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Arthur Le Bars
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#!/usr/bin/env python3
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import argparse
import logging as log
import os
import subprocess
import time
from subprocess import CalledProcessError
from bioblend.galaxy.objects import GalaxyInstance
import yaml
class DataLibLoader:
def __init__(self):
self.existing_folders_cache = {}
self.bam_metadata_cache = {}
def create_deep_folder(self, prj_lib, path, parent_folder=None, deep_name=""):
segments = path.split(os.sep)
deeper_name = os.sep.join([deep_name, segments[0]])
if deeper_name in self.existing_folders_cache:
new_folder = self.existing_folders_cache[deeper_name]
else:
new_folder = prj_lib.create_folder(segments[0], base_folder=parent_folder)
self.existing_folders_cache[deeper_name] = new_folder
if len(segments) > 1:
new_folder = self.create_deep_folder(prj_lib, os.sep.join(segments[1:]), new_folder, deeper_name)
return new_folder
def get_bam_label(self, dirname, bam_file):
bam_id = bam_file
if bam_id.endswith('.bam'):
bam_id = bam_id[:-4]
if dirname in self.bam_metadata_cache:
if bam_id in self.bam_metadata_cache[dirname] and 'label' in self.bam_metadata_cache[dirname][bam_id] and self.bam_metadata_cache[dirname][bam_id]['label']:
return self.bam_metadata_cache[dirname][bam_id]['label']
else:
return None
else:
meta_file = os.path.join(dirname, 'metadata.yml')
if os.path.exists(meta_file):
with open(meta_file) as f:
self.bam_metadata_cache[dirname] = yaml.safe_load(f)
log.info("Found metadata in %s " % meta_file)
else:
self.bam_metadata_cache[dirname] = {}
log.info("Did not find metadata in %s " % meta_file)
return self.get_bam_label(dirname, bam_file)
def main(self, args, data_dir_root='/project_data'):
"""
Load files into a Galaxy data library.
"""
log.info("Importing data libraries.")
url = "http://localhost"
# The environment variables are set by the parent container
admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', 'admin@galaxy.org')
admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'password')
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# Establish connection to galaxy instance
gio = GalaxyInstance(url=url, email=admin_email, password=admin_pass)
log.info("Looking for project data in %s" % data_dir_root)
folders = dict()
for root, dirs, files in os.walk(data_dir_root, followlinks=True):
file_list = [os.path.join(root, filename) for filename in files]
folders[root] = file_list
post_renaming = {}
if folders:
# Delete pre-existing lib (probably created by a previous call)
existing = gio.libraries.get_previews(name='Project Data')
for lib in existing:
if not lib.deleted:
log.info('Pre-existing "Project Data" library %s found, removing it.' % lib.id)
gio.libraries.delete(lib.id)
log.info("Creating new 'Project Data' library.")
prj_lib = gio.libraries.create('Project Data', 'Data for current genome annotation project')
for fname, files in folders.items():
if fname and files:
folder_name = fname[len(data_dir_root) + 1:]
log.info("Creating folder: %s" % folder_name)
folder = None
if not args.dry_run:
folder = self.create_deep_folder(prj_lib, folder_name)
for single_file in files:
ftype = 'auto'
clean_name = os.path.basename(single_file)
clean_name = clean_name.replace('_', ' ')
if single_file.endswith('.bam'):
ftype = 'bam'
bam_label = self.get_bam_label(fname, os.path.basename(single_file))
if bam_label:
clean_name = bam_label
else:
clean_name = os.path.splitext(clean_name)[0]
if clean_name.endswith("Aligned.sortedByCoord.out"): # Stupid thing for many local bam files
clean_name = clean_name[:-25]
elif single_file.endswith('.fasta') or single_file.endswith('.fa') or single_file.endswith('.faa') or single_file.endswith('.fna'):
ftype = 'fasta'
elif single_file.endswith('.gff') or single_file.endswith('.gff3'):
ftype = 'gff3'
clean_name = os.path.splitext(clean_name)[0]
elif single_file.endswith('.xml'):
ftype = 'xml'
elif single_file.endswith('.bw'):
ftype = 'bigwig'
elif single_file.endswith('.gaf'):
ftype = 'tabular'
elif single_file.endswith('_tree.txt'):
# We don't want to pollute the logs with 20000 useless lines
log.debug("Skipping useless file '%s'." % single_file)
continue
elif single_file.endswith('.tar.gz') and 'newick' in fname:
ftype = 'tar'
elif single_file.endswith('.bai') or single_file.endswith('.tar.gz') or single_file.endswith('.tar.bz2') or single_file.endswith('.raw') or single_file.endswith('.pdf'):
log.info("Skipping useless file '%s'." % single_file)
continue
log.info("Adding file '%s' with type '%s' and name '%s'." % (single_file, ftype, clean_name))
if not args.dry_run:
datasets = prj_lib.upload_from_galaxy_fs(
single_file,
folder=folder,
link_data_only='link_to_files',
file_type=ftype,
tag_using_filenames=False
)
# Rename dataset
# Need to do it AFTER the datasets import is finished, otherwise the new names are not kept by galaxy
# (erased by metadata generation I guess)
post_renaming[datasets[0]] = clean_name
time.sleep(1)
if args.dry_run:
log.info("Finished in DRY RUN mode")
return
# Wait for uploads to complete
log.info("Waiting for import jobs to finish... please wait")
while True:
try:
# "C" state means the job is completed, no need to wait for it
ret = subprocess.check_output("squeue | grep -v \"C debug\" | grep -v \"JOBID\" || true", shell=True)
if not len(ret):
break
time.sleep(3)
except CalledProcessError as inst:
if inst.returncode == 153: # queue is empty
break
else:
raise
time.sleep(10)
log.info("Import finished, now renaming datasets with pretty names")
for dataset in post_renaming:
dataset.update(name=post_renaming[dataset])
log.info("Finished importing data.")
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Populate the Galaxy data library with files.'
)
parser.add_argument("-v", "--verbose", help="Increase output verbosity.",
action="store_true")
parser.add_argument("-d", "--dry-run", help="Don't update the data library, just show what it would do.",
action="store_true")
args = parser.parse_args()
if args.verbose:
log.basicConfig(level=log.DEBUG)
else:
log.basicConfig(level=log.INFO)
dll = DataLibLoader()
dll.main(args)