Commit 628dddb7 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch 'devel_12.2.x' into merge-12.1.8

parents bb8865c3 c16fe709
Pipeline #8679 failed with stage
in 9 minutes and 22 seconds
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
annotation/minerva-big/
debian/src/
debian/minerva*
debian/src/*.sql
builds/
map_images/
minerva-big/
*/target/
web/src/main/webapp/svnversion.txt
*.war
/target/
service/minerva-big/
npm-debug.log
converter-sbml/jsbml.log
#log files
*.log
#IntelliJ files
.idea/
*.iml
#eclipse files
/target/
.classpath
.settings
#debian build files
debian/src/
debian/minerva*
debian/src/*.sql
/bin/
......@@ -10,7 +10,6 @@ variables:
POSTGRES_USER: map_viewer
POSTGRES_PASSWORD: "123qweasdzxc"
test_frontend:
stage: test
script:
......@@ -18,24 +17,179 @@ test_frontend:
- npm install
- npm test
test_backend 1 15:
image: maven:3.6.0-jdk-8
stage: test
script:
#xvfb is for X11 connection used by some parts of the java code: https://stackoverflow.com/a/47575851/1127920
- apt-get update
- apt-get install -y xvfb
- Xvfb :99 &
- export DISPLAY=:99
- mvn -DskipTests=true clean install -pl commons -am
- mvn test -pl commons
test_backend 2 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl annotation -am
- mvn test -pl annotation
test_backend 3 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl CellDesigner-plugin -am
- mvn test -pl CellDesigner-plugin
test_backend 4 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl converter -am
- mvn test -pl converter
test_backend 5 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl converter-graphics -am
- mvn test -pl converter-graphics
test_backend 6 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl converter-CellDesigner -am
- mvn test -pl converter-CellDesigner
test_backend 7 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl converter-SBGNML -am
- mvn test -pl converter-SBGNML
test_backend 8 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl converter-sbml -am
- mvn test -pl converter-sbml
test_backend 9 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl model -am
- mvn test -pl model
test_backend 10 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl model-command -am
- mvn test -pl model-command
test_backend 11 15:
image: maven:3.6.0-jdk-8
stage: test
script:
- mvn -DskipTests=true clean install -pl pathvisio -am
- mvn test -pl pathvisio
test_backend 12 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl persist -am
- mvn test -pl persist
test_backend 13 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl reactome -am
- mvn test -pl reactome
test_backend 14 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl rest-api -am
- mvn test -pl rest-api
test_backend 15 15:
image: maven:3.6.0-jdk-8
services:
- postgres:9.6
stage: test
script:
- mkdir /etc/minerva/
- cp test-db-ci.properties /etc/minerva/db.properties
- mvn -DskipTests=true clean install -pl service -am
- mvn test -pl service
build_war:
image: debian
image: maven:3.6.0-jdk-8
stage: build
only:
- tags
tags:
- privileged
artifacts:
expire_in: 1 day
paths:
- minerva.war
script:
- apt-get update
- apt-get install -y curl sudo gnupg git openjdk-8-jdk ant maven
- curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
- sudo apt-get install -y nodejs
- apt-get install -y curl gnupg git ant
- curl -sL https://deb.nodesource.com/setup_9.x | bash -
- apt-get install -y nodejs
- ant maven-build
- cp web/target/web-1.0.war minerva.war
dependency_conflict_check:
image: maven:3.6.0-jdk-8
stage: test
script:
- apt-get update
- apt-get install -y curl gnupg git ant
- curl -sL https://deb.nodesource.com/setup_9.x | bash -
- apt-get install -y nodejs
- mvn clean install -DskipTests=true
- set +e
- mvn dependency:tree -Dverbose | grep conflict | cat > conflicts.txt
- set -e
- conflicts=`cat conflicts.txt| wc -l`
- echo Found conflicts $conflicts ':'
- cat conflicts.txt
- test 0 = $conflicts
build_debian_package:
image: debian
stage: packaging
......@@ -43,17 +197,67 @@ build_debian_package:
- tags
tags:
- privileged
dependencies:
- build_war
artifacts:
paths:
- "debian/*.deb"
script:
- mkdir web/target/
- mv minerva.war web/target/web-1.0.war
- apt-get update
- apt-get install -y curl sudo gnupg git openjdk-8-jdk ant maven dh-make build-essential lintian devscripts xsltproc fakeroot xsltproc docbook-xsl
- curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
- sudo apt-get install -y nodejs
- apt-get install -y dh-make build-essential lintian devscripts xsltproc fakeroot xsltproc docbook-xsl
- export DEBFULLNAME="Piotr Gawron"
- export DEBEMAIL="piotr.gawron@uni.lu"
- ant debian-pkg
- debian/create-debian-pkg.sh
test_upgrade_debian_package:
image: debian
stage: test
only:
- tags
# we need to run it in privileged mode due to: https://stackoverflow.com/questions/29683231/tomcat7-fail-to-start-inside-ubuntu-docker-container
tags:
- privileged
services:
- name: piotrgawron/debian-repo
alias: debian-repo
dependencies:
- build_debian_package
script:
- apt-get update
- apt-get install -y ssh software-properties-common dirmngr wget curl apt-transport-https
- debian_file=$(ls debian/*.deb)
- 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
- chmod 0755 /usr/sbin/policy-rc.d
- apt-get install -y --allow-unauthenticated minerva
#local repository with new version
- apt-add-repository "deb http://debian-repo/ unstable main"
- apt-get update
- apt-get dist-upgrade -y --allow-unauthenticated
- mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d
- service tomcat8 start
#we need to wait a bit for tomcat start
- sleep 15
- wget http://localhost:8080/minerva/
#test if we can login and get configuration using new version
- test 200 = $(curl --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
- test 200 = $(curl --write-out %{http_code} --silent --output configuration.json --cookie cookie.txt http://localhost:8080/minerva/api/configuration/)
- test 1 = $(cat configuration.json| grep $version | wc -l)
test_install_debian_package:
image: debian
......@@ -82,7 +286,8 @@ test_install_debian_package:
- 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 Docker/policy-rc.d /usr/sbin/policy-rc.d
- mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d
- chmod 0755 /usr/sbin/policy-rc.d
- apt-get install -y --allow-unauthenticated minerva
- mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d
- service tomcat8 start
......
eclipse.preferences.version=1
encoding/<project>=UTF-8
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
activeProfiles=
eclipse.preferences.version=1
resolveWorkspaceProjects=true
version=1
DELEGATES_PREFERENCE=delegateValidatorList
USER_BUILD_PREFERENCE=enabledBuildValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
USER_MANUAL_PREFERENCE=enabledManualValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
USER_PREFERENCE=overrideGlobalPreferencesfalse
eclipse.preferences.version=1
override=false
suspend=false
vals/org.eclipse.jst.jsf.facelet.ui.FaceletHTMLValidator/global=FF01
vals/org.eclipse.jst.jsp.core.JSPBatchValidator/global=FF01
vals/org.eclipse.jst.jsp.core.JSPContentValidator/global=FF01
vals/org.eclipse.jst.jsp.core.TLDValidator/global=FF01
vals/org.eclipse.wst.dtd.core.dtdDTDValidator/global=FF01
vals/org.eclipse.wst.html.core.HTMLValidator/global=FF01
vals/org.eclipse.wst.wsdl.validation.wsdl/global=FF02158org.eclipse.wst.wsdl.validation.internal.eclipse.Validator
vals/org.eclipse.wst.xml.core.xml/global=FF03
vals/org.eclipse.wst.xsd.core.xsd/global=FF02162org.eclipse.wst.xsd.core.internal.validation.eclipse.Validator
vals/org.eclipse.wst.xsl.core.xsl/global=FF02
vf.version=3
inerva (12.2.0~beta.1) unstable; urgency=medium
* Small improvement: list of publication can be filtered by submap (#614)
* Small improvement: report bug utility shows confirmation dialog on success
(#648)
* Small improvement: size of add overlay window adjusted to show more data
without scrollbars (#657)
* Small improvement: all popup dialogs in the app have dialog specific css
class names (#665)
* Bug fix: loading icon is not overlapping input in the search panel (#404)
* Bug fix: position of transcription sites in genes are computed properly
(#553)
* Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
(#626)
* Bug fix: layout exported to SBML can be properly visualized by COPASI
(#654)
* Bug fix: working with too many maps within the single session could crash
connection to server (#651)
* Bug fix: invalid pubmed id could crash listing/downloading publications
(#656)
* Bug fix: icons in safari sometimes disappear (#661)
* Bug fix: downloading reference genome for the second time resulted in an
error (#670)
* Bug fix: plugin validation in admin panel improved to catch more problems
(#672)
* Bug fix: drawing corrupted heterodimer association in CellDesigner could
crash map upload (#673)
* Bug fix: custom semantic zooming didn't work with pathways imported from
CellDesigner layers (#678)
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 7 Feb 2019 14:00:00 +0200
minerva (12.2.0~beta.0) unstable; urgency=medium
* Feature: bug report utility
* Small improvement: JS plugin can create listener that is triggered on
search results focus change
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 23 Jan 2019 15:00:00 +0200
minerva (12.2.0~alpha.1) unstable; urgency=medium
* Bug fix: problems with SBML-CellDesigner translation fixed
* Bug fix: gitlab CI tests fixed
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 17 Jan 2019 15:00:00 +0200
minerva (12.2.0~alpha.0) unstable; urgency=medium
* Feature: url GET parameters support all kind of search and selected overlays
highlight
* Feature: user can create custom logging configuration in file
/etc/minerva/log4j.properties
* Feature: plugin panel in admin allows to configure set of available plugins
* Feature: import export from SBML supports RENDER package
* Feature: import export from SBML supports MULTI package
* Feature: API tool providing possibility to transform different types of
file formats
* Feature: current state of the browsed map is reflected in the url (position,
zoom, overlays, search queries, etc.)
* Small improvement: export to SBML includes unit factors
* Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
* Small improvement: genetics information allows to provide information about
modification on peptide level that could be visualized in MolArt
* Small improvement: allow to control the background and font color of areas
drawn from text areas in CellDesigner "layers"
* Small improvement: config logo location is relative to the root minerva
deployment directory
* Small improvement: there is branding minerva logo in the left panel
* Small improvement: there is possibility to download part of the map limited
to set of reactions/elements
* Small improvement: allow admin to configure parameters displayed in the
left panel
* Small improvement: arrows for Transcription Starting Sites looks more like
in CellDesigner
* Small improvement: popup window appear with info about exceeding max number
of search results when necessary
* Small improvement: plugins can define default width of the container tab
* Small improvement: new miriam type is handled: ClinicalTrials.gov
* Small improvement: click on the border of compartment select the
compartment
* Small improvement: there is max size of the map in configuration panel that
disables upload of too big files
* Small improvement: hitting enter on login page logs in the user (no need to
click on the login button)
* Small improvement: refresh button in overlays panel (useful when data
overlays are uploaded separately in using API calls)
* Small improvement: list of publications is downloadable
* Small improvement: export of reactions support filtering by reaction type
* Small improvement: 'BACK TO MAP' link is available only when guest account
has proper access level
* Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
email account is provided
* Small improvement: Plugin API allows to show/hide data overlays
* Bug fix: export to CellDesigner align inhibition reaction properly
* Bug fix: export/import to/from SBML handles Heterodimer Association
reaction properly
* Bug fix: logo doesn't need to be square
* Bug fix: when clicking on a search link (in overview window), input in the
left tab was not modified
* Bug fix: in admin panel changing of genome version is blocking interface
until data about url is retrieved
* Bug fix: export of species inside complex into CellDesigner was causing
problems when reading the file in CellDesigner
* Bug fix: export to SBGN did not export compartments
* Bug fix: export of complex states to SBGN did not work
* Bug fix: type of the data overlay can be defined in the file content
(useful when uploading genetic variants)
* Bug fix: CLEAR button clears comment checkbox if necessary
* Bug fix: minerva install problem on ubuntu 16 fixed
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 11 Jan 2019 12:00:00 +0200
minerva (12.1.8) stable; urgency=medium
* Bug fix: add a project reset users custom overlays limit to default (#679)
* Bug fix: edit/remove project button was disabled based on Configuration
Manage Privilege, but should be based on Project Manage Privilege (#681)
* Bug fix: another minor problem with updating privileges introduced in
* Bug fix: another minor problem with updating privileges introduced in
12.1.6 fixed (#659)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 8 Feb 2019 15:30:00 +0200
......@@ -29,18 +138,18 @@ minerva (12.1.5) stable; urgency=medium
* Bug fix: word wrapping fixed in overlay table for long overlay names
in Firefox browser
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 10 Jan 2019 14:00:00 +0200
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 10 Jan 2019 14:00:00 +0200
minerva (12.1.4) stable; urgency=medium
* Bug fix: no check for limit on custom data overlays fixed
* Bug fix: error message improved when there is privilege problem during
* Bug fix: error message improved when there is privilege problem during
data overlay upload
* Bug fix: upload of data overlay from admin panel didn't work
* Bug fix: add project button is disabled when user doesn't have proper
* Bug fix: add project button is disabled when user doesn't have proper
privileges ("Add project" privilege)
* Bug fix: there are no more extra markers due to map wrapping
* Bug fix: upload of the project failed when another project was removed
during upload
* Bug fix: upload of the project failed when another project was removed
during upload
* Bug fix: word wrapping fixed in overlay table for long overlay names
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 28 Dec 2018 14:00:00 +0200
......@@ -48,20 +157,20 @@ minerva (12.1.4) stable; urgency=medium
minerva (12.1.3) stable; urgency=medium
* Bug fix: add project button is disabled when user has no privileges
* Bug fix: projectId was missing in the edit window
* Bug fix: user could provide invalid mesh ID that caused errors when
browsing map
* Bug fix: user created from LDAP connection doesn't have a password
stored in the database
* Bug fix: user could provide invalid mesh ID that caused errors when
browsing map
* Bug fix: user created from LDAP connection doesn't have a password
stored in the database
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 14 Dec 2018 14:00:00 +0200
minerva (12.1.2) stable; urgency=medium
* Bug fix: vmh annotations should be properly matching id entered in the input
* Bug fix: opacity was not working when highliting objects in plugins
* Bug fix: integer configurtion options (like SMTP_PORT) are properly
* Bug fix: integer configurtion options (like SMTP_PORT) are properly
validated before saving
* Bug fix: inside of reaction box wasn't properly aligned
* Bug fix: too long data overlay name disturbed size of the map div and
* Bug fix: too long data overlay name disturbed size of the map div and
interaction with the map
* Bug fix: search for some drugs resulted in internal server error
* Bug fix: LDAP login is case insensitive
......@@ -108,16 +217,16 @@ minerva (12.1.0) stable; urgency=medium
* Bug fix: loading invalid plugin doesn't render empty div anymore
* Bug fix: sorting of custom overlays was broken when description of overlay
was present
* Bug fix: when there is a problem with adjusting font in complexes (because
* Bug fix: when there is a problem with adjusting font in complexes (because
the font should be smaller than 1pt) description is not drawn anymore
* Bug fix: going to export page and back was breaking a map
* Bug fix: coordinates of selected area wasn't processed properly when they
exceeded canvas
* Bug fix: postgres migration script fixed to work with new docker compose
* Bug fix: double click on user add button disabled
* Bug fix: double click on user add button disabled
* Bug fix: privileges are mirrored correctly across different popups
* Bug fix: plugin tab css fixed
* Bug fix: uploading sbml file with no ids in glyphs returned error that
* Bug fix: uploading sbml file with no ids in glyphs returned error that
could not be easily understand
* Bug fix: ds_store files in subfolders crashed zip upload
* Bug fix: when creating new user default privileges were not filled
......
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
#eclipse files
target
.classpath
.settings
/bin/
eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
encoding//src/test/resources=UTF-8
encoding/<project>=UTF-8
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.8
activeProfiles=
eclipse.preferences.version=1
resolveWorkspaceProjects=true
version=1
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>1.0</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
<repositories>
<repository>
<id>central</id>
<url>http://repo.maven.apache.org/maven2/</url>
</repository>
<repository>
<id>repo</id>
<releases>
<enabled>true</enabled>
<checksumPolicy>ignore</checksumPolicy>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
<url>file://${project.basedir}/repo</url>