Merge remote-tracking branch 'origin/develop' into fb_filesystemlike

Author: labkey-matthewb

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java

@@ -3,6 +3,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.directory.api.ldap.model.exception.LdapException;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.security.ValidEmail;
@@ -112,13 +113,13 @@ public static void setLdapSettings(Map<String, String> props, Map<String, String
             }
         }
 
-        PropertyManager.PropertyMap writableProps = PropertyManager.getWritableProperties(PROPERTY_CATEGORY, true);
+        WritablePropertyMap writableProps = PropertyManager.getWritableProperties(PROPERTY_CATEGORY, true);
         writableProps.clear();
 
         writableProps.putAll(props);
         writableProps.save();
 
-        PropertyManager.PropertyMap encryptedWritableProps = PropertyManager.getEncryptedStore().getWritableProperties(PROPERTY_CATEGORY_ENCRYPTED, true);
+        WritablePropertyMap encryptedWritableProps = PropertyManager.getEncryptedStore().getWritableProperties(PROPERTY_CATEGORY_ENCRYPTED, true);
         encryptedWritableProps.clear();
 
         encryptedWritableProps.putAll(encryptedProps);

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -19,6 +19,8 @@
 import htsjdk.tribble.TribbleException;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.ArrayUtils;
@@ -59,6 +61,7 @@
 import org.labkey.api.data.ConvertHelper;
 import org.labkey.api.data.DataRegionSelection;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.Results;
 import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.SQLFragment;
@@ -174,8 +177,6 @@
 import org.springframework.web.bind.ServletRequestParameterPropertyValues;
 import org.springframework.web.servlet.ModelAndView;
 
-import jakarta.servlet.http.HttpServletRequest;
-import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -4972,7 +4973,7 @@ public static class SetSequenceImportDefaultsAction extends MutatingApiAction<Se
         public ApiResponse execute(SetSequenceImportDefaultsForm form, BindException errors) throws Exception
         {
             Container target = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
-            PropertyManager.PropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
+            WritablePropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
             configMap.put(INPUT_FILE_TREATMENT, form.getInputFileTreatment());
 
             configMap.save();

blast/src/org/labkey/blast/BLASTManager.java

@@ -23,6 +23,7 @@
 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.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
@@ -45,7 +46,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.FileSystems;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Date;
 import java.util.Map;
@@ -70,7 +70,7 @@ public static BLASTManager get()
 
     public void saveSettings(Map<String, String> props) throws IllegalArgumentException
     {
-        PropertyManager.PropertyMap configMap = PropertyManager.getWritableProperties(BLASTManager.CONFIG_PROPERTY_DOMAIN, true);
+        WritablePropertyMap configMap = PropertyManager.getWritableProperties(BLASTManager.CONFIG_PROPERTY_DOMAIN, true);
 
         //validate bin dir
         String binDir = StringUtils.trimToNull(props.get(BLAST_BIN_DIR));

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -16,6 +16,7 @@
 
 package org.labkey.singlecell;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
@@ -37,6 +38,7 @@
 import org.labkey.api.data.ContainerType;
 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.TableInfo;
 import org.labkey.api.data.TableSelector;
@@ -66,7 +68,6 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 
-import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
@@ -522,7 +523,7 @@ public static class SetTenXImportDefaultsAction extends MutatingApiAction<SetSeq
         public ApiResponse execute(SetSequenceImportDefaultsForm form, BindException errors) throws Exception
         {
             Container target = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
-            PropertyManager.PropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
+            WritablePropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
             configMap.put(REQUIRE_ASSAY_TYPE, Boolean.valueOf(form.isRequireAssayType()).toString());
             configMap.put(COMBINE_HASHING_CITE, Boolean.valueOf(form.isCombineHashingCite()).toString());