From: gmungoc Date: Thu, 25 Oct 2018 14:41:21 +0000 (+0100) Subject: JAL-3143 comma-delimited feature attributes for alleles, X-Git-Tag: Release_2_11_1_0~58^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e4eca89202963f5f7c95ac002efd64fe0e79a25c;p=jalview.git JAL-3143 comma-delimited feature attributes for alleles, clinical_significance --- diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java index a133381..9a45dda 100644 --- a/src/jalview/ext/ensembl/EnsemblFeatures.java +++ b/src/jalview/ext/ensembl/EnsemblFeatures.java @@ -26,6 +26,7 @@ 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; @@ -129,15 +130,11 @@ class EnsemblFeatures extends EnsemblRestClient int end = Integer.parseInt(obj.get("end").toString()); String source = obj.get("source").toString(); String strand = obj.get("strand").toString(); - Object value = obj.get("consequence_type"); - value = obj.get("alleles"); - JSONArray allelesArray = (JSONArray) value; - String alleles = allelesArray == null ? null - : allelesArray.toString(); // todo need as a List? - value = obj.get("clinical_significance"); - JSONArray clinSigArray = (JSONArray) value; - String clinSig = clinSigArray == null ? null - : clinSigArray.toString(); + 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' diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 7a37c8a..5dc701d 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -915,10 +915,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /** * Answers true if the feature type is either 'NMD_transcript_variant' or - * 'transcript' or one of its sub-types in the Sequence Ontology. This is - * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl + * 'transcript' (or one of its sub-types in the Sequence Ontology). This is + * because NMD_transcript_variant behaves like 'transcript' in Ensembl * although strictly speaking it is not (it is a sub-type of * sequence_variant). + *

+ * (This test was needed when fetching transcript features as GFF. As we are + * now fetching as JSON, all features have type 'transcript' so the check for + * NMD_transcript_variant is redundant. Left in for any future case arising.) * * @param featureType * @return diff --git a/src/jalview/util/JSONUtils.java b/src/jalview/util/JSONUtils.java new file mode 100644 index 0000000..cdfc88e --- /dev/null +++ b/src/jalview/util/JSONUtils.java @@ -0,0 +1,34 @@ +package jalview.util; + +import org.json.simple.JSONArray; + +public class JSONUtils +{ + + /** + * Converts a JSONArray of values to a string as a comma-separated list. + * Answers null if the array is null or empty. + * + * @param jsonArray + * @return + */ + public static String arrayToList(JSONArray jsonArray) + { + if (jsonArray == null) + { + return null; + } + + StringBuilder sb = new StringBuilder(); + for (int i = 0; i < jsonArray.size(); i++) + { + if (i > 0) + { + sb.append(","); + } + sb.append(jsonArray.get(i).toString()); + } + return sb.length() == 0 ? null : sb.toString(); + } + +} diff --git a/test/jalview/util/JSONUtilsTest.java b/test/jalview/util/JSONUtilsTest.java new file mode 100644 index 0000000..45f1c48 --- /dev/null +++ b/test/jalview/util/JSONUtilsTest.java @@ -0,0 +1,26 @@ +package jalview.util; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertNull; + +import org.json.JSONException; +import org.json.simple.JSONArray; +import org.testng.annotations.Test; + +public class JSONUtilsTest +{ + @Test(groups = "Functional") + public void testArrayToList() throws JSONException + { + assertNull(JSONUtils.arrayToList(null)); + + JSONArray ja = new JSONArray(); + assertNull(JSONUtils.arrayToList(null)); + + ja.add("hello"); + assertEquals(JSONUtils.arrayToList(ja), "hello"); + + ja.add("world"); + assertEquals(JSONUtils.arrayToList(ja), "hello,world"); + } +}