Made it possible o read not only compressed biopax data, etc.

PathwayCommons · Jun 2, 2024 · c1dbbd6 · c1dbbd6
1 parent c912daa
commit c1dbbd6
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Showing 5 changed files with 33 additions and 35 deletions.
diff --git a/build.gradle b/build.gradle
@@ -33,7 +33,8 @@ dependencies {
     implementation "org.springframework.boot:spring-boot-configuration-processor"
     implementation 'org.springdoc:springdoc-openapi-ui:1.7.0'
 
-    implementation 'org.biopax.paxtools:sbgn-converter:6.0.0-SNAPSHOT'
+    implementation 'org.biopax.paxtools:sbgn-converter:6.0.0'
+    implementation 'org.biopax.paxtools:paxtools-core:6.0.0'
     implementation 'com.google.code.gson:gson:2.9.0'
     implementation 'org.apache.commons:commons-collections4:4.4'
 

diff --git a/src/main/java/factoid/converter/BiopaxToFactoid.java b/src/main/java/factoid/converter/BiopaxToFactoid.java
@@ -2,14 +2,12 @@
 
 import java.util.ArrayList;
 import java.util.HashSet;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 import org.biopax.paxtools.model.Model;
 import org.biopax.paxtools.model.level3.BioSource;
@@ -28,21 +26,18 @@
 import org.biopax.paxtools.model.level3.EvidenceCodeVocabulary;
 import org.biopax.paxtools.model.level3.Interaction;
 import org.biopax.paxtools.model.level3.ModificationFeature;
-import org.biopax.paxtools.model.level3.MolecularInteraction;
 import org.biopax.paxtools.model.level3.PhysicalEntity;
 import org.biopax.paxtools.model.level3.Process;
 import org.biopax.paxtools.model.level3.Protein;
 import org.biopax.paxtools.model.level3.ProteinReference;
 import org.biopax.paxtools.model.level3.Rna;
-import org.biopax.paxtools.model.level3.SequenceEntity;
 import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
 import org.biopax.paxtools.model.level3.SmallMolecule;
 import org.biopax.paxtools.model.level3.TemplateReaction;
 import org.biopax.paxtools.model.level3.TemplateReactionRegulation;
 import org.biopax.paxtools.model.level3.Xref;
 
 import com.google.gson.JsonArray;
-import com.google.gson.JsonNull;
 import com.google.gson.JsonObject;
 
 
@@ -64,7 +59,7 @@ public JsonObject convert(Model model) {
 				.collect(Collectors.toSet());
 
 		for (Interaction intn : intns) {
-			Set<String> markedPmids = new HashSet<String>();
+			Set<String> markedPmids = new HashSet<>();
 			Process controlled = getControlled(intn);
 			for ( Evidence evidence : controlled.getEvidence() ) {
 				for (Xref xref : evidence.getXref()) {
@@ -153,7 +148,6 @@ private boolean keepIntn(Interaction intn) {
 				}
 			}
 		}
-
 		return false;
 	}
 
@@ -225,11 +219,11 @@ private JsonObject makeEntityJson(Entity entity) {
 
 		if ( originalDb.contains("uniprot") ) {
 			db = "uniprot";
-		}
-		else if ( originalDb.equals("hgnc symbol") || originalDb.equals("refseq") ) {
+		} else if (  originalDb.equalsIgnoreCase("hgnc.symbol")
+				|| originalDb.equalsIgnoreCase("hgnc symbol")
+				|| originalDb.equalsIgnoreCase("refseq") ) {
 			db = originalDb;
-		}
-		else {
+		} else {
 			logger.warning("Unhandled xref database: " + originalDb);
 			// if the entity db is not handled return null
 			// which will signal that the related interaction must be skipped as well

diff --git a/src/main/java/factoid/web/Controller.java b/src/main/java/factoid/web/Controller.java
@@ -15,14 +15,7 @@
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.server.ResponseStatusException;
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.StringWriter;
-import java.io.Writer;
+import java.io.*;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.zip.GZIPInputStream;
@@ -120,12 +113,12 @@ public String biopaxToFactoid(
     produces = "application/json"
   )
   public String biopaxUrlToFactoid(
-		  @Parameter(description = "URL of a TAR-GZ compressed BioPAX RDF/XML file") @RequestBody String url) {
+		  @Parameter(description = "URL of a BioPAX RDF/XML file") @RequestBody String url) {
 	  BiopaxToFactoid converter = new BiopaxToFactoid();
 	  try {
 		  String body = getContentFromUrl(url);
 		  InputStream is = new ByteArrayInputStream(body.getBytes(StandardCharsets.UTF_8));
-	      Model model = new SimpleIOHandler().convertFromOWL(is);
+      Model model = new SimpleIOHandler().convertFromOWL(is);
 		  return converter.convert(model).toString();
 	  } catch (IllegalStateException | JsonSyntaxException | JsonIOException e) {
 		  throw new ResponseStatusException(HttpStatus.BAD_REQUEST, e.getMessage());
@@ -136,26 +129,26 @@ public String biopaxUrlToFactoid(
 
   private String getContentFromUrl(String url) {
 		InputStream is = null;
-		GZIPInputStream gzipInputStream = null;
 		try {
-			is = new URL(url).openStream();
-			gzipInputStream = new GZIPInputStream(is);
+      try {
+			  is = new GZIPInputStream(new URL(url).openStream());
+      } catch (IOException e) {
+        //e.printStackTrace();
+        is = new URL(url).openStream();
+      }
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
-		InputStreamReader reader = new InputStreamReader(gzipInputStream);
-		BufferedReader in = new BufferedReader(reader);
+    Reader reader = new InputStreamReader(is);
 		Writer writer = new StringWriter();
-
 		char[] buffer = new char[10240];
 	    try {
-			for (int length = 0; (length = reader.read(buffer)) > 0;) {
+			for (int length; (length = reader.read(buffer)) > 0;) {
 			    writer.write(buffer, 0, length);
 			}
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
-
 	  String body = writer.toString();
 	  return body;
 	}

diff --git a/src/test/java/factoid/converter/BiopaxToFactoidTest.java b/src/test/java/factoid/converter/BiopaxToFactoidTest.java
@@ -32,8 +32,8 @@ public void testToJson() throws IOException {
 		Set<Map.Entry<String, JsonElement>> entries = js.entrySet();
 
 		for ( Map.Entry<String, JsonElement> entry : entries ) {
-			Set<String> entityIds1 = new HashSet<String>();
-			Set<String> entityIds2 = new HashSet<String>();
+			Set<String> entityIds1 = new HashSet<>();
+			Set<String> entityIds2 = new HashSet<>();
 			JsonArray arr = entry.getValue().getAsJsonArray();
 			for ( JsonElement el : arr ) {
 				JsonObject obj = el.getAsJsonObject();
@@ -49,7 +49,6 @@ public void testToJson() throws IOException {
 
 			assertEquals(entityIds1, entityIds2);
 		}
-
-
+
 	}
 }
diff --git a/src/test/java/factoid/web/ControllerT.java b/src/test/java/factoid/web/ControllerT.java
@@ -1,5 +1,6 @@
 package factoid.web;
 
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
@@ -70,7 +71,7 @@ public void testBiopaxToFactoid() throws IOException {
   }
 
   @Test
-  public void testBiopaxUrlToFactoid() {
+  public void testBiopaxArchiveUrlToFactoid() {
     String url = "https://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.psp.BIOPAX.owl.gz";
     HttpHeaders headers = new HttpHeaders();
     headers.set("Content-Type", "text/plain");
@@ -79,4 +80,14 @@ public void testBiopaxUrlToFactoid() {
     assertNotNull(res);
     assertTrue(res.contains("interaction"));
   }
+
+  @Test
+  @Disabled
+  public void testPc2UrlToFactoid() {
+    String url = "https://beta.pathwaycommons.org/pc2/get?uri=biofactoid:74ea0716-473c-4a6c-96e0-113a33112827";
+    HttpHeaders headers = new HttpHeaders();
+    HttpEntity<String> request = new HttpEntity<>(url, headers);
+    String res = template.postForObject("/v2/biopax-url-to-json", request, String.class);
+    assertNotNull(res);
+  }
 }