Merge branch 'master' of github.com:VEuPathDB/ApiCommonWebsite

VEuPathDB · Dec 6, 2023 · 54795c9 · 54795c9
2 parents cd7bea4 + 965573f
commit 54795c9
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Showing 4 changed files with 58 additions and 24 deletions.
diff --git a/...rc/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java b/...rc/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java
@@ -85,17 +85,26 @@ public List<List<String>> getRecordAsBedFields(RecordInstance record) throws Wdk
     int featureEnd = Integer.valueOf(m.group(3));
 
     StrandDirection strand = StrandDirection.fromSign(m.group(4));
-    if(_reverseAndComplement) {
-      strand = strand.opposite();
-    }
+
     int fivePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_FIVE_PRIME_UTR_LENGTH);
     int threePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_THREE_PRIME_UTR_LENGTH);
 
-    Integer segmentStart = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength);
-    Integer segmentEnd = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength);
+    Integer upstreamPosition = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand);
+    Integer downstreamPosition = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand);
+
+    Integer segmentStart = upstreamPosition;
+    Integer segmentEnd = downstreamPosition;
+    if(strand.getSign().equals("-")) {
+        segmentStart = downstreamPosition;
+        segmentEnd = upstreamPosition;
+    }
 
     DeflineBuilder defline = new DeflineBuilder(featureId);
 
+    if(_reverseAndComplement) {
+      strand = strand.opposite();
+    }
+
     if(_requestedDeflineFields.contains("organism")){
       defline.appendRecordAttribute(record, ATTR_ORGANISM);
     }
@@ -132,18 +141,35 @@ private Matcher matchLocationCoords(RecordInstance record, String key, Pattern p
   private static int getPositionGenomic(
       Integer featureStart, Integer featureEnd, 
       int offset, OffsetSign sign, Anchor anchor,
-      int fivePrimeUtrLength, int threePrimeUtrLength
+      int fivePrimeUtrLength, int threePrimeUtrLength,
+      StrandDirection strand 
       ) throws WdkModelException{
-    if (sign == OffsetSign.minus) {
-      offset = - offset;
-    }
-    switch(anchor) {
-      case Start: return featureStart + offset;
-      case CodeStart: return featureStart + fivePrimeUtrLength + offset;
-      case End: return featureEnd + offset;
-      case CodeEnd: return featureEnd - threePrimeUtrLength + offset;
-      default: throw new WdkModelException("Unsupported anchor type: " + anchor);
-    }
+
+      if(strand.getSign().equals("-")) {
+
+          if (sign == OffsetSign.plus) {
+              offset = - offset;
+          }
+          switch(anchor) {
+          case Start: return featureEnd + offset;
+          case CodeStart: return featureEnd - fivePrimeUtrLength + offset;
+          case End: return featureStart + offset;
+          case CodeEnd: return featureStart + threePrimeUtrLength + offset;
+          default: throw new WdkModelException("Unsupported anchor type: " + anchor);
+          }
+      }
+      else {
+          if (sign == OffsetSign.minus) {
+              offset = - offset;
+          }
+          switch(anchor) {
+          case Start: return featureStart + offset;
+          case CodeStart: return featureStart + fivePrimeUtrLength + offset;
+          case End: return featureEnd + offset;
+          case CodeEnd: return featureEnd - threePrimeUtrLength + offset;
+          default: throw new WdkModelException("Unsupported anchor type: " + anchor);
+          }
+      }
   }
 
   private static String getPositionDescGenomic(int offset, OffsetSign sign, Anchor anchor) throws WdkModelException{

diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java
@@ -1,6 +1,7 @@
 package org.apidb.apicommon.model.report.bed.util;
 
 import java.util.List;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
@@ -30,6 +31,12 @@ public static List<String> bed6(String featureId, Integer start, Integer end, De
 
 
   public static List<String> bed12(String featureId, DeflineBuilder defline, StrandDirection strand, List<Integer> subfeatureStarts, List<Integer> subfeatureEnds){
+
+      if(strand.getSign().equals("-")) {
+          Collections.reverse(subfeatureStarts);
+          Collections.reverse(subfeatureEnds);
+      }
+
     Integer start = Collections.min(subfeatureStarts);
     Integer end = Collections.max(subfeatureEnds);
 
@@ -44,9 +51,10 @@ public static List<String> bed12(String featureId, DeflineBuilder defline, Stran
       .collect(Collectors.joining(","));
 
     String blockStartsStr =
-      IntStream.range(0, numBlocks)
-      .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString())
-      .collect(Collectors.joining(","));
+        IntStream.range(0, numBlocks)
+        .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString())
+        .collect(Collectors.joining(","));
+
 
     Integer zeroBasedStart = locationToZeroBased(start);
 

diff --git a/...src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java b/...src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java
@@ -444,7 +444,7 @@ private Optional<String> getBulkSubfeatureSql(String feature,
   private static void appendAttributes(JSONObject json, ResultSet rs) throws SQLException {
     String attrsStr = rs.getString("ATTS");
     if (rs.wasNull()) return;
-    String attrs[] = attrsStr.split(";");
+    String attrs[] = attrsStr.split(";;");
     for (int i = 0; i < attrs.length; i++) {
       String attr[] = attrs[i].split("=");
       if (attr.length > 1) {
@@ -499,7 +499,7 @@ private Optional<String> getSequenceId(String idColName, String attrsTableName,
   private static String replaceSqlMacros(String sql, String start, String end, String seqId, Map<String, String> qp) {
     sql = sql.replaceAll("\\$base_start", start);
     sql = sql.replaceAll("\\$rend", end);
-    sql = sql.replaceAll("\\$dlm",";");
+    sql = sql.replaceAll("\\$dlm",";;");
     sql = sql.replaceAll("\\$srcfeature_id", seqId);
 
     // skip query params we know are used for "control" purposes (not SQL macros)

diff --git a/Site/yarn.lock b/Site/yarn.lock
@@ -3,6 +3,6 @@
 
 
 "@veupathdb/genomics-site@^1.0.49":
-  version "1.0.87"
-  resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.87.tgz#2a1484957a0f54054664f333e7b099317b20fa0e"
-  integrity sha512-q2Jc1ifh+INBsxo3SJaX/ZC1ys5BfsTfpbKbRwS1dIeANC97nkMVMaj5OHH/tDA8B1ToxCKfokiweBIVoMmqLg==
+  version "1.0.100"
+  resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.100.tgz#ebb7d5a5fcd56d069d101a3ab71797d839b89f8f"
+  integrity sha512-xGdEKfqMAFOfhDxoIIynU6o7cGIq7xQJri2y0g3fFJNwHnOPavJnwEIADmx81i9vwAHaCAW8GG/r1sLW8pJbLA==