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

Author: labkey-matthewb

api/schemas/expTypes.xsd

@@ -96,7 +96,7 @@
 			<xs:element name="Comments" type="string" minOccurs="0"/>
             <xs:element name="ExperimentLSID" type="string" minOccurs="0" maxOccurs="1" />
 			<xs:element name="Properties" type="exp:PropertyCollectionType" minOccurs="0"/>
-            <xs:element name="WorkflowTaskLSID" type="string" minOccurs="0" maxOccurs="1" />
+            <xs:element name="WorkflowTaskId" type="string" minOccurs="0" maxOccurs="1" />
             <xs:element name="ReplacedByRunLSID" type="string" minOccurs="0">
 				<xs:annotation>
 					<xs:documentation>Reference to another run that defines an updated version of this data</xs:documentation>

api/schemas/folder.xsd

@@ -93,6 +93,7 @@
                 <xs:element name="moduleProperties" minOccurs="0" type="modulePropertiesType"/>
                 <xs:element name="xar" minOccurs="0" type="exportDirType" />
                 <xs:element name="inventory" minOccurs="0" type="exportDirType"/>
+                <xs:element name="workflow" minOccurs="0" type="exportDirType"/>
                 <xs:element name="fileBrowserConfig" minOccurs="0" maxOccurs="1">
                     <xs:complexType>
                         <xs:attribute name="file" type="xs:string">

api/src/org/labkey/api/admin/FolderArchiveDataTypes.java

@@ -51,4 +51,5 @@ private FolderArchiveDataTypes() {}
     public static final String DATA_CLASS_DATA = "Data Class Data";
     public static final String INVENTORY = "Inventory locations and items";
     public static final String VIEW_CATEGORIES = "Categories";
+    public static final String WORKFLOW = "Workflow jobs, templates, tasks, actions and entities";
 }

api/src/org/labkey/api/admin/FolderImportContext.java

@@ -51,6 +51,7 @@ public class FolderImportContext extends AbstractFolderContext
     private String _xarJobId;
 
     private final HashSet<String> _importedReports = new HashSet<>();
+    private Map<Long, Long> _assayRunWorkflowTaskMap = new HashMap<>();
 
     private static final String FOLDER_IMPORT_DB_SEQUENCE_PREFIX = "FolderImportJobCounter-";
 
@@ -180,6 +181,16 @@ public void addImportedReport(ReportDescriptor d)
         _importedReports.add(ReportUtil.getSerializedName(d));
     }
 
+    public Map<Long, Long> getAssayRunWorkflowTaskMap()
+    {
+        return _assayRunWorkflowTaskMap;
+    }
+
+    public void setAssayRunWorkflowTaskMap(Map<Long, Long> assayRunWorkflowTaskMap)
+    {
+        _assayRunWorkflowTaskMap = assayRunWorkflowTaskMap;
+    }
+
     @Override
     public AuditBehaviorType getAuditBehaviorType() throws Exception
     {

api/src/org/labkey/api/data/SQLParameterException.java

@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) 2011 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.api.data;
+
+import org.labkey.api.util.SkipMothershipLogging;
+
+/**
+ * Signals there was a problem with a SQL parameter, such as a conversion problem.
+ */
+public class SQLParameterException extends SQLGenerationException implements SkipMothershipLogging
+{
+    public SQLParameterException(String message)
+    {
+        super(message);
+    }
+}

api/src/org/labkey/api/data/SqlExecutingSelector.java

@@ -567,7 +567,9 @@ public void handleSqlException(SQLException e, @Nullable Connection conn)
             if (null != _sql)
                 ExceptionUtil.decorateException(e, ExceptionUtil.ExceptionInfo.DialectSQL, _sql.toDebugString(), false);
 
-            throw getExceptionFramework().translate(getScope(), "ExecutingSelector", e);
+            RuntimeException translated = getExceptionFramework().translate(getScope(), "ExecutingSelector", e);
+            ExceptionUtil.copyDecorations(e, translated);
+            throw translated;
         }
     }
 }

api/src/org/labkey/api/data/Table.java

@@ -19,6 +19,7 @@
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.beanutils.PropertyUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
@@ -50,6 +51,7 @@
 import org.labkey.api.query.RuntimeValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.util.BaseScanner;
+import org.labkey.api.util.ExceptionUtil;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.MemTracker;
@@ -571,7 +573,7 @@ Object getObject(ResultSet rs) throws SQLException
     // Standard SQLException catch block: log exception, query SQL, and params
     static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, SQLException e, Level logLevel)
     {
-        if (SqlDialect.isCancelException(e))
+        if (SqlDialect.isCancelException(e) || ExceptionUtil.isIgnorable(e))
         {
             return;
         }
@@ -585,7 +587,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S
             String trim = sql.getSQL().trim();
 
             // Treat a ConstraintException during INSERT/UPDATE as a WARNING. Treat all other SQLExceptions as an ERROR.
-            if (RuntimeSQLException.isConstraintException(e) && (StringUtils.startsWithIgnoreCase(trim, "INSERT") || StringUtils.startsWithIgnoreCase(trim, "UPDATE")))
+            if (RuntimeSQLException.isConstraintException(e) && (Strings.CI.startsWith(trim, "INSERT") || Strings.CI.startsWith(trim, "UPDATE")))
             {
                 // Log this ConstraintException if log Level is WARN (the default) or lower. Skip logging for callers that request just ERRORs.
                 if (Level.WARN.isMoreSpecificThan(logLevel))
@@ -1409,7 +1411,7 @@ public void testSelect() throws SQLException
             //noinspection EmptyTryBlock,UnusedDeclaration
             try (ResultSet rs = new TableSelector(tinfo).getResultSet()){}
 
-            Map[] maps = new TableSelector(tinfo).getMapArray();
+            Map<?, ?>[] maps = new TableSelector(tinfo).getMapArray();
             assertNotNull(maps);
 
             Principal[] principals = new TableSelector(tinfo).getArray(Principal.class);
@@ -1739,7 +1741,7 @@ public static ParameterMapStatement deleteStatement(Connection conn, TableInfo t
         //
 
         Domain domain = tableDelete.getDomain();
-        DomainKind domainKind = tableDelete.getDomainKind();
+        DomainKind<?> domainKind = tableDelete.getDomainKind();
         if (null != domain && null != domainKind && StringUtils.isEmpty(domainKind.getStorageSchemaName()))
         {
             if (!d.isPostgreSQL() && !d.isSqlServer())

api/src/org/labkey/api/data/TableSelector.java

@@ -396,7 +396,7 @@ public Results getResultsAsync(final boolean cache, final boolean scrollable, Ht
     }
 
     /**
-     * Setting this options asks the TableSelector to add additional display columns to the generated SQL, as well
+     * Setting this option asks the TableSelector to add additional display columns to the generated SQL, as well
 
      * as forcing the results to be sorted.
      * @return this

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

@@ -165,21 +165,5 @@ default String getDocumentId()
         return String.join(":",getContainer().getId(), "assay", String.valueOf(getRowId()));
     }
 
-    static boolean isSampleWorkflowJobProtocol(String lsid)
-    {
-        return lsid.contains(ExperimentService.SAMPLE_MANAGEMENT_JOB_PROTOCOL_PREFIX);
-    }
-
-    static boolean isSampleWorkflowTaskProtocol(String lsid)
-    {
-        return lsid.contains(ExperimentService.SAMPLE_MANAGEMENT_TASK_PROTOCOL_PREFIX);
-    }
-
-    // TODO remove this and its relatives once the workflow folder import/export rewrite has happened.
-    static boolean isSampleWorkflowProtocol(String lsid)
-    {
-        return isSampleWorkflowTaskProtocol(lsid) || isSampleWorkflowJobProtocol(lsid);
-    }
-
     Map<String, Object> getAuditRecordMap(AssayProvider provider);
 }

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

@@ -393,6 +393,8 @@ ValidationException updateDataClass(
      */
     @NotNull List<? extends ExpMaterial> getExpMaterialsByName(String name, @Nullable Container container, User user);
 
+    @NotNull List<? extends ExpMaterial> getExpMaterialsByName(@NotNull Collection<String> names, @NotNull String sampleTypeName, @NotNull Container container, User user);
+
     @Nullable ExpData findExpData(
         Container c,
         User user,