Update Galaxy in CVMFS

galaxyproject · Jun 3, 2016 · ade5239 · ade5239
1 parent 9d2ecd4
commit ade5239
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Showing 8 changed files with 101 additions and 47 deletions.
diff --git a/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml b/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
@@ -415,6 +415,7 @@
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.1.0.20140616.0" />
     </section>
     <section id="group" name="Join, Subtract and Group" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1" />
         <tool id="join1" />
         <tool id="comp1" />

diff --git a/galaxy.yml b/galaxy.yml
@@ -2,50 +2,88 @@
 
 # FIXME: can't notify for restart across plays
 
-- name: Galaxy web code and dependencies, manage static configs
-  hosts: galaxyservers
-  remote_user: "{{ galaxy_privileged_user }}"
-  vars_files:
-    - "{{ deploy_env }}/secret_vars/galaxyservers.yml"
-  vars:
-    instance_root: "{{ galaxy_root }}"
-    galaxy_config: "{{ galaxy_config_hash }}"
-  roles:
-    # set up local galaxy clone and local config
-    - role: galaxyprojectdotorg.galaxy
-      galaxy_manage_clone: no
-      galaxy_manage_static_setup: yes
-      galaxy_manage_mutable_setup: no
-      galaxy_manage_database: no
-      galaxy_fetch_dependencies: no
-  post_tasks:
-    # create impersonation config on Main
-    - name: Set galaxy_config to impersonate_config_hash
-      set_fact:
-        galaxy_config: "{{ impersonate_config_hash }}"
-      when: deploy_env == "production"
+- name: Update Galaxy on CVMFS stratum 0 server
+  hosts: cvmfsstratum0servers
+  remote_user: "{{ galaxy_user }}"
+  tasks:
+    - name: Begin CVMFS transaction
+      command: /usr/bin/cvmfs_server transaction {{ galaxy_instance_codename }}.galaxyproject.org
 
-    - name: Create Galaxy impersonation configuration file
-      template: src=roles/galaxyprojectdotorg.galaxy/templates/galaxy.ini.j2 dest={{ galaxy_config_dir }}/impersonate.ini backup=yes
-      when: deploy_env == "production"
+    - name: Restart docker
+      service:
+        name: docker
+        state: restarted
 
-    # create installer config
-    - name: Set galaxy_config to installer_config_hash
-      set_fact:
-        galaxy_config: "{{ installer_config_hash }}"
+    - name: Fetch Galaxy commit
+      command: "/usr/bin/git rev-parse HEAD"
+      args:
+        chdir: /cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy
+      register: galaxy_commit_old
 
-    - name: Create Galaxy installer configuration file
-      template: src=roles/galaxyprojectdotorg.galaxy/templates/galaxy.ini.j2 dest={{ galaxy_config_dir }}/installer.ini backup=yes
+    - name: Update Galaxy
+      # TODO: use docker_container maybe?
+      command: docker run --rm -v /cvmfs:/cvmfs galaxy/update /cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/bin/update_galaxy.sh
 
-    # create data manager config
-    - name: Set galaxy_config to datamanager_config_hash
-      set_fact:
-        galaxy_config: "{{ datamanager_config_hash }}"
+    # TODO: store these somewhere in the playbook
+    - name: Fetch Galaxy version
+      command: "/usr/bin/docker run --rm -v /cvmfs:/cvmfs -e PYTHONPATH=/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy/lib galaxy/update /cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/venv/bin/python -c 'from galaxy.version import VERSION; print VERSION'"
+      register: galaxy_version
 
-    - name: Create Galaxy data manager configuration file
-      template: src=roles/galaxyprojectdotorg.galaxy/templates/galaxy.ini.j2 dest={{ galaxy_config_dir }}/datamanager.ini backup=yes
+    - name: Fetch Galaxy commit
+      command: "/usr/bin/git rev-parse HEAD"
+      args:
+        chdir: /cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy
+      register: galaxy_commit
 
-- name: Galaxy database and mutable configs
+    - name: Fetch Galaxy short commit
+      command: "/usr/bin/git rev-parse --short HEAD"
+      args:
+        chdir: /cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy
+      register: galaxy_commit_short
+
+    - name: Abort CVMFS transaction
+      command: /usr/bin/cvmfs_server abort -f {{ galaxy_instance_codename }}.galaxyproject.org
+      when: galaxy_commit_old.stdout == galaxy_commit.stdout
+
+    - name: Exit if no changes
+      fail:
+        msg: Galaxy commit ID did not change after updating, transaction aborted
+      when: galaxy_commit_old.stdout == galaxy_commit.stdout
+
+    - name: Store updated version information
+      local_action:
+        module: copy
+        # Fixme: should probably use to_nice_yaml
+        content: |
+          ---
+          galaxy_version: {{ galaxy_version.stdout }}
+          galaxy_commit: {{ galaxy_commit.stdout }}
+          galaxy_commit_short: {{ galaxy_commit_short.stdout }}
+        dest: "{{ deploy_env }}/galaxy_version.yml"
+
+    - name: Publish CVMFS transaction
+      command: /usr/bin/cvmfs_server publish -a "galaxy_{{ galaxy_version.stdout }}_{{ galaxy_commit_short.stdout }}" -m "Update Galaxy to version {{ galaxy_version.stdout }} commit {{ galaxy_commit.stdout }} via Ansible" {{ galaxy_instance_codename }}.galaxyproject.org
+
+- name: Snapshot CVMFS changes on stratum 1 servers
+  hosts: cvmfsstratum1servers
+  remote_user: "{{ galaxy_user }}"
+  tasks:
+    - name: CVMFS snapshot
+      command: /usr/bin/cvmfs_server snapshot {{ galaxy_instance_codename }}.galaxyproject.org
+
+    - name: Clear squid cache (restart)
+      service:
+        name: squid
+        state: restarted
+
+- name: Wipe CVMFS cache on Galaxy servers
+  hosts: galaxyservers
+  remote_user: "{{ galaxy_user }}"
+  tasks:
+    - name: Wipe CVMFS cache
+      command: /usr/local/bin/cvmfs_wipecache
+
+- name: Galaxy database and interactive environments
   hosts: galaxyservers
   remote_user: "{{ galaxy_user }}"
   vars_files:
@@ -58,24 +96,25 @@
     - role: galaxyprojectdotorg.galaxy
       galaxy_manage_clone: no
       galaxy_manage_static_setup: no
-      galaxy_manage_mutable_setup: yes
+      galaxy_manage_mutable_setup: no
       galaxy_manage_database: yes
       galaxy_fetch_eggs: no
       when: inventory_hostname in groups['galaxymasters']
-    # fetch and distribute mutable configs (needs the galaxy_mutable_configs
-    # var set in galaxyprojectdotorg.galaxy)
-    - role: usegalaxy
     # Set up interactive environments
+    # FIXME: clone the version in galaxy_version.yml
     - role: galaxyprojectdotorg.interactive_environments
+  post_tasks:
+    # FIXME: still need to kill hung uWSGI workers
+    - name: Restart Galaxy
+      command: /home/g2{{ galaxy_instance_codename }}/bin/galaxy graceful
 
-- name: Galaxy privileged user tasks and static content setup
+- name: Update version in welcome.html
   hosts: galaxyservers
   remote_user: "{{ galaxy_privileged_user }}"
   vars_files:
     - "{{ deploy_env }}/secret_vars/galaxyservers.yml"
+    - "{{ deploy_env }}/galaxy_version.yml"
   roles:
-    - role: usegalaxy_privileged
-    # welcome page
     - role: usegalaxy_static
 
 - name: Update Galaxy on Pulsar servers

diff --git a/galaxy_static.yml b/galaxy_static.yml
@@ -3,5 +3,7 @@
 
 - hosts: galaxyservers
   remote_user: "{{ galaxy_privileged_user }}"
+  vars_files:
+    - "{{ deploy_env }}/galaxy_version.yml"
   roles:
     - role: usegalaxy_static
diff --git a/stage/galaxy_version.yml b/stage/galaxy_version.yml
@@ -0,0 +1,4 @@
+---
+galaxy_version: 16.07.dev
+galaxy_commit: 789c3009369c0f3712cc140d404ad0a8b1151f48
+galaxy_commit_short: 789c300
diff --git a/stage/group_vars/all.yml b/stage/group_vars/all.yml
@@ -5,3 +5,4 @@ deploy_env: stage
 galaxy_changeset_id: 25a26d8c9c4f21e84e39741c98755f10c4519d8b
 galaxy_vcs: git
 galaxy_instance_codename: test
+galaxy_user: g2test
diff --git a/stage/group_vars/galaxyservers.yml b/stage/group_vars/galaxyservers.yml
@@ -26,7 +26,6 @@ galaxy_log_dir: "{{ galaxy_root }}/log"
 
 
 ## used by: the play itself
-galaxy_user: g2test
 # As of Ansible 2.0, a variable name matching a word used in a with_items loop
 # (as in supervisord_group_configs) will be expanded, despite the fact that
 # bare word expansion is deprecated. D=

diff --git a/stage/inventory b/stage/inventory
@@ -24,3 +24,11 @@ radegast.galaxyproject.org
 
 [virtualhosts]
 radegast.galaxyproject.org
+
+[cvmfsstratum0servers]
+cvmfs0-tacc0.galaxyproject.org
+
+[cvmfsstratum1servers]
+cvmfs1-tacc0.galaxyproject.org
+cvmfs1-iu0.galaxyproject.org
+cvmfs1-psu0.galaxyproject.org
diff --git a/templates/galaxy/common/static/welcome.html.j2 b/templates/galaxy/common/static/welcome.html.j2
@@ -160,7 +160,7 @@
 
                 <p style="font-size: 90%;">This is a free, public, internet accessible resource. Data transfer and data storage are not encrypted. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to any public site, including this Galaxy server.  If you have protected data, large data storage requirements, or short deadlines you are encouraged to setup your own <a href="http://getgalaxy.org/" target="_blank">local Galaxy instance</a> or run <a href="http://usegalaxy.org/cloud" target="_blank">Galaxy on the cloud</a>.</p>
 
-                <p class="text-center"><small>Galaxy version {{ version_major.stdout }}, commit <code><a href="https://github.com/galaxyproject/galaxy/commit/{{ galaxy_changeset_id }}" target="_blank">{{ galaxy_changeset_id }}</a></code></small></p>
+                <p class="text-center"><small>Galaxy version {{ galaxy_version }}, commit <code><a href="https://github.com/galaxyproject/galaxy/commit/{{ galaxy_commit }}" target="_blank">{{ galaxy_commit }}</a></code></small></p>
 
             </div>
         </div>