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Merged
labkey-jeckels merged 3 commits into from
Jun 11, 2025
Merged

Minor auto-refactor code cleanup on a massive scale #822

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c462b11
Minor auto-refactor code cleanup on a massive scale
labkey-jeckels Jun 8, 2025
3d19bfc
Additional cleanup
labkey-jeckels Jun 10, 2025
d91c354
Restore explicit type declaration per request
labkey-jeckels Jun 11, 2025
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9 changes: 3 additions & 6 deletions snprc_ehr/src/org/labkey/snprc_ehr/SNPRCBeanFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@
public class SNPRCBeanFactory<K> extends BeanObjectFactory<K>
{

private static Logger _log = LogManager.getLogger(BeanObjectFactory.class);
private Class<K> _class;
private static final Logger _log = LogManager.getLogger(BeanObjectFactory.class);
private final Class<K> _class;


public SNPRCBeanFactory(Class<K> clss)
Expand All @@ -55,9 +55,6 @@ public SNPRCBeanFactory(Class<K> clss)
/**
* Maps property fooBar to key foo_bar, in preparation for CRUD operations
*
* @param bean
* @param m
* @return
*/
@Override
public
Expand Down Expand Up @@ -128,7 +125,7 @@ public K fromMap(K bean, Map<String, ?> m)
}
catch (IllegalAccessException | InvocationTargetException x)
{
throw new UnexpectedException(x);
throw UnexpectedException.wrap(x);
}
catch (IllegalArgumentException x)
{
Expand Down
30 changes: 15 additions & 15 deletions snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@ public void setBaseURL(String baseURL)
}

@RequiresPermission(AdminPermission.class)
public class SSRSConfigAction extends FormViewAction<SSRSConfigForm>
public static class SSRSConfigAction extends FormViewAction<SSRSConfigForm>
{
@Override
public void validateCommand(SSRSConfigForm target, Errors errors)
Expand Down Expand Up @@ -174,7 +174,7 @@ public void addNavTrail(NavTree root)
}

@RequiresPermission(ManageLookupTablesPermission.class)
public class EditLookupTablesAction extends SimpleViewAction
public static class EditLookupTablesAction extends SimpleViewAction<Object>
{

@Override
Expand All @@ -192,7 +192,7 @@ public ModelAndView getView(Object o, BindException errors)


@RequiresPermission(UpdatePermission.class)
public class UpdateQueryAction extends SimpleViewAction<QueryForm>
public static class UpdateQueryAction extends SimpleViewAction<QueryForm>
{
private QueryForm _form;

Expand Down Expand Up @@ -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<SimpleApiJsonForm>
public static class getNextAnimalIdAction extends MutatingApiAction<SimpleApiJsonForm>
{
@Override
public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors)
Expand Down Expand Up @@ -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<Object>
{
@Override
public URLHelper getRedirectURL(Object o)
Expand All @@ -312,7 +312,7 @@ public URLHelper getRedirectURL(Object o)
}

@RequiresPermission(SNPRCColonyAdminPermission.class)
public class SsrsReportsAction extends SimpleRedirectAction
public static class SsrsReportsAction extends SimpleRedirectAction<Object>
{
@Override
public URLHelper getRedirectURL(Object o)
Expand All @@ -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)
Expand All @@ -332,7 +332,7 @@ public URLHelper getRedirectURL(Object o)
}

@RequiresPermission(EHRDataEntryPermission.class)
public class SndEventViewAction extends SimpleRedirectAction
public static class SndEventViewAction extends SimpleRedirectAction<Object>
{
@Override
public URLHelper getRedirectURL(Object o)
Expand All @@ -342,7 +342,7 @@ public URLHelper getRedirectURL(Object o)
}

@RequiresPermission(SNPRCColonyAdminPermission.class)
public class NewAnimalWizardAction extends SimpleRedirectAction
public static class NewAnimalWizardAction extends SimpleRedirectAction<Object>
{
@Override
public URLHelper getRedirectURL(Object o)
Expand All @@ -355,13 +355,13 @@ public URLHelper getRedirectURL(Object o)
* Get all New Animals
*/
@RequiresPermission(SNPRCColonyAdminPermission.class)
public class GetNewAnimalDataAction extends ReadOnlyApiAction<NewAnimalData>
public static class GetNewAnimalDataAction extends ReadOnlyApiAction<NewAnimalData>
{
@Override
public ApiResponse execute(NewAnimalData o, BindException errors)
{

Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();


SimpleFilter filter = new SimpleFilter();
Expand All @@ -387,7 +387,7 @@ public ApiResponse execute(NewAnimalData o, BindException errors)
* Update/Add new animal
*/
@RequiresPermission(SNPRCColonyAdminPermission.class)
public class UpdateAnimalDataAction extends MutatingApiAction<NewAnimalData>
public static class UpdateAnimalDataAction extends MutatingApiAction<NewAnimalData>
{
@Override
public void validateForm(NewAnimalData newAnimalData, Errors errors)
Expand Down Expand Up @@ -480,12 +480,12 @@ public ApiResponse execute(NewAnimalData newAnimalData, BindException errors)
}

@RequiresPermission(EHRDataEntryPermission.class)
public class RemoveCategoryAction extends MutatingApiAction<AnimalGroupCategory>
public static class RemoveCategoryAction extends MutatingApiAction<AnimalGroupCategory>
{
@Override
public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindException errors)
{
Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();
try
{
UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer());
Expand All @@ -504,7 +504,7 @@ public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindExceptio
categoriesFilter.addCondition(FieldKey.fromString("category_code"), animalGroupCategory.getCategoryCode(), CompareType.EQUAL);
Map<String, Object> animalGroupsCategory = new TableSelector(categoriesTable, categoriesFilter, null).getObject(Map.class);

List<Map<String, Object>> keys = new ArrayList<Map<String, Object>>();
List<Map<String, Object>> keys = new ArrayList<>();

Map<String, Object> idMap = new HashMap<>();
idMap.put("category_code", animalGroupsCategory.get("category_code"));
Expand Down
44 changes: 20 additions & 24 deletions snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ public AnimalGroupsController()
}

@RequiresPermission(EHRDataEntryPermission.class)
public class GroupCategoriesAction extends SimpleViewAction<AnimalGroupCategory>
public static class GroupCategoriesAction extends SimpleViewAction<AnimalGroupCategory>
{
@Override
public void addNavTrail(NavTree root)
Expand All @@ -114,13 +114,13 @@ public ModelAndView getView(AnimalGroupCategory animalGroupCategory, BindExcepti
* Get all defined categories
*/
@RequiresPermission(EHRDataEntryPermission.class)
public class GetCategoriesAction extends ReadOnlyApiAction<AnimalGroupCategory>
public static class GetCategoriesAction extends ReadOnlyApiAction<AnimalGroupCategory>
{
@Override
public ApiResponse execute(AnimalGroupCategory o, BindException errors)
{

Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();

Sort sort = SortFilterHelper.getSort(o.getSort(), true);

Expand Down Expand Up @@ -149,7 +149,7 @@ public ApiResponse execute(AnimalGroupCategory o, BindException errors)
* Update/Add category
*/
@RequiresPermission(EHRDataEntryPermission.class)
public class UpdateCategoriesAction extends MutatingApiAction<AnimalGroupCategory>
public static class UpdateCategoriesAction extends MutatingApiAction<AnimalGroupCategory>
{
@Override
public ApiResponse execute(AnimalGroupCategory o, BindException errors)
Expand Down Expand Up @@ -225,12 +225,12 @@ private Integer getNextCategoryId()
}

@RequiresPermission(EHRDataEntryPermission.class)
public class RemoveCategoryAction extends MutatingApiAction<AnimalGroupCategory>
public static class RemoveCategoryAction extends MutatingApiAction<AnimalGroupCategory>
{
@Override
public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindException errors)
{
Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();
try
{
UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer());
Expand All @@ -249,7 +249,7 @@ public ApiResponse execute(AnimalGroupCategory animalGroupCategory, BindExceptio
categoriesFilter.addCondition(FieldKey.fromString("category_code"), animalGroupCategory.getCategoryCode(), CompareType.EQUAL);
Map<String, Object> animalGroupsCategory = new TableSelector(categoriesTable, categoriesFilter, null).getObject(Map.class);

List<Map<String, Object>> keys = new ArrayList<Map<String, Object>>();
List<Map<String, Object>> keys = new ArrayList<>();

Map<String, Object> idMap = new HashMap<>();
idMap.put("category_code", animalGroupsCategory.get("category_code"));
Expand Down Expand Up @@ -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<AnimalSpecies>
public static class GetSpeciesAction extends ReadOnlyApiAction<AnimalSpecies>
{
@Override
public ApiResponse execute(AnimalSpecies o, BindException errors)
{
List<JSONObject> jsonRows = new ArrayList<>();
Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();

try
{
Expand Down Expand Up @@ -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<AnimalGroup>
public static class GetGroupsByCategoryAction extends ReadOnlyApiAction<AnimalGroup>
{
@Override
public ApiResponse execute(AnimalGroup animalGroup, BindException errors)
{
Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();
UserSchema us = new SNPRC_EHRUserSchema(getUser(), getContainer());

ArrayList<AnimalGroup> rows = new TableSelector(us.getTable("animal_groups", null, true, false),
Expand All @@ -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<GroupMember>
public static class GetAnimalsByGroupAction extends ReadOnlyApiAction<GroupMember>
{
@Override
public ApiResponse execute(GroupMember groupMember, BindException errors)
Expand All @@ -385,7 +385,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors)
animals.add(member.toJSON());
}

Map<String, Object> props = new HashMap<String, Object>();
Map<String, Object> props = new HashMap<>();
props.put("animals", animals);
props.put("success", true);
return new ApiSimpleResponse(props);
Expand All @@ -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<GroupMember>
public static class GetAnimalsByNameAction extends ReadOnlyApiAction<GroupMember>
{
@Override
public ApiResponse execute(GroupMember groupMember, BindException errors)
Expand Down Expand Up @@ -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<SimpleApiJsonForm>
public static class UpdateGroupsAction extends MutatingApiAction<SimpleApiJsonForm>
{
@Override
public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors)
Expand Down Expand Up @@ -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)
{
Expand All @@ -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)
Expand Down Expand Up @@ -567,7 +563,7 @@ private Integer getNextGroupCode()
}

@RequiresPermission(EHRDataEntryPermission.class)
public class DeleteGroupsAction extends MutatingApiAction<SimpleApiJsonForm>
public static class DeleteGroupsAction extends MutatingApiAction<SimpleApiJsonForm>
{
@Override
public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors)
Expand Down Expand Up @@ -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<GroupMember>
public static class UpdateGroupMembersAction extends MutatingApiAction<GroupMember>
{
@Override
public ApiResponse execute(GroupMember groupMember, BindException errors)
Expand All @@ -655,7 +651,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors)

AnimalsGroupAssignor animalsGroupAssignor = new AnimalsGroupAssignor(this.getViewContext(), groupMember.getGroupid());

List<GroupMember> groupMembers = new ArrayList<GroupMember>();
List<GroupMember> groupMembers = new ArrayList<>();
for (String animal : groupMember.getId().split("\n"))
{
GroupMember animalForm = new GroupMember();
Expand Down Expand Up @@ -687,7 +683,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors)
}

@RequiresPermission(ManageGroupMembersPermission.class)
public class DeleteGroupMembersAction extends MutatingApiAction<GroupMember>
public static class DeleteGroupMembersAction extends MutatingApiAction<GroupMember>
{
@Override
public ApiResponse execute(GroupMember groupMember, BindException errors)
Expand All @@ -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<Map<String, Object>> keys = new ArrayList<Map<String, Object>>();
List<Map<String, Object>> keys = new ArrayList<>();
List<GroupMember> members = tableSelector.getArrayList(GroupMember.class);
for (GroupMember member : members)
{
Expand Down
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