Merge branch 'main' of github.com:CESNET/usegalaxy into main

Author: martindemko

.gitignore

@@ -3,17 +3,11 @@
 *.retry
 .venv
 *.log
-
-### Values and Secrets ###
-.vault-password.*
-hosts
-ansible.log
-
-# Python bytecode
+.DS_Store
 *.pyc
 
-# Macs
-.DS_Store
+# vault secrets
+.vault-password.*
 
-# ideally no local roles changes are present
+# installed roles
 roles

README.md

@@ -60,8 +60,9 @@ rabbitmq_users_password:
   mqadmin: a-really-long-password-here
   pulsar: a-really-long-DIFFERENT-password-here
 vault_rabbitmq_password_galaxy: good-password-here
-oidc_client_id: string-with-client-id
-oidc_client_secret: string-with-client-secret
+einfracz_client_id: string-with-client-id
+einfracz_client_secret: string-with-client-secret
+
 # Galaxy admin API key for tool installation
 api_key: dont-be-lazy-a-really-long-password-here
 # see https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/special_topics/vault.md
@@ -91,6 +92,31 @@ and external repository that contains the lists of tools for every instance: htt
 
 Following are troubleshooting notes gathered through the learning process.
 
+
+### client build OOM
+
+- stop app before building
+- do not build maps (`make client-production` only)
+- set reasonable heap (e.g. `NODE_OPTIONS: --max_old_space_size=4096`)
+- disable webpack parallel minimizer
+
+```diff
+diff --git a/client/webpack.config.js b/client/webpack.config.js
+index 8202237857..99f86ec25d 100644
+--- a/client/webpack.config.js
++++ b/client/webpack.config.js
+@@ -43,7 +43,7 @@ module.exports = (env = {}, argv = {}) => {
+     if (targetEnv == "production") {
+         minimizations = {
+             minimize: true,
+-            minimizer: [new TerserPlugin(), new CssMinimizerPlugin()],
++            minimizer: [new TerserPlugin({parallel: false,}), new CssMinimizerPlugin()],
+         };
+     } else {
+         minimizations = {
+```
+
+
 ### glibc
 
 On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therefore playbook ends in error.

extra_scripts/shed_tools_shadow_script.sh

@@ -0,0 +1,21 @@
+#!/bin/env bash
+
+set -e
+
+FROM=$1
+TO=$2
+LIST=/tmp/dirs_to_move.$$
+
+cd "${FROM}"
+find shed_tools/ -mindepth 7 -maxdepth 7 -type d \( -name '.hg' -o -name 'test-data' \) > ${LIST}
+
+cat ${LIST} | while read DIR; do
+    if [ -n "$DIR" ]; then
+        SRC="$FROM/$DIR";
+        TARGET="$TO/$DIR";
+        echo "moving $SRC -> $TARGET";
+        rsync -av --mkpath "$SRC/" "$TARGET" && rm -rf "$SRC" && ln -s "$TARGET" "$SRC" || echo "rsync must failed, directory is missing!";
+    else
+        echo "line is empty!"
+    fi
+done

files/galaxy-umsa.grid.cesnet.cz/all_tools.yml

@@ -43,6 +43,7 @@ items:
   - matchms
   - mfassignr
   - qcxms
+  - ipapy2
   - pre_processing
   - post_processing
   - proteomics

files/galaxy/static/usegalaxy-cz.png

@@ -8,7 +8,8 @@
         name:
         - python3-pip
         - python-is-python3
-        update_cache: yes
+        # this is not needed often and can fail the run since the machines have many repos
+        # update_cache: yes
       when: ansible_os_family == 'Debian'
 
 - hosts: production
@@ -176,11 +177,22 @@
     - git:
         repo: 'https://github.com/usegalaxy-eu/libraries-training-repo'
         dest: /libraries/
+
     - name: stop galaxy to free mem for client build
       become: true
       become_user: root
       ansible.builtin.command: galaxyctl stop
       when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'galaxy-qa2.galaxy.cloud.e-infra.cz']"
+
+    # this needs to be in the correct spot, not here, either via fork or enabling this configuration upstream
+
+    # - name: client building optimization for small machines
+    #   replace:
+    #     path: "{{ galaxy_root }}/server/client/webpack.config.js"
+    #     regexp: 'TerserPlugin\(\)'
+    #     replace: 'TerserPlugin({parallel: false,})'
+    #   when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'galaxy-qa2.galaxy.cloud.e-infra.cz']"
+
   roles:
     - galaxyproject.tusd
     - usegalaxy_eu.apptainer
@@ -214,6 +226,13 @@
         state: restarted
         name: nginx
 
+    # not detected automatically due to a bug: https://github.com/galaxyproject/galaxy/issues/20483
+    - name: Install conditional dependencies
+      pip:
+        name: fs.onedatarestfs==21.2.5.2
+        virtualenv: "{{ galaxy_venv_dir }}"
+      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz','usegalaxy.cz']"
+
     - name: Creates entry in crontab "chmod on _files for ngnix access"
       ansible.builtin.cron:
         name: "chmod on _files for ngnix access"
@@ -246,11 +265,22 @@
       when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
       no_log: true
 
+    # set up cron to propagate einfra users to einfra galaxy group
+    - name: Ensure the user_group cron script directory exists
+      ansible.builtin.file:
+        path: "{{ galaxy_root }}/cron/user_group"
+        state: directory
+        owner: postgres
+        group: postgres
+        mode: '0755'
+      when: "'usegalaxy.cz' in inventory_hostname"
+      tags: cron
     - name: Copy user - group association script
       ansible.builtin.copy:
         src: "{{ playbook_dir }}/extra_scripts/add_group_users.py"
-        dest: "/var/lib/postgresql/add_group_users.py"
+        dest: "{{ galaxy_root }}/cron/user_group/add_group_users.py"
         owner: postgres
+        group: postgres
       when: "'usegalaxy.cz' in inventory_hostname"
       tags: cron
     - name: Setup user - group association rutine
@@ -259,10 +289,40 @@
         user: postgres
         minute: "0"
         hour: "*" # every hour
-        job: "python3 /var/lib/postgresql/add_group_users.py {{ inventory_hostname }} $(cat /home/{{ galaxy_user_name }}/.galaxy_api_key)"
+        job: "python3 {{ galaxy_root }}/cron/user_group/add_group_users.py {{ inventory_hostname }} $(cat /home/{{ galaxy_user_name }}/.galaxy_api_key)"
       when: "'usegalaxy.cz' in inventory_hostname"
       tags: cron
 
+    # set up cron to shadow some shed_tools contents to minimize space consumption
+    - name: Ensure the shadow cron script directory exists
+      ansible.builtin.file:
+        path: "{{ galaxy_root }}/cron/shadow"
+        state: directory
+        owner: "{{ galaxy_user_name }}"
+        group: "{{ galaxy_user_group_name }}"
+        mode: '0755'
+      when: "shed_tools_shadowing"
+      tags: cron
+    - name: Copy shed_tools shadowing script
+      ansible.builtin.copy:
+        src: "{{ playbook_dir }}/extra_scripts/shed_tools_shadow_script.sh"
+        dest: "{{ galaxy_root }}/cron/shadow/shed_tools_shadow_script.sh"
+        owner: "{{ galaxy_user_name }}"
+        group: "{{ galaxy_user_group_name }}"
+        mode: '0755'
+      when: "shed_tools_shadowing"
+      tags: cron
+    - name: Setup shed_tools shadowing rutine
+      ansible.builtin.cron:
+        name: "Shadow shed-tools directories"
+        user: "{{ galaxy_user_name }}"
+        minute: "0"
+        hour: "2" # 2 am daily
+        job: "{{ galaxy_root }}/cron/shadow/shed_tools_shadow_script.sh {{ galaxy_root }}/var {{ galaxy_mutable_data_dir }} 2>&1 | logger -t shed_tools_shadowing"
+      when: "shed_tools_shadowing"
+      tags: cron
+
+    # set up cron to automate tool installation from https://github.com/CESNET/galaxy_tools repository
     - name: Ensure the tools cron script directory exists
       ansible.builtin.file:
         path: "{{ galaxy_root }}/cron/tools"
@@ -291,6 +351,7 @@
       tags: cron
       when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
 
+
     - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py
       replace:
         path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py"
@@ -311,6 +372,7 @@
         user: "{{ galaxy_user_name }}"
         state: present
         key: "{{ lookup('file','files/{{ inventory_hostname }}/pulsar.pub') }}"
+
     - name: Restart galaxy
       become: true
       become_user: root