Merge pull request #2408 from intermine/dev

Release 5.0.4

.github/workflows/im-build.yml

@@ -37,10 +37,10 @@ jobs:
       uses: actions/setup-java@v1
       with:
         java-version: '11'
-    - name: Set up python 2.7
+    - name: Set up python 3.7
       uses: actions/setup-python@v2
       with:
-        python-version: '2.7'  
+        python-version: '3.7'
     - name: Install PostgreSQL client
       run: |
         sudo apt-get update -y
@@ -83,10 +83,10 @@ jobs:
       uses: actions/setup-java@v1
       with:
         java-version: '11'
-    - name: Set up python 2.7
+    - name: Set up python 3.7
       uses: actions/setup-python@v2
       with:
-        python-version: '2.7'  
+        python-version: '3.7'
     - name: Install PostgreSQL client
       run: |
         sudo apt-get update -y

README.md

@@ -3,7 +3,7 @@ InterMine
 
 Master: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=master)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
 Dev: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=dev)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
-[![Version](http://img.shields.io/badge/version-5.0.3-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
+[![Version](http://img.shields.io/badge/version-5.0.4-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
 [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE)
 [![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine)
 [![Conda](https://anaconda.org/anaconda/conda-build/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine)

RELEASE_NOTES

@@ -7,6 +7,19 @@
  * information or http://www.gnu.org/copyleft/lesser.html.
  *
  */
+InterMine 5.0.4 (Dicember 2021)
+
+#2324 - Remove dependency from EBI maven nexus repo
+#2377 - Updated GFF3Record (thanks @sammyjava)
+#2396 - Biogrid extension
+#2392 - Public name can be taken by deleted account
+#2397 - Implement a new WS to summarise templates
+#2398 - Implement a new WS to precompute templates
+#2399 - Update the GET /templates WS to show which templates user can make change
+#2400 - Update the PUT /bluegenes-properties WS to use body
+#2402 - WebProperties WS returns blugenes properties too
+#2404 - Update CI to use Python 3.7
+
 InterMine 5.0.3 (June 2021)
 
 #2375 - Update interpro_keys.properties

bio/build.gradle

@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version = '5.0.3'
+    version = '5.0.4'
 
     apply plugin: "java"
     apply plugin: "maven"
@@ -14,7 +14,7 @@ subprojects {
         mavenLocal()
         mavenCentral()
         maven {
-            url 'https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/'
+            url 'https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/'
         }
     }
 

bio/core/src/main/java/org/intermine/bio/io/gff3/GFF3Record.java

@@ -330,6 +330,18 @@ public List<String> getNames() {
         return null;
     }
 
+    /**
+    * Return the list of the Symbol field from the attributes of this record.
+    * @return the Symbol from the attributes of this record or null if there isn't a value
+    */
+    public List<String> getSymbols() {
+        if (getAttributes().containsKey("Symbol")) {
+            return getAttributes().get("Symbol");
+        } else {
+            return null;
+        }
+    }
+
     /**
      * Return the first value of the Alias field from the attributes of this record.
      * @return the Alias from the attributes of this record or null of there isn't a value

bio/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.3
-systemProp.bioVersion=5.0.3
+systemProp.imVersion=5.0.4
+systemProp.bioVersion=5.0.4
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

bio/postprocess-test/build.gradle

@@ -17,7 +17,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.3'
+    version = '5.0.4'
 
     apply plugin: 'java'
     apply plugin: 'maven'

bio/postprocess-test/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.3
-systemProp.bioVersion=5.0.3
+systemProp.imVersion=5.0.4
+systemProp.bioVersion=5.0.4
 
 systemProp.flymineVersion=4.0.0
 

bio/postprocess/build.gradle

@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.3'
+    version = '5.0.4'
 
     apply plugin: 'java'
     apply plugin: 'maven'

bio/postprocess/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.3
-systemProp.bioVersion=5.0.3
+systemProp.imVersion=5.0.4
+systemProp.bioVersion=5.0.4
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

bio/sources/biogrid/src/main/java/org/intermine/bio/dataconversion/BioGridConverter.java

@@ -198,7 +198,8 @@ private void readConfig() {
                 config = new Config();
                 configs.put(taxonId, config);
             }
-            if ("xref".equals(attributes[1])) {
+            String attribute = attributes[1];
+            if ("xref".equals(attribute)) {
                 String attribute2 = attributes[2];
                 if (StringUtils.isNotEmpty(attribute2)) {
                     // e.g. primaryIdentifier
@@ -208,18 +209,17 @@ private void readConfig() {
                     //e.g. mgd/mgi
                     config.setXref(value.toLowerCase());
                 }
+            } else if ("alias".equals(attribute)) {
+                config.setAlias(value);
+            } else if ("strain".equals(attribute)) {
+                strains.put(value, taxonId);
+            } else if ("prefix".equals(attribute)) {
+                // e.g. MGI:
+                config.setPrefix(value);
             } else {
-                String attribute = attributes[1];
-                if ("strain".equals(attribute)) {
-                    strains.put(value, taxonId);
-                } else if ("prefix".equals(attribute)) {
-                    // e.g. MGI:
-                    config.setPrefix(value);
-                } else {
-                    // e.g. 9606.symbol = shortLabel
-                    config.setIdentifierName(attribute);
-                    config.setNameSource(value);
-                }
+                // e.g. 9606.symbol = shortLabel
+                config.setIdentifierName(attribute);
+                config.setNameSource(value);
             }
         }
     }
@@ -266,6 +266,7 @@ class BioGridHandler extends DefaultHandler
         private String participantId = null;
         private Stack<String> stack = new Stack<String>();
         private String attName = null;
+        private String aliasType = null;
         private StringBuffer attValue = null;
 
         /**
@@ -324,7 +325,11 @@ public void startElement(String uri, String localName, String qName, Attributes
                     db = db.toLowerCase();
                     interactorHolder.xrefs.put(db, attrs.getValue("id"));
                 }
-
+            // <interactorList><interactor id="4">
+            // <names><alias type="systematic name">SPAC23G3.09</alias><names>
+            } else if ("alias".equals(qName) && stack.search("interactor") == 2) {
+                attName = "alias";
+                aliasType = attrs.getValue("type");
             // <interactorList><interactor id="4"><names><shortLabel>YFL039C</shortLabel>
             } else if ("shortLabel".equals(qName) && stack.search("interactor") == 2) {
                 attName = "shortLabel";
@@ -447,7 +452,11 @@ public void endElement(String uri, String localName, String qName)
                     shortLabel = shortLabel.trim();
                 }
                 interactorHolder.shortLabel = shortLabel;
-
+            // <interactorList><interactor id="4">
+            // <names><alias type="systematic name">SPAC23G3.09</alias><names>
+            } else if (attName != null && "alias".equals(attName)
+                    && "alias".equals(qName) && stack.search("interactor") == 2) {
+                interactorHolder.alias.put(aliasType, attValue.toString());
             /******************* INTERACTIONS ***************************************************/
             //<interactionList><interaction>   <participantList><participant id="68259">
             //<interactorRef>1</interactorRef>
@@ -618,6 +627,8 @@ private boolean setGene(String taxonId, InteractorHolder ih, Config config)
 
             if ("shortLabel".equalsIgnoreCase(config.getNameSource())) {
                 identifier = ih.shortLabel;
+            } else if (config.getAlias() != null && ih.alias.get(config.getAlias()) != null) {
+                identifier = ih.alias.get(config.getAlias());
             } else {
                 identifier = ih.xrefs.get(config.getIdentifierSource());
             }
@@ -888,6 +899,8 @@ protected class InteractorHolder
             protected Participant participant = null;
             // db to identifier, eg. FlyBase --> FBgn
             protected Map<String, String> xrefs = new HashMap<String, String>();
+            // alias type to value, eg. "systematic name" --> SPAC23G3.09
+            protected Map<String, String> alias = new HashMap<String, String>();
             // symbol
             protected String shortLabel;
             protected boolean valid = true;
@@ -1016,6 +1029,7 @@ protected class Config
         private String taxonId;
         private String prefix;
         private String xref;
+        private String alias;
         private String identifierName = DEFAULT_IDENTIFIER_FIELD;
         private String nameSource;
 
@@ -1064,6 +1078,21 @@ protected void setXref(String xref) {
             this.xref = xref;
         }
 
+        /**
+          * @return the alias type to determine the identifier for the gene
+         */
+        public String getAlias() {
+            return alias;
+        }
+
+        /**
+         * @param alias the aliad type to use to determine the identifier for this gene,
+         * e.g. systematic name
+         */
+        public void setAlias(String alias) {
+            this.alias = alias;
+        }
+
         /**
          * @return name of identifier to set on the gene object, e.g. primaryIdentifier or symbol
          */

bio/sources/biogrid/src/main/resources/biogrid_config.properties

@@ -47,3 +47,7 @@
 # A. thaliana
 3702.xref.primaryIdentifier = TAIR
 
+# pombe
+4896.alias.primaryIdentifier = systematic name
+4896.strain = 284812
+

bio/sources/build.gradle

@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.3'
+    version = '5.0.4'
 
     apply plugin: 'java'
     apply plugin: 'maven'
@@ -32,7 +32,7 @@ subprojects {
         mavenLocal()
         mavenCentral()
         maven {
-            url 'https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/'
+            url 'https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/'
         }
     }