convert options from json to yaml

README.md

@@ -34,6 +34,7 @@ sequenceserver_blast_db:
       users: ['fbar','jsmith']
       web_page_title: 'blablabla'
       placeholders: [{key: 'key1', value: 'value1'}, {key: 'key2', value: 'value2'}]
+      conf_options: [{key: 'job_lifetime', value: '10080'}, {key: 'databases_widget', value: 'tree'}, {key: 'options', value: {'blastn': {'default': ['-task blastn', '-evalue 1e-5'], 'short-seq': ['-task blastn-short', '-evalue 1e-1']}}}]
 ```
 This is the variable used to define the BLAST databases.
 
@@ -55,7 +56,7 @@ Each database is defined as a dictionary of the following parameters:
 - `group` Optional. Useful if the database needs restricted access. An LDAP group ("gid"). LDAP users who are member of this group 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'}]`.
-- `conf_options` Optional. A list of supplementary SequenceServer configuration options dictionaries `{key: 'key_item', value: 'value_item'}` (see [SequenceServer documentation](https://sequenceserver.com/doc/#basics)). For example `conf_options: [{key: 'job_lifetime', value: '10080'}, {key: 'databases_widget', value: 'tree'}]`.
+- `conf_options` Optional. A list of supplementary SequenceServer configuration options as dictionaries `{key: 'key_item', value: 'value_item'}` (see [SequenceServer documentation](https://sequenceserver.com/doc/#basics)). For example `[{key: 'job_lifetime', value: '10080'}, {key: 'databases_widget', value: 'tree'}, {key: 'options', value: {'blastn': {'default': ['-task blastn', '-evalue 1e-5'], 'short-seq': ['-task blastn-short', '-evalue 1e-1']}}}]`
 
 Unique `name` and `port` are mandatory for each database.
 `users`, `ldap_businesscategory` and `group` are optional and can be used to add an authentication layer with the nginx-auth-ldap module. Choose one single authentication mode for each database.

molecule/default/converge.yml

@@ -12,7 +12,7 @@
         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>'}]
-        conf_options: [{key: 'job_lifetime', value: '10080'}, {key: 'databases_widget', value: 'tree'}]
+        conf_options: [{key: 'job_lifetime', value: '10080'}, {key: 'databases_widget', value: 'tree'}, {key: 'options', value: {'blastn': {'default': ['-task blastn', '-evalue 1e-5'], 'short-seq': ['-task blastn-short', '-evalue 1e-1']}}}]
     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"

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
@@ -26,6 +26,17 @@
     - name: Display SequenceServer service logs
       debug:
         msg: "{{ log.content | b64decode }}"
+    - name: Get the SequenceServer configuration file of my_db
+      slurp:
+        src: "/etc/sequenceserver/config/sequenceserver.my_db.conf"
+      register: my_db_conf
+    - name: Display content of the SequenceServer configuration file of my_db
+      debug:
+        msg: "{{ my_db_conf.content | b64decode }}"
+    - name: Check that conf_option is in the SequenceServer configuration file of my_db
+      set_fact:
+        grep_slurm_batch: "{{ my_db_conf.content | b64decode | regex_findall('databases_widget') | first }}"
+      failed_when: grep_slurm_batch != 'databases_widget'
     - name: Test that SequenceServer service is running for my_db
       systemd:
         name: sequenceserver-my_db.service
@@ -35,8 +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
@@ -48,27 +59,27 @@
       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'
       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:[email protected]'
       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
@@ -83,14 +94,3 @@
       set_fact:
         grep_slurm_batch: "{{ lib_modified_for_hpc_integration.content | b64decode | regex_findall('slurm_sbatch.sh') | first }}"
       failed_when: grep_slurm_batch != 'slurm_sbatch.sh'
-    - name: Get the SequenceServer configuration file of my_db
-      slurp:
-        src: "/etc/sequenceserver/config/sequenceserver.my_db.conf"
-      register: my_db_conf
-    - name: Display content of the SequenceServer configuration file of my_db
-      debug:
-        msg: "{{ my_db_conf.content | b64decode }}"
-    - name: Check that conf_option is in the SequenceServer configuration file of my_db
-      set_fact:
-        grep_slurm_batch: "{{ my_db_conf.content | b64decode | regex_findall('databases_widget') | first }}"
-      failed_when: grep_slurm_batch != 'databases_widget'

templates/sequenceserver.conf.j2

@@ -1,9 +1,22 @@
 :port: '{{ item.port }}'
 :database_dir: '{{ item.path }}'
 {% if item.conf_options is defined and item.conf_options %}
-{% for option in item.conf_options %}
-{% if option.key is defined and option.key and option.value is defined and option.value %}
-:{{ option.key }}: '{{ option.value }}'
+{% for conf_option in item.conf_options %}
+{% if conf_option.key is defined and conf_option.key and conf_option.value is defined and conf_option.value %}
+{% if conf_option.key != 'options' %}
+:{{ conf_option.key }}: '{{ conf_option.value }}'
+{% else %}
+:options:
+{% for blast_type, blast_configs in conf_option.value.items() %}
+  :{{ blast_type }}:
+{% for blast_config, blast_params in blast_configs.items() %}
+    :{{ blast_config }}:
+{% for blast_param in blast_params %}
+    - {{ blast_param }}
+{% endfor %}
+{% endfor %}
+{% endfor %}
+{% endif %}
 {% endif %}
 {% endfor %}
 {% endif %}