Merge branch 'merge-13.0.0' into 'master'

Merge 13.0.0

See merge request !770

.gitlab-ci.yml

@@ -268,13 +268,9 @@ test_upgrade_debian_package:
      - version=$(echo $debian_file| cut -f2 -d"_")
      - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
      - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
-     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
      - apt-add-repository "deb http://repo-r3lab.uni.lu/debian/ stable main"
      - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412
      - apt-get update
-# auto accept oracle license
-     - echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
 #hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
      - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
      - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d
@@ -315,12 +311,8 @@ test_install_debian_package:
      - debian_file=$(ls debian/*.deb)
      - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
      - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
-     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
      - apt-add-repository "deb http://debian-repo/ unstable main"
      - apt-get update
-# auto accept oracle license
-     - echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
 #hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
      - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
      - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d

CHANGELOG

-minerva (12.3.0~alpha.0) unstable; urgency=low
+minerva (13.1.0~alpha.0) unstable; urgency=low
   * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)
   * Feature: changes in admin panel doesn't require saving - they are saved
@@ -46,7 +46,7 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Small improvement: when adding new project columns "Root map", "Mapping
     file" and "Map type" are merged (#700)
   * Small improvement: allow admin to disable CORS check (#802)
-  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to 
+  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
     SemanticZoomLevelTransparency (#801)
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
@@ -64,6 +64,15 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
     wrapped in more than one line (#758)
   * Bug fix: export to CellDesigner preserve font size (#803)
 
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 7 May 2019 15:00:00 +0200
+
+minerva (13.0.0) stable; urgency=medium
+  * Bug fix: Since Oracle Java cannot be installed as debian dependency we use
+    openjdk-8. Due to this dependency minerva can be no longer installed on
+    Ubuntu-14 (#223)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 6 May 2019 18:00:00 +0200
+
 minerva (12.2.3) stable; urgency=medium
   * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
   * Bug fix: searching of chemicals stopped working due to expired SSL

debian/template/control

@@ -13,4 +13,4 @@ Description: Standalone web application for visualization, exploration and
  Tomcat server later to change the address.
 Section: science
 Homepage: http://r3lab.uni.lu/web/minerva-website/
-Depends: ${misc:Depends}, tomcat7 | tomcat8, oracle-java8-set-default, postgresql (>=9.3)
+Depends: ${misc:Depends}, openjdk-8-jre-headless, tomcat7 | tomcat8, postgresql (>=9.3)

debian/template/preinst

@@ -14,14 +14,6 @@ log "Running preinst" $1 $2;
 # we execute it here because if some packages are missing then dpkg will return non-zero exit code
 set -e
 
-DEFAULT_JAVA_SYMLINK="/usr/lib/jvm/default-java"
-
-log "changing \$DEFAULT_JAVA_SYMLINK";
-path="/usr/lib/jvm/java-8-oracle";
-log "Creating symlink between $path and $DEFAULT_JAVA_SYMLINK";
-rm -f $DEFAULT_JAVA_SYMLINK
-ln -s $path $DEFAULT_JAVA_SYMLINK
-
 case "$1" in
     install|upgrade)
 	invoke-rc.d $TOMCAT_PACKAGE stop || true

frontend-js/package-lock.json

@@ -3307,6 +3307,12 @@
         }
       }
     },
+    "log4js-memory-appender": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/log4js-memory-appender/-/log4js-memory-appender-1.0.5.tgz",
+      "integrity": "sha1-e4I2NDpCuLEgidjX+kebD22aNME=",
+      "dev": true
+    },
     "longest": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/longest/-/longest-1.0.1.tgz",
@@ -5072,15 +5078,6 @@
         }
       }
     },
-    "stream-to-blob": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/stream-to-blob/-/stream-to-blob-1.0.1.tgz",
-      "integrity": "sha512-aRy4neA4rf+qMtLT9fCRLPGWdrsIKtCx4kUdNTIPgPQ2hkHkdxbViVAvABMx9oRM6yCWfngHx6pwXfbYkVuPuw==",
-      "dev": true,
-      "requires": {
-        "once": "^1.3.3"
-      }
-    },
     "streamroller": {
       "version": "1.0.4",
       "resolved": "https://registry.npmjs.org/streamroller/-/streamroller-1.0.4.tgz",