JAL-2254 map error text in root node of EMBL XML response

diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
index 01b921a..3b80821 100644 (file)
--- a/resources/embl_mapping.xml
+++ b/resources/embl_mapping.xml
@@ -28,6 +28,9 @@
        -->
        <class name="jalview.datamodel.xdb.embl.EmblFile">
                <map-to xml="ROOT"/>
+               <field name="text" type="string">
+                       <bind-xml node="text"/>
+               </field>
                <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
                        <bind-xml name="entry"/>
                </field>

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index a95f6e5..1dd854a 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -46,6 +46,8 @@ public class EmblFile
 
   Vector<EmblError> errors;
 
+  String text;
+
   /**
    * @return the entries
    */
@@ -187,4 +189,14 @@ public class EmblFile
       }
     }
   }
+
+  public String getText()
+  {
+    return text;
+  }
+
+  public void setText(String text)
+  {
+    this.text = text;
+  }
 }

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index f672e8b..b139574 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -102,6 +102,11 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
     }
 
+    /*
+     * invalid accession gets a reply with no <entry> elements, text content of
+     * EmbFile reads something like (e.g.) this ungrammatical phrase
+     * Entry: <acc> display type is either not supported or entry is not found.
+     */
     List<SequenceI> peptides = new ArrayList<SequenceI>();
     if (efile != null && efile.getEntries() != null)
     {