fix: nextflow_poll_period_secdonds now minutes. And better nextflow a…

…nsible task names

ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml

@@ -81,7 +81,7 @@
   when:
   - not combined_file.stat.exists
 
-- name: Set nextflow command
+- name: Set nextflow command (Deduplicate)
   set_fact:
     nextflow_cmd: >-
       nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -91,27 +91,33 @@
   when:
   - not combined_file.stat.exists
 
-- name: Display nextflow command
+- name: Display nextflow command (Deduplicate)
   debug:
     var: nextflow_cmd
   when:
   - not combined_file.stat.exists
 
-- name: Run nextflow (async)
+- name: Display nextflow command timeout (Deduplicate)
+  debug:
+    msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
+  when:
+  - not combined_file.stat.exists
+
+- name: Run nextflow (Deduplicate) (async)
   command: "{{ nextflow_cmd }}"
   async: "{{ nextflow_timeout_minutes|int * 60 }}"
   poll: 0
   register: nextflow_async
   when:
   - not combined_file.stat.exists
 
-- name: Wait for nextflow (async)
+- name: Wait for nextflow (Deduplicate)
   async_status:
     jid: "{{ nextflow_async.ansible_job_id }}"
   register: nextflow_result
   until: nextflow_result.finished
-  delay: "{{ nextflow_poll_period_seconds|int }}"
-  retries: "{{ (nextflow_timeout_minutes|int / (nextflow_poll_period_seconds|int / 60))|int }}"
+  delay: "{{ nextflow_poll_period_minutes | int * 60 }}"
+  retries: "{{ (nextflow_timeout_minutes | int / nextflow_poll_period_minutes | int) | int }}"
   when:
   - not combined_file.stat.exists
 
@@ -149,7 +155,7 @@
   register: compress_task
   when: not file_type_file.stat.exists
 
-- name: Add this tasy to the list of compress tasks
+- name: Add this task to the list of compress tasks
   set_fact:
     compress_tasks: "{{ compress_tasks + [ compress_task ] }}"
   when: not file_type_file.stat.exists

ansible/roles/combine/tasks/nextflow-merge-file-type.yaml

@@ -81,7 +81,7 @@
   when:
   - not combined_file.stat.exists
 
-- name: Set nextflow command
+- name: Set nextflow command (Merge)
   set_fact:
     nextflow_cmd: >-
       nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -91,27 +91,33 @@
   when:
   - not combined_file.stat.exists
 
-- name: Display nextflow command
+- name: Display nextflow command (Merge)
   debug:
     var: nextflow_cmd
   when:
   - not combined_file.stat.exists
 
-- name: Run nextflow (async)
+- name: Display nextflow command timeout (Merge)
+  debug:
+    msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
+  when:
+  - not combined_file.stat.exists
+
+- name: Run nextflow (Merge) (async)
   command: "{{ nextflow_cmd }}"
   async: "{{ nextflow_timeout_minutes|int * 60 }}"
   poll: 0
   register: nextflow_async
   when:
   - not combined_file.stat.exists
 
-- name: Wait for nextflow (async)
+- name: Wait for nextflow (Merge)
   async_status:
     jid: "{{ nextflow_async.ansible_job_id }}"
   register: nextflow_result
   until: nextflow_result.finished
-  delay: "{{ nextflow_poll_period_seconds|int }}"
-  retries: "{{ (nextflow_timeout_minutes|int / (nextflow_poll_period_seconds|int / 60))|int }}"
+  delay: "{{ nextflow_poll_period_minutes | int * 60 }}"
+  retries: "{{ (nextflow_timeout_minutes | int / nextflow_poll_period_minutes | int) | int }}"
   when:
   - not combined_file.stat.exists
 
@@ -149,7 +155,7 @@
   register: compress_task
   when: not file_type_file.stat.exists
 
-- name: Add this tasy to the list of compress tasks
+- name: Add this task to the list of compress tasks
   set_fact:
     compress_tasks: "{{ compress_tasks + [ compress_task ] }}"
   when: not file_type_file.stat.exists

ansible/roles/combine/vars/main.yaml

@@ -39,7 +39,7 @@ shatterfile_large_threshold_kb: 1048576
 # and poll period for the (asynchronous) Nextflow process
 # Timeouts (minutes):  1440 (24 hours)
 nextflow_timeout_minutes: 1440
-nextflow_poll_period_seconds: 30
+nextflow_poll_period_minutes: 1
 
 compress_timeout_minutes: 1440
 compress_poll_period_minutes: 1

ansible/roles/fragment/tasks/fragmentation.yaml

@@ -60,21 +60,13 @@
     that:
     - nextflow_timeout_minutes | int > 0
 
-- name: Display nextflow timeout (minutes)
-  debug:
-    var: nextflow_timeout_minutes
-
 # Set nextflow_poll_period_minutes based on nextflow_timeout_minutes/30.
 # If this is development then this defaults.
 - name: Set nextflow_poll_period_minutes
   set_fact:
     nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes|int/60)|int }}"
   when: deployment=="production"
 
-- name: Display nextflow poll period (minutes)
-  debug:
-    var: nextflow_poll_period_minutes
-
 - name: Log line to report
   blockinfile:
     marker: "<!-- {fragmentation-nextflow} ANSIBLE MANAGED BLOCK -->"
@@ -99,7 +91,7 @@
   - "fragmentation.nf.j2"
   - "{{ deployment }}/nextflow.config.j2"
 
-- name: Set nextflow command
+- name: Set nextflow command (Fragmentation)
   set_fact:
     nextflow_cmd: >-
       nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -112,17 +104,21 @@
        --max_hac {{ vendors[vendor].fraghac }}
        --max_frag {{ vendors[vendor].fragmaxfrags }}
 
-- name: Display nextflow command
+- name: Display nextflow command (Fragmentation)
   debug:
     var: nextflow_cmd
 
-- name: Run nextflow (async)
+- name: Display nextflow command timeout (Fragmentation)
+  debug:
+    msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
+
+- name: Run nextflow (Fragmentation) (async)
   command: "{{ nextflow_cmd }}"
   async: "{{ nextflow_timeout_minutes|int * 60 }}"
   poll: 0
   register: nextflow_async
 
-- name: Wait for nextflow (async)
+- name: Wait for nextflow (Fragmentation)
   async_status:
     jid: "{{ nextflow_async.ansible_job_id }}"
   register: nextflow_result

ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml

@@ -63,9 +63,6 @@
     nextflow_timeout_minutes: "{{ nextflow_timeout_calc|int }}"
   when: nextflow_timeout_calc|int>nextflow_timeout_minutes
 
-- debug:
-    var: nextflow_timeout_minutes
-
 # Set nextflow_poll_period_minutes based on nextflow_timeout_minutes/30.
 # If this is development then this defaults.
 - name: Set nextflow_poll_period_minutes
@@ -88,7 +85,7 @@
 # python -m frag.network.scripts.generate_inchi -i $FRAGPATH/fragment/$FRAGNODEFILE -o $FRAGPATH/fragment/$INCHITAB -n
 #
 
-- name: Set nextflow command
+- name: Set nextflow command (Generate Isomol Inchi)
   set_fact:
     nextflow_cmd: >-
       nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -100,17 +97,21 @@
       --outputfile {{ isoinchitab }}
       --chunk_size {{ inchigenchunk|int }}
 
-- name: Display nextflow command
+- name: Display nextflow command (Generate Isomol Inchi)
   debug:
     var: nextflow_cmd
 
-- name: Run nextflow (async)
+- name: Display nextflow command timeout (Generate Isomol Inchi)
+  debug:
+    msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
+
+- name: Run nextflow (Generate Isomol Inchi) (async)
   command: "{{ nextflow_cmd }}"
   async: "{{ nextflow_timeout_minutes|int * 60 }}"
   poll: 0
   register: nextflow_async
 
-- name: Wait for nextflow (async)
+- name: Wait for nextflow (Generate Isomol Inchi)
   async_status:
     jid: "{{ nextflow_async.ansible_job_id }}"
   register: nextflow_result

ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml

@@ -69,7 +69,7 @@
 # Move the nextflow workflow and config into place (from templates)
 # so they move from "<templates>/{{ deployment }}" to "{{ reppath }}/nextflow"...
 
-- name: Translate nextflow files
+- name: Translate nextflow files (Generate Inchi)
   template:
     src: "{{ item }}"
     dest: "{{ reppath }}/nextflow/{{ item|regex_replace(deployment + '/')|regex_replace('.j2') }}"
@@ -81,7 +81,7 @@
 # python -m frag.network.scripts.generate_inchi -i $FRAGPATH/fragment/$FRAGNODEFILE -o $FRAGPATH/fragment/$INCHITAB -n -s
 #
 
-- name: Set nextflow command
+- name: Set nextflow command (Generate Non-Isomol Inchi)
   set_fact:
     nextflow_cmd: >-
       nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -94,17 +94,17 @@
       --chunk_size {{ inchigenchunk|int }}
       --standard '{{ standard }}'
 
-- name: Display nextflow command
+- name: Display nextflow command (Generate Non-Isomol Inchi)
   debug:
     var: nextflow_cmd
 
-- name: Run nextflow (async)
+- name: Run nextflow (Generate Non-Isomol Inchi) (async)
   command: "{{ nextflow_cmd }}"
   async: "{{ nextflow_timeout_minutes|int * 60 }}"
   poll: 0
   register: nextflow_async
 
-- name: Wait for nextflow (async)
+- name: Wait for nextflow (Generate Non-Isomol Inchi)
   async_status:
     jid: "{{ nextflow_async.ansible_job_id }}"
   register: nextflow_result

ansible/roles/standardise/tasks/standardise-file.yaml

@@ -79,21 +79,13 @@
       that:
       - nextflow_timeout_minutes | int > 0
 
-  - name: Display nextflow timeout (minutes)
-    debug:
-      var: nextflow_timeout_minutes
-
   # Set nextflow_poll_period_minutes based on nextflow_timeout_minutes/30.
   # If this is development then this defaults.
   - name: Set nextflow_poll_period_minutes
     set_fact:
       nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes|int/30)|int }}"
     when: deployment == "production"
 
-  - name: Display nextflow poll period (minutes)
-    debug:
-      var: nextflow_poll_period_minutes
-
   - name: Log line to report
     blockinfile:
       marker: "<!-- {standardise-nextflow} ANSIBLE MANAGED BLOCK -->"
@@ -118,7 +110,7 @@
     - "standardizer.nf.j2"
     - "{{ deployment }}/nextflow.config.j2"
 
-  - name: Set nextflow command
+  - name: Set nextflow command (Standardise)
     set_fact:
       nextflow_cmd: >-
         nextflow run -c {{ reppath }}/nextflow/nextflow.config
@@ -133,17 +125,21 @@
         --compound_id_field {{ standard_compound_id_field }}
         --split_token {{ standsplittoken }}
 
-  - name: Display nextflow command
+  - name: Display nextflow command (Standardise)
     debug:
       var: nextflow_cmd
 
-  - name: Run nextflow (async)
+  - name: Display nextflow command timeout (Standardise)
+    debug:
+      msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
+
+  - name: Run nextflow (Standardize) (async)
     command: "{{ nextflow_cmd }}"
     async: "{{ nextflow_timeout_minutes|int * 60 }}"
     poll: 0
     register: nextflow_async
 
-  - name: Wait for nextflow (async)
+  - name: Wait for nextflow (Standardise)
     async_status:
       jid: "{{ nextflow_async.ansible_job_id }}"
     register: nextflow_result