Merge pull request #49 from RBVI/feature/switch-resolving

Merge the new feature that uses jensenlab for resolving instead of STITCH and Viruses
RBVI · May 2, 2024 · 23cfcdc · 23cfcdc
2 parents 5d4eed5 + 9a82e04
commit 23cfcdc
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Showing 8 changed files with 100 additions and 36 deletions.
diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/Annotation.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/Annotation.java
@@ -1,14 +1,15 @@
 package edu.ucsf.rbvi.stringApp.internal.model;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 
-import edu.ucsf.rbvi.stringApp.internal.model.Species;
 import edu.ucsf.rbvi.stringApp.internal.utils.ModelUtils;
 
 public class Annotation {
@@ -77,9 +78,9 @@ public String toString() {
 	public boolean isResolved() {return resolved;}
 	public void setResolved(boolean resolved) {this.resolved = resolved;}
 
-	public static Map<String, List<Annotation>> getAnnotations(JSONObject json, String queryTerms, Species species) {
+	public static Map<String, List<Annotation>> getAnnotations(JSONObject json, String queryTerms, Species species, String useDATABASE) {
 		Map<String, List<Annotation>> map = new HashMap<>();
-		return getAnnotations(json, queryTerms, map, species);
+		return getAnnotations(json, queryTerms, map, species, useDATABASE);
 	}
 
 	public static boolean allResolved(List<Annotation> annotations) {
@@ -91,9 +92,11 @@ public static boolean allResolved(List<Annotation> annotations) {
 	}
 
 	public static Map<String, List<Annotation>> getAnnotations(JSONObject json, String queryTerms,
-	                                                           Map<String, List<Annotation>> map, Species species) {
+	                                                           Map<String, List<Annotation>> map, Species species, String useDATABASE) {
 		String[] terms = queryTerms.trim().split("\n");
 		JSONArray annotationArray = ModelUtils.getResultsFromJSON(json, JSONArray.class);
+		if (useDATABASE.equals(Databases.JENSENLAB.getAPIName()))
+			annotationArray = (JSONArray) annotationArray.get(0);
 		Integer version = ModelUtils.getVersionFromJSON(json);
 
 		// If we switch the API back to use a start of 0, this will need to change
@@ -110,13 +113,16 @@ public static Map<String, List<Annotation>> getAnnotations(JSONObject json, Stri
 			String taxonName = null;
 			int taxId = -1;
 			int queryIndex = -1;
+			String query = null;
 			String uniprot = null;
 			String sequence = null;
 			String image = null;
 			String color = null;
 
+			// Fields coming from string-db
 			if (ann.containsKey("preferredName"))
 				preferredName = (String)ann.get("preferredName");
+			// annotation contains the description of the entity as it comes from STRING-DB
 			if (ann.containsKey("annotation"))
 				annotation = (String)ann.get("annotation");
 			if (ann.containsKey("stringId"))
@@ -143,6 +149,7 @@ public static Map<String, List<Annotation>> getAnnotations(JSONObject json, Stri
 					species.setOfficialName(taxonName);
 				}
 			}
+			// Fields coming from string-db with csdata=1
 			if (ann.containsKey("uniprot"))
 				uniprot = (String)ann.get("uniprot");
 			if (ann.containsKey("sequence"))
@@ -152,6 +159,30 @@ public static Map<String, List<Annotation>> getAnnotations(JSONObject json, Stri
 			if (ann.containsKey("image"))
 				image = (String)ann.get("image");
 
+			// Fields coming from jensenlab
+			if(ann.containsKey("primary")) {
+				preferredName = (String)ann.get("primary");
+				if (description != null && !description.equals(""))
+					annotation = description;
+			}
+			// TODO: type is actually the taxId, but do we need it?
+			//if (ann.containsKey("type"))
+			//	taxId = (Long)ann.get("type");
+			if(ann.containsKey("id")) {
+				if (ann.containsKey("type") && (Long)ann.get("type") != -1)
+					stringId = (Long)ann.get("type") + "." +(String)ann.get("id");
+				else
+					stringId = (String)ann.get("id");
+			}
+			// TODO: [N] Currently, we still get both CIDm and CIDs
+			// We only have networks for the CIDm, so we ignore the others for now
+			if (stringId.startsWith("CIDs"))
+				continue;
+			if(ann.containsKey("query")) {
+				query = (String)ann.get("query");
+				queryIndex = Arrays.asList(terms).indexOf(query);
+			}
+
 			// Temporary HACK
 			// if (stringId.startsWith("-1.CID1"))
 			// 	stringId = stringId.replaceFirst("-1.CID1","CIDm");

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/Databases.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/Databases.java
@@ -10,7 +10,8 @@ public enum Databases {
 	// AGOTOOL("aGOtool", "agotool")
 	VIRUSES("Viruses", "viruses"),
 	STITCH("Stitch", "stitch"),
-	STRINGDB("String-db", "string-db");
+	STRINGDB("String-db", "string-db"),
+	JENSENLAB("Jensenlab", "jensenlab");
 
 	String dbName;
 	String apiName;

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/StringNetwork.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/model/StringNetwork.java
@@ -391,48 +391,72 @@ private Map<String, List<Annotation>> getAnnotationBatch(Species species, final
 		try {
 			results = HttpUtils.postJSON(url, args, manager);
 			// System.out.println(results.toString());
+			if (results != null) {
+				// System.out.println("Got results");
+				annotations = Annotation.getAnnotations(results, encTerms, annotations, species, Databases.STRING.getAPIName());
+				// System.out.println("Get annotations returns "+annotations.size());
+			}
 		} catch (ConnectionException ex) {
 			if (ex instanceof UnknownSpeciesException && manager.isVirusesEnabled() && annotations.size() == 0 && includeViruses) {
 				// also call the viruses API
 				// http://viruses.string-db.org/cgi/webservice_handler.pl?species=11320&identifiers=NS1_I34A1
 				// &caller_identity=string_app_v1_1_1&output=json&request=resolveList
-				url = manager.getResolveURL(Databases.VIRUSES.getAPIName());
+				//url = manager.getResolveURL(Databases.VIRUSES.getAPIName());
+				//args = new HashMap<>();
+				//args.put("species", speciesId);
+				//args.put("identifiers", encTerms);
+				//args.put("caller_identity", StringManager.CallerIdentity);
+				//args.put("output", "json");
+				//args.put("request", "resolveList");
+				//manager.info("URL:" + url + "?species=" + speciesId + "&caller_identity="
+				//		+ StringManager.CallerIdentity + "&identifiers=" + HttpUtils.truncate(encTerms));
+
+				url = manager.getEntityQueryURL();
 				args = new HashMap<>();
-				args.put("species", speciesId);
-				args.put("identifiers", encTerms);
-				args.put("caller_identity", StringManager.CallerIdentity);
-				args.put("output", "json");
-				args.put("request", "resolveList");
-				manager.info("URL:" + url + "?species=" + speciesId + "&caller_identity="
-						+ StringManager.CallerIdentity + "&identifiers=" + HttpUtils.truncate(encTerms));
+				args.put("limit", "5");
+				args.put("types", speciesId);
+				args.put("format", "json");
+				args.put("query", encTerms);
+				manager.info("URL: "+url+"?types=" + speciesId + "&limit=5&format=json"+"&identifiers="+HttpUtils.truncate(encTerms));
+
 				// Get the results
 				// System.out.println("Getting VIRUSES term resolution");
 				results = HttpUtils.postJSON(url, args, manager);
+				if (results != null) {
+					// System.out.println("Got results");
+					annotations = Annotation.getAnnotations(results, encTerms, annotations, species, Databases.JENSENLAB.getAPIName());
+					// System.out.println("Get annotations returns "+annotations.size());
+				}
 			}
 		}
 
-		if (results != null) {
-			// System.out.println("Got results");
-			annotations = Annotation.getAnnotations(results, encTerms, annotations, species);
-			// System.out.println("Get annotations returns "+annotations.size());
-		}
 		results = null;
 
 		// then, call other APIs to get resolve them
 		// resolve compounds 
 		if (useDATABASE.equals(Databases.STITCH.getAPIName())) {
-			url = manager.getResolveURL(Databases.STITCH.getAPIName())+"json/resolveList";
+			//url = manager.getResolveURL(Databases.STITCH.getAPIName())+"json/resolveList";
+			//args = new HashMap<>();
+			//args.put("species", "CIDm");
+			//args.put("identifiers", encTerms);
+			//args.put("caller_identity", StringManager.CallerIdentity);
+			// manager.info("URL: "+url+"?species="+speciesId+"&caller_identity="+StringManager.CallerIdentity+"&identifiers="+HttpUtils.truncate(encTerms));
+
+			url = manager.getEntityQueryURL();
 			args = new HashMap<>();
-			args.put("species", "CIDm");
-			args.put("identifiers", encTerms);
-			args.put("caller_identity", StringManager.CallerIdentity);
-			manager.info("URL: "+url+"?species="+speciesId+"&caller_identity="+StringManager.CallerIdentity+"&identifiers="+HttpUtils.truncate(encTerms));
+			// we ask for 10 since half of them are CIDs, which we ignore
+			args.put("limit", "10");
+			args.put("types", "-1");
+			args.put("format", "json");
+			args.put("query", encTerms);
+			manager.info("URL: "+url+"?types=-1&limit=10&format=json"+"&identifiers="+HttpUtils.truncate(encTerms));
+
 			// Get the results
 			// System.out.println("Getting STITCH term resolution");
 			results = HttpUtils.postJSON(url, args, manager);
 
 			if (results != null) {
-				updateAnnotations(results, encTerms, species);
+				updateAnnotations(results, encTerms, species, Databases.JENSENLAB.getAPIName());
 			}
 			results = null;
 		} 
@@ -526,9 +550,9 @@ public List<String> combineIds(Map<String, String> reverseMap) {
 		return ids;
 	}
 
-	private void updateAnnotations(JSONObject results, String terms, Species species) {
+	private void updateAnnotations(JSONObject results, String terms, Species species, String useDATABASE) {
 		Map<String, List<Annotation>> newAnnotations = Annotation.getAnnotations(results,
-				terms, species);
+				terms, species, useDATABASE);
 		for (String newAnn : newAnnotations.keySet()) {
 			List<Annotation> allAnn = new ArrayList<Annotation>(newAnnotations.get(newAnn));
 			if (annotations.containsKey(newAnn)) {

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/ExpandNetworkTask.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/ExpandNetworkTask.java
@@ -194,7 +194,7 @@ public void run(TaskMonitor monitor) {
 		Map<String, String> args = new HashMap<>();
 		if (selectedType.equals(ModelUtils.COMPOUND)) {
 			useDatabase = Databases.STITCH.getAPIName();
-			args.put("filter", "CIDm%%");			
+			args.put("filter", "CIDm%");			
 			args.put("existing",existing.trim());
 			args.put("score", conf.toString());
 			args.put("database", database);
@@ -215,7 +215,7 @@ public void run(TaskMonitor monitor) {
 		} else {
 			useDatabase = Databases.STRING.getAPIName();
 			filterString = String.valueOf(selSpecies.getTaxId());
-			args.put("filter", filterString + ".%%");
+			args.put("filter", filterString + ".%");
 			args.put("existing",existing.trim());
 			args.put("score", conf.toString());
 			args.put("database", database);

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/LoadInteractions.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/LoadInteractions.java
@@ -121,9 +121,9 @@ else if (useDATABASE.equals(Databases.STRINGDB.getAPIName()))
 			if (additionalNodes > 0) {
 				args.put("additional", Integer.toString(additionalNodes));
 				if (useDATABASE.equals(Databases.STRING.getAPIName())) {
-					args.put("filter", String.valueOf(species.getTaxId()) + ".%%");
+					args.put("filter", String.valueOf(species.getTaxId()) + ".%");
 				} else {
-					args.put("filter", String.valueOf(species.getTaxId()) + ".%%|CIDm%%");
+					args.put("filter", String.valueOf(species.getTaxId()) + ".%|CIDm%");
 				}
 			}
 		}

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/LoadTermsTask.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/tasks/LoadTermsTask.java
@@ -118,9 +118,9 @@ public void run(TaskMonitor monitor) {
 			if (additionalNodes > 0) {
 				args.put("additional", Integer.toString(additionalNodes));
 				if (useDATABASE.equals(Databases.STRING.getAPIName())) {
-					args.put("filter", taxString + ".%%");
+					args.put("filter", taxString + ".%");
 				} else if (useDATABASE.equals(Databases.STITCH.getAPIName())) {
-					args.put("filter", taxString + ".%%|CIDm%%");
+					args.put("filter", taxString + ".%|CIDm%");
 				}
 			}
 		}

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/ui/GetTermsPanel.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/ui/GetTermsPanel.java
@@ -506,14 +506,16 @@ private void showTableRow(JTable table, String term, Map<String, ResolveTableMod
 		TableRowSorter sorter = new TableRowSorter(tableModelMap.get(term));
 		sorter.setSortable(0, false);
 		sorter.setSortable(1, true);
-		sorter.setSortable(2, false);
+		sorter.setSortable(2, true);
+		sorter.setSortable(3, false);
 		table.setModel(tableModelMap.get(term));
 		table.setRowSorter(sorter);
 		table.setAutoResizeMode( JTable.AUTO_RESIZE_OFF );
-		table.getColumnModel().getColumn(2).setCellRenderer(new TextAreaRenderer());
+		table.getColumnModel().getColumn(3).setCellRenderer(new TextAreaRenderer());
 		table.getColumnModel().getColumn(0).setPreferredWidth(50);
 		table.getColumnModel().getColumn(1).setPreferredWidth(75);
-		table.getColumnModel().getColumn(2).setPreferredWidth(525);
+		table.getColumnModel().getColumn(2).setPreferredWidth(75);
+		table.getColumnModel().getColumn(3).setPreferredWidth(525);
 	}
 
 	public void cancel() {

diff --git a/src/main/java/edu/ucsf/rbvi/stringApp/internal/ui/ResolveTableModel.java b/src/main/java/edu/ucsf/rbvi/stringApp/internal/ui/ResolveTableModel.java
@@ -32,7 +32,7 @@ public ResolveTableModel(GetTermsPanel wsClient, String term, List<Annotation> a
 	}
 
 	@Override
-	public int getColumnCount() { return 3; }
+	public int getColumnCount() { return 4; }
 
 	@Override
 	public int getRowCount() { 
@@ -48,6 +48,8 @@ public String getColumnName(int columnIndex) {
 		case 1:
 			return "Name";
 		case 2:
+			return "ID";
+		case 3:
 			return "Description";
 		}
 		return "";
@@ -62,6 +64,8 @@ public Class<?> getColumnClass(int columnIndex) {
 			return String.class;
 		case 2:
 			return String.class;
+		case 3:
+			return String.class;
 		}
 		return null;
 	}
@@ -75,6 +79,8 @@ public Object getValueAt(int rowIndex, int columnIndex) {
 		case 1:
 			return ann.getPreferredName();
 		case 2:
+			return ann.getStringId();
+		case 3:
 			return ann.getAnnotation();
 		}
 		return null;