Merge pull request #2434 from intermine/dev

im 5.0.7
intermine · Apr 27, 2022 · f6360f9 · f6360f9
2 parents ae73e20 + 6faa52c
commit f6360f9
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diff --git a/README.md b/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-5.0.6-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
+[![Version](http://img.shields.io/badge/version-5.0.7-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)
@@ -56,7 +56,7 @@ You can build InterMine using Docker. See https://github.com/intermine/docker-in
 Copyright and Licence
 ------------------------
 
-Copyright (C) 2002-2021 FlyMine
+Copyright (C) 2002-2022 FlyMine
 
 See [LICENSE](LICENSE) file for licensing information.
 

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -1,12 +1,24 @@
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should
  * be distributed with the code.  See the LICENSE file for more
  * information or http://www.gnu.org/copyleft/lesser.html.
  *
  */
+InterMine 5.0.7 (April 2022)
+
+#2419 - Updated the WS /templates to return dataTypes
+#2425 - Fix XSS issue
+#2427 - Create a WS returning all the templates
+#2428 - Superuser can run whatever template
+#2027 - Added a new generic TSV data source
+      - Completly removed dependencies on jcenter
+      - Added pombe organims to the taxon id to be ingnored by the idresolver
+      - Copyright updated
+	  - Fixed typo in the go evidence code
+
 InterMine 5.0.6 (Dicember 2021)
 
 #2414 - Upgraded psi lib version (thanks @asherpasha)

diff --git a/bio/build.gradle b/bio/build.gradle
@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version = '5.0.6'
+    version = '5.0.7'
 
     apply plugin: "java"
     apply plugin: "maven"

diff --git a/bio/core/build.gradle b/bio/core/build.gradle
@@ -11,11 +11,6 @@ buildscript {
 apply plugin: 'dbmodel'
 apply plugin: 'biocore-dbmodel'
 
-repositories {
-    //temporary for bio-source-flymine-static
-    jcenter()
-}
-
 sourceSets {
     main {
         java {

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/BioDBConverter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/BioDBConverter.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/BioDirectoryConverter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/BioDirectoryConverter.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/BioFileConverter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/BioFileConverter.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/BioStoreHook.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/BioStoreHook.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/DoNothingIdResolver.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/DoNothingIdResolver.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/DoNothingIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/DoNothingIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/EnsemblIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/EnsemblIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/EntrezGeneIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/EntrezGeneIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/FlyBaseIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/FlyBaseIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3Converter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3Converter.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3RecordHandler.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3RecordHandler.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3SeqHandler.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/GFF3SeqHandler.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/GeneInfoRecord.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/GeneInfoRecord.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/HgncIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/HgncIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/HumanIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/HumanIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolver.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolver.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolverService.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/IdResolverService.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/MgiIdentifiersResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/MgiIdentifiersResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/MockIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/MockIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/NcbiGeneInfoParser.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/NcbiGeneInfoParser.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/OboConverter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/OboConverter.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/OntologyIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/OntologyIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/RgdIdentifiersResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/RgdIdentifiersResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/WormBaseIdResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/WormBaseIdResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/ZfinIdentifiersResolverFactory.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/ZfinIdentifiersResolverFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.dataconversion;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/io/bed/BEDRecord.java b/bio/core/src/main/java/org/intermine/bio/io/bed/BEDRecord.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.io.bed;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/io/gff3/GFF3Parser.java b/bio/core/src/main/java/org/intermine/bio/io/gff3/GFF3Parser.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.io.gff3;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/io/gff3/GFF3Record.java b/bio/core/src/main/java/org/intermine/bio/io/gff3/GFF3Record.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.io.gff3;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/OboParser.java b/bio/core/src/main/java/org/intermine/bio/ontology/OboParser.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/OboRelation.java b/bio/core/src/main/java/org/intermine/bio/ontology/OboRelation.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/OboTerm.java b/bio/core/src/main/java/org/intermine/bio/ontology/OboTerm.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/OboTermSynonym.java b/bio/core/src/main/java/org/intermine/bio/ontology/OboTermSynonym.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/OboTypeDefinition.java b/bio/core/src/main/java/org/intermine/bio/ontology/OboTypeDefinition.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/SequenceOntology.java b/bio/core/src/main/java/org/intermine/bio/ontology/SequenceOntology.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/ontology/SequenceOntologyFactory.java b/bio/core/src/main/java/org/intermine/bio/ontology/SequenceOntologyFactory.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.ontology;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should

diff --git a/bio/core/src/main/java/org/intermine/bio/query/range/ChromosomeLocationHelper.java b/bio/core/src/main/java/org/intermine/bio/query/range/ChromosomeLocationHelper.java
@@ -1,7 +1,7 @@
 package org.intermine.bio.query.range;
 
 /*
- * Copyright (C) 2002-2021 FlyMine
+ * Copyright (C) 2002-2022 FlyMine
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should