Minor update - set unif xref.db from data instead of using 'MeSH 2013'

PathwayCommons · Sep 2, 2019 · 3d315ba · 3d315ba
1 parent 9e7d7cf
commit 3d315ba
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Showing 4 changed files with 7 additions and 10 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>pathwaycommons</groupId>
     <artifactId>ctd-to-biopax</artifactId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>1.0.1-SNAPSHOT</version>
     <name>ctd-to-biopax</name>
 
     <description>
@@ -64,8 +64,8 @@
                     <artifactId>maven-compiler-plugin</artifactId>
                     <version>3.5.1</version>
                     <configuration>
-                        <source>1.6</source>
-                        <target>1.6</target>
+                        <source>1.8</source>
+                        <target>1.8</target>
                     </configuration>
                 </plugin>
             </plugins>

diff --git a/src/main/java/org/ctdbase/converter/CTDChemicalConverter.java b/src/main/java/org/ctdbase/converter/CTDChemicalConverter.java
@@ -36,7 +36,7 @@ public Model convert(InputStream inputStream) throws IOException {
                 2 - CasRN
                 3 - Definition
                 4 - ParentIDs (MESH:*)
-                5- TreeNumber
+                5 - TreeNumber
                 6 - ParentTreeNumber
                 7 - Synonyms (sep w/ |)
                 8 - DrugBank IDs
@@ -126,10 +126,10 @@ private RelationshipXref createDrugBankXref(Model model, String dbId) {
     }
 
     private UnificationXref createUnificationXrefFromId(Model model, String chemicalId) {
-        String[] tokens = chemicalId.split(":");
+        String[] tokens = chemicalId.split(":"); //length=2 always
         String uri = CtdUtil.sanitizeId("rxref_" + chemicalId + "_" + UUID.randomUUID());
         UnificationXref xref = create(UnificationXref.class, uri);
-        xref.setDb("MeSH 2013");
+        xref.setDb(tokens[0]); //mesh
         xref.setId(tokens[1]);
         model.add(xref);
         return xref;

diff --git a/src/main/java/org/ctdbase/converter/CTDGeneConverter.java b/src/main/java/org/ctdbase/converter/CTDGeneConverter.java
@@ -61,7 +61,7 @@ private EntityReference generateReference(
             2 - GeneID
             3 - AltGeneIDs
             4 - Synonyms
-            5- BioGRIDIds
+            5 - BioGRIDIds
             6 - PharmGKBs
             7 - UniProtIds
          */

diff --git a/src/test/java/org/ctdbase/converter/CTDInteractionConverterTest.java b/src/test/java/org/ctdbase/converter/CTDInteractionConverterTest.java
@@ -1,12 +1,9 @@
 package org.ctdbase.converter;
 
-import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.model.Model;
 import org.biopax.paxtools.model.level3.*;
 import org.biopax.paxtools.trove.TProvider;
 import org.biopax.paxtools.util.BPCollections;
-import org.ctdbase.util.CtdUtil;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import static org.junit.Assert.*;