package-run-projects

export GIT_SSL_NO_VERIFY=true

import git
import glob
import os
import subprocess
from biosimulators_utils.combine import data_model
from biosimulators_utils.combine import io
from biosimulators_utils.simulator import exec
from biosimulators_utils.biosimulations.utils import get_file_extension_combine_uri_map

file_extension_combine_uri_map = get_file_extension_combine_uri_map()

repo = git.Repo('.')

projects = [
    {
        'id': 'e/105',
        'workspace': 'yc_poh/poh_2012',
        'changeset': '713cd2940e5d99350a907e3199e29acf2180e094',
    }
]
for project in projects:
    # download project
    git.Submodule.add(repo, project['id'], 'projects/' + project['id'], url='https://models.physiomeproject.org/w/' + project['workspace'])
    subprocess.run(['git', 'checkout', project['changeset']], cwd='projects/' + project['id'])

    # create archive
    archive = data_model.CombineArchive()

    # add files to archive
    for filename in glob.glob('projects/' + project['id'] + '/**/*', recursive=True):
        _, ext = os.path.splitext(filename)        
        if ext:
            formats = file_extension_combine_uri_map.get(ext[1:], None)
            if len(formats) == 1:
                format = list(formats)[0]
            else:
                format = 'http://purl.org/NET/mediatypes/application/octet-stream'
        else:
            format = 'http://purl.org/NET/mediatypes/application/octet-stream'

        master = format == 'http://identifiers.org/combine.specifications/sed-ml'
        archive.contents.append(data_model.CombineArchiveContent(filename, format, master))

    # save archive
    in_dir = '/home/jonrkarr/Documents/biosimulations-physiome/' + project['id']
    archive_file = '/home/jonrkarr/Documents/biosimulations-physiome/' + project['id'] + '/archive.omex'
    io.CombineArchiveWriter().run(archive, in_dir, archive_file)

    # simulate archive
    out_dir = '/home/jonrkarr/Documents/biosimulations-physiome/' + project['id'] + '/out'
    docker_image = 'ghcr.io/biosimulators/opencor:latest'
    exec.exec_sedml_docs_in_archive_with_containerized_simulator(archive_file, out_dir, docker_image)

    # read results