Workflow inst data & fix var binding id issues

Author: hvarg

server/src/main/java/org/diskproject/server/api/impl/DiskResource.java

@@ -40,7 +40,6 @@
 import org.diskproject.shared.classes.util.WorkflowTemplateResponse;
 import org.diskproject.shared.classes.vocabulary.Vocabulary;
 import org.diskproject.shared.classes.workflow.WorkflowVariable;
-import org.diskproject.shared.classes.workflow.WorkflowTemplate;
 import org.diskproject.shared.classes.workflow.WorkflowRun;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -174,7 +173,7 @@ public List<TriggeredLOI> queryGoal(
     response.setContentType("application/json");
     response.setCharacterEncoding("utf-8");
     try {
-      return this.repo.queryHypothesis(id);
+      return this.repo.queryGoal(id);
     } catch (NotFoundException e) {
       try {
         ErrorMessage error = new ErrorMessage(e.getMessage());

server/src/main/java/org/diskproject/server/db/DiskDB.java

@@ -6,6 +6,8 @@
 import java.util.Date;
 import java.util.List;
 
+import org.checkerframework.checker.units.qual.t;
+
 import org.diskproject.server.repository.DiskRDF;
 import org.diskproject.server.util.KBCache;
 import org.diskproject.server.util.KBUtils;
@@ -530,7 +532,7 @@ private DataQueryTemplate loadDataQueryTemplate (KBObject objTemplate)  {
     }
 
     private KBObject writeDataQueryResults (DataQueryResult queryResults) {
-        KBObject dq = domainKB.createObjectOfClass(GUID.randomId("dqt"), DISKOnt.getClass(DISK.DATA_QUERY_TEMPLATE));
+        KBObject dq = domainKB.createObjectOfClass(GUID.randomId("dqr"), DISKOnt.getClass(DISK.DATA_QUERY_RESULTS));
         KBObject qr = _writeDataQueryTemplate(queryResults, dq);
         if (queryResults.getQuery() != null)
             domainKB.setPropertyValue(qr, DISKOnt.getProperty(DISK.HAS_QUERY), domainKB.createLiteral(queryResults.getQuery()));
@@ -700,10 +702,10 @@ public List<LineOfInquiry> listLOIPreviews() {
     private KBObject writeWorkflowSeed (WorkflowSeed seed, String parentId) {
         String prefix = parentId != null ? parentId + "/seeds/" : null;
         KBObject seedObj = domainKB.createObjectOfClass(prefix != null ? prefix + GUID.randomId("") : null , DISKOnt.getClass(DISK.WORKFLOW_SEED));
-        return _writeWorkflowSeed(seed, seedObj, parentId);
+        return _writeWorkflowSeed(seed, seedObj);
     }
 
-    private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj, String parentId) {
+    private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj) {
         if (seed.getName() != null)
             domainKB.setLabel(seedObj, seed.getName());
         if (seed.getDescription() != null)
@@ -717,19 +719,19 @@ private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj, String
         if (parameters != null && parameters.size() > 0) {
             for (VariableBinding vBinding: parameters) {
                 domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_PARAMETER), 
-                    writeVariableBinding(vBinding, parentId));
+                    writeVariableBinding(vBinding, seedObj.getID()));
             }
         }
         if (inputs != null && inputs.size() > 0) {
             for (VariableBinding vBinding: inputs) {
                 domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_INPUT), 
-                    writeVariableBinding(vBinding, parentId));
+                    writeVariableBinding(vBinding, seedObj.getID()));
             }
         }
         if (outputs != null && outputs.size() > 0) {
             for (VariableBinding vBinding: outputs) {
                 domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_OUTPUT), 
-                    writeVariableBinding(vBinding, parentId));
+                    writeVariableBinding(vBinding, seedObj.getID()));
             }
         }
         return seedObj;
@@ -775,7 +777,8 @@ private WorkflowSeed loadWorkflowSeed (KBObject seedObj) {
     private KBObject writeWorkflowInstantiation (WorkflowInstantiation inst, String parentId) {
         String prefix = parentId != null ? parentId + "/instantiations/" : null;
         KBObject seedObj = domainKB.createObjectOfClass(prefix != null ? prefix + GUID.randomId("") : null , DISKOnt.getClass(DISK.WORKFLOW_INSTANTIATION));
-        KBObject instObj = _writeWorkflowSeed(inst, seedObj, parentId);
+        KBObject instObj = _writeWorkflowSeed(inst, seedObj);
+        String instId = instObj.getID();
 
         if (inst.getStatus() != null)
             domainKB.setPropertyValue(instObj, DISKOnt.getClass(DISK.HAS_STATUS), domainKB.createLiteral(getStringFromStatus(inst.getStatus())) );
@@ -784,15 +787,15 @@ private KBObject writeWorkflowInstantiation (WorkflowInstantiation inst, String
         if (data != null && data.size() > 0) {
             for (VariableBinding vBinding: data) {
                 domainKB.addPropertyValue(instObj, DISKOnt.getProperty(DISK.HAS_DATA_BINDINGS), 
-                    writeVariableBinding(vBinding, parentId));
+                    writeVariableBinding(vBinding, instId));
             }
         }
 
         List<Execution> execs = inst.getExecutions();
         if (execs != null && execs.size() > 0) {
             for (Execution exec: execs) {
                 domainKB.addPropertyValue(instObj, DISKOnt.getProperty(DISK.HAS_EXECUTION), 
-                    writeExecution(exec, parentId));
+                    writeExecution(exec, instId));
             }
         }
         return instObj;
@@ -1052,7 +1055,6 @@ public boolean writeTLOI(TriggeredLOI tloi) {
         Boolean newTLOI = tloi.getId() == null || tloi.getId().equals("");
         if (newTLOI) tloi.setId(createTloiURI(GUID.randomId("TriggeredLOI")));
         String tloiId = tloi.getId();
-        //if (domainKB == null) return false;
 
         this.rdf.startWrite();
         KBObject tloiItem = writeCommonResource(tloi, tloiId, DISKOnt.getClass(DISK.TRIGGERED_LINE_OF_INQUIRY));
@@ -1112,27 +1114,27 @@ public TriggeredLOI loadTLOI(String id) {
             KBObject status = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_STATUS));
             if (status != null)
                 tloi.setStatus(getStatusFromString(status.getValueAsString()));
-            KBObject queryResult = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_RESULT));
+            KBObject queryResult = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_QUERY_RESULTS));
             if (queryResult != null)
                 tloi.setQueryResults(loadDataQueryResult(queryResult));
 
             List<KBObject> wfInst = domainKB.getPropertyValues(obj, DISKOnt.getProperty(DISK.HAS_WORKFLOW_INST));
             List<KBObject> mwfInst = domainKB.getPropertyValues(obj, DISKOnt.getProperty(DISK.HAS_META_WORKFLOW_INST));
+            List<WorkflowInstantiation> wfList = new ArrayList<WorkflowInstantiation>();
+            List<WorkflowInstantiation> metaWfList = new ArrayList<WorkflowInstantiation>();
 
             if (wfInst != null && wfInst.size() > 0) {
-                List<WorkflowInstantiation> list = new ArrayList<WorkflowInstantiation>();
                 for (KBObject t : wfInst) {
-                    list.add(loadWorkflowInstantiation(t));
+                    wfList.add(loadWorkflowInstantiation(t));
                 }
-                tloi.setWorkflows(list);
             }
             if (mwfInst != null && mwfInst.size() > 0) {
-                List<WorkflowInstantiation> list = new ArrayList<WorkflowInstantiation>();
                 for (KBObject t : mwfInst) {
-                    list.add(loadWorkflowInstantiation(t));
+                    metaWfList.add(loadWorkflowInstantiation(t));
                 }
-                tloi.setMetaWorkflows(list);
             }
+            tloi.setWorkflows(wfList);
+            tloi.setMetaWorkflows(metaWfList);
 
             this.rdf.end();
             return tloi;
@@ -1167,9 +1169,11 @@ public List<TriggeredLOI> listTLOIs() {
         List<String> ids = listObjectIdPerClass(DISKOnt.getClass(DISK.TRIGGERED_LINE_OF_INQUIRY));
         for (String fullId: ids) {
             String id = getLocalId(fullId);
-            list.add(this.loadTLOI(id));
+            TriggeredLOI cur = this.loadTLOI(id);
+            if (cur != null) {
+                list.add(cur);
+            }
         }
-                //TriggeredLOI tloi = loadTLOI(username, tloiId.replaceAll("^.*\\/", ""));
         return list;
     }
 

server/src/main/java/org/diskproject/server/db/DiskOrchestrator.java

@@ -280,7 +280,7 @@ public QuestionVariable LoadQuestionVariableFromKB (KBObject var, KBAPI kb) {
         return null;
     }
 
-    public List<Question> listHypothesesQuestions() {
+    public List<Question> listQuestions() {
         return new ArrayList<Question>(this.allQuestions.values());
     }
 
@@ -356,6 +356,14 @@ private List<VariableOption> queryForOptions (String varName, String query) thro
         return options;
     }
 
+    public Question getQuestion (String id) {
+        return this.allQuestions.get(id);
+    }
+
+    public QuestionVariable getVariable (String id) {
+        return this.allVariables.get(id);
+    }
+
     public String createQuestionOptionsQuery (Question q, List<QuestionVariable> includedVariables) {
         if (q != null) {
             String queryConstraint = q.getConstraint();

server/src/main/java/org/diskproject/server/db/QuestionDB.java

@@ -12,9 +12,12 @@
 import org.diskproject.server.util.ConfigKeys;
 import org.diskproject.shared.classes.adapters.DataAdapter;
 import org.diskproject.shared.classes.common.Endpoint;
+import org.diskproject.shared.classes.loi.DataQueryTemplate;
+import org.diskproject.shared.classes.loi.LineOfInquiry;
 
 public class DataAdapterManager {
     protected Map<String, DataAdapter> byUrl, byName;
+    protected Map<String, DataAdapter> byId;  // By endpoints ID
 
     public DataAdapterManager () {
         this.byUrl = new HashMap<String, DataAdapter>();
@@ -87,10 +90,53 @@ public Collection<DataAdapter> values () {
         return this.byUrl.values();
     }
 
+    /**
+     * Create records for each adapter into the RDF database.
+     * @param db Diskdb where to register the adapters.
+     */
     public void registerAdapters (DiskDB db) {
+        this.byId = new HashMap<String, DataAdapter>();
         for (DataAdapter adp: this.values()) {
             Endpoint cur = db.registerEndpoint(new Endpoint(adp.getName(), adp.getEndpointUrl()));
-            adp.setId(cur.getId());
+            String id = cur.getId();
+            adp.setId(id);
+            this.byId.put(id, adp);
         }
     }
+
+    /**
+     * Finds a data adapter by their endpoint id.
+     * Only works after registerAdapters, as the id is dependent of the database.
+     * @param   id    Id of the endpoint that represents the data adapter.
+     * @return  The data adater with that endpoint id.
+     */
+    public DataAdapter getMethodAdapterById (String id) {
+        if (this.byId != null && this.byId.containsKey(id))
+            return this.byId.get(id);
+        return null;
+    }
+
+    /**
+     * Finds a data adapter by their endpoint.
+     * Only works after registerAdapters, as endpoints are dependent of the database.
+     * @param   endpoint    Endpoint that represents the data adapter.
+     * @return  The data adater for that endpoint.
+     */
+    public DataAdapter getMethodAdapterByEndpoint (Endpoint endpoint) {
+        if (endpoint != null && endpoint.getId() != null)
+            return this.getMethodAdapterById(endpoint.getId());
+        return null;
+    }
+
+    /**
+     * Finds a data adapter by their endpoint.
+     * Only works after registerAdapters, as endpoints are dependent of the database.
+     * @param   endpoint    Endpoint that represents the data adapter.
+     * @return  The data adater for that endpoint.
+     */
+    public DataAdapter getMethodAdapterByLOI (LineOfInquiry loi) {
+        DataQueryTemplate dqt = loi.getDataQueryTemplate();
+        Endpoint e = dqt == null ? null : dqt.getEndpoint();
+        return e == null ? null : getMethodAdapterByEndpoint(e);
+    }
 }

server/src/main/java/org/diskproject/server/managers/DataAdapterManager.java

@@ -20,7 +20,11 @@
 
 public class MethodAdapterManager {
     protected Map<String, MethodAdapter> byUrl, byName;
+    protected Map<String, MethodAdapter> byId;  // By endpoints ID
 
+    /**
+     * Manages and indexes a group of method adapters.
+     */
     public MethodAdapterManager () {
         this.byUrl = new HashMap<String, MethodAdapter>();
         this.byName = new HashMap<String, MethodAdapter>();
@@ -63,6 +67,11 @@ public MethodAdapter getMethodAdapterByUrl (String url) {
         return null;
     }
 
+    /**
+     * Finds a method adapter by its name.
+     * @param   name    Name of the method adapter.
+     * @return  The method adater with that name.
+     */
     public MethodAdapter getMethodAdapterByName (String name) {
         if (this.byName.containsKey(name))
             return this.byName.get(name);
@@ -107,10 +116,41 @@ public String toString () {
         return txt;
     }
 
+    /**
+     * Create records for each adapter into the RDF database.
+     * @param db Diskdb where to register the adapters.
+     */
     public void registerAdapters (DiskDB db) {
+        this.byId = new HashMap<String, MethodAdapter>();
         for (MethodAdapter adp: this.values()) {
             Endpoint cur = db.registerEndpoint(new Endpoint(adp.getName(), adp.getEndpointUrl()));
-            adp.setId(cur.getId());
+            String id = cur.getId();
+            adp.setId(id);
+            byId.put(id, adp);
         }
     }
+
+    /**
+     * Finds a method adapter by their endpoint id.
+     * Only works after registerAdapters, as the id is dependent of the database.
+     * @param   id    Id of the endpoint that represents the method adapter.
+     * @return  The method adater with that endpoint id.
+     */
+    public MethodAdapter getMethodAdapterById (String id) {
+        if (this.byId != null && this.byId.containsKey(id))
+            return this.byId.get(id);
+        return null;
+    }
+
+    /**
+     * Finds a method adapter by their endpoint.
+     * Only works after registerAdapters, as endpoints are dependent of the database.
+     * @param   endpoint    Endpoint that represents the method adapter.
+     * @return  The method adater for that endpoint.
+     */
+    public MethodAdapter getMethodAdapterByEndpoint (Endpoint endpoint) {
+        if (endpoint != null && endpoint.getId() != null)
+            return this.getMethodAdapterById(endpoint.getId());
+        return null;
+    }
 }

server/src/main/java/org/diskproject/server/managers/MethodAdapterManager.java

@@ -106,7 +106,7 @@ private Vocabulary initializeVocabularyFromKB(KBAPI kb, String ns, String prefix
     public String getPrefixes() {
         String txt = "";
         for (Vocabulary v: this.vocabularies.values()) {
-            txt += String.format("PREFIX %s: <%s>\n", v.getNamespace(), v.getPrefix());
+            txt += String.format("PREFIX %s: <%s>\n", v.getPrefix(), v.getNamespace());
         }
         return txt;
     }