Assay: resolve a single provider/protocol before creating protocol schema

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -881,22 +881,37 @@ private Set<String> getPropertyDomains(ExpProtocol protocol)
     }
 
     @Override
-    public List<Pair<Domain, Map<DomainProperty, Object>>> getDomains(ExpProtocol protocol)
+    public @NotNull List<Domain> getDomains(ExpProtocol protocol)
     {
-        List<Pair<Domain, Map<DomainProperty, Object>>> domains = new ArrayList<>();
+        List<Domain> domains = new ArrayList<>();
         for (String uri : getPropertyDomains(protocol))
         {
             Domain domain = PropertyService.get().getDomain(protocol.getContainer(), uri);
             if (domain != null)
-            {
-                Map<DomainProperty, Object> values = DefaultValueService.get().getDefaultValues(domain.getContainer(), domain);
-                domains.add(new Pair<>(domain, values));
-            }
+                domains.add(domain);
         }
-        sortDomainList(domains);
+
+        // Rely on the assay provider to return a list of default domains in the right order (Collections.sort() is
+        // stable so that domains that haven't been inserted and have id 0 stay in the same order), and rely on the fact
+        // that they get inserted in the same order, so they will have ascending ids.
+        domains.sort(Comparator.comparing(Domain::getTypeId));
+
         return domains;
     }
 
+    @Override
+    public @NotNull List<Pair<Domain, Map<DomainProperty, Object>>> getDomainsAndDefaultValues(ExpProtocol protocol)
+    {
+        List<Pair<Domain, Map<DomainProperty, Object>>> domainAndDefaultValues = new ArrayList<>();
+        for (Domain domain : getDomains(protocol))
+        {
+            Map<DomainProperty, Object> values = DefaultValueService.get().getDefaultValues(domain.getContainer(), domain);
+            domainAndDefaultValues.add(Pair.of(domain, values));
+        }
+
+        return domainAndDefaultValues;
+    }
+
     @Override
     public Pair<ExpProtocol, List<Pair<Domain, Map<DomainProperty, Object>>>> getAssayTemplate(User user, Container targetContainer)
     {
@@ -905,14 +920,6 @@ public Pair<ExpProtocol, List<Pair<Domain, Map<DomainProperty, Object>>>> getAss
         return new Pair<>(copy, createDefaultDomains(targetContainer, user));
     }
 
-    protected void sortDomainList(List<Pair<Domain, Map<DomainProperty, Object>>> domains)
-    {
-        // Rely on the assay provider to return a list of default domains in the right order (Collections.sort() is
-        // stable so that domains that haven't been inserted and have id 0 stay in the same order), and rely on the fact
-        // that they get inserted in the same order, so they will have ascending ids.
-        domains.sort(Comparator.comparingInt(pair -> pair.getKey().getTypeId()));
-    }
-
     @Override
     public Pair<ExpProtocol, List<Pair<Domain, Map<DomainProperty, Object>>>> getAssayTemplate(User user, Container targetContainer, ExpProtocol toCopy)
     {
@@ -925,7 +932,7 @@ public Pair<ExpProtocol, List<Pair<Domain, Map<DomainProperty, Object>>>> getAss
         }
         copy.setObjectProperties(copiedProps);
 
-        List<Pair<Domain, Map<DomainProperty, Object>>> originalDomains = getDomains(toCopy);
+        List<Pair<Domain, Map<DomainProperty, Object>>> originalDomains = getDomainsAndDefaultValues(toCopy);
         List<Pair<Domain, Map<DomainProperty, Object>>> copiedDomains = new ArrayList<>(originalDomains.size());
         for (Pair<Domain, Map<DomainProperty, Object>> domainInfo : originalDomains)
         {
@@ -1113,18 +1120,15 @@ public ModelAndView createResultDetailsView(ViewContext context, ExpProtocol pro
     @Override
     public void deleteProtocol(ExpProtocol protocol, User user, @Nullable final String auditUserComment) throws ExperimentException
     {
-        List<Pair<Domain, Map<DomainProperty, Object>>> domainInfos =  getDomains(protocol);
-        List<Domain> domains = new ArrayList<>();
-        for (Pair<Domain, Map<DomainProperty, Object>> domainInfo : domainInfos)
-            domains.add(domainInfo.getKey());
+        List<Domain> domains = getDomains(protocol);
 
         Set<Container> defaultValueContainers = new HashSet<>();
         defaultValueContainers.add(protocol.getContainer());
         defaultValueContainers.addAll(protocol.getExpRunContainers());
         clearDefaultValues(defaultValueContainers, domains);
-        for (Pair<Domain, Map<DomainProperty, Object>> domainInfo : domainInfos)
+
+        for (Domain domain : domains)
         {
-            Domain domain = domainInfo.getKey();
             for (DomainProperty prop : domain.getProperties())
             {
                 prop.delete();
@@ -1537,12 +1541,14 @@ private NavTree getManageMenuNavTree(ViewContext context, ExpProtocol protocol)
     {
         Container protocolContainer = protocol.getContainer();
         Container contextContainer = context.getContainer();
-
         NavTree manageMenu = new NavTree(MANAGE_ASSAY_DESIGN_LINK);
 
+        final AssayUrls assayUrls = Objects.requireNonNull(PageFlowUtil.urlProvider(AssayUrls.class));
+        final ExperimentUrls experimentUrls = Objects.requireNonNull(PageFlowUtil.urlProvider(ExperimentUrls.class));
+
         if (allowUpdate(context, protocol))
         {
-            ActionURL editURL = PageFlowUtil.urlProvider(AssayUrls.class).getDesignerURL(protocolContainer, protocol, false, context.getActionURL());
+            ActionURL editURL = assayUrls.getDesignerURL(protocolContainer, protocol, false, context.getActionURL());
             if (editURL != null)
             {
                 var child = manageMenu.addChild("Edit assay design","");
@@ -1552,32 +1558,30 @@ private NavTree getManageMenuNavTree(ViewContext context, ExpProtocol protocol)
                     child.setScript("if (window.confirm('This assay is defined in the " + protocolContainer.getPath() + " folder. Would you still like to edit it?')) { window.location = " + jsString(editURL.toString()) + "; } return false;");
             }
 
-            ActionURL copyURL = PageFlowUtil.urlProvider(AssayUrls.class).getChooseCopyDestinationURL(protocol, protocolContainer);
+            ActionURL copyURL = assayUrls.getChooseCopyDestinationURL(protocol, protocolContainer);
             if (copyURL != null)
                 manageMenu.addChild("Copy assay design", copyURL.toString());
         }
 
         if (allowDelete(context, protocol))
         {
-            manageMenu.addChild("Delete assay design", PageFlowUtil.urlProvider(ExperimentUrls.class).getDeleteProtocolURL(protocol, PageFlowUtil.urlProvider(AssayUrls.class).getAssayListURL(contextContainer)));
+            manageMenu.addChild("Delete assay design", experimentUrls.getDeleteProtocolURL(protocol, assayUrls.getAssayListURL(contextContainer)));
         }
 
-        ActionURL exportURL = PageFlowUtil.urlProvider(ExperimentUrls.class).getExportProtocolURL(protocolContainer, protocol);
+        ActionURL exportURL = experimentUrls.getExportProtocolURL(protocolContainer, protocol);
         manageMenu.addChild("Export assay design", exportURL.toString());
 
         if (contextContainer.hasPermission(context.getUser(), AdminPermission.class))
         {
-            List<Pair<Domain, Map<DomainProperty, Object>>> domainInfos = getDomains(protocol);
-            if (!domainInfos.isEmpty())
+            List<Domain> domains = getDomains(protocol);
+            if (!domains.isEmpty())
             {
                 NavTree setDefaultsTree = new NavTree(SET_DEFAULT_VALUES_LINK);
-                AssayUrls urls = PageFlowUtil.urlProvider(AssayUrls.class);
-                for (Pair<Domain, Map<DomainProperty, Object>> domainInfo : domainInfos)
+                for (Domain domain : domains)
                 {
-                    Domain domain = domainInfo.getKey();
                     if (allowDefaultValues(domain) && !domain.getProperties().isEmpty())
                     {
-                        ActionURL url = urls.getSetDefaultValuesAssayURL(contextContainer, getName(), domain, context.getActionURL());
+                        ActionURL url = assayUrls.getSetDefaultValuesAssayURL(contextContainer, getName(), domain, context.getActionURL());
                         setDefaultsTree.addChild(domain.getName(), url);
                     }
                 }

api/src/org/labkey/api/assay/AssayDomainService.java

@@ -16,7 +16,6 @@
 
 package org.labkey.api.assay;
 
-import org.labkey.api.gwt.client.assay.AssayException;
 import org.labkey.api.gwt.client.assay.model.GWTProtocol;
 import org.labkey.api.query.ValidationException;
 

api/src/org/labkey/api/assay/AssayProvider.java

@@ -163,7 +163,9 @@ default String getLabel()
 
     List<ParticipantVisitResolverType> getParticipantVisitResolverTypes();
 
-    List<Pair<Domain, Map<DomainProperty, Object>>> getDomains(ExpProtocol protocol);
+    @NotNull List<Domain> getDomains(ExpProtocol protocol);
+
+    @NotNull List<Pair<Domain, Map<DomainProperty, Object>>> getDomainsAndDefaultValues(ExpProtocol protocol);
 
     Pair<ExpProtocol, List<Pair<Domain, Map<DomainProperty, Object>>>> getAssayTemplate(User user, Container targetContainer);
 

api/src/org/labkey/api/assay/AssayService.java

@@ -232,11 +232,6 @@ ParticipantVisitResolver createResolver(User user, ExpRun run, @Nullable ExpProt
      */
     <FlagType extends ExpQCFlag> List<FlagType> getFlags(AssayProvider provider, int runId, Class<FlagType> cls);
 
-    /**
-     * Returns the TableInfo for the given assay domain based on the assay domain ID.
-     */
-    TableInfo getTableInfoForDomainId(User user, Container container, int domainId, @Nullable ContainerFilter cf);
-
     void onBeforeAssayResultDelete(Container container, User user, ExpRun run, Map<String, Object> resultRow);
 
     /**

api/src/org/labkey/api/exp/property/AbstractDomainKind.java

@@ -53,11 +53,6 @@
 import static org.labkey.api.exp.api.ExpData.DATA_INPUTS_PREFIX;
 import static org.labkey.api.exp.api.SampleTypeService.MATERIAL_INPUTS_PREFIX;
 
-/**
- * User: kevink
- * Date: Jun 4, 2010
- * Time: 3:29:46 PM
- */
 public abstract class AbstractDomainKind<T> extends DomainKind<T>
 {
     public static final String OBJECT_URI_COLUMN_NAME = "lsid";
@@ -181,10 +176,8 @@ public boolean hasNullValues(Domain domain, DomainProperty prop)
             long nonBlankRows = new SqlSelector(ExperimentService.get().getSchema(), nonBlankRowsSQL).getRowCount();
             return totalRows != nonBlankRows;
         }
-        else
-        {
-            return false;
-        }
+
+        return false;
     }
 
     protected boolean getTotalAndNonBlankSql(Domain domain, DomainProperty prop, SQLFragment allRowsSQL, SQLFragment nonBlankRowsSQL)
@@ -205,7 +198,8 @@ protected boolean getTotalAndNonBlankSql(Domain domain, DomainProperty prop, SQL
 
             return true;
         }
-        else if (domain.getStorageTableName() != null)
+
+        if (domain.getStorageTableName() != null)
         {
             String table = domain.getStorageTableName();
             allRowsSQL.append("SELECT * FROM " + getStorageSchemaName() + "." + table);
@@ -224,12 +218,11 @@ else if (domain.getStorageTableName() != null)
                 nonBlankRowsSQL.append(mvColumn.getName().toLowerCase());
                 nonBlankRowsSQL.append(" IS NOT NULL");
             }
+
             return true;
         }
-        else
-        {
-            return false;
-        }
+
+        return false;
     }
 
     @Override
@@ -252,7 +245,6 @@ protected DomainTemplate getDomainTemplate(Domain domain)
         return DomainTemplate.findTemplate(domain.getTemplateInfo(), getKindName());
     }
 
-
     @Override
     public Set<String> getNonProvisionedTableNames()
     {
@@ -315,10 +307,17 @@ public boolean exceedsMaxLength(Domain domain, DomainProperty prop)
     }
 
     @Override
+    @Nullable
     public List<String> getDomainNamePreviews(String schemaName, String queryName, Container container, User user)
     {
         String domainURI = PropertyService.get().getDomainURI(schemaName, queryName, container, user);
-        GWTDomain gwtDomain = DomainUtil.getDomainDescriptor(user, domainURI, container, true);
+        if (domainURI == null)
+            return null;
+
+        GWTDomain<?> gwtDomain = DomainUtil.getDomainDescriptor(user, domainURI, container, true);
+        if (gwtDomain == null)
+            return null;
+
         Domain domain = PropertyService.get().getDomain(container, gwtDomain.getDomainURI());
         if (null != domain && null != domain.getDomainKind())
         {

api/src/org/labkey/api/exp/property/DomainKind.java

@@ -53,7 +53,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-abstract public class DomainKind<T>  implements Handler<String>
+abstract public class DomainKind<T> implements Handler<String>
 {
     abstract public String getKindName();
 
@@ -110,6 +110,7 @@ public Map<String, Object> processArguments(Container container, User user, Map<
      * @return set of strings containing the names. This will be compared ignoring case
      */
     abstract public Set<String> getReservedPropertyNames(Domain domain, User user);
+
     public Set<String> getReservedPropertyNames(Domain domain, User user, boolean forCreate)
     {
         return getReservedPropertyNames(domain, user);
@@ -256,19 +257,18 @@ public boolean hasPropertiesIncludeBaseProperties()
 
     /**
      * Default for all domain kinds is to not delete data. Lists and Datasets override this.
-     * @return
      */
     public boolean isDeleteAllDataOnFieldImport()
     {
         return false;
     }
 
-    public TableInfo getTableInfo(User user, Container container, String name, @Nullable ContainerFilter cf)
+    public @Nullable TableInfo getTableInfo(User user, Container container, String name, @Nullable ContainerFilter cf)
     {
         return null;
     }
 
-    public TableInfo getTableInfo(User user, Container container, Domain domain, @Nullable ContainerFilter cf)
+    public @Nullable TableInfo getTableInfo(User user, Container container, Domain domain, @Nullable ContainerFilter cf)
     {
         return getTableInfo(user, container, domain.getName(), cf);
     }
@@ -348,6 +348,7 @@ public DefaultValueType getDefaultDefaultType(Domain domain)
     {
         return DefaultValueType.FIXED_EDITABLE;
     }
+
     public String getObjectUriColumnName()
     {
         return null;
@@ -385,14 +386,11 @@ public NameExpressionValidationResult validateNameExpressions(T options, GWTDoma
     }
 
     /**
-     * @param schemaName
-     * @param queryName
-     * @param container
-     * @param user
-     * @return  Return preview name(s) based on the name expression configured for the designer. For DataClass, up to one preview names is returned.
-     * For samples, up to 2 names can be returned, with the 1st one being the sample preview name and the 2nd being the aliquot preview name.
+     * @return Return preview name(s) based on the name expression configured for the designer. For DataClass,
+     * up to one preview names is returned. For samples, up to 2 names can be returned, with the 1st one being
+     * the sample preview name and the 2nd being the aliquot preview name.
      */
-    public List<String> getDomainNamePreviews(String schemaName, String queryName, Container container, User user)
+    public @Nullable List<String> getDomainNamePreviews(String schemaName, String queryName, Container container, User user)
     {
         return null;
     }