*/
package jalview.ext.ensembl;
+import jalview.analysis.AlignmentUtils;
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
{
// domain properties lookup keys:
- protected static final String ENSEMBL_DOMAIN = "ENSEMBL_DOMAIN";
- protected static final String ENSEMBL_GENOMES_DOMAIN = "ENSEMBL_GENOMES_DOMAIN";
+ protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
+
+ protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
// domain properties default values:
- protected static final String DEFAULT_ENSEMBL_DOMAIN = "http://rest.ensembl.org";
- protected static final String DEFAULT_ENSEMBL_GENOMES_DOMAIN = "http://rest.ensemblgenomes.org";
+ protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
+
+ // ensemblgenomes REST service merged to ensembl 9th April 2019
+ protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
/*
* accepts ENSG/T/E/P with 11 digits
protected final String ensemblDomain;
+ protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
+
+ protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+
+ protected static final String OBJECT_TYPE_GENE = "Gene";
+
+ protected static final String PARENT = "Parent";
+
+ protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
+
+ protected static final String OBJECT_TYPE = "object_type";
+
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
* the default domain names may be overridden in .jalview_properties;
* this allows an easy change from http to https in future if needed
*/
- ensemblDomain = Cache.getDefault(ENSEMBL_DOMAIN, DEFAULT_ENSEMBL_DOMAIN);
- ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_DOMAIN,
- DEFAULT_ENSEMBL_GENOMES_DOMAIN);
+ ensemblDomain = Cache
+ .getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
+ ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+ DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
domain = ensemblDomain;
}
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- if (ensemblGenomesDomain.equals(getDomain()))
- {
- return DBRefSource.ENSEMBLGENOMES;
- }
return DBRefSource.ENSEMBL;
}
protected void setDomain(String d)
{
- domain = d;
+ domain = d == null ? null : d.trim();
}
}