Merge pull request #104 from VEuPathDB/platform-excludes

Add ability to include/exclude sql queries based on DB platform of the App DB

Model/lib/rng/wdkModel.rng

@@ -83,6 +83,16 @@
     </optional>
   </define>
 
+  <!-- define inclusion/exclusion attributes for DB platform -->
+  <define name="DbPlatformIncludeExclude">
+    <optional>
+      <attribute name="includeDbPlatforms" />
+    </optional>
+    <optional>
+      <attribute name="excludeDbPlatforms" />
+    </optional>
+  </define>
+
   <!-- define constants -->
   <define name="constant">
     <element name="constant">
@@ -1105,6 +1115,7 @@
   <define name="sqlQuery">
     <element name="sqlQuery">
       <ref name="QueryBaseContents" />
+      <ref name="DbPlatformIncludeExclude" />
       <optional>
         <attribute name="attributeMetaQueryRef" />
       </optional>

Model/src/main/java/org/gusdb/wdk/model/WdkModel.java

@@ -903,7 +903,7 @@ private void excludeResources() throws WdkModelException {
     // remove query sets
     for (QuerySet querySet : querySetList) {
       if (querySet.include(_projectId)) {
-        querySet.excludeResources(_projectId);
+        querySet.excludeResources(_projectId, _modelConfig.getAppDB().getPlatformEnum());
         addSet(querySet, querySets);
       }
     }
@@ -1041,7 +1041,7 @@ private void createInternalSets() throws WdkModelException {
       internalQuerySet.setName(Utilities.INTERNAL_QUERY_SET);
       internalQuerySet.setDoNotTest(true);
       addQuerySet(internalQuerySet);
-      internalQuerySet.excludeResources(_projectId);
+      internalQuerySet.excludeResources(_projectId, _modelConfig.getAppDB().getPlatformEnum());
     }
 
     // create a query set to hold all internal questions, that is, the

Model/src/main/java/org/gusdb/wdk/model/WdkModelBase.java

@@ -2,13 +2,16 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.log4j.Logger;
+import org.gusdb.fgputil.db.platform.SupportedPlatform;
 import org.gusdb.wdk.model.RngAnnotations.RngUndefined;
 
 /**
@@ -40,12 +43,17 @@ public abstract class WdkModelBase {
   private Set<String> _includeProjects;
   private Set<String> _excludeProjects;
 
+  private Set<SupportedPlatform> _includeDbPlatforms;
+  private Set<SupportedPlatform> _excludeDbPlatforms;
+
   private List<PropertyList> _propertyLists;
   private Map<String, String[]> _propertyListMap;
 
   public WdkModelBase() {
     _includeProjects = new LinkedHashSet<>();
     _excludeProjects = new LinkedHashSet<>();
+    _includeDbPlatforms = new LinkedHashSet<>();
+    _excludeDbPlatforms = new LinkedHashSet<>();
     _propertyLists = new ArrayList<>();
     _propertyListMap = new LinkedHashMap<>();
   }
@@ -55,6 +63,8 @@ public WdkModelBase(WdkModelBase base) {
     _resolved = base._resolved;
     _includeProjects = new LinkedHashSet<>(base._includeProjects);
     _excludeProjects = new LinkedHashSet<>(base._excludeProjects);
+    _includeDbPlatforms = new LinkedHashSet<>(base._includeDbPlatforms);
+    _excludeDbPlatforms = new LinkedHashSet<>(base._excludeDbPlatforms);
     if (base._propertyLists != null)
       _propertyLists = new ArrayList<>(base._propertyLists);
     if (base._propertyListMap != null)
@@ -78,14 +88,7 @@ public WdkModelBase clone() {
    */
   @RngUndefined
   public void setExcludeProjects(String excludeProjects) {
-    excludeProjects = excludeProjects.trim();
-    if (excludeProjects.isEmpty())
-      return;
-
-    String[] projects = excludeProjects.split(",");
-    for (String project : projects) {
-      _excludeProjects.add(project.trim());
-    }
+    _excludeProjects.addAll(parseCommaDelimitedValues(excludeProjects));
   }
 
   /**
@@ -94,14 +97,42 @@ public void setExcludeProjects(String excludeProjects) {
    */
   @RngUndefined
   public void setIncludeProjects(String includeProjects) {
-    includeProjects = includeProjects.trim();
-    if (includeProjects.isEmpty())
-      return;
+    _includeProjects.addAll(parseCommaDelimitedValues(includeProjects));
+  }
 
-    String[] projects = includeProjects.split(",");
-    for (String project : projects) {
-      _includeProjects.add(project.trim());
+  /**
+   * @param excludeDbPlatforms
+   *          the excludeDbPlatforms to set
+   */
+  @RngUndefined
+  public void setExcludeDbPlatforms(String excludeDbPlatforms) {
+    _excludeDbPlatforms.addAll(
+        parseCommaDelimitedValues(excludeDbPlatforms)
+        .stream().map(SupportedPlatform::toPlatform).collect(Collectors.toSet()));
+  }
+
+  /**
+   * @param includeDbPlatforms
+   *          the includeDbPlatforms to set
+   */
+  @RngUndefined
+  public void setIncludeDbPlatforms(String includeDbPlatforms) {
+    _includeDbPlatforms.addAll(
+        parseCommaDelimitedValues(includeDbPlatforms)
+        .stream().map(SupportedPlatform::toPlatform).collect(Collectors.toSet()));
+  }
+
+  private Set<String> parseCommaDelimitedValues(String unparsedList) {
+    unparsedList = unparsedList.trim();
+    if (unparsedList.isEmpty())
+      return Collections.emptySet();
+
+    String[] rawValues = unparsedList.split(",");
+    Set<String> values = new LinkedHashSet<>();
+    for (String value : rawValues) {
+      values.add(value.trim());
     }
+    return values;
   }
 
   /**
@@ -115,6 +146,17 @@ public boolean include(String projectId) {
     }
   }
 
+  /**
+   * @return true if the object is included in the current AppDB platform
+   */
+  public boolean include(SupportedPlatform dbPlatform) {
+    if (_includeDbPlatforms.isEmpty()) { // no inclusions assigned
+      return !_excludeDbPlatforms.contains(dbPlatform);
+    } else { // has inclusions
+      return _includeDbPlatforms.contains(dbPlatform);
+    }
+  }
+
   /**
    * @return the resolved
    */

Model/src/main/java/org/gusdb/wdk/model/WdkModelException.java

@@ -33,6 +33,8 @@ public static WdkModelException translateFrom(Exception e) {
   }
 
   public static WdkModelException translateFrom(Exception e, String newMessage) {
+    // if passed message is null, use name of original exception
+    if (newMessage == null) newMessage = e.getClass().getSimpleName();
     // if exception is already a WdkModelException, simply return
     if (e instanceof WdkModelException) return (WdkModelException)e;
     // check underlying exception; a WdkModelException may simply have been wrapped

Model/src/main/java/org/gusdb/wdk/model/query/QuerySet.java

@@ -8,6 +8,7 @@
 import java.util.stream.Collectors;
 
 import org.apache.log4j.Logger;
+import org.gusdb.fgputil.db.platform.SupportedPlatform;
 import org.gusdb.wdk.model.ModelSetI;
 import org.gusdb.wdk.model.Utilities;
 import org.gusdb.wdk.model.WdkModel;
@@ -215,10 +216,14 @@ public String toString() {
   }
 
   @Override
-  public void excludeResources(String projectId) throws WdkModelException {
+  public void excludeResources(String projectId) {
+    throw new UnsupportedOperationException("QuerySet excludes must be handled by excludeResources(projectId,supportedPlatform");
+  }
+
+  public void excludeResources(String projectId, SupportedPlatform supportedPlatform) throws WdkModelException {
     // exclude queries
     for (Query query : _queryList) {
-      if (query.include(projectId)) {
+      if (query.include(projectId) && query.include(supportedPlatform)) {
         query.excludeResources(projectId);
         String queryName = query.getName();
         if (_queries.containsKey(queryName))