From 43fcc0777e53252f270994dc4215790a9e61dc65 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Wed, 21 Feb 2024 12:48:02 +0530
Subject: [PATCH 1/3] Use gxadmin for cleanup

---
 roles/galaxy-pg-cleanup/tasks/main.yml             |  9 +--------
 .../galaxy-pg-cleanup/templates/run_cleanup.sh.j2  | 14 --------------
 2 files changed, 1 insertion(+), 22 deletions(-)
 delete mode 100644 roles/galaxy-pg-cleanup/templates/run_cleanup.sh.j2

diff --git a/roles/galaxy-pg-cleanup/tasks/main.yml b/roles/galaxy-pg-cleanup/tasks/main.yml
index c06bef8b1..30e8b129e 100644
--- a/roles/galaxy-pg-cleanup/tasks/main.yml
+++ b/roles/galaxy-pg-cleanup/tasks/main.yml
@@ -1,10 +1,3 @@
-- name: Template run_cleanup.sh script   
-  template:
-    src: run_cleanup.sh.j2
-    dest: /home/galaxy/run_cleanup.sh
-    mode: "744"
-    owner: galaxy
-    group: galaxy
 - name: Add cron job for galaxy
   cron:
     name: "galaxy_pg_cleanup"    
@@ -12,4 +5,4 @@
     weekday: "{{ galaxy_pg_cleanup_cron_weekday }}"
     hour: "{{ galaxy_pg_cleanup_cron_hour }}"
     minute: "00"
-    job: bash /home/galaxy/run_cleanup.sh 2>> /home/galaxy/pgcleanup.log
+    job: gxadmin galaxy cleanup 10
diff --git a/roles/galaxy-pg-cleanup/templates/run_cleanup.sh.j2 b/roles/galaxy-pg-cleanup/templates/run_cleanup.sh.j2
deleted file mode 100644
index a2556150d..000000000
--- a/roles/galaxy-pg-cleanup/templates/run_cleanup.sh.j2
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-cd {{ galaxy_server_dir }}
-
-. {{ galaxy_venv_dir }}/bin/activate
-
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml delete_userless_histories
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml delete_exported_histories
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml purge_deleted_histories
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml purge_deleted_hdas
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml purge_historyless_hdas
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml purge_hdas_of_purged_histories
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml delete_datasets
-python ./scripts/cleanup_datasets/pgcleanup.py -o 10 -c {{ galaxy_config_dir }}/galaxy.yml purge_datasets
\ No newline at end of file

From 4f1c05e399c3658187630b45ebe8a3852d806ce8 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Wed, 21 Feb 2024 13:10:00 +0530
Subject: [PATCH 2/3] Add log dir env var

---
 roles/galaxy-pg-cleanup/tasks/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/roles/galaxy-pg-cleanup/tasks/main.yml b/roles/galaxy-pg-cleanup/tasks/main.yml
index 30e8b129e..1ace608c2 100644
--- a/roles/galaxy-pg-cleanup/tasks/main.yml
+++ b/roles/galaxy-pg-cleanup/tasks/main.yml
@@ -5,4 +5,4 @@
     weekday: "{{ galaxy_pg_cleanup_cron_weekday }}"
     hour: "{{ galaxy_pg_cleanup_cron_hour }}"
     minute: "00"
-    job: gxadmin galaxy cleanup 10
+    job: GALAXY_LOG_DIR=/var/log/galaxy gxadmin galaxy cleanup 10

From c8d79c7bb7992361b12ac268c9f1924f870f1f71 Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Thu, 22 Feb 2024 09:05:51 +1100
Subject: [PATCH 3/3] add more env

---
 roles/galaxy-pg-cleanup/tasks/main.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/roles/galaxy-pg-cleanup/tasks/main.yml b/roles/galaxy-pg-cleanup/tasks/main.yml
index 1ace608c2..e5d53625e 100644
--- a/roles/galaxy-pg-cleanup/tasks/main.yml
+++ b/roles/galaxy-pg-cleanup/tasks/main.yml
@@ -1,3 +1,9 @@
+- name: Create log directory that galaxy can write to
+  file:
+    state: directory
+    path: /var/log/galaxy
+    owner: galaxy
+    group: galaxy
 - name: Add cron job for galaxy
   cron:
     name: "galaxy_pg_cleanup"    
@@ -5,4 +11,4 @@
     weekday: "{{ galaxy_pg_cleanup_cron_weekday }}"
     hour: "{{ galaxy_pg_cleanup_cron_hour }}"
     minute: "00"
-    job: GALAXY_LOG_DIR=/var/log/galaxy gxadmin galaxy cleanup 10
+    job: ". {{ galaxy_venv_dir }}/bin/activate; GALAXY_LOG_DIR=/var/log/galaxy GALAXY_ROOT={{ galaxy_server_dir }} GALAXY_CONFIG_FILE={{ galaxy_config_file }} /usr/local/bin/gxadmin galaxy cleanup 10"