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Merged
labkey-adam merged 1 commit into from
Oct 2, 2024
Merged

Use WritablePropertyMap #809

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5 changes: 3 additions & 2 deletions elispotassay/src/org/labkey/elispot/ElispotModule.java
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Expand Up @@ -32,6 +32,7 @@

import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Set;

public class ElispotModule extends DefaultModule
Expand Down Expand Up @@ -70,9 +71,9 @@ public boolean hasScripts()

@NotNull
@Override
public Set<String> getSchemaNames()
public Collection<String> getSchemaNames()
{
return Set.of(
return List.of(
ElispotProtocolSchema.ELISPOT_DBSCHEMA_NAME,
ElispotProtocolSchema.ELISPOT_ANTIGEN_SCHEMA_NAME
);
Expand Down
5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/FlowSettings.java
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Expand Up @@ -20,6 +20,7 @@
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.util.FileUtil;

import java.io.File;
Expand Down Expand Up @@ -74,7 +75,7 @@ static public String getWorkingDirectoryPath()
static public void setWorkingDirectoryPath(String path)
{
Container container = ContainerManager.getRoot();
PropertyManager.PropertyMap map = PropertyManager.getWritableProperties(container, PROPCAT_FLOW, path != null);
WritablePropertyMap map = PropertyManager.getWritableProperties(container, PROPCAT_FLOW, path != null);
if (map == null)
{
assert path == null;
Expand All @@ -87,7 +88,7 @@ static public void setWorkingDirectoryPath(String path)
public static void setDeleteFiles(boolean deleteFiles)
{
Container container = ContainerManager.getRoot();
PropertyManager.PropertyMap map = PropertyManager.getWritableProperties(container, PROPCAT_FLOW, !deleteFiles);
WritablePropertyMap map = PropertyManager.getWritableProperties(container, PROPCAT_FLOW, !deleteFiles);
if (map == null)
return;

Expand Down
9 changes: 5 additions & 4 deletions luminex/src/org/labkey/luminex/AnalyteDefaultValueService.java
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Expand Up @@ -18,6 +18,7 @@
import org.apache.commons.lang3.StringUtils;
import org.labkey.api.data.Container;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.exp.property.DomainProperty;
import org.labkey.api.security.User;
Expand Down Expand Up @@ -174,7 +175,7 @@ public static Map<String, String> getContainerDefaultValues(Container container,
return PropertyManager.getProperties(container, getAnalyteColumnCategory(protocol));
}

public static PropertyManager.PropertyMap getWritableContainerDefaultValues(Container container, ExpProtocol protocol)
public static WritablePropertyMap getWritableContainerDefaultValues(Container container, ExpProtocol protocol)
{
return PropertyManager.getWritableProperties(container, AnalyteDefaultValueService.getAnalyteColumnCategory(protocol), true);
}
Expand All @@ -184,7 +185,7 @@ public static Map<String, String> getUserDefaultValues(User user, Container cont
return PropertyManager.getProperties(user, container, getAnalyteColumnCategory(protocol));
}

public static PropertyManager.PropertyMap getWritableUserDefaultValues(User user, Container container, ExpProtocol protocol)
public static WritablePropertyMap getWritableUserDefaultValues(User user, Container container, ExpProtocol protocol)
{
return PropertyManager.getWritableProperties(user, container, AnalyteDefaultValueService.getAnalyteColumnCategory(protocol), true);
}
Expand Down Expand Up @@ -253,7 +254,7 @@ public static List<String> getAnalyteProperty(List<String> analytes, Container c

public static void setAnalyteDefaultValues(Map<String, Map<String, String>> analyteProperties, Container container, ExpProtocol protocol)
{
PropertyManager.PropertyMap defaultAnalyteColumnValues = getWritableContainerDefaultValues(container, protocol);
WritablePropertyMap defaultAnalyteColumnValues = getWritableContainerDefaultValues(container, protocol);
defaultAnalyteColumnValues.clear(); // NOTE: an empty property map would work too.
for(Map.Entry<String, Map<String, String>> entry : analyteProperties.entrySet())
{
Expand All @@ -280,7 +281,7 @@ public static void setAnalyteDefaultValues(Map<String, Map<String, String>> anal
// TODO: merge with the method above
public static void setAnalyteDefaultValues(List<String> analytes, List<String> positivityThresholds, List<String> negativeBeads, Container container, ExpProtocol protocol)
{
PropertyManager.PropertyMap defaultAnalyteColumnValues = getWritableContainerDefaultValues(container, protocol);
WritablePropertyMap defaultAnalyteColumnValues = getWritableContainerDefaultValues(container, protocol);
defaultAnalyteColumnValues.clear(); // NOTE: an empty property map would work too.
if (analytes != null)
{
Expand Down
9 changes: 5 additions & 4 deletions luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
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Expand Up @@ -16,6 +16,7 @@

package org.labkey.luminex;

import jakarta.servlet.ServletException;
import org.apache.commons.collections4.keyvalue.MultiKey;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.action.LabKeyError;
Expand All @@ -36,6 +37,7 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.DisplayColumnGroup;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.data.RenderContext;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SqlSelector;
Expand Down Expand Up @@ -68,7 +70,6 @@
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;

import jakarta.servlet.ServletException;
import java.io.File;
import java.io.IOException;
import java.io.Writer;
Expand Down Expand Up @@ -759,7 +760,7 @@ public boolean executeStep(LuminexRunUploadForm form, BindException errors) thro
saveExperimentRun(form);

// Save user last entered default values for analytes
PropertyManager.PropertyMap defaultAnalyteColumnValues = AnalyteDefaultValueService.getWritableUserDefaultValues(getUser(), getContainer(), form.getProtocol());
WritablePropertyMap defaultAnalyteColumnValues = AnalyteDefaultValueService.getWritableUserDefaultValues(getUser(), getContainer(), form.getProtocol());
for (String analyteName : form.getAnalyteNames())
{
// for analyte domain properties use the standard assay default value persistance
Expand All @@ -782,7 +783,7 @@ public boolean executeStep(LuminexRunUploadForm form, BindException errors) thro
defaultAnalyteColumnValues.save();

// save the default values for the analyte standards/titrations information in 2 categories: well roles and titrations
PropertyManager.PropertyMap defaultWellRoleValues = PropertyManager.getWritableProperties(
WritablePropertyMap defaultWellRoleValues = PropertyManager.getWritableProperties(
getUser(), getContainer(), form.getProtocol().getName() + ": Well Role", true);

for (final Map.Entry<String, Titration> titrationEntry : form.getParser().getTitrationsWithTypes().entrySet())
Expand Down Expand Up @@ -816,7 +817,7 @@ public boolean executeStep(LuminexRunUploadForm form, BindException errors) thro
propertyName = getShowStandardCheckboxColumnName(titrationEntry.getValue());
if (!titrationEntry.getValue().isUnknown() && getViewContext().getRequest().getParameter(propertyName).equals("true"))
{
PropertyManager.PropertyMap defaultTitrationValues = PropertyManager.getWritableProperties(
WritablePropertyMap defaultTitrationValues = PropertyManager.getWritableProperties(
getUser(), getContainer(),
form.getProtocol().getName() + ": " + titrationEntry.getValue().getName(), true);
for (String analyteName : form.getAnalyteNames())
Expand Down
13 changes: 7 additions & 6 deletions ms2/src/org/labkey/ms2/MS2Controller.java
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Expand Up @@ -55,6 +55,7 @@
import org.labkey.api.data.MenuButton;
import org.labkey.api.data.NestableQueryView;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.data.RenderContext;
import org.labkey.api.data.ResultsImpl;
import org.labkey.api.data.RuntimeSQLException;
Expand Down Expand Up @@ -1105,7 +1106,7 @@ public boolean handlePost(ManageViewsForm form, BindException errors)

if (null != viewNames)
{
PropertyManager.PropertyMap m = PropertyManager.getWritableProperties(getUser(), ContainerManager.getRoot(), MS2_VIEWS_CATEGORY, true);
WritablePropertyMap m = PropertyManager.getWritableProperties(getUser(), ContainerManager.getRoot(), MS2_VIEWS_CATEGORY, true);

for (String viewName : viewNames)
m.remove(viewName);
Expand Down Expand Up @@ -1142,7 +1143,7 @@ else if (viewType == DefaultViewType.Manual)
viewName = form.getDefaultViewName();
}

PropertyManager.PropertyMap m = PropertyManager.getWritableProperties(getUser(), ContainerManager.getRoot(), MS2_DEFAULT_VIEW_CATEGORY, true);
WritablePropertyMap m = PropertyManager.getWritableProperties(getUser(), ContainerManager.getRoot(), MS2_DEFAULT_VIEW_CATEGORY, true);
m.put(DEFAULT_VIEW_NAME, viewName);
m.save();

Expand Down Expand Up @@ -2106,12 +2107,12 @@ public ModelAndView getView(FormType form, boolean reshow, BindException errors)

private void savePreferences(Map<String, String> prefs)
{
if (prefs instanceof PropertyManager.PropertyMap)
if (prefs instanceof WritablePropertyMap writable)
{
// Non-guests are stored in the database, guests get it stored in their session
try (var ignored = SpringActionController.ignoreSqlUpdates())
{
((PropertyManager.PropertyMap) prefs).save();
writable.save();
}
}
}
Expand Down Expand Up @@ -3069,7 +3070,7 @@ public boolean handlePost(MS2ViewForm form, BindException errors)
String viewParams = (null == form.getViewParams() ? "" : form.getViewParams());

String name = form.name;
PropertyManager.PropertyMap m;
WritablePropertyMap m;
if (form.isShared() && getContainer().hasPermission(getUser(), InsertPermission.class))
m = PropertyManager.getWritableProperties(getContainer(), MS2_VIEWS_CATEGORY, true);
else
Expand Down Expand Up @@ -4279,7 +4280,7 @@ public static class MS2SearchOptionsAction extends MutatingApiAction<MS2SearchOp
@Override
public Object execute(MS2SearchOptions form, BindException errors)
{
PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), CATEGORY, true);
WritablePropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), CATEGORY, true);

Map<String, String> valuesToPersist = form.getOptions();
if (!valuesToPersist.isEmpty())
Expand Down
10 changes: 4 additions & 6 deletions ms2/src/org/labkey/ms2/pipeline/mascot/MascotConfig.java
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Expand Up @@ -17,12 +17,9 @@

import org.labkey.api.data.Container;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.settings.AbstractWriteableSettingsGroup;

/**
* Created by: jeckels
* Date: 2/7/16
*/
public class MascotConfig extends AbstractWriteableSettingsGroup
{
protected static final String MASCOT_SERVER_PROP = "MascotServer";
Expand Down Expand Up @@ -116,8 +113,9 @@ protected boolean isPasswordProperty(String propName)

public static void reset(Container container)
{
PropertyManager.PropertyMap props = PropertyManager.getProperties(SITE_CONFIG_USER, container, GROUP_NAME);
props.delete();
WritablePropertyMap props = PropertyManager.getWritableProperties(SITE_CONFIG_USER, container, GROUP_NAME, false);
if (props != null)
props.delete();
}

public static MascotConfig getWriteableMascotConfig(Container container)
Expand Down