Merge discvr-24.11 to develop

bbimber · bbimber · commit ea8dbfc486c8 · 2024-12-13T23:28:01.000Z
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.305-12.306.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.305-12.306.sql
@@ -0,0 +1,11 @@
+ALTER TABLE laboratory.species ADD rowid SERIAL;
+ALTER TABLE laboratory.species ADD container entityid;
+ALTER TABLE laboratory.species ADD created timestamp;
+ALTER TABLE laboratory.species ADD createdby int;
+ALTER TABLE laboratory.species ADD modified timestamp;
+ALTER TABLE laboratory.species ADD modifiedby int;
+
+UPDATE laboratory.species SET container = (SELECT entityid FROM core.containers WHERE name = 'Shared');
+
+ALTER TABLE laboratory.species DROP CONSTRAINT PK_species;
+ALTER TABLE laboratory.species ADD CONSTRAINT PK_species PRIMARY KEY (rowid);
diff --git a/laboratory/resources/schemas/dbscripts/sqlserver/laboratory-12.305-12.306.sql b/laboratory/resources/schemas/dbscripts/sqlserver/laboratory-12.305-12.306.sql
@@ -0,0 +1,11 @@
+ALTER TABLE laboratory.species ADD rowid INT identity(1,1);
+ALTER TABLE laboratory.species ADD container entityid;
+ALTER TABLE laboratory.species ADD created datetime;
+ALTER TABLE laboratory.species ADD createdby int;
+ALTER TABLE laboratory.species ADD modified datetime;
+ALTER TABLE laboratory.species ADD modifiedby int;
+GO
+UPDATE laboratory.species SET container = (SELECT entityid FROM core.containers WHERE name = 'Shared');
+
+ALTER TABLE laboratory.species DROP CONSTRAINT PK_species;
+ALTER TABLE laboratory.species ADD CONSTRAINT PK_species PRIMARY KEY (rowid);
diff --git a/laboratory/resources/schemas/laboratory.xml b/laboratory/resources/schemas/laboratory.xml
@@ -841,6 +841,9 @@
         <javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
         <auditLogging>DETAILED</auditLogging>
         <columns>
+            <column columnName="rowid">
+                <isHidden>true</isHidden>
+            </column>
             <column columnName="common_name">
             </column>
             <column columnName="scientific_name">
@@ -850,6 +853,29 @@
                 <nullable>true</nullable>
                 <columnTitle>MHC Prefix</columnTitle>
             </column>
+            <column columnName="container">
+                <isHidden>false</isHidden>
+            </column>
+            <column columnName="createdby">
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="created">
+                <isUserEditable>false</isUserEditable>
+                <shownInInsertView>false</shownInInsertView>
+                <shownInUpdateView>false</shownInUpdateView>
+                <nullable>true</nullable>
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="modifiedby">
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="modified">
+                <isUserEditable>false</isUserEditable>
+                <shownInInsertView>false</shownInInsertView>
+                <shownInUpdateView>false</shownInUpdateView>
+                <nullable>true</nullable>
+                <isHidden>true</isHidden>
+            </column>
         </columns>
     </table>
     <table tableName="geographic_origins" tableDbType="TABLE" useColumnOrder="true">
diff --git a/laboratory/resources/views/populateInitialValues.html b/laboratory/resources/views/populateInitialValues.html
@@ -13,7 +13,7 @@
                     LABKEY.Ajax.request({
                         url : LABKEY.ActionURL.buildURL('laboratory', 'populateDefaults'),
                         params: {
-                            tableNames: ['sample_type']
+                            tableNames: ['sample_type', 'species']
                         },
                         method : 'POST',
                         scope: this,
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java b/laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java
@@ -63,7 +63,7 @@ public void containerCreated(Container c, User user)
         {
             try
             {
-                LaboratoryManager.get().populateDefaultData(user, c, null);
+                LaboratoryManager.get().populateDefaultData(user, c);
             }
             catch (IllegalArgumentException e)
             {
@@ -208,7 +208,7 @@ private void possiblyInitializeOnActiveModuleChange(PropertyChangeEvent evt)
 
             try
             {
-                LaboratoryManager.get().populateDefaultData(u, ce.container, null);
+                LaboratoryManager.get().populateDefaultData(u, ce.container);
             }
             catch (Exception e)
             {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryManager.java b/laboratory/src/org/labkey/laboratory/LaboratoryManager.java
@@ -18,6 +18,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
@@ -336,26 +337,33 @@ public void updateWorkbookTags(User u, Container c, Collection<String> tags, boo
         }
     }
 
+    public void populateDefaultData(User u, Container c)
+    {
+        populateDefaultData(u, c, Arrays.asList(LaboratorySchema.TABLE_SAMPLE_TYPE, LaboratorySchema.TABLE_SPECIES));
+    }
+
     //pass null to populate all supported tables
-    public void populateDefaultData(User u, Container c, @Nullable List<String> tableNames)
+    public void populateDefaultData(User u, Container c, @NotNull List<String> tableNames)
     {
         if (c.isWorkbook())
         {
             return;
         }
 
-        if (tableNames == null)
-        {
-            tableNames = new ArrayList<>();
-            tableNames.add(LaboratorySchema.TABLE_SAMPLE_TYPE);
-        }
-
         for (String name : tableNames)
         {
-            if (LaboratorySchema.TABLE_SAMPLE_TYPE.equalsIgnoreCase(name))
+            if (LaboratorySchema.TABLE_SAMPLE_TYPE.equalsIgnoreCase(name) )
             {
                 populateDefaultDataForTable(u, c, "laboratory", LaboratorySchema.TABLE_SAMPLE_TYPE, PageFlowUtil.set("type"), "type");
             }
+            else if (LaboratorySchema.TABLE_SPECIES.equalsIgnoreCase(name) )
+            {
+                populateDefaultDataForTable(u, c, "laboratory", LaboratorySchema.TABLE_SPECIES, PageFlowUtil.set("common_name", "scientific_name", "mhc_prefix"), "common_name");
+            }
+            else
+            {
+                throw new IllegalArgumentException("Unknown table: " + name);
+            }
         }
     }
 
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryModule.java b/laboratory/src/org/labkey/laboratory/LaboratoryModule.java
@@ -76,7 +76,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 12.305;
+        return 12.306;
     }
 
     @Override
diff --git a/laboratory/src/org/labkey/laboratory/LaboratorySchema.java b/laboratory/src/org/labkey/laboratory/LaboratorySchema.java
@@ -38,6 +38,7 @@ public class LaboratorySchema
     public static final String TABLE_WORKBOOKS = "workbooks";
     public static final String TABLE_WORKBOOK_TAGS = "workbook_tags";
     public static final String TABLE_ASSAY_RUN_TEMPLATES = "assay_run_templates";
+    public static final String TABLE_SPECIES = "species";
 
     public static LaboratorySchema getInstance()
     {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryUserSchema.java b/laboratory/src/org/labkey/laboratory/LaboratoryUserSchema.java
@@ -49,6 +49,8 @@ protected TableInfo createWrappedTable(String name, @NotNull TableInfo sourceTab
             return getSubjectsTable(name, sourceTable, cf);
         else if (LaboratorySchema.TABLE_FREEZERS.equalsIgnoreCase(name))
             return getContainerScopedTable(name, sourceTable, cf, "name");
+        else if (LaboratorySchema.TABLE_SPECIES.equalsIgnoreCase(name))
+            return getContainerScopedTable(name, sourceTable, cf, "common_name");
         else if (LaboratorySchema.TABLE_SAMPLE_TYPE.equalsIgnoreCase(name))
             return getContainerScopedTable(name, sourceTable, cf, "type");
         else if (LaboratorySchema.TABLE_DNA_OLIGOS.equalsIgnoreCase(name))

Original file line number	Diff line number	Diff line change
`@@ -63,7 +63,7 @@ public void containerCreated(Container c, User user)`
`63`	`63`	`{`
`64`	`64`	`try`
`65`	`65`	`{`
`66`		`- LaboratoryManager.get().populateDefaultData(user, c, null);`
	`66`	`+ LaboratoryManager.get().populateDefaultData(user, c);`
`67`	`67`	`}`
`68`	`68`	`catch (IllegalArgumentException e)`
`69`	`69`	`{`
`@@ -208,7 +208,7 @@ private void possiblyInitializeOnActiveModuleChange(PropertyChangeEvent evt)`
`208`	`208`
`209`	`209`	`try`
`210`	`210`	`{`
`211`		`- LaboratoryManager.get().populateDefaultData(u, ce.container, null);`
	`211`	`+ LaboratoryManager.get().populateDefaultData(u, ce.container);`
`212`	`212`	`}`
`213`	`213`	`catch (Exception e)`
`214`	`214`	`{`
Original file line number	Diff line number	Diff line change
`@@ -18,6 +18,7 @@`
`18`	`18`	`import org.apache.commons.lang3.StringUtils;`
`19`	`19`	`import org.apache.logging.log4j.Logger;`
`20`	`20`	`import org.apache.logging.log4j.LogManager;`
	`21`	`+import org.jetbrains.annotations.NotNull;`
`21`	`22`	`import org.jetbrains.annotations.Nullable;`
`22`	`23`	`import org.labkey.api.assay.AssayProvider;`
`23`	`24`	`import org.labkey.api.assay.AssayService;`
`@@ -336,26 +337,33 @@ public void updateWorkbookTags(User u, Container c, Collection<String> tags, boo`
`336`	`337`	`}`
`337`	`338`	`}`
`338`	`339`
	`340`	`+ public void populateDefaultData(User u, Container c)`
	`341`	`+ {`
	`342`	`+ populateDefaultData(u, c, Arrays.asList(LaboratorySchema.TABLE_SAMPLE_TYPE, LaboratorySchema.TABLE_SPECIES));`
	`343`	`+ }`
	`344`	`+`
`339`	`345`	`//pass null to populate all supported tables`
`340`		`- public void populateDefaultData(User u, Container c, @Nullable List<String> tableNames)`
	`346`	`+ public void populateDefaultData(User u, Container c, @NotNull List<String> tableNames)`
`341`	`347`	`{`
`342`	`348`	`if (c.isWorkbook())`
`343`	`349`	`{`
`344`	`350`	`return;`
`345`	`351`	`}`
`346`	`352`
`347`		`- if (tableNames == null)`
`348`		`- {`
`349`		`- tableNames = new ArrayList<>();`
`350`		`- tableNames.add(LaboratorySchema.TABLE_SAMPLE_TYPE);`
`351`		`- }`
`352`		`-`
`353`	`353`	`for (String name : tableNames)`
`354`	`354`	`{`
`355`		`- if (LaboratorySchema.TABLE_SAMPLE_TYPE.equalsIgnoreCase(name))`
	`355`	`+ if (LaboratorySchema.TABLE_SAMPLE_TYPE.equalsIgnoreCase(name) )`
`356`	`356`	`{`
`357`	`357`	`populateDefaultDataForTable(u, c, "laboratory", LaboratorySchema.TABLE_SAMPLE_TYPE, PageFlowUtil.set("type"), "type");`
`358`	`358`	`}`
	`359`	`+ else if (LaboratorySchema.TABLE_SPECIES.equalsIgnoreCase(name) )`
	`360`	`+ {`
	`361`	`+ populateDefaultDataForTable(u, c, "laboratory", LaboratorySchema.TABLE_SPECIES, PageFlowUtil.set("common_name", "scientific_name", "mhc_prefix"), "common_name");`
	`362`	`+ }`
	`363`	`+ else`
	`364`	`+ {`
	`365`	`+ throw new IllegalArgumentException("Unknown table: " + name);`
	`366`	`+ }`
`359`	`367`	`}`
`360`	`368`	`}`
`361`	`369`
Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,7 @@ public String getName()`
`76`	`76`	`@Override`
`77`	`77`	`public @Nullable Double getSchemaVersion()`
`78`	`78`	`{`
`79`		`- return 12.305;`
	`79`	`+ return 12.306;`
`80`	`80`	`}`
`81`	`81`
`82`	`82`	`@Override`
Original file line number	Diff line number	Diff line change
`@@ -38,6 +38,7 @@ public class LaboratorySchema`
`38`	`38`	`public static final String TABLE_WORKBOOKS = "workbooks";`
`39`	`39`	`public static final String TABLE_WORKBOOK_TAGS = "workbook_tags";`
`40`	`40`	`public static final String TABLE_ASSAY_RUN_TEMPLATES = "assay_run_templates";`
	`41`	`+ public static final String TABLE_SPECIES = "species";`
`41`	`42`
`42`	`43`	`public static LaboratorySchema getInstance()`
`43`	`44`	`{`