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

Author: XingY

api/src/org/labkey/api/exp/OntologyManager.java

@@ -2561,13 +2561,11 @@ public static Pair<String, GUID> getURICacheKey(DomainDescriptor dd)
         return getCacheKey(dd.getDomainURI(), dd.getContainer());
     }
 
-
     public static Pair<String, GUID> getCacheKey(PropertyDescriptor pd)
     {
         return getCacheKey(pd.getPropertyURI(), pd.getContainer());
     }
 
-
     public static Pair<String, GUID> getCacheKey(String uri, Container c)
     {
         Container proj = c.getProject();
@@ -2661,7 +2659,6 @@ public static PropertyDescriptor insertOrUpdatePropertyDescriptor(PropertyDescri
         }
     }
 
-
     static final String parameters = "propertyuri,name,description,rangeuri,concepturi,label," +
             "format,container,project,lookupcontainer,lookupschema,lookupquery,defaultvaluetype,hidden," +
             "mvenabled,importaliases,url,urltarget,shownininsertview,showninupdateview,shownindetailsview,measure,dimension,scale," +
@@ -2704,71 +2701,6 @@ else if ("propertyuri".equals(p))
         return new ParameterMapStatement(t.getSchema().getScope(), conn, sql, null);
     }
 
-    static ParameterMapStatement getUpdateStmt(Connection conn, User user, TableInfo t) throws SQLException
-    {
-        user = null==user ? User.guest : user;
-        SQLFragment sql = new SQLFragment("UPDATE exp.propertydescriptor SET ");
-        ColumnInfo c;
-        String comma = "";
-        for (var p : parametersArray)
-        {
-            if (null == (c = t.getColumn(p)))
-                continue;
-            sql.append(comma).append(p).append("=?");
-            comma = ", ";
-            sql.add(new Parameter(p, c.getJdbcType()));
-        }
-        sql.append(", modifiedby=" + user.getUserId() + ", modified={fn now()}");
-        sql.append("\nWHERE propertyid=?");
-        sql.add(new Parameter("propertyid", JdbcType.INTEGER));
-        return new ParameterMapStatement(t.getSchema().getScope(), conn, sql, null);
-    }
-
-
-    public static void insertPropertyDescriptors(User user, List<PropertyDescriptor> pds) throws SQLException
-    {
-        if (null == pds || pds.isEmpty())
-            return;
-        TableInfo t = getTinfoPropertyDescriptor();
-        try (Connection conn = t.getSchema().getScope().getConnection();
-             ParameterMapStatement stmt = getInsertStmt(conn, user, t, false))
-        {
-            ObjectFactory<PropertyDescriptor> f = ObjectFactory.Registry.getFactory(PropertyDescriptor.class);
-            Map<String, Object> m = null;
-            for (PropertyDescriptor pd : pds)
-            {
-                m = f.toMap(pd, m);
-                stmt.clearParameters();
-                stmt.putAll(m);
-                stmt.addBatch();
-            }
-            stmt.executeBatch();
-        }
-    }
-
-
-    public static void updatePropertyDescriptors(User user, List<PropertyDescriptor> pds) throws SQLException
-    {
-        if (null == pds || pds.isEmpty())
-            return;
-        TableInfo t = getTinfoPropertyDescriptor();
-        try (Connection conn = t.getSchema().getScope().getConnection();
-             ParameterMapStatement stmt = getUpdateStmt(conn, user, t))
-        {
-            ObjectFactory<PropertyDescriptor> f = ObjectFactory.Registry.getFactory(PropertyDescriptor.class);
-            Map<String, Object> m = null;
-            for (PropertyDescriptor pd : pds)
-            {
-                m = f.toMap(pd, m);
-                stmt.clearParameters();
-                stmt.putAll(m);
-                stmt.addBatch();
-            }
-            stmt.executeBatch();
-        }
-    }
-
-
     public static PropertyDescriptor insertPropertyDescriptor(PropertyDescriptor pd) throws ChangePropertyDescriptorException
     {
         assert pd.getPropertyId() == 0;
@@ -2779,7 +2711,6 @@ public static PropertyDescriptor insertPropertyDescriptor(PropertyDescriptor pd)
         return pd;
     }
 
-
     //todo:  we automatically update a pd to the last  one in?
     public static PropertyDescriptor updatePropertyDescriptor(PropertyDescriptor pd)
     {

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -21,6 +21,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.assay.AssayProvider;
+import org.labkey.api.attachments.AttachmentParent;
 import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
 import org.labkey.api.data.Container;
@@ -248,6 +249,15 @@ ExpRun createRunForProvenanceRecording(Container container, User user,
     @Nullable
     ExpData getExpData(ExpDataClass dataClass, long rowId);
 
+    /**
+     * Build an {@link org.labkey.api.attachments.AttachmentParent} that points at an ExpData's
+     * attachment storage. Useful for callers outside the experiment module (for example, module
+     * triggers) that need to move, read, or delete ExpData attachments without referencing
+     * experiment-internal classes.
+     */
+    @NotNull
+    AttachmentParent getDataClassAttachmentParent(@NotNull Container container, @NotNull String dataLsid);
+
     /**
      * Get a Data with name at a specific time.
      */
@@ -1152,10 +1162,6 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
 
     int aliasMapRowContainerUpdate(TableInfo aliasMapTable, List<Long> dataIds, Container targetContainer);
 
-    Map<String, Integer> moveDataClassObjects(Collection<? extends ExpData> dataObjects, @NotNull Container sourceContainer, @NotNull Container targetContainer, @NotNull User user, @Nullable String userComment, @Nullable AuditBehaviorType auditBehavior) throws ExperimentException, BatchValidationException;
-
-    int moveAuditEvents(Container targetContainer, List<String> runLsids);
-
     /**
      * From a list of barcodes, find material lsids
      * @param uniqueIds A list of barcodes

experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java

@@ -1221,7 +1221,7 @@ public Map<String, Object> moveRows(User user, Container container, Container ta
 
                     try
                     {
-                        Map<String, Integer> response = ExperimentService.get().moveDataClassObjects(containerObjects.get(c), c, targetContainer, user, auditUserComment, auditType);
+                        Map<String, Integer> response = ExperimentServiceImpl.get().moveDataClassObjects(containerObjects.get(c), c, targetContainer, user, errors, auditUserComment, auditType);
                         incrementCounts(allContainerResponse, response);
                     }
                     catch (ExperimentException e)