Resolve LabworkTypes in module dependency order to remove need for registerLabworkOverrides (#738)

Author: bbimber

ehr/api-src/org/labkey/api/ehr/EHRService.java

@@ -328,8 +328,6 @@ public EHRQCState getQCState(@NotNull Container c)
     /** The EHR expects certain QC states to exist. This will inspect the current study and create any missing QC states. **/
     abstract public List<String> ensureStudyQCStates(Container c, final User u, final boolean commitChanges);
 
-    abstract public void registerLabWorkOverrides(Module module, String fromType, LabworkType toType);
-
     /**
      * The EHR has a built-in GeneticsCalculations pipeline job that computes inbreeding and kinship based on the pedigree.
      * These are normally calculated in R, saved as TSVs, and imported using java code. This method is a separate entrypoint

ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java

@@ -79,7 +79,7 @@ public class DefaultLabworkType implements LabworkType
     @NotNull
     private final Module _declaringModule;
 
-        public DefaultLabworkType(String name, String schemaName, String queryName, Module declaringModule)
+        public DefaultLabworkType(String name, String schemaName, String queryName, @NotNull Module declaringModule)
     {
         _name = name;
         _schemaName = schemaName;
@@ -118,6 +118,11 @@ public boolean isEnabled(Container c)
         return c.getActiveModules().contains(_declaringModule);
     }
 
+    public Module getDeclaringModule()
+    {
+        return _declaringModule;
+    }
+
     @Override
     public List<String> getResults(Container c, User u, String runId, boolean redacted)
     {

ehr/src/org/labkey/ehr/EHRServiceImpl.java

@@ -113,7 +113,6 @@ public class EHRServiceImpl extends EHRService
     private final List<DemographicsProvider> _demographicsProviders = new ArrayList<>();
     private final Map<REPORT_LINK_TYPE, List<ReportLink>> _reportLinks = new HashMap<>();
     private final MultiValuedMap<String, Pair<Module, Path>> _actionOverrides = new ArrayListValuedHashMap<>();
-    private final Map<String, Pair<Module, LabworkType>> _labWorkOverrides = new HashMap<>();
     private final List<Pair<Module, Resource>> _extraTriggerScripts = new ArrayList<>();
     private final Map<Module, List<Supplier<ClientDependency>>> _clientDependencies = new HashMap<>();
     private final Map<String, Map<String, List<Pair<Module, Class<? extends TableCustomizer>>>>> _tableCustomizers = new CaseInsensitiveHashMap<>();
@@ -1055,16 +1054,6 @@ public void appendSNOMEDCols(AbstractTableInfo ti, String displayColumnName, Str
         }
     }
 
-    public void registerLabWorkOverrides(Module module, String fromType, LabworkType toType)
-    {
-        _labWorkOverrides.put(fromType, Pair.of(module, toType));
-    }
-
-    public Map<String, Pair<Module, LabworkType>> getLabWorkOverrides()
-    {
-        return _labWorkOverrides;
-    }
-
     @Override
     public void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
     {

ehr/src/org/labkey/ehr/history/LabworkManager.java

@@ -28,6 +28,7 @@
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -57,24 +58,20 @@ public void registerType(LabworkType type)
 
     public Collection<LabworkType> getTypes(Container c)
     {
-        List<LabworkType> result = new ArrayList<>(_types.size());
-        Map<String, Pair<Module, LabworkType>> labworkTypeOverrides = EHRServiceImpl.get().getLabWorkOverrides();
+        Map<String, LabworkType> map = new LinkedHashMap<>();
         for (LabworkType type : _types)
         {
+            // NOTE: Because modules initialize in dependency order, they will be registered in order and the code below should allow
+            // center modules to override default EHR labwork types.
+            // Also, if it ever becomes necessary for a center module to simply eliminate a built-in labwork type we could consider making a
+            // NoOpLabworkType. A module could register this to replace a built-in Labwork type with one that doesnt do anything.
             if (type.isEnabled(c))
             {
-                if (labworkTypeOverrides.containsKey(type.getName()))
-                {
-                    Pair<Module, LabworkType> override = labworkTypeOverrides.get(type.getName());
-                    result.add(override.getValue());
-                }
-                else
-                {
-                    result.add(type);
-                }
+                map.put(type.getName(), type);
             }
         }
-        return Collections.unmodifiableCollection(result);
+
+        return Collections.unmodifiableCollection(map.values());
     }
 
     public List<String> getResults(Container c, User u, String runId, boolean redacted)