/usr/lib/python3/dist-packages/bioblend/galaxy/libraries/__init__.py is in python3-bioblend 0.7.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 | """
Contains possible interactions with the Galaxy Data Libraries
"""
from bioblend.galaxy.client import Client
from bioblend.util import attach_file
class LibraryClient(Client):
def __init__(self, galaxy_instance):
self.module = 'libraries'
super(LibraryClient, self).__init__(galaxy_instance)
def create_library(self, name, description=None, synopsis=None):
"""
Create a data library with the properties defined in the arguments.
Return a list of JSON dicts, looking like so::
: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:
{"id": "f740ab636b360a70",
"name": "Library from bioblend",
"url": "/api/libraries/f740ab636b360a70"}
"""
payload = {'name': name}
if description:
payload['description'] = description
if synopsis:
payload['synopsis'] = synopsis
return Client._post(self, payload)
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.
"""
payload = {}
return Client._delete(self, payload, 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 Client._get(self, url=url)
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 Client._delete(self, url=url, payload={'purged': purged})
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)
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']
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 Client._post(self, payload, id=library_id, contents=True)
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
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 = Client._get(self, 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
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 Client._get(self, 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'
# 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 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)
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)
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)
def upload_file_from_server(self, library_id, server_dir, folder_id=None,
file_type='auto', dbkey='?', link_data_only=None,
roles=""):
"""
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: ???
"""
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)
def upload_from_galaxy_filesystem(self, library_id, filesystem_paths, folder_id=None,
file_type="auto", dbkey="?", link_data_only=None,
roles=""):
"""
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_library_path_paste`` 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: ???
"""
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)
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 Client._post(self, payload, id=library_id, contents=True)
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 Client._get(self, url=url)
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 Client._post(self, payload, url=url)
|