A fix - refs #294.

PathwayCommons · Apr 23, 2018 · 8b80461 · 8b80461
1 parent 7de37f7
commit 8b80461
Showing 1 changed file with 33 additions and 27 deletions.
diff --git a/cpath-cli/src/main/java/cpath/analysis/LandingAndLinkout.java b/cpath-cli/src/main/java/cpath/analysis/LandingAndLinkout.java
@@ -11,6 +11,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
 
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
@@ -24,37 +25,42 @@ public class LandingAndLinkout implements Analysis<Model> {
 //    public static final String JAVA_OPTION_IDTYPE = "cpath.analysis.linkout.type";
     private static final CPathSettings cpath = CPathSettings.getInstance();
 
-    @Autowired
-    CPathService service;
-
     @Override
     public void execute(Model model) {
-        //export the list of unique UniProt primary accession numbers
-        LOG.info("creating the list of primary uniprot IDs...");
-        Set<String> acs = new TreeSet<>();
-        //exclude publication xrefs
-        Set<Xref> xrefs = new HashSet<>(model.getObjects(UnificationXref.class));
-        xrefs.addAll(model.getObjects(RelationshipXref.class));
-        long left = xrefs.size();
-        for(Xref x : xrefs) {
-            String id = x.getId();
-            if (CPathUtils.startsWithAnyIgnoreCase(x.getDb(),"uniprot")
-                    && id != null && !acs.contains(id))
-                acs.addAll(service.map(id, "UNIPROT"));
-            if(--left % 10000 == 0)
-                LOG.info(left + " xrefs to map...");
-        }
-
-        PrintWriter writer;
+        ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext(
+                new String[] { "classpath:META-INF/spring/applicationContext-jpa.xml" });
         try {
-            writer = new PrintWriter("uniprot.txt");
-        } catch (FileNotFoundException e) {
-            throw new RuntimeException("", e);
+            final CPathService service = context.getBean(CPathService.class);
+            //export the list of unique UniProt primary accession numbers
+            LOG.info("creating the list of primary uniprot IDs...");
+            Set<String> acs = new TreeSet<>();
+            //exclude publication xrefs
+            Set<Xref> xrefs = new HashSet<>(model.getObjects(UnificationXref.class));
+            xrefs.addAll(model.getObjects(RelationshipXref.class));
+            long left = xrefs.size();
+            for (Xref x : xrefs) {
+                String id = x.getId();
+                if (CPathUtils.startsWithAnyIgnoreCase(x.getDb(), "uniprot")
+                        && id != null && !acs.contains(id))
+                    acs.addAll(service.map(id, "UNIPROT"));
+                if (--left % 10000 == 0)
+                    LOG.info(left + " xrefs to map...");
+            }
+
+            PrintWriter writer;
+            try {
+                writer = new PrintWriter("uniprot.txt");
+            } catch (FileNotFoundException e) {
+                throw new RuntimeException("", e);
+            }
+            writer.println(String.format("#PathwayCommons v%s - primary UniProt accession numbers:", cpath.getVersion()));
+            for (String ac : acs)
+                writer.println(ac);
+            writer.close();
+
+        } finally {
+            context.close();
         }
-        writer.println(String.format("#PathwayCommons v%s - primary UniProt accession numbers:", cpath.getVersion()));
-        for(String ac : acs)
-            writer.println(ac);
-        writer.close();
 
         LOG.info("generated uniprot.txt");
     }