Update tpv on production to version 2.2.0

.github/workflows/check_tpv_config.yml

@@ -31,26 +31,72 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install total-perspective-vortex==$TPV_VERSION pyyaml galaxy-data
+        pip install total-perspective-vortex==$TPV_VERSION pyyaml galaxy-app
       env:
-        TPV_VERSION: '1.2.0'
-    # Run check files script
-    - name: Check vortex destination ids against job conf environment ids (aarnet)
+        TPV_VERSION: '2.2.0'
+    - name: Check TPV files and job conf
       env:
         SETTING: github
-      run: |
-        import yaml
-        with open('templates/galaxy/config/aarnet_job_conf.yml.j2') as handle:
-            job_conf_destinations = yaml.safe_load(handle).get('execution', {}).get('environments', [])
-        with open('files/galaxy/dynamic_job_rules/production/total_perspective_vortex/destinations.yml') as handle:
-            vortex_destinations = yaml.safe_load(handle).get('destinations', [])
-        for vd in vortex_destinations:
-            try:
-                job_conf_env = job_conf_destinations[vd]
-            except KeyError as e:
-                raise Exception(f'Destination id {vd} not found in job config file')        
       shell: python
-    - name: Run tpv lint on all vortex config files
-      env:
-        SETTING: github
-      run: for f in files/galaxy/dynamic_job_rules/production/total_perspective_vortex/*; do tpv lint $f; done
+      run: |
+        """This code uses ansible to template out the jinja templates for tpv configs and job config,
+              then runs the tpv linter on the resultant files."""
+        import re
+        import subprocess
+        import os
+        import shutil
+
+        working_dir = '.github/workflows/check_tpv_config'
+        hosts_file = os.path.join(working_dir, 'hosts')
+        playbook_file = os.path.join(working_dir, 'template_playbook.yml')
+        files_dir = os.path.join(working_dir, 'files')
+        templates_dir = os.path.join(working_dir, 'templates')
+        os.mkdir(files_dir)
+        os.mkdir(templates_dir)
+
+        tpv_dir = 'files/galaxy/dynamic_job_rules/production/total_perspective_vortex'
+        tpv_config_files = [os.path.join(tpv_dir, f) for f in os.listdir(tpv_dir)]
+        job_conf_template = 'templates/galaxy/config/aarnet_job_conf.yml.j2'
+        tpv_files = []
+
+        replace_patterns = ['\{\{\s?vault_\w+\s?\}\}', '\{\{\s?hostname\s?\}\}']
+
+        with open('.vault_pass.txt', 'w') as password_file:
+          password_file.write('FalsePassword')
+
+        def template_file(fname):
+          output_fname = fname.replace(templates_dir, files_dir).replace('.j2', '')
+          extra_vars = f'src={fname.replace(templates_dir+"/", "")} dest={os.path.realpath(output_fname)}'
+          ansible_command = f'ansible-playbook -i {hosts_file} {playbook_file} --extra-vars \'{extra_vars}\''
+          try:
+            subprocess.check_output(ansible_command, shell=True)
+          except subprocess.CalledProcessError as e:
+            print(e.output)
+            raise Exception('Failed to template {os.path.basename(fname)}')
+          return output_fname
+
+        def sanitize_text(fname):
+          """Replaces any references to vault variables with a constant string as the
+               vault is not decrypted during tests"""
+          with open(fname) as handle:
+            text = handle.read()
+            for rp in replace_patterns:
+              text = re.sub(rp, 'text_replaced', text)
+          with open(fname, 'w') as handle:
+            handle.write(text)
+
+        for t in tpv_config_files + [job_conf_template]:
+          if t.endswith('.yml'):
+            test_fname = os.path.join(files_dir, os.path.basename(t))
+            shutil.copy(t, test_fname)
+            tpv_files.append(test_fname)
+          elif t.endswith('.yml.j2'):
+            test_fname = os.path.join(templates_dir, os.path.basename(t))
+            shutil.copy(t, test_fname)
+            sanitize_text(test_fname)
+            templated_file = template_file(test_fname)
+            if 'tpv_dir' in t:
+              tpv_files.append(templated_file)
+
+        for t in tpv_files:
+          subprocess.check_output(f'tpv lint {t}', shell=True)

.github/workflows/check_tpv_config/hosts

@@ -0,0 +1,2 @@
+[defaults]
+localhost ansible_connection=local

.github/workflows/check_tpv_config/template_playbook.yml

@@ -0,0 +1,11 @@
+---
+- hosts: localhost
+  vars_files:
+  - ../../../group_vars/aarnet.yml
+  - ../../../group_vars/galaxyservers.yml
+  - ../../../host_vars/aarnet.usegalaxy.org.au.yml
+  tasks:
+  - name: Template file
+    template:
+      src: "{{ src }}"
+      dest: "{{ dest }}"

aarnet_update_configs_playbook.yml

@@ -8,40 +8,38 @@
       - group_vars/aarnet_slurm.yml
       - host_vars/aarnet.usegalaxy.org.au.yml
       - secret_group_vars/stats_server_vault
-  vars:
-    - tpv_files:
-        - tools.yml
-        - users.yml
-        - roles.yml
-        - destinations.yml
-    - tpv_templates:
-        - default_tool.yml.j2
   handlers:
     - name: galaxy gravity restart
       become: True
       become_user: galaxy
       command: "{{ galaxy_venv_dir }}/bin/galaxyctl graceful"
       environment:
         GRAVITY_STATE_DIR: "{{ galaxy_gravity_state_dir }}"
+    - name: galaxy handler restart
+      become: True
+      become_user: galaxy
+      command: "{{ galaxy_venv_dir }}/bin/galaxyctl handler_0 handler_1 handler_2 handler_3 handler_4"
+      environment:
+        GRAVITY_STATE_DIR: "{{ galaxy_gravity_state_dir }}"
   tasks:
     - name: copy job_conf file
       template:
         src: "{{ galaxy_config_template_src_dir }}/config/aarnet_job_conf.yml.j2"
         dest: "{{ galaxy_config_dir }}/job_conf.yml"
-      notify: galaxy gravity restart
+      notify: galaxy handler restart
       # TODO: better linting of job conf, then it is probably entirely acceptable to let the jenkins_bot trigger a graceful restart of handlers
       when: not ansible_user == 'jenkins_bot'  # do not let the automatic process update the job conf
     - name: template object store conf file
       template:
         src: "{{ galaxy_config_template_src_dir }}/config/aarnet_object_store_conf.xml.j2"
         dest: "{{ galaxy_config_dir }}/object_store_conf.xml"
-      # notify: Restart Galaxy # TODO: appropriate handler for galaxyctl restart
+      notify: galaxy gravity restart
       when: not ansible_user == 'jenkins_bot'  # do not let the automatic process object store or restart galaxy
     - name: template toolbox filters
       template:
         src: "{{ galaxy_config_template_src_dir }}/toolbox/filters/ga_filters.py.j2"
         dest: "{{ galaxy_server_dir }}/lib/galaxy/tools/toolbox/filters/ga_filters.py"
-      notify: galaxy gravity restart # TODO: check whether graceful restart is enough in this case
+      notify: galaxy gravity restart
       when: not ansible_user == 'jenkins_bot'  # do not let the automatic process restart galaxy
     - name: Copy local tool conf file
       copy:
@@ -50,13 +48,19 @@
       with_items:
         - local_tool_conf.xml
       when: not ansible_user == 'jenkins_bot'
-    - name: copy total perspective vortex files
+    - name: Install dynamic job rules (static) # dynamic job rules tasks copied from https://github.com/galaxyproject/ansible-galaxy/blob/main/tasks/static_setup.yml
       copy:
-        src: "{{ galaxy_dynamic_job_rules_src_dir }}/total_perspective_vortex/{{ item }}"
-        dest: "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/{{ item }}"
-      with_items: "{{ tpv_files }}"
-    - name: copy total perspective vortex templates
+        src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
+        dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item }}"
+        mode: 0644
+      with_items: "{{ galaxy_dynamic_job_rules }}"
+      when: not item.endswith(".j2")
+    - name: Install dynamic job rules (template)
       template:
-        src: "{{ galaxy_dynamic_job_rules_src_dir }}/total_perspective_vortex/{{ item }}"
-        dest: "{{ galaxy_dynamic_job_rules_dir }}/total_perspective_vortex/{{ item | replace('.j2', '') }}"
-      with_items: "{{ tpv_templates }}"
+        src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
+        dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | regex_replace(regex) }}"
+        mode: 0644
+      vars:
+        regex: '\.j2$'
+      with_items: "{{ galaxy_dynamic_job_rules }}"
+      when: item.endswith(".j2")