Feature/ensembl ref db

checkstyle.xml

@@ -3,7 +3,7 @@
         "https://checkstyle.org/dtds/configuration_1_3.dtd">
 <module name="Checker">
     <module name="LineLength">
-        <property name="max" value="150"/>
+        <property name="max" value="250"/>
     </module>
     <!-- Add more modules as needed -->
 </module>

pom.xml

@@ -70,7 +70,7 @@
 		<dependency>
 			<groupId>org.reactome.base</groupId>
 			<artifactId>reactome-base</artifactId>
-			<version>2.2.4-SNAPSHOT</version>
+			<version>2.0.0</version>
 		</dependency>
 		<!-- Test dependencies -->
 		<dependency>

src/main/java/org/reactome/orthoinference/EWASInferrer.java

@@ -12,12 +12,13 @@
 import static org.gk.model.ReactomeJavaConstants.*;
 
 import org.gk.model.InstanceDisplayNameGenerator;
+import org.gk.model.ReactomeJavaConstants;
 import org.gk.persistence.MySQLAdaptor;
-import org.gk.schema.GKSchemaClass;
-import org.gk.schema.InvalidAttributeException;
-import org.gk.schema.SchemaClass;
+import org.gk.schema.*;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
 
 public class EWASInferrer {
 
@@ -98,7 +99,11 @@ public static List<GKInstance> inferEWAS(GKInstance ewasInst) throws InvalidAttr
 					for (int endCoord : (Collection<Integer>) ewasInst.getAttributeValuesList(endCoordinate)) {
 						infEWASInst.addAttributeValue(endCoordinate, endCoord);
 					}
-					if (infEWASInst.getAttributeValue(startCoordinate) != null && (int) infEWASInst.getAttributeValue(startCoordinate) > 1 || infEWASInst.getAttributeValue(endCoordinate) != null && (int) infEWASInst.getAttributeValue(endCoordinate) > 1) {
+					if (infEWASInst.getAttributeValue(startCoordinate) != null &&
+						(int) infEWASInst.getAttributeValue(startCoordinate) > 1 ||
+						infEWASInst.getAttributeValue(endCoordinate) != null &&
+						(int) infEWASInst.getAttributeValue(endCoordinate) > 1) {
+
 						List<String> infEWASInstNames = (ArrayList<String>) (ewasInst).getAttributeValuesList(name);
 						infEWASInst.addAttributeValue(name, infEWASInstNames.get(0));
 						infEWASInst.addAttributeValue(name, homologueId);
@@ -339,53 +344,41 @@ public static void readENSGMappingFile(String toSpecies, String pathToOrthopairs
 
 	// Fetches Uniprot DB instance
 	@SuppressWarnings("unchecked")
-	public static void fetchAndSetUniprotDbInstance() throws Exception
-	{
+	public static void fetchAndSetUniprotDbInstance() throws Exception {
 		Collection<GKInstance> uniprotDbInstances = (Collection<GKInstance>) dba.fetchInstanceByAttribute(ReferenceDatabase, name, "=", "UniProt");
 		uniprotDbInst = uniprotDbInstances.iterator().next();
 	}
 
-	// Creates instance pertaining to the species Ensembl Protein DB
-	public static void createEnsemblProteinDbInstance(String toSpeciesLong, String toSpeciesReferenceDbUrl, String toSpeciesEnspAccessUrl) throws Exception
-	{
-		String enspSpeciesDb = "ENSEMBL_" + toSpeciesLong + "_PROTEIN";
-		enspDbInst = new GKInstance(dba.getSchema().getClassByName(ReferenceDatabase));
-		enspDbInst.setDbAdaptor(dba);
-		enspDbInst.addAttributeValue(created, instanceEditInst);
-		enspDbInst.addAttributeValue(name, "Ensembl");
-		enspDbInst.addAttributeValue(name, enspSpeciesDb);
-		enspDbInst.addAttributeValue(url, toSpeciesReferenceDbUrl);
-		enspDbInst.addAttributeValue(accessUrl, toSpeciesEnspAccessUrl);
-		enspDbInst.setAttributeValue(_displayName, "Ensembl");
-		dba.storeInstance(enspDbInst);
-	}
+	public static void fetchAndSetEnsemblDbInstance(String ensemblDatabaseType, String pathToRefDbConfig)
+		throws Exception {
 
-	// Creates instance pertaining to the species Ensembl Gene DB
-	public static void createEnsemblGeneDBInstance(String toSpeciesLong, String toSpeciesReferenceDbUrl, String toSpeciesEnsgAccessUrl) throws Exception
-	{
-		String ensgSpeciesDb = "ENSEMBL_" + toSpeciesLong + "_GENE";
-		ensgDbInst = new GKInstance(dba.getSchema().getClassByName(ReferenceDatabase));
-		ensgDbInst.setDbAdaptor(dba);
-		ensgDbInst.addAttributeValue(created, instanceEditInst);
-		ensgDbInst.addAttributeValue(name, "ENSEMBL");
-		ensgDbInst.addAttributeValue(name, ensgSpeciesDb);
-		ensgDbInst.addAttributeValue(url, toSpeciesReferenceDbUrl);
-		ensgDbInst.addAttributeValue(accessUrl, toSpeciesEnsgAccessUrl);
-		ensgDbInst.setAttributeValue(_displayName, "ENSEMBL");
-		dba.storeInstance(ensgDbInst);
+		GKInstance ensemblDbInst = fetchOrCreateEnsemblDbInstance(ensemblDatabaseType, pathToRefDbConfig);
+		if (ensemblDbInst == null) {
+			throw new IllegalStateException(
+				"Unable to fetch EnsEMBL Reference Database for type: " + ensemblDatabaseType
+			);
+		}
+
+		ensgDbInst = ensemblDbInst;
+		enspDbInst = ensemblDbInst;
 	}
 
 	// Create instance pertaining to any alternative reference DB for the species
 	public static void createAlternateReferenceDBInstance(JSONObject altRefDbJSON) throws Exception
 	{
-		alternateDbInst = new GKInstance(dba.getSchema().getClassByName(ReferenceDatabase));
-		alternateDbInst.setDbAdaptor(dba);
-		alternateDbInst.addAttributeValue(created, instanceEditInst);
-		alternateDbInst.addAttributeValue(name, ((JSONArray) altRefDbJSON.get("dbname")).get(0));
-		alternateDbInst.addAttributeValue(url, altRefDbJSON.get("url"));
-		alternateDbInst.addAttributeValue(accessUrl, altRefDbJSON.get("access"));
-		alternateDbInst.setAttributeValue(_displayName, ((JSONArray) altRefDbJSON.get("dbname")).get(0));
-		alternateDbInst = InstanceUtilities.checkForIdenticalInstances(alternateDbInst, null);
+		String altRefDbDisplayName = (String) ((JSONArray) altRefDbJSON.get("dbname")).get(0);
+		if (refDbExistsInDb(altRefDbDisplayName)) {
+			alternateDbInst = getRefDbFromDb(altRefDbDisplayName);
+		} else {
+			alternateDbInst = new GKInstance(dba.getSchema().getClassByName(ReferenceDatabase));
+			alternateDbInst.setDbAdaptor(dba);
+			alternateDbInst.addAttributeValue(created, instanceEditInst);
+			alternateDbInst.addAttributeValue(name, altRefDbDisplayName);
+			alternateDbInst.addAttributeValue(url, altRefDbJSON.get("url"));
+			alternateDbInst.addAttributeValue(accessUrl, altRefDbJSON.get("access"));
+			alternateDbInst.setAttributeValue(_displayName, altRefDbDisplayName);
+			alternateDbInst = InstanceUtilities.checkForIdenticalInstances(alternateDbInst, null);
+		}
 		if (altRefDbJSON.get("alt_id") != null)
 		{
 			altRefDbId = (String) altRefDbJSON.get("alt_id");
@@ -412,4 +405,76 @@ public static void setWormbaseMappings(Map<String, List<String>> wormbaseMapping
 	public static void setGeneNameMappingFile(Map<String, String> geneNameMappingsCopy) {
 		geneNameMappings = geneNameMappingsCopy;
 	}
+
+	private static boolean refDbExistsInDb(String refDbDisplayName) throws Exception {
+		Collection<GKInstance> refDbInstances =
+			dba.fetchInstanceByAttribute(ReferenceDatabase, _displayName, "=", refDbDisplayName);
+		return refDbInstances != null && !refDbInstances.isEmpty();
+	}
+
+	private static GKInstance getRefDbFromDb(String refDbDisplayName) throws Exception {
+		return (GKInstance) dba.fetchInstanceByAttribute(
+			ReferenceDatabase, _displayName, "=", refDbDisplayName
+		).iterator().next();
+	}
+
+	private static GKInstance fetchOrCreateEnsemblDbInstance(String ensemblDatabaseType, String pathToRefDbConfig)
+		throws Exception {
+
+		String ensemblRefDBDisplayName;
+		if (ensemblDatabaseType.equals("main")) {
+			ensemblRefDBDisplayName = "ENSEMBL";
+		} else if (ensemblDatabaseType.equals("fungi")) {
+			ensemblRefDBDisplayName = "ENSEMBL Fungi";
+		} else if (ensemblDatabaseType.equals("protist")) {
+			ensemblRefDBDisplayName = "ENSEMBL Protist";
+		} else {
+			throw new IllegalStateException(ensemblDatabaseType + " is not a valid EnsEMBL database type");
+		}
+
+		return refDbExistsInDb(ensemblRefDBDisplayName) ?
+			getRefDbFromDb(ensemblRefDBDisplayName) :
+			createRefDb(ensemblRefDBDisplayName, pathToRefDbConfig);
+	}
+
+	private static GKInstance createRefDb(String refDbDisplayName, String pathToRefDbConfig)
+		throws Exception {
+
+		JSONObject refDbJsonObject = getRefDBJSONObject(refDbDisplayName, pathToRefDbConfig);
+
+		GKInstance refDbInstance = new GKInstance(fetchSchema().getClassByName(ReferenceDatabase));
+		refDbInstance.setDbAdaptor(dba);
+		refDbInstance.setAttributeValue(ReactomeJavaConstants.created, instanceEditInst);
+		refDbInstance.setAttributeValue(ReactomeJavaConstants.accessUrl, refDbJsonObject.get("accessUrl"));
+		refDbInstance.setAttributeValue("identifiersPrefix", refDbJsonObject.get("identifiersPrefix"));
+		refDbInstance.setAttributeValue(ReactomeJavaConstants.resourceIdentifier,
+			refDbJsonObject.get("resourceIdentifier"));
+		refDbInstance.setAttributeValue(ReactomeJavaConstants.url, refDbJsonObject.get("url"));
+		refDbInstance.setAttributeValue(ReactomeJavaConstants.name, Collections.singletonList(refDbDisplayName));
+		InstanceDisplayNameGenerator.setDisplayName(refDbInstance);
+
+		return refDbInstance;
+	}
+
+	private static JSONObject getRefDBJSONObject(String refDbDisplayName, String pathToRefDbConfig) {
+		JSONParser parser = new JSONParser();
+		JSONObject refDbsJsonObject;
+		try {
+			refDbsJsonObject = (JSONObject) parser.parse(new FileReader(pathToRefDbConfig));
+		} catch (IOException | ParseException e) {
+			throw new RuntimeException("Unable to read/parse JSON from " + pathToRefDbConfig, e);
+		}
+		return (JSONObject) refDbsJsonObject.get(refDbDisplayName);
+	}
+
+	private static Schema fetchSchema() {
+		if (dba.getSchema() == null) {
+			try {
+				return dba.fetchSchema();
+			} catch (Exception e) {
+				throw new RuntimeException("Unable to fetch schema from " + dba, e);
+			}
+		}
+		return dba.getSchema();
+	}
 }

src/main/java/org/reactome/orthoinference/EventsInferrer.java

@@ -77,6 +77,7 @@ public static void inferEvents(Properties props, String species) throws Exceptio
 		releaseVersion = props.getProperty("releaseNumber");
 		String pathToOrthopairs = props.getProperty("pathToOrthopairs", "orthopairs");
 		String pathToSpeciesConfig = props.getProperty("pathToSpeciesConfig", "src/main/resources/Species.json");
+		String pathToRefDbConfig = props.getProperty("pathToRefDbConfig", "src/main/resources/refdb.json");
 		String dateOfRelease = props.getProperty("dateOfRelease");
 		int personId = Integer.valueOf(props.getProperty("personId"));
 		setReleaseDates(dateOfRelease);
@@ -95,9 +96,7 @@ public static void inferEvents(Properties props, String species) throws Exceptio
 		logger.info("Beginning orthoinference of " + speciesName);
 
 		JSONObject refDb = (JSONObject) speciesObject.get("refdb");
-		String refDbUrl = (String) refDb.get("url");
-		String refDbProteinUrl = (String) refDb.get("access");
-		String refDbGeneUrl = (String) refDb.get("ensg_access");
+		String ensemblDatabaseType = (String) refDb.get("use_gk_central_ensembl_ref_db");
 
 		// Creates two files that a) list reactions that are eligible for inference and b) those that are successfully inferred
 		String eligibleFilename = "eligible_" + species	+ "_75.txt";
@@ -120,8 +119,7 @@ public static void inferEvents(Properties props, String species) throws Exceptio
 		}
 		EWASInferrer.readENSGMappingFile(species, pathToOrthopairs);
 		EWASInferrer.fetchAndSetUniprotDbInstance();
-		EWASInferrer.createEnsemblProteinDbInstance(speciesName, refDbUrl, refDbProteinUrl);
-		EWASInferrer.createEnsemblGeneDBInstance(speciesName, refDbUrl, refDbGeneUrl);
+		EWASInferrer.fetchAndSetEnsemblDbInstance(ensemblDatabaseType, pathToRefDbConfig);
 
 		JSONObject altRefDbJSON = (JSONObject) speciesObject.get("alt_refdb");
 		if (altRefDbJSON != null)
@@ -348,7 +346,14 @@ private static void setSummationInstance() throws Exception
 		GKInstance summationInst = new GKInstance(dbAdaptor.getSchema().getClassByName(Summation));
 		summationInst.setDbAdaptor(dbAdaptor);
 		summationInst.addAttributeValue(created, instanceEditInst);
-		String summationText = "This event has been computationally inferred from an event that has been demonstrated in another species.<p>The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.<p><a href='/electronic_inference_compara.html' target = 'NEW'>More details and caveats of the event inference in Reactome.</a> For details on PANTHER see also: <a href='http://www.pantherdb.org/about.jsp' target='NEW'>http://www.pantherdb.org/about.jsp</a>";
+		String summationText = "This event has been computationally inferred from an event that has been " +
+			"demonstrated in another species.<p>The inference is based on the homology mapping from PANTHER. " +
+			"Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a " +
+			"mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are " +
+			"inferred to the other species. High level events are also inferred for these events to allow for " +
+			"easier navigation.<p><a href='/electronic_inference_compara.html' target = 'NEW'>More details and " +
+			"caveats of the event inference in Reactome.</a> For details on PANTHER see also: " +
+			"<a href='http://www.pantherdb.org/about.jsp' target='NEW'>http://www.pantherdb.org/about.jsp</a>";
 		summationInst.addAttributeValue(text, summationText);
 		summationInst.addAttributeValue(_displayName, summationText);
 		summationInst = InstanceUtilities.checkForIdenticalInstances(summationInst, null);

src/main/java/org/reactome/orthoinference/OrthologousEntityGenerator.java

@@ -313,7 +313,9 @@ private static GKInstance createInfEntitySet(GKInstance entitySetInst, boolean o
 				for (GKInstance candidateInst : candidateInstances)
 				{
 					GKInstance infCandidateInst = createOrthoEntity(candidateInst, false);
-					if (infCandidateInst != null && !existingMemberInstances.contains(infCandidateInst.getAttributeValue(name).toString()) && !existingCandidateInstances.contains(infCandidateInst.getAttributeValue(name).toString()))
+					if (infCandidateInst != null &&
+						!existingMemberInstances.contains(infCandidateInst.getAttributeValue(name).toString()) &&
+						!existingCandidateInstances.contains(infCandidateInst.getAttributeValue(name).toString()))
 					{
 						existingCandidateInstances.add(infCandidateInst.getAttributeValue(name).toString());
 						infCandidatesList.add(infCandidateInst);