Source code for bioblend.galaxy.libraries

"""
Contains possible interactions with the Galaxy Data Libraries
"""
import logging
import time

from six.moves import range

from bioblend.galaxy.client import Client
from bioblend.galaxy.datasets import DatasetTimeoutException, terminal_states
from bioblend.util import attach_file

log = logging.getLogger(__name__)


[docs]class LibraryClient(Client): def __init__(self, galaxy_instance): self.module = 'libraries' super(LibraryClient, self).__init__(galaxy_instance)
[docs] def create_library(self, name, description=None, synopsis=None): """ Create a data library with the properties defined in the arguments. :type name: str :param name: Name of the new data library :type description: str :param description: Optional data library description :type synopsis: str :param synopsis: Optional data library synopsis :rtype: dict :return: Details of the created library. For example:: {'id': 'f740ab636b360a70', 'name': 'Library from bioblend', 'url': '/api/libraries/f740ab636b360a70'} """ payload = {'name': name} if description: payload['description'] = description if synopsis: payload['synopsis'] = synopsis return self._post(payload)
[docs] def delete_library(self, library_id): """ Delete a data library. :type library_id: str :param library_id: Encoded data library ID identifying the library to be deleted .. warning:: Deleting a data library is irreversible - all of the data from the library will be permanently deleted. """ return self._delete(id=library_id)
def _show_item(self, library_id, item_id): """ Get details about a given library item. """ url = self.gi._make_url(self, library_id, contents=True) url = '/'.join([url, item_id]) return self._get(url=url)
[docs] def delete_library_dataset(self, library_id, dataset_id, purged=False): """ Delete a library dataset in a data library. :type library_id: str :param library_id: library id where dataset is found in :type dataset_id: str :param dataset_id: id of the dataset to be deleted :type purged: bool :param purged: Indicate that the dataset should be purged (permanently deleted) :rtype: dict :return: A dictionary containing the dataset id and whether the dataset has been deleted. For example:: {u'deleted': True, u'id': u'60e680a037f41974'} """ url = self.gi._make_url(self, library_id, contents=True) # Append the dataset_id to the base history contents URL url = '/'.join([url, dataset_id]) return self._delete(payload={'purged': purged}, url=url)
[docs] def update_library_dataset(self, dataset_id, **kwds): """ Update library dataset metadata. Some of the attributes that can be modified are documented below. :type dataset_id: str :param dataset_id: id of the dataset to be deleted :type name: str :param name: Replace library dataset name with the given string :type misc_info: str :param misc_info: Replace library dataset misc_info with given string :type file_ext: str :param file_ext: Replace library dataset extension (must exist in the Galaxy registry) :type genome_build: str :param genome_build: Replace library dataset genome build (dbkey) :rtype: dict :return: details of the updated dataset """ url = '/'.join([self.gi._make_url(self), 'datasets', dataset_id]) return self._patch(payload=kwds, url=url)
[docs] def show_dataset(self, library_id, dataset_id): """ Get details about a given library dataset. The required ``library_id`` can be obtained from the datasets's library content details. :type library_id: str :param library_id: library id where dataset is found in :type dataset_id: str :param dataset_id: id of the dataset to be inspected :rtype: dict :return: A dictionary containing information about the dataset in the library """ return self._show_item(library_id, dataset_id)
[docs] def wait_for_dataset(self, library_id, dataset_id, maxwait=12000, interval=3): """ Wait until the library dataset state is terminal ('ok', 'empty', 'error', 'discarded' or 'failed_metadata'). :type library_id: str :param library_id: library id where dataset is found in :type dataset_id: str :param dataset_id: id of the dataset to wait for :type maxwait: float :param maxwait: Total time (in seconds) to wait for the dataset state to become terminal. If the dataset state is not terminal within this time, a ``DatasetTimeoutException`` will be thrown. :type interval: float :param interval: Time (in seconds) to wait between 2 consecutive checks. :rtype: dict :return: A dictionary containing information about the dataset in the library """ assert maxwait > 0 assert interval > 0 for time_left in range(maxwait, 0, -interval): dataset = self.show_dataset(library_id, dataset_id) state = dataset['state'] if state in terminal_states: return dataset if time_left > 0: log.warning("Waiting for library %s dataset %s to complete. Will wait another %i s", library_id, dataset_id, time_left) time.sleep(min(time_left, interval)) else: raise DatasetTimeoutException("Waited too long for library %s dataset %s to complete" % (library_id, dataset_id))
[docs] def show_folder(self, library_id, folder_id): """ Get details about a given folder. The required ``folder_id`` can be obtained from the folder's library content details. :type library_id: str :param library_id: library id to inspect folders in :type folder_id: str :param folder_id: id of the folder to be inspected """ return self._show_item(library_id, folder_id)
def _get_root_folder_id(self, library_id): """ Find the root folder (i.e. '/') of a library. :type library_id: str :param library_id: library id to find root of """ l = self.show_library(library_id=library_id) if 'root_folder_id' in l: return l['root_folder_id'] # Galaxy previous to release_13.04 does not have root_folder_id in # library dictionary, so resort to find the folder with name '/' library_contents = self.show_library(library_id=library_id, contents=True) for f in library_contents: if f['name'] == '/': return f['id']
[docs] def create_folder(self, library_id, folder_name, description=None, base_folder_id=None): """ Create a folder in a library. :type library_id: str :param library_id: library id to use :type folder_name: str :param folder_name: name of the new folder in the data library :type description: str :param description: description of the new folder in the data library :type base_folder_id: str :param base_folder_id: id of the folder where to create the new folder. If not provided, the root folder will be used """ # Get root folder ID if no ID was provided if base_folder_id is None: base_folder_id = self._get_root_folder_id(library_id) # Compose the payload payload = {} payload['name'] = folder_name payload['folder_id'] = base_folder_id payload['create_type'] = 'folder' if description is not None: payload['description'] = description return self._post(payload, id=library_id, contents=True)
[docs] def get_folders(self, library_id, folder_id=None, name=None): """ Get all the folders or filter specific one(s) via the provided ``name`` or ``folder_id`` in data library with id ``library_id``. Provide only one argument: ``name`` or ``folder_id``, but not both. :type folder_id: str :param folder_id: filter for folder by folder id :type name: str :param name: filter for folder by name. For ``name`` specify the full path of the folder starting from the library's root folder, e.g. ``/subfolder/subsubfolder``. :rtype: list :return: list of dicts each containing basic information about a folder """ if folder_id is not None and name is not None: raise ValueError('Provide only one argument between name or folder_id, but not both') library_contents = self.show_library(library_id=library_id, contents=True) if folder_id is not None: folder = next((_ for _ in library_contents if _['type'] == 'folder' and _['id'] == folder_id), None) folders = [folder] if folder is not None else [] elif name is not None: folders = [_ for _ in library_contents if _['type'] == 'folder' and _['name'] == name] else: folders = [_ for _ in library_contents if _['type'] == 'folder'] return folders
[docs] def get_libraries(self, library_id=None, name=None, deleted=False): """ Get all the libraries or filter for specific one(s) via the provided name or ID. Provide only one argument: ``name`` or ``library_id``, but not both. :type library_id: str :param library_id: filter for library by library id :type name: str :param name: If ``name`` is set and multiple names match the given name, all the libraries matching the argument will be returned :type deleted: bool :param deleted: If set to ``True``, return libraries that have been deleted :rtype: list :return: list of dicts each containing basic information about a library """ if library_id is not None and name is not None: raise ValueError('Provide only one argument between name or library_id, but not both') libraries = self._get(deleted=deleted) if library_id is not None: library = next((_ for _ in libraries if _['id'] == library_id), None) libraries = [library] if library is not None else [] if name is not None: libraries = [_ for _ in libraries if _['name'] == name] return libraries
[docs] def show_library(self, library_id, contents=False): """ Get information about a library. :type library_id: str :param library_id: filter for library by library id :type contents: bool :param contents: True if want to get contents of the library (rather than just the library details) :rtype: dict :return: details of the given library """ return self._get(id=library_id, contents=contents)
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'] = str(keywords.get('tag_using_filenames', True)) payload['preserve_dirs'] = str(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()
[docs] def upload_file_from_url(self, library_id, file_url, folder_id=None, file_type='auto', dbkey='?'): """ Upload a file to a library from a URL. :type library_id: str :param library_id: id of the library where to place the uploaded file :type file_url: str :param file_url: URL of the file to upload :type folder_id: str :param folder_id: id of the folder where to place the uploaded file. If not provided, the root folder will be used :type file_type: str :param file_type: Galaxy file format name :type dbkey: str :param dbkey: Dbkey """ return self._do_upload(library_id, file_url=file_url, folder_id=folder_id, file_type=file_type, dbkey=dbkey)
[docs] def upload_file_contents(self, library_id, pasted_content, folder_id=None, file_type='auto', dbkey='?'): """ Upload pasted_content to a data library as a new file. :type library_id: str :param library_id: id of the library where to place the uploaded file :type pasted_content: str :param pasted_content: Content to upload into the library :type folder_id: str :param folder_id: id of the folder where to place the uploaded file. If not provided, the root folder will be used :type file_type: str :param file_type: Galaxy file format name :type dbkey: str :param dbkey: Dbkey """ return self._do_upload(library_id, pasted_content=pasted_content, folder_id=folder_id, file_type=file_type, dbkey=dbkey)
[docs] def upload_file_from_local_path(self, library_id, file_local_path, folder_id=None, file_type='auto', dbkey='?'): """ Read local file contents from file_local_path and upload data to a library. :type library_id: str :param library_id: id of the library where to place the uploaded file :type file_local_path: str :param file_local_path: path of local file to upload :type folder_id: str :param folder_id: id of the folder where to place the uploaded file. If not provided, the root folder will be used :type file_type: str :param file_type: Galaxy file format name :type dbkey: str :param dbkey: Dbkey """ return self._do_upload(library_id, file_local_path=file_local_path, folder_id=folder_id, file_type=file_type, dbkey=dbkey)
[docs] def upload_file_from_server(self, library_id, server_dir, folder_id=None, file_type='auto', dbkey='?', link_data_only=None, roles="", preserve_dirs=False, tag_using_filenames=True): """ Upload all files in the specified subdirectory of the Galaxy library import directory to a library. .. note:: For this method to work, the Galaxy instance must have the ``library_import_dir`` option configured in the ``config/galaxy.ini`` configuration file. :type library_id: str :param library_id: id of the library where to place the uploaded file :type server_dir: str :param server_dir: relative path of the subdirectory of ``library_import_dir`` to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded :type folder_id: str :param folder_id: id of the folder where to place the uploaded files. If not provided, the root folder will be used :type file_type: str :param file_type: Galaxy file format name :type dbkey: str :param dbkey: Dbkey :type link_data_only: str :param link_data_only: either 'copy_files' (default) or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files :type roles: str :param roles: ??? :type preserve_dirs: bool :param preserve_dirs: Indicate whether to preserve the directory structure when importing dir :type tag_using_filenames: bool :param tag_using_filenames: Indicate whether to generate dataset tags from filenames """ return self._do_upload(library_id, server_dir=server_dir, folder_id=folder_id, file_type=file_type, dbkey=dbkey, link_data_only=link_data_only, roles=roles, preserve_dirs=preserve_dirs, tag_using_filenames=tag_using_filenames)
[docs] def upload_from_galaxy_filesystem(self, library_id, filesystem_paths, folder_id=None, file_type="auto", dbkey="?", link_data_only=None, roles="", preserve_dirs=False, tag_using_filenames=True): """ Upload a set of files already present on the filesystem of the Galaxy server to a library. .. note:: For this method to work, the Galaxy instance must have the ``allow_path_paste`` (``allow_library_path_paste`` in Galaxy ``release_17.05`` and earlier) option set to ``True`` in the ``config/galaxy.ini`` configuration file. :type library_id: str :param library_id: id of the library where to place the uploaded file :type filesystem_paths: str :param filesystem_paths: file paths on the Galaxy server to upload to the library, one file per line :type folder_id: str :param folder_id: id of the folder where to place the uploaded files. If not provided, the root folder will be used :type file_type: str :param file_type: Galaxy file format name :type dbkey: str :param dbkey: Dbkey :type link_data_only: str :param link_data_only: either 'copy_files' (default) or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files :type roles: str :param roles: ??? :type preserve_dirs: bool :param preserve_dirs: Indicate whether to preserve the directory structure when importing dir :type tag_using_filenames: bool :param tag_using_filenames: Indicate whether to generate dataset tags from filenames """ return self._do_upload(library_id, filesystem_paths=filesystem_paths, folder_id=folder_id, file_type=file_type, dbkey=dbkey, link_data_only=link_data_only, roles=roles, preserve_dirs=preserve_dirs, tag_using_filenames=tag_using_filenames)
[docs] def copy_from_dataset(self, library_id, dataset_id, folder_id=None, message=''): """ Copy a Galaxy dataset into a library. :type library_id: str :param library_id: id of the library where to place the uploaded file :type dataset_id: str :param dataset_id: id of the dataset to copy from :type folder_id: str :param folder_id: id of the folder where to place the uploaded files. If not provided, the root folder will be used :type message: str :param message: message for copying action """ if folder_id is None: folder_id = self._get_root_folder_id(library_id) payload = {} payload['folder_id'] = folder_id payload['create_type'] = 'file' payload['from_hda_id'] = dataset_id payload['ldda_message'] = message return self._post(payload, id=library_id, contents=True)
[docs] def get_library_permissions(self, library_id): """ Get the permessions for a library. :type library_id: str :param library_id: id of the library :rtype: dict :return: dictionary with all applicable permissions' values """ url = '/'.join([self.gi._make_url(self, library_id), 'permissions']) return self._get(url=url)
[docs] def set_library_permissions(self, library_id, access_in=None, modify_in=None, add_in=None, manage_in=None): """ Set the permissions for a library. Note: it will override all security for this library even if you leave out a permission type. :type library_id: str :param library_id: id of the library :type access_in: list :param access_in: list of role ids :type modify_in: list :param modify_in: list of role ids :type add_in: list :param add_in: list of role ids :type manage_in: list :param manage_in: list of role ids """ payload = {} if access_in: payload['LIBRARY_ACCESS_in'] = access_in if modify_in: payload['LIBRARY_MODIFY_in'] = modify_in if add_in: payload['LIBRARY_ADD_in'] = add_in if manage_in: payload['LIBRARY_MANAGE_in'] = manage_in url = '/'.join([self.gi._make_url(self, library_id), 'permissions']) return self._post(payload, url=url)