Updates neccessary for new InterPro Scan version 5 SOAP API

git-svn-id: svn://rarepos.cs.uni-tuebingen.de/tfpredict@100 71221333-9ef9-431f-bb7f-117e0a61b720
draeger-lab · Apr 23, 2015 · 659d2d5 · 659d2d5
1 parent d35d9f5
commit 659d2d5
Show file tree

Hide file tree

Showing 19 changed files with 1,524 additions and 24 deletions.
diff --git a/lib/IPRScan5_Axis1.jar b/lib/IPRScan5_Axis1.jar
diff --git a/lib/IPRScan_JAXWS.jar b/lib/IPRScan_JAXWS.jar
diff --git a/lib/ebiws-lib/activation-1.1.1.jar b/lib/ebiws-lib/activation-1.1.1.jar
diff --git a/lib/ebiws-lib/axis-1.4.jar b/lib/ebiws-lib/axis-1.4.jar
diff --git a/lib/ebiws-lib/axis-jaxrpc-1.4.jar b/lib/ebiws-lib/axis-jaxrpc-1.4.jar
diff --git a/lib/ebiws-lib/axis-saaj-1.4.jar b/lib/ebiws-lib/axis-saaj-1.4.jar
diff --git a/lib/ebiws-lib/axis-wsdl4j-1.5.1.jar b/lib/ebiws-lib/axis-wsdl4j-1.5.1.jar
diff --git a/lib/commons-cli-1.2.jar → lib/ebiws-lib/commons-cli-1.2.jar b/lib/commons-cli-1.2.jar → lib/ebiws-lib/commons-cli-1.2.jar
diff --git a/lib/ebiws-lib/commons-codec-1.2.jar b/lib/ebiws-lib/commons-codec-1.2.jar
diff --git a/lib/ebiws-lib/commons-discovery-0.2.jar b/lib/ebiws-lib/commons-discovery-0.2.jar
diff --git a/lib/ebiws-lib/commons-httpclient-3.1.jar b/lib/ebiws-lib/commons-httpclient-3.1.jar
diff --git a/lib/ebiws-lib/commons-logging-1.0.4.jar b/lib/ebiws-lib/commons-logging-1.0.4.jar
diff --git a/lib/ebiws-lib/mail-1.4.1.jar b/lib/ebiws-lib/mail-1.4.1.jar
diff --git a/src/ipr/AbstractWsToolClient.java b/src/ipr/AbstractWsToolClient.java
diff --git a/src/ipr/IPRScan5Client.java b/src/ipr/IPRScan5Client.java
diff --git a/src/ipr/IPRextract.java b/src/ipr/IPRextract.java
@@ -51,19 +51,19 @@ public static Map<String, IprEntry> getSeq2DomainMap(List<String[]> IPRoutput, B
 		Map<String, IprEntry> seq2domain = new HashMap<String, IprEntry>();
 
 		for (int i=0; i < IPRoutput.size(); i++) {
-
 			String[] domain_entry = IPRoutput.get(i);
+			if (domain_entry.length < 12) continue;
 			String sequence_id = domain_entry[0].trim();
 			String domain_id = domain_entry[11].trim();
 			int domain_start = Integer.parseInt(domain_entry[6]);
 			int domain_end = Integer.parseInt(domain_entry[7]);
 			int curr_domain_length = domain_end - domain_start + 1;
-
 			String domain_interval = domain_id + "    " + domain_start + "\t" + domain_end;
 
 			// skip domains for which no InterPro-ID is given
 			if (domain_id.equals("NULL")) {
-				continue;
+				System.out.println("WARNING: Skipped domain " + domain_id + " with missing InterPro-ID");
+			  continue;
 			}
 
 			IprEntry curr_entry;
@@ -146,11 +146,11 @@ public static Map<String, IprRaw> parseIPRoutput(List<String[]> IPRoutput) {
 
 			String[] domain_entry = IPRoutput.get(i);
 
+			if (domain_entry.length < 13) {
+			  continue;
+			}
 			String domain_id = domain_entry[11].trim();
 			// skip domains for which no InterPro-ID is given
-			if (domain_id.equals("NULL")) {
-				continue;
-			}
 			// skip domain IDs which were already added
 			if (ipr_domains.containsKey(domain_id)) {
 				continue;
@@ -174,15 +174,8 @@ public static Map<String, IprRaw> parseIPRoutput(List<String[]> IPRoutput) {
 
 				// parse GO terms for current InterPro domain entry			
 				domain_GOterms = new ArrayList<String>(); 
-				for (String go_entry : domain_go.split(",")) {
-
-					if (go_entry.contains("GO:")) {
-						int start_pos = go_entry.indexOf("(GO:")+1;
-						int end_pos = go_entry.indexOf(")", start_pos);
-
-						go_entry = go_entry.substring(start_pos, end_pos);
-						domain_GOterms.add(go_entry);
-					}
+				for (String go_entry : domain_go.split("\\|")) {
+				  domain_GOterms.add(go_entry);
 				}
 			}
 			IprRaw ipr_domain = new IprRaw(domain_id, domain_names, domain_GOterms);

diff --git a/src/ipr/IPRrun.java b/src/ipr/IPRrun.java
@@ -44,7 +44,7 @@
 
 import javax.xml.rpc.ServiceException;
 
-import uk.ac.ebi.webservices.jaxws.IPRScanClient;
+import uk.ac.ebi.webservices.axis1.stubs.iprscan5.WsResultType;
 
 /**
  * 
@@ -54,7 +54,7 @@
  */
 public class IPRrun {
 
-	public static boolean addSpacerLine = true;
+	public static boolean addSpacerLine = false;
 
 	// fixes bug in current version of InterProScan which removes first line of sequence if header is given
 	private static void addSpacerLine(String seqfile) {
@@ -134,7 +134,7 @@ public ArrayList<String[]> run(String seqfile, String iprpath, String basedir, b
 
 			// submit job
 			try {
-				IPRScanClient.main(param);
+				IPRScan5Client.main(param);
 			} catch (Exception e) {	}
 
 			// restore System.exit
@@ -146,14 +146,15 @@ public ArrayList<String[]> run(String seqfile, String iprpath, String basedir, b
 			// restore System.out
 			System.setOut(orig_stdout);
 
-			IPRScanClient webIPR = new IPRScanClient();
+			IPRScan5Client webIPR = new IPRScan5Client();
 
 			if (!silent) System.out.println("Waiting for " + jobs.size() + " job(s) to finish ...");
 			for (String jobid : jobs) {
 				if (!silent) System.out.println("Polling job \"" + jobid + "\" ...");
 					try {
-						webIPR.getResults(jobid, basedir + jobid, "out");
-						webIPR.getResults(jobid, basedir + jobid, "visual-png");
+					  new File(basedir).mkdirs();
+						webIPR.getResults(jobid, basedir + jobid, "tsv");
+						webIPR.getResults(jobid, basedir + jobid, "svg");
 					} catch (IOException e) {
 						e.printStackTrace();
 					} catch (ServiceException e) {
@@ -166,6 +167,7 @@ public ArrayList<String[]> run(String seqfile, String iprpath, String basedir, b
 			if (silent) {
 				System.setErr(orig_stderr);
 			}
+
 			IPRoutput = readIPROutput(basedir, jobs);
 
 		} else { // local
@@ -199,7 +201,7 @@ private static ArrayList<String[]> readIPROutput(String basedir, ArrayList<Strin
 
 		for (String job : jobs) {
 			try {
-				 BufferedReader br = new BufferedReader(new FileReader(basedir+job+".out.txt"));
+				 BufferedReader br = new BufferedReader(new FileReader(basedir+job+".tsv.txt"));
 				 while ((line = br.readLine()) != null) {
 					 String[] tabpos = line.split("\t");
 					 String seqID = tabpos[0].trim();

diff --git a/src/main/TFpredictMain.java b/src/main/TFpredictMain.java
@@ -53,7 +53,7 @@ public class TFpredictMain {
 	private static boolean trainMode = false;
 
 	private static final String[] validClassifiers = new String[] {"SVM_linear", "KNN", "NaiveBayes"}; 
-	private static final String version = "1.2";
+	private static final String version = "1.3";
 
 	public static final String sabineSpeciesList = "organism_list.txt";
 	public static final String classMappingFile = "class_mapping.txt"; 

diff --git a/src/modes/Predict.java b/src/modes/Predict.java
@@ -820,7 +820,7 @@ private void writeHTMLoutput() {
 					    if (!seq2job.isEmpty() && seq2job.containsKey(seq)) {
 					    	String job = seq2job.get(seq);
 							bw.write("<table>\n");
-							bw.write("  <tr><th> <img src=\"" + job + ".visual-png.png\"/>" + "</th></tr>\n");	
+							bw.write("  <tr><th> <img src=\"" + job + ".svg.svg\"/>" + "</th></tr>\n");	
 							bw.write("  <tr><th> Illustration generated by <a href=https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId="+job+"&tool=iprscan&analysis=visual target=\"_blank\"> InterProScan </a> </th></tr>\n");
 							bw.write("</table>\n\n");
 							bw.write("<br>\n\n");