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JAL-2679 use object_type=Transcript for lookup of Parent for Protein
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSymbol.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSymbol.java
b/src/jalview/ext/ensembl/EnsemblSymbol.java
index
671bfec
..
e3b6c93
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/
src/jalview/ext/ensembl/EnsemblSymbol.java
@@
-42,6
+42,8
@@
import org.json.simple.parser.ParseException;
*/
public class EnsemblSymbol extends EnsemblXref
{
*/
public class EnsemblSymbol extends EnsemblXref
{
+ private static final String GENE = "gene";
+ private static final String TYPE = "type";
/**
* Constructor given the target domain to fetch data from
*
/**
* Constructor given the target domain to fetch data from
*
@@
-73,9
+75,9
@@
public class EnsemblSymbol extends EnsemblXref
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String id = val.get("id").toString();
- String type = val.get("type").toString();
- if (id != null && "gene".equals(type))
+ String id = val.get(ID).toString();
+ String type = val.get(TYPE).toString();
+ if (id != null && GENE.equals(type))
{
result = id;
break;
{
result = id;
break;
@@
-105,7
+107,7
@@
public class EnsemblSymbol extends EnsemblXref
StringBuilder sb = new StringBuilder();
sb.append(getDomain()).append("/xrefs/symbol/")
.append(species.toString()).append("/").append(id)
StringBuilder sb = new StringBuilder();
sb.append(getDomain()).append("/xrefs/symbol/")
.append(species.toString()).append("/").append(id)
- .append("?content-type=application/json");
+ .append(CONTENT_TYPE_JSON);
for (String t : type)
{
sb.append("&object_type=").append(t);
for (String t : type)
{
sb.append("&object_type=").append(t);
@@
-139,21
+141,19
@@
public class EnsemblSymbol extends EnsemblXref
{
for (String query : queries)
{
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
{
- if (taxon.isModelOrganism())
+ URL url = getUrl(query, taxon, GENE);
+ if (url != null)
{
{
- URL url = getUrl(query, taxon, "gene");
- if (url != null)
+ br = getHttpResponse(url, ids);
+ if (br != null)
{
{
- br = getHttpResponse(url, ids);
- if (br != null)
+ String geneId = parseSymbolResponse(br);
+ System.out.println(url + " returned " + geneId);
+ if (geneId != null && !result.contains(geneId))
{
{
- String geneId = parseSymbolResponse(br);
- if (geneId != null && !result.contains(geneId))
- {
- result.add(geneId);
- }
+ result.add(geneId);
}
}
}
}
}
}