fix: Ensure nextflow_poll_period_minutes is not zero

InformaticsMatters · Oct 15, 2024 · d5f02b6 · d5f02b6
1 parent 6fe6c2d
commit d5f02b6
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Showing 6 changed files with 31 additions and 1 deletion.
diff --git a/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml b/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml
@@ -97,6 +97,11 @@
   when:
   - not combined_file.stat.exists
 
+- name: Ensure nextflow_poll_period_minutes is not zero
+  set_fact:
+    nextflow_poll_period_minutes: 1
+  when: nextflow_poll_period_minutes | int == 0
+
 - name: Display nextflow command timeout (Deduplicate)
   debug:
     msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}

diff --git a/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml b/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml
@@ -97,6 +97,11 @@
   when:
   - not combined_file.stat.exists
 
+- name: Ensure nextflow_poll_period_minutes is not zero
+  set_fact:
+    nextflow_poll_period_minutes: 1
+  when: nextflow_poll_period_minutes | int == 0
+
 - name: Display nextflow command timeout (Merge)
   debug:
     msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}

diff --git a/ansible/roles/fragment/tasks/fragmentation.yaml b/ansible/roles/fragment/tasks/fragmentation.yaml
@@ -73,6 +73,11 @@
     nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}"
   when: deployment=="production"
 
+- name: Ensure nextflow_poll_period_minutes is not zero
+  set_fact:
+    nextflow_poll_period_minutes: 1
+  when: nextflow_poll_period_minutes | int == 0
+
 - name: Log line to report
   blockinfile:
     marker: "<!-- {fragmentation-nextflow} ANSIBLE MANAGED BLOCK -->"

diff --git a/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml b/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml
@@ -72,6 +72,11 @@
     nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}"
   when: deployment=="production"
 
+- name: Ensure nextflow_poll_period_minutes is not zero
+  set_fact:
+    nextflow_poll_period_minutes: 1
+  when: nextflow_poll_period_minutes | int == 0
+
 # Move the nextflow workflow and config into place (from templates)
 # so they move from "<templates>/{{ deployment }}" to "{{ reppath }}/nextflow"...
 

diff --git a/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml b/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml
@@ -60,6 +60,11 @@
     nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}"
   when: deployment=="production"
 
+- name: Ensure nextflow_poll_period_minutes is not zero
+  set_fact:
+    nextflow_poll_period_minutes: 1
+  when: nextflow_poll_period_minutes | int == 0
+
 # Move the nextflow workflow and config into place (from templates)
 # so they move from "<templates>/{{ deployment }}" to "{{ reppath }}/nextflow"...
 
@@ -92,7 +97,7 @@
   debug:
     var: nextflow_cmd
 
-- name: Display nextflow command timeout (Fragmentation)
+- name: Display nextflow command timeout (Generate Non-Isomol Inchi)
   debug:
     msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }}
 

diff --git a/ansible/roles/standardise/tasks/standardise-file.yaml b/ansible/roles/standardise/tasks/standardise-file.yaml
@@ -84,6 +84,11 @@
       nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}"
     when: deployment == "production"
 
+  - name: Ensure nextflow_poll_period_minutes is not zero
+    set_fact:
+      nextflow_poll_period_minutes: 1
+    when: nextflow_poll_period_minutes | int == 0
+
   - name: Log line to report
     blockinfile:
       marker: "<!-- {standardise-nextflow} ANSIBLE MANAGED BLOCK -->"