Fb 7140 sample set to sample type (#35)

Author: labkey-adam

laboratory/resources/web/laboratory/utils.js

@@ -13,8 +13,8 @@ Laboratory.Utils = new function(){
         },
 
         /**
-         * The purpose of this helper is to provide a listing of all items to display in the laboratory module navigation pages.  It draws from
-         * assays, sample sets, and other other NavItems that have been registered with LaboratoryService.
+         * The purpose of this helper is to provide a listing of all items to display in the laboratory module navigation pages. It draws from
+         * assays, sample types, and other other NavItems that have been registered with LaboratoryService.
          * @param [config.types] Optional.
          * @param [config.includeHidden] Optional. If true, non-visible items will be included.
          * @param config.success Success callback.  Will be passed a single object as an argument with the following properties

laboratory/src/org/labkey/laboratory/LaboratoryModule.java

@@ -156,7 +156,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         RoleManager.registerRole(new LaboratoryAdminRole());
 
         LaboratoryService.get().registerDataProvider(new LaboratoryDataProvider(this));
-        LaboratoryService.get().registerDataProvider(new SampleSetDataProvider());
+        LaboratoryService.get().registerDataProvider(new SampleTypeDataProvider());
         LaboratoryService.get().registerDataProvider(new ExtraDataSourcesDataProvider(this));
 
         DetailsURL details = DetailsURL.fromString("/laboratory/siteLabSettings.view");

…ey/laboratory/SampleSetDataProvider.java …y/laboratory/SampleTypeDataProvider.javalaboratory/src/org/labkey/laboratory/SampleSetDataProvider.java renamed to laboratory/src/org/labkey/laboratory/SampleTypeDataProvider.java laboratory/src/org/labkey/laboratory/SampleSetDataProvider.java renamed to laboratory/src/org/labkey/laboratory/SampleTypeDataProvider.java

@@ -21,8 +21,8 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
-import org.labkey.api.exp.api.ExpSampleSet;
-import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.exp.api.ExpSampleType;
+import org.labkey.api.exp.api.SampleTypeService;
 import org.labkey.api.laboratory.AbstractDataProvider;
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.laboratory.QueryCountNavItem;
@@ -47,13 +47,12 @@
  * Date: 10/8/12
  * Time: 9:06 AM
  */
-public class SampleSetDataProvider extends AbstractDataProvider
+public class SampleTypeDataProvider extends AbstractDataProvider
 {
-    public static final String NAME = "SampleSetDataProvider";
+    public static final String NAME = "SampleTypeDataProvider";
 
-    public SampleSetDataProvider()
+    public SampleTypeDataProvider()
     {
-
     }
 
     @Override
@@ -77,12 +76,12 @@ public List<NavItem> getDataNavItems(Container c, User u)
     @Override
     public List<NavItem> getSampleNavItems(Container c, User u)
     {
-        //also append all sample sets in this container
+        //also append all sample types in this container
         List<NavItem> navItems = new ArrayList<NavItem>();
 
-        for (ExpSampleSet ss : ExperimentService.get().getSampleSets(c, u, true))
+        for (ExpSampleType st : SampleTypeService.get().getSampleTypes(c, u, true))
         {
-            navItems.add(new SampleSetNavItem(this, LaboratoryService.NavItemCategory.samples, ss));
+            navItems.add(new SampleTypeNavItem(this, LaboratoryService.NavItemCategory.samples, st));
         }
         return navItems;
     }
@@ -116,12 +115,12 @@ public Module getOwningModule()
     public List<SummaryNavItem> getSummary(Container c, User u)
     {
         List<SummaryNavItem> items = new ArrayList<>();
-        for (ExpSampleSet ss : ExperimentService.get().getSampleSets(c, u, true))
+        for (ExpSampleType st : SampleTypeService.get().getSampleTypes(c, u, true))
         {
-            SampleSetNavItem nav = new SampleSetNavItem(this, LaboratoryService.NavItemCategory.samples, ss);
+            SampleTypeNavItem nav = new SampleTypeNavItem(this, LaboratoryService.NavItemCategory.samples, st);
             if (nav.isVisible(c, u))
             {
-                items.add(new QueryCountNavItem(this, "Samples", ss.getName(), LaboratoryService.NavItemCategory.samples, "Samples", ss.getName()));
+                items.add(new QueryCountNavItem(this, "Samples", st.getName(), LaboratoryService.NavItemCategory.samples, "Samples", st.getName()));
             }
         }
 
@@ -132,18 +131,18 @@ public List<SummaryNavItem> getSummary(Container c, User u)
     public List<NavItem> getSubjectIdSummary(Container c, User u, String subjectId)
     {
         List<NavItem> items = new ArrayList<NavItem>();
-        for (ExpSampleSet ss : ExperimentService.get().getSampleSets(c, u, true))
+        for (ExpSampleType st : SampleTypeService.get().getSampleTypes(c, u, true))
         {
             UserSchema us = QueryService.get().getUserSchema(u, c, "Samples");
             if (us != null)
             {
-                TableInfo ti = us.getTable(ss.getName());
+                TableInfo ti = us.getTable(st.getName());
                 if (ti != null)
                 {
                     ColumnInfo ci = getSubjectColumn(ti);
                     if (ci != null)
                     {
-                        QueryCountNavItem qc = new QueryCountNavItem(this, "Samples", ss.getName(), LaboratoryService.NavItemCategory.samples, "Samples", ss.getName());
+                        QueryCountNavItem qc = new QueryCountNavItem(this, "Samples", st.getName(), LaboratoryService.NavItemCategory.samples, "Samples", st.getName());
                         qc.setFilter(new SimpleFilter(FieldKey.fromString(ci.getName()), subjectId));
                         items.add(qc);
                     }

…/labkey/laboratory/SampleSetNavItem.java …labkey/laboratory/SampleTypeNavItem.javalaboratory/src/org/labkey/laboratory/SampleSetNavItem.java renamed to laboratory/src/org/labkey/laboratory/SampleTypeNavItem.java laboratory/src/org/labkey/laboratory/SampleSetNavItem.java renamed to laboratory/src/org/labkey/laboratory/SampleTypeNavItem.java

@@ -16,7 +16,7 @@
 package org.labkey.laboratory;
 
 import org.labkey.api.data.Container;
-import org.labkey.api.exp.api.ExpSampleSet;
+import org.labkey.api.exp.api.ExpSampleType;
 import org.labkey.api.exp.api.ExperimentUrls;
 import org.labkey.api.exp.query.SamplesSchema;
 import org.labkey.api.laboratory.AbstractImportingNavItem;
@@ -35,14 +35,14 @@
  * Date: 10/1/12
  * Time: 8:51 AM
  */
-public class SampleSetNavItem extends AbstractImportingNavItem
+public class SampleTypeNavItem extends AbstractImportingNavItem
 {
-    private ExpSampleSet _sampleSet;
+    private final ExpSampleType _sampleType;
 
-    public SampleSetNavItem(DataProvider provider, LaboratoryService.NavItemCategory itemType, ExpSampleSet sampleSet)
+    public SampleTypeNavItem(DataProvider provider, LaboratoryService.NavItemCategory itemType, ExpSampleType sampleType)
     {
-        super(provider, sampleSet.getName(), sampleSet.getName(), itemType, LaboratoryService.NavItemCategory.samples.name());
-        _sampleSet = sampleSet;
+        super(provider, sampleType.getName(), sampleType.getName(), itemType, LaboratoryService.NavItemCategory.samples.name());
+        _sampleType = sampleType;
     }
 
     @Override
@@ -56,7 +56,7 @@ public boolean getDefaultVisibility(Container c, User u)
     {
         //by default, only show if defined in current container
         Container toCompare = c.isWorkbook() ? c.getParent() : c;
-        return _sampleSet.getContainer().equals(toCompare);
+        return _sampleType.getContainer().equals(toCompare);
     }
 
     @Override
@@ -65,19 +65,19 @@ public ActionURL getImportUrl(Container c, User u)
         if (!c.hasPermission(u, InsertPermission.class))
             return null;
 
-        ActionURL url = PageFlowUtil.urlProvider(ExperimentUrls.class).getImportSamplesURL(c, _sampleSet.getName());
+        ActionURL url = PageFlowUtil.urlProvider(ExperimentUrls.class).getImportSamplesURL(c, _sampleType.getName());
         return url;
     }
 
     @Override
     public ActionURL getSearchUrl(Container c, User u)
     {
-        return PageFlowUtil.urlProvider(LaboratoryUrls.class).getSearchUrl(c, SamplesSchema.SCHEMA_NAME, _sampleSet.getName());
+        return PageFlowUtil.urlProvider(LaboratoryUrls.class).getSearchUrl(c, SamplesSchema.SCHEMA_NAME, _sampleType.getName());
     }
 
     @Override
     public ActionURL getBrowseUrl(Container c, User u)
     {
-        return QueryService.get().urlFor(u, c, QueryAction.executeQuery, SamplesSchema.SCHEMA_NAME, _sampleSet.getName());
+        return QueryService.get().urlFor(u, c, QueryAction.executeQuery, SamplesSchema.SCHEMA_NAME, _sampleType.getName());
     }
 }