diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRCBeanFactory.java b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRCBeanFactory.java index 2e9a23c3e..fb3a10a15 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRCBeanFactory.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRCBeanFactory.java @@ -42,8 +42,8 @@ public class SNPRCBeanFactory extends BeanObjectFactory { - private static Logger _log = LogManager.getLogger(BeanObjectFactory.class); - private Class _class; + private static final Logger _log = LogManager.getLogger(BeanObjectFactory.class); + private final Class _class; public SNPRCBeanFactory(Class clss) @@ -55,9 +55,6 @@ public SNPRCBeanFactory(Class clss) /** * Maps property fooBar to key foo_bar, in preparation for CRUD operations * - * @param bean - * @param m - * @return */ @Override public @@ -128,7 +125,7 @@ public K fromMap(K bean, Map m) } catch (IllegalAccessException | InvocationTargetException x) { - throw new UnexpectedException(x); + throw UnexpectedException.wrap(x); } catch (IllegalArgumentException x) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRController.java b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRController.java index b6755e014..9c645b0fb 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRController.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRController.java @@ -126,7 +126,7 @@ public void setBaseURL(String baseURL) } @RequiresPermission(AdminPermission.class) - public class SSRSConfigAction extends FormViewAction + public static class SSRSConfigAction extends FormViewAction { @Override public void validateCommand(SSRSConfigForm target, Errors errors) @@ -174,7 +174,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(ManageLookupTablesPermission.class) - public class EditLookupTablesAction extends SimpleViewAction + public static class EditLookupTablesAction extends SimpleViewAction { @Override @@ -192,7 +192,7 @@ public ModelAndView getView(Object o, BindException errors) @RequiresPermission(UpdatePermission.class) - public class UpdateQueryAction extends SimpleViewAction + public static class UpdateQueryAction extends SimpleViewAction { private QueryForm _form; @@ -265,7 +265,7 @@ public void addNavTrail(NavTree root) // http://localhost:8080/labkey/snprc_ehr/snprc/getNextAnimalId @RequiresPermission(EHRDataEntryPermission.class) - public class getNextAnimalIdAction extends MutatingApiAction + public static class getNextAnimalIdAction extends MutatingApiAction { @Override public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors) @@ -302,7 +302,7 @@ public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException er } @RequiresPermission(SNPRCColonyAdminPermission.class) - public class BirthReportAction extends SimpleRedirectAction + public static class BirthReportAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -312,7 +312,7 @@ public URLHelper getRedirectURL(Object o) } @RequiresPermission(SNPRCColonyAdminPermission.class) - public class SsrsReportsAction extends SimpleRedirectAction + public static class SsrsReportsAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -322,7 +322,7 @@ public URLHelper getRedirectURL(Object o) } @RequiresPermission(ReadPermission.class) - public class IdChipReaderAction extends SimpleRedirectAction + public static class IdChipReaderAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -332,7 +332,7 @@ public URLHelper getRedirectURL(Object o) } @RequiresPermission(EHRDataEntryPermission.class) - public class SndEventViewAction extends SimpleRedirectAction + public static class SndEventViewAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -342,7 +342,7 @@ public URLHelper getRedirectURL(Object o) } @RequiresPermission(SNPRCColonyAdminPermission.class) - public class NewAnimalWizardAction extends SimpleRedirectAction + public static class NewAnimalWizardAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -355,13 +355,13 @@ public URLHelper getRedirectURL(Object o) * Get all New Animals */ @RequiresPermission(SNPRCColonyAdminPermission.class) - public class GetNewAnimalDataAction extends ReadOnlyApiAction + public static class GetNewAnimalDataAction extends ReadOnlyApiAction { @Override public ApiResponse execute(NewAnimalData o, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); SimpleFilter filter = new SimpleFilter(); @@ -387,7 +387,7 @@ public ApiResponse execute(NewAnimalData o, BindException errors) * Update/Add new animal */ @RequiresPermission(SNPRCColonyAdminPermission.class) - public class UpdateAnimalDataAction extends MutatingApiAction + public static class UpdateAnimalDataAction extends MutatingApiAction { @Override public void validateForm(NewAnimalData newAnimalData, Errors errors) @@ -480,12 +480,12 @@ public ApiResponse execute(NewAnimalData newAnimalData, BindException errors) } @RequiresPermission(EHRDataEntryPermission.class) - public class RemoveCategoryAction extends MutatingApiAction + public static class RemoveCategoryAction extends MutatingApiAction { @Override public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); try { UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer()); @@ -504,7 +504,7 @@ public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindExceptio categoriesFilter.addCondition(FieldKey.fromString("category_code"), animalGroupCategory.getCategoryCode(), CompareType.EQUAL); Map animalGroupsCategory = new TableSelector(categoriesTable, categoriesFilter, null).getObject(Map.class); - List> keys = new ArrayList>(); + List> keys = new ArrayList<>(); Map idMap = new HashMap<>(); idMap.put("category_code", animalGroupsCategory.get("category_code")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java index fede9771d..cbf395195 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java @@ -95,7 +95,7 @@ public AnimalGroupsController() } @RequiresPermission(EHRDataEntryPermission.class) - public class GroupCategoriesAction extends SimpleViewAction + public static class GroupCategoriesAction extends SimpleViewAction { @Override public void addNavTrail(NavTree root) @@ -114,13 +114,13 @@ public ModelAndView getView(AnimalGroupCategory animalGroupCategory, BindExcepti * Get all defined categories */ @RequiresPermission(EHRDataEntryPermission.class) - public class GetCategoriesAction extends ReadOnlyApiAction + public static class GetCategoriesAction extends ReadOnlyApiAction { @Override public ApiResponse execute(AnimalGroupCategory o, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); Sort sort = SortFilterHelper.getSort(o.getSort(), true); @@ -149,7 +149,7 @@ public ApiResponse execute(AnimalGroupCategory o, BindException errors) * Update/Add category */ @RequiresPermission(EHRDataEntryPermission.class) - public class UpdateCategoriesAction extends MutatingApiAction + public static class UpdateCategoriesAction extends MutatingApiAction { @Override public ApiResponse execute(AnimalGroupCategory o, BindException errors) @@ -225,12 +225,12 @@ private Integer getNextCategoryId() } @RequiresPermission(EHRDataEntryPermission.class) - public class RemoveCategoryAction extends MutatingApiAction + public static class RemoveCategoryAction extends MutatingApiAction { @Override public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); try { UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer()); @@ -249,7 +249,7 @@ public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindExceptio categoriesFilter.addCondition(FieldKey.fromString("category_code"), animalGroupCategory.getCategoryCode(), CompareType.EQUAL); Map animalGroupsCategory = new TableSelector(categoriesTable, categoriesFilter, null).getObject(Map.class); - List> keys = new ArrayList>(); + List> keys = new ArrayList<>(); Map idMap = new HashMap<>(); idMap.put("category_code", animalGroupsCategory.get("category_code")); @@ -289,13 +289,13 @@ public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindExceptio * Get all defined species, needed when editing categories */ @RequiresPermission(EHRDataEntryPermission.class) - public class GetSpeciesAction extends ReadOnlyApiAction + public static class GetSpeciesAction extends ReadOnlyApiAction { @Override public ApiResponse execute(AnimalSpecies o, BindException errors) { List jsonRows = new ArrayList<>(); - Map props = new HashMap(); + Map props = new HashMap<>(); try { @@ -334,12 +334,12 @@ public ApiResponse execute(AnimalSpecies o, BindException errors) * Given a category, get all its groups */ @RequiresPermission(EHRDataEntryPermission.class) - public class GetGroupsByCategoryAction extends ReadOnlyApiAction + public static class GetGroupsByCategoryAction extends ReadOnlyApiAction { @Override public ApiResponse execute(AnimalGroup animalGroup, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer()); ArrayList rows = new TableSelector(us.getTable("animal_groups", null, true, false), @@ -359,7 +359,7 @@ public ApiResponse execute(AnimalGroup animalGroup, BindException errors) * Given a group, load all animals that are assigned to it */ @RequiresPermission(EHRDataEntryPermission.class) - public class GetAnimalsByGroupAction extends ReadOnlyApiAction + public static class GetAnimalsByGroupAction extends ReadOnlyApiAction { @Override public ApiResponse execute(GroupMember groupMember, BindException errors) @@ -385,7 +385,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) animals.add(member.toJSON()); } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("animals", animals); props.put("success", true); return new ApiSimpleResponse(props); @@ -396,7 +396,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) * Get Animals by name (animal id) - defined to present a list of valid animals to the user */ @RequiresPermission(EHRDataEntryPermission.class) - public class GetAnimalsByNameAction extends ReadOnlyApiAction + public static class GetAnimalsByNameAction extends ReadOnlyApiAction { @Override public ApiResponse execute(GroupMember groupMember, BindException errors) @@ -425,7 +425,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) * validation of the data takes place in the animal_groups.js trigger script */ @RequiresPermission(EHRDataEntryPermission.class) - public class UpdateGroupsAction extends MutatingApiAction + public static class UpdateGroupsAction extends MutatingApiAction { @Override public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors) @@ -506,9 +506,6 @@ public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException er /** * Get a group code to be assigned to a new group * - * @param categoryCode - * @param ignoreCategory - if true, this will return the next code regardless of the category the group belongs to - * @return */ private Integer getNextGroupCode(int categoryCode, boolean ignoreCategory) { @@ -524,7 +521,6 @@ private Integer getNextGroupCode(int categoryCode, boolean ignoreCategory) /** * Get a group code to be assigned to a new group * - * @param categoryCode * @return next code to be used for insert */ private Integer getNextGroupCode(int categoryCode) @@ -567,7 +563,7 @@ private Integer getNextGroupCode() } @RequiresPermission(EHRDataEntryPermission.class) - public class DeleteGroupsAction extends MutatingApiAction + public static class DeleteGroupsAction extends MutatingApiAction { @Override public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors) @@ -637,7 +633,7 @@ public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException er * Assigns animals to a group using an instance of {@link AnimalsGroupAssignor} */ @RequiresPermission(ManageGroupMembersPermission.class) - public class UpdateGroupMembersAction extends MutatingApiAction + public static class UpdateGroupMembersAction extends MutatingApiAction { @Override public ApiResponse execute(GroupMember groupMember, BindException errors) @@ -655,7 +651,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) AnimalsGroupAssignor animalsGroupAssignor = new AnimalsGroupAssignor(this.getViewContext(), groupMember.getGroupid()); - List groupMembers = new ArrayList(); + List groupMembers = new ArrayList<>(); for (String animal : groupMember.getId().split("\n")) { GroupMember animalForm = new GroupMember(); @@ -687,7 +683,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) } @RequiresPermission(ManageGroupMembersPermission.class) - public class DeleteGroupMembersAction extends MutatingApiAction + public static class DeleteGroupMembersAction extends MutatingApiAction { @Override public ApiResponse execute(GroupMember groupMember, BindException errors) @@ -707,7 +703,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors) filter.addCondition(FieldKey.fromString("date"), groupMember.getDate(), CompareType.EQUAL); TableSelector tableSelector = new TableSelector(table, filter, null); - List> keys = new ArrayList>(); + List> keys = new ArrayList<>(); List members = tableSelector.getArrayList(GroupMember.class); for (GroupMember member : members) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalsHierarchyController.java b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalsHierarchyController.java index b8406bae3..2a7353cd6 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalsHierarchyController.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalsHierarchyController.java @@ -26,7 +26,6 @@ import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; -import org.labkey.api.ehr.dataentry.DataEntryForm; import org.labkey.api.query.FieldKey; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; @@ -45,6 +44,7 @@ import org.springframework.web.servlet.ModelAndView; import java.util.ArrayList; +import java.util.Collection; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -80,16 +80,13 @@ public void setViewBy(String viewBy) } @RequiresPermission(ReadPermission.class) - public class GetViewAction extends SimpleViewAction + public static class GetViewAction extends SimpleViewAction { @Override public ModelAndView getView(ViewByForm form, BindException errors) { - - JspView view = new JspView("/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp", this); - String viewBy = form.getViewBy(); - if (viewBy == null) viewBy = "locations"; + JspView view = new JspView<>("/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp"); view.setTitle("Animal Tree View Navigation"); view.setHidePageTitle(true); view.setFrame(WebPartView.FrameType.PORTAL); @@ -123,7 +120,7 @@ public Object execute(Node nodeForm, BindException errors) jsonRootLocations.add(node.toJSON()); } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("nodes", jsonRootLocations); @@ -151,7 +148,7 @@ public Object execute(Node nodeForm, BindException errors) jsonRootLocations.add(animal.toJSON()); } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("nodes", jsonRootLocations); @@ -203,12 +200,12 @@ public void setIncludeAllAnimals(boolean includeAllAnimals) } @RequiresPermission(ReadPermission.class) - public class GetAnimals extends ReadOnlyApiAction + public static class GetAnimals extends ReadOnlyApiAction { @Override public Object execute(AnimalsBy animalsBy, BindException errors) { - List animals = new ArrayList(); + List animals = new ArrayList<>(); Node node = new Node(); switch (animalsBy.getBy().toLowerCase()) { @@ -266,7 +263,7 @@ public Object execute(AnimalsBy animalsBy, BindException errors) jsonRootLocations.add(animal.toJSON()); } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("animals", jsonRootLocations); @@ -295,7 +292,7 @@ public ApiResponse execute(Animal animal, BindException errors) jsonLocationsPath.add(node.toJSON()); } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("path", jsonLocationsPath); @@ -309,26 +306,21 @@ public ApiResponse execute(Animal animal, BindException errors) private HierarchyService getHierarchyService(String viewBy) { - HierarchyService hierarchyService; if (viewBy == null) { return new LocationHierarchyServiceImpl(this.getViewContext()); } - switch (viewBy) + return switch (viewBy) { - case "locations": - return new LocationHierarchyServiceImpl(this.getViewContext()); - case "groups": - return new GroupsHierarchyServiceImpl(this.getViewContext()); - case "protocols": - return new ProtocolHierarchyServiceImpl(this.getViewContext()); - default: - return new GroupsHierarchyServiceImpl(this.getViewContext()); - } + case "locations" -> new LocationHierarchyServiceImpl(this.getViewContext()); + case "groups" -> new GroupsHierarchyServiceImpl(this.getViewContext()); + case "protocols" -> new ProtocolHierarchyServiceImpl(this.getViewContext()); + default -> new GroupsHierarchyServiceImpl(this.getViewContext()); + }; } @RequiresPermission(ReadPermission.class) - public class GetReportsAction extends ReadOnlyApiAction + public static class GetReportsAction extends ReadOnlyApiAction { @Override public Object execute(Object o, BindException errors) @@ -344,11 +336,11 @@ public Object execute(Object o, BindException errors) sort.appendSortColumn(FieldKey.fromString("sort_order"), Sort.SortDirection.ASC, false); - List reports = new TableSelector(reportsTable, filter, sort).getArrayList(Map.class); + Collection> reports = new TableSelector(reportsTable, filter, sort).getMapCollection(); JSONObject reportsJson = new JSONObject(); - for (Map m : reports) + for (var m : reports) { JSONObject reportObject = new JSONObject(); @@ -361,7 +353,7 @@ public Object execute(Object o, BindException errors) } - Map props = new HashMap(); + Map props = new HashMap<>(); props.put("reports", reportsJson); return new ApiSimpleResponse(props); } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java index dc85e57c2..e0fddab73 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java @@ -95,7 +95,7 @@ public ActionURL getRedirectURL(PipelinePathForm form) throws Exception * Landing page for a Fee Schedule Import */ @RequiresPermission(AdminPermission.class) - public class FeeScheduleImportAction extends FormViewAction + public static class FeeScheduleImportAction extends FormViewAction { private String _navTrail = "Import Fee Schedule"; private File _fsFile; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinicalObservationsFormSection.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinicalObservationsFormSection.java index ee1d47635..5aba34597 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinicalObservationsFormSection.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinicalObservationsFormSection.java @@ -28,7 +28,7 @@ */ public class ClinicalObservationsFormSection extends SimpleFormSection { - private boolean _allowAdd = true; + private boolean _allowAdd; public ClinicalObservationsFormSection() { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathFormSection.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathFormSection.java index 78388fbf4..93e91751a 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathFormSection.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathFormSection.java @@ -36,7 +36,7 @@ public ClinpathFormSection(String schemaName, String queryName, String label) @Override public List getTbarButtons() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.add("COPYFROMCLINPATHRUNS"); defaultButtons.addAll(super.getTbarButtons()); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathRunsFormSection.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathRunsFormSection.java index 7bd400fbf..704fb7bdb 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathRunsFormSection.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/ClinpathRunsFormSection.java @@ -29,7 +29,7 @@ */ public class ClinpathRunsFormSection extends SimpleGridPanel { - boolean _isRequest = false; + boolean _isRequest; public ClinpathRunsFormSection(boolean isRequest) { @@ -44,7 +44,7 @@ public ClinpathRunsFormSection(boolean isRequest) @Override public List getTbarButtons() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.addAll(super.getTbarButtons()); if (!_isRequest) diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/EncounterChildFormSection.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/EncounterChildFormSection.java index 297c01187..db3f0b122 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/EncounterChildFormSection.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/EncounterChildFormSection.java @@ -31,7 +31,7 @@ */ public class EncounterChildFormSection extends SimpleGridPanel { - private boolean _allowAddDefaults; + private final boolean _allowAddDefaults; public EncounterChildFormSection(String schemaName, String queryName, String label, boolean allowAddDefaults) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/LabworkFormSection.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/LabworkFormSection.java index 7467e3f4f..bb44d0ff7 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/LabworkFormSection.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/LabworkFormSection.java @@ -31,7 +31,7 @@ */ public class LabworkFormSection extends SimpleGridPanel { - private boolean _allowPanelEdit = false; + private boolean _allowPanelEdit; public LabworkFormSection(String schemaName, String queryName, String label) { @@ -54,7 +54,7 @@ public LabworkFormSection(String schemaName, String queryName, String label, boo @Override public List getTbarButtons() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.add("COPYFROMCLINPATHRUNS"); defaultButtons.addAll(super.getTbarButtons()); defaultButtons.remove("ADDANIMALS"); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SNPRCTaskForm.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SNPRCTaskForm.java index 31debcdb1..681479b48 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SNPRCTaskForm.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SNPRCTaskForm.java @@ -36,7 +36,7 @@ public SNPRCTaskForm(DataEntryFormContext ctx, Module owner, String name, String @Override protected List getButtonConfigs() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.add("SAVEDRAFT"); defaultButtons.add("SUBMIT"); //defaultButtons.add("REVIEW"); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SingleSurgeryFormType.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SingleSurgeryFormType.java index b989a25ca..e1c61e477 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SingleSurgeryFormType.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SingleSurgeryFormType.java @@ -25,7 +25,6 @@ import org.labkey.api.ehr.dataentry.TaskFormSection; import org.labkey.api.ehr.security.EHRSurgeryEntryPermission; import org.labkey.api.module.Module; -import org.labkey.api.module.ModuleLoader; import org.labkey.api.security.PrincipalType; import org.labkey.api.security.SecurityManager; import org.labkey.api.security.UserPrincipal; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SurgeryFormType.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SurgeryFormType.java index d31e26243..ba2a22258 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SurgeryFormType.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/SurgeryFormType.java @@ -25,7 +25,6 @@ import org.labkey.api.ehr.dataentry.TaskFormSection; import org.labkey.api.ehr.security.EHRSurgeryEntryPermission; import org.labkey.api.module.Module; -import org.labkey.api.module.ModuleLoader; import org.labkey.api.security.PrincipalType; import org.labkey.api.security.SecurityManager; import org.labkey.api.security.UserPrincipal; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/UnsaveableTask.java b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/UnsaveableTask.java index 3b2324633..49018a198 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/UnsaveableTask.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/dataentry/dataentry/UnsaveableTask.java @@ -46,7 +46,7 @@ protected boolean canInsert() @Override protected List getButtonConfigs() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.add("SUBMIT"); return defaultButtons; @@ -55,7 +55,7 @@ protected List getButtonConfigs() @Override protected List getMoreActionButtonConfigs() { - List defaultButtons = new ArrayList(); + List defaultButtons = new ArrayList<>(); defaultButtons.add("VALIDATEALL"); defaultButtons.add("FORCESUBMIT"); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveAssignmentsDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveAssignmentsDemographicsProvider.java index fad851d5d..46897e26f 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveAssignmentsDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveAssignmentsDemographicsProvider.java @@ -40,7 +40,7 @@ public ActiveAssignmentsDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveCasesDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveCasesDemographicsProvider.java index 53ab906ec..ad7a93a28 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveCasesDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveCasesDemographicsProvider.java @@ -15,28 +15,15 @@ */ package org.labkey.snprc_ehr.demographics; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.Results; -import org.labkey.api.data.ResultsImpl; -import org.labkey.api.data.Selector; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Sort; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; import org.labkey.api.ehr.demographics.AbstractListDemographicsProvider; import org.labkey.api.module.Module; import org.labkey.api.query.FieldKey; -import org.labkey.api.security.User; -import java.sql.ResultSet; -import java.sql.SQLException; import java.util.Collection; -import java.util.Collections; -import java.util.HashMap; import java.util.HashSet; -import java.util.Map; import java.util.Set; /** @@ -53,7 +40,7 @@ public ActiveCasesDemographicsProvider(Module module) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("objectid")); keys.add(FieldKey.fromString("Id")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveFlagsDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveFlagsDemographicsProvider.java index 29614771e..7bc665958 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveFlagsDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/ActiveFlagsDemographicsProvider.java @@ -16,28 +16,14 @@ package org.labkey.snprc_ehr.demographics; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.Results; -import org.labkey.api.data.ResultsImpl; -import org.labkey.api.data.Selector; import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; import org.labkey.api.ehr.demographics.AbstractListDemographicsProvider; import org.labkey.api.module.Module; import org.labkey.api.query.FieldKey; -import org.labkey.api.security.User; -import java.sql.ResultSet; -import java.sql.SQLException; import java.util.Collection; -import java.util.Collections; -import java.util.HashMap; import java.util.HashSet; -import java.util.Map; import java.util.Set; /** @@ -54,7 +40,7 @@ public ActiveFlagsDemographicsProvider(Module module) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/BirthDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/BirthDemographicsProvider.java index 439062475..b9f28a2c8 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/BirthDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/BirthDemographicsProvider.java @@ -41,7 +41,7 @@ public BirthDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentAccountsDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentAccountsDemographicsProvider.java index b4149cf74..1a1d1a21b 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentAccountsDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentAccountsDemographicsProvider.java @@ -15,28 +15,15 @@ */ package org.labkey.snprc_ehr.demographics; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.Results; -import org.labkey.api.data.ResultsImpl; -import org.labkey.api.data.Selector; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Sort; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; import org.labkey.api.ehr.demographics.AbstractListDemographicsProvider; import org.labkey.api.module.Module; import org.labkey.api.query.FieldKey; -import org.labkey.api.security.User; -import java.sql.ResultSet; -import java.sql.SQLException; import java.util.Collection; -import java.util.Collections; -import java.util.HashMap; import java.util.HashSet; -import java.util.Map; import java.util.Set; /** diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentDietDemographicsProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentDietDemographicsProvider.java index 959ab7c6e..48281112d 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentDietDemographicsProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/demographics/CurrentDietDemographicsProvider.java @@ -22,7 +22,6 @@ import org.labkey.api.query.FieldKey; import java.util.Collection; -import java.util.Date; import java.util.HashSet; import java.util.Set; @@ -42,7 +41,7 @@ public CurrentDietDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("code")); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/enums/AssignmentFailureReason.java b/snprc_ehr/src/org/labkey/snprc_ehr/enums/AssignmentFailureReason.java index c86fb5c99..2b73b5544 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/enums/AssignmentFailureReason.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/enums/AssignmentFailureReason.java @@ -34,7 +34,7 @@ public enum AssignmentFailureReason INVALID_START_OR_END_DATE("End Date must be greater than Start Date."), END_DATE_REQUIRED("Group member must have an end date when the group has an end date."); - private String reason; + private final String reason; AssignmentFailureReason(String reason) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/helpers/CustomizerQueryProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/helpers/CustomizerQueryProvider.java index b00f888a7..c5434668f 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/helpers/CustomizerQueryProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/helpers/CustomizerQueryProvider.java @@ -42,14 +42,6 @@ public CustomizerQueryProvider() { * Checks if the passed table exists, the primary key and id columns, * and builds table with calculated fields from SQL query. Returns false if any checks fail and * true if all checks pass and the table is successfully built - * @param tableInfo - * @param columnName - * @param dateColumnName - * @param queryString - * @param ehrSchema - * @param calculatedColumns - * @param isRemovingDefaultCustomizerColumns - * @return */ public AbstractTableInfo getCalculatedColumnsTable(AbstractTableInfo tableInfo, String columnName, String dateColumnName, String queryString, UserSchema ehrSchema, @@ -85,8 +77,6 @@ public AbstractTableInfo getCalculatedColumnsTable(AbstractTableInfo tableInfo, /** * Obtain the column info for the primary key of a given table - * @param tableInfo - * @return */ private ColumnInfo getPrimaryKeyColumn(TableInfo tableInfo) { List primaryKeys = tableInfo.getPkColumns(); @@ -95,13 +85,6 @@ private ColumnInfo getPrimaryKeyColumn(TableInfo tableInfo) { /** * Returns a new query info object to be used for calculating a column's info - * @param tableInfo - * @param primaryKeyColumn - * @param idColumn - * @param ehrSchema - * @param label - * @param calculatedColumns - * @return */ private CalculatedColumnQueryInfo getQueryInfo(AbstractTableInfo tableInfo, ColumnInfo primaryKeyColumn, ColumnInfo idColumn, UserSchema ehrSchema, @@ -120,9 +103,6 @@ private CalculatedColumnQueryInfo getQueryInfo(AbstractTableInfo tableInfo, Colu /** * Returns a wrapped column object from a given query and it's information - * @param queryInfo - * @param queryString - * @return */ private WrappedColumn getWrappedCalculatedColumn(CalculatedColumnQueryInfo queryInfo, String queryString) { WrappedColumn column = new WrappedColumn(queryInfo.getPrimaryKeyColumn(), CaseUtils.toCamelCase(queryInfo.getLabel(), @@ -139,10 +119,6 @@ private WrappedColumn getWrappedCalculatedColumn(CalculatedColumnQueryInfo query /** * Maps values from the query object's data to the variable names within the SQL query string * (formatted for the Apache Commons Lang StrSubstitor where ${variableName} maps to variableName) - * @param queryString - * @param queryInfo - * @param dateColumnName - * @return */ private String mapQueryStringValues(String queryString, CalculatedColumnQueryInfo queryInfo, String dateColumnName) { Map queryByValues = new HashMap<>(); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/helpers/SortFilterHelper.java b/snprc_ehr/src/org/labkey/snprc_ehr/helpers/SortFilterHelper.java index 7168e28f3..f8e5fde4d 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/helpers/SortFilterHelper.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/helpers/SortFilterHelper.java @@ -37,7 +37,7 @@ public static Sort getSort(String sortBy, boolean toUnderScore) { Sort sort = new Sort(); - if (sortBy == null || sortBy.equals("")) + if (sortBy == null || sortBy.isEmpty()) { return sort; } @@ -65,13 +65,12 @@ public static Sort getSort(String sortBy, boolean toUnderScore) /** * @param filterBy json string of the form [{"property":"columnName","value":"foo"}] - * @return */ public static SimpleFilter getFilter(String filterBy) { SimpleFilter filter = new SimpleFilter(); - if (filterBy == null || filterBy.equals("")) + if (filterBy == null || filterBy.isEmpty()) { return filter; } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultObservationsDataSource.java b/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultObservationsDataSource.java index 105cc93c5..87c24ff29 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultObservationsDataSource.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultObservationsDataSource.java @@ -20,8 +20,6 @@ import org.labkey.api.ehr.history.AbstractDataSource; import org.labkey.api.module.Module; -import java.sql.SQLException; - /** * Created by Marty on 12/8/2016. */ diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultTreatmentOrdersDataSource.java b/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultTreatmentOrdersDataSource.java index c0d3f217a..d96fae35d 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultTreatmentOrdersDataSource.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/history/DefaultTreatmentOrdersDataSource.java @@ -37,22 +37,21 @@ public DefaultTreatmentOrdersDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, null, "code")); - sb.append(safeAppend(rs, "Category", "category")); - sb.append(safeAppendDateAndTime(rs, "Start Date", "date")); - sb.append(safeAppend(rs, "Amount", "amount")); - sb.append(safeAppend(rs, "Units", "amount_units")); - sb.append(safeAppend(rs, "Route", "route")); - sb.append(safeAppend(rs, "Frequency", "frequency")); - sb.append(safeAppend(rs, "Duration", "duration")); - sb.append(safeAppend(rs, "Reason", "reason")); - sb.append(safeAppend(rs, "Remark", "remark")); - sb.append(safeAppend(rs, "Description", "description")); - sb.append(safeAppendDateAndTime(rs, "End Date", "enddate")); + String sb = safeAppend(rs, null, "code") + + safeAppend(rs, "Category", "category") + + safeAppendDateAndTime(rs, "Start Date", "date") + + safeAppend(rs, "Amount", "amount") + + safeAppend(rs, "Units", "amount_units") + + safeAppend(rs, "Route", "route") + + safeAppend(rs, "Frequency", "frequency") + + safeAppend(rs, "Duration", "duration") + + safeAppend(rs, "Reason", "reason") + + safeAppend(rs, "Remark", "remark") + + safeAppend(rs, "Description", "description") + + safeAppendDateAndTime(rs, "End Date", "enddate"); - return sb.toString(); + return sb; } protected String safeAppendDateAndTime(Results rs, String label, String field) throws SQLException { FieldKey fk = FieldKey.fromString(field); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkDataSource.java b/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkDataSource.java index e6aaa9368..d25a26128 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkDataSource.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkDataSource.java @@ -155,7 +155,7 @@ public Map> getFlags(Container c, User u, String id, Date m TableSelector ts = new TableSelector(ti, PageFlowUtil.set("parentid", "flag", "value"), filter, null); final Map> map = new HashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkType.java b/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkType.java index 468870a32..d2787e6fb 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkType.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/history/LabworkType.java @@ -63,8 +63,8 @@ public class LabworkType extends DefaultLabworkType private static String _serviceId; private static String _serviceType; - private String _testCol = "TestId"; - private String _sortCol = "sortOrder"; + private final String _testCol = "TestId"; + private final String _sortCol = "sortOrder"; private Map _tests = null; public LabworkType(Module module) diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/history/OffspringDataSource.java b/snprc_ehr/src/org/labkey/snprc_ehr/history/OffspringDataSource.java index 86509d6d6..94498ef32 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/history/OffspringDataSource.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/history/OffspringDataSource.java @@ -36,13 +36,12 @@ public OffspringDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Offspring ID", "Offspring")); - sb.append(safeAppend(rs, "Sex", "sex")); - sb.append(safeAppend(rs, "Sire", "sire")); - sb.append(safeAppend(rs, "Dam", "dam")); + String sb = safeAppend(rs, "Offspring ID", "Offspring") + + safeAppend(rs, "Sex", "sex") + + safeAppend(rs, "Sire", "sire") + + safeAppend(rs, "Dam", "dam"); - return sb.toString(); + return sb; } } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/model/CalculatedColumnQueryInfo.java b/snprc_ehr/src/org/labkey/snprc_ehr/model/CalculatedColumnQueryInfo.java index 33b61634f..73cf012c5 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/model/CalculatedColumnQueryInfo.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/model/CalculatedColumnQueryInfo.java @@ -8,7 +8,6 @@ import org.labkey.api.query.UserSchema; import org.labkey.snprc_ehr.model.CalculatedColumn; -import java.util.List; import java.util.Set; /** diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/notification/AbstractSSRSNotification.java b/snprc_ehr/src/org/labkey/snprc_ehr/notification/AbstractSSRSNotification.java index 945c77f99..84fae29fc 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/notification/AbstractSSRSNotification.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/notification/AbstractSSRSNotification.java @@ -203,13 +203,13 @@ public MimeMessage createMessage(Container c, User u) } catch (MessagingException e) { - throw new UnexpectedException(e); + throw UnexpectedException.wrap(e); } } } catch (URISyntaxException | IOException e) { - throw new UnexpectedException(e); + throw UnexpectedException.wrap(e); } } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeScheduleExcelParser.java b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeScheduleExcelParser.java index 5c2a89c36..21555e58b 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeScheduleExcelParser.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeScheduleExcelParser.java @@ -55,8 +55,8 @@ public class FeeScheduleExcelParser private boolean _parsed; private String _feeScheduleSheetName; // = "Capped Fee Schedule"; //"Actual Cost Fee Schedule"; private final int _numberOfSkipHeaderRows = 2; - private Map _feeScheduleMap = new LinkedHashMap<>(); - private Map _columnNameMap = new LinkedHashMap<>(); + private final Map _feeScheduleMap = new LinkedHashMap<>(); + private final Map _columnNameMap = new LinkedHashMap<>(); private String _yearPublished; private Container _container; private User _user; @@ -125,7 +125,7 @@ public List getTabPageNames() throws PipelineJobException } } } - if (tabPageNames.size() == 0) + if (tabPageNames.isEmpty()) { throw new PipelineJobException("No Fee Schedule found in workbook."); } @@ -156,8 +156,8 @@ public void parseFile() throws PipelineJobException // tab page selected in jsp int rowIdx; String value; - Double doubleValue; - boolean hasData = false; + double doubleValue; + boolean hasData; Workbook workbook = null; Sheet sheet; @@ -230,7 +230,7 @@ public void parseFile() throws PipelineJobException if (row != null) { FeeScheduleDataRow dataRow = new FeeScheduleDataRow(); - Map costValueMap = new LinkedHashMap(); + Map costValueMap = new LinkedHashMap<>(); for (int col = 0; col < _columnNameMap.size(); col++) //row.getLastCellNum(); col++) { @@ -259,7 +259,7 @@ else if ("Activity ID".equalsIgnoreCase(columnName)) if (ExcelFactory.isCellNumeric(cell)) { doubleValue = cell.getNumericCellValue(); - dataRow.setActivityId(doubleValue.intValue()); + dataRow.setActivityId((int) doubleValue); } else { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java index ef08d2c19..12d3c7f67 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java @@ -22,12 +22,10 @@ import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.security.User; import org.labkey.api.util.FileUtil; -import org.labkey.api.util.Path; import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.vfs.FileLike; -import org.labkey.vfs.FileSystemLike; import java.io.File; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineProvider.java b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineProvider.java index 1df06ca7b..4e550030a 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineProvider.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineProvider.java @@ -36,7 +36,7 @@ public class FeeSchedulePipelineProvider extends PipelineProvider { public static final String NAME = "FeeSchedulePipeline"; - FileFilter _fileMaskFilter = null; + FileFilter _fileMaskFilter; public FeeSchedulePipelineProvider(Module owningModule) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/query/CalculatedColumnForeignKey.java b/snprc_ehr/src/org/labkey/snprc_ehr/query/CalculatedColumnForeignKey.java index 5e9eb5abe..1e0b74b75 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/query/CalculatedColumnForeignKey.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/query/CalculatedColumnForeignKey.java @@ -4,9 +4,7 @@ import org.apache.logging.log4j.Logger; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.TableInfo; -import org.labkey.api.ldk.table.AbstractTableCustomizer; import org.labkey.api.query.DetailsURL; import org.labkey.api.query.LookupForeignKey; import org.labkey.api.query.QueryDefinition; @@ -20,24 +18,20 @@ import org.labkey.snprc_ehr.model.CalculatedColumnQueryInfo; import java.util.ArrayList; -import java.util.HashMap; import java.util.List; -import java.util.Map; public class CalculatedColumnForeignKey extends LookupForeignKey { private static final Logger _log = LogManager.getLogger(CalculatedColumnForeignKey.class); /* Query info object */ - private CalculatedColumnQueryInfo _queryInfo; + private final CalculatedColumnQueryInfo _queryInfo; /* SQL query to be used to calculate column values */ - private String _queryString; + private final String _queryString; /** * Constructor - * @param queryInfo - * @param queryString */ public CalculatedColumnForeignKey(CalculatedColumnQueryInfo queryInfo, String queryString) { _queryInfo = queryInfo; @@ -46,7 +40,6 @@ public CalculatedColumnForeignKey(CalculatedColumnQueryInfo queryInfo, String qu /** * Returns a table that contains the new foreign key columns that were calculated via SQL query - * @return */ @Override public TableInfo getLookupTableInfo() { @@ -63,7 +56,7 @@ public TableInfo getLookupTableInfo() { List errors = new ArrayList<>(); TableInfo lookupTable = queryDefinition.getTable(errors, true); - if (errors.size() > 0) { + if (!errors.isEmpty()) { _log.error("Error creating lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); errors.forEach(error -> _log.error(error.getMessage(), error)); return null; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java b/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java index 20099b485..1efec61c1 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java @@ -55,9 +55,9 @@ public class SNPRC_EHRTriggerHelper { private static final Logger _log = LogManager.getLogger(SNPRC_EHRTriggerHelper.class); - private Container _container = null; - private User _user = null; - private Map _cachedTables = new HashMap<>(); + private final Container _container; + private final User _user; + private final Map _cachedTables = new HashMap<>(); @@ -235,7 +235,7 @@ public Integer getNextCaseId() public Map getExtraContext() { - Map map = new HashMap(); + Map map = new HashMap<>(); map.put("quickValidation", true); map.put("generatedByServer", true); @@ -313,22 +313,14 @@ public void exec(ResultSet rs) throws SQLException try { - if (rows.size() > 0) + if (!rows.isEmpty()) { Map extraContext = getExtraContext(); extraContext.put("skipAnnounceChangedParticipants", true); qus.updateRows(getUser(), flagsTable.getUserSchema().getContainer(), rows, oldKeys, null, extraContext); } } - catch (InvalidKeyException e) - { - throw new RuntimeException(e); - } - catch (BatchValidationException e) - { - throw new RuntimeException(e); - } - catch (QueryUpdateServiceException e) + catch (InvalidKeyException | QueryUpdateServiceException | BatchValidationException e) { throw new RuntimeException(e); } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java b/snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java index d9964e737..790e09825 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java @@ -56,8 +56,8 @@ public class AnimalsGroupAssignor { ViewContext viewContext; - private AnimalGroup group; - private AnimalGroupCategory category; + private final AnimalGroup group; + private final AnimalGroupCategory category; @@ -201,7 +201,7 @@ public void assign(List groupMembers) throws ValidationException selector = new SqlSelector(dbStudySchema, sql); if (selector.exists()) - throw new ValidationException(AssignmentFailureReason.ALREADY_IN_GROUP.toString() + ": " + groupMember.getParticipantid()); + throw new ValidationException(AssignmentFailureReason.ALREADY_IN_GROUP + ": " + groupMember.getParticipantid()); } // if category groups are mutually exclusive, then we need to make sure animal @@ -232,7 +232,7 @@ public void assign(List groupMembers) throws ValidationException selector = new SqlSelector(dbStudySchema, sql); if (selector.exists()) - throw new ValidationException(AssignmentFailureReason.ALREADY_IN_CATEGORY.toString() + ": " + groupMember.getParticipantid()); + throw new ValidationException(AssignmentFailureReason.ALREADY_IN_CATEGORY + ": " + groupMember.getParticipantid()); } // if future dates are not allowed, then we need to make sure a future date is not being entered @@ -272,7 +272,7 @@ public void assign(List groupMembers) throws ValidationException if (!animal_species.equalsIgnoreCase(category_speciesCode)) { - throw new ValidationException(AssignmentFailureReason.NOT_APPLICABLE_SPECIES.toString() + " Id: " + groupMember.getParticipantid() + " Species: " + animal_species); + throw new ValidationException(AssignmentFailureReason.NOT_APPLICABLE_SPECIES + " Id: " + groupMember.getParticipantid() + " Species: " + animal_species); } } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/services/GroupsHierarchyServiceImpl.java b/snprc_ehr/src/org/labkey/snprc_ehr/services/GroupsHierarchyServiceImpl.java index 8dec55ff2..82f90df49 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/services/GroupsHierarchyServiceImpl.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/services/GroupsHierarchyServiceImpl.java @@ -42,7 +42,7 @@ */ public class GroupsHierarchyServiceImpl implements HierarchyService { - private ViewContext viewContext; + private final ViewContext viewContext; public GroupsHierarchyServiceImpl(ViewContext viewContext) { @@ -52,7 +52,7 @@ public GroupsHierarchyServiceImpl(ViewContext viewContext) @Override public List getRootNodes() { - List categoryNodes = new ArrayList(); + List categoryNodes = new ArrayList<>(); SimpleFilter displayable = new SimpleFilter(); displayable.addCondition(FieldKey.fromString("displayable"), "Y", CompareType.EQUAL); @@ -72,7 +72,7 @@ public List getRootNodes() @Override public List getSubNodes(Node node) { - List categoryGroupNodes = new ArrayList(); + List categoryGroupNodes = new ArrayList<>(); try { Integer categoryCode = Integer.parseInt(node.getNode().replace("CATEGORY-", "")); @@ -150,7 +150,7 @@ public List getAnimals(Node node) TableInfo demographicsTable = schema.getTable("demographics"); SimpleFilter animalFilter = new SimpleFilter(); - List animalIds = new ArrayList(); + List animalIds = new ArrayList<>(); for (Animal animal : animals) { animalIds.add(animal.getText()); @@ -165,7 +165,7 @@ public List getAnimals(Node node) oneAnimalDemographicsMap.put("status", a.get("calculated_status")); demographicsMap.put((String) a.get("id"), oneAnimalDemographicsMap); } - List notAliveAnimals = new ArrayList(); + List notAliveAnimals = new ArrayList<>(); for (Animal animal : animals) { if (demographicsMap.containsKey(animal.getText())) @@ -208,7 +208,7 @@ public Node getRootNode(Node node) return null; } Node rootNode = new Node(); - Map props = new HashMap(); + Map props = new HashMap<>(); UserSchema us = new SNPRC_EHRUserSchema(this.viewContext.getUser(), this.viewContext.getContainer()); AnimalGroup group = new TableSelector(us.getTable("animal_groups"), new SimpleFilter().addCondition(FieldKey.fromString("code"), @@ -231,7 +231,7 @@ public AnimalNodePath getNodePath(Animal animal) Animal animalRecord = new TableSelector(demographicsTable, demographicsFilter, null).getObject(Animal.class); - List locationsPath = new ArrayList(); + List locationsPath = new ArrayList<>(); AnimalNodePath animalNodePath = new AnimalNodePath(); animalNodePath.setAnimalId(animal.getParticipantid()); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/services/LocationHierarchyServiceImpl.java b/snprc_ehr/src/org/labkey/snprc_ehr/services/LocationHierarchyServiceImpl.java index 587e0fb7c..992f55184 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/services/LocationHierarchyServiceImpl.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/services/LocationHierarchyServiceImpl.java @@ -47,7 +47,7 @@ */ public class LocationHierarchyServiceImpl implements HierarchyService { - private ViewContext viewContext; + private final ViewContext viewContext; public LocationHierarchyServiceImpl(ViewContext viewContext) { @@ -73,7 +73,7 @@ public List getRootNodes() List maps = new TableSelector(housingTable, currentHousingRecordsFilter, sort).getArrayList(Map.class); List rootNodes = new ArrayList<>(); - List alreadySeenNodes = new ArrayList(); + List alreadySeenNodes = new ArrayList<>(); for (Map map : maps) { @@ -184,7 +184,7 @@ public List getAnimals(Node node) TableInfo demographicsTable = userSchema.getTable("demographics"); SimpleFilter filter = new SimpleFilter(); - List animalIds = new ArrayList(); + List animalIds = new ArrayList<>(); for (Animal animal : animals) { animalIds.add(animal.getId()); @@ -200,7 +200,7 @@ public List getAnimals(Node node) oneAnimalDemographicsMap.put("status", a.get("calculated_status")); demographicsMap.put((String) a.get("id"), oneAnimalDemographicsMap); } - List notAliveAnimals = new ArrayList(); + List notAliveAnimals = new ArrayList<>(); for (Animal animal : animals) { if (demographicsMap.containsKey(animal.getId())) @@ -221,7 +221,6 @@ public List getAnimals(Node node) /** - * @param node * @return true if node is a root node, false otherwise */ @Override @@ -274,7 +273,7 @@ public AnimalNodePath getNodePath(Animal animal) AnimalNodePath animalNodePath = new AnimalNodePath(); animalNodePath.setAnimalId(animal.getParticipantid()); - List locationsPath = new ArrayList(); + List locationsPath = new ArrayList<>(); animalNodePath.setLocations(locationsPath); if (map == null) diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/services/ProtocolHierarchyServiceImpl.java b/snprc_ehr/src/org/labkey/snprc_ehr/services/ProtocolHierarchyServiceImpl.java index 020cd56d2..fe8151228 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/services/ProtocolHierarchyServiceImpl.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/services/ProtocolHierarchyServiceImpl.java @@ -38,7 +38,7 @@ */ public class ProtocolHierarchyServiceImpl implements HierarchyService { - private ViewContext viewContext; + private final ViewContext viewContext; public ProtocolHierarchyServiceImpl(ViewContext viewContext) { @@ -60,7 +60,7 @@ public List getRootNodes() List maps = new TableSelector(assignmentTable, currentAssignmentsRecordsFilter, sort).getArrayList(Map.class); List rootNodes = new ArrayList<>(); - List alreadySeenNodes = new ArrayList(); + List alreadySeenNodes = new ArrayList<>(); for (Map map : maps) { @@ -129,8 +129,8 @@ public List getAnimals(Node node) sort.insertSortColumn(FieldKey.fromString("participantid"), Sort.SortDirection.ASC); List animals = new TableSelector(assignmentTable, currentAssignmentRecordsFilter, sort).getArrayList(Animal.class); - List distinctAnimals = new ArrayList(); - List animalIds = new ArrayList(); + List distinctAnimals = new ArrayList<>(); + List animalIds = new ArrayList<>(); for (Animal animal : animals) { @@ -156,7 +156,7 @@ public List getAnimals(Node node) oneAnimalDemographicsMap.put("status", a.get("calculated_status")); demographicsMap.put((String) a.get("id"), oneAnimalDemographicsMap); } - List notAliveAnimals = new ArrayList(); + List notAliveAnimals = new ArrayList<>(); for (Animal animal : distinctAnimals) { if (demographicsMap.containsKey(animal.getText())) @@ -206,7 +206,7 @@ public AnimalNodePath getNodePath(Animal animal) Animal animalDemographicsRecord = new TableSelector(demographicsTable, demographicsFilter, null).getObject(Animal.class); - List locationsPath = new ArrayList(); + List locationsPath = new ArrayList<>(); AnimalNodePath animalNodePath = new AnimalNodePath(); animalNodePath.setAnimalId(animal.getParticipantid()); diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/services/SNPRC_EHRValidator.java b/snprc_ehr/src/org/labkey/snprc_ehr/services/SNPRC_EHRValidator.java index 3731cb0e2..458a76bba 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/services/SNPRC_EHRValidator.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/services/SNPRC_EHRValidator.java @@ -12,7 +12,6 @@ import org.labkey.api.security.User; import org.labkey.snprc_ehr.domain.NewAnimalData; -import java.util.Date; import java.util.Map; public class SNPRC_EHRValidator diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/BloodDrawTrigger.java b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/BloodDrawTrigger.java index c8c91652f..83ce5214a 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/BloodDrawTrigger.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/BloodDrawTrigger.java @@ -141,7 +141,7 @@ private void validateTotalBloodDraws(Container c, User u, String id, Date date, // Currently this queries study.blood. This is still pending tying SND with SNPRC study queries TableInfo ti = TriggerHelper.getTableInfo(c, u,"study", "Blood Draws", errors); - if (ti == null || errors.size() > 0) + if (ti == null || !errors.isEmpty()) { // if ti is null, there will be an error in errors return; @@ -195,7 +195,7 @@ private Map getBloodInfoForSpecies(Container c, User u, String s { TableInfo ti = TriggerHelper.getTableInfo(c, u,"snprc_ehr", "species", errors); Map speciesBlood = null; - if (errors.size() == 0 && ti != null) + if (errors.isEmpty() && ti != null) { // Cols to retrieve Set cols = new HashSet<>(); @@ -269,7 +269,7 @@ private void validateBloodDraw(Container c, User u, TriggerAction triggerAction) List errors = new ArrayList<>(); Map bloodBySpecies = getBloodInfoForSpecies(c, u, species, errors); - if (errors.size() > 0) + if (!errors.isEmpty()) { eventData.setException(event, errors.get(0)); return; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/FemaleOnlyTrigger.java b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/FemaleOnlyTrigger.java index 773a79f3c..e3638c3da 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/FemaleOnlyTrigger.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/FemaleOnlyTrigger.java @@ -40,7 +40,7 @@ public void onInsert(Container c, User u, TriggerAction triggerAction, Map errors = new ArrayList<>(); boolean genderMatches = TriggerHelper.verifyGender(c, triggerAction.getEvent().getSubjectId(), expectedGender, errors); - if (errors.size() > 0) + if (!errors.isEmpty()) { event.setException(errors.get(0)); } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/MaleOnlyTrigger.java b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/MaleOnlyTrigger.java index 55204d400..d368f21ff 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/MaleOnlyTrigger.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/snd/triggers/MaleOnlyTrigger.java @@ -40,7 +40,7 @@ public void onInsert(Container c, User u, TriggerAction triggerAction, Map errors = new ArrayList<>(); boolean genderMatches = TriggerHelper.verifyGender(c, triggerAction.getEvent().getSubjectId(), expectedGender, errors); - if (errors.size() > 0) + if (!errors.isEmpty()) { event.setException(errors.get(0)); } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/steps/SuperPackageLoadTask.java b/snprc_ehr/src/org/labkey/snprc_ehr/steps/SuperPackageLoadTask.java index d8950c5bf..d0b1555e2 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/steps/SuperPackageLoadTask.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/steps/SuperPackageLoadTask.java @@ -62,7 +62,7 @@ private void importSuperPackages(PipelineJob job) throws PipelineJobException TableSelector ts = new TableSelector(ti, filter, sort); List superPackages = ts.getArrayList(SuperPackage.class); - if (superPackages == null || superPackages.size() == 0) + if (superPackages == null || superPackages.isEmpty()) { job.getLogger().info("No new super packages found in " + SNPRC_EHRSchema.TABLE_SND_SUPER_PACKAGE_STAGING); return; diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAccountDisplayColumnFactory.java b/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAccountDisplayColumnFactory.java index 3c6f08bc4..50d1613ff 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAccountDisplayColumnFactory.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAccountDisplayColumnFactory.java @@ -57,7 +57,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo) return new AnimalAccountDisplayColumn(colInfo); } - public class AnimalAccountDisplayColumn extends DataColumn + public static class AnimalAccountDisplayColumn extends DataColumn { public AnimalAccountDisplayColumn(ColumnInfo col) @@ -98,14 +98,13 @@ public HtmlString getFormattedHtml(RenderContext ctx) ArrayList errors = new ArrayList<>(); SimpleDateFormat dateFormat = new SimpleDateFormat("MM-dd-yy"); - StringBuilder sb = new StringBuilder(); - sb.append(""); - //sb.append(""); - sb.append("" ); - sb.append(""); - sb.append("
AccountStart DateGroup
" + PageFlowUtil.filter(dataMap.get("account")) + "" + dateFormat.format(dataMap.get("date")) + "" + PageFlowUtil.filter(dataMap.get("accountGroup")) + "
"); + String sb = "" + + //sb.append(""); + "" + + "" + + "
AccountStart DateGroup
" + PageFlowUtil.filter(dataMap.get("account")) + "" + dateFormat.format(dataMap.get("date")) + "" + PageFlowUtil.filter(dataMap.get("accountGroup")) + "
"; - String html = PageFlowUtil.validateHtml(sb.toString(), errors, false); + String html = PageFlowUtil.validateHtml(sb, errors, false); if (errors.isEmpty()) return HtmlString.unsafe(html); else @@ -124,15 +123,11 @@ public Object getExcelCompatibleValue(RenderContext ctx) if (dataMap.isEmpty()) return ""; - ArrayList errors = new ArrayList<>(); SimpleDateFormat dateFormat = new SimpleDateFormat("MM-dd-yy"); - StringBuilder sb = new StringBuilder(); - sb.append("Account: " + dataMap.get("account") + " " ); - sb.append("Date: " + dateFormat.format(dataMap.get("date")) + " "); - sb.append("Account Groups: " + dataMap.get("accountGroup")); - - return sb.toString(); + return "Account: " + dataMap.get("account") + " " + + "Date: " + dateFormat.format(dataMap.get("date")) + " " + + "Account Groups: " + dataMap.get("accountGroup"); } } diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAssignmentDisplayColumnFactory.java b/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAssignmentDisplayColumnFactory.java index c7132573b..8ec84815b 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAssignmentDisplayColumnFactory.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/table/AnimalAssignmentDisplayColumnFactory.java @@ -57,19 +57,16 @@ public class AnimalAssignmentDisplayColumnFactory implements DisplayColumnFactor @Override public DisplayColumn createRenderer(ColumnInfo colInfo) { - return new AnimalAssignmentDisplayColumnFactory.AnimalAssignmentDisplayColumn(colInfo); + return new AnimalAssignmentDisplayColumn(colInfo); } - public class AnimalAssignmentDisplayColumn extends DataColumn + public static class AnimalAssignmentDisplayColumn extends DataColumn { - private ColumnInfo col; - public AnimalAssignmentDisplayColumn(ColumnInfo col) { super(col,false); setRequiresHtmlFiltering(false); - this.col = col; } private TableSelector getTs(RenderContext ctx) @@ -117,7 +114,7 @@ public HtmlString getFormattedHtml(RenderContext ctx) sb.append(""); //sb.append(""); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -126,9 +123,8 @@ public void exec(ResultSet rs) throws SQLException String date = dateFormat.format(rs.getDate("date")); String assignmentStatus = PageFlowUtil.filter(rs.getString("assignmentStatus")); String remark = PageFlowUtil.filter(rs.getString("remark")); - //remark = (remark == null) ? "" : remark; sb.append(""); - sb.append("" + ""); + sb.append("" + ""); } }); sb.append("
ProtocolDateStatusComment
" + protocol + "" + date + "" + assignmentStatus + "" + remark + "
" + remark + "
"); @@ -156,7 +152,7 @@ public Object getExcelCompatibleValue(RenderContext ctx) SimpleDateFormat dateFormat = new SimpleDateFormat("MM-dd-yy"); StringBuilder sb = new StringBuilder(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/table/EventNarrativeDisplayColumnFactory.java b/snprc_ehr/src/org/labkey/snprc_ehr/table/EventNarrativeDisplayColumnFactory.java index a7ad4d824..8e23fb3f7 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/table/EventNarrativeDisplayColumnFactory.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/table/EventNarrativeDisplayColumnFactory.java @@ -12,10 +12,10 @@ public class EventNarrativeDisplayColumnFactory implements DisplayColumnFactory @Override public DisplayColumn createRenderer(ColumnInfo colInfo) { - return new EventNarrativeDisplayColumnFactory.EventNarrativeDisplayColumn(colInfo); + return new EventNarrativeDisplayColumn(colInfo); } - public class EventNarrativeDisplayColumn extends DataColumn + public static class EventNarrativeDisplayColumn extends DataColumn { public EventNarrativeDisplayColumn(ColumnInfo col) { diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java b/snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java index 950a39926..8da6ec560 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java @@ -15,7 +15,6 @@ */ package org.labkey.snprc_ehr.table; -import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -59,7 +58,7 @@ public class SNPRC_EHRCustomizer extends AbstractTableCustomizer { private static final Logger _log = LogHelper.getLogger(SNPRC_EHRCustomizer.class, "SNPRC_EHR Table Customizer Class"); - private CustomizerQueryProvider _provider; + private final CustomizerQueryProvider _provider; private Set calculatedColumns; @@ -170,7 +169,7 @@ public void doTableSpecificCustomizations(AbstractTableInfo ti) } if (matches(ti, "study", "housing")) { - customizeHousingTable((AbstractTableInfo) ti); + customizeHousingTable(ti); } // if (matches(ti, "ehr", "project")) { // customizeProjectTable((AbstractTableInfo) ti); @@ -201,18 +200,16 @@ public void doTableSpecificCustomizations(AbstractTableInfo ti) /** * Performs table customizations for columns that are calculated by SQL queries - * @param tableInfo */ public void doCalculatedCustomizations(AbstractTableInfo tableInfo) { if (tableInfo.getColumn(DATE_COLUMN) != null) { - addCalculatedColumns((AbstractTableInfo) tableInfo); + addCalculatedColumns(tableInfo); } } /** * Checks the user schema and whether the table is 'demographics' and performs the necessary column calculations - * @param table */ private void addCalculatedColumns(AbstractTableInfo table) { @@ -227,9 +224,6 @@ private void addCalculatedColumns(AbstractTableInfo table) /** * Checks the table and schema information and invokes provider method to build the table with the * IACUC Assignment Calculated columns - * @param ehrSchema - * @param tableInfo - * @param dateColumnName */ private void appendAssignmentAtTimeColumn(UserSchema ehrSchema, AbstractTableInfo tableInfo, final String dateColumnName) { @@ -249,9 +243,6 @@ private void appendAssignmentAtTimeColumn(UserSchema ehrSchema, AbstractTableInf /** * Checks the table and schema information and invokes provider method to build the table with the * Age At Time calculated columns - * @param ehrSchema - * @param tableInfo - * @param dateColumnName */ private void appendAgeAtTimeColumn(UserSchema ehrSchema, AbstractTableInfo tableInfo, String dateColumnName) { @@ -277,8 +268,6 @@ private void appendAgeAtTimeColumn(UserSchema ehrSchema, AbstractTableInfo table /** * Checks if the current table has a lookup value in the animal table - * @param tableInfo - * @return */ private boolean hasAnimalLookup(AbstractTableInfo tableInfo) { var idCol = tableInfo.getMutableColumn(ID_COLUMN); @@ -287,8 +276,6 @@ private boolean hasAnimalLookup(AbstractTableInfo tableInfo) { /** * Checks if the current table is demographics - * @param tableInfo - * @return */ private boolean isDemographicsTable(TableInfo tableInfo) { return tableInfo.getName().equalsIgnoreCase(DEMOGRAPHICS_TABLE) && tableInfo.getPublicSchemaName().equalsIgnoreCase(STUDY_SCHEMA); diff --git a/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java b/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java index 24210e098..a3f2031ac 100644 --- a/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java +++ b/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java @@ -149,7 +149,7 @@ public List getAssociatedModules() @BeforeClass public static void setupProject() throws Exception { - SNPRC_EHRTest initTest = (SNPRC_EHRTest) getCurrentTest(); + SNPRC_EHRTest initTest = getCurrentTest(); initTest.doSetup(); } @@ -304,22 +304,22 @@ protected void populateHardTableRecords() throws Exception // Valid accounts List> accountRows = Arrays.asList( - new HashMap(Maps.of("account", "1000-100-10", + new HashMap<>(Maps.of("account", "1000-100-10", "description", "Doe, 1111MM", "accountStatus", "A", "accountGroup", "Doe", "date", DATE_FORMAT.format(DateUtils.addDays(new Date(), -20)))), - new HashMap(Maps.of("account", "2000-200-20", + new HashMap<>(Maps.of("account", "2000-200-20", "description", "Smith, 2222PC", "accountStatus", "A", "accountGroup", "Smith 2222", "date", DATE_FORMAT.format(DateUtils.addDays(new Date(), -15)))), - new HashMap(Maps.of("account", "3000-300-30", + new HashMap<>(Maps.of("account", "3000-300-30", "description", "Yu, Reseach 1212", "accountStatus", "A", "accountGroup", "Undefined", "date", DATE_FORMAT.format(DateUtils.addDays(new Date(), -2)))), - new HashMap(Maps.of("account", "4000-400-40", + new HashMap<>(Maps.of("account", "4000-400-40", "description", "General clinical", "accountStatus", "I", "accountGroup", "Clinical", @@ -609,7 +609,7 @@ public void testAnimalHistoryNoFilter() //check count and links for one subject final WebElement overview = PortalHelper.Locators.webPart("Overview").waitForElement(getDriver(), WAIT_FOR_JAVASCRIPT); DataRegionTable tbl = DataRegion(getDriver()).find(overview); - assertEquals(tbl.getDataRowCount(), 49); + assertEquals(49, tbl.getDataRowCount()); assertElementPresent(Locator.linkWithText("TEST1020148")); assertElementPresent(Locator.linkWithText("Male")); assertElementPresent(Locator.linkWithText("Alive")); @@ -902,12 +902,12 @@ public void testKinshipReport() historyPage.clickReportTab("Kinship"); DataRegionTable tbl = historyPage.getActiveReportDataRegion(); - assertEquals(tbl.getDataRowCount(), 20); + assertEquals(20, tbl.getDataRowCount()); _ext4Helper.checkCheckbox(Locator.ehrCheckboxIdContaining("limitRawDataToSelection")); tbl = historyPage.getActiveReportDataRegion(); - assertEquals(tbl.getDataRowCount(), 2); + assertEquals(2, tbl.getDataRowCount()); String[] idCols = {"Id", "Id2", "Coefficient"}; List> rows = tbl.getRows(idCols); diff --git a/snprc_r24/resources/transform/src/AbstractAssayValidator.java b/snprc_r24/resources/transform/src/AbstractAssayValidator.java index efbbb35b0..7abbba06a 100644 --- a/snprc_r24/resources/transform/src/AbstractAssayValidator.java +++ b/snprc_r24/resources/transform/src/AbstractAssayValidator.java @@ -26,11 +26,11 @@ public abstract class AbstractAssayValidator private String _email; private String _password; private File _errorFile; - private Map _runProperties = new HashMap<>(); - private Map _transformFile = new HashMap<>(); - private List _errors = new ArrayList<>(); + private final Map _runProperties = new HashMap<>(); + private final Map _transformFile = new HashMap<>(); + private final List _errors = new ArrayList<>(); private String _host; - private String ERROR_FILE = "c:\\temp\\Labkey\\error.txt"; + private final String ERROR_FILE = "c:\\temp\\Labkey\\error.txt"; public enum Props { assayId, // the assay id from the run properties field diff --git a/snprc_r24/resources/transform/src/MicrobiomeTransform.java b/snprc_r24/resources/transform/src/MicrobiomeTransform.java index 45364c2ca..7377a57f3 100644 --- a/snprc_r24/resources/transform/src/MicrobiomeTransform.java +++ b/snprc_r24/resources/transform/src/MicrobiomeTransform.java @@ -25,14 +25,12 @@ import org.apache.poi.xssf.usermodel.XSSFWorkbook; import org.apache.poi.ss.usermodel.DateUtil; -import com.google.common.collect.*; - public class MicrobiomeTransform extends AbstractAssayValidator { private File _errorFile; - private Map _runProperties = new HashMap<>(); - private Map _colMap = new HashMap<>(); - private Map _dictionary = new HashMap<>(); + private final Map _runProperties = new HashMap<>(); + private final Map _colMap = new HashMap<>(); + private final Map _dictionary = new HashMap<>(); private final int numHeaderCols = 4; public static void main(String[] args) @@ -121,7 +119,7 @@ private String getColumns(Row row) } else { - writeError("Encountered Invalid column header: " + getValue(cell) + " " + sb.toString(), ""); + writeError("Encountered Invalid column header: " + getValue(cell) + " " + sb, ""); //throw new IllegalArgumentException("Encountered Invalid column header: " + getValue(cell) + "\n"); } @@ -146,7 +144,7 @@ private String getColumns(Row row) // Can add more checking here private boolean isValid(String common) { - return !common.isEmpty() && common.trim().length() > 0; + return !common.isEmpty() && !common.trim().isEmpty(); } @@ -159,7 +157,7 @@ private String processRow(Row row) Cell cell; int i = 0; - Integer rowNum = 0; + int rowNum; for (Map.Entry entry : _colMap.entrySet()) { @@ -179,7 +177,7 @@ private String processRow(Row row) else { rowNum = row.getRowNum(); - writeError("Missing row identifyer informaion on row: " + rowNum.toString(), ""); + writeError("Missing row identifyer informaion on row: " + rowNum, ""); } } catch (IOException e) @@ -258,7 +256,7 @@ public void runTransform(File inputFile) { sb.append(getColumns(nextRow)); - System.out.println(sb.toString()); + System.out.println(sb); first = false; } @@ -267,7 +265,7 @@ public void runTransform(File inputFile) sb.append(processRow(nextRow)); } - writer.print(sb.toString()); + writer.print(sb); } } diff --git a/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Controller.java b/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Controller.java index 0f36941e9..22d02b77a 100644 --- a/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Controller.java +++ b/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Controller.java @@ -36,12 +36,12 @@ public snprc_r24Controller() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { @Override public ModelAndView getView(Object o, BindException errors) throws Exception { - return new JspView("/org/labkey/snprc_r24/view/hello.jsp"); + return new JspView<>("/org/labkey/snprc_r24/view/hello.jsp"); } @Override diff --git a/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Module.java b/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Module.java index cb4e440c5..11b47dd65 100644 --- a/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Module.java +++ b/snprc_r24/src/org/labkey/snprc_r24/snprc_r24Module.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerController.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerController.java index 80a18c723..711a267ba 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerController.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerController.java @@ -32,7 +32,6 @@ import org.springframework.validation.Errors; import java.text.ParseException; -import java.time.DateTimeException; import java.util.ArrayList; import java.util.Date; import java.util.HashMap; @@ -55,7 +54,7 @@ public SNPRC_schedulerController() //http://localhost:8080/labkey/snprc_scheduler/snprc/Begin.view? @RequiresPermission(SNPRC_schedulerReadersPermission.class) //@RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleRedirectAction + public static class BeginAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -66,7 +65,7 @@ public URLHelper getRedirectURL(Object o) // http://localhost:8080/labkey/snprc_scheduler/snprc/getActiveTimelines.view?ProjectObjectId=55130483-F7DD-4366-8FA3-55ED58115482 @RequiresPermission(SNPRC_schedulerReadersPermission.class) - public class getActiveTimelinesAction extends ReadOnlyApiAction + public static class getActiveTimelinesAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Timeline timeline, BindException errors) @@ -101,7 +100,7 @@ public ApiResponse execute(Timeline timeline, BindException errors) // on the specified date. @RequiresPermission(SNPRC_schedulerReadersPermission.class) - public class getScheduledTimelinesForSpeciesAction extends ReadOnlyApiAction + public static class getScheduledTimelinesForSpeciesAction extends ReadOnlyApiAction { @Override public ApiResponse execute(SimpleApiJsonForm form, BindException errors) @@ -176,7 +175,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) */ @RequiresPermission(SNPRC_schedulerReadersPermission.class) - public class getActiveProjectsAction extends ReadOnlyApiAction + public static class getActiveProjectsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors) @@ -250,7 +249,7 @@ else if (parentObjectId != null ) List> projects = SNDService.get().getActiveProjects(getContainer(), getUser(), filters, true, eventDate); - if (projects.size() > 0) + if (!projects.isEmpty()) { // SND returned the project table data, need to add Iacuc and CostAccount fields from ehr.project table UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), "ehr"); @@ -297,7 +296,7 @@ else if (parentObjectId != null ) // http://localhost:8080/labkey/snprc_scheduler/snprc/updateTimeline.view? @RequiresPermission(SNPRC_schedulerEditorsPermission.class) - public class updateTimelineAction extends MutatingApiAction + public static class updateTimelineAction extends MutatingApiAction { @Override public void validateForm(SimpleApiJsonForm form, Errors errors) diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerManager.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerManager.java index 2b58291a5..f3d5ddd89 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerManager.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerManager.java @@ -315,7 +315,7 @@ public void deleteTimeline(@NotNull Container c, @NotNull User u, Timeline time { Set cols; SimpleFilter filter; - Map row = new HashMap<>(); + Map row; List> rows = new ArrayList<>(); @@ -356,7 +356,7 @@ public void deleteTimeline(@NotNull Container c, @NotNull User u, Timeline time row.put(TimelineItem.TIMELINEITEM_TIMELINE_ITEM_ID, timelineItemId); rows.add(row); } - if (rows.size() > 0) + if (!rows.isEmpty()) { qus.deleteRows(u, c, rows, null, null); } @@ -816,7 +816,7 @@ public void updateTimelineAnimalItems(@NotNull Container c, @NotNull User u, @No timelineAnimalItem.setObjectId(new GUID().toString()); timelineAnimalItemRows.add(timelineAnimalItem.toMap(c)); - if (timelineAnimalItemRows.size() > 0 ) + if (!timelineAnimalItemRows.isEmpty()) { List> insertedRow = qus.insertRows(u, c, timelineAnimalItemRows, errors, null, null); diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerSequencer.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerSequencer.java index 61ab66b8f..406c3bc35 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerSequencer.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerSequencer.java @@ -9,8 +9,8 @@ public enum SNPRC_schedulerSequencer { TIMELINEID ("org.labkey.snprc_scheduler.domain.Timeline", 100); - private String sequenceName; - private int minId; + private final String sequenceName; + private final int minId; SNPRC_schedulerSequencer(String name, int id) { sequenceName = name; diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerUserSchema.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerUserSchema.java index 9d05bf8f8..9f92d4706 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerUserSchema.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/SNPRC_schedulerUserSchema.java @@ -21,7 +21,7 @@ public class SNPRC_schedulerUserSchema extends SimpleUserSchema { - private boolean _permissionCheck = true; + private final boolean _permissionCheck = true; public SNPRC_schedulerUserSchema(User user, Container container) { diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/domains/Timeline.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/domains/Timeline.java index 6bc4e33ac..7a98e28c3 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/domains/Timeline.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/domains/Timeline.java @@ -555,7 +555,7 @@ public Map toMap(Container c, User u) values.put(TIMELINE_PROTOCOL, getProtocol()); values.put(TIMELINE_ANIMAL_ACCOUNT, getAnimalAccount()); - if (getTimelineItems().size() > 0) + if (!getTimelineItems().isEmpty()) { List> listTimelineItems = new ArrayList<>(); for (TimelineItem timelineItem : getTimelineItems()) @@ -564,7 +564,7 @@ public Map toMap(Container c, User u) } values.put(TIMELINE_TIMELINE_ITEMS, listTimelineItems); } - if (getTimelineProjectItems().size() > 0) + if (!getTimelineProjectItems().isEmpty()) { List> listTimelineProjectItems = new ArrayList<>(); for (TimelineProjectItem timelineProjectItem : getTimelineProjectItems()) @@ -573,7 +573,7 @@ public Map toMap(Container c, User u) } values.put(TIMELINE_TIMELINE_PROJECT_ITEMS, listTimelineProjectItems); } - if (getTimelineAnimalItems().size() > 0) + if (!getTimelineAnimalItems().isEmpty()) { List> listTimelineAnimalItems = new ArrayList<>(); for (TimelineAnimalJunction timelineAnimalItem : getTimelineAnimalItems()) @@ -582,7 +582,7 @@ public Map toMap(Container c, User u) } values.put(TIMELINE_ANIMAL_ITEMS, listTimelineAnimalItems); } - if (getStudyDayNotes().size() > 0) + if (!getStudyDayNotes().isEmpty()) { List> listStudyDayNotes = new ArrayList<>(); for (StudyDayNotes studyDayNote : getStudyDayNotes()) @@ -636,7 +636,7 @@ public JSONObject toJSON(Container c, User u) json.put(TIMELINE_PROTOCOL, getProtocol()); json.put(TIMELINE_ANIMAL_ACCOUNT, getAnimalAccount()); - if (getTimelineItems().size() > 0) + if (!getTimelineItems().isEmpty()) { JSONArray jsonTimelineItems = new JSONArray(); for (TimelineItem timelineItem : getTimelineItems()) @@ -645,7 +645,7 @@ public JSONObject toJSON(Container c, User u) } json.put(TIMELINE_TIMELINE_ITEMS, jsonTimelineItems); } - if (getTimelineProjectItems().size() > 0) + if (!getTimelineProjectItems().isEmpty()) { JSONArray jsonTimelineProjectItems = new JSONArray(); for (TimelineProjectItem timelineProjectItem : getTimelineProjectItems()) @@ -654,7 +654,7 @@ public JSONObject toJSON(Container c, User u) } json.put(TIMELINE_TIMELINE_PROJECT_ITEMS, jsonTimelineProjectItems); } - if (getTimelineAnimalItems().size() > 0) + if (!getTimelineAnimalItems().isEmpty()) { JSONArray jsonTimelineAnimalItems = new JSONArray(); for (TimelineAnimalJunction timelineAnimalItem : getTimelineAnimalItems()) @@ -663,7 +663,7 @@ public JSONObject toJSON(Container c, User u) } json.put(TIMELINE_ANIMAL_ITEMS, jsonTimelineAnimalItems); } - if (getStudyDayNotes().size() > 0) + if (!getStudyDayNotes().isEmpty()) { JSONArray jsonStudyDayNotes = new JSONArray(); for (StudyDayNotes studyDayNote : getStudyDayNotes()) diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/StudyDayNotesTable.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/StudyDayNotesTable.java index 677d08986..51efe8ff4 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/StudyDayNotesTable.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/StudyDayNotesTable.java @@ -40,9 +40,9 @@ public SimpleUserSchema.SimpleTable init() @Override public QueryUpdateService getUpdateService() { - return new StudyDayNotesTable.UpdateService(this); + return new UpdateService(this); } - protected class UpdateService extends SimpleQueryUpdateService + protected static class UpdateService extends SimpleQueryUpdateService { public UpdateService(SimpleUserSchema.SimpleTable ti) { diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineAnimalJunctionTable.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineAnimalJunctionTable.java index 301957a62..50443343e 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineAnimalJunctionTable.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineAnimalJunctionTable.java @@ -41,9 +41,9 @@ public SimpleUserSchema.SimpleTable init() @Override public QueryUpdateService getUpdateService() { - return new TimelineAnimalJunctionTable.UpdateService(this); + return new UpdateService(this); } - protected class UpdateService extends SimpleQueryUpdateService + protected static class UpdateService extends SimpleQueryUpdateService { public UpdateService(SimpleUserSchema.SimpleTable ti) { diff --git a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineItemTable.java b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineItemTable.java index 229d0a485..a154be34e 100644 --- a/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineItemTable.java +++ b/snprc_scheduler/src/org/labkey/snprc_scheduler/query/TimelineItemTable.java @@ -27,8 +27,6 @@ public class TimelineItemTable extends SimpleUserSchema.SimpleTable *

* Create the simple table. * - * @param schema - * @param table */ public TimelineTable(SNPRC_schedulerUserSchema schema, TableInfo table, ContainerFilter cf) diff --git a/snprc_scheduler/test/src/org/labkey/test/tests/snprc_scheduler/SNPRC_schedulerTest.java b/snprc_scheduler/test/src/org/labkey/test/tests/snprc_scheduler/SNPRC_schedulerTest.java index af1570798..c9291680f 100644 --- a/snprc_scheduler/test/src/org/labkey/test/tests/snprc_scheduler/SNPRC_schedulerTest.java +++ b/snprc_scheduler/test/src/org/labkey/test/tests/snprc_scheduler/SNPRC_schedulerTest.java @@ -88,7 +88,7 @@ public String getContainerPath() @BeforeClass public static void setupProject() { - SNPRC_schedulerTest init = (SNPRC_schedulerTest) getCurrentTest(); + SNPRC_schedulerTest init = getCurrentTest(); init.doSetup(); } @@ -152,6 +152,7 @@ public String getModulePath() return SNPRC_EHR_PATH; // Retrieve reference study from snprc_ehr, not snprc_scheduler } + @Override protected boolean skipStudyImportQueryValidation() { return true; @@ -338,7 +339,7 @@ private String getTestProjectObjectId() String projectObjectId = ""; - SelectRowsResponse response = null; + SelectRowsResponse response; try { response = selectCmd.execute(cn, getCurrentContainerPath()); @@ -372,7 +373,7 @@ private ArrayList> getProjectItems(String parentObjectId) SelectRowsResponse response = selectCmd.execute(cn, getCurrentContainerPath()); Rowset rows = response.getRowset(); - Map rowMap = null; + Map rowMap; for (Row row : rows) { @@ -409,7 +410,7 @@ private ArrayList> getTimelineItems(String timelineObjectId) SelectRowsResponse response = selectCmd.execute(cn, getCurrentContainerPath()); Rowset rows = response.getRowset(); - Map rowMap = null; + Map rowMap; for (Row row : rows) { @@ -445,7 +446,7 @@ private ArrayList> getStudyDayNotes(String timelineObjectId) SelectRowsResponse response = selectCmd.execute(cn, getCurrentContainerPath()); Rowset rows = response.getRowset(); - Map rowMap = null; + Map rowMap; for (Row row : rows) {