release 2.2.0 (#21)

* closes #19

* closes #20

.github/workflows/ci.yml

@@ -1,7 +1,7 @@
 ---
 name: CI
 'on':
-  pull_request:
+#  pull_request:
   push:
   schedule:
     - cron: "30 5 3 * *"

README.md

@@ -26,7 +26,7 @@ Variable to set the version of SequenceServer to install. This role can be used
 
 ```yaml
 sequenceserver_blast_db:
-#   - { name: 'my_db', port: '4567', path: '/path/to/my/db', users: ['fbar','jsmith'], web_page_title: 'blablabla' }
+#   - { name: 'my_db', port: '4567', path: '/path/to/my/db', users: ['fbar','jsmith'], web_page_title: 'blablabla', placeholders: [{key: 'key1', value: 'value1'}, {key: 'key2', value: 'value2'}] }
 ```
 This is the variable used to define the BLAST databases.
 
@@ -46,6 +46,7 @@ Each database is defined as a dictionary of the following parameters:
 - `users` Optional. Useful if the database needs restricted access. List of authorized users (LDAP "uid").
 - `ldap_businesscategory` Optional. Useful if the database needs restricted access. A ldap businessCategory value. LDAP users with this "businessCategory" value will have access to the database.
 - `web_page_title` Optional. The title displayed at the top of the web page. If not provided, the default title is "BLAST server for `name`".
+- `placeholders` Optional. A list of placeholder dictionaries `{key: 'key_item', value: 'value_item'}` that are used to customize top or bottom supplementary HTML code (see `sequenceserver_top_web_page_html_path` and `sequenceserver_bottom_web_page_html_path`). For example `placeholders: [{key: 'key1', value: 'value1'}, {key: 'key2', value: 'value2'}]`.
 
 Unique `name` and `port` are mandatory for each database.
 `users` and `ldap_businesscategory` are optional and can be used to add an authentication layer with the nginx-auth-ldap module. It is planned to add a `groups` parameter soon to list authorized groups.
@@ -76,10 +77,13 @@ sequenceserver_home_url: "http://sequenceserver.com"
 sequenceserver_support_email: "http://www.sequenceserver.com/#license-and-support"
 # Path to the file containing the supplementary HTML code to display at the top of the web page
 sequenceserver_top_web_page_html_path: "~/top_web_page.html"
+# Path to the file containing the supplementary HTML code to display at the bottom of the web page
+sequenceserver_bottom_web_page_html_path: "~/bottom_web_page.html"
 ```
 These variables allow to customize the BLAST server web page. They are optional.
 Two variables are available to set the logo displayed on the BLAST server: `sequenceserver_logo_url` or `sequenceserver_logo_path`. If both are set, the logo given with `sequenceserver_logo_path` will override the logo given with `sequenceserver_logo_url`.
-If the file `sequenceserver_top_web_page_html_path` exists, its content will be added in the base RUBY template used to display the web page and will be rendered at the top of the web page. This file must contain HTML code. This can be used, for example, to display information or warning messages to users (service shutdown, etc).
+If the files `sequenceserver_top_web_page_html_path` or `sequenceserver_bottom_web_page_html_path` exist, their content will be added in the base RUBY template used to display the web page and will be rendered at the top and bottom of the web page. These files must contain HTML code. This can be used, for example, to display information or warning messages to users (service shutdown, etc).
+Placeholders set in the database parameter `placeholders` (see above) can be used to customize the HTML code in these files. For example, if the database has the parameter `placeholders: [{key: 'key_item', value: 'value_item'}]`, the snippet `<%= SequenceServer::Key_item %>` will be replaced by the string `value_item` in the rendered HTML code. Please note that the first letter must be upper case in the snippet to be correctly interpreted as a Ruby constant by SequenceServer.
 
 ```yaml
 # User running the sequenceserver service (systemd) and running SLURM blast jobs

defaults/main.yml

@@ -15,9 +15,10 @@ sequenceserver_version: 2.0.0
 # groups: TODO. Optional. Useful if the database needs restricted access. List of authorized groups.
 # ldap_businesscategory: Optional. Useful if the database needs restricted access. A ldap businessCategory value. Ldap users with this businessCategory value will have access to the database.
 # web_page_title: Optional. The title displayed at the top of the web page. If not provided, the default title is "BLAST server for <name>".
+# placeholders: Optional. A list of placeholder dictionaries `{key: 'key_item', value: 'value_item'}` that are used to customize top or bottom supplementary HTML code (`sequenceserver_top_web_page_html_path` and `sequenceserver_bottom_web_page_html_path`)
 #
 sequenceserver_blast_db:
-#   - { name: 'my_db', port: '4567', path: '/path/to/my/db', users: ['fbar','jsmith'], web_page_title: 'blablabla' }
+#   - { name: 'my_db', port: '4567', path: '/path/to/my/db', users: ['fbar','jsmith'], web_page_title: 'blablabla', placeholders: [{ key: 'key1', value: 'value1'}, { key: 'key2', value: 'value2'}] }
 
 # NCBI BLAST and SLURM variables
 # Used in the slurm bash scripts
@@ -45,6 +46,8 @@ sequenceserver_home_url: "http://sequenceserver.com"
 sequenceserver_support_email: "http://www.sequenceserver.com/#license-and-support"
 # Path to the file containing the supplementary HTML code to display at the top of the web page
 sequenceserver_top_web_page_html_path: "~/top_web_page.html"
+# Path to the file containing the supplementary HTML code to display at the bottom of the web page
+sequenceserver_bottom_web_page_html_path: "~/bottom_web_page.html"
 
 # Service (systemd)
 #

molecule/default/converge.yml

@@ -8,7 +8,8 @@
     sequenceserver_blast_binaries: /usr/local/anaconda/envs/blast/bin
     sequenceserver_blast_db:
       # yamllint disable-line rule:braces
-      - { name: 'my_db', port: '4567', path: '/tmp/test-data' }
+      - { name: 'my_db', port: '4567', path: '/tmp/test-data', placeholders: [{ key: 'key_string', value: 'value1'}, { key: 'key_link', value: '<a href="http://testplaceholder.com">my favorite link</a>'}] }
     sequenceserver_top_web_page_html_path: "/tmp/top_web_page.html"
+    sequenceserver_bottom_web_page_html_path: "/tmp/bottom_web_page.html"
     sequenceserver_home_url: "http://myfavoritewebsite.com"
     sequenceserver_support_email: "mailto:[email protected]"

molecule/default/prepare.yml

@@ -6,6 +6,10 @@
     - name: Update apt cache.
       apt: update_cache=true cache_valid_time=600
       when: ansible_os_family == 'Debian'
+    - name: Install dependencies.
+      package:
+        name:
+          - curl
     - name: Install rsyslog
       include_role:
         name: robertdebock.rsyslog
@@ -39,3 +43,9 @@
         dest: /tmp/
         owner: root
         mode: 0644
+    - name: Copy bottom_web_page.html
+      copy:
+        src: tests/bottom_web_page.html
+        dest: /tmp/
+        owner: root
+        mode: 0644

molecule/default/tests/bottom_web_page.html

@@ -0,0 +1,4 @@
+<div id="bottomsupplementarycontent">
+	Render custom string for this database: <%= SequenceServer::Key_string %></br>
+	Render custom link for this database: <%= SequenceServer::Key_link %></br>
+</div>

molecule/default/verify.yml

@@ -43,3 +43,24 @@
         name: sequenceserver-my_db.service
       register: service_result
       failed_when: service_result.status.SubState != 'running'
+    - name: Test NGINX home page
+      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
+    - name: Get SequenceServer home page content
+      slurp:
+        src: "/tmp/home.html"
+      register: sequenceserver_page
+    - name: Display SequenceServer home page content
+      debug:
+        msg: "{{ sequenceserver_page.content | b64decode }}"
+    - name: Test that the SequenceServer 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: sequenceserver_command
+      failed_when: sequenceserver_command.rc > 0

tasks/main.yml

@@ -92,27 +92,48 @@
     - {regexp: '{{ sequenceserver_logo_title_regexp }}', replace: '{{ sequenceserver_logo_title_replace }}'}
     - {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
+- 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:
     path: "{{ sequenceserver_top_web_page_html_path }}"
   register: top_web_page_html_path
 
-- name: Modify source erb file for custom web page title | Insert supplementary HTML code on the top of the web page | Get the file content
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the bottom of the web page | Check if the file exists
+  stat:
+    path: "{{ sequenceserver_bottom_web_page_html_path }}"
+  register: bottom_web_page_html_path
+
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the top of the web page | Get the file content
   slurp:
     src: "{{ sequenceserver_top_web_page_html_path }}"
   register: top_web_page_html_file
   when: top_web_page_html_path.stat.exists
 
+- name: Modify source erb file for custom web page title | Insert supplementary HTML code at the bottom of the web page | Get the file content
+  slurp:
+    src: "{{ sequenceserver_bottom_web_page_html_path }}"
+  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
   blockinfile:
     path: "{{ sequenceserver_file_to_modify_for_custom_web_page }}"
     block: "{{ top_web_page_html_file['content'] | b64decode }}"
     insertafter: "<body>"
-    marker: "<!-- {mark} ANSIBLE MANAGED BLOCK -->"
+    marker: "<!-- {mark} ANSIBLE MANAGED BLOCK - TOP -->"
     backup: yes
   when: top_web_page_html_path.stat.exists
   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
+  blockinfile:
+    path: "{{ sequenceserver_file_to_modify_for_custom_web_page }}"
+    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
+  notify: Restart all sequenceserver services
+
 - name: Add slurm_sbatch.sh for HPC integration (https://sequenceserver.com/doc/#hpc)
   template:
     src: slurm_sbatch.sh.j2

templates/sequenceserver.rb.j2

@@ -4,4 +4,11 @@ module SequenceServer
 {% else %}
   WEB_PAGE_TITLE = 'BLAST server for {{ item.name }}'
 {% endif %}
+{% if item.placeholders is defined and item.placeholders %}
+  {% for placeholder in item.placeholders %}
+    {% if placeholder.key is defined and placeholder.key and placeholder.value is defined and placeholder.value %}
+  {{ placeholder.key[0]|upper}}{{placeholder.key[1:] }} = '{{ placeholder.value }}'
+    {% endif %}
+  {% endfor %}
+{% endif %}
 end