSkylineName(), pxMod.getPossibleUnimodMatches().size() == 0); + assertTrue("Unexpected possible mods for isotopic modification " + pxMod.getSkylineName(), pxMod.getPossibleUnimodMatches().isEmpty()); } else if (expectedMatches.size() == 1) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/Formula.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/Formula.java index eeea9d65..7b994b56 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/Formula.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/Formula.java @@ -59,7 +59,7 @@ public SortedMap getElementCounts() negative.append(formulaPart); } } - String separator = positive.length() > 0 && negative.length() > 0 ? " - " : (negative.length() > 0 ? "-" : ""); + String separator = !positive.isEmpty() && !negative.isEmpty() ? " - " : (!negative.isEmpty() ? "-" : ""); return positive + separator + negative; } @@ -168,7 +168,7 @@ private static Formula parse(String input, Formula formula, boolean negative) // from the total mass. Only one negative part is allowed. We will parse the positive and negative parts separately. input = input.trim(); - while (input.length() > 0) + while (!input.isEmpty()) { if (input.startsWith("-")) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxXmlWriter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxXmlWriter.java index 2c1e6153..022a49ef 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxXmlWriter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxXmlWriter.java @@ -391,7 +391,7 @@ void writeModificationList(Status validationStatus) throws PxException */ Element mod_list = new Element("ModificationList"); var mods = validationStatus.getModifications(); - if(mods.size() == 0 || mods.stream().noneMatch(Modification::isValid)) + if(mods.isEmpty() || mods.stream().noneMatch(Modification::isValid)) { mod_list.addChild(new CvParamElement("MS", "MS:1002864", "No PTMs are included in the dataset")); } @@ -688,7 +688,7 @@ private void writeElement(XMLStreamWriter writer, Element element, String indent { writer.writeCharacters("\n"); writer.writeCharacters(indent); - if(StringUtils.isBlank(element.getText()) && element.getChildren().size() == 0) + if(StringUtils.isBlank(element.getText()) && element.getChildren().isEmpty()) { writer.writeEmptyElement(element.getName()); } @@ -712,9 +712,9 @@ private void writeElement(XMLStreamWriter writer, Element element, String indent writeElement(writer, child, indent + INDENT); } - if(!StringUtils.isBlank(element.getText()) || element.getChildren().size() != 0) + if(!StringUtils.isBlank(element.getText()) || !element.getChildren().isEmpty()) { - if(element.getChildren().size() != 0) + if(!element.getChildren().isEmpty()) { writer.writeCharacters("\n"); writer.writeCharacters(indent); diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodModification.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodModification.java index 892b8959..7acc771d 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodModification.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodModification.java @@ -191,12 +191,12 @@ public boolean matches(String normFormula, @NotNull Set sites, Term { return false; } - if (sites.size() == 0 && terminus == null) + if (sites.isEmpty() && terminus == null) { // Cannot find an exact match based on just the formula return false; } - if (sites.size() > 0) + if (!sites.isEmpty()) { for (Specificity site: sites) { @@ -243,7 +243,7 @@ public String toString() sb.append("UNIMOD:").append(getId()); sb.append(", ").append(getName()); sb.append(", ").append(getNormalizedFormula()); - if(_modSites.size() > 0) + if(!_modSites.isEmpty()) { sb.append(", Sites: ").append(StringUtils.join(_modSites, ":")); } @@ -279,7 +279,7 @@ public TermSpecificity getcTerm() public String getModSitesWithPosition() { - if(_modSites.size() > 0) + if(!_modSites.isEmpty()) { return StringUtils.join(_modSites.stream().map(Specificity::toString).collect(Collectors.toSet()), ":"); } @@ -300,7 +300,7 @@ public String getTerminus() } if (_cTerm != null) { - terminus = terminus + (terminus.length() > 0 ? ", " : "") + _cTerm; + terminus = terminus + (!terminus.isEmpty() ? ", " : "") + _cTerm; } return terminus; } diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java index 9c65d4d8..25a3d463 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java @@ -215,13 +215,13 @@ private static boolean isIsotopicDiff(Formula diffFormula) elements.remove(element); } } - return elements.size() == 0; + return elements.isEmpty(); } private UnimodModification parseModification(Element modEl) throws PxException { String title = modEl.getAttribute("title"); - Integer id = Integer.parseInt(modEl.getAttribute("record_id")); + int id = Integer.parseInt(modEl.getAttribute("record_id")); NodeList deltaEl = modEl.getElementsByTagNameNS(NAMESPACE, "delta"); UnimodModification uMod = new UnimodModification(id, title, getFormula(deltaEl)); @@ -302,7 +302,7 @@ private Formula getFormula(NodeList nl) throws PxException { throw new PxException("Unrecognized element in formula: " + symbol); } - Integer number = Integer.parseInt(el.getAttribute("number")); + int number = Integer.parseInt(el.getAttribute("number")); formula.addElement(chemElement, number); } } diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/DataValidator.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/DataValidator.java index 2ab181d6..7f797aa3 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/DataValidator.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/DataValidator.java @@ -191,7 +191,7 @@ private ExperimentModInfo saveModInfoForWildCardSkylineMod(ExperimentModificatio { List sites = ModificationInfoManager.getIsotopeModificationSites(pxMod.getDbModId(), runs, user); var uModsList = UnimodUtil.getMatchesIfWildcardSkylineMod(pxMod, sites); - if (uModsList.size() > 0) + if (!uModsList.isEmpty()) { var modInfo = new ExperimentIsotopeModInfo(); modInfo.setExperimentAnnotationsId(expAnnotations.getId()); @@ -281,7 +281,7 @@ private void validateContainerSampleFiles(List skylineDocs, // name but different paths imported into separate replicates of a document. Skyline allows this but it can get // confusing even for the user. Set ambiguousFiles = sampleFileNameAndKeys.keySet().stream().filter(k -> sampleFileNameAndKeys.get(k).size() > 1).collect(Collectors.toSet()); - if (ambiguousFiles.size() > 0) + if (!ambiguousFiles.isEmpty()) { for (SkylineDocValidator skyDoc : skylineDocs) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/ValidatorStatus.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/ValidatorStatus.java index b0bfcef8..08d365f0 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/ValidatorStatus.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/validator/ValidatorStatus.java @@ -7,7 +7,6 @@ import java.util.ArrayList; import java.util.Collections; -import java.util.LinkedHashMap; import java.util.List; public class ValidatorStatus extends GenericValidationStatus diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ContainerJoin.java b/panoramapublic/src/org/labkey/panoramapublic/query/ContainerJoin.java index 1532775b..7d3935f4 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/ContainerJoin.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/ContainerJoin.java @@ -76,7 +76,7 @@ public ContainerJoin addJoin(@NotNull String joinCol, @NotNull TableInfo table, public @NotNull SQLFragment getContainerSql() { SQLFragment sql = new SQLFragment(); - if (_joinList.size() > 0) + if (!_joinList.isEmpty()) { // We expect the last table in the join sequence to have the container column sql.append(getLastJoinTableAlias()).append("."); @@ -91,7 +91,7 @@ private String getLastJoinTableAlias() public @Nullable FieldKey getContainerFieldKey() { - if (_joinList.size() > 0) + if (!_joinList.isEmpty()) { var parts = _joinList.stream().map(InnerJoinClause::getJoinCol).collect(Collectors.toList()); parts.add(CONTAINER); diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java index b66e36f3..e3ed9b7f 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/DataValidationManager.java @@ -125,7 +125,7 @@ public static boolean isValidationOutdated(@NotNull DataValidation validation, @ SimpleFilter filter = new SimpleFilter(); filter.addCondition(FieldKey.fromParts("Created"), validation.getCreated(), CompareType.GT); filter.addCondition(FieldKey.fromParts("Container"), container.getId()); - if (AuditLogService.get().getAuditEvents(container, user, FileSystemAuditProvider.EVENT_TYPE, filter, null).size() > 0) + if (!AuditLogService.get().getAuditEvents(container, user, FileSystemAuditProvider.EVENT_TYPE, filter, null).isEmpty()) { return true; } @@ -417,7 +417,7 @@ public static void specLibInfoDeleted(@NotNull ExperimentAnnotations expAnnotati // Get the libraries associated with the given SpecLibInfo List specLibList = getLibrariesForSpecLibInfo(specLibInfo, validation); - if (specLibList.size() > 0) + if (!specLibList.isEmpty()) { try (DbScope.Transaction transaction = PanoramaPublicSchema.getSchema().getScope().ensureTransaction()) { @@ -440,7 +440,7 @@ public static void specLibInfoChanged(@NotNull ExperimentAnnotations expAnnotati if (validation != null) { // Get the libraries associated with the given SpecLibInfo - if (getLibrariesForSpecLibInfo(specLibInfo, validation).size() > 0) + if (!getLibrariesForSpecLibInfo(specLibInfo, validation).isEmpty()) { recalculateStatus(validation, user); } @@ -463,7 +463,7 @@ public static void specLibInfoAdded(ExperimentAnnotations expAnnotations, SpecLi // Get the libraries associated with the given SpecLibInfo List specLibList = getLibrariesMatchingSpecLibInfo(specLibInfo, validation, user); - if (specLibList.size() > 0) + if (!specLibList.isEmpty()) { try (DbScope.Transaction transaction = PanoramaPublicSchema.getSchema().getScope().ensureTransaction()) { @@ -725,12 +725,11 @@ private static void validateOrganisms(ExperimentAnnotations expAnnot, MissingMet notFound.add(orgName); } } - if(notFound.size() > 0) + if(!notFound.isEmpty()) { - StringBuilder err = new StringBuilder("No taxonomy ID found for organism"); - err.append(notFound.size() > 1 ? "s: " : ": "); - err.append(StringUtils.join(notFound, ',')); - errors.add(err.toString()); + String err = "No taxonomy ID found for organism" + (notFound.size() > 1 ? "s: " : ": ") + + StringUtils.join(notFound, ','); + errors.add(err); } } @@ -757,12 +756,11 @@ private static void validateInstruments(ExperimentAnnotations expAnnot, MissingM notFound.add(instrumentName); } } - if(notFound.size() > 0) + if(!notFound.isEmpty()) { - StringBuilder err = new StringBuilder("Unrecognized instrument"); - err.append(notFound.size() > 1 ? "s: " : ": "); - err.append(StringUtils.join(notFound, ',')); - errors.add(err.toString()); + String err = "Unrecognized instrument" + (notFound.size() > 1 ? "s: " : ": ") + + StringUtils.join(notFound, ','); + errors.add(err); } } diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java index 1bc6a474..230369b6 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsManager.java @@ -360,7 +360,7 @@ public static ExperimentAnnotations getExperimentInContainer(Container container SimpleFilter filter = container != null ? SimpleFilter.createContainerFilter(container) : null; List expAnnotations = new TableSelector(PanoramaPublicManager.getTableInfoExperimentAnnotations(), filter, null).getArrayList(ExperimentAnnotations.class); - if(expAnnotations.size() > 0) + if(!expAnnotations.isEmpty()) { // 09.04.14 // Return the first experiment in the container. @@ -374,7 +374,7 @@ public static ExperimentAnnotations getExperimentInContainer(Container container public static boolean hasExperimentsInSubfolders(Container container, User user) { Collection containerIds = ContainerFilter.Type.CurrentAndSubfolders.create(container, user).getIds(); - if(containerIds == null || containerIds.size() == 0) + if(containerIds == null || containerIds.isEmpty()) { return false; } @@ -394,7 +394,7 @@ public static boolean hasExperimentsInSubfolders(Container container, User user) List expAnnotations = new TableSelector(PanoramaPublicManager.getTableInfoExperimentAnnotations(), filter, null).getArrayList(ExperimentAnnotations.class); - return expAnnotations.size() > 0; + return !expAnnotations.isEmpty(); } public static ExperimentAnnotations getExperimentForShortUrl(ShortURLRecord shortUrl) @@ -546,7 +546,6 @@ public static boolean hasProteomicData(ExperimentAnnotations experimentAnnotatio } /** - * @param experimentAnnotations * @return true if the given experiment is a journal copy, and is the most recent version. */ public static boolean isCurrentVersion(ExperimentAnnotations experimentAnnotations) @@ -577,8 +576,6 @@ public static List getPublishedVersionsOfExperiment(int s } /** - * @param container - * @param user * @return List of instruments that were used to acquire the data for the Skyline documents in the given container. * The list will only include instrument model names that have a match in the PSI-MS controlled vocabulary. We are not able * to get specific instrument model names from Bruker, Agilent or Waters raw data. The instrument name for data from these @@ -596,7 +593,7 @@ public static List getPublishedVersionsOfExperiment(int s private static List getInstrumentModelNames(List runIds, User user, Container container) { - if (runIds.size() > 0) + if (!runIds.isEmpty()) { SimpleFilter filter = new SimpleFilter().addInClause(FieldKey.fromParts("runId"), runIds); return new TableSelector(TargetedMSService.get().getUserSchema(user, container).getTable("instrument"), diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java index 45d926f8..b743b15e 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java @@ -491,7 +491,7 @@ public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class grpMembers = SecurityManager.getAllGroupMembers(group, MemberType.ACTIVE_USERS); - if(grpMembers.size() != 0) + if(!grpMembers.isEmpty()) { return grpMembers.stream().min(Comparator.comparing(User::getUserId)).orElse(null); } diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ModificationInfoManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/ModificationInfoManager.java index e08caecc..5e14f7cc 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/ModificationInfoManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/ModificationInfoManager.java @@ -178,7 +178,7 @@ public static void deleteIsotopeModInfoForExperiment(ExperimentAnnotations expAn new SimpleFilter(FieldKey.fromParts("experimentAnnotationsId"), expAnnotations.getId()), null ).getArrayList(Integer.class); - if (modInfoIds.size() > 0) + if (!modInfoIds.isEmpty()) { SimpleFilter filter = new SimpleFilter(new SimpleFilter.InClause(FieldKey.fromParts("modInfoId"), modInfoIds)); Table.delete(PanoramaPublicManager.getTableInfoIsotopeUnimodInfo(), filter); @@ -252,7 +252,7 @@ public static boolean runsHaveIsotopeModifications(List runIds, User user, private static boolean runsHaveModifications(List runIds, TableInfo tableInfo, User user, Container container) { - if (runIds.size() == 0) return false; + if (runIds.isEmpty()) return false; TargetedMSService svc = TargetedMSService.get(); SQLFragment sql = new SQLFragment("SELECT mod.Id FROM ") diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/PxXmlManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/PxXmlManager.java index a06094d2..43cfd9b7 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/PxXmlManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/PxXmlManager.java @@ -10,7 +10,6 @@ import org.labkey.panoramapublic.model.PxXml; import java.util.Collections; -import java.util.List; public class PxXmlManager { diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionManager.java index ee3d53e9..d9fc46f4 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionManager.java @@ -117,7 +117,7 @@ public static void deleteSubmission(@NotNull Submission submission, @NotNull Use List allSubmissions = getSubmissionsNewestFirst(submission.getJournalExperimentId()); allSubmissions.removeIf(Submission::isObsolete); - if (allSubmissions.size() == 0) + if (allSubmissions.isEmpty()) { // Delete the JournalExperiment if there are no submissions left after removing any obsolete ones JournalExperiment je = getJournalExperiment(submission.getJournalExperimentId()); @@ -436,7 +436,7 @@ public static void beforeSubmittedExperimentDeleted(@NotNull ExperimentAnnotatio JournalSubmission js = getJournalSubmission(expAnnotations.getId(), journal.getId(), expAnnotations.getContainer()); if (js != null) { - if (js.getCopiedSubmissions().size() == 0) + if (js.getCopiedSubmissions().isEmpty()) { // Experiment was submitted but not yet copied so we can delete the rows in the Submission and JournalExperiment tables. try (DbScope.Transaction transaction = PanoramaPublicManager.getSchema().getScope().ensureTransaction()) diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionTableInfo.java b/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionTableInfo.java index 6f8b3127..ff0fd6da 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionTableInfo.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/SubmissionTableInfo.java @@ -13,7 +13,6 @@ import org.labkey.api.query.FilteredTable; import org.labkey.api.util.HtmlString; import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.writer.HtmlWriter; import org.labkey.panoramapublic.PanoramaPublicController; diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/speclib/EditLibInfoDisplayColumnFactory.java b/panoramapublic/src/org/labkey/panoramapublic/query/speclib/EditLibInfoDisplayColumnFactory.java index 6769a09f..eb873db2 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/speclib/EditLibInfoDisplayColumnFactory.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/speclib/EditLibInfoDisplayColumnFactory.java @@ -8,7 +8,6 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.writer.HtmlWriter; diff --git a/panoramapublic/src/org/labkey/panoramapublic/view/PanoramaPublicRunListView.java b/panoramapublic/src/org/labkey/panoramapublic/view/PanoramaPublicRunListView.java index 31bcbbc5..79bbb154 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/view/PanoramaPublicRunListView.java +++ b/panoramapublic/src/org/labkey/panoramapublic/view/PanoramaPublicRunListView.java @@ -18,7 +18,7 @@ public class PanoramaPublicRunListView extends ExperimentRunListView { - private ExperimentAnnotations _expAnnotations; + private final ExperimentAnnotations _expAnnotations; public PanoramaPublicRunListView(ExperimentAnnotations expAnnotations, UserSchema schema, QuerySettings settings) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp b/panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp index 3844a318..7216d8e5 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp +++ b/panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp @@ -139,7 +139,7 @@ String publishButtonText = "Submit"; if (js != null && !annot.isJournalCopy()) { - journal = JournalManager.getJournal(js.getJournalId()); + JournalManager.getJournal(js.getJournalId()); Submission submission = js.getLatestSubmission(); if (submission != null) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/view/unimodMatchInfo.jsp b/panoramapublic/src/org/labkey/panoramapublic/view/unimodMatchInfo.jsp index 8d9c2b98..5aeb644b 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/view/unimodMatchInfo.jsp +++ b/panoramapublic/src/org/labkey/panoramapublic/view/unimodMatchInfo.jsp @@ -39,7 +39,7 @@
-<%if (bean.getUnimodMatches().size() == 0 && !bean.isIsotopicMod()) { %> +<%if (bean.getUnimodMatches().isEmpty() && !bean.isIsotopicMod()) { %>
Define a custom <%=button("Combination Modification").href(defineCombinationModUrl)%> if this modification is a combination of two modifications.
@@ -85,7 +85,7 @@ }, { xtype: 'component', - <% if (unimodMatches.size() == 0) { %> + <% if (unimodMatches.isEmpty()) { %> cls: 'alert labkey-error alert-warning', <% } %> html: unimodMatchesHtml() diff --git a/panoramapublic/test/src/org/labkey/test/components/panoramapublic/PanoramaPublicSearchWebPart.java b/panoramapublic/test/src/org/labkey/test/components/panoramapublic/PanoramaPublicSearchWebPart.java index 46d7d243..cb25c4a1 100644 --- a/panoramapublic/test/src/org/labkey/test/components/panoramapublic/PanoramaPublicSearchWebPart.java +++ b/panoramapublic/test/src/org/labkey/test/components/panoramapublic/PanoramaPublicSearchWebPart.java @@ -15,7 +15,7 @@ public class PanoramaPublicSearchWebPart extends BodyWebPart { - private static String title = "Panorama Public Search"; + private static final String title = "Panorama Public Search"; private final WebDriverWait tabWait = new WebDriverWait(getDriver(), Duration.ofSeconds(1)); @@ -30,6 +30,7 @@ protected PanoramaPublicSearchWebPart.ElementCache newElementCache() return new PanoramaPublicSearchWebPart.ElementCache(); } + @Override public String getTitle() { return elementCache().title.get(); diff --git a/panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java b/panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java index 80f33a52..53d523b5 100644 --- a/panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java +++ b/panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java @@ -2,7 +2,6 @@ import org.labkey.test.BaseWebDriverTest; import org.labkey.test.Locator; -import org.labkey.test.WebTestHelper; import org.labkey.test.components.BodyWebPart; import org.labkey.test.util.DataRegionTable; import org.openqa.selenium.WebElement; diff --git a/panoramapublic/test/src/org/labkey/test/pages/panoramapublic/DataValidationPage.java b/panoramapublic/test/src/org/labkey/test/pages/panoramapublic/DataValidationPage.java index cb6c4e35..16d1e2f7 100644 --- a/panoramapublic/test/src/org/labkey/test/pages/panoramapublic/DataValidationPage.java +++ b/panoramapublic/test/src/org/labkey/test/pages/panoramapublic/DataValidationPage.java @@ -106,7 +106,7 @@ public void verifySampleFileStatus(String skylineDocName, List found, Li scrollIntoView(panel); expandSkyDocRow(panel, skylineDocName); - verifySkyDocStatus(skylineDocName, missing.size() == 0 ? "COMPLETE" : "INCOMPLETE"); + verifySkyDocStatus(skylineDocName, missing.isEmpty() ? "COMPLETE" : "INCOMPLETE"); var sampleFilesTable = panel.findElement(getFilesTableLocator(skylineDocName, "pxv-tpl-table")); for (var file: missing) @@ -201,8 +201,8 @@ public void verifySpectralLibraryStatus(String libraryFile, String fileSize, Str scrollIntoView(panel); expandLibraryRow(panel, libraryFile, fileSize); verifySpecLibStatus(libraryFile, fileSize, - (spectrumFiles.size() == 0 || idFiles.size() == 0 - || spectrumFilesMissing.size() > 0 || idFilesMissing.size() > 0) ? "INCOMPLETE" : "COMPLETE"); + (spectrumFiles.isEmpty() || idFiles.isEmpty() + || !spectrumFilesMissing.isEmpty() || !idFilesMissing.isEmpty()) ? "INCOMPLETE" : "COMPLETE"); var panelText = panel.getText(); List expectedTexts = new ArrayList<>(skylineDocNames); @@ -279,7 +279,7 @@ public void verifyWildCardModStatus(String modName, boolean inferred, List cellValues.add(cell.getText())); assertTrue(modName + " was not found in modification row " + rowIdx, cells.get(MOD_COL_NAME).getText().contains(modName)); - if (unimodMatches == null || unimodMatches.size() == 0) + if (unimodMatches == null || unimodMatches.isEmpty()) { assertTrue(cells.get(MOD_COL_UNIMOD_NAME).getText().startsWith("MISSING")); } @@ -300,7 +300,7 @@ public void verifyWildCardModStatus(String modName, boolean inferred, List files, List filesMissing, WebElement specLibsPanel, String tblCls) { - if (files.size() > 0 || filesMissing.size() > 0) + if (!files.isEmpty() || !filesMissing.isEmpty()) { var filesTable = specLibsPanel.findElement(getFilesTableLocator(libraryName, tblCls)); for (var file : filesMissing) diff --git a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicBaseTest.java b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicBaseTest.java index 189bcf47..8960bcdf 100644 --- a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicBaseTest.java +++ b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicBaseTest.java @@ -102,7 +102,7 @@ protected String getProjectName() @BeforeClass public static void initProject() { - PanoramaPublicBaseTest init = (PanoramaPublicBaseTest)getCurrentTest(); + PanoramaPublicBaseTest init = getCurrentTest(); init.createPanoramaPublicJournalProject(); // Create the test project diff --git a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicModificationsTest.java b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicModificationsTest.java index 61319c24..8ccd12c0 100644 --- a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicModificationsTest.java +++ b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicModificationsTest.java @@ -356,7 +356,7 @@ private int checkModRow(DataRegionTable modsTable, String modificationName, Stri private int checkModificationRow(DataRegionTable modsTable, List matches, String modificationName) { String expectedText = ""; - if (matches != null && matches.size() > 0) + if (matches != null && !matches.isEmpty()) { for (var unimod: matches) { diff --git a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMyDataViewTest.java b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMyDataViewTest.java index 6bbdbbf9..4d2e8da4 100644 --- a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMyDataViewTest.java +++ b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMyDataViewTest.java @@ -34,7 +34,7 @@ public class PanoramaPublicMyDataViewTest extends PanoramaPublicBaseTest @BeforeClass public static void initialSetUp() { - PanoramaPublicMyDataViewTest test = (PanoramaPublicMyDataViewTest) getCurrentTest(); + PanoramaPublicMyDataViewTest test = getCurrentTest(); test.init(); } diff --git a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaWebPublicSearchTest.java b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaWebPublicSearchTest.java index 3fb9c64b..ddf8f40f 100644 --- a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaWebPublicSearchTest.java +++ b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaWebPublicSearchTest.java @@ -1,10 +1,8 @@ package org.labkey.test.tests.panoramapublic; -import org.apache.commons.collections4.MultiValuedMap; import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; -import org.labkey.api.view.Portal; import org.labkey.test.BaseWebDriverTest; import org.labkey.test.Locator; import org.labkey.test.TestTimeoutException; @@ -19,9 +17,7 @@ import org.openqa.selenium.support.ui.ExpectedConditions; import java.util.Arrays; -import java.util.List; import java.util.Set; -import java.util.stream.Collectors; @Category({External.class, MacCossLabModules.class}) @BaseWebDriverTest.ClassTimeout(minutes = 5) @@ -43,7 +39,7 @@ public class PanoramaWebPublicSearchTest extends PanoramaPublicBaseTest @BeforeClass public static void initialSetUp() { - PanoramaWebPublicSearchTest init = (PanoramaWebPublicSearchTest) getCurrentTest(); + PanoramaWebPublicSearchTest init = getCurrentTest(); init.initialSetupHelper(); } diff --git a/pwebdashboard/src/org/labkey/pwebdashboard/ProjectAdminsTable.java b/pwebdashboard/src/org/labkey/pwebdashboard/ProjectAdminsTable.java index 471a65ef..1ded0784 100644 --- a/pwebdashboard/src/org/labkey/pwebdashboard/ProjectAdminsTable.java +++ b/pwebdashboard/src/org/labkey/pwebdashboard/ProjectAdminsTable.java @@ -90,7 +90,7 @@ public ProjectAdminsTable(@NotNull PwebDashboardSchema userSchema, ContainerFilt addCondition(sql); } - class AdminsColumn extends DataColumn + static class AdminsColumn extends DataColumn { public AdminsColumn(ColumnInfo col) { diff --git a/signup/src/org/labkey/signup/SignUpAdmin.jsp b/signup/src/org/labkey/signup/SignUpAdmin.jsp index b1757893..e25a92cc 100644 --- a/signup/src/org/labkey/signup/SignUpAdmin.jsp +++ b/signup/src/org/labkey/signup/SignUpAdmin.jsp @@ -140,7 +140,7 @@ Set keySet = groupToGroup.keySet(); for(String key: keySet) { List rules = Arrays.asList(groupToGroup.get(key).split("\\s*,\\s*")); - for(String rule: rules) { if(!rule.equals("")) {%> + for(String rule: rules) { if(!rule.isEmpty()) {%> <%=h(SecurityManager.getGroup(Integer.parseInt(key)))%> (<%=h(key)%>) <%=h(SecurityManager.getGroup(Integer.parseInt(rule)))%> (<%=h(rule)%>) diff --git a/signup/src/org/labkey/signup/SignUpController.java b/signup/src/org/labkey/signup/SignUpController.java index 78597865..a81f690a 100644 --- a/signup/src/org/labkey/signup/SignUpController.java +++ b/signup/src/org/labkey/signup/SignUpController.java @@ -104,7 +104,7 @@ public static ActionURL getShowSignUpAdminUrl() } @RequiresSiteAdmin - public class ShowSignUpAdminAction extends SimpleViewAction + public static class ShowSignUpAdminAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -123,7 +123,7 @@ public void addNavTrail(NavTree root) } @RequiresSiteAdmin - public class AddPropertyAction extends FormHandlerAction + public static class AddPropertyAction extends FormHandlerAction { @Override public URLHelper getSuccessURL(AddPropertyForm addPropertyForm) @@ -160,7 +160,7 @@ public void validateCommand(AddPropertyForm target, Errors errors) } @RequiresSiteAdmin - public class RemovePropertyAction extends FormHandlerAction + public static class RemovePropertyAction extends FormHandlerAction { @Override public URLHelper getSuccessURL(ContainerIdForm containerIdForm) @@ -192,7 +192,7 @@ public void validateCommand(ContainerIdForm target, Errors errors) } @RequiresSiteAdmin - public class AddGroupChangeProperty extends FormHandlerAction + public static class AddGroupChangeProperty extends FormHandlerAction { @Override public URLHelper getSuccessURL(AddGroupChangeForm containerIdForm) @@ -228,7 +228,7 @@ public void validateCommand(AddGroupChangeForm target, Errors errors) } @RequiresSiteAdmin - public class RemoveGroupChangeProperty extends FormHandlerAction + public static class RemoveGroupChangeProperty extends FormHandlerAction { @Override public URLHelper getSuccessURL(AddGroupChangeForm containerIdForm) @@ -251,7 +251,7 @@ public boolean handlePost(AddGroupChangeForm addGroupChangeForm, BindException e rules.remove(String.valueOf(newgroup)); String newProperties = StringUtils.join(rules, ','); m.put(String.valueOf(oldgroup), newProperties); - if(rules.size() == 0 || (rules.size() == 1 && rules.contains(""))) + if(rules.isEmpty() || (rules.size() == 1 && rules.contains(""))) m.remove(oldgroup); m.save(); @@ -336,7 +336,7 @@ public void setNewgroup(int newgroup) // Class ConfirmAction handles a user trying to confirm an account creation. If the email and confirmation code match // that in our database they will be added to the LabKey user base @RequiresNoPermission - public class ConfirmAction extends FormViewAction + public static class ConfirmAction extends FormViewAction { protected URLHelper _successUrl = null; private TempUser _tempUser = null; @@ -722,7 +722,7 @@ public void setNewSignUp(boolean newSignUp) } @RequiresLogin - public class ChangeGroupsApiAction extends MutatingApiAction + public static class ChangeGroupsApiAction extends MutatingApiAction { @Override public ApiResponse execute(AddGroupChangeForm addGroupChangeForm, BindException errors) throws Exception diff --git a/signup/src/org/labkey/signup/SignUpModule.java b/signup/src/org/labkey/signup/SignUpModule.java index 0d360850..ecca9ed5 100644 --- a/signup/src/org/labkey/signup/SignUpModule.java +++ b/signup/src/org/labkey/signup/SignUpModule.java @@ -71,7 +71,7 @@ protected Collection createWebPartFactories() @Override public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) { - JspView view = new JspView("/org/labkey/signup/signupPage.jsp", new SignUpController.SignupForm()); + JspView view = new JspView<>("/org/labkey/signup/signupPage.jsp", new SignUpController.SignupForm()); view.setTitle("Sign Up"); return view; diff --git a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java index 806dcdd7..ebb956ee 100644 --- a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java +++ b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java @@ -44,7 +44,7 @@ public class SendTestResultsEmail implements org.quartz.Job public static final String TEST_GET_HTML_EMAIL = "gethtml"; public static final String MORNING_EMAIL = "morningemail"; - private Date _date; + private final Date _date; public interface DEFAULT_EMAIL { String RECIPIENT = "skyline-dev@proteinms.net"; @@ -119,7 +119,7 @@ public Pair getHTMLEmail(org.labkey.api.security.User from) ActionURL containerUrl = PageFlowUtil.urlProvider(ProjectUrls.class).getBeginURL(container).addParameter("end", mdyFormatter.format(end)); String testResultsUrl = AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath() + containerUrl.getEncodedLocalURIString(); message.append("
") - .append("

").append(PageFlowUtil.filter(container.getName())).append("
starting: ").append(start.toString()).append("

") + .append("

").append(PageFlowUtil.filter(container.getName())).append("
starting: ").append(start).append("

") .append("
View Full TestResults
") .append("
"); diff --git a/testresults/src/org/labkey/testresults/TestResultsController.java b/testresults/src/org/labkey/testresults/TestResultsController.java index 44ce98ea..8d6e1394 100644 --- a/testresults/src/org/labkey/testresults/TestResultsController.java +++ b/testresults/src/org/labkey/testresults/TestResultsController.java @@ -143,13 +143,13 @@ public TestResultsController() * action to view rundown.jsp and also the landing page for module */ @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception { RunDownBean bean = getRunDownBean(getUser(), getContainer(), getViewContext()); - return new JspView("/org/labkey/testresults/view/rundown.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/rundown.jsp", bean); } @Override @@ -163,7 +163,7 @@ public static RunDownBean getRunDownBean(org.labkey.api.security.User user, Cont String viewType = viewContext.getRequest().getParameter("viewType"); Calendar cal = Calendar.getInstance(); - cal.setTime(end != null && !end.equals("") ? MDYFormat.parse(end) : new Date()); + cal.setTime(end != null && !end.isEmpty() ? MDYFormat.parse(end) : new Date()); setToEightAM(cal); Date endDate = cal.getTime(); cal.add(Calendar.DATE, -1); @@ -335,7 +335,7 @@ public static User[] getUsers(Container trainingDataContainer, String username) * action to view trainging data for each user */ @RequiresPermission(ReadPermission.class) - public class TrainingDataViewAction extends SimpleViewAction + public static class TrainingDataViewAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -355,7 +355,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception User[] users = getUsers(getContainer(), null); TestsDataBean bean = new TestsDataBean(runs, users); - return new JspView("/org/labkey/testresults/view/trainingdata.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/trainingdata.jsp", bean); } @Override @@ -450,7 +450,7 @@ else if ((train && !foundRuns.isEmpty()) || (!train && foundRuns.isEmpty())) * accepts url parameter "start" and "end" which will be the date range of selected runs for that user to display */ @RequiresPermission(ReadPermission.class) - public class ShowUserAction extends SimpleViewAction + public static class ShowUserAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -480,7 +480,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception ensureRunDataCached(runs, false); TestsDataBean bean = new TestsDataBean(runs, user == null ? new User[0] : new User[]{user}); - return new JspView("/org/labkey/testresults/view/user.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/user.jsp", bean); } @Override @@ -494,7 +494,7 @@ public void addNavTrail(NavTree root) * accepts a url parameter "runId" which will be the run that the jsp displays the information of */ @RequiresPermission(ReadPermission.class) - public class ShowRunAction extends SimpleViewAction + public static class ShowRunAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -504,7 +504,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception { runId = Integer.parseInt(getViewContext().getRequest().getParameter("runId")); } catch (Exception e) { - return new JspView("/org/labkey/testresults/view/runDetail.jsp", null); + return new JspView<>("/org/labkey/testresults/view/runDetail.jsp", null); } String filterTestPassesBy = getViewContext().getRequest().getParameter("filter"); @@ -526,10 +526,10 @@ public ModelAndView getView(Object o, BindException errors) throws Exception RunDetail[] runs = executeGetRunsSQLFragment(sqlFragment, getContainer(), false, true); if (runs.length == 0) - return new JspView("/org/labkey/testresults/view/runDetail.jsp", null); + return new JspView<>("/org/labkey/testresults/view/runDetail.jsp", null); RunDetail run = runs[0]; if (run == null) - return new JspView("/org/labkey/testresults/view/runDetail.jsp", null); + return new JspView<>("/org/labkey/testresults/view/runDetail.jsp", null); if (filterTestPassesBy != null) { if (filterTestPassesBy.equals("duration")) { List filteredPasses = Arrays.asList(passes); @@ -554,7 +554,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception run.setHang(hangs[0]); run.setPasses(passes); TestsDataBean bean = new TestsDataBean(runs, new User[0]); - return new JspView("/org/labkey/testresults/view/runDetail.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/runDetail.jsp", bean); } @Override @@ -568,7 +568,7 @@ public void addNavTrail(NavTree root) * accepts a url parameter "viewType" of either wk(week), mo(month), or yr(year) and defaults to month */ @RequiresPermission(ReadPermission.class) - public class LongTermAction extends SimpleViewAction + public static class LongTermAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -589,7 +589,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception bean.setNonAssociatedFailures(failures); ensureRunDataCached(runs, true); - return new JspView("/org/labkey/testresults/view/longTerm.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/longTerm.jsp", bean); } @Override @@ -604,7 +604,7 @@ public void addNavTrail(NavTree root) * accepts parameter viewType as 'wk', 'mo', or 'yr'. defaults to 'day' */ @RequiresPermission(ReadPermission.class) - public class ShowFailures extends SimpleViewAction + public static class ShowFailures extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -636,11 +636,11 @@ public ModelAndView getView(Object o, BindException errors) throws Exception (run.getLeaks() != null && Arrays.stream(run.getLeaks()).anyMatch(leak -> leak.getTestName().equals(failedTest))) ).toArray(RunDetail[]::new)); - return new JspView("/org/labkey/testresults/view/failureDetail.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/failureDetail.jsp", bean); } bean.setRuns(runs); - return new JspView("/org/labkey/testresults/view/multiFailureDetail.jsp", bean); + return new JspView<>("/org/labkey/testresults/view/multiFailureDetail.jsp", bean); } @Override @@ -713,7 +713,7 @@ public Object execute(Object o, BindException errors) * action to show all flagged runs flagged.jsp */ @RequiresNoPermission - public class ShowFlaggedAction extends SimpleViewAction + public static class ShowFlaggedAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception @@ -721,7 +721,7 @@ public ModelAndView getView(Object o, BindException errors) throws Exception SimpleFilter filter = new SimpleFilter(); filter.addCondition(FieldKey.fromParts("flagged"), true); RunDetail[] details = new TableSelector(TestResultsSchema.getTableInfoTestRuns(), filter, null).getArray(RunDetail.class); - return new JspView("/org/labkey/testresults/view/flagged.jsp", new TestsDataBean(details, new User[0])); + return new JspView<>("/org/labkey/testresults/view/flagged.jsp", new TestsDataBean(details, new User[0])); } @Override public void addNavTrail(NavTree root) @@ -730,7 +730,8 @@ public void addNavTrail(NavTree root) } @RequiresSiteAdmin - public class ChangeBoundaries extends MutatingApiAction { + public static class ChangeBoundaries extends MutatingApiAction + { @Override public Object execute(Object o, BindException errors) throws Exception { @@ -785,7 +786,7 @@ public Object execute(Object o, BindException errors) throws Exception } @RequiresPermission(ReadPermission.class) - public class ViewLogAction extends ReadOnlyApiAction + public static class ViewLogAction extends ReadOnlyApiAction { @Override public Object execute(Object o, BindException errors) @@ -809,7 +810,7 @@ public Object execute(Object o, BindException errors) } @RequiresPermission(ReadPermission.class) - public class ViewXmlAction extends ReadOnlyApiAction + public static class ViewXmlAction extends ReadOnlyApiAction { @Override public Object execute(Object o, BindException errors) @@ -833,7 +834,7 @@ public Object execute(Object o, BindException errors) } @RequiresNoPermission - public class SendEmailNotificationAction extends ReadOnlyApiAction + public static class SendEmailNotificationAction extends ReadOnlyApiAction { @Override public Object execute(Object o, BindException errors) @@ -951,12 +952,12 @@ public Object execute(Object o, BindException errors) throws Exception else error += "Email 'To' not valid."; - if (error.equals("")) { + if (error.isEmpty()) { org.labkey.api.security.User y = UserManager.getUser(from); if (y == null) error += "Sender email not a registered user."; } - if (error.equals("")) { + if (error.isEmpty()) { res.put("Message", "Email sent from " + from.getEmailAddress() + " to " + to.getEmailAddress()); res.put("Response", "true"); testCustom.execute(SendTestResultsEmail.TEST_CUSTOM, UserManager.getUser(from), to.getEmailAddress()); @@ -999,7 +1000,8 @@ private Date getGenerateDate() { } @RequiresSiteAdmin - public class SetUserActive extends MutatingApiAction { + public static class SetUserActive extends MutatingApiAction + { @Override public Object execute(Object o, BindException errors) { @@ -1038,19 +1040,18 @@ public Object execute(Object o, BindException errors) * action for posting test output as an xml file */ @RequiresNoPermission - public class PostAction extends MutatingApiAction { + public static class PostAction extends MutatingApiAction + { @Override public Object execute(Object o, BindException errors) throws Exception { // DebugRequest(getViewContext().getRequest()); - if (!(getViewContext().getRequest() instanceof MultipartRequest)) + if (!(getViewContext().getRequest() instanceof MultipartRequest request)) { - throw new Exception("Expected a request of type MultipartRequest got " + getViewContext().getRequest().getClass().toString()); + throw new Exception("Expected a request of type MultipartRequest got " + getViewContext().getRequest().getClass()); } - MultipartRequest request = (MultipartRequest) getViewContext().getRequest(); - MultipartFile file = request.getFile("xml_file"); if (file == null) { @@ -1092,7 +1093,7 @@ else if (xml.isEmpty()) private void DebugRequest(HttpServletRequest hsRequest) { - _log.info("Request is " + hsRequest.getClass().toString()); + _log.info("Request is " + hsRequest.getClass()); _log.info("Content length is : "+ hsRequest.getContentLength()); _log.info("Content type: " + hsRequest.getContentType()); Enumeration headerNames = hsRequest.getHeaderNames(); @@ -1102,9 +1103,8 @@ private void DebugRequest(HttpServletRequest hsRequest) _log.info("Header " + headerName + ": " + hsRequest.getHeader(headerName)); } - if (hsRequest instanceof MultipartRequest) + if (hsRequest instanceof MultipartRequest request) { - MultipartRequest request = (MultipartRequest) hsRequest; _log.info("Multi part content type for xml: " + request.getMultipartContentType("xml")); _log.info("Multi part content type for xml_file: " + request.getMultipartContentType("xml_file")); } @@ -1113,7 +1113,7 @@ private void DebugRequest(HttpServletRequest hsRequest) @RequiresPermission(ReadPermission.class) - public class ErrorFilesAction extends SimpleViewAction + public static class ErrorFilesAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) @@ -1122,7 +1122,7 @@ public ModelAndView getView(Object o, BindException errors) File[] files = local.listFiles(); if (files == null) files = new File[0]; - return new JspView("/org/labkey/testresults/view/errorFiles.jsp", files); + return new JspView<>("/org/labkey/testresults/view/errorFiles.jsp", files); } @Override @@ -1132,7 +1132,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(ReadPermission.class) - public class PostErrorFilesAction extends MutatingApiAction + public static class PostErrorFilesAction extends MutatingApiAction { @Override public Object execute(Object o, BindException errors) @@ -1753,7 +1753,7 @@ static void populateFailures(RunDetail[] runs) { int runId = run.getId(); List failList = testFailDetails.get(runId); run.setFailures(failList != null - ? failList.toArray(new TestFailDetail[failList.size()]) + ? failList.toArray(new TestFailDetail[0]) : new TestFailDetail[0]); } } diff --git a/testresults/src/org/labkey/testresults/TestResultsWebPart.java b/testresults/src/org/labkey/testresults/TestResultsWebPart.java index 2e377c77..0a714ce5 100644 --- a/testresults/src/org/labkey/testresults/TestResultsWebPart.java +++ b/testresults/src/org/labkey/testresults/TestResultsWebPart.java @@ -30,11 +30,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNul { bean = TestResultsController.getRunDownBean(portalCtx.getUser(), c, portalCtx); } - catch (ParseException e) - { - e.printStackTrace(); - } - catch (IOException e) + catch (ParseException | IOException e) { e.printStackTrace(); } diff --git a/testresults/src/org/labkey/testresults/model/GlobalSettings.java b/testresults/src/org/labkey/testresults/model/GlobalSettings.java index 200bc807..8fdb9c65 100644 --- a/testresults/src/org/labkey/testresults/model/GlobalSettings.java +++ b/testresults/src/org/labkey/testresults/model/GlobalSettings.java @@ -1,9 +1,5 @@ package org.labkey.testresults.model; -import org.labkey.api.data.Container; - -import java.util.Date; - public class GlobalSettings { diff --git a/testresults/src/org/labkey/testresults/model/RunDetail.java b/testresults/src/org/labkey/testresults/model/RunDetail.java index 919fb345..8202cdac 100644 --- a/testresults/src/org/labkey/testresults/model/RunDetail.java +++ b/testresults/src/org/labkey/testresults/model/RunDetail.java @@ -288,7 +288,7 @@ public Double[] getPoints() throws IOException { List values = new ArrayList<>(); try ( ByteArrayInputStream bais = new ByteArrayInputStream(pointsummary); - DataInputStream in = new DataInputStream(bais); + DataInputStream in = new DataInputStream(bais) ) { StringBuilder str = new StringBuilder(); while (in.available() > 0) diff --git a/testresults/src/org/labkey/testresults/model/TestFailDetail.java b/testresults/src/org/labkey/testresults/model/TestFailDetail.java index f83879cf..24b0b39c 100644 --- a/testresults/src/org/labkey/testresults/model/TestFailDetail.java +++ b/testresults/src/org/labkey/testresults/model/TestFailDetail.java @@ -120,7 +120,7 @@ public void setTimestamp(Date timestamp) @Override public int compareTo(TestFailDetail o) { - int diff = 0; + int diff; if(this.timestamp == null) { diff = Integer.compare(this.testId, o.testId); } else { diff --git a/testresults/src/org/labkey/testresults/model/User.java b/testresults/src/org/labkey/testresults/model/User.java index 957277ce..02634279 100644 --- a/testresults/src/org/labkey/testresults/model/User.java +++ b/testresults/src/org/labkey/testresults/model/User.java @@ -108,37 +108,35 @@ public boolean fitsMemoryTrainingData(double avgMemory, int stdDeviations) { public static double upperBound(double mean, double stdDev, int stdDevs) { return mean + stdDev * stdDevs; } public String runBoundHtmlString(int warningBoundary, int errorBoundary) { - StringBuilder sb = new StringBuilder(); - sb.append("Good: "); - sb.append("> "); - sb.append((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), warningBoundary)) - 1); - sb.append("\n"); - sb.append("Warn: "); - sb.append((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), errorBoundary))); - sb.append(" - "); - sb.append((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), warningBoundary)) - 1); - sb.append("\n"); - sb.append("Error: "); - sb.append("< "); - sb.append((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), errorBoundary))); - return sb.toString(); + String sb = "Good: " + + "> " + + ((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), warningBoundary)) - 1) + + "\n" + + "Warn: " + + (int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), errorBoundary)) + + " - " + + ((int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), warningBoundary)) - 1) + + "\n" + + "Error: " + + "< " + + (int) Math.round(lowerBound(getMeantestsrun(), getStddevtestsrun(), errorBoundary)); + return sb; } public String memBoundHtmlString(int warningBoundary, int errorBoundary) { - StringBuilder sb = new StringBuilder(); - sb.append("Good: "); - sb.append("< "); - sb.append((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), warningBoundary)) + 1); - sb.append("\n"); - sb.append("Warn: "); - sb.append((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), warningBoundary)) + 1); - sb.append(" - "); - sb.append((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), errorBoundary))); - sb.append("\n"); - sb.append("Error: "); - sb.append("> "); - sb.append((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), errorBoundary))); - return sb.toString(); + String sb = "Good: " + + "< " + + ((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), warningBoundary)) + 1) + + "\n" + + "Warn: " + + ((int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), warningBoundary)) + 1) + + " - " + + (int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), errorBoundary)) + + "\n" + + "Error: " + + "> " + + (int) Math.round(upperBound(getMeanmemory(), getStddevmemory(), errorBoundary)); + return sb; } @Override diff --git a/testresults/src/org/labkey/testresults/view/RunDownBean.java b/testresults/src/org/labkey/testresults/view/RunDownBean.java index 2220f1c2..58522c47 100644 --- a/testresults/src/org/labkey/testresults/view/RunDownBean.java +++ b/testresults/src/org/labkey/testresults/view/RunDownBean.java @@ -228,9 +228,9 @@ public JSONObject getTodaysCompactMemoryJson(Date day) throws Exception MathStat stats = service.getStats(ArrayUtils.toPrimitive(list.toArray(new Double[0]))); double median = stats.getMedian(); - int largestkey = averagePassPointMap.keySet().size() == 0 ? 0 : Collections.max(averagePassPointMap.keySet()); + int largestkey = averagePassPointMap.keySet().isEmpty() ? 0 : Collections.max(averagePassPointMap.keySet()); int tolerance = 500; // pases must be at least 500 runs away from eachother - if (averagePassPointMap.size() == 0 || + if (averagePassPointMap.isEmpty() || (averagePassPointMap.get(largestkey) != null && median > tolerance + averagePassPointMap.get(largestkey))) { averagePassPointMap.put(largestkey+1, median); } diff --git a/testresults/src/org/labkey/testresults/view/TestsDataBean.java b/testresults/src/org/labkey/testresults/view/TestsDataBean.java index 07f93aa9..55685314 100644 --- a/testresults/src/org/labkey/testresults/view/TestsDataBean.java +++ b/testresults/src/org/labkey/testresults/view/TestsDataBean.java @@ -28,7 +28,6 @@ import org.labkey.testresults.model.TestFailDetail; import org.labkey.testresults.model.TestPassDetail; -import java.lang.String; import java.util.ArrayList; import java.util.Arrays; import java.util.Calendar; diff --git a/testresults/src/org/labkey/testresults/view/multiFailureDetail.jsp b/testresults/src/org/labkey/testresults/view/multiFailureDetail.jsp index e21b8222..6f457e75 100644 --- a/testresults/src/org/labkey/testresults/view/multiFailureDetail.jsp +++ b/testresults/src/org/labkey/testresults/view/multiFailureDetail.jsp @@ -29,7 +29,7 @@ Container c = getContainer(); RunDetail[] runs = data.getStatRuns(); if(runs.length > 1) { - Arrays.sort(runs, new Comparator() + Arrays.sort(runs, new Comparator<>() { @Override public int compare(RunDetail o1, RunDetail o2) @@ -100,7 +100,7 @@ <% Collections.reverse(Arrays.asList(runs)); // so most recent is on top - Map dates = new TreeMap(); // maps dates to count of failures per run + Map dates = new TreeMap<>(); // maps dates to count of failures per run for(RunDetail run: runs) { %> @@ -141,10 +141,10 @@ <% Map lang =languageBreakdown.get(""); for(String l: lang.keySet()) { - Double percent = lang.get(l) * 100; + double percent = lang.get(l) * 100; %> - ['<%=h(l)%>', <%=percent.intValue()%>], + ['<%=h(l)%>', <%=(int)percent%>], <%}%> ], type : 'pie' }, diff --git a/testresults/src/org/labkey/testresults/view/rundown.jsp b/testresults/src/org/labkey/testresults/view/rundown.jsp index 45a30b03..1fae2331 100644 --- a/testresults/src/org/labkey/testresults/view/rundown.jsp +++ b/testresults/src/org/labkey/testresults/view/rundown.jsp @@ -52,7 +52,7 @@ DateFormat df = new SimpleDateFormat("MM/dd/yyyy"); String viewType = data.getViewType(); - if (viewType == null || viewType.equals("")) + if (viewType == null || viewType.isEmpty()) viewType = ViewType.MONTH; String viewTypeWord = "Month"; if (viewType.equals(ViewType.WEEK)) diff --git a/testresults/src/org/labkey/testresults/view/user.jsp b/testresults/src/org/labkey/testresults/view/user.jsp index a392f80a..0f84b87d 100644 --- a/testresults/src/org/labkey/testresults/view/user.jsp +++ b/testresults/src/org/labkey/testresults/view/user.jsp @@ -52,7 +52,7 @@ String startDate = req.getParameter("start"); String endDate = req.getParameter("end"); String user = req.getParameter("user"); - boolean showSingleUser = user != null && !user.equals(""); + boolean showSingleUser = user != null && !user.isEmpty(); DateFormat df = new SimpleDateFormat("MM/dd/yyyy"); Date today = new Date(); if (startDate == null)