Upgrade default sequenceserver and blast version (#7)

* Upgrade default sequenceserver version to 2.0.0 * Upgrade default blast version to 2.12.0 * Add variable for the path to the log file * Fix regexp to change the logo and the title * Molecule test: add tasks to display logs
abims-sbr · Feb 21, 2022 · f44b227 · f44b227
1 parent 88dbfbb
commit f44b227
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Showing 8 changed files with 19 additions and 8 deletions.
diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ Available variables are listed below, along with default values (see `defaults/m
 
 ```yaml
 # Version of the ruby gem to install (>= 2.0.0)
-sequenceserver_version: 2.0.0.rc8
+sequenceserver_version: 2.0.0
 ```
 Variable to set the version of SequenceServer to install. This role can be used with SequenceServer version >= 2.0.0.
 
@@ -57,7 +57,7 @@ SequenceServer logs are stored in `/var/log/sequenceserver/sequenceserver.log`.
 
 ```yaml
 # Version of BLAST to use in sequenceserver (called with "module load" in the slurm bash script)
-sequenceserver_blast_version: 2.9.0
+sequenceserver_blast_version: 2.12.0
 # Absolute path to the blast binaries
 sequenceserver_blast_binaries: "~/conda3/envs/blast-{{ sequenceserver_blast_version }}/bin"
 # --cpus-per-task (SLURM option)

diff --git a/defaults/main.yml b/defaults/main.yml
@@ -3,7 +3,7 @@
 # Ruby gem
 #
 # Version of the ruby gem to install (>= 2.0.0)
-sequenceserver_version: 2.0.0.rc8
+sequenceserver_version: 2.0.0
 
 # List of blast databases
 #
@@ -23,7 +23,7 @@ sequenceserver_blast_db:
 # Used in the slurm bash scripts
 #
 # Version of BLAST to use in sequenceserver (called with "module load" in the slurm bash script)
-sequenceserver_blast_version: 2.9.0
+sequenceserver_blast_version: 2.12.0
 # Absolute path to the blast binaries
 sequenceserver_blast_binaries: "~/conda3/envs/blast-{{ sequenceserver_blast_version }}/bin"
 # --cpus-per-task (SLURM option)

diff --git a/molecule/default/converge.yml b/molecule/default/converge.yml
@@ -10,3 +10,5 @@
     # yamllint disable-line rule:braces
       - { name: 'my_db', port: '4567', path: '/tmp/test-data' }
     sequenceserver_top_web_page_html_path: "/tmp/top_web_page.html"
+    sequenceserver_home_url: "http://myfavoritewebsite.com"
+    sequenceserver_support_email: "mailto:[email protected]"
diff --git a/molecule/default/tests/env.yml b/molecule/default/tests/env.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - blast=2.9.0
+  - blast=2.12.0
diff --git a/molecule/default/verify.yml b/molecule/default/verify.yml
@@ -25,6 +25,13 @@
       when: (ansible_distribution == "CentOS" or ansible_distribution == "RedHat") and ansible_distribution_major_version == "7"
       register: sequenceserver_command
       failed_when: sequenceserver_command.rc > 0
+    - name: Get SequenceServer service logs
+      slurp:
+        src: "/var/log/sequenceserver/sequenceserver.log"
+      register: log
+    - name: Display SequenceServer service logs
+      debug:
+        msg: "{{ log.content | b64decode }}"
     - name: Test that SequenceServer service is running for my_db
       systemd:
         name: sequenceserver-my_db.service

diff --git a/tasks/main.yml b/tasks/main.yml
@@ -79,7 +79,7 @@
     replace: "{{ item.replace }}"
     backup: yes
   with_items:
-    - {regexp: '      <a\n        class="navbar-brand"\n        href="http://sequenceserver.com" target="_blank">\n        <img class="logo" src="SequenceServer_logo.png" alt="sequenceserver_logo">\n        <small>\n          <%= SequenceServer::VERSION %>\n        </small>\n      </a>', replace: '      <a\n        class="navbar-left"\n        href="{{ sequenceserver_home_url }}" target="_blank">\n        <img src="{{ sequenceserver_logo }}" alt="logo" height="40px" style="margin-top:5px;margin-right:30px;">\n      </a>\n      <div\n        class="navbar-brand" style="margin-top:10px;">\n        <%= SequenceServer::WEB_PAGE_TITLE %>\n      </div>'} # noqa 204
+    - {regexp: '\s+<a\n\s+class="navbar-brand"\n\s+href="https://sequenceserver.com" target="_blank">\n\s+<img class="logo" src="SequenceServer_logo.png" alt="sequenceserver_logo">\n\s+<small>\n\s+<%= SequenceServer::VERSION %>\n\s+</small>\n\s+</a>', replace: '      <a\n        class="navbar-left"\n        href="{{ sequenceserver_home_url }}" target="_blank">\n        <img src="{{ sequenceserver_logo }}" alt="logo" height="40px" style="margin-top:5px;margin-right:30px;">\n      </a>\n      <div\n        class="navbar-brand" style="margin-top:10px;">\n        <%= SequenceServer::WEB_PAGE_TITLE %>\n      </div>'} # noqa 204
     - {regexp: 'http://www.sequenceserver.com/#license-and-support', replace: '{{ sequenceserver_support_email }}'}
 
 - name: Modify source erb file for custom web page title | Insert supplementary HTML code on the top of the web page | Check if the file exists

diff --git a/templates/syslog.j2 b/templates/syslog.j2
@@ -1,3 +1,3 @@
-if $programname == 'sequenceserver' then /var/log/sequenceserver/sequenceserver.log
-if $programname == 'scl' then /var/log/sequenceserver/sequenceserver.log
+if $programname == 'sequenceserver' then {{ sequenceserver_log_file }}
+if $programname == 'scl' then {{ sequenceserver_log_file }}
 & stop
diff --git a/vars/main.yml b/vars/main.yml
@@ -24,6 +24,8 @@ sequenceserver_config_dir: config
 sequenceserver_extension_dir: extension
 # Contains SLURM scripts
 sequenceserver_hpc_dir: hpc_script
+# Absolute path to the log file
+sequenceserver_log_file: /var/log/sequenceserver/sequenceserver.log
 # Default logo image name (used if sequenceserver_logo_url and sequenceserver_logo_path are not provided)
 sequenceserver_logo: SequenceServer_logo.png