trinity: Remove `-XX:MaxPermSize=2G` from `_JAVA_OPTIONS` #288

Workflow file for this run

	---
	name: Total Perspective Vortex

	'on':
	pull_request:
	paths:
	- 'files/galaxy/tpv/**'
	push:
	branches:
	- master
	paths:
	- 'files/galaxy/tpv/**'

	jobs:
	lint:
	name: Total Perspective Vortex linter
	runs-on: ubuntu-latest
	steps:

	- name: Check out the codebase.
	uses: actions/checkout@v2
	with:
	path: 'infrastructure-playbook'

	- name: Update git submodules.
	working-directory: 'infrastructure-playbook'
	run: \|
	git submodule update --init --recursive --remote --checkout

	- name: Set up Python 3.
	uses: actions/setup-python@v2
	with:
	python-version: '3.x'
	cache: 'pip'

	# Install Ansible.
	- name: Cache Ansible.
	id: cache-ansible
	uses: actions/cache@v3
	with:
	path: /opt/hostedtoolcache/Python///lib/python/site-packages/ansible
	key: ${{ hashFiles('infrastructure-playbook/requirements.txt') }}
	- name: Install Ansible (fast when an existing installation was already cached).
	working-directory: 'infrastructure-playbook'
	run: \|
	# Install an Ansible version compatible with the version of
	# ansible-core specified in requirements.txt for the
	# infrastructure-playbook repo.
	ANSIBLE_CORE_REQ=$(perl -pe 's/\\\n/ /' requirements.txt \| grep ansible-core)
	pip3 install --use-feature=fast-deps ansible "$ANSIBLE_CORE_REQ"
	- name: Save Ansible cache.
	uses: actions/cache/save@v3
	if: ${{ steps.cache-ansible.outputs.cache-hit != 'true' }}
	with:
	path: /opt/hostedtoolcache/Python///lib/python/site-packages/ansible
	key: ${{ hashFiles('infrastructure-playbook/requirements.txt') }}

	# Total Perspective Vortex needs the Galaxy logic, which should be
	# installed automatically when running `pip3 install
	# total-perspective-vortex[cli]` (the `galaxy-app` package).
	# However:
	# - `galaxy-app` package on PyPI is outdated (see issue #15999 on
	# the Galaxy repo: https://github.com/galaxyproject/galaxy/issues/15999)
	# - Ideally the version of Galaxy should exactly match the one running on
	# usegalaxy.eu.
	# Therefore, we clone Galaxy and add it to the PYTHONPATH.
	- name: Get Galaxy repo and commit id.
	working-directory: 'infrastructure-playbook'
	run: \|
	# Get the Galaxy repository URL and commit from Ansible variables.
	export TMP_FILE=`mktemp`
	openssl rand -base64 24 > .vault_password
	ansible localhost --connection local \
	--inventory hosts --module-name copy \
	--args "content={{hostvars['sn06.galaxyproject.eu']}} dest=${TMP_FILE}" \
	> /dev/null
	export GALAXY_COMMIT_ID=$(cat ${TMP_FILE} \| jq -r .galaxy_commit_id)
	export GALAXY_REPO=$(cat ${TMP_FILE} \| jq -r .galaxy_repo)
	rm ${TMP_FILE}
	echo $GALAXY_COMMIT_ID > ../galaxy_commit_id
	echo $GALAXY_REPO > ../galaxy_repo
	- name: Cache Galaxy
	id: cache-galaxy
	uses: actions/cache@v3
	with:
	path: galaxy
	key: ${{ hashFiles('galaxy_repo') }}-${{ hashFiles('galaxy_commit_id') }}
	- name: Clone Galaxy
	if: ${{ steps.cache-galaxy.outputs.cache-hit != 'true' }}
	run: \|
	export GALAXY_COMMIT_ID="$(cat ./galaxy_commit_id)"
	export GALAXY_REPO="$(cat ./galaxy_repo)"
	# git clone -b $GALAXY_COMMIT_ID --single-branch --depth=1 $GALAXY_REPO galaxy # does not work with commit hashes
	git clone $GALAXY_REPO galaxy && cd galaxy && git checkout $GALAXY_COMMIT_ID
	- name: Save Galaxy cache.
	uses: actions/cache/save@v3
	if: ${{ steps.cache-galaxy.outputs.cache-hit != 'true' }}
	with:
	path: galaxy
	key: ${{ hashFiles('galaxy_repo') }}-${{ hashFiles('galaxy_commit_id') }}
	- name: Install Galaxy requirements.
	working-directory: 'galaxy'
	run: pip install -r requirements.txt

	# Install the Total Perspective Vortex version that should be running on
	# usegalaxy.eu
	- name: Install Total Perspective Vortex.
	working-directory: 'galaxy'
	run: \|
	TPV_REQ=$(perl -pe 's/\\\n/ /' lib/galaxy/dependencies/conditional-requirements.txt \| grep total-perspective-vortex)
	pip3 install --upgrade "$TPV_REQ"

	- name: Install port of Ansible filters for Jinja (required for the next step).
	run: \|
	pip3 install jinja2-ansible-filters

	- name: Create mounts vars file.
	working-directory: 'infrastructure-playbook/mounts'
	run: \|
	make dest/all.yml

	- name: Create a playbook to template the TPV files.
	shell: python -u {0}
	working-directory: 'infrastructure-playbook'
	run: \|
	import glob
	import importlib
	import sys

	# import tpv.py
	spec = importlib.util.spec_from_file_location('tpv_ci', '.github/workflows/tpv.py')
	module = importlib.util.module_from_spec(spec)
	spec.loader.exec_module(module)
	make_playbook = module.make_playbook

	tpv_path = "files/galaxy/tpv/"
	templates = tuple(
	(file, '.'.join(file.split('.')[:-1])) # remove j2 extension
	for file in glob.glob(f"{tpv_path}/.yaml.j2") + glob.glob(f"{tpv_path}/.yml.j2")
	)

	playbook = make_playbook('sn06.yml', templates=templates)
	with open('../playbook_path', 'w') as file:
	file.write(str(playbook))

	- name: Render TPV configuration files.
	run: \|
	PLAYBOOK="$(cat playbook_path)"
	BASENAME="$(basename $PLAYBOOK)"
	DIRNAME="$(dirname $PLAYBOOK)"
	cd "$DIRNAME"

	shopt -s nullglob

	ansible-playbook --connection=local "$BASENAME"

	- name: Run Total Perspective Vortex linter.
	run: \|
	export PYTHONPATH=$(realpath ./galaxy/lib)

	PLAYBOOK="$(cat playbook_path)"
	BASENAME="$(basename $PLAYBOOK)"
	DIRNAME="$(dirname $PLAYBOOK)"
	cd "$DIRNAME"

	shopt -s nullglob

	for file in files/galaxy/tpv/*.{yml,yaml}; do
	echo Running TPV linter on "$file"...
	tpv lint $file \|\| exit 1
	done

	dry-run:
	name: Total Perspective Vortex dry-run
	runs-on: ubuntu-latest
	steps:

	- name: Check out the codebase.
	uses: actions/checkout@v3
	with:
	fetch-depth: ${{ github.event_name == 'pull_request' && 2 \|\| 0 }}
	path: 'infrastructure-playbook'

	- name: Update git submodules.
	working-directory: 'infrastructure-playbook'
	run: \|
	git submodule update --init --recursive --remote --checkout

	- name: Set up Python 3.
	uses: actions/setup-python@v2
	with:
	python-version: '3.x'
	cache: 'pip'

	# Install Ansible.
	- name: Cache Ansible.
	id: cache-ansible
	uses: actions/cache@v3
	with:
	path: /opt/hostedtoolcache/Python///lib/python/site-packages/ansible
	key: ${{ hashFiles('infrastructure-playbook/requirements.txt') }}
	- name: Install Ansible.
	working-directory: 'infrastructure-playbook'
	run: \|
	# Install an Ansible version compatible with the version of
	# ansible-core specified in requirements.txt for the
	# infrastructure-playbook repo.
	ANSIBLE_CORE_REQ=$(perl -pe 's/\\\n/ /' requirements.txt \| grep ansible-core)
	pip3 install --use-feature=fast-deps ansible "$ANSIBLE_CORE_REQ"
	- name: Save Ansible cache.
	uses: actions/cache/save@v3
	if: ${{ steps.cache-ansible.outputs.cache-hit != 'true' }}
	with:
	path: /opt/hostedtoolcache/Python///lib/python/site-packages/ansible
	key: ${{ hashFiles('infrastructure-playbook/requirements.txt') }}

	# Total Perspective Vortex needs the Galaxy logic, which should be
	# installed automatically when running `pip3 install
	# total-perspective-vortex[cli]` (the `galaxy-app` package).
	# However:
	# - `galaxy-app` package on PyPI is outdated (see issue #15999 on
	# the Galaxy repo: https://github.com/galaxyproject/galaxy/issues/15999)
	# - Ideally the version of Galaxy should exactly match the one running on
	# usegalaxy.eu.
	# Therefore, we clone Galaxy and add it to the PYTHONPATH.
	- name: Get Galaxy repo and commit id.
	id: commits-galaxy
	working-directory: 'infrastructure-playbook'
	run: \|
	# Get the Galaxy repository URL and commit from Ansible variables.
	export TMP_FILE=`mktemp`
	openssl rand -base64 24 > .vault_password
	ansible localhost --connection local \
	--inventory hosts --module-name copy \
	--args "content={{hostvars['sn06.galaxyproject.eu']}} dest=${TMP_FILE}" \
	> /dev/null
	export GALAXY_COMMIT_ID=$(cat ${TMP_FILE} \| jq -r .galaxy_commit_id)
	export GALAXY_REPO=$(cat ${TMP_FILE} \| jq -r .galaxy_repo)
	rm ${TMP_FILE}
	echo "commit=$GALAXY_COMMIT_ID" >> $GITHUB_OUTPUT
	echo "repo=$GALAXY_REPO" >> $GITHUB_OUTPUT
	- name: Cache Galaxy
	id: cache-galaxy
	uses: actions/cache@v3
	with:
	path: galaxy
	key: ${{ steps.commits-galaxy.outputs.repo }}-${{ steps.commits-galaxy.outputs.commit }}
	- name: Clone Galaxy
	if: ${{ steps.cache-galaxy.outputs.cache-hit != 'true' }}
	run: \|
	# git clone -b ${{ steps.commits-galaxy.outputs.commit }} \
	# --single-branch \
	# --depth=1 ${{ steps.commits-galaxy.outputs.repo }} \
	# galaxy # does not work with commit hashes
	git clone ${{ steps.commits-galaxy.outputs.repo }} galaxy && cd galaxy && git checkout ${{ steps.commits-galaxy.outputs.commit }}
	- name: Save Galaxy cache.
	uses: actions/cache/save@v3
	if: ${{ steps.cache-galaxy.outputs.cache-hit != 'true' }}
	with:
	path: galaxy
	key: ${{ steps.commits-galaxy.outputs.repo }}-${{ steps.commits-galaxy.outputs.commit }}
	- name: Install Galaxy requirements.
	working-directory: 'galaxy'
	run: pip install -r requirements.txt

	# Install the Total Perspective Vortex version that should be running on
	# usegalaxy.eu
	- name: Install Total Perspective Vortex.
	working-directory: 'galaxy'
	run: \|
	TPV_REQ=$(perl -pe 's/\\\n/ /' lib/galaxy/dependencies/conditional-requirements.txt \| grep total-perspective-vortex)
	pip3 install --upgrade "$TPV_REQ"

	- name: Install port of Ansible filters for Jinja.
	run: \|
	pip3 install jinja2-ansible-filters

	- name: Create mounts vars file.
	working-directory: 'infrastructure-playbook/mounts'
	run: \|
	make dest/all.yml

	- name: Get commit ids before/after push or pull request.
	id: commits-infrastructure-playbook
	working-directory: 'infrastructure-playbook'
	run: \|
	set -Eeo pipefail
	if ${{ github.event_name == 'pull_request' }}; then
	echo "before=$(git rev-parse HEAD^1)" >> $GITHUB_OUTPUT
	echo "after=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT
	else
	echo "before=${{ github.event.before }}" >> $GITHUB_OUTPUT
	echo "after=${{ github.event.after }}" >> $GITHUB_OUTPUT
	fi

	- name: Create playbooks to template the TPV files.
	id: playbooks
	shell: python -u {0}
	working-directory: 'infrastructure-playbook'
	run: \|
	import glob
	import importlib
	import os
	import subprocess
	import sys

	# import make_playbook from tpv.py
	spec = importlib.util.spec_from_file_location('tpv_ci', '.github/workflows/tpv.py')
	module = importlib.util.module_from_spec(spec)
	spec.loader.exec_module(module)
	make_playbook = module.make_playbook

	tpv_path = 'files/galaxy/tpv/'
	templates = tuple(
	# TPV configuration files
	(file, '.'.join(file.split('.')[:-1])) # remove j2 extension
	for file in glob.glob(f'{tpv_path}/.yaml.j2') + glob.glob(f'{tpv_path}/.yml.j2')
	) + (
	# job_conf.yml
	('templates/galaxy/config/job_conf.yml.j2', 'templates/galaxy/config/job_conf.yml'),
	)

	# template files based on the new version
	playbook = make_playbook('sn06.yml', templates=templates)
	with open(os.environ["GITHUB_OUTPUT"], "a") as file:
	file.write(f"new={playbook}\n")

	# template files based on the old version
	subprocess.run(
	["git", "checkout", "${{ steps.commits-infrastructure-playbook.outputs.before }}"]
	)
	playbook = make_playbook('sn06.yml', templates=templates)
	with open(os.environ["GITHUB_OUTPUT"], "a") as file:
	file.write(f"old={playbook}\n")

	- name: Render TPV configuration files.
	run: \|
	shopt -s nullglob

	PLAYBOOK="${{ steps.playbooks.outputs.old }}"
	BASENAME="$(basename $PLAYBOOK)"
	DIRNAME="$(dirname $PLAYBOOK)"
	cd "$DIRNAME"
	ansible-playbook --connection=local "$BASENAME"

	PLAYBOOK="${{ steps.playbooks.outputs.new }}"
	BASENAME="$(basename $PLAYBOOK)"
	DIRNAME="$(dirname $PLAYBOOK)"
	cd "$DIRNAME"
	ansible-playbook --connection=local "$BASENAME"

	- name: Change paths of TPV configuration files in job_conf.yml
	shell: python -u {0}
	run: \|
	import os
	from pathlib import Path
	from urllib.parse import urlparse

	import yaml

	repository = Path("${{ steps.playbooks.outputs.new }}").parent
	job_conf_path = Path('templates/galaxy/config/job_conf.yml')
	tpv_path = Path('files/galaxy/tpv/')

	job_conf = yaml.safe_load(open(repository / job_conf_path, 'r'))
	tpv_config_files = job_conf['execution']['environments']['tpv_dispatcher']['tpv_config_files']
	for i, file in enumerate(tpv_config_files):
	if urlparse(file).scheme in {'file', ''}:
	tpv_config_files[i] = str(repository / tpv_path / Path(file).name)
	job_conf['execution']['environments']['tpv_dispatcher']['tpv_config_files'] = tpv_config_files

	yaml.dump(job_conf, open(repository / job_conf_path, 'w'))

	- name: Detect tools that have changed.
	id: tools-changed
	shell: python -u {0}
	run: \|
	import glob
	import hashlib
	import os
	from pathlib import Path

	import yaml

	playbooks = {
	'old': Path("${{ steps.playbooks.outputs.old }}"),
	'new': Path("${{ steps.playbooks.outputs.new }}"),
	}
	os.chdir(playbooks['new'].parent)

	tpv_path = Path('files/galaxy/tpv/')

	changed = set()
	for file in (Path(path) for path in glob.glob(f"{tpv_path}/.yml") + glob.glob(f"{tpv_path}/.yaml")):
	comparison = {}
	for key, playbook in playbooks.items():
	comparison[key] = yaml.safe_load(open(playbooks[key].parent / file, 'r')).get("tools", {})
	comparison[key] = {
	key: hashlib.sha256(yaml.dump(value, sort_keys=True).encode('utf-8')).hexdigest()
	for key, value in comparison[key].items()
	}
	changed \|= set(comparison['new']) - set(comparison['old'])
	changed \|= {key for key in set(comparison['new']) & set(comparison['old']) if comparison['new'][key] != comparison['old'][key]}

	with open(os.environ["GITHUB_OUTPUT"], 'a') as file:
	file.write(f"changed={' '.join(changed)}\n")

	- name: Run Total Perspective Vortex dry-run.
	env:
	TOOLS: ${{ steps.tools-changed.outputs.changed }}
	PLAYBOOK: ${{ steps.playbooks.outputs.new }}
	run: \|
	set -Eeo pipefail
	shopt -s nullglob

	export PYTHONPATH=$(realpath ./galaxy/lib)

	BASENAME="$(basename $PLAYBOOK)"
	DIRNAME="$(dirname $PLAYBOOK)"
	cd "$DIRNAME"

	IFS=" " read -a tools <<< "$TOOLS"
	for tool in "${tools[@]}"; do
	echo Running TPV dry-run for "$tool..."
	tpv dry-run --job-conf templates/galaxy/config/job_conf.yml --tool "$tool"
	done

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trinity: Remove `-XX:MaxPermSize=2G` from `_JAVA_OPTIONS` #288

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trinity: Remove `-XX:MaxPermSize=2G` from `_JAVA_OPTIONS` #288

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trinity: Remove -XX:MaxPermSize=2G from _JAVA_OPTIONS #288

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Workflow file for this run

trinity: Remove `-XX:MaxPermSize=2G` from `_JAVA_OPTIONS` #288