cati_portal_ctl

#! /usr/bin/env python3

import glob
import os
import os.path as osp
import sys
import shutil
import subprocess
import tempfile

import click

class Singularity:
    def __init__(self):
        self.directory = osp.dirname(osp.dirname(osp.abspath(__file__)))
        self.sif = osp.join(self.directory, 'cati_portal.sif')
        self.tmp = osp.join(self.directory, 'tmp')
        self.env = os.environ.copy()
        self.env['SINGULARITY_TMPDIR'] = self.tmp

    def __call__(self, cmd, **kwargs):
        check_call(['singularity', 'run', '-B', '%s:/cati_portal' % self.directory, self.sif] + cmd,
                   env=self.env, **kwargs)

    def output(self, cmd, **kwargs):
        return check_output(['singularity', 'run', '-B', '%s:/cati_portal' % self.directory, self.sif] + cmd,
                   env=self.env, **kwargs)

    def start(self, name):
        check_call(['singularity', 'instance', 'start', '-B', '%s:/cati_portal' % self.directory, self.sif, name],
                   env=self.env)

    def stop(self, name):
        check_call(['singularity', 'instance', 'stop', name],
                   env=self.env)
        for f in glob.glob(osp.join(self.tmp, 'cati_portal.sif.%s.*' % name)):
            os.remove(f)

    def shell(self, name):
        instance_name = 'instance://%s' % name

        # Check if the Singularity instance is running
        running = False
        process = subprocess.Popen(['singularity', 'instance','list'], stdout=subprocess.PIPE)
        output, unused_err = process.communicate()
        output=output.decode()
        instances = set(line.split()[0] for line in output.split('\n')[1:] if line)
        if instance_name in instances:
            check_call(['singularity', 'shell', instance_name],
                    env=self.env)
        else:
            check_call(['singularity', 'shell',  '-B', '%s:/cati_portal' % self.directory, self.sif],
                    env=self.env)

    def build(self, output_image, singularity_dir, recipe_file):
        # Try to write in output directory with root. If not possible,
        # image must be created in a temporary directory and copied.
        try:
            test_file = output_image + '.test'
            subprocess.check_call(['sudo', 'touch', test_file])
        except subprocess.CalledProcessError:
            use_tmp = True
        else:
            use_tmp = False
            subprocess.check_call(['sudo', 'rm', test_file])
        if use_tmp:
            tmp = tempfile.NamedTemporaryFile(suffix='.sif')
            os.remove(tmp.name)
            check_call(['sudo', 'singularity', 'build', tmp.name, osp.join(singularity_dir, recipe_file)], cwd=singularity_dir)
            subprocess.check_call(['sudo', 'chown', '%s:%s' % (os.environ['USER'],os.environ['USER']), tmp.name])
            check_call(['cp', tmp.name, output_image])
        else:
            check_call(['sudo', 'singularity', 'build', output_image, osp.join(singularity_dir, recipe_file)], cwd=singularity_dir)


@click.group()
def cli():
    pass

def check_call(cmd, **kwargs):
    print('-'*60)
    print(' '.join("'{0}'".format(i) for i in cmd))
    print('-'*60)
    if input is not None and 'universal_newlines' not in kwargs:
        kwargs['universal_newlines'] = True
    subprocess.run(cmd, check=True, **kwargs)

def check_output(cmd, input=None, **kwargs):
    print('-'*60)
    print(' '.join("'{0}'".format(i) for i in cmd))
    print('-'*60)
    if input is not None and 'universal_newlines' not in kwargs:
        kwargs['universal_newlines'] = True
    return subprocess.run(cmd,  check=True, stdout=subprocess.PIPE, **kwargs).stdout

@cli.command()
@click.option('--delete-existing', is_flag=True)
@click.option('--pg_port', default='54321')  # instead of PostgreSQL default port 5432
@click.option('--http_port', default='8080')  # instead of HTTP default port 80
def install(delete_existing, pg_port, http_port):
    directory = osp.dirname(osp.dirname(osp.abspath(__file__)))
    print('Creating new cati_portal instance in', directory)
    base_sif = osp.join(directory, 'base.sif')
    cati_portal_sif = osp.join(directory, 'cati_portal.sif')
    git = osp.join(directory, 'git')
    venv = osp.join(directory, 'venv')

    singularity = Singularity()

    if delete_existing:
        if osp.exists(venv):
            print('Delete', venv)
            shutil.rmtree(venv)

    singularity_dir =  osp.join(git, 'singularity')
    if not osp.exists(base_sif):
        singularity.build(base_sif, singularity_dir, 'base.recipe')
    if not osp.exists(cati_portal_sif):
        singularity.build(cati_portal_sif, singularity_dir, 'cati_portal.recipe')

    if not osp.exists(venv):
        singularity(['python3', '-m', 'venv', '--system-site-packages', '/cati_portal/venv'])
        pip = '/cati_portal/venv/bin/pip'
        singularity([pip, 'install', '--upgrade', 'pip'])
        singularity([pip, 'install', '--editable', '/cati_portal/git'])

    singularity(['/cati_portal/venv/bin/python', '-m', 'cati_portal.install', str(delete_existing), pg_port, http_port])


@cli.command()
def start():
    singularity = Singularity()
    singularity.start('cati_portal')

@cli.command()
def stop():
    singularity = Singularity()
    singularity.stop('cati_portal')

@cli.command()
def restart():
    singularity = Singularity()
    singularity.stop('cati_portal')
    singularity.start('cati_portal')

@cli.command()
def shell():
    singularity = Singularity()
    singularity.shell('cati_portal')


if __name__ == '__main__':
    try:
        cli()
    except Exception as e:
        print('-'*60)
        print('ERROR:', e, file=sys.stderr)
        raise
        sys.exit(1)
    sys.exit(0)