Merge pull request #2267 from intermine/dev

Release 4.2.0

README.md

@@ -3,7 +3,7 @@ InterMine
 
 Master: [![Build Status: master][travis-badge-master]][ci]
 Dev: [![Build Status: dev][travis-badge-dev]][ci]
-[![Version](http://img.shields.io/badge/version-4.1.3-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
+[![Version](http://img.shields.io/badge/version-4.2.0-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)
@@ -63,6 +63,11 @@ See [LICENSE](LICENSE) file for licensing information.
 This product includes software developed by the
 [Apache Software Foundation][apache]
 
+InterMine Development Roadmap
+-----------------------------
+
+For more information about the upcoming releases, please visit the [InterMine Development Roadmap](https://intermine.readthedocs.io/en/latest/intermine/roadmap/#intermine-development-roadmap). For the roadmap, please see [here](https://github.com/intermine/intermine/projects/7).
+
 Please cite
 ------------------------
 

RELEASE_NOTES

@@ -7,6 +7,32 @@
  * information or http://www.gnu.org/copyleft/lesser.html.
  *
  */
+InterMine 4.2.0 (June 2020)
+
+#1650 - Need way to upgrade anonymous sessions via web service
+#1969 - FAIR: add profile Gene and Protein markup to the report page
+#2099 - Need webservice endpoint that identifies if superuser
+#2142 - Create a new logout service
+#2144 - Update the /user endpoint to allow to change password
+#2148 - Add PUT method to the /lists webservice to update the description
+#2149 - Update the /users endpoint to attach to the user just created the lists created anonymously
+#2155 - FAIR: adopt DataRecord type in the report page
+#2199 - Invalid JSON response to POST /user/queries
+#2205 - Update change password webservice to require current password
+#2207 - Add clearLocation() to removeFeature() (thanks @sammyjava)
+#2215 - Fix organism short name formation (thanks @ahmedihafez)
+#2236 - Remove BioEntity.ontologyAnnotations because redundant (thanks @sammyjava)
+#2237 - Editing  a Date filter on the results table shows Service failed message
+#2239 - BAR ThaleMine - 6: Fixed a minor bug in reports page long fields (thanks @asherpasha)
+#2240 - BAR ThaleMine - 7: go-annotation loader (thanks @asherpasha)
+#2242 - /service/templates is missing optional constraint if format=json
+#2246 - Issues related to fields with type Date
+#2252 - Added a new bio source to load ISA files in json format
+#2253 - src.data.dir.includes and src.data.dir in project.xml not always work as expected
+#2255 - Added BioChemEntity (via configuration) markup
+#2259 - UniProtFastaLoader doesn't extract the organism name composed by more than 2 words
+#2264 - Add licence to the OboConverter
+
 InterMine 4.1.3 (March 2020)
 
 #2208 Delete a template -> it's still displayed on the Templates tab

bio/build.gradle

@@ -10,7 +10,7 @@ buildscript {
 
 subprojects {
     group = 'org.intermine'
-    version = '4.1.3'
+    version = '4.2.0'
 
     apply plugin: "java"
     apply plugin: "maven"
@@ -127,9 +127,9 @@ subprojects {
             vcsUrl = 'https://github.com/intermine/intermine.git'
             publicDownloadNumbers = true
             version {
-                name = '4.1.3'
-                desc = 'InterMine 4.1.3'
-                vcsTag = 'intermine-4.1.3'
+                name = '4.2.0'
+                desc = 'InterMine 4.2.0'
+                vcsTag = 'intermine-4.2.0'
             }
         }
         configurations = ['archives']

bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3RecordHandler.java

@@ -158,14 +158,16 @@ protected Item getFeature() {
     }
 
     /**
-     * Remove the feature item that was set with setFeature() and associated synonyms
+     * Remove the feature item that was set with setFeature() and associated synonyms,
+     * as well as the associated Location.
      */
     protected void removeFeature() {
         items.remove("_feature");
         for (Item synonym : synonyms) {
             items.remove(synonym.getIdentifier());
         }
         synonyms.clear();
+        clearLocation();
     }
 
     /**

bio/core/src/main/java/org/intermine/bio/dataconversion/OboConverter.java

@@ -16,6 +16,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Arrays;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
@@ -199,10 +200,11 @@ private void storeDataset(Item ontology) throws ObjectStoreException {
         Item datasetItem = createItem("DataSet");
         datasetItem.setAttribute("name", dataset);
         if (licence != null) {
-            datasetItem.setAttribute("licence", licence);
+            datasetItem.setAttributeIfNotNull("licence", licence);
         }
         datasetItem.setReference("dataSource", datasourceItem);
         store(datasetItem);
+        ontology.setCollection("dataSets", Arrays.asList(datasetItem.getIdentifier()));
     }
 
     /**

bio/core/src/main/java/org/intermine/bio/task/OboConverterTask.java

@@ -75,7 +75,14 @@ public void setTermClass(String termClass) {
         this.termClass = termClass;
     }
 
-
+    /**
+     * Set the licence retrieved from the {bio-source}.properties file
+     *
+     * @param licence the licence
+     */
+    public void setLicence(String licence) {
+        this.licence = licence;
+    }
 
     /**
      * Run the task
@@ -106,6 +113,9 @@ public void execute() {
             OboConverter converter;
             if (file.endsWith(".obo")) {
                 converter = new OboConverter(writer, model, file, ontologyName, url, termClass);
+                if (licence != null) {
+                    converter.setLicence(licence);
+                }
             } else {
                 throw new IllegalArgumentException("Don't know how to deal with file " + file);
             }

bio/core/src/test/resources/OboConverterTest.xml

@@ -10,6 +10,7 @@
 <item id="0_1" class="Ontology">
 <attribute name="name" value="SO"/>
 <attribute name="url" value="http://www.flymine.org"/>
+<collection name="dataSets"><reference ref_id="2_1"/></collection>
 </item>
 <item id="5_2" class="OntologyRelation">
 <attribute name="direct" value="false"/>

bio/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=4.1.+
-systemProp.bioVersion=4.1.+
+systemProp.imVersion=4.2.+
+systemProp.bioVersion=4.2.+
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

bio/model/core.xml

@@ -20,7 +20,6 @@
         <reference name="organism" referenced-type="Organism"/>
         <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/>
         <collection name="locations" referenced-type="Location" reverse-reference="feature" />
-        <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
         <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/>
         <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
         <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/>

bio/postprocess-test/build.gradle

@@ -22,7 +22,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '4.1.3'
+    version = '4.2.0'
 
     apply plugin: 'java'
     apply plugin: 'maven'

bio/postprocess-test/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=4.1.+
-systemProp.bioVersion=4.1.+
+systemProp.imVersion=4.2.+
+systemProp.bioVersion=4.2.+
 
 systemProp.flymineVersion=4.0.+
 

bio/postprocess/build.gradle

@@ -21,7 +21,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '4.1.3'
+    version = '4.2.0'
 
     apply plugin: 'java'
     apply plugin: 'maven'
@@ -171,9 +171,9 @@ subprojects {
             vcsUrl = 'https://github.com/intermine/intermine.git'
             publicDownloadNumbers = true
             version {
-                name = '4.1.3'
-                desc = 'InterMine 4.1.3'
-                vcsTag = 'intermine-4.1.3'
+                name = '4.2.0'
+                desc = 'InterMine 4.2.0'
+                vcsTag = 'intermine-4.2.0'
             }
         }
         configurations = ['archives']

bio/postprocess/gradle.properties

@@ -1,4 +1,4 @@
-systemProp.imVersion=4.1.+
-systemProp.bioVersion=4.1.+
+systemProp.imVersion=4.2.+
+systemProp.bioVersion=4.2.+
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl

bio/sources/build.gradle

@@ -21,7 +21,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '4.1.3'
+    version = '4.2.0'
 
     apply plugin: 'java'
     apply plugin: 'maven'
@@ -59,6 +59,12 @@ subprojects {
         testCompile group: "org.intermine", name: "intermine-integrate", version: System.getProperty("imVersion"), classifier: "testClasses"
         testCompile group: 'xmlunit', name: 'xmlunit', version: '1.0'
         mergeModel group : "org.intermine", name: "intermine-objectstore", version: System.getProperty("imVersion")
+
+	    // JAX-B dependencies for JDK 9+
+    implementation "jakarta.xml.bind:jakarta.xml.bind-api:2.3.2"
+    implementation "org.glassfish.jaxb:jaxb-runtime:2.3.2"
+    implementation "javax.annotation:javax.annotation-api:1.3.2"
+
     }
 
     dbModelConfig {
@@ -194,9 +200,9 @@ subprojects {
             vcsUrl = 'https://github.com/intermine/intermine.git'
             publicDownloadNumbers = true
             version {
-                name = '4.1.3'
-                desc = 'InterMine 4.1.3'
-                vcsTag = 'intermine-4.1.3'
+                name = '4.2.0'
+                desc = 'InterMine 4.2.0'
+                vcsTag = 'intermine-4.2.0'
             }
         }
         configurations = ['archives']

bio/sources/do/do.properties

@@ -14,3 +14,4 @@ obo.ontology.url = http://www.disease-ontology.org
 # this class in a do_additions.xml file for this source
 obo.term.class = DOTerm
 
+obo.ontology.licence = https://creativecommons.org/publicdomain/zero/1.0/

bio/sources/eco/eco.properties

@@ -14,3 +14,4 @@ obo.ontology.url = http://www.evidenceontology.org/
 # this class in a eco_additions.xml file for this source
 obo.term.class = ECOTerm
 
+obo.ontology.licence = https://creativecommons.org/publicdomain/zero/1.0/

bio/sources/entrez-organism/src/main/java/org/intermine/bio/dataconversion/EntrezOrganismRetriever.java

@@ -295,8 +295,14 @@ public void endElement(String uri, String localName, String qName) {
                                 text.substring(0, spaceIndex));
                         organism.setAttribute("species",
                                 text.substring(spaceIndex + 1));
-                        organism.setAttribute("shortName", text.charAt(0)
-                                + ". " + text.substring(spaceIndex + 1));
+                        // Organism name could have [] in it , as a result the shortname
+                        // will start with [. toFix : check if it does not start with [
+                        String shortName = text.charAt(0)
+                                + ". " + text.substring(spaceIndex + 1);
+                        if (text.startsWith("[") ) {
+                            shortName = text.charAt(1) + ". " + text.substring(spaceIndex + 1);
+                        }
+                        organism.setAttribute("shortName", shortName);
                     }
                 }
             } else if ("CommonName".equals(name)) {

bio/sources/fasta/src/main/java/org/intermine/bio/dataconversion/UniProtFastaLoaderTask.java

@@ -16,6 +16,7 @@
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.intermine.model.bio.Organism;
 import org.intermine.objectstore.ObjectStoreException;
+import org.apache.commons.lang.StringUtils;
 
 /**
  * Code for loading fasta for uniprot proteins.
@@ -31,11 +32,12 @@ public class UniProtFastaLoaderTask extends FastaLoaderTask
     @Override
     protected Organism getOrganism(ProteinSequence bioJavaSequence) throws ObjectStoreException {
         String header = bioJavaSequence.getOriginalHeader();
-        final String regexp = "OS\\=\\w+\\s\\w+";
+        final String regexp = "OS\\=(\\w+(\\s)*)*";
         Pattern p = Pattern.compile(regexp);
         Matcher m = p.matcher(header);
         if (m.find()) {
             header = m.group();
+            header = cleanHeader(header);
             String[] bits = header.split("=");
             if (bits.length != 2) {
                 return null;
@@ -55,4 +57,21 @@ protected Organism getOrganism(ProteinSequence bioJavaSequence) throws ObjectSto
         }
         return null;
     }
+
+    /**
+     * the header might end with OX, GN, PE or SV (due to the new regular expression)
+     * Example: OS=Severe acute respiratory syndrome coronavirus 2 OX
+     *
+     * @param header a partial header
+     * @return the header without suffix
+     */
+    private String cleanHeader(String header) {
+        String[] suffixes = {" OX", " GN", " PE", " SV"};
+        for (String suffix : suffixes) {
+            if (StringUtils.endsWith(header, suffix)) {
+                return StringUtils.removeEnd(header, suffix);
+            }
+        }
+        return header;
+    }
 }

bio/sources/go-annotation/src/main/resources/go-annotation_config.properties

@@ -19,8 +19,8 @@
 #10090.typeAnnotated=gene
 
 # Arabidopsis
-3702.identifier=symbol
-3702.readColumn=symbol
+3702.identifier=secondaryIdentifier
+3702.readColumn=identifier
 3702.typeAnnotated=gene
 
 226900.typeAnnotated=protein

bio/sources/go/go.properties

@@ -2,3 +2,5 @@ have.file.obo = true
 obo.ontology.name=GO
 obo.ontology.url=http://www.geneontology.org
 obo.term.class=GOTerm
+
+obo.ontology.licence = https://creativecommons.org/licenses/by/4.0/

bio/sources/gradle.properties

@@ -1,5 +1,5 @@
-systemProp.imVersion=4.1.+
-systemProp.bioVersion=4.1.+
+systemProp.imVersion=4.2.+
+systemProp.bioVersion=4.2.+
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!
 

bio/sources/isa/build.gradle

@@ -0,0 +1,32 @@
+sourceSets {
+    main {
+        java {
+            srcDirs = ['src/main/java', 'build/gen']
+        }
+        resources {
+            srcDirs = ['src/main/resources']
+        }
+    }
+    test {
+        java {
+            srcDirs = ['src/test/java']
+        }
+        resources {
+            srcDirs = ['src/test/resources']
+        }
+    }
+}
+
+dependencies {
+    compile group: 'org.intermine', name: 'bio-model', version: bioVersion, transitive: false
+    compile group: 'org.intermine', name: 'intermine-integrate', version: imVersion
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.9.8'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.8'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.9.8'
+    runtime fileTree(dir: 'libs', include: '*.jar') //antlr-2.7.6-caching.jar
+    bioModel group: 'org.intermine', name: 'bio-model', version: bioVersion, transitive: false
+}
+
+processResources {
+    from('.') { include ("*.properties")}
+}

bio/sources/isa/isa.properties

@@ -0,0 +1,8 @@
+compile.dependencies = intermine/objectstore/main, \
+           bio/core/main, \
+           intermine/integrate/main, \
+           bio/sources/isa/main
+
+have.file.custom.tgt = true
+converter.class = org.intermine.bio.dataconversion.IsaConverter
+