+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.io.FeaturesFile;
-import jalview.io.FileParse;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.JSONUtils;
+import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
/**
* A client for fetching and processing Ensembl feature data in GFF format by
* calling the overlap REST service
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
- List<String> queries = new ArrayList<String>();
+ List<String> queries = new ArrayList<>();
queries.add(query);
- FileParse fp = getSequenceReader(queries);
- FeaturesFile fr = new FeaturesFile(fp);
- return new Alignment(fr.getSeqsAsArray());
+ BufferedReader fp = getSequenceReader(queries);
+ if (fp == null)
+ {
+ return null;
+ }
+
+ SequenceI seq = parseFeaturesJson(fp);
+ return new Alignment(new SequenceI[] { seq });
+ }
+
+ /**
+ * Parses the JSON response into Jalview sequence features and attaches them
+ * to a dummy sequence
+ *
+ * @param br
+ * @return
+ */
+ private SequenceI parseFeaturesJson(BufferedReader br)
+ {
+ SequenceI seq = new Sequence("Dummy", "");
+
+ JSONParser jp = new JSONParser();
+ try
+ {
+ JSONArray responses = (JSONArray) jp.parse(br);
+ Iterator rvals = responses.iterator();
+ while (rvals.hasNext())
+ {
+ try
+ {
+ JSONObject obj = (JSONObject) rvals.next();
+ String type = obj.get("feature_type").toString();
+ int start = Integer.parseInt(obj.get("start").toString());
+ int end = Integer.parseInt(obj.get("end").toString());
+ String source = obj.get("source").toString();
+ String strand = obj.get("strand").toString();
+ Object phase = obj.get("phase");
+ String alleles = JSONUtils
+ .arrayToList((JSONArray) obj.get("alleles"));
+ String clinSig = JSONUtils
+ .arrayToList(
+ (JSONArray) obj.get("clinical_significance"));
+
+ /*
+ * convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
+ * so as to have a valid SO term for the feature type
+ * ('gene', 'exon', 'transcript' don't need any conversion)
+ */
+ if ("variation".equals(type))
+ {
+ type = SequenceOntologyI.SEQUENCE_VARIANT;
+ }
+ else if (SequenceOntologyI.CDS.equalsIgnoreCase((type)))
+ {
+ type = SequenceOntologyI.CDS;
+ }
+
+ String desc = getFirstNotNull(obj, "alleles", "external_name",
+ JSON_ID);
+ SequenceFeature sf = new SequenceFeature(type, desc, start, end,
+ source);
+ sf.setStrand("1".equals(strand) ? "+" : "-");
+ if (phase != null)
+ {
+ sf.setPhase(phase.toString());
+ }
+ setFeatureAttribute(sf, obj, "id");
+ setFeatureAttribute(sf, obj, "Parent");
+ setFeatureAttribute(sf, obj, "consequence_type");
+ sf.setValue("alleles", alleles);
+ sf.setValue("clinical_significance", clinSig);
+
+ seq.addSequenceFeature(sf);
+ } catch (Throwable t)
+ {
+ // ignore - keep trying other features
+ }
+ }
+ } catch (ParseException | IOException e)
+ {
+ // ignore
+ }
+
+ return seq;
+ }
+
+ /**
+ * Returns the first non-null attribute found (if any) as a string, formatted
+ * suitably for display as feature description or tooltip. Answers null if
+ * none of the attribute keys is present.
+ *
+ * @param obj
+ * @param keys
+ * @return
+ */
+ protected String getFirstNotNull(JSONObject obj, String... keys)
+ {
+ String desc = null;
+
+ for (String key : keys)
+ {
+ Object val = obj.get(key);
+ if (val != null)
+ {
+ String s = val instanceof JSONArray
+ ? JSONUtils.arrayToList((JSONArray) val)
+ : val.toString();
+ if (!s.isEmpty())
+ {
+ return s;
+ }
+ }
+ }
+ return desc;
+ }
+
+ /**
+ * A helper method that reads the 'key' entry in the JSON object, and if not
+ * null, sets its string value as an attribute on the sequence feature
+ *
+ * @param sf
+ * @param obj
+ * @param key
+ */
+ protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+ String key)
+ {
+ Object object = obj.get(key);
+ if (object != null)
+ {
+ sf.setValue(key, object.toString());
+ }
}
/**
urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
- urlstring.append("?content-type=text/x-gff3");
+ urlstring.append("?content-type=" + getResponseMimeType());
+
+ /*
+ * specify object_type=gene in case is shared by transcript and/or protein;
+ * currently only fetching features for gene sequences;
+ * refactor in future if needed to fetch for transcripts
+ */
+ urlstring.append("&").append(OBJECT_TYPE).append("=")
+ .append(OBJECT_TYPE_GENE);
/*
* specify features to retrieve
* @see http://rest.ensembl.org/documentation/info/overlap_id
- * could make the list a configurable entry in jalview.properties
+ * could make the list a configurable entry in .jalview_properties
*/
for (EnsemblFeatureType feature : featuresWanted)
{
* describes the required encoding of the response.
*/
@Override
- protected String getRequestMimeType(boolean multipleIds)
+ protected String getRequestMimeType()
{
- return "text/x-gff3";
+ return "application/json";
}
/**
- * Returns the MIME type for GFF3.
+ * Returns the MIME type wanted for the response
*/
@Override
protected String getResponseMimeType()
{
- return "text/x-gff3";
+ return "application/json";
}
/**
git://source.jalview.org / jalview.git / blobdiff