Merge pull request #92 from MICommunity/develop

Develop > Master
MICommunity · Sep 27, 2024 · 22b8767 · 22b8767
2 parents c621f90 + f92762f
commit 22b8767
Show file tree

Hide file tree

Showing 46 changed files with 728 additions and 419 deletions.
diff --git a/jami-batch/pom.xml b/jami-batch/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami</groupId>
         <artifactId>psi-jami</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-batch</artifactId>

diff --git a/jami-bridges/bridges-core/pom.xml b/jami-bridges/bridges-core/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>bridges-core</artifactId>

diff --git a/jami-bridges/jami-chebi/pom.xml b/jami-bridges/jami-chebi/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-chebi</artifactId>

diff --git a/jami-bridges/jami-ensembl/pom.xml b/jami-bridges/jami-ensembl/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-ensembl</artifactId>

diff --git a/...jami-ensembl/src/main/java/psidev/psi/mi/jami/bridges/ensembl/AbstractEnsemblFetcher.java b/...jami-ensembl/src/main/java/psidev/psi/mi/jami/bridges/ensembl/AbstractEnsemblFetcher.java
@@ -54,13 +54,7 @@ public abstract class AbstractEnsemblFetcher<T extends Interactor> implements In
 
     private final CachedOlsOntologyTermFetcher ontologyFetcher = new CachedOlsOntologyTermFetcher();
 
-    private final Map<String, CvTerm> biotypeToCVId = new HashMap<>(Map.of(
-            "protein_coding", this.getCVByMIId("MI:0324"), // mRNA
-            "protein_coding_CDS_not_defined", this.getCVByMIId("MI:2190"), // lncRNA
-            "lncRNA", this.getCVByMIId("MI:2190"), // lncRNA
-            "miRNA", this.getCVByMIId("MI:2204"), // miRNA
-            "snRNA", this.getCVByMIId("MI:0607") // snRNA
-    ));
+    private final Map<String, CvTerm> biotypeToCVId = this.buildInitialBioTypeMap();
 
     private final Map<String, String> biotypeToShortestType = new HashMap<>();
 
@@ -230,6 +224,16 @@ private String extractPureIdentifier(String id) {
         return id.split("\\.")[0];
     }
 
+    private Map<String, CvTerm> buildInitialBioTypeMap() {
+        Map<String, CvTerm> map = new HashMap<>();
+        map.computeIfAbsent("protein_coding", k -> this.getCVByMIId("MI:0324")); // mRNA
+        map.computeIfAbsent("protein_coding_CDS_not_defined", k -> this.getCVByMIId("MI:2190")); // lncRNA
+        map.computeIfAbsent("lncRNA", k -> this.getCVByMIId("MI:2190")); // lncRNA
+        map.computeIfAbsent("miRNA", k -> this.getCVByMIId("MI:2204")); // miRNA
+        map.computeIfAbsent("snRNA", k -> this.getCVByMIId("MI:0607")); // snRNA
+        return map;
+    }
+
     private CvTerm getCVByMIId(String id) {
         if (id == null) return null;
         try {

diff --git a/jami-bridges/jami-europubmedcentral/pom.xml b/jami-bridges/jami-europubmedcentral/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <artifactId>jami-bridges</artifactId>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-europubmedcentral</artifactId>
@@ -36,7 +36,7 @@
             <plugin>
                 <groupId>com.helger.maven</groupId>
                 <artifactId>jaxws-maven-plugin</artifactId>
-                <version>2.6</version>
+                <version>2.6.2</version>
                 <executions>
                     <execution>
                         <id>wsimport-from-jdk</id>

diff --git a/jami-bridges/jami-imexcentral/pom.xml b/jami-bridges/jami-imexcentral/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-imexcentral</artifactId>
@@ -16,7 +16,7 @@
             <plugin>
                 <groupId>com.helger.maven</groupId>
                 <artifactId>jaxws-maven-plugin</artifactId>
-                <version>2.6</version>
+                <version>2.6.2</version>
                 <executions>
                     <execution>
                         <goals>

diff --git a/jami-bridges/jami-obo/pom.xml b/jami-bridges/jami-obo/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-obo</artifactId>

diff --git a/jami-bridges/jami-ols/pom.xml b/jami-bridges/jami-ols/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-ols</artifactId>

diff --git a/jami-bridges/jami-ontology-manager/pom.xml b/jami-bridges/jami-ontology-manager/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-ontology-manager</artifactId>

diff --git a/jami-bridges/jami-rna-central/pom.xml b/jami-bridges/jami-rna-central/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-rna-central</artifactId>

diff --git a/...idges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/ApiXrefs.java b/...idges/jami-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/ApiXrefs.java
@@ -61,7 +61,7 @@ static class Result {
         private String gencodeTranscriptId;
         private URL gencodeEnsemblUrl;
 
-        private List<URL> quickgoHits;
+        private Integer quickgoHits;
 
         @Jacksonized
         @Data

diff --git a/...i-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java b/...i-rna-central/src/main/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcher.java
@@ -60,7 +60,8 @@ public Collection<NucleicAcid> fetchByIdentifier(String identifier, int taxID) t
                 nucleicAcid.setSequence(entree.getSequence());
                 nucleicAcid.setFullName(entree.getDescription());
                 addXRefs(nucleicAcid, pureIdentifier, organism);
-                if (type == OLSUtils.rnaCV) nucleicAcid.getAnnotations().add(new DefaultAnnotation(OLSUtils.getCVByName("comment"), "RNA-Central type: " + entree.getRnaType()));
+                if (type == OLSUtils.rnaCV)
+                    nucleicAcid.getAnnotations().add(new DefaultAnnotation(OLSUtils.getCVByName("comment"), "RNA-Central type: " + entree.getRnaType()));
 
                 return List.of(nucleicAcid);
             } else return List.of();
@@ -73,14 +74,19 @@ public Collection<NucleicAcid> fetchByIdentifier(String identifier, int taxID) t
     private void addXRefs(NucleicAcid nucleicAcid, String pureIdentifier, Organism organism) {
         try {
             URL url = new URL(String.format(XREFS_URL, pureIdentifier));
+            int count = 0;
+            int targetCount;
 
-            while (url != null) {
+            do {
                 ApiXrefs xrefs = OLSUtils.mapper.readValue(url, ApiXrefs.class);
+                targetCount = xrefs.getCount();
+                count += xrefs.getResults().size();
                 url = xrefs.getNext() != null ? new URL(xrefs.getNext().toString().replace("http", "https")) : null;
                 xrefs.getResults().stream()
-                        .filter(result -> result.getAccession().getSpecies().equals(organism.getScientificName()) || result.getTaxid().equals(organism.getTaxId()))
+                        .filter(result -> result.getTaxid().equals(organism.getTaxId()) ||
+                                (result.getAccession().getSpecies() != null && result.getAccession().getSpecies().equals(organism.getScientificName())))
                         .forEach(result -> this.extractXrefsAndAliases(nucleicAcid, result));
-            }
+            } while (count < targetCount);
 
         } catch (IOException e) {
             throw new RuntimeException(e);

diff --git a/...a-central/src/test/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcherTest.java b/...a-central/src/test/java/psidev/psi/mi/jami/bridges/rna/central/RNACentralFetcherTest.java
@@ -41,9 +41,11 @@ public void testPDBeXref() throws BridgeFailedException {
         NucleicAcid acid = nucleicAcids.iterator().next();
         assertEquals("transfer rna", acid.getInteractorType().getFullName());
         List<Xref> xrefs = acid.getXrefs().stream().filter(xref -> xref.getDatabase().getShortName().equals("pdbe")).collect(Collectors.toList());
-        assertFalse(xrefs.isEmpty());
+        assertTrue(xrefs.isEmpty());
+        List<Xref> identifiers = acid.getIdentifiers().stream().filter(xref -> xref.getDatabase().getShortName().equals("pdbe")).collect(Collectors.toList());
+        assertFalse(identifiers.isEmpty());
         assertTrue("URS0002311975_9606 should have a PDB Xref to 7ONU",
-                xrefs.stream().anyMatch(xref -> xref.getId().equals("7ONU")));
+                identifiers.stream().anyMatch(xref -> xref.getId().equals("7ONU")));
     }
 
 
@@ -70,36 +72,38 @@ public void testEnsemblXref() throws BridgeFailedException {
         // Side tests
 
         assertTrue("URS0000031E12_9606 should have a RefSeq Xref to NR_029480",
-                acid.getXrefs().stream().anyMatch(x -> x.getId().equals("NR_029480")));
+                acid.getIdentifiers().stream().anyMatch(x -> x.getId().equals("NR_029480")));
 
         assertTrue("URS0000031E12_9606 should have a miRBase Xref to MI0000064",
-                acid.getXrefs().stream().anyMatch(x -> x.getId().equals("MI0000064")));
+                acid.getIdentifiers().stream().anyMatch(x -> x.getId().equals("MI0000064")));
 
         assertTrue("All xrefs should have a qualifier",
-                acid.getXrefs().stream().allMatch(xref -> xref.getQualifier() != null));
+                acid.getIdentifiers().stream().allMatch(xref -> xref.getQualifier() != null));
     }
 
     @Test
     public void testRefSeqXref() throws BridgeFailedException {
-        // https://rnacentral.org/api/v1/rna/URS000075C808_9606.json
-        // https://rnacentral.org/api/v1/rna/URS000075C808/xrefs.json
-        Collection<NucleicAcid> nucleicAcids = fetcher.fetchByIdentifier("URS000075C808_9606");
+        // https://rnacentral.org/api/v1/rna/URS00026A23F2_9606.json
+        // https://rnacentral.org/api/v1/rna/URS00026A23F2/xrefs.json
+        Collection<NucleicAcid> nucleicAcids = fetcher.fetchByIdentifier("URS00026A23F2_9606");
         NucleicAcid acid = nucleicAcids.iterator().next();
         List<Xref> xrefs = acid.getXrefs().stream().filter(xref -> xref.getDatabase().getShortName().equals("refseq")).collect(Collectors.toList());
-        assertFalse(xrefs.isEmpty());
-        assertTrue("URS000075C808_9606 should have a RefSeq Xref to NR_003716",
-                xrefs.stream().anyMatch(xref -> xref.getId().equals("NR_003716")));
+        assertTrue(xrefs.isEmpty());
+        List<Xref> identifiers = acid.getIdentifiers().stream().filter(xref -> xref.getDatabase().getShortName().equals("refseq")).collect(Collectors.toList());
+        assertFalse(identifiers.isEmpty());
+        assertTrue("URS00026A23F2_9606 should have a RefSeq Xref to NR_003716",
+                identifiers.stream().anyMatch(xref -> xref.getId().equals("NR_003716")));
     }
 
     @Test
     public void testGeneNameAlias() throws BridgeFailedException {
-        // https://rnacentral.org/api/v1/rna/URS000075C808_9606.json
-        // https://rnacentral.org/api/v1/rna/URS000075C808/xrefs.json
-        Collection<NucleicAcid> nucleicAcids = fetcher.fetchByIdentifier("URS000075C808_9606");
+        // https://rnacentral.org/api/v1/rna/URS00026A23F2_9606.json
+        // https://rnacentral.org/api/v1/rna/URS00026A23F2/xrefs.json
+        Collection<NucleicAcid> nucleicAcids = fetcher.fetchByIdentifier("URS00026A23F2_9606");
         NucleicAcid acid = nucleicAcids.iterator().next();
         List<Alias> aliases = acid.getAliases().stream().filter(alias -> alias.getType().getShortName().equals("gene name")).collect(Collectors.toList());
-        assertEquals("URS000075C808_9606 should only have one Gene Name alias", 1, aliases.size());
-        assertTrue("URS000075C808_9606 gene name should be HOTAIR",
+        assertEquals("URS00026A23F2_9606 should only have one Gene Name alias", 1, aliases.size());
+        assertTrue("URS00026A23F2_9606 gene name should be HOTAIR",
                 aliases.stream().anyMatch(alias -> alias.getName().equals("HOTAIR")));
     }
 }
diff --git a/jami-bridges/jami-uniprot-protein-api/pom.xml b/jami-bridges/jami-uniprot-protein-api/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-uniprot-protein-api</artifactId>

diff --git a/...pi/src/test/java/psidev/psi/mi/jami/bridges/uniprot/rest/UniprotProteinAPIClientTest.java b/...pi/src/test/java/psidev/psi/mi/jami/bridges/uniprot/rest/UniprotProteinAPIClientTest.java
@@ -43,7 +43,7 @@ public void getTremblIdsForAccession() throws UniprotProteinAPIClientException {
         for (String upi : upis) {
             System.out.println(upi);
         }
-        Assert.assertEquals(8, upis.size());
+        Assert.assertEquals(3, upis.size());
 
     }
 
@@ -128,7 +128,7 @@ public void getTremblIdsForSequence() throws UniprotProteinAPIClientException {
         for (String upi : upis) {
             System.out.println(upi);
         }
-        Assert.assertEquals(8, upis.size());
+        Assert.assertEquals(3, upis.size());
 
     }
 
@@ -152,7 +152,7 @@ public void getUPEntriesForSequence() throws UniprotProteinAPIClientException {
         System.out.println(upi.getAccession());
         Assert.assertNotNull(upi);
         Assert.assertEquals("UPI000003EADC", upi.getAccession());
-        Assert.assertEquals(12, upi.getDbReference().size());
+        Assert.assertEquals(7, upi.getDbReference().size());
 
     }
 

diff --git a/jami-bridges/jami-uniprot-taxonomy/pom.xml b/jami-bridges/jami-uniprot-taxonomy/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-uniprot-taxonomy</artifactId>

diff --git a/jami-bridges/jami-uniprot/pom.xml b/jami-bridges/jami-uniprot/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-uniprot</artifactId>

diff --git a/jami-bridges/jami-unisave/pom.xml b/jami-bridges/jami-unisave/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.5.1-SNAPSHOT</version>
+        <version>3.6.0</version>
     </parent>
 
     <artifactId>jami-unisave</artifactId>