def update_repository(self, id, tar_ball_path, commit_message=None):
"""
Update the contents of a Tool Shed repository with specified tar ball.
:type id: str
:param id: Encoded repository ID
:type tar_ball_path: str
:param tar_ball_path: Path to file containing tar ball to upload.
:type commit_message: str
:param commit_message: Commit message used for the underlying Mercurial
repository backing Tool Shed repository.
:rtype: dict
:return: Returns a dictionary that includes repository content warnings.
Most valid uploads will result in no such warning and an exception
will be raised generally if there are problems.
For example a successful upload will look like::
{'content_alert': '',
'message': ''}
.. versionadded:: 0.5.2
"""
url = self._make_url(id) + '/changeset_revision'
payload = {
'file': attach_file(tar_ball_path)
}
if commit_message is not None:
payload['commit_message'] = commit_message
try:
return self._post(payload=payload, files_attached=True, url=url)
finally:
payload['file'].close()
def upload_file(self, path, history_id, **keywords):
"""
Upload file specified by ``path`` to the history specified by
``history_id``.
:type path: str
:param path: path of the file to upload
:type history_id: str
:param history_id: id of the history where to upload the file
:type file_name: str
:param file_name: (optional) name of the new history dataset
:type file_type: str
:param file_type: Galaxy datatype for the new dataset, default is auto
:type dbkey: str
:param dbkey: (optional) genome dbkey
"""
default_file_name = basename(path)
if "file_name" not in keywords:
keywords["file_name"] = default_file_name
payload = self._upload_payload(history_id, **keywords)
payload["files_0|file_data"] = attach_file(path, name=keywords["file_name"])
try:
return self._tool_post(payload, files_attached=True)
finally:
payload["files_0|file_data"].close()
def update_repository(self, id, tar_ball_path, commit_message=None):
"""
Update the contents of a Tool Shed repository with specified tar ball.
:type id: str
:param id: Encoded repository ID
:type tar_ball_path: str
:param tar_ball_path: Path to file containing tar ball to upload.
:type commit_message: str
:param commit_message: Commit message used for the underlying Mercurial
repository backing Tool Shed repository.
:rtype: dict
:return: Returns a dictionary that includes repository content warnings.
Most valid uploads will result in no such warning and an exception
will be raised generally if there are problems.
For example a successful upload will look like::
{u'content_alert': u'',
u'message': u''}
.. versionadded:: 0.5.2
"""
url = '/'.join([self.gi._make_url(self, id), 'changeset_revision'])
payload = {
'file': attach_file(tar_ball_path)
}
if commit_message is not None:
payload['commit_message'] = commit_message
try:
return self._post(payload=payload, files_attached=True, url=url)
finally:
payload['file'].close()
def _attach_file(upload_payload, uri, index=0):
uri = path_or_uri_to_uri(uri)
is_path = uri.startswith("file://")
if not is_path or config.use_path_paste:
upload_payload["inputs"]["files_%d|url_paste" % index] = uri
else:
files_attached[0] = True
path = uri[len("file://"):]
upload_payload["files_%d|file_data" % index] = attach_file(path)
def _attach_file(upload_payload, uri, index=0):
uri = path_or_uri_to_uri(uri)
is_path = uri.startswith("file://")
if not is_path or config.use_path_paste:
upload_payload["inputs"]["files_%d|url_paste" % index] = uri
else:
files_attached[0] = True
path = uri[len("file://"):]
upload_payload["files_%d|file_data" % index] = attach_file(path)
def _do_upload(self, **keywords):
"""
Set up the POST request and do the actual data upload to a data library.
This method should not be called directly but instead refer to the methods
specific for the desired type of data upload.
"""
library_id = keywords['library_id']
folder_id = keywords.get('folder_id', None)
if folder_id is None:
folder_id = self._get_root_folder_id(library_id)
files_attached = False
# Compose the payload dict
payload = {}
payload['folder_id'] = folder_id
payload['file_type'] = keywords.get('file_type', 'auto')
payload['dbkey'] = keywords.get('dbkey', '?')
payload['create_type'] = 'file'
if keywords.get("roles", None):
payload["roles"] = keywords["roles"]
if keywords.get("link_data_only", None) and keywords['link_data_only'] != 'copy_files':
payload["link_data_only"] = 'link_to_files'
if keywords.get('remote_dataset', None):
payload['remote_dataset'] = keywords['remote_dataset'];
if keywords.get('uuid_list', None):
payload['uuid_list'] = keywords['uuid_list'];
if keywords.get('remote_dataset_type_list', None):
payload['remote_dataset_type_list'] = keywords['remote_dataset_type_list'];
if keywords.get('file_size_list', None):
payload['file_size_list'] = keywords['file_size_list'];
if keywords.get('line_count_list', None):
payload['line_count_list'] = keywords['line_count_list'];
# upload options
if keywords.get('file_url', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|url_paste'] = keywords['file_url']
elif keywords.get('pasted_content', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|url_paste'] = keywords['pasted_content']
elif keywords.get('server_dir', None) is not None:
payload['upload_option'] = 'upload_directory'
payload['server_dir'] = keywords['server_dir']
elif keywords.get('file_local_path', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|file_data'] = attach_file(keywords['file_local_path'])
files_attached = True
elif keywords.get("filesystem_paths", None) is not None:
payload["upload_option"] = "upload_paths"
payload["filesystem_paths"] = keywords["filesystem_paths"]
try:
return Client._post(self, payload, id=library_id, contents=True,
files_attached=files_attached)
finally:
if payload.get('files_0|file_data', None) is not None:
payload['files_0|file_data'].close()
def _do_upload(self, library_id, **keywords):
"""
Set up the POST request and do the actual data upload to a data library.
This method should not be called directly but instead refer to the
methods specific for the desired type of data upload.
"""
folder_id = keywords.get('folder_id', None)
if folder_id is None:
folder_id = self._get_root_folder_id(library_id)
files_attached = False
# Compose the payload dict
payload = {}
payload['folder_id'] = folder_id
payload['file_type'] = keywords.get('file_type', 'auto')
payload['dbkey'] = keywords.get('dbkey', '?')
payload['create_type'] = 'file'
if keywords.get("roles", None):
payload["roles"] = keywords["roles"]
if keywords.get("link_data_only",
None) and keywords['link_data_only'] != 'copy_files':
payload["link_data_only"] = 'link_to_files'
payload['tag_using_filenames'] = keywords.get('tag_using_filenames',
False)
if keywords.get('tags'):
payload['tags'] = keywords['tags']
payload['preserve_dirs'] = keywords.get('preserve_dirs', False)
# upload options
if keywords.get('file_url', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|url_paste'] = keywords['file_url']
elif keywords.get('pasted_content', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|url_paste'] = keywords['pasted_content']
elif keywords.get('server_dir', None) is not None:
payload['upload_option'] = 'upload_directory'
payload['server_dir'] = keywords['server_dir']
elif keywords.get('file_local_path', None) is not None:
payload['upload_option'] = 'upload_file'
payload['files_0|file_data'] = attach_file(
keywords['file_local_path'])
files_attached = True
elif keywords.get("filesystem_paths", None) is not None:
payload["upload_option"] = "upload_paths"
payload["filesystem_paths"] = keywords["filesystem_paths"]
try:
return self._post(payload,
id=library_id,
contents=True,
files_attached=files_attached)
finally:
if payload.get('files_0|file_data', None) is not None:
payload['files_0|file_data'].close()
def import_history(self, file_path=None, url=None):
"""
Import a history from an archive on disk or a URL.
:type file_path: str
:param file_path: Path to exported history archive on disk.
:type url: str
:param url: URL for an exported history archive
"""
if file_path:
archive_file = attach_file(file_path)
payload = dict(archive_source='', archive_file=archive_file, archive_type="file")
else:
payload = dict(archive_source=url, archive_type='url')
return self._post(payload=payload, files_attached=file_path is not None)
def upload_file(self, path, history_id, **keywords):
"""
Upload the file specified by ``path`` to the history specified by
``history_id``.
:type path: str
:param path: path of the file to upload
:type history_id: str
:param history_id: id of the history where to upload the file
:type file_name: str
:param file_name: (optional) name of the new history dataset
:type file_type: str
:param file_type: (optional) Galaxy datatype for the new dataset, default is auto
:type dbkey: str
:param dbkey: (optional) genome dbkey
:type to_posix_lines: bool
:param to_posix_lines: if ``True`` (the default), convert universal line
endings to POSIX line endings. Set to ``False`` when uploading a gzip,
bz2 or zip archive containing a binary file
:type space_to_tab: bool
:param space_to_tab: whether to convert spaces to tabs. Default is
``False``. Applicable only if to_posix_lines is ``True``
:rtype: dict
:return: Information about the created upload job
"""
if "file_name" not in keywords:
keywords["file_name"] = basename(path)
payload = self._upload_payload(history_id, **keywords)
payload["files_0|file_data"] = attach_file(path,
name=keywords["file_name"])
try:
return self._post(payload, files_attached=True)
finally:
payload["files_0|file_data"].close()
def upload_file(self, path, history_id, **keywords):
"""
Upload the file specified by ``path`` to the history specified by
``history_id``.
:type path: str
:param path: path of the file to upload
:type history_id: str
:param history_id: id of the history where to upload the file
:type file_name: str
:param file_name: (optional) name of the new history dataset
:type file_type: str
:param file_type: (optional) Galaxy datatype for the new dataset, default is auto
:type dbkey: str
:param dbkey: (optional) genome dbkey
:type to_posix_lines: bool
:param to_posix_lines: if ``True`` (the default), convert universal line
endings to POSIX line endings. Set to ``False`` when uploading a gzip,
bz2 or zip archive containing a binary file
:type space_to_tab: bool
:param space_to_tab: whether to convert spaces to tabs. Default is
``False``. Applicable only if to_posix_lines is ``True``
:rtype: dict
:return: Information about the created upload job
"""
if "file_name" not in keywords:
keywords["file_name"] = basename(path)
payload = self._upload_payload(history_id, **keywords)
payload["files_0|file_data"] = attach_file(path, name=keywords["file_name"])
try:
return self._post(payload, files_attached=True)
finally:
payload["files_0|file_data"].close()
def _attach_file(self, path):
return attach_file(path)
