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https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
refactor the rest of the module to use new manager
This commit is contained in:
Martin Cech
@@ -85,23 +85,22 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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@expose_api_anonymous
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def show_version(self, trans, encoded_dataset_id, encoded_ldda_id, **kwd):
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"""
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show_version( self, trans, encoded_dataset_id, encoded_ldda_id, **kwd ):
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* GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
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Displays information about specific version of the library_dataset (i.e. ldda).
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Display a specific version of a library dataset (i.e. ldda).
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:param encoded_dataset_id: the encoded id of the dataset to query
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* GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
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:param encoded_dataset_id: the encoded id of the related library dataset
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:type encoded_dataset_id: an encoded id string
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:param encoded_ldda_id: the encoded id of the ldda to query
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:type encoded_ldda_id: an encoded id string
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:rtype: dictionary
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:returns: dict of ldda's details
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:rtype: dictionary
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:raises: ObjectNotFound
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"""
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try:
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library_dataset = self.get_library_dataset(trans, id=encoded_dataset_id, check_ownership=False, check_accessible=True)
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except Exception:
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raise exceptions.ObjectNotFound('Requested library_dataset was not found.')
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library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
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try:
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ldda = self.get_library_dataset_dataset_association(trans, id=encoded_ldda_id, check_ownership=False, check_accessible=False)
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@@ -117,10 +116,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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@expose_api
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def show_roles(self, trans, encoded_dataset_id, **kwd):
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"""
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show_roles( self, trans, id, **kwd ):
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Display information about current or available roles for a given dataset permission.
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* GET /api/libraries/datasets/{encoded_dataset_id}/permissions
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Displays information about current or available roles
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for a given dataset permission.
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:param encoded_dataset_id: the encoded id of the dataset to query
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:type encoded_dataset_id: an encoded id string
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@@ -128,16 +126,14 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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:param scope: either 'current' or 'available'
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:type scope: string
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:returns: either dict of current roles for all permission types
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or dict of available roles to choose from (is the same for any permission type)
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:rtype: dictionary
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:returns: either dict of current roles for all permission types or
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dict of available roles to choose from (is the same for any permission type)
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"""
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:raises: InsufficientPermissionsException
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"""
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current_user_roles = trans.get_current_user_roles()
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try:
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library_dataset = self.get_library_dataset(trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False)
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except Exception as e:
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raise exceptions.ObjectNotFound('Requested dataset was not found.' + str(e))
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library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
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dataset = library_dataset.library_dataset_dataset_association.dataset
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# User has to have manage permissions permission in order to see the roles.
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@@ -202,8 +198,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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@expose_api
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def update_permissions(self, trans, encoded_dataset_id, payload=None, **kwd):
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"""
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Set permissions of the given library dataset to the given role ids.
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*POST /api/libraries/datasets/{encoded_dataset_id}/permissions
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Set permissions of the given dataset to the given role ids.
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:param encoded_dataset_id: the encoded id of the dataset to update permissions of
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:type encoded_dataset_id: an encoded id string
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@@ -218,6 +215,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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:param modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item
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:type modify_ids[]: string or list
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:type: dictionary
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:returns: dict of current roles for all available permission types
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:rtype: dictionary
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@@ -226,10 +224,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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"""
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if payload:
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kwd.update(payload)
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try:
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library_dataset = self.get_library_dataset(trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False)
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except Exception as e:
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raise exceptions.ObjectNotFound('Requested dataset was not found.' + str(e))
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library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
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dataset = library_dataset.library_dataset_dataset_association.dataset
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current_user_roles = trans.get_current_user_roles()
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can_manage = trans.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin()
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@@ -330,62 +325,59 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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@expose_api
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def delete(self, trans, encoded_dataset_id, **kwd):
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"""
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delete( self, trans, encoded_dataset_id, **kwd ):
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Mark the dataset deleted or undeleted.
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* DELETE /api/libraries/datasets/{encoded_dataset_id}
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Marks the dataset deleted or undeleted based on the value
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of the undelete flag.
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If the flag is not present it is considered False and the
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item is marked deleted.
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:param encoded_dataset_id: the encoded id of the dataset to change
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:type encoded_dataset_id: an encoded id string
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:param undelete: flag whether to undeleted instead of deleting
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:type undelete: bool
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:returns: dict containing information about the dataset
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:rtype: dictionary
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"""
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undelete = util.string_as_bool(kwd.get('undelete', False))
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try:
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dataset = self.get_library_dataset(trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False)
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except Exception as e:
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raise exceptions.ObjectNotFound('Requested dataset was not found.' + str(e))
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library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
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current_user_roles = trans.get_current_user_roles()
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allowed = trans.app.security_agent.can_modify_library_item(current_user_roles, dataset)
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allowed = trans.app.security_agent.can_modify_library_item(current_user_roles, library_dataset)
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if (not allowed) and (not trans.user_is_admin()):
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raise exceptions.InsufficientPermissionsException('You do not have proper permissions to delete this dataset.')
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if undelete:
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dataset.deleted = False
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library_dataset.deleted = False
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else:
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dataset.deleted = True
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library_dataset.deleted = True
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trans.sa_session.add(dataset)
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trans.sa_session.add(library_dataset)
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trans.sa_session.flush()
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rval = trans.security.encode_all_ids(dataset.to_dict())
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nice_size = util.nice_size(int(dataset.library_dataset_dataset_association.get_size()))
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rval = trans.security.encode_all_ids(library_dataset.to_dict())
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nice_size = util.nice_size(int(library_dataset.library_dataset_dataset_association.get_size()))
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rval['file_size'] = nice_size
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rval['update_time'] = dataset.update_time.strftime("%Y-%m-%d %I:%M %p")
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rval['deleted'] = dataset.deleted
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rval['update_time'] = library_dataset.update_time.strftime("%Y-%m-%d %I:%M %p")
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rval['deleted'] = library_dataset.deleted
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rval['folder_id'] = 'F' + rval['folder_id']
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return rval
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@expose_api
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def load(self, trans, payload=None, **kwd):
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"""
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Load dataset(s) from the given source into the library.
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* POST /api/libraries/datasets
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Load dataset from the given source into the library.
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Source can be:
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user directory - root folder specified in galaxy.ini as "$user_library_import_dir"
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example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here}
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the folder with the user login has to be created beforehand
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(admin)import directory - root folder specified in galaxy ini as "$library_import_dir"
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example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}
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(admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini
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:param payload: dictionary structure containing:
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:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
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:type encoded_folder_id: an encoded id string
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:param source: source the datasets should be loaded from
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Source can be:
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user directory - root folder specified in galaxy.ini as "$user_library_import_dir"
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example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here}
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the folder with the user login has to be created beforehand
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(admin)import directory - root folder specified in galaxy ini as "$library_import_dir"
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example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}
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(admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini
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:type source: str
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:param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy
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while linking is set to True all symlinks will be resolved _once_
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@@ -400,8 +392,10 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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:param tag_using_filenames: flag whether to generate dataset tags from filenames
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:type tag_using_filenames: bool
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:type dictionary
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:returns: dict containing information about the created upload job
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:rtype: dictionary
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:raises: RequestParameterMissingException, AdminRequiredException, ConfigDoesNotAllowException, RequestParameterInvalidException
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InsufficientPermissionsException, ObjectNotFound
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"""
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@@ -508,10 +502,10 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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# TODO convert to expose_api
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def download(self, trans, format, **kwd):
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"""
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download( self, trans, format, **kwd )
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Download requested datasets (identified by encoded IDs) in requested format.
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* GET /api/libraries/datasets/download/{format}
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* POST /api/libraries/datasets/download/{format}
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Downloads requested datasets (identified by encoded IDs) in requested format.
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example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ld_ids%255B%255D=a0d84b45643a2678&ld_ids%255B%255D=fe38c84dcd46c828``
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@@ -524,8 +518,8 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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:param folder_ids[]: an array of encoded folder ids
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:type folder_ids[]: an array
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:rtype: file
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:returns: either archive with the requested datasets packed inside or a single uncompressed dataset
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:rtype: file
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:raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound
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"""
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@@ -634,7 +628,8 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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zpath = os.path.split(path)[-1] # comes as base_name/fname
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outfname, zpathext = os.path.splitext(zpath)
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if is_composite: # need to add all the components from the extra_files_path to the zip
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if is_composite:
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# need to add all the components from the extra_files_path to the zip
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if zpathext == '':
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zpath = '%s.html' % zpath # fake the real nature of the html file
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try:
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@@ -669,10 +664,9 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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log.exception("Requested dataset %s does not exist on the host.", fpath)
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raise exceptions.ObjectNotFound("Requested dataset not found.")
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except Exception as e:
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log.exception("Unable to add %s to temporary library download archive %s", fname, outfname)
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log.exception("Unable to add %s to temporary library download archive %s" % (fname, outfname))
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raise exceptions.InternalServerError("Unable to add dataset to temporary library download archive . " + str(e))
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else: # simple case
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else:
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try:
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if format == 'zip':
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archive.add(ldda.dataset.file_name, path)
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@@ -735,8 +729,8 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
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:type: list
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"""
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path_to_root = []
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# We are almost in root
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if folder.parent_id is None:
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# We are almost in root
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path_to_root.append(('F' + trans.security.encode_id(folder.id), folder.name))
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else:
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# We add the current folder and traverse up one folder.
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