Merge remote-tracking branch 'origin/develop' into fb_javascriptfragm…

…ent_asjson
LabKey · Jan 26, 2024 · eeefddc · eeefddc
2 parents 1346e3c + afad4da
commit eeefddc
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diff --git a/api/src/org/labkey/api/admin/AdminBean.java b/api/src/org/labkey/api/admin/AdminBean.java
@@ -29,6 +29,7 @@
 import org.labkey.api.security.UserManager;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.DateUtil;
+import org.labkey.api.util.Formats;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.HtmlStringBuilder;
 import org.labkey.api.util.MothershipReport;
@@ -77,6 +78,7 @@ public static class RecentUser
     public static final String serverGuid = AppProps.getInstance().getServerGUID();
     public static final String serverSessionGuid = AppProps.getInstance().getServerSessionGUID();
     public static final String servletContainer = ModuleLoader.getServletContext().getServerInfo();
+    public static final String sessionTimeout = Formats.commaf0.format(ModuleLoader.getServletContext().getSessionTimeout());
     @SuppressWarnings("unused") // Available substitution property, not used directly in code
     public static final String buildTime = ModuleLoader.getInstance().getCoreModule().getBuildTime();
     @SuppressWarnings("unused") // Available substitution property, not used directly in code

diff --git a/api/src/org/labkey/api/reader/HTMLDataLoader.java b/api/src/org/labkey/api/reader/HTMLDataLoader.java
@@ -21,6 +21,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.JSoupUtil;
+import org.w3c.dom.DOMException;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
@@ -82,12 +83,19 @@ public boolean isHeaderMatch(@NotNull byte[] header)
             String s = new String(header, StringUtilsLabKey.DEFAULT_CHARSET);
 
             List<String> errors = new ArrayList<>();
-            Document doc = JSoupUtil.convertHtmlToDocument(s, true, errors);
-            if (!errors.isEmpty() || doc == null)
-                return false;
+            try
+            {
+                Document doc = JSoupUtil.convertHtmlToDocument(s, true, errors);
+                if (!errors.isEmpty() || doc == null)
+                    return false;
 
-            // Look for a html>body>table element
-            return findTable(doc) != null;
+                // Look for a html>body>table element
+                return findTable(doc) != null;
+            }
+            catch (DOMException e)
+            {
+                return false;
+            }
         }
     };
 

diff --git a/api/src/org/labkey/api/util/JsonUtil.java b/api/src/org/labkey/api/util/JsonUtil.java
@@ -561,7 +561,10 @@ public void testJavascript() throws Exception
         {
             // just verifying current behavior: JSONObject escapes /, ObjectMapper does not escape /
             assertEquals("{\"key<\\/\":\"<\\/script>\"}", new JSONObject(Map.of("key</","</script>")).toString());
-            assertEquals("{\"key</\":\"</script>\"}", new ObjectMapper().writeValueAsString(Map.of("key</","</script>")));
+            // This is the default ObjectMapper behavior
+            //assertEquals("{\"key</\":\"</script>\"}", new ObjectMapper().writeValueAsString(Map.of("key</","</script>")));
+            // This is the "hacked" ObjectMapper behavior see the fix-up code in CoreModule static
+            assertEquals("{\"key<\\/\":\"<\\/script>\"}", new ObjectMapper().writeValueAsString(Map.of("key</","</script>")));
 
             // our ObjectMapper should act like JSONObject.toString()
             assertEquals("{\"key<\\/\":\"<\\/script>\"}", DEFAULT_MAPPER.writeValueAsString(Map.of("key</","</script>")));

diff --git a/api/webapp/WEB-INF/web.xml b/api/webapp/WEB-INF/web.xml
@@ -66,7 +66,6 @@
         <url-pattern>*.post</url-pattern>
     </filter-mapping>
 
-
     <welcome-file-list>
         <welcome-file>/</welcome-file>
     </welcome-file-list>

diff --git a/...assay/plate/AbstractPlateTypeHandler.java → ...say/plate/AbstractPlateLayoutHandler.java b/...assay/plate/AbstractPlateTypeHandler.java → ...say/plate/AbstractPlateLayoutHandler.java
@@ -18,17 +18,22 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
+import org.labkey.api.util.Pair;
 
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 /**
  * User: klum
  * Date: Jun 13, 2012
  */
-public abstract class AbstractPlateTypeHandler implements PlateTypeHandler
+public abstract class AbstractPlateLayoutHandler implements PlateLayoutHandler
 {
+    Map<Pair<Integer, Integer>, PlateType> _plateTypeMap;
+
     @Override
     public void validateTemplate(Container container, User user, Plate template) throws ValidationException
     {
@@ -40,6 +45,28 @@ public Map<String, List<String>> getDefaultGroupsForTypes()
         return Collections.emptyMap();
     }
 
+    abstract protected List<Pair<Integer, Integer>> getSupportedPlateSizes();
+
+    protected void validatePlateType(PlateType plateType)
+    {
+        if (!getSupportedPlateTypes().contains(plateType))
+            throw new IllegalStateException("The plate type : " + plateType.getDescription() + " is not supported for this layout handler.");
+    }
+
+    @Override
+    public List<PlateType> getSupportedPlateTypes()
+    {
+        if (_plateTypeMap == null)
+        {
+            _plateTypeMap = new HashMap<>();
+            for (PlateType type : PlateService.get().getPlateTypes())
+            {
+                _plateTypeMap.put(new Pair<>(type.getRows(), type.getColumns()), type);
+            }
+        }
+        return getSupportedPlateSizes().stream().filter(size -> _plateTypeMap.containsKey(size)).map(size -> _plateTypeMap.get(size)).collect(Collectors.toList());
+    }
+
     @Override
     public boolean showEditorWarningPanel()
     {

diff --git a/assay/api-src/org/labkey/api/assay/plate/Plate.java b/assay/api-src/org/labkey/api/assay/plate/Plate.java
@@ -40,6 +40,8 @@ public interface Plate extends PropertySet, Identifiable
 
     boolean isTemplate();
 
+    @NotNull PlateType getPlateTypeObject();
+
     @Nullable PlateSet getPlateSetObject();
 
     /**
@@ -76,7 +78,7 @@ public interface Plate extends PropertySet, Identifiable
 
     int getWellGroupCount(WellGroup.Type type);
 
-    String getType();
+    String getAssayType();
 
     @Override
     @Nullable ActionURL detailsURL();

diff --git a/...key/api/assay/plate/PlateTypeHandler.java → ...y/api/assay/plate/PlateLayoutHandler.java b/...key/api/assay/plate/PlateTypeHandler.java → ...y/api/assay/plate/PlateLayoutHandler.java
@@ -16,33 +16,33 @@
 
 package org.labkey.api.assay.plate;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
-import org.labkey.api.util.Pair;
 
-import java.util.List;
 import java.sql.SQLException;
+import java.util.List;
 import java.util.Map;
 
 /**
- * User: jeckels
- * Date: Apr 23, 2007
+ * Represents a handler that can create assay specific plate layouts
  */
-public interface PlateTypeHandler
+public interface PlateLayoutHandler
 {
+    @NotNull
     String getAssayType();
 
-    List<String> getTemplateTypes(Pair<Integer, Integer> size);
+    @NotNull List<String> getLayoutTypes(PlateType plateType);
 
     /**
      * createTemplate will be given a null value for templateTypeName when it is creating a new template which is a
      * default for that assay type.
      */
-    Plate createTemplate(@Nullable String templateTypeName, Container container, int rowCount, int colCount) throws SQLException;
+    Plate createTemplate(@Nullable String templateTypeName, Container container, @NotNull PlateType plateType) throws SQLException;
 
-    List<Pair<Integer, Integer>> getSupportedPlateSizes();
+    List<PlateType> getSupportedPlateTypes();
 
     List<WellGroup.Type> getWellGroupTypes();
 

diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateService.java b/assay/api-src/org/labkey/api/assay/plate/PlateService.java
@@ -88,23 +88,21 @@ static PlateService get()
      * Creates a new plate
      * @param container The template's container.
      * @param templateType The type of plate, if associated with a particular assay.
-     * @param rowCount The number of columns in the plate.
-     * @param columnCount The number of rows in the plate.
+     * @param plateType Specifies the overall shape of the plate
      * @return A newly created plate instance
      * @throws IllegalArgumentException Thrown if a template of the specified name already exists in the container.
      */
-    @NotNull Plate createPlate(Container container, String templateType, int rowCount, int columnCount);
+    @NotNull Plate createPlate(Container container, String templateType, @NotNull PlateType plateType);
 
     /**
      * Creates a new plate template.
      * @param container The template's container.
      * @param templateType The type of plate template, if associated with a particular assay.
-     * @param rowCount The number of columns in the plate.
-     * @param columnCount The number of rows in the plate.
+     * @param plateType Specifies the overall shape of the plate
      * @return A newly created plate template instance.
      * @throws IllegalArgumentException Thrown if a template of the specified name already exists in the container.
      */
-    @NotNull Plate createPlateTemplate(Container container, String templateType, int rowCount, int columnCount);
+    @NotNull Plate createPlateTemplate(Container container, String templateType, @NotNull PlateType plateType);
 
     /**
      * Adds a new well group to the plate
@@ -164,6 +162,17 @@ static PlateService get()
      */
     @Nullable PlateSet getPlateSet(Container container, int plateSetId);
 
+    /**
+     * Returns the list of available plate types.
+     * @return
+     */
+    @NotNull List<? extends PlateType> getPlateTypes();
+
+    /**
+     * Returns the plate type matching the specified shape.
+     */
+    @Nullable PlateType getPlateType(int rows, int columns);
+
     /**
      * Returns the number of assay runs that are linked to the specified plate. Currently, this only works
      * for the standard assay with plate support since other assays types do not store the plate ID with the
@@ -235,7 +244,7 @@ static PlateService get()
     /**
      * Registers a handler for a particular type of plate
      */
-    void registerPlateTypeHandler(PlateTypeHandler handler);
+    void registerPlateLayoutHandler(PlateLayoutHandler handler);
 
     /**
      * Calculates a dilution curve for the specified well groups.

diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateSet.java b/assay/api-src/org/labkey/api/assay/plate/PlateSet.java
@@ -15,6 +15,8 @@ public interface PlateSet
 
     String getName();
 
+    String getPlateSetId();
+
     boolean isArchived();
 
     List<Plate> getPlates(User user);

diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateType.java b/assay/api-src/org/labkey/api/assay/plate/PlateType.java
@@ -0,0 +1,9 @@
+package org.labkey.api.assay.plate;
+
+public interface PlateType
+{
+    Integer getRowId();
+    String getDescription();
+    Integer getRows();
+    Integer getColumns();
+}
diff --git a/assay/resources/schemas/assay.xml b/assay/resources/schemas/assay.xml
@@ -29,6 +29,11 @@
       <column columnName="Name">
         <description>The unique admin-provided name of each plate template (""NAb: 5 specimens in duplicate", for example).</description>
       </column>
+      <column columnName="Description"/>
+      <column columnName="PlateId">
+        <columnTitle>Plate ID</columnTitle>
+        <isUserEditable>false</isUserEditable>
+      </column>
       <column columnName="PlateSet">
         <description>The Plate Set that this plate is assigned to.</description>
         <fk>
@@ -37,6 +42,14 @@
           <fkDbSchema>assay</fkDbSchema>
         </fk>
       </column>
+      <column columnName="PlateType">
+        <description>The plate type of this plate.</description>
+        <fk>
+          <fkColumnName>RowId</fkColumnName>
+          <fkTable>PlateType</fkTable>
+          <fkDbSchema>assay</fkDbSchema>
+        </fk>
+      </column>
       <column columnName="CreatedBy">
         <datatype>int</datatype>
         <columnTitle>Created By</columnTitle>
@@ -79,20 +92,12 @@
         <description>Boolean indicating whether each plate is a template versus an uploaded instance of a plate template.</description>
         <shownInUpdateView>false</shownInUpdateView>
       </column>
-      <column columnName="Rows">
-        <description>The number of rows in each plate.</description>
-        <shownInUpdateView>false</shownInUpdateView>
-      </column>
-      <column columnName="Columns">
-        <description>The number of columns in each plate.</description>
-        <shownInUpdateView>false</shownInUpdateView>
-      </column>
       <column columnName="DataFileId">
         <isUserEditable>false</isUserEditable>
         <description>A unique text identifier (a GUID) for the data file associated with each plate.</description>
       </column>
-      <column columnName="Type">
-        <description>A text label of the plate type ("NAb", for example).</description>
+      <column columnName="AssayType">
+        <description>A text label of the plate assay type ("NAb", for example).</description>
       </column>
     </columns>
   </table>
@@ -178,6 +183,11 @@
     <columns>
       <column columnName="RowId"/>
       <column columnName="Name"/>
+      <column columnName="Description"/>
+      <column columnName="PlateSetId">
+        <columnTitle>Plate Set ID</columnTitle>
+        <isUserEditable>false</isUserEditable>
+      </column>
       <column columnName="Container"/>
       <column columnName="CreatedBy"/>
       <column columnName="Created"/>
@@ -186,4 +196,16 @@
       <column columnName="Archived"/>
     </columns>
   </table>
+  <table tableName="PlateType" tableDbType="TABLE">
+    <description>Contains one row per plate type.</description>
+    <columns>
+      <column columnName="RowId">
+        <isHidden>true</isHidden>
+      </column>
+      <column columnName="Rows"/>
+      <column columnName="Columns"/>
+      <column columnName="Description"/>
+      <column columnName="Archived"/>
+    </columns>
+  </table>
 </tables>
diff --git a/assay/resources/schemas/dbscripts/postgresql/assay-24.001-24.002.sql b/assay/resources/schemas/dbscripts/postgresql/assay-24.001-24.002.sql
@@ -0,0 +1,61 @@
+CREATE TABLE assay.PlateType
+(
+    RowId SERIAL,
+    Rows INT NOT NULL,
+    Columns INT NOT NULL,
+    Description VARCHAR(300) NOT NULL,
+    Archived BOOLEAN NOT NULL DEFAULT FALSE,
+
+    CONSTRAINT PK_PlateType PRIMARY KEY (RowId),
+    CONSTRAINT UQ_PlateType_Rows_Cols UNIQUE (Rows, Columns)
+);
+
+INSERT INTO assay.PlateType (Rows, Columns, Description) VALUES (3, 4, '12 well (3x4)');
+INSERT INTO assay.PlateType (Rows, Columns, Description) VALUES (4, 6, '24 well (4x6)');
+INSERT INTO assay.PlateType (Rows, Columns, Description) VALUES (6, 8, '48 well (6x8)');
+INSERT INTO assay.PlateType (Rows, Columns, Description) VALUES (8, 12, '96 well (8x12)');
+INSERT INTO assay.PlateType (Rows, Columns, Description) VALUES (16, 24, '384 well (16x24)');
+INSERT INTO assay.PlateType (Rows, Columns, Description, Archived) VALUES (32, 48, '1536 well (32x48)', TRUE);
+INSERT INTO assay.PlateType (Rows, Columns, Description, Archived) VALUES (0, 0, 'Invalid Plate Type (Plates which were created with non-valid row & column combinations)', TRUE);
+
+-- Rename type column to assayType
+ALTER TABLE assay.Plate RENAME COLUMN Type TO AssayType;
+-- Add plateType as a FK to assay.PlateType
+ALTER TABLE assay.Plate ADD COLUMN PlateType INTEGER;
+ALTER TABLE assay.Plate ADD CONSTRAINT FK_Plate_PlateType FOREIGN KEY (PlateType) REFERENCES assay.PlateType (RowId);
+
+-- Add ID and description columns to Plate and PlateSet tables
+ALTER TABLE assay.Plate ADD COLUMN PlateId VARCHAR(200);
+ALTER TABLE assay.Plate ADD COLUMN Description VARCHAR(300);
+ALTER TABLE assay.PlateSet ADD COLUMN PlateSetId VARCHAR(200);
+ALTER TABLE assay.PlateSet ADD COLUMN Description VARCHAR(300);
+
+-- Most existing plate sets will have a generated name, but mutated ones will get fixed up by the java upgrade script
+UPDATE assay.PlateSet SET PlateSetId = Name;
+
+UPDATE assay.Plate
+SET PlateType =
+        CASE
+            WHEN (Rows = 3 AND Columns = 4) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 3 AND Columns = 4)
+            WHEN (Rows = 4 AND Columns = 6) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 4 AND Columns = 6)
+            WHEN (Rows = 6 AND Columns = 8) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 6 AND Columns = 8)
+            WHEN (Rows = 8 AND Columns = 12) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 8 AND Columns = 12)
+            WHEN (Rows = 16 AND Columns = 24) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 16 AND Columns = 24)
+            WHEN (Rows = 32 AND Columns = 48) THEN (SELECT RowId FROM assay.PlateType WHERE Rows = 32 AND Columns = 48)
+            ELSE (SELECT RowId FROM assay.PlateType WHERE Rows = 0 AND Columns = 0)
+            END
+WHERE PlateType IS NULL;
+
+ALTER TABLE assay.Plate ALTER COLUMN PlateType SET NOT NULL;
+ALTER TABLE assay.Plate DROP COLUMN Rows;
+ALTER TABLE assay.Plate DROP COLUMN Columns;
+
+-- upgrade script to initialize plate and plateSet IDs
+SELECT core.executeJavaUpgradeCode('initializePlateAndPlateSetIDs');
+
+-- finalize plate and plateSet ID columns
+ALTER TABLE assay.Plate ALTER COLUMN PlateId SET NOT NULL;
+ALTER TABLE assay.Plate ADD CONSTRAINT UQ_Plate_PlateId UNIQUE (PlateId);
+
+ALTER TABLE assay.PlateSet ALTER COLUMN PlateSetId SET NOT NULL;
+ALTER TABLE assay.PlateSet ADD CONSTRAINT UQ_PlateSet_PlateSetId UNIQUE (PlateSetId);