Modified console command: -i (reindex), etc. to delete all biopax el.…

… idx. documents first...

src/main/java/cpath/service/ConsoleApplication.java

@@ -194,16 +194,22 @@ private void modifyModel(String analysisClass) throws IOException {
     LOG.info("Over-writing model: {}...", service.settings().mainModelFile());
     new SimpleIOHandler(BioPAXLevel.L3).convertToOWL(model,
         new GZIPOutputStream(new FileOutputStream(service.settings().mainModelFile())));
-    //init the lucene index as read-write
-    service.initIndex(model, service.settings().indexDir(), false);
-    //re-index the model
-    service.index().save(model);
+    //re-index
+    reindex(model);
   }
 
-  private void reindex() throws IOException {
+  private void reindex() {
     Model model = CPathUtils.importFromTheArchive(service.settings().mainModelFile());
+    reindex(model);
+  }
+
+  private void reindex(Model model) {
     service.initIndex(model, service.settings().indexDir(), false);
+    //remove biopax but not id-mapping docs
+    service.index().drop();
+    //re-index
     service.index().save(model);
+    service.index().close();
   }
 
   /*

src/main/java/cpath/service/IndexImpl.java

@@ -179,10 +179,10 @@ private SearchResponse transform(Query query, IndexSearcher searcher, TopDocs to
 			throw new IllegalArgumentException("topDocs is null");
 		}
 		SearchResponse response = new SearchResponse();
-		response.setMaxHitsPerPage(maxHitsPerPage);
-		long numTotalHits = topDocs.totalHits.value; //todo: call searcher.count(q) instead or it's same?..
+		response.setMaxHitsPerPage(getMaxHitsPerPage());
+		long numTotalHits = topDocs.totalHits.value; //todo: call searcher.count(q) instead or it's the same?
 		response.setNumHits(numTotalHits);
-		List<SearchHit> hits = response.getSearchHit();//empty list
+		List<SearchHit> hits = response.getSearchHit();//empty list to be filled from top docs
 		assert hits!=null && hits.isEmpty();
 		LOG.debug("transform, no. TopDocs to process:" + topDocs.scoreDocs.length);
 		for(ScoreDoc scoreDoc : topDocs.scoreDocs) {
@@ -459,6 +459,7 @@ public void save(BioPAXElement bpe) {
 
 	@Override
 	public void save(Model model) {
+		setModel(model);
 		final int numObjectsToIndex = model.getObjects(Entity.class).size()
 				+ model.getObjects(EntityReference.class).size()
 				+ model.getObjects(Provenance.class).size();
@@ -477,15 +478,13 @@ public void save(Model model) {
 		commit();
 		//force refreshing the index state (for new readers)
 		refresh();
-		setModel(model);
 		LOG.info("build(), all done.");
 	}
 
 	@Override
 	public void commit() {
 		try {
 			indexWriter.commit();
-			indexWriter.flush();
 		} catch (Exception e) {
 			throw new RuntimeException(e);
 		}
@@ -495,7 +494,7 @@ public void commit() {
 	public void close() {
 		try {
 			if (indexWriter != null && indexWriter.isOpen()) {
-				indexWriter.flush();
+				indexWriter.commit();
 				indexWriter.close();
 			}
 		} catch (Exception e) {
@@ -513,21 +512,25 @@ public synchronized void refresh() {
 	}
 
 	@Override
-	public boolean isClosed() {
-		return indexWriter == null || !indexWriter.isOpen();
-	}
-
-	@Override
-	public long count(String queryString) {
-		return 0;
+	public void drop() {
+		if(indexWriter==null) {
+			throw new IllegalStateException("read-only index");
+		}
+		try {
+			Query q = new FieldExistsQuery(FIELD_KEYWORD);
+			indexWriter.deleteDocuments(q);
+			indexWriter.commit();
+			indexWriter.deleteUnusedFiles();
+			setModel(null);
+			LOG.info("dropped (deleted) BioPAX index");
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
 	}
 
 	private void addDatasources(Set<Provenance> set, Document doc) {
 		for (Provenance p : set) {
-			//store but do not index/tokenize the URI
-//			doc.add(new StoredField(FIELD_DATASOURCE, p.getUri()));
 			doc.add(new TextField(FIELD_DATASOURCE, p.getUri(), Field.Store.YES));
-
 			//index names (including the datasource identifier from metadata json config; see premerge/merge)
 			//different data sources can have the same name e.g. 'intact'; tokenized - to search by partial name
 			for (String s : p.getName()) {
@@ -538,7 +541,6 @@ private void addDatasources(Set<Provenance> set, Document doc) {
 
 	private void addOrganisms(Set<BioSource> set, Document doc) {	
 		for(BioSource bs : set) {
-			//doc.add(new StoredField(FIELD_ORGANISM, bs.getUri()));
 			doc.add(new TextField(FIELD_ORGANISM,  bs.getUri(), Field.Store.YES));
 
 			// add organism names
@@ -815,6 +817,6 @@ public void save(Mapping mapping) {
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
-		//call commit(), refresh() after one or several save(mapping)
+		//call commit(), refresh() after several save(mapping)
 	}
 }

src/main/java/cpath/service/Merger.java

@@ -81,8 +81,9 @@ public void merge() {
 			simpleMerger.merge(m, providerModel);
 		}
 
-		//remove dangling SPEs (such non-participant/components molecules are not useful for pathway analyses...)
+		//remove dangling SPEs and Genes (such non-participant/components are not useful for pathway analyses...)
     ModelUtils.removeObjectsIfDangling(m, SimplePhysicalEntity.class);
+		ModelUtils.removeObjectsIfDangling(m, Gene.class);
 		//now, remove dangling xrefs, CV et al. utility type individuals
 		ModelUtils.removeObjectsIfDangling(m, UtilityClass.class);
 

src/main/java/cpath/service/ServiceImpl.java

@@ -139,14 +139,6 @@ public void setBlacklist(Blacklist blacklist) {
     this.blacklist = blacklist;
   }
 
-  IndexImpl getIndex() {
-    return index;
-  }
-
-  void setIndex(IndexImpl index) {
-    this.index = index;
-  }
-
   public ServiceResponse search(String queryStr,
                                 int page, Class<? extends BioPAXElement> biopaxClass,
                                 String[] dsources, String[] organisms) {

src/main/java/cpath/service/metadata/Index.java

@@ -37,7 +37,7 @@ public interface Index {
 	/**
 	* Full-text search for an object.
 	* 
-    * @param query String (keywords or Lucene query string)
+  * @param query String (keywords or Lucene query string)
 	* @param page hits page number (when the number of hits exceeds a threshold)
 	* @param type - filter by class
 	* @param datasources  - filter by datasource
@@ -56,5 +56,5 @@ public interface Index {
 
 	void refresh();
 
-	boolean isClosed();
+	void drop();
 }

src/main/java/cpath/service/metadata/Mappings.java

@@ -27,12 +27,4 @@ public interface Mappings {
 
 	void close();
 
-	boolean isClosed();
-
-	/**
-	 * Total number of search hits for the given lucene query.
-	 * @param queryString
-	 * @return
-	 */
-	long count(String queryString);
 }

src/test/java/cpath/service/ConsoleApplicationIT.java

@@ -272,8 +272,7 @@ public void premergeAndMerge() throws IOException {
     merger.replaceConflictingUris(providerModel, mainModel);
     mainModel.merge(providerModel);
 
-//    //in prod, we bremove dangling SPEs, but here/below we need them for merge assertions; so commented out...
-//    ModelUtils.removeObjectsIfDangling(mainModel, SimplePhysicalEntity.class);
+    //in prod, we also remove dangling SPEs and Genes but here below we need them for merge assertions...
     ModelUtils.removeObjectsIfDangling(mainModel, UtilityClass.class);
 
     //it's vital to save to and then read the main model back from file,

src/test/java/cpath/service/IndexIT.java

@@ -31,7 +31,6 @@ public final void search() throws IOException {
       .getResource("classpath:merge/pathwaydata1.owl").getInputStream());
     IndexImpl index = new IndexImpl(model, "target/test-idx", false);
     index.save(model);
-    index.refresh();
 
     //close index writer and re-open the index searcher in the read-only mode
     //(optional; tests should pass regardless; if you remove the following two lines, keep index.close() at the end)
@@ -209,6 +208,13 @@ public final void search() throws IOException {
     assertFalse(response.getSearchHit().isEmpty());
     assertEquals(1, response.getSearchHit().size());
 
+    //re-open to write
+    index.close();
+    index = new IndexImpl(model, "target/test-idx", false);
+    index.drop();
+    response = index.search("*", 1, null, null, null);
+    assertTrue(response.getSearchHit().isEmpty());
+
     index.close();
   }