ome · jburel · Mar 4, 2022 · Jan 15, 2022 · Jan 15, 2022 · Jan 17, 2022
diff --git a/README.md b/README.md
@@ -51,7 +51,17 @@ The following instructions explain how to deploy a devspace on a Docker host.
 *   Copy the SSH and Git configuration files used for fetching and pushing the
     Git repositories under `slave/.ssh` and `slave/.gitconfig`. This is usually
     your own SSH and Git configuration files.
-
+    You need to use a public key without a passphrase and a `.gitconfig` file containing
+    the following sections:
+    ```
+    [user]
+       name = YOUR_NAME
+       email = YOUR_EMAIL
+    [github]
+        token = YOUR_GITHUB_TOKEN
+        user = YOUR_GITHUB_NAME
+    ```
+
  *  Run `rename.py` to match your topic name. Specify the Git user corresponding to
     the confguration files used above. If you do not yet have
     topic branches available on origin, use `develop` or one of the
@@ -71,9 +81,13 @@ The following instructions explain how to deploy a devspace on a Docker host.
 
 Start and configure:
 
+*   Build devspace using `docker-compose`:
+
+        $ docker-compose -f docker-compose.yml build 
+
 *   Start devspace using `docker-compose`:
 
-        $ docker-compose up -d
+        $ docker-compose -f docker-compose.yml up -d
 
     By default, this will use the name of the directory as the project name. In the case of a shared Docker host, it is possible to override the project name using
 
@@ -85,6 +99,10 @@ Start and configure:
 
         $ docker-compose -p my_project port nginxjenkins 443
 
+*   Create the `maven-internal` Nexus repository:
+
+        $ docker-compose exec nexus /nexus-data/createRepoMavenInternal.sh
+
 *   [Optional] Turn on Basic HTTP authentication for Jenkins
 
         sudo htpasswd -c jenkins/conf.d/passwdfile nginx
@@ -94,10 +112,6 @@ Start and configure:
         auth_basic "Restricted";
         auth_basic_user_file /etc/nginx/conf.d/passwdfile;
 
-*   [Optional] Create the `maven-internal` Nexus repository:
-
-        $ docker-compose exec nexus /nexus-data/createRepoMavenInternal.sh
-
 
 # GitHub OAuth
 
@@ -118,6 +132,8 @@ After the script has completed you can either leave it in place so it will overr
 
 # Job configurations
 
+*   When running the OMERO-build job for the first time, select the ``PURGE_DATA`` option to create the database.
+
 # Job workflow
 
 The default deployment initializes a Jenkins server with a [predefined set of

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -56,7 +56,7 @@ services:
         networks:
             - omero-network
         volumes:
-            - ./server:/home/omero
+            - ./server:/home/omero-server
         environment:
             - SLAVE_NAME=omero
             - SLAVE_EXECUTORS=2
@@ -74,8 +74,8 @@ services:
         networks:
             - omero-network
         volumes:
-            - ./web:/home/omero
-            - ./nginx/conf.d:/home/omero/nginx
+            - ./web:/home/omero-web
+            - ./nginx/conf.d:/home/omero-web/nginx
         environment:
             - SLAVE_NAME=web
             - SLAVE_EXECUTORS=2
@@ -91,7 +91,7 @@ services:
             - omero-network
         volumes:
             - ./nginx/conf.d:/etc/nginx/conf.d
-            - ./web/static:/home/omero/static
+            - ./web/static:/home/omero-web/static
             - ./nginx/log:/var/log/nginx
             - ./nginx/sslcert:/etc/nginx/ssl
         environment:

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM openmicroscopy/devslave-c7:0.6.1
+FROM openmicroscopy/devslave-c7:0.7.2
 
 MAINTAINER OME
 

diff --git a/home/config.xml b/home/config.xml
@@ -3,7 +3,7 @@
   <disabledAdministrativeMonitors>
     <string>jenkins.security.s2m.MasterKillSwitchWarning</string>
   </disabledAdministrativeMonitors>
-  <version>2.150.3</version>
+  <version>2.319.2</version>
   <installStateName>RESTART</installStateName>
   <numExecutors>0</numExecutors>
   <mode>NORMAL</mode>
@@ -29,8 +29,8 @@
       <properties>
         <hudson.tools.InstallSourceProperty>
           <installers>
-            <hudson.tools.JDKInstaller plugin="jdk-tool@1.2">
-              <id>jdk-8u192-oth-JPR</id>
+            <hudson.tools.JDKInstaller plugin="jdk-tool@1.5">
+              <id>jdk-8u221-oth-JPR</id>
               <acceptLicense>true</acceptLicense>
             </hudson.tools.JDKInstaller>
           </installers>

diff --git a/home/hudson.plugins.copyartifact.CopyArtifactConfigurat b/home/hudson.plugins.copyartifact.CopyArtifactConfigurat
@@ -0,0 +1,4 @@
+<?xml version='1.1' encoding='UTF-8'?>
+<hudson.plugins.copyartifact.CopyArtifactConfiguration plugin="copyartifact@1.46.2">
+  <mode>PRODUCTION</mode>
+</hudson.plugins.copyartifact.CopyArtifactConfiguration>
diff --git a/home/hudson.plugins.git.GitTool.xml b/home/hudson.plugins.git.GitTool.xml
@@ -1,5 +1,5 @@
 <?xml version='1.1' encoding='UTF-8'?>
-<hudson.plugins.git.GitTool_-DescriptorImpl plugin="git-client@2.7.2">
+<hudson.plugins.git.GitTool_-DescriptorImpl plugin="git-client@3.11.0">
   <installations class="hudson.plugins.git.GitTool-array">
     <hudson.plugins.git.GitTool>
       <name>Default</name>

diff --git a/home/hudson.plugins.gradle.Gradle.xml b/home/hudson.plugins.gradle.Gradle.xml
@@ -0,0 +1,4 @@
+<?xml version='1.1' encoding='UTF-8'?>
+<hudson.plugins.gradle.Gradle_-DescriptorImpl plugin="gradle@1.38">
+  <installations/>
+</hudson.plugins.gradle.Gradle_-DescriptorImpl>
diff --git a/home/hudson.tasks.Ant.xml b/home/hudson.tasks.Ant.xml
@@ -1,5 +1,5 @@
 <?xml version='1.1' encoding='UTF-8'?>
-<hudson.tasks.Ant_-DescriptorImpl plugin="ant@1.8">
+<hudson.tasks.Ant_-DescriptorImpl plugin="ant@1.13">
   <installations>
     <hudson.tasks.Ant_-AntInstallation>
       <name>Ant 1.9</name>

diff --git a/home/jobs/BIOFORMATS-build/config.xml b/home/jobs/BIOFORMATS-build/config.xml
@@ -1,5 +1,5 @@
 <?xml version='1.1' encoding='UTF-8'?>
-<matrix-project plugin="matrix-project@1.14">
+<matrix-project>
   <actions/>
   <description></description>
   <keepDependencies>false</keepDependencies>
@@ -22,7 +22,7 @@
       </parameterDefinitions>
     </hudson.model.ParametersDefinitionProperty>
   </properties>
-  <scm class="hudson.plugins.git.GitSCM" plugin="git@4.0.0-rc">
+  <scm class="hudson.plugins.git.GitSCM">
     <configVersion>2</configVersion>
     <userRemoteConfigs>
       <hudson.plugins.git.UserRemoteConfig>

diff --git a/home/jobs/BIOFORMATS-push/config.xml b/home/jobs/BIOFORMATS-push/config.xml
@@ -32,7 +32,7 @@
       </parameterDefinitions>
     </hudson.model.ParametersDefinitionProperty>
   </properties>
-  <scm class="hudson.plugins.git.GitSCM" plugin="git@4.0.0-rc">
+  <scm class="hudson.plugins.git.GitSCM">
     <configVersion>2</configVersion>
     <userRemoteConfigs>
       <hudson.plugins.git.UserRemoteConfig>
@@ -123,7 +123,7 @@ foreach-get-version-as-property &gt; ${WORKSPACE}/target/version.properties</com
   </builders>
   <publishers>
     <hudson.tasks.ArtifactArchiver>
-      <artifacts>target/version.tsv</artifacts>
+      <artifacts>target/version.tsv, target/version.properties</artifacts>
       <allowEmptyArchive>false</allowEmptyArchive>
       <onlyIfSuccessful>false</onlyIfSuccessful>
       <fingerprint>false</fingerprint>

diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml
@@ -57,14 +57,26 @@
   <triggers/>
   <concurrentBuild>false</concurrentBuild>
   <builders>
+    <hudson.plugins.copyartifact.CopyArtifact plugin="copyartifact">
+      <project>OMERO-python-superbuild-build</project>
+      <filter></filter>
+      <target></target>
+      <excludes></excludes>
+      <selector class="hudson.plugins.copyartifact.StatusBuildSelector"/>
+      <flatten>false</flatten>
+      <doNotFingerprintArtifacts>false</doNotFingerprintArtifacts>
+    </hudson.plugins.copyartifact.CopyArtifact>
     <hudson.tasks.Shell>
-      <command>cd src
+      <command>
+mv omero-scripts/dist/*.tar.gz .
+cd src
 export OMERO_BRANCH=$MERGE_PUSH_BRANCH
-
+        
 virtualenv $WORKSPACE/omero-virtualenv --system-site-packages
+
 source $WORKSPACE/omero-virtualenv/bin/activate
 pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl
-pip install -U setuptools &apos;omero-py&gt;=5.6.0.dev9&apos;
+pip install -U setuptools omero-py
 source docs/hudson/OMERO.sh
 </command>
     </hudson.tasks.Shell>

diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml
@@ -49,7 +49,7 @@ source $WORKSPACE/.venv3/bin/activate
 pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl
 pip install -U pip future
 pip install markdown
-pip install reportlab # For figure
+pip install &quot;reportlab<3.6&quot; # For figure
 pip install omego
 pip install tables
 pip install jinja2
@@ -106,7 +106,6 @@ OMERO_DATA_DIR=$DATA_DIR
 
 mkdir -p $OMERO_DATA_DIR
 
-# UNZIP SERVER
 OMERO_DIST=$WORKSPACE/OMERO.server
 export OMERODIR=$OMERO_DIST
 
@@ -122,7 +121,6 @@ unzip $ZIP
 rm -f $ZIP
 mv $WORKSPACE/$DIST $OMERO_DIST
 
-# INSTALL PYTHON PACKAGES
 source $WORKSPACE/.venv3/bin/activate
 pip install git+https://github.com/$SPACE_USER/omero-metadata.git@$MERGE_PUSH_BRANCH#egg=omero-metadata
 pip install git+https://github.com/$SPACE_USER/omero-cli-render.git@$MERGE_PUSH_BRANCH#egg=omero-cli-render
@@ -132,12 +130,7 @@ for x in *.tar.gz; do
     pip install -U $x # Install marshal, etc. *after* requirements
 done
 
-## LOAD CONFIG
 
-# LOAD EXTRA CONFIG
-#omero load configfile.omero
-
-# DEFAULT CONFIG
 omero config set omero.db.name $OMERO_DB_NAME
 omero config set omero.db.host $OMERO_DB_HOST
 omero config set omero.db.user $OMERO_DB_USER
@@ -147,10 +140,6 @@ omero config set omero.db.poolsize 25
 omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
 omero config set omero.security.trustStorePassword changeit
 omero certificates
-## END LOAD CONFIG
-
-
-## PURGE
 
 if [ &quot;$PURGE_DATA&quot; = &quot;true&quot; ]; then
     createdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME
@@ -160,14 +149,11 @@ else
     omego db -vvv upgrade --serverdir $OMERO_DIST --dbname $OMERO_DB_NAME
 fi
 
-## END PURGE
-
 export LANG=&apos;en_US.UTF-8&apos;
 export LANGUAGE=&apos;en_US:en&apos;
 export LC_ALL=&apos;en_US.UTF-8&apos;
 BUILD_ID=DONT_KILL_ME omero admin start
 
-# WAIT FOR OMERO TO START UP AND ACCEPT CONNECTIONS
 omero admin waitup
 omero admin diagnostics
 

diff --git a/home/org.jenkinsci.plugins.docker.commons.tools.DockerT b/home/org.jenkinsci.plugins.docker.commons.tools.DockerT
@@ -0,0 +1,4 @@
+<?xml version='1.1' encoding='UTF-8'?>
+<org.jenkinsci.plugins.docker.commons.tools.DockerTool_-DescriptorImpl plugin="docker-commons@1.18">
+  <installations class="org.jenkinsci.plugins.docker.commons.tools.DockerTool-array"/>
+</org.jenkinsci.plugins.docker.commons.tools.DockerTool_-DescriptorImpl>
diff --git a/home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml b/home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml
@@ -0,0 +1,4 @@
+<?xml version='1.1' encoding='UTF-8'?>
+<org.jenkinsci.plugins.gitclient.JGitApacheTool_-DescriptorImpl plugin="git-client@3.11.0">
+  <installations class="hudson.plugins.git.GitTool-array"/>
+</org.jenkinsci.plugins.gitclient.JGitApacheTool_-DescriptorImpl>
diff --git a/home/org.jenkinsci.plugins.gitclient.JGitTool.xml b/home/org.jenkinsci.plugins.gitclient.JGitTool.xml
@@ -1,4 +1,4 @@
 <?xml version='1.1' encoding='UTF-8'?>
-<org.jenkinsci.plugins.gitclient.JGitTool_-DescriptorImpl plugin="git-client@2.7.2">
+<org.jenkinsci.plugins.gitclient.JGitTool_-DescriptorImpl plugin="git-client@3.11.0">
   <installations class="hudson.plugins.git.GitTool-array"/>
 </org.jenkinsci.plugins.gitclient.JGitTool_-DescriptorImpl>
diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile
@@ -1,10 +1,11 @@
-FROM jenkins/jenkins:2.150.3
+FROM jenkins/jenkins:2.319.2-lts-jdk11
 MAINTAINER OME
 
 # Temp fix robot test results
-ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP="
+ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" -Djenkins.install.runSetupWizard=false
 
 COPY plugins.txt /usr/share/jenkins/ref/plugins.txt
+
 RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt
 
 USER root