galaxy_irods_interface: irods_upload.py comparison

comparison irods_upload.py @ 2:0641ea2f75b1 draft

"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"

author	rhohensinner
date	Fri, 02 Jul 2021 09:40:25 +0000
parents
children	d2be2eb8350f

comparison

equal deleted inserted replaced

-:19c1cecdfdfd
+:0641ea2f75b1
+#!/usr/bin/env python
+# Processes uploads from the user.
+# WARNING: Changes in this tool (particularly as related to parsing) may need
+# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
+from __future__ import print_function
+import errno
+import os
+import shutil
+import sys
+sys.path.append("/home/richard/galaxy/lib")
+from json import dump, load, loads
+from galaxy.datatypes import sniff
+from galaxy.datatypes.registry import Registry
+from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
+from galaxy.util import (
+bunch,
+safe_makedirs,
+unicodify
+)
+from galaxy.util.compression_utils import CompressedFile
+assert sys.version_info[:2] >= (2, 7)
+_file_sources = None
+def get_file_sources():
+global _file_sources
+if _file_sources is None:
+from galaxy.files import ConfiguredFileSources
+file_sources = None
+if os.path.exists("file_sources.json"):
+file_sources_as_dict = None
+with open("file_sources.json") as f:
+file_sources_as_dict = load(f)
+if file_sources_as_dict is not None:
+file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict)
+if file_sources is None:
+ConfiguredFileSources.from_dict([])
+_file_sources = file_sources
+return _file_sources
+def file_err(msg, dataset):
+# never remove a server-side upload
+if dataset.type not in ('server_dir', 'path_paste'):
+try:
+os.remove(dataset.path)
+except Exception:
+pass
+return dict(type='dataset',
+ext='data',
+dataset_id=dataset.dataset_id,
+stderr=msg,
+failed=True)
+def safe_dict(d):
+"""Recursively clone JSON structure with unicode dictionary keys."""
+if isinstance(d, dict):
+return {unicodify(k): safe_dict(v) for k, v in d.items()}
+elif isinstance(d, list):
+return [safe_dict(x) for x in d]
+else:
+return d
+def parse_outputs(args):
+rval = {}
+for arg in args:
+id, files_path, path = arg.split(':', 2)
+rval[int(id)] = (path, files_path)
+return rval
+def add_file(dataset, registry, output_path):
+ext = None
+compression_type = None
+line_count = None
+link_data_only_str = dataset.get('link_data_only', 'copy_files')
+if link_data_only_str not in ['link_to_files', 'copy_files']:
+raise UploadProblemException("Invalid setting '%s' for option link_data_only - upload request misconfigured" % link_data_only_str)
+link_data_only = link_data_only_str == 'link_to_files'
+# run_as_real_user is estimated from galaxy config (external chmod indicated of inputs executed)
+# If this is True we always purge supplied upload inputs so they are cleaned up and we reuse their
+# paths during data conversions since this user already owns that path.
+# Older in_place check for upload jobs created before 18.01, TODO remove in 19.XX. xref #5206
+run_as_real_user = dataset.get('run_as_real_user', False) or dataset.get("in_place", False)
+# purge_source defaults to True unless this is an FTP import and
+# ftp_upload_purge has been overridden to False in Galaxy's config.
+# We set purge_source to False if:
+# - the job does not have write access to the file, e.g. when running as the
+#   real user
+# - the files are uploaded from external paths.
+purge_source = dataset.get('purge_source', True) and not run_as_real_user and dataset.type not in ('server_dir', 'path_paste')
+# in_place is True unless we are running as a real user or importing external paths (i.e.
+# this is a real upload and not a path paste or ftp import).
+# in_place should always be False if running as real user because the uploaded file will
+# be owned by Galaxy and not the user and it should be False for external paths so Galaxy doesn't
+# modify files not controlled by Galaxy.
+in_place = not run_as_real_user and dataset.type not in ('server_dir', 'path_paste', 'ftp_import')
+# Base on the check_upload_content Galaxy config option and on by default, this enables some
+# security related checks on the uploaded content, but can prevent uploads from working in some cases.
+check_content = dataset.get('check_content' , True)
+# auto_decompress is a request flag that can be swapped off to prevent Galaxy from automatically
+# decompressing archive files before sniffing.
+auto_decompress = dataset.get('auto_decompress', True)
+try:
+dataset.file_type
+except AttributeError:
+raise UploadProblemException('Unable to process uploaded file, missing file_type parameter.')
+if dataset.type == 'url':
+try:
+dataset.path = sniff.stream_url_to_file(dataset.path, file_sources=get_file_sources())
+except Exception as e:
+raise UploadProblemException('Unable to fetch %s\n%s' % (dataset.path, unicodify(e)))
+# See if we have an empty file
+if not os.path.exists(dataset.path):
+raise UploadProblemException('Uploaded temporary file (%s) does not exist.' % dataset.path)
+stdout, ext, datatype, is_binary, converted_path = handle_upload(
+registry=registry,
+path=dataset.path,
+requested_ext=dataset.file_type,
+name=dataset.name,
+tmp_prefix='data_id_%s_upload_' % dataset.dataset_id,
+tmp_dir=output_adjacent_tmpdir(output_path),
+check_content=check_content,
+link_data_only=link_data_only,
+in_place=in_place,
+auto_decompress=auto_decompress,
+convert_to_posix_lines=dataset.to_posix_lines,
+convert_spaces_to_tabs=dataset.space_to_tab,
+)
+# Strip compression extension from name
+if compression_type and not getattr(datatype, 'compressed', False) and dataset.name.endswith('.' + compression_type):
+dataset.name = dataset.name[:-len('.' + compression_type)]
+# Move dataset
+if link_data_only:
+# Never alter a file that will not be copied to Galaxy's local file store.
+if datatype.dataset_content_needs_grooming(dataset.path):
+err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \
+'<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.'
+raise UploadProblemException(err_msg)
+if not link_data_only:
+# Move the dataset to its "real" path. converted_path is a tempfile so we move it even if purge_source is False.
+if purge_source or converted_path:
+try:
+# If user has indicated that the original file to be purged and have converted_path tempfile
+if purge_source and converted_path:
+shutil.move(converted_path, output_path)
+os.remove(dataset.path)
+else:
+shutil.move(converted_path or dataset.path, output_path)
+except OSError as e:
+# We may not have permission to remove the input
+if e.errno != errno.EACCES:
+raise
+else:
+shutil.copy(dataset.path, output_path)
+# Write the job info
+stdout = stdout or 'uploaded %s file' % ext
+info = dict(type='dataset',
+dataset_id=dataset.dataset_id,
+ext=ext,
+stdout=stdout,
+name=dataset.name,
+line_count=line_count)
+if dataset.get('uuid', None) is not None:
+info['uuid'] = dataset.get('uuid')
+# FIXME: does this belong here? also not output-adjacent-tmpdir aware =/
+if not link_data_only and datatype and datatype.dataset_content_needs_grooming(output_path):
+# Groom the dataset content if necessary
+datatype.groom_dataset_content(output_path)
+return info
+def add_composite_file(dataset, registry, output_path, files_path):
+datatype = None
+# Find data type
+if dataset.file_type is not None:
+datatype = registry.get_datatype_by_extension(dataset.file_type)
+def to_path(path_or_url):
+is_url = path_or_url.find('://') != -1  # todo fixme
+if is_url:
+try:
+temp_name = sniff.stream_url_to_file(path_or_url, file_sources=get_file_sources())
+except Exception as e:
+raise UploadProblemException('Unable to fetch %s\n%s' % (path_or_url, unicodify(e)))
+return temp_name, is_url
+return path_or_url, is_url
+def make_files_path():
+safe_makedirs(files_path)
+def stage_file(name, composite_file_path, is_binary=False):
+dp = composite_file_path['path']
+path, is_url = to_path(dp)
+if is_url:
+dataset.path = path
+dp = path
+auto_decompress = composite_file_path.get('auto_decompress', True)
+if auto_decompress and not datatype.composite_type and CompressedFile.can_decompress(dp):
+# It isn't an explicitly composite datatype, so these are just extra files to attach
+# as composite data. It'd be better if Galaxy was communicating this to the tool
+# a little more explicitly so we didn't need to dispatch on the datatype and so we
+# could attach arbitrary extra composite data to an existing composite datatype if
+# if need be? Perhaps that would be a mistake though.
+CompressedFile(dp).extract(files_path)
+else:
+tmpdir = output_adjacent_tmpdir(output_path)
+tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
+sniff.handle_composite_file(
+datatype,
+dp,
+files_path,
+name,
+is_binary,
+tmpdir,
+tmp_prefix,
+composite_file_path,
+)
+# Do we have pre-defined composite files from the datatype definition.
+if dataset.composite_files:
+make_files_path()
+for name, value in dataset.composite_files.items():
+value = bunch.Bunch(**value)
+if value.name not in dataset.composite_file_paths:
+raise UploadProblemException("Failed to find file_path %s in %s" % (value.name, dataset.composite_file_paths))
+if dataset.composite_file_paths[value.name] is None and not value.optional:
+raise UploadProblemException('A required composite data file was not provided (%s)' % name)
+elif dataset.composite_file_paths[value.name] is not None:
+composite_file_path = dataset.composite_file_paths[value.name]
+stage_file(name, composite_file_path, value.is_binary)
+# Do we have ad-hoc user supplied composite files.
+elif dataset.composite_file_paths:
+make_files_path()
+for key, composite_file in dataset.composite_file_paths.items():
+stage_file(key, composite_file)  # TODO: replace these defaults
+# Move the dataset to its "real" path
+primary_file_path, _ = to_path(dataset.primary_file)
+shutil.move(primary_file_path, output_path)
+# Write the job info
+return dict(type='dataset',
+dataset_id=dataset.dataset_id,
+stdout='uploaded %s file' % dataset.file_type)
+def __read_paramfile(path):
+with open(path) as fh:
+obj = load(fh)
+# If there's a single dataset in an old-style paramfile it'll still parse, but it'll be a dict
+assert type(obj) == list
+return obj
+def __read_old_paramfile(path):
+datasets = []
+with open(path) as fh:
+for line in fh:
+datasets.append(loads(line))
+return datasets
+def __write_job_metadata(metadata):
+# TODO: make upload/set_metadata compatible with https://github.com/galaxyproject/galaxy/pull/4437
+with open('galaxy.json', 'w') as fh:
+for meta in metadata:
+dump(meta, fh)
+fh.write('\n')
+def output_adjacent_tmpdir(output_path):
+""" For temp files that will ultimately be moved to output_path anyway
+just create the file directly in output_path's directory so shutil.move
+will work optimally.
+"""
+return os.path.dirname(output_path)
+def __main__():
+if len(sys.argv) < 4:
+print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr)
+sys.exit(1)
+output_paths = parse_outputs(sys.argv[4:])
+registry = Registry()
+registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2])
+try:
+datasets = __read_paramfile(sys.argv[3])
+except (ValueError, AssertionError):
+datasets = __read_old_paramfile(sys.argv[3])
+metadata = []
+for dataset in datasets:
+dataset = bunch.Bunch(**safe_dict(dataset))
+try:
+output_path = output_paths[int(dataset.dataset_id)][0]
+except Exception:
+print('Output path for dataset %s not found on command line' % dataset.dataset_id, file=sys.stderr)
+sys.exit(1)
+try:
+if dataset.type == 'composite':
+files_path = output_paths[int(dataset.dataset_id)][1]
+metadata.append(add_composite_file(dataset, registry, output_path, files_path))
+else:
+metadata.append(add_file(dataset, registry, output_path))
+except UploadProblemException as e:
+metadata.append(file_err(unicodify(e), dataset))
+__write_job_metadata(metadata)
+if __name__ == '__main__':
+__main__()

Mercurial > repos > rhohensinner > galaxy_irods_interface

comparison irods_upload.py @ 2:0641ea2f75b1 draft