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271 lines
11 KiB
Python
271 lines
11 KiB
Python
#!/usr/bin/env python
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# Processes uploads from the user.
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# WARNING: Changes in this tool (particularly as related to parsing) may need
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# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
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from __future__ import print_function
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import errno
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import os
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import shutil
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import sys
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from json import dump, load, loads
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from six.moves.urllib.request import urlopen
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from galaxy import util
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from galaxy.datatypes import sniff
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from galaxy.datatypes.registry import Registry
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from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
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assert sys.version_info[:2] >= (2, 7)
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def file_err(msg, dataset):
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# never remove a server-side upload
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if dataset.type not in ('server_dir', 'path_paste'):
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try:
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os.remove(dataset.path)
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except Exception:
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pass
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return dict(type='dataset',
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ext='data',
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dataset_id=dataset.dataset_id,
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stderr=msg,
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failed=True)
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def safe_dict(d):
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"""
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Recursively clone json structure with UTF-8 dictionary keys
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http://mellowmachines.com/blog/2009/06/exploding-dictionary-with-unicode-keys-as-python-arguments/
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"""
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if isinstance(d, dict):
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return dict([(k.encode('utf-8'), safe_dict(v)) for k, v in d.items()])
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elif isinstance(d, list):
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return [safe_dict(x) for x in d]
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else:
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return d
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def parse_outputs(args):
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rval = {}
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for arg in args:
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id, files_path, path = arg.split(':', 2)
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rval[int(id)] = (path, files_path)
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return rval
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def add_file(dataset, registry, output_path):
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ext = None
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compression_type = None
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line_count = None
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link_data_only_str = dataset.get('link_data_only', 'copy_files')
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if link_data_only_str not in ['link_to_files', 'copy_files']:
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raise UploadProblemException("Invalid setting '%s' for option link_data_only - upload request misconfigured" % link_data_only_str)
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link_data_only = link_data_only_str == 'link_to_files'
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# run_as_real_user is estimated from galaxy config (external chmod indicated of inputs executed)
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# If this is True we always purge supplied upload inputs so they are cleaned up and we reuse their
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# paths during data conversions since this user already owns that path.
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# Older in_place check for upload jobs created before 18.01, TODO remove in 19.XX. xref #5206
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run_as_real_user = dataset.get('run_as_real_user', False) or dataset.get("in_place", False)
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# purge_source defaults to True unless this is an FTP import and
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# ftp_upload_purge has been overridden to False in Galaxy's config.
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# We set purge_source to False if:
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# - the job does not have write access to the file, e.g. when running as the
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# real user
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# - the files are uploaded from external paths.
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purge_source = dataset.get('purge_source', True) and not run_as_real_user and dataset.type not in ('server_dir', 'path_paste')
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# in_place is True unless we are running as a real user or importing external paths (i.e.
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# this is a real upload and not a path paste or ftp import).
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# in_place should always be False if running as real user because the uploaded file will
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# be owned by Galaxy and not the user and it should be False for external paths so Galaxy doesn't
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# modify files not controlled by Galaxy.
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in_place = not run_as_real_user and dataset.type not in ('server_dir', 'path_paste', 'ftp_import')
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# Base on the check_upload_content Galaxy config option and on by default, this enables some
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# security related checks on the uploaded content, but can prevent uploads from working in some cases.
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check_content = dataset.get('check_content' , True)
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# auto_decompress is a request flag that can be swapped off to prevent Galaxy from automatically
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# decompressing archive files before sniffing.
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auto_decompress = dataset.get('auto_decompress', True)
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try:
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dataset.file_type
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except AttributeError:
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raise UploadProblemException('Unable to process uploaded file, missing file_type parameter.')
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if dataset.type == 'url':
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try:
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dataset.path = sniff.stream_url_to_file(dataset.path)
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except Exception as e:
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raise UploadProblemException('Unable to fetch %s\n%s' % (dataset.path, str(e)))
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# See if we have an empty file
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if not os.path.exists(dataset.path):
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raise UploadProblemException('Uploaded temporary file (%s) does not exist.' % dataset.path)
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if not os.path.getsize(dataset.path) > 0:
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raise UploadProblemException('The uploaded file is empty')
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stdout, ext, datatype, is_binary, converted_path = handle_upload(
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registry=registry,
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path=dataset.path,
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requested_ext=dataset.file_type,
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name=dataset.name,
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tmp_prefix='data_id_%s_upload_' % dataset.dataset_id,
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tmp_dir=output_adjacent_tmpdir(output_path),
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check_content=check_content,
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link_data_only=link_data_only,
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in_place=in_place,
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auto_decompress=auto_decompress,
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convert_to_posix_lines=dataset.to_posix_lines,
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convert_spaces_to_tabs=dataset.space_to_tab,
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)
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# Strip compression extension from name
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if compression_type and not getattr(datatype, 'compressed', False) and dataset.name.endswith('.' + compression_type):
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dataset.name = dataset.name[:-len('.' + compression_type)]
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# Move dataset
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if link_data_only:
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# Never alter a file that will not be copied to Galaxy's local file store.
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if datatype.dataset_content_needs_grooming(dataset.path):
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err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \
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'<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.'
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raise UploadProblemException(err_msg)
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if not link_data_only:
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# Move the dataset to its "real" path. converted_path is a tempfile so we move it even if purge_source is False.
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if purge_source or converted_path:
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try:
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shutil.move(converted_path or dataset.path, output_path)
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except OSError as e:
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# We may not have permission to remove the input
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if e.errno != errno.EACCES:
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raise
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else:
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shutil.copy(dataset.path, output_path)
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# Write the job info
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stdout = stdout or 'uploaded %s file' % ext
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info = dict(type='dataset',
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dataset_id=dataset.dataset_id,
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ext=ext,
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stdout=stdout,
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name=dataset.name,
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line_count=line_count)
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if dataset.get('uuid', None) is not None:
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info['uuid'] = dataset.get('uuid')
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# FIXME: does this belong here? also not output-adjacent-tmpdir aware =/
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if not link_data_only and datatype and datatype.dataset_content_needs_grooming(output_path):
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# Groom the dataset content if necessary
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datatype.groom_dataset_content(output_path)
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return info
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def add_composite_file(dataset, output_path, files_path):
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if dataset.composite_files:
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os.mkdir(files_path)
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for name, value in dataset.composite_files.items():
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value = util.bunch.Bunch(**value)
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if dataset.composite_file_paths[value.name] is None and not value.optional:
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raise UploadProblemException('A required composite data file was not provided (%s)' % name)
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elif dataset.composite_file_paths[value.name] is not None:
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dp = dataset.composite_file_paths[value.name]['path']
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isurl = dp.find('://') != -1 # todo fixme
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if isurl:
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try:
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temp_name = sniff.stream_to_file(urlopen(dp), prefix='url_paste')
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except Exception as e:
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raise UploadProblemException('Unable to fetch %s\n%s' % (dp, str(e)))
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dataset.path = temp_name
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dp = temp_name
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if not value.is_binary:
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tmpdir = output_adjacent_tmpdir(output_path)
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tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
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if dataset.composite_file_paths[value.name].get('space_to_tab', value.space_to_tab):
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sniff.convert_newlines_sep2tabs(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
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else:
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sniff.convert_newlines(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
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shutil.move(dp, os.path.join(files_path, name))
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# Move the dataset to its "real" path
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shutil.move(dataset.primary_file, output_path)
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# Write the job info
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return dict(type='dataset',
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dataset_id=dataset.dataset_id,
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stdout='uploaded %s file' % dataset.file_type)
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def __read_paramfile(path):
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with open(path) as fh:
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obj = load(fh)
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# If there's a single dataset in an old-style paramfile it'll still parse, but it'll be a dict
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assert type(obj) == list
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return obj
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def __read_old_paramfile(path):
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datasets = []
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with open(path) as fh:
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for line in fh:
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datasets.append(loads(line))
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return datasets
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def __write_job_metadata(metadata):
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# TODO: make upload/set_metadata compatible with https://github.com/galaxyproject/galaxy/pull/4437
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with open('galaxy.json', 'w') as fh:
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for meta in metadata:
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dump(meta, fh)
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fh.write('\n')
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def output_adjacent_tmpdir(output_path):
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""" For temp files that will ultimately be moved to output_path anyway
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just create the file directly in output_path's directory so shutil.move
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will work optimially.
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"""
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return os.path.dirname(output_path)
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def __main__():
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if len(sys.argv) < 4:
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print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr)
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sys.exit(1)
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output_paths = parse_outputs(sys.argv[4:])
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registry = Registry()
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registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2])
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try:
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datasets = __read_paramfile(sys.argv[3])
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except (ValueError, AssertionError):
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datasets = __read_old_paramfile(sys.argv[3])
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metadata = []
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for dataset in datasets:
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dataset = util.bunch.Bunch(**safe_dict(dataset))
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try:
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output_path = output_paths[int(dataset.dataset_id)][0]
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except Exception:
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print('Output path for dataset %s not found on command line' % dataset.dataset_id, file=sys.stderr)
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sys.exit(1)
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try:
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if dataset.type == 'composite':
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files_path = output_paths[int(dataset.dataset_id)][1]
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metadata.append(add_composite_file(dataset, output_path, files_path))
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else:
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metadata.append(add_file(dataset, registry, output_path))
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except UploadProblemException as e:
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metadata.append(file_err(e.message, dataset))
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__write_job_metadata(metadata)
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if __name__ == '__main__':
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__main__()
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