comparison create_or_update_organism.py @ 14:bda202275e70 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"

13:a5388eab6383

#!/usr/bin/env python
from __future__ import print_function

import argparse
import glob
import json
import logging
import os
import shutil
import stat
import subprocess
import sys
import tarfile
import tempfile
import time

from apollo import accessible_organisms
from apollo.util import GuessOrg, OrgOrGuess

from arrow.apollo import get_apollo_instance

    return False


def IsRemote():
    return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
    parser.add_argument('jbrowse_src', help='Source JBrowse Data Directory')

        log.info("\tUpdating Organism")
        if IsRemote():
            with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                with tarfile.open(archive.name, mode="w:gz") as tar:
                    dataset_data_dir = args.jbrowse_src
                    for file in glob.glob(dataset_data_dir):
                        tar.add(file, arcname=file.replace(dataset_data_dir, './'))
                    if IsBlatEnabled():
                        tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
                data = wa.remote.update_organism(
                    org['id'],
                    archive,

        if IsRemote():
            with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                with tarfile.open(archive.name, mode="w:gz") as tar:
                    dataset_data_dir = args.jbrowse_src
                    for file in glob.glob(dataset_data_dir):
                        tar.add(file, arcname=file.replace(dataset_data_dir, './'))
                    if IsBlatEnabled():
                        with tempfile.TemporaryDirectory() as empty_dir:
                            os.chmod(empty_dir, stat.S_IRUSR | stat.S_IXUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
                            tar.add(empty_dir, arcname="./searchDatabaseData/")
                            tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")

14:bda202275e70

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json
import logging
import os
import re
import shutil
import stat
import subprocess
import sys
import tarfile
import tempfile
import time
from pathlib import Path

from apollo import accessible_organisms
from apollo.util import GuessOrg, OrgOrGuess

from arrow.apollo import get_apollo_instance

    return False


def IsRemote():
    return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0


def zip_data_dir(dataset_data_dir, tar):
    tar.add(dataset_data_dir, arcname='./', recursive=False)
    for r, d, f in os.walk(dataset_data_dir):
        for file_name in f:
            abs_file = os.path.join(r, file_name)
            rel_dir = os.path.relpath(r, dataset_data_dir)
            rel_file = os.path.join(rel_dir, file_name)
            if not rel_file.startswith('./'):
                rel_file = './' + rel_file
            if os.path.islink(abs_file):
                target = Path(abs_file).resolve().absolute().as_posix()
                if re.match(r'.*/_metadata_files/[0-9]+/metadata_[0-9]+.dat', target):
                    # This is a metadata file generated by galaxy, symlink would certainly be dead on remote host, resolve it
                    abs_file = target
            tar.add(abs_file, arcname=rel_file)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
    parser.add_argument('jbrowse_src', help='Source JBrowse Data Directory')

        log.info("\tUpdating Organism")
        if IsRemote():
            with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                with tarfile.open(archive.name, mode="w:gz") as tar:
                    dataset_data_dir = args.jbrowse_src
                    zip_data_dir(dataset_data_dir, tar)
                    if IsBlatEnabled():
                        tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
                data = wa.remote.update_organism(
                    org['id'],
                    archive,

        if IsRemote():
            with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                with tarfile.open(archive.name, mode="w:gz") as tar:
                    dataset_data_dir = args.jbrowse_src
                    zip_data_dir(dataset_data_dir, tar)
                    if IsBlatEnabled():
                        with tempfile.TemporaryDirectory() as empty_dir:
                            os.chmod(empty_dir, stat.S_IRUSR | stat.S_IXUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
                            tar.add(empty_dir, arcname="./searchDatabaseData/")
                            tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")