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restyle docstring for consistency

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This commit is contained in:
Martin Cech
2019-08-29 13:30:27 -04:00
parent 2d6cb9c5e9
commit ef187ad37e
4 changed files with 61 additions and 51 deletions
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lib/galaxy/webapps/galaxy/api/folder_contents.py
+4 -3
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@@ -251,8 +251,9 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
@expose_api
def create(self, trans, encoded_folder_id, payload, **kwd):
"""
* POST /api/folders/{encoded_id}/contents
create a new library file from an HDA
POST /api/folders/{encoded_id}/contents
Create a new library file from an HDA.
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
:type encoded_folder_id: an encoded id string
@@ -299,7 +300,7 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
def __decode_library_content_id(self, trans, encoded_folder_id):
"""
Identifies whether the id provided is properly encoded
Identify whether the id provided is properly encoded
LibraryFolder.
:param encoded_folder_id: encoded id of Galaxy LibraryFolder
lib/galaxy/webapps/galaxy/api/folders.py
+21 -13
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@@ -24,7 +24,8 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def index(self, trans, **kwd):
"""
*GET /api/folders/
GET /api/folders/
This would normally display a list of folders. However, that would
be across multiple libraries, so it's not implemented.
"""
@@ -33,8 +34,7 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def show(self, trans, id, **kwd):
"""
show( self, trans, id, **kwd )
*GET /api/folders/{encoded_folder_id}
GET /api/folders/{encoded_folder_id}
Displays information about a folder.
@@ -52,8 +52,9 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def create(self, trans, encoded_parent_folder_id, payload=None, **kwd):
"""
*POST /api/folders/{encoded_parent_folder_id}
Create a new folder object underneath the one specified in the parameters.
POST /api/folders/{encoded_parent_folder_id}
Create a new folder object underneath the one specified in the parameters.
:param encoded_parent_folder_id: (required) the parent folder's id
:type encoded_parent_folder_id: an encoded id string (should be prefixed by 'F')
@@ -81,7 +82,7 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def get_permissions(self, trans, encoded_folder_id, **kwd):
"""
* GET /api/folders/{id}/permissions
GET /api/folders/{id}/permissions
Load all permissions for the given folder id and return it.
@@ -132,8 +133,9 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def set_permissions(self, trans, encoded_folder_id, payload=None, **kwd):
"""
*POST /api/folders/{encoded_folder_id}/permissions
Set permissions of the given folder to the given role ids.
POST /api/folders/{encoded_folder_id}/permissions
Set permissions of the given folder to the given role ids.
:param encoded_folder_id: the encoded id of the folder to set the permissions of
:type encoded_folder_id: an encoded id string
@@ -224,9 +226,10 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def delete(self, trans, encoded_folder_id, **kwd):
"""
delete( self, trans, encoded_folder_id, **kwd )
* DELETE /api/folders/{encoded_folder_id}
marks the folder with the given ``encoded_folder_id`` as `deleted` (or removes the `deleted` mark if the `undelete` param is true)
DELETE /api/folders/{encoded_folder_id}
Mark the folder with the given ``encoded_folder_id`` as `deleted`
(or remove the `deleted` mark if the `undelete` param is true).
.. note:: Currently, only admin users can un/delete folders.
@@ -249,19 +252,24 @@ class FoldersController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIte
@expose_api
def update(self, trans, encoded_folder_id, payload=None, **kwd):
"""
* PATCH /api/folders/{encoded_folder_id}
Update the folder defined by an ``encoded_folder_id`` with the data in the payload.
PATCH /api/folders/{encoded_folder_id}
Update the folder defined by an ``encoded_folder_id``
with the data in the payload.
.. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
:param id: the encoded id of the folder
:type id: an encoded id string
:param payload: (required) dictionary structure containing::
'name': new folder's name, cannot be empty
'description': new folder's description
:type payload: dict
:returns: detailed folder information
:rtype: dict
:raises: RequestParameterMissingException
"""
decoded_folder_id = self.folder_manager.cut_and_decode(trans, encoded_folder_id)
lib/galaxy/webapps/galaxy/api/library_contents.py
+18 -18
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@@ -43,12 +43,12 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def index(self, trans, library_id, **kwd):
"""
index( self, trans, library_id, **kwd )
* GET /api/libraries/{library_id}/contents:
Returns a list of library files and folders.
GET /api/libraries/{library_id}/contents:
.. note:: May be slow! Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a non-recursive solution
Return a list of library files and folders.
.. note:: This endpoint is slow for large libraries. Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a faster non-recursive solution
:param library_id: the encoded id of the library
:type library_id: str
@@ -123,9 +123,9 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def show(self, trans, id, library_id, **kwd):
"""
show( self, trans, id, library_id, **kwd )
* GET /api/libraries/{library_id}/contents/{id}
Returns information about library file or folder.
GET /api/libraries/{library_id}/contents/{id}
Returns information about library file or folder.
:param id: the encoded id of the library item to return
:type id: str
@@ -160,9 +160,9 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def create(self, trans, library_id, payload, **kwd):
"""
create( self, trans, library_id, payload, **kwd )
* POST /api/libraries/{library_id}/contents:
create a new library file or folder
POST /api/libraries/{library_id}/contents:
Create a new library file or folder.
To copy an HDA into a library send ``create_type`` of 'file' and
the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_message``).
@@ -374,9 +374,10 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def update(self, trans, id, library_id, payload, **kwd):
"""
update( self, trans, id, library_id, payload, **kwd )
* PUT /api/libraries/{library_id}/contents/{id}
create a ImplicitlyConvertedDatasetAssociation
PUT /api/libraries/{library_id}/contents/{id}
Create an ImplicitlyConvertedDatasetAssociation.
.. seealso:: :class:`galaxy.model.ImplicitlyConvertedDatasetAssociation`
:type id: str
@@ -412,9 +413,9 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def delete(self, trans, library_id, id, **kwd):
"""
delete( self, trans, library_id, id, **kwd )
* DELETE /api/libraries/{library_id}/contents/{id}
delete the LibraryDataset with the given ``id``
DELETE /api/libraries/{library_id}/contents/{id}
Delete the LibraryDataset with the given ``id``.
:type id: str
:param id: the encoded id of the library dataset to delete
@@ -430,7 +431,6 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
* deleted: if the library dataset was marked as deleted,
* purged: if the library dataset was purged
"""
# a request body is optional here
purge = False
if kwd.get('payload', None):
purge = util.string_as_bool(kwd['payload'].get('purge', False))
lib/galaxy/webapps/galaxy/api/library_datasets.py
+18 -17
View File
@@ -49,9 +49,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api_anonymous
def show(self, trans, id, **kwd):
"""
Show the details of a library dataset.
GET /api/libraries/datasets/{encoded_dataset_id}
* GET /api/libraries/datasets/{encoded_dataset_id}
Show the details of a library dataset.
:param id: the encoded id of the library dataset to query
:type id: an encoded id string
@@ -66,9 +66,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api_anonymous
def show_version(self, trans, encoded_dataset_id, encoded_ldda_id, **kwd):
"""
Display a specific version of a library dataset (i.e. ldda).
GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
* GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
Display a specific version of a library dataset (i.e. ldda).
:param encoded_dataset_id: the encoded id of the related library dataset
:type encoded_dataset_id: an encoded id string
@@ -97,9 +97,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api
def show_roles(self, trans, encoded_dataset_id, **kwd):
"""
Display information about current or available roles for a given dataset permission.
GET /api/libraries/datasets/{encoded_dataset_id}/permissions
* GET /api/libraries/datasets/{encoded_dataset_id}/permissions
Display information about current or available roles for a given dataset permission.
:param encoded_dataset_id: the encoded id of the dataset to query
:type encoded_dataset_id: an encoded id string
@@ -159,9 +159,10 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api
def update(self, trans, encoded_dataset_id, payload=None, **kwd):
"""Update the given library dataset (the latest linked ldda).
"""
PATCH /api/libraries/datasets/{encoded_dataset_id}
* PATCH /api/libraries/datasets/{encoded_dataset_id}
Update the given library dataset (the latest linked ldda).
:param encoded_dataset_id: the encoded id of the library dataset to update
:type encoded_dataset_id: an encoded id string
@@ -187,9 +188,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api
def update_permissions(self, trans, encoded_dataset_id, payload=None, **kwd):
"""
Set permissions of the given library dataset to the given role ids.
POST /api/libraries/datasets/{encoded_dataset_id}/permissions
*POST /api/libraries/datasets/{encoded_dataset_id}/permissions
Set permissions of the given library dataset to the given role ids.
:param encoded_dataset_id: the encoded id of the dataset to update permissions of
:type encoded_dataset_id: an encoded id string
@@ -294,9 +295,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api
def delete(self, trans, encoded_dataset_id, **kwd):
"""
Mark the dataset deleted or undeleted.
DELETE /api/libraries/datasets/{encoded_dataset_id}
* DELETE /api/libraries/datasets/{encoded_dataset_id}
Mark the dataset deleted or undeleted.
:param encoded_dataset_id: the encoded id of the dataset to change
:type encoded_dataset_id: an encoded id string
@@ -332,9 +333,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
@expose_api
def load(self, trans, payload=None, **kwd):
"""
Load dataset(s) from the given source into the library.
POST /api/libraries/datasets
* POST /api/libraries/datasets
Load dataset(s) from the given source into the library.
:param payload: dictionary structure containing:
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
@@ -497,10 +498,10 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
# TODO convert to expose_api
def download(self, trans, format, **kwd):
"""
Download requested datasets (identified by encoded IDs) in requested format.
GET /api/libraries/datasets/download/{format}
POST /api/libraries/datasets/download/{format}
* GET /api/libraries/datasets/download/{format}
* POST /api/libraries/datasets/download/{format}
Download requested datasets (identified by encoded IDs) in requested format.
example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ld_ids%255B%255D=a0d84b45643a2678&ld_ids%255B%255D=fe38c84dcd46c828``