Option to migrate SQL Server hard tables to PostgreSQL (#907)

labkey-adam · web-flow · commit 1c7b2afaff72 · 2025-08-01T14:46:13.000-07:00
diff --git a/flow/src/org/labkey/flow/controllers/FlowController.java b/flow/src/org/labkey/flow/controllers/FlowController.java
@@ -46,6 +46,7 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.JobRunner;
 import org.labkey.api.util.TestContext;
+import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
@@ -72,8 +73,6 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import java.net.URI;
-
 @Marshal(Marshaller.Jackson)
 public class FlowController extends BaseFlowController
 {
@@ -367,8 +366,8 @@ public class SavePreferencesAction extends SimpleViewAction<Object>
         public ModelAndView getView(Object o, BindException errors) throws Exception
         {
             FlowPreference.update(getRequest());
-            URI uri = new URI(getRequest().getContextPath() + "/_.gif");
-            return HttpView.redirect(uri.toString());
+            URLHelper url = new URLHelper(getRequest().getContextPath() + "/_.gif");
+            return HttpView.redirect(url, false);
         }
 
         @Override
diff --git a/protein/resources/schemas/dbscripts/postgresql/prot-0.000-21.000.sql b/protein/resources/schemas/dbscripts/postgresql/prot-0.000-21.000.sql
@@ -70,6 +70,7 @@ CREATE TABLE prot.InfoSources
 
 /*** Initializations */
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO prot.InfoSources (Name, Url, InsertDate) VALUES ('Genbank', 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term={}', '2005-03-04 12:08:10');
 INSERT INTO prot.InfoSources (Name, Url, InsertDate) VALUES ('NiceProt', 'http://au.expasy.org/cgi-bin/niceprot.pl?{}', '2005-03-04 12:08:10');
 INSERT INTO prot.InfoSources (Name, Url, InsertDate) VALUES ('GeneCards', 'http://www.genecards.org/cgi-bin/carddisp?{}&alias=yes', '2005-03-04 12:08:10');
@@ -80,6 +81,7 @@ UPDATE prot.InfoSources SET Url = 'http://www.genecards.org/cgi-bin/carddisp.pl?
 UPDATE prot.InfoSources SET URL = 'http://www.uniprot.org/uniprot/{}' WHERE Name = 'NiceProt';
 UPDATE prot.InfoSources SET URL = 'http://www.ncbi.nlm.nih.gov/protein/{}' WHERE Name = 'Genbank';
 UPDATE prot.infosources SET url = 'http://amigo.geneontology.org/amigo/term/{}' WHERE Name = 'GO';
+-- @SkipOnEmptySchemasEnd
 
 /****** AnnotationTypes                                 */
 CREATE TABLE prot.AnnotationTypes
@@ -97,13 +99,15 @@ CREATE TABLE prot.AnnotationTypes
 );
 CREATE UNIQUE INDEX UQ_ProtAnnotationTypes ON prot.AnnotationTypes(Name);
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO prot.AnnotationTypes (Name,SourceId,EntryDate) VALUES ('GO_F',5,'2005-03-04 11:37:15');
 INSERT INTO prot.AnnotationTypes (Name,SourceId,EntryDate) VALUES ('GO_P',5,'2005-03-04 11:37:15');
 INSERT INTO prot.AnnotationTypes (Name,EntryDate) VALUES ('keyword','2005-03-04 11:37:15');
 INSERT INTO prot.AnnotationTypes (Name,EntryDate) VALUES ('feature','2005-03-04 11:37:15');
 INSERT INTO prot.AnnotationTypes (Name,SourceId,EntryDate) VALUES ('GO_C',5,'2005-03-04 11:38:13');
 INSERT INTO prot.AnnotationTypes (Name,EntryDate) VALUES ('FullOrganismName',now());
 INSERT INTO prot.AnnotationTypes (Name,EntryDate) VALUES ('LookupString',now());
+-- @SkipOnEmptySchemasEnd
 
 CREATE INDEX IX_AnnotationTypes_SourceId ON prot.annotationtypes(SourceId);
 
@@ -124,6 +128,7 @@ CREATE TABLE prot.IdentTypes
 CREATE UNIQUE INDEX UQ_ProtIdentTypes ON prot.IdentTypes(Name);
 CREATE INDEX IX_IdentTypes_cannonicalsourceid ON prot.IdentTypes(cannonicalsourceid);
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO prot.IdentTypes (Name,CannonicalSourceId,EntryDate) VALUES ('Genbank',1,'2005-03-04 11:37:14');
 INSERT INTO prot.IdentTypes (Name,CannonicalSourceId,EntryDate) VALUES ('SwissProt',2,'2005-03-04 11:37:14');
 INSERT INTO prot.IdentTypes (Name,CannonicalSourceId,EntryDate) VALUES ('GeneName',3,'2005-03-04 11:37:14');
@@ -193,6 +198,7 @@ INSERT INTO prot.IdentTypes (Name,EntryDate) VALUES ('PhosSite','2005-03-04 12:4
 INSERT INTO prot.IdentTypes (Name,EntryDate) VALUES ('REBASE','2005-03-04 13:25:29');
 INSERT INTO prot.IdentTypes (Name,EntryDate) VALUES ('Maize-2DPAGE','2005-03-04 15:10:53');
 INSERT INTO prot.IdentTypes (Name,EntryDate) VALUES ('HIV','2005-03-04 22:13:40');
+-- @SkipOnEmptySchemasEnd
 
 /****** Organisms                                       */
 CREATE TABLE prot.Organisms
@@ -209,7 +215,9 @@ CREATE TABLE prot.Organisms
 );
 CREATE UNIQUE INDEX UQ_ProtOrganisms_Genus_Species ON prot.Organisms(Genus, Species);
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO prot.Organisms (CommonName,Genus,Species,Comments) VALUES ('Unknown organism','Unknown','unknown','Organism is unknown');
+-- @SkipOnEmptySchemasEnd
 
 CREATE INDEX IX_Organisms_IdentId ON prot.Organisms(IdentId);
 
@@ -497,6 +505,7 @@ CREATE FUNCTION prot.drop_go_indexes() RETURNS void AS $$
     END;
     $$ LANGUAGE plpgsql;
 
+-- @SkipOnEmptySchemasBegin
 -- add most common ncbi Taxonomy id's
 
 CREATE TEMPORARY TABLE idents
@@ -568,6 +577,7 @@ UPDATE prot.Organisms
     WHERE i.OrgId = Organisms.OrgId;
 
 DROP TABLE idents;
+-- @SkipOnEmptySchemasEnd
 
 CREATE TABLE prot.FastaSequences
 (
diff --git a/protein/resources/schemas/dbscripts/postgresql/prot-25.000-25.001.sql b/protein/resources/schemas/dbscripts/postgresql/prot-25.000-25.001.sql
@@ -0,0 +1,8 @@
+-- These columns are unused and, due to data type differences, are problematic for SQL Server -> PostgreSQL migration
+ALTER TABLE prot.InfoSources DROP COLUMN Deleted;
+ALTER TABLE prot.AnnotationTypes DROP COLUMN Deleted;
+ALTER TABLE prot.IdentTypes DROP COLUMN Deleted;
+ALTER TABLE prot.Organisms DROP COLUMN Deleted;
+ALTER TABLE prot.Sequences DROP COLUMN Deleted;
+ALTER TABLE prot.Identifiers DROP COLUMN Deleted;
+ALTER TABLE prot.Annotations DROP COLUMN Deleted;
diff --git a/protein/resources/schemas/dbscripts/sqlserver/prot-25.000-25.001.sql b/protein/resources/schemas/dbscripts/sqlserver/prot-25.000-25.001.sql
@@ -0,0 +1,8 @@
+-- These columns are unused and, due to data type differences, are problematic for SQL Server -> PostgreSQL migration
+EXEC core.fn_dropifexists 'InfoSources', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'AnnotationTypes', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'IdentTypes', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'Organisms', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'Sequences', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'Identifiers', 'prot', 'COLUMN', 'Deleted';
+EXEC core.fn_dropifexists 'Annotations', 'prot', 'COLUMN', 'Deleted';
diff --git a/protein/resources/schemas/dbscripts/sqlserver/prot-25.001-25.002.sql b/protein/resources/schemas/dbscripts/sqlserver/prot-25.001-25.002.sql
@@ -0,0 +1,3 @@
+-- Move foreign key to the correct table. Issue 53523.
+ALTER TABLE prot.Organisms DROP CONSTRAINT FK_ProtSequences_ProtOrganisms;
+ALTER TABLE prot.Sequences ADD CONSTRAINT FK_ProtSequences_ProtOrganisms FOREIGN KEY (OrgId) REFERENCES prot.Organisms (OrgId);
diff --git a/protein/resources/schemas/prot.xml b/protein/resources/schemas/prot.xml
@@ -38,9 +38,6 @@
 			</column>
 			<column columnName="StartPos"/>
 			<column columnName="EndPos"/>
-			<column columnName="Deleted">
-				<isHidden>true</isHidden>
-			</column>
 		</columns>
 	</table>
 	<table tableName="AnnotationTypes" tableDbType="TABLE">
@@ -53,7 +50,6 @@
 			<column columnName="Description"/>
 			<column columnName="EntryDate"/>
 			<column columnName="ModDate"/>
-			<column columnName="Deleted"/>
 		</columns>
 	</table>
 	<table tableName="AnnotInsertions" tableDbType="TABLE">
@@ -135,9 +131,6 @@
 			<column columnName="SourceVersion">
 				<isHidden>true</isHidden>
 			</column>
-			<column columnName="Deleted">
-				<isHidden>true</isHidden>
-			</column>
 		</columns>
 	</table>
 	<table tableName="IdentTypes" tableDbType="TABLE">
@@ -151,9 +144,6 @@
 			</column>
 			<column columnName="EntryDate"/>
 			<column columnName="Description"/>
-			<column columnName="Deleted">
-				<isHidden>true</isHidden>
-			</column>
 		</columns>
 	</table>
 	<table tableName="InfoSources" tableDbType="TABLE">
@@ -169,7 +159,6 @@
 			<column columnName="LastUpdate"/>
 			<column columnName="InsertDate"/>
 			<column columnName="ModDate"/>
-			<column columnName="Deleted"/>
 		</columns>
 	</table>
 	<table tableName="Organisms" tableDbType="TABLE">
@@ -185,9 +174,6 @@
 			<column columnName="IdentId">
 				<isHidden>true</isHidden>
 			</column>
-			<column columnName="Deleted">
-				<isHidden>true</isHidden>
-			</column>
 		</columns>
 	</table>
 	<table tableName="Sequences" tableDbType="TABLE">
@@ -229,9 +215,6 @@
             <column columnName="BestName"/>
 			<column columnName="BestGeneName"/>
 			<column columnName="Length"/>
-			<column columnName="Deleted">
-                <isHidden>true</isHidden>
-            </column>
         </columns>
         <description>Contains a row per protein known to this server installation.</description>
 	</table>
diff --git a/protein/src/org/labkey/protein/ProteinModule.java b/protein/src/org/labkey/protein/ProteinModule.java
@@ -20,9 +20,13 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.files.TableUpdaterFileListener;
+import org.labkey.api.module.DatabaseMigration;
+import org.labkey.api.module.DatabaseMigration.DefaultMigrationHandler;
 import org.labkey.api.module.DefaultModule;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.pipeline.PipelineService;
@@ -62,7 +66,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 25.000;
+        return 25.001;
     }
 
     @Override
@@ -125,6 +129,20 @@ public void doStartup(ModuleContext moduleContext)
         }
 
         ProteinService.get().registerProteinSearchView(new ProteinSearchViewProvider());
+        DatabaseMigration.registerHandler(ProteinSchema.getSchema(), new DefaultMigrationHandler()
+        {
+            @Override
+            public void beforeSchema(DbSchema targetSchema)
+            {
+                new SqlExecutor(targetSchema).execute("ALTER TABLE prot.Organisms DROP CONSTRAINT FK_ProtOrganisms_ProtIdentifiers");
+            }
+
+            @Override
+            public void afterSchema(DbSchema targetSchema)
+            {
+                new SqlExecutor(targetSchema).execute("ALTER TABLE prot.Organisms ADD CONSTRAINT FK_ProtOrganisms_ProtIdentifiers FOREIGN KEY (IdentId) REFERENCES prot.Identifiers (IdentId)");
+            }
+        });
     }
 
     @Override

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+-- Move foreign key to the correct table. Issue 53523.`
	`2`	`+ALTER TABLE prot.Organisms DROP CONSTRAINT FK_ProtSequences_ProtOrganisms;`
	`3`	`+ALTER TABLE prot.Sequences ADD CONSTRAINT FK_ProtSequences_ProtOrganisms FOREIGN KEY (OrgId) REFERENCES prot.Organisms (OrgId);`