Merge pull request #7 from nicolasmoreau/master

Guided query interface

portal.ejb/src/main/java/org/vamdc/portal/RedirectPage.java

@@ -2,6 +2,7 @@
 
 public class RedirectPage {
 	public static final String QUERY="query";
+	public static final String QUERYTREE="queryTree";
 	public static final String PREVIEW="preview";
 	public static final String QUERY_LOG="queryLog";
 	public static final String SPECIES="species";

portal.ejb/src/main/java/org/vamdc/portal/session/preview/PersistableQueryInterface.java

@@ -0,0 +1,16 @@
+package org.vamdc.portal.session.preview;
+
+import java.util.List;
+
+import org.vamdc.portal.entity.query.HttpHeadResponse;
+import org.vamdc.portal.entity.security.User;
+import org.vamdc.portal.session.queryBuilder.FormHolder;
+import org.vamdc.portal.session.queryBuilder.QueryData;
+import org.vamdc.portal.session.queryLog.QueryLog;
+
+public interface PersistableQueryInterface {
+	public List<HttpHeadResponse> getNodesResponse();
+	public User getUser();
+	public QueryLog getQueryLog();
+	public QueryData getQueryData();
+}

portal.ejb/src/main/java/org/vamdc/portal/session/preview/PreviewManager.java

@@ -48,6 +48,7 @@ public class PreviewManager implements Serializable{
 	private long startTime;
 
 	public void initiate(){
+
 		if (nodeFutureResponses.size()>0)
 			return;
 
@@ -153,7 +154,10 @@ public void clear(){
 
 	public String refine(){
 		clear();
-		return RedirectPage.QUERY;
+		if(!queryData.isGuidedQuery())
+			return RedirectPage.QUERY;
+		else
+			return RedirectPage.QUERYTREE;
 	}
 
 	/**

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/QueryController.java

@@ -17,8 +17,9 @@
 import org.jboss.seam.log.Log;
 import org.vamdc.portal.RedirectPage;
 import org.vamdc.portal.entity.query.HttpHeadResponse;
-import org.vamdc.portal.entity.query.HttpHeadResponse.Response;
 import org.vamdc.portal.entity.query.Query;
+import org.vamdc.portal.entity.security.User;
+import org.vamdc.portal.session.preview.PersistableQueryInterface;
 import org.vamdc.portal.session.preview.PreviewManager;
 import org.vamdc.portal.session.queryBuilder.forms.AtomsForm;
 import org.vamdc.portal.session.queryBuilder.forms.BranchesForm;
@@ -40,7 +41,7 @@
  */
 @Name("query")
 @Scope(ScopeType.EVENT)
-public class QueryController {
+public class QueryController implements PersistableQueryInterface{
 
 	@Logger
 	Log log;
@@ -60,11 +61,8 @@ public class QueryController {
 
 	@End
 	public String saveQuery(){
-
 		if (queryData.isValid()){
-			persistQuery();
-
-
+			persistQuery();			
 			conversation.endAndRedirect();
 			log.info("Save action");
 			return RedirectPage.QUERY_LOG;
@@ -75,11 +73,12 @@ public String saveQuery(){
 	}
 
 	private void persistQuery() {
-		Query query = constructQuery();
+		QueryPersister p = new QueryPersister(this);		
+		Query query = p.constructQuery();//constructQuery();
 		queryLog.save(query,queryData.getEditQueryId());
 	}
 
-	private Query constructQuery(){
+	/*private Query constructQuery(){
 		Query result=null;
 		if (queryData.getEditQueryId()!=null)
 			result = queryLog.getQuery(queryData.getEditQueryId());
@@ -103,16 +102,17 @@ private List<HttpHeadResponse> selectRespondedNodes() {
 				responses.add(response);
 		}
 		return responses;
-	}
+	}*/
 
 
 
 	public String preview(){
 
 		if (queryData.isValid()){
 			return RedirectPage.PREVIEW;
-		}else 
+		}else{
 			return RedirectPage.QUERY;
+		}
 	}
 
 	public String edit(String queryID){
@@ -168,5 +168,24 @@ public void addFormUtil(){
 		queryData.addForm(new UtilForm());
 	}
 
+	@Override
+	public List<HttpHeadResponse> getNodesResponse() {
+		return preview.getNodes();
+	}
+
+	@Override
+	public User getUser() {
+		return auth.getUser();
+	}
+
+	@Override
+	public QueryLog getQueryLog(){
+		return this.queryLog;
+	}
+
+	@Override
+	public QueryData getQueryData(){
+		return this.queryData;
+	}
 
 }

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/QueryData.java

@@ -30,6 +30,7 @@
 import org.vamdc.tapservice.vss2.RestrictExpression;
 import org.vamdc.tapservice.vss2.VSSParser;
 
+
 @Name("queryData")
 @Scope(ScopeType.CONVERSATION)
 public class QueryData implements FormHolder,Serializable{
@@ -39,6 +40,7 @@ public class QueryData implements FormHolder,Serializable{
 	//All forms and lists are serialized explicitly
 	private transient Collection<Form> forms;
 	private transient List<Form> formsList;
+	private transient List<Form> unsortedFormsList;
 
 	//Species-related forms
 	private transient Collection<SpeciesForm> speciesForms;
@@ -54,6 +56,9 @@ public class QueryData implements FormHolder,Serializable{
 	private transient Collection<Restrictable> activeKeywords;
 	private transient Collection<String> activeNodes;
 
+	private Integer speciesFormPosition;
+	private Boolean guidedQuery = false;
+
 	@In(create=true) private transient RegistryFacade registryFacade;
 
 	public QueryData(){
@@ -63,6 +68,7 @@ public QueryData(){
 	private void initCollections(){
 		formCounts=Collections.synchronizedMap(new TreeMap<Integer,Integer>());
 		forms=Collections.synchronizedSet(new TreeSet<Form>(new Order()));
+		unsortedFormsList = Collections.synchronizedList(new ArrayList<Form>());
 		formsList = Collections.synchronizedList(new ArrayList<Form>());
 		speciesForms=Collections.synchronizedSet(new TreeSet<SpeciesForm>(new Order()));
 		request = EnumSet.noneOf(Requestable.class);
@@ -124,8 +130,7 @@ private Collection<Restrictable> getKeywordsFromForms(){
 		for (Form form:getForms()){
 			result.addAll(form.getKeywords());
 		}
-		return result;
-
+		return result;			
 	}
 
 	private Collection<Restrictable> getKeywordsFromQuery(String query){
@@ -148,12 +153,11 @@ private Collection<Restrictable> getKeywordsFromQuery(String query){
 	}
 
 
-
 	public String getQueryString(){
 		if (isUserModified())
 			return customQueryString;
 		return QueryGenerator.buildQueryString(request,formsList); 
-	}
+ 	}
 
 
 	private boolean isUserModified(){
@@ -172,6 +176,10 @@ public List<Form> getForms(){
 		return formsList;
 	}
 
+	public List<Form> getUnsortedForms(){
+		return this.unsortedFormsList;
+	}
+
 	public Collection<SpeciesForm> getSpeciesForms(){
 		return new ArrayList<SpeciesForm>(speciesForms);
 	}
@@ -205,13 +213,36 @@ private boolean quickAddForm(Form form){
 			form.setQueryData(this);
 			forms.add(form);
 			formCounts.put(form.getOrder(), getFormTypeCount(form)+1);
+
+			if(form.getOrder() == Order.GuidedSpeciesType)
+				this.speciesFormPosition = forms.size()-1;
+
 			if (form instanceof SpeciesForm)
 				speciesForms.add((SpeciesForm) form);
+			else
+				unsortedFormsList.add(form);
+
 			return true;
 		}
 		return false;
 	}
 
+	public List<Form> getOrderedGuidedForm(){
+		if(this.getSpeciesForms().size() > 0 && this.speciesFormPosition != null){
+			List<Form> result = new ArrayList<Form>();
+			for(Form f : this.unsortedFormsList){
+				result.add(f);
+			}
+			int i = this.speciesFormPosition;
+			for(Form f : this.speciesForms){
+				result.add(i+1, f);
+				i++;
+			}
+			return result;
+		}else
+			return this.unsortedFormsList;
+	}
+
 	public Integer getFormTypeCount(Form form){
 		Integer count;
 		if ((count=formCounts.get(form.getOrder()))!=null){
@@ -231,13 +262,15 @@ public void deleteForm(Form form){
         }
         formCounts.put(form.getOrder(), getFormTypeCount(form)-1);
 		forms.remove(form);
+		unsortedFormsList.remove(form);
 		if (form.getOrder()<Order.SPECIES_LIMIT)
-			speciesForms.remove(form);
+			speciesForms.remove(form);		
+
 		rebuildLists();
 	}
 
 	public String getComments() { return comments; }
-	public void setComments(String comments) { this.comments = comments; }
+	public void setComments(String comments) {this.comments = comments; }
 
 	public String getEditQueryId() { return editedQueryId; }
 	public void setEditQueryId(String editQueryId) { this.editedQueryId = editQueryId; }
@@ -291,4 +324,13 @@ public void setCustomQueryString(String customQueryString) {
 		this.customQueryString = customQueryString;
 	}
 
+	public void setGuidedQuery(Boolean guidedQuery){
+		this.guidedQuery = guidedQuery;
+	}
+
+	public Boolean isGuidedQuery(){
+		return this.guidedQuery;
+	}
+
+
 }

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/QueryGenerator.java

@@ -33,7 +33,7 @@ public int compare(Form o1, Form o2) {
 	}
 
 	public static String getFormsQuery(Collection<Form> forms){
-
+		
 		SortedSet<Form> sorted = new TreeSet<Form>(new NewOrder()); 
 		sorted.addAll(forms);
 

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/QueryPersister.java

@@ -0,0 +1,46 @@
+package org.vamdc.portal.session.queryBuilder;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+
+import org.vamdc.portal.entity.query.HttpHeadResponse;
+import org.vamdc.portal.entity.query.Query;
+import org.vamdc.portal.entity.query.HttpHeadResponse.Response;
+import org.vamdc.portal.session.preview.PersistableQueryInterface;
+
+
+public class QueryPersister {
+	private PersistableQueryInterface queryManager;
+
+	public QueryPersister(PersistableQueryInterface queryManager){
+		this.queryManager = queryManager;
+	}
+
+	public Query constructQuery(){
+		Query result=null;
+		if (queryManager.getQueryData().getEditQueryId() !=null)
+			result = queryManager.getQueryLog().getQuery(queryManager.getQueryData().getEditQueryId());
+		else
+			result = new Query();
+		result.setComments(queryManager.getQueryData().getComments());
+		result.setQueryString(queryManager.getQueryData().getQueryString());
+		result.setResponses(selectRespondedNodes());
+		result.setUser(queryManager.getUser());
+		result.setDate(new Date());
+		return result;
+	}
+
+	private List<HttpHeadResponse> selectRespondedNodes() {
+		ArrayList<HttpHeadResponse> responses = new ArrayList<HttpHeadResponse>();
+
+		for (HttpHeadResponse response:queryManager.getNodesResponse()){
+			if (response.getStatus()==Response.OK || response.getStatus()==Response.TRUNCATED)
+				responses.add(response);
+		}
+		return responses;
+	}
+
+
+}