sequenceserver 3.1.2

README.md

@@ -22,7 +22,7 @@ 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: 2.2.0
+sequenceserver_version: 3.1.2
 ```
 Variable to set the version of SequenceServer to install. This role can be used with SequenceServer version >= 2.0.0.
 
@@ -66,7 +66,7 @@ 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: 2.14.0
+sequenceserver_blast_version: 2.15.0
 # Absolute path to the blast binaries
 sequenceserver_blast_binaries: "~/conda3/envs/blast-{{ sequenceserver_blast_version }}/bin"
 # --cpus-per-task (SLURM option)

defaults/main.yml

@@ -3,7 +3,7 @@
 # Ruby gem
 #
 # Version of the ruby gem to install (>= 2.0.0)
-sequenceserver_version: 2.2.0
+sequenceserver_version: 3.1.2
 
 # List of blast databases
 #
@@ -30,7 +30,7 @@ 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: 2.14.0
+sequenceserver_blast_version: 2.15.0
 # Absolute path to the blast binaries
 sequenceserver_blast_binaries: "~/conda3/envs/blast-{{ sequenceserver_blast_version }}/bin"
 # --cpus-per-task (SLURM option)

molecule/default/tests/env.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - blast=2.14.0
+  - blast=2.15.0

molecule/default/verify.yml

@@ -4,17 +4,17 @@
   become: true
   tasks:
     - name: Test blast installation
       shell: # noqa 301 305
         cmd: "/usr/local/anaconda/envs/blast/bin/blastn -version"
       register: blast_command
       failed_when: blast_command.rc > 0
     - name: Test my_db
       shell: # noqa 301 305
         cmd: "/usr/local/anaconda/envs/blast/bin/blastdbcmd -db /tmp/test-data/my_db -entry all"
       register: blastdbcmd_command
       failed_when: blastdbcmd_command.rc > 0
     - name: Ubuntu 20 | Test SequenceServer installation
       shell: # noqa 301
         cmd: "export GEM_PATH=/usr/local/share/gems && /usr/local/share/gems/bin/sequenceserver --version"
       when: ansible_distribution == "Ubuntu" and ansible_distribution_major_version == "20"
       register: sequenceserver_command
@@ -46,8 +46,8 @@
       get_url:
         url: "http://localhost"
         dest: "/tmp/nginx.html"
     - name: Test SequenceServer home page with curl # same thing tried with the ansible get_url module without success
       shell: # noqa 301
         cmd: "curl -sL http://localhost:4567 -o /tmp/home.html"
       register: sequenceserver_command
       failed_when: sequenceserver_command.rc > 0
@@ -59,33 +59,33 @@
       debug:
         msg: "{{ sequenceserver_page.content | b64decode }}"
     - name: Check title in home page content
       shell: # noqa 301
-        cmd: curl -sL http://localhost:4567 | grep -q 'http://myfavoritewebsite.com'
+        cmd: curl -sL http://localhost:4567 | grep -q 'BLAST server for my_db'
       register: grep_title
       failed_when: grep_title.rc > 0
     - name: Check support email in home page content
       shell: # noqa 301
         cmd: curl -sL http://localhost:4567 | grep -q 'mailto:amazingsupport@myfavoritewebsite.com'
       register: grep_support
       failed_when: grep_support.rc > 0
     - name: Check custom html in home page content (top)
       shell: # noqa 301
         cmd: curl -sL http://localhost:4567 | grep -q 'My message'
       register: grep_custom_html_top
       failed_when: grep_custom_html_top.rc > 0
     - name: Check custom html in home page content (bottom)
       shell: # noqa 301
         cmd: curl -sL http://localhost:4567 | grep -q 'Render custom string for this database'
       register: grep_custom_html_bottom
       failed_when: grep_custom_html_bottom.rc > 0
     - name: Check that the home page is rendering the values of the placeholders set for my_db
       shell: # noqa 301
         cmd: curl -sL http://localhost:4567 | grep -q '<a href="http://testplaceholder.com">my favorite link</a>'
       register: grep_placeholder
       failed_when: grep_placeholder.rc > 0
     - name: Get the lib modified for hpc integration
       slurp:
-        src: "/usr/local/share/gems/gems/sequenceserver-2.2.0/lib/sequenceserver/blast/job.rb"
+        src: "/usr/local/share/gems/gems/sequenceserver-3.1.2/lib/sequenceserver/blast/job.rb"
       register: lib_modified_for_hpc_integration
     - name: Display content of the lib modified for hpc integration
       debug:

tasks/main.yml

@@ -94,11 +94,23 @@
   when: (sequenceserver_logo_url is defined and sequenceserver_logo_url) or (sequenceserver_logo_path is defined and sequenceserver_logo_path)
 
 - name: Modify source erb file for custom web page title and source lib for HPC integration | Set regexp | Default
+  set_fact:
+    sequenceserver_home_url_regexp: 'https://sequenceserver.com'
+    sequenceserver_home_url_replace: '{{ sequenceserver_home_url }}'
+    sequenceserver_logo_regexp: 'sequenceserver_logo.webp'
+    sequenceserver_logo_replace: '{{ sequenceserver_logo }}'
+    sequenceserver_title_regexp: '<%= SequenceServer::VERSION %>'
+    sequenceserver_title_replace: '<%= SequenceServer::WEB_PAGE_TITLE %>'
+    sequenceserver_support_regexp: 'https://sequenceserver.com/support'
+    sequenceserver_hpc_command_regexp: '(\s+def command\n.+\n.+\n\s+end\n)(\n\s+def raise!\n)'
+
+- name: Modify source erb file for custom web page title and source lib for HPC integration | Set regexp | Version 2.2.0
   set_fact:
     sequenceserver_logo_title_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>' # noqa 204
     sequenceserver_logo_title_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
     sequenceserver_support_regexp: 'https://www.sequenceserver.com/#support'
     sequenceserver_hpc_command_regexp: '(      def command\n.+\n.+\n      end\n)(\n(?:      #.*\n)+      def raise!\n)'
+  when: sequenceserver_version is defined and sequenceserver_version == "2.2.0"
 
 - name: Modify source erb file for custom web page title and source lib for HPC integration | Set regexp | Version 2.0.0rc8
   set_fact:
@@ -107,15 +119,41 @@
     sequenceserver_hpc_command_regexp: '(      def command\n.+\n.+\n      end\n)(\n(?:      #.*\n){4}      def raise!\n)'
   when: sequenceserver_version is defined and sequenceserver_version == "2.0.0.rc8"
 
-- name: Modify source erb file for custom web page title | Customize logo, title, support email  | Replace
+- name: Modify source layout.erb file for custom web page title | Customize logo, title, support email | Replace | Default
   replace:
-    path: "{{ sequenceserver_file_to_modify_for_custom_web_page }}"
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
+    regexp: "{{ item.regexp }}"
+    replace: "{{ item.replace }}"
+    backup: yes
+  with_items:
+    - {regexp: '{{ sequenceserver_home_url_regexp }}', replace: '{{ sequenceserver_home_url_replace }}'}
+    - {regexp: '{{ sequenceserver_logo_regexp }}', replace: '{{ sequenceserver_logo_replace }}'}
+    - {regexp: '{{ sequenceserver_title_regexp }}', replace: '{{ sequenceserver_title_replace }}'}
+    - {regexp: '{{ sequenceserver_support_regexp }}', replace: '{{ sequenceserver_support_email }}'}
+  when: sequenceserver_version is defined and sequenceserver_version != "2.2.0" and sequenceserver_version != "2.0.0.rc8"
+
+- name: Modify source search_layout.erb file for custom web page title | Customize logo, title, support email | Replace | Default
+  replace:
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page_second }}"
+    regexp: "{{ item.regexp }}"
+    replace: "{{ item.replace }}"
+    backup: yes
+  with_items:
+    - {regexp: '{{ sequenceserver_logo_regexp }}', replace: '{{ sequenceserver_logo_replace }}'}
+    - {regexp: '{{ sequenceserver_title_regexp }}', replace: '{{ sequenceserver_title_replace }}'}
+    - {regexp: '{{ sequenceserver_support_regexp }}', replace: '{{ sequenceserver_support_email }}'}
+  when: sequenceserver_version is defined and sequenceserver_version != "2.2.0" and sequenceserver_version != "2.0.0.rc8"
+
+- name: Modify source erb file for custom web page title | Customize logo, title, support email | Replace | Version 2.2.0 or 2.0.0rc8
+  replace:
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
     regexp: "{{ item.regexp }}"
     replace: "{{ item.replace }}"
     backup: yes
   with_items:
     - {regexp: '{{ sequenceserver_logo_title_regexp }}', replace: '{{ sequenceserver_logo_title_replace }}'}
     - {regexp: '{{ sequenceserver_support_regexp }}', replace: '{{ sequenceserver_support_email }}'}
+  when: sequenceserver_version is defined and (sequenceserver_version == "2.2.0" or sequenceserver_version == "2.0.0.rc8")
 
 - name: Modify source erb file for custom web page title | Insert supplementary HTML code at the top of the web page | Check if the file exists
   stat:
@@ -139,24 +177,50 @@
   register: bottom_web_page_html_file
   when: bottom_web_page_html_path.stat.exists
 
-- name: Modify source erb file for custom web page title | Insert supplementary HTML code on the top of the web page | Insert or update with file content
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code on the top of the web page | Insert or update with file content | Default
   blockinfile:
-    path: "{{ sequenceserver_file_to_modify_for_custom_web_page }}"
+    path: "{{ item }}"
     block: "{{ top_web_page_html_file['content'] | b64decode }}"
     insertafter: "<body>"
     marker: "<!-- {mark} ANSIBLE MANAGED BLOCK - TOP -->"
     backup: yes
-  when: top_web_page_html_path.stat.exists
+  with_items:
+    - "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
+    - "{{ sequenceserver_file_to_modify_for_custom_web_page_second }}"
+  when: top_web_page_html_path.stat.exists and sequenceserver_version is defined and sequenceserver_version != "2.2.0" and sequenceserver_version != "2.0.0.rc8"
   notify: Restart all sequenceserver services
 
-- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the bottom of the web page | Insert or update with file content
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the bottom of the web page | Insert or update with file content | Default
   blockinfile:
-    path: "{{ sequenceserver_file_to_modify_for_custom_web_page }}"
+    path: "{{ item }}"
     block: "{{ bottom_web_page_html_file['content'] | b64decode }}"
     insertafter: "<%= yield %>"
     marker: "<!-- {mark} ANSIBLE MANAGED BLOCK - BOTTOM -->"
     backup: yes
-  when: bottom_web_page_html_path.stat.exists
+  with_items:
+    - "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
+    - "{{ sequenceserver_file_to_modify_for_custom_web_page_second }}"
+  when: bottom_web_page_html_path.stat.exists and sequenceserver_version is defined and sequenceserver_version != "2.2.0" and sequenceserver_version != "2.0.0.rc8"
+  notify: Restart all sequenceserver services
+
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code on the top of the web page | Insert or update with file content | Version 2.2.0 or 2.0.0rc8
+  blockinfile:
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
+    block: "{{ top_web_page_html_file['content'] | b64decode }}"
+    insertafter: "<body>"
+    marker: "<!-- {mark} ANSIBLE MANAGED BLOCK - TOP -->"
+    backup: yes
+  when: top_web_page_html_path.stat.exists and (sequenceserver_version == "2.2.0" or sequenceserver_version == "2.0.0.rc8")
+  notify: Restart all sequenceserver services
+
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the bottom of the web page | Insert or update with file content | Version 2.2.0 or 2.0.0rc8
+  blockinfile:
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page_first }}"
+    block: "{{ bottom_web_page_html_file['content'] | b64decode }}"
+    insertafter: "<%= yield %>"
+    marker: "<!-- {mark} ANSIBLE MANAGED BLOCK - BOTTOM -->"
+    backup: yes
+  when: bottom_web_page_html_path.stat.exists and (sequenceserver_version == "2.2.0" or sequenceserver_version == "2.0.0.rc8")
   notify: Restart all sequenceserver services
 
 - name: Add slurm_sbatch.sh for HPC integration (https://sequenceserver.com/doc/#hpc)

vars/main.yml

@@ -11,9 +11,10 @@ sequenceserver_ruby_download_url: "http://cache.ruby-lang.org/pub/ruby/3.3/ruby-
 sequenceserver_gem_install_dir: "{{ sequenceserver_gem_root_path }}/usr/local/share/gems"
 # Absolute path to the directory where the logo image is copied
 sequenceserver_web_public_repository: "{{ sequenceserver_gem_install_dir }}/gems/sequenceserver-{{ sequenceserver_version }}/public"
-# File that is modified to customize the blast server (logo, title and support link)
+# Files that are modified to customize the blast server (logo, title and support link)
 # Need sequenceserver version >= 2.0.0
-sequenceserver_file_to_modify_for_custom_web_page: "{{ sequenceserver_gem_install_dir }}/gems/sequenceserver-{{ sequenceserver_version }}/views/layout.erb"
+sequenceserver_file_to_modify_for_custom_web_page_first: "{{ sequenceserver_gem_install_dir }}/gems/sequenceserver-{{ sequenceserver_version }}/views/layout.erb"
+sequenceserver_file_to_modify_for_custom_web_page_second: "{{ sequenceserver_gem_install_dir }}/gems/sequenceserver-{{ sequenceserver_version }}/views/search_layout.erb"
 # File that is modified for HPC integration (SLURM)
 # Need sequenceserver version >= 2.0.0
 sequenceserver_lib_to_modify_for_hpc_integration: "{{ sequenceserver_gem_install_dir }}/gems/sequenceserver-{{ sequenceserver_version }}/lib/sequenceserver/blast/job.rb"