From 1055858fb1c685f77ec3398723cf58f6a591f998 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 6 Oct 2016 16:16:08 +0100
Subject: [PATCH] JAL-2254 map error text in root node of EMBL XML response

---
 resources/embl_mapping.xml                   |    3 +++
 src/jalview/datamodel/xdb/embl/EmblFile.java |   12 ++++++++++++
 src/jalview/ws/dbsources/EmblXmlSource.java  |    5 +++++
 3 files changed, 20 insertions(+)

diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
index 01b921a..3b80821 100644
--- 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
--- 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
--- 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)
     {
-- 
1.7.10.2