Merge pull request #40 from bimberlabinternal/24.11_fb_species

Convert species table to be container-scoped
bimberlabinternal · Dec 13, 2024 · c0368c5 · c0368c5
2 parents c570a60 + cb8a748
commit c0368c5
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Showing 9 changed files with 71 additions and 12 deletions.
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))