LabKey · labkey-adam · Oct 2, 2024 · Oct 1, 2024
diff --git a/lincs/src/org/labkey/lincs/LincsController.java b/lincs/src/org/labkey/lincs/LincsController.java
@@ -19,14 +19,14 @@
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.json.JSONObject;
-import org.labkey.api.action.MutatingApiAction;
-import org.labkey.api.action.ReadOnlyApiAction;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.ApiUsageException;
 import org.labkey.api.action.FormHandlerAction;
 import org.labkey.api.action.FormViewAction;
 import org.labkey.api.action.LabKeyError;
+import org.labkey.api.action.MutatingApiAction;
+import org.labkey.api.action.ReadOnlyApiAction;
 import org.labkey.api.action.SimpleErrorView;
 import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
@@ -37,6 +37,7 @@
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.data.SimpleDisplayColumn;
 import org.labkey.api.data.TableInfo;
@@ -1017,7 +1018,7 @@ public void validateCommand(ClueCredentialsForm target, Errors errors) {}
         @Override
         public boolean handlePost(ClueCredentialsForm form, BindException errors)
         {
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(getContainer(), LINCS_CLUE_CREDENTIALS, true);
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(getContainer(), LINCS_CLUE_CREDENTIALS, true);
             map.put(CLUE_SERVER_URI, form.getServerUri());
             map.put(CLUE_API_KEY, form.getApiKey());
             map.save();
@@ -1045,8 +1046,8 @@ public ModelAndView getSuccessView(ClueCredentialsForm form)
         @Override
         public ModelAndView getView(ClueCredentialsForm form, boolean reshow, BindException errors)
         {
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(getContainer(), LINCS_CLUE_CREDENTIALS, false);
-            if(map != null)
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(getContainer(), LINCS_CLUE_CREDENTIALS, false);
+            if (map != null)
             {
                 form.setServerUri(map.get(CLUE_SERVER_URI));
                 form.setApiKey(map.get(CLUE_API_KEY));

diff --git a/lincs/src/org/labkey/lincs/cromwell/CromwellConfig.java b/lincs/src/org/labkey/lincs/cromwell/CromwellConfig.java
@@ -6,6 +6,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -68,7 +69,7 @@ public URI getAbortUri(String cromwellJobId)
 
     public void save(@NotNull Container container)
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(container, PROPS_CROMWELL, true);
+        WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(container, PROPS_CROMWELL, true);
         map.put(PROP_CROMWELL_SERVER_URL, getCromwellServerUrl());
         map.put(PROP_CROMWELL_SERVER_PORT, String.valueOf(getCromwellServerPort()));
         map.save();

diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java b/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java
@@ -8,6 +8,7 @@
 import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.security.User;
 import org.labkey.api.targetedms.ITargetedMSRun;
@@ -35,7 +36,7 @@ public static PspEndpoint getPspEndpoint(Container container) throws LincsPspExc
         try
         {
             // Only run if the psp endpoint configuration has been saved in the container
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(container, LincsController.LINCS_CLUE_CREDENTIALS, false);
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(container, LincsController.LINCS_CLUE_CREDENTIALS, false);
             if(map != null)
             {
                 pspUrl = map.get(LincsController.CLUE_SERVER_URI);

diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
@@ -63,6 +63,7 @@
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.NormalContainerType;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
@@ -127,7 +128,6 @@
 import org.labkey.api.util.ExceptionUtil;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.HtmlStringBuilder;
 import org.labkey.api.util.Link;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
@@ -204,7 +204,6 @@
 import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
-import org.springframework.validation.ObjectError;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.ByteArrayOutputStream;
@@ -981,7 +980,7 @@ public void validateCommand(DataCiteCredentialsForm form, Errors errors)
         @Override
         public boolean handlePost(DataCiteCredentialsForm form, BindException errors)
         {
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, true);
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, true);
             map.put(DataCiteService.USER, form.getProdUser());
             map.put(DataCiteService.PASSWORD, form.getPassword());
             map.put(DataCiteService.PREFIX, form.getDoiPrefix());
@@ -1013,7 +1012,7 @@ public ModelAndView getView(DataCiteCredentialsForm form, boolean reshow, BindEx
         {
             if(!reshow)
             {
-                PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
+                WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
                 if(map != null)
                 {
                     // Force the user to re-enter the passwords; do not set them in the form
@@ -1132,7 +1131,7 @@ public void validateCommand(PXCredentialsForm form, Errors errors)
         @Override
         public boolean handlePost(PXCredentialsForm form, BindException errors)
         {
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, true);
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, true);
             map.put(ProteomeXchangeService.PX_USER, form.getUserName());
             map.put(ProteomeXchangeService.PX_PASSWORD, form.getPassword());
             map.save();
@@ -1160,7 +1159,7 @@ public ModelAndView getView(PXCredentialsForm form, boolean reshow, BindExceptio
         {
             if(!reshow)
             {
-                PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
+                WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
                 if(map != null)
                 {
                     String user = map.get(ProteomeXchangeService.PX_USER);
@@ -4277,7 +4276,7 @@ public void addNavTrail(NavTree root)
         @Override
         public boolean handlePost(PxActionsForm form, BindException errors) throws ProteomeXchangeServiceException, PxException
         {
-            PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
+            WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
             String pxUser = null;
             String pxPassword = null;
             if(map != null)

diff --git a/panoramapublic/src/org/labkey/panoramapublic/datacite/DataCiteService.java b/panoramapublic/src/org/labkey/panoramapublic/datacite/DataCiteService.java
@@ -6,6 +6,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.util.Link;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 
@@ -182,7 +183,7 @@ private static DataCiteResponse doRequest(DataCiteConfig config, @Nullable JSONO
      */
     private static DataCiteConfig getDataCiteConfig(boolean test) throws DataCiteException
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
+        WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
         return getConfig(map, null, test);
     }
 
@@ -195,7 +196,7 @@ private static DataCiteConfig getDataCiteConfig(boolean test) throws DataCiteExc
     @NotNull
     private static DataCiteConfig getDataCiteConfig(@NotNull String doi) throws DataCiteException
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
+        WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(DataCiteService.CREDENTIALS, false);
         DataCiteConfig testConfig = getConfig(map, doi, true);
         DataCiteConfig config = getConfig(map, doi, false);
         if(testConfig.hasPrefix(doi))
@@ -209,7 +210,7 @@ private static DataCiteConfig getDataCiteConfig(@NotNull String doi) throws Data
         throw new DataCiteException("Unrecognized prefix in DOI: " + doi);
     }
 
-    private static DataCiteConfig getConfig(PropertyManager.PropertyMap map, @Nullable String doi, boolean test) throws DataCiteException
+    private static DataCiteConfig getConfig(WritablePropertyMap map, @Nullable String doi, boolean test) throws DataCiteException
     {
         if(map == null)
         {

diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
@@ -22,6 +22,7 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.PropertyMap;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.files.FileContentService;
@@ -750,8 +751,8 @@ private static void addChar(List<Character> categoryChars, List<Character> passw
 
     private void assignPxId(ExperimentAnnotations targetExpt, boolean useTestDb) throws ProteomeXchangeServiceException
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
-        if(map != null)
+        PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(ProteomeXchangeService.PX_CREDENTIALS, false);
+        if (map != null)
         {
             String user = map.get(ProteomeXchangeService.PX_USER);
             String password = map.get(ProteomeXchangeService.PX_PASSWORD);

diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyLibraryStateTask.java
@@ -6,6 +6,7 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.exp.api.ExpExperiment;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.pipeline.AbstractTaskFactory;
@@ -120,7 +121,7 @@ private static void copyLibraryState(Container container, Container sourceContai
         if (null != versionStr)
         {
             log.info(String.format("Setting the value of property '%s' to '%s'.", TargetedMSService.PROP_CHROM_LIB_REVISION, versionStr));
-            PropertyManager.PropertyMap targetPropMap = PropertyManager.getWritableProperties(container, TargetedMSService.MODULE_NAME, true);
+            WritablePropertyMap targetPropMap = PropertyManager.getWritableProperties(container, TargetedMSService.MODULE_NAME, true);
             targetPropMap.put(TargetedMSService.PROP_CHROM_LIB_REVISION, versionStr);
             targetPropMap.save();
 

diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/CatalogEntryManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/CatalogEntryManager.java
@@ -11,16 +11,17 @@
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
 import org.labkey.api.view.ShortURLRecord;
+import org.labkey.panoramapublic.PanoramaPublicManager;
 import org.labkey.panoramapublic.catalog.CatalogEntrySettings;
 import org.labkey.panoramapublic.catalog.CatalogImageAttachmentParent;
-import org.labkey.panoramapublic.PanoramaPublicManager;
 import org.labkey.panoramapublic.model.CatalogEntry;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 
@@ -210,7 +211,7 @@ private static List<Integer> getSubList(List<Integer> entryIdList, int displayCo
 
     public static CatalogEntrySettings getCatalogEntrySettings()
     {
-        PropertyManager.PropertyMap map = PropertyManager.getNormalStore().getWritableProperties(PANORAMA_PUBLIC_CATALOG, false);
+        WritablePropertyMap map = PropertyManager.getNormalStore().getWritableProperties(PANORAMA_PUBLIC_CATALOG, false);
         if (map != null)
         {
             if (Boolean.parseBoolean(map.get(CATALOG_ENTRY_ENABLED)))
@@ -231,7 +232,7 @@ public static void saveCatalogEntrySettings(boolean enabled, @Nullable Long maxF
                                                 @Nullable Integer imgHeight, @Nullable Integer maxTextChars,
                                                 @Nullable Integer maxEntries)
     {
-        PropertyManager.PropertyMap map = PropertyManager.getNormalStore().getWritableProperties(CatalogEntryManager.PANORAMA_PUBLIC_CATALOG, true);
+        WritablePropertyMap map = PropertyManager.getNormalStore().getWritableProperties(CatalogEntryManager.PANORAMA_PUBLIC_CATALOG, true);
         map.put(CatalogEntryManager.CATALOG_ENTRY_ENABLED, Boolean.toString(enabled));
         map.put(CatalogEntryManager.CATALOG_MAX_FILE_SIZE, maxFileSize != null ? String.valueOf(maxFileSize) : null);
         map.put(CatalogEntryManager.CATALOG_IMG_WIDTH, imgWidth !=null ? String.valueOf(imgWidth) : null);

diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java
@@ -21,6 +21,7 @@
 import org.labkey.api.admin.FolderExportPermission;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlSelector;
@@ -367,7 +368,7 @@ public static User getJournalAdminUser(Journal journal)
 
     public static @Nullable PublicDataUser getPublicDataUser(@NotNull Journal journal)
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(journal.getProject(), PUBLIC_DATA_USER, false);
+        WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(journal.getProject(), PUBLIC_DATA_USER, false);
         if(map != null && map.get(USER_ID) != null)
         {
             User user = UserManager.getUser(Integer.parseInt(map.get(USER_ID)));
@@ -382,7 +383,7 @@ public static User getJournalAdminUser(Journal journal)
 
     public static void savePublicDataUser(@NotNull Journal journal, @NotNull User user, @NotNull String password)
     {
-        PropertyManager.PropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(journal.getProject(), PUBLIC_DATA_USER, true);
+        WritablePropertyMap map = PropertyManager.getEncryptedStore().getWritableProperties(journal.getProject(), PUBLIC_DATA_USER, true);
         map.put(USER_ID, String.valueOf(user.getUserId()));
         map.put(USER_PASSWORD, password);
         map.save();

diff --git a/signup/src/org/labkey/signup/SignUpAdmin.jsp b/signup/src/org/labkey/signup/SignUpAdmin.jsp
@@ -3,11 +3,13 @@
 <%@ page import="org.labkey.api.data.Container" %>
 <%@ page import="org.labkey.api.data.ContainerManager" %>
 <%@ page import="org.labkey.api.data.PropertyManager" %>
+<%@ page import="org.labkey.api.data.PropertyManager.WritablePropertyMap" %>
 <%@ page import="org.labkey.api.security.Group" %>
 <%@ page import="org.labkey.api.security.SecurityManager" %>
 <%@ page import="org.labkey.api.security.User" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.signup.SignUpController.AddGroupChangeProperty" %>
 <%@ page import="org.labkey.signup.SignUpController.AddPropertyAction" %>
 <%@ page import="org.labkey.signup.SignUpController.RemoveGroupChangeProperty" %>
@@ -18,7 +20,6 @@
 <%@ page import="java.util.List" %>
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.Set" %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%!
@@ -135,7 +136,7 @@
         <th>Group B</th>
         <th>&nbsp;</th>
     </tr>
-    <%  PropertyManager.PropertyMap groupToGroup = PropertyManager.getWritableProperties(SignUpModule.SIGNUP_GROUP_TO_GROUP, true);
+    <%  WritablePropertyMap groupToGroup = PropertyManager.getWritableProperties(SignUpModule.SIGNUP_GROUP_TO_GROUP, true);
         Set<String> keySet = groupToGroup.keySet();
         for(String key: keySet) {
         List<String> rules = Arrays.asList(groupToGroup.get(key).split("\\s*,\\s*"));