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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
galaxy.webapps.galaxy.api package¶
Submodules¶
galaxy.webapps.galaxy.api.annotations module¶
API operations on annotations.
-
class
galaxy.webapps.galaxy.api.annotations.
BaseAnnotationsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesStoredWorkflowMixin
,galaxy.model.item_attrs.UsesAnnotations
-
class
galaxy.webapps.galaxy.api.annotations.
HistoryAnnotationsController
(app)[source]¶ Bases:
galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController
-
controller_name
= 'history_annotations'¶
-
tagged_item_id
= 'history_id'¶
-
-
class
galaxy.webapps.galaxy.api.annotations.
HistoryContentAnnotationsController
(app)[source]¶ Bases:
galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController
-
controller_name
= 'history_content_annotations'¶
-
tagged_item_id
= 'history_content_id'¶
-
-
class
galaxy.webapps.galaxy.api.annotations.
WorkflowAnnotationsController
(app)[source]¶ Bases:
galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController
-
controller_name
= 'workflow_annotations'¶
-
tagged_item_id
= 'workflow_id'¶
-
galaxy.webapps.galaxy.api.authenticate module¶
API key retrieval through BaseAuth Sample usage:
curl –user zipzap@foo.com:password http://localhost:8080/api/authenticate/baseauth
Returns:
- {
- “api_key”: “baa4d6e3a156d3033f05736255f195f9”
}
galaxy.webapps.galaxy.api.cloud module¶
API operations on Cloud-based storages, such as Amazon Simple Storage Service (S3).
-
class
galaxy.webapps.galaxy.api.cloud.
CloudController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTfull controller for interaction with Amazon S3.
-
index
(trans, *args, **kwargs)[source]¶ - GET /api/cloud/storage
- Lists cloud-based buckets (e.g., S3 bucket, Azure blob) user has defined.
Parameters: - trans –
- kwargs –
Returns: A list of cloud-based buckets user has defined.
-
get
(trans, *args, **kwargs)[source]¶ - POST /api/cloud/storage/get
- gets given objects from a given cloud-based bucket to a Galaxy history.
Parameters: - trans (galaxy.web.framework.webapp.GalaxyWebTransaction) – Galaxy web transaction
- payload (dict) –
A dictionary structure containing the following keys: * history_id: the (encoded) id of history to which the object should be received to. * bucket: the name of a bucket from which data should be fetched from (e.g., a bucket name on AWS S3). * objects: a list of the names of objects to be fetched. * authz_id: the encoded ID of CloudAuthz to be used for authorizing access to the resource
provider. You may get a list of the defined authorizations via /api/cloud/authz. Also, you can use /api/cloud/authz/create to define a new authorization.- input_args [Optional; default value is an empty dict] a dictionary containing the following keys:
- ** dbkey: [Optional; default value: is ?]
- Sets the genome (e.g., hg19) of the objects being fetched to Galaxy.
- ** file_type: [Optional; default value is auto]
- Sets the Galaxy datatype (e.g., bam) for the objects being fetched to Galaxy. See the following link for a complete list of Galaxy data types: https://galaxyproject.org/learn/datatypes/
- ** space_to_tab: [Optional; default value is False]
- A boolean value (“true” or “false”) that sets if spaces should be converted to tab in the objects being fetched to Galaxy. Applicable only if to_posix_lines is True
- ** to_posix_lines: [Optional; default value is Yes]
- A boolean value (“true” or “false”); if “Yes”, converts universal line endings to POSIX line endings. Set to “False” if you upload a gzip, bz2 or zip archive containing a binary file.
- input_args [Optional; default value is an empty dict] a dictionary containing the following keys:
- kwargs –
Return type: dictionary
Returns: a dictionary containing a summary view of the datasets copied from the given cloud-based storage.
-
send
(trans, *args, **kwargs)[source]¶ - POST /api/cloud/storage/send
- Sends given dataset(s) in a given history to a given cloud-based bucket. Each dataset is named using the label assigned to the dataset in the given history (see HistoryDatasetAssociation.name). If no dataset ID is given, this API sends all the datasets belonging to a given history to a given cloud-based bucket.
Parameters: - trans (galaxy.web.framework.webapp.GalaxyWebTransaction) – Galaxy web transaction
- payload (dictionary) –
A dictionary structure containing the following keys: * history_id the (encoded) id of history from which the object should be downloaed. * bucket: the name of a bucket to which data should be sent (e.g., a bucket name on AWS S3). * authz_id: the encoded ID of CloudAuthz to be used for authorizing access to the resource
provider. You may get a list of the defined authorizations via /api/cloud/authz. Also, you can use /api/cloud/authz/create to define a new authorization.- dataset_ids: [Optional; default: None]
- A list of encoded dataset IDs belonging to the specified history that should be sent to the given bucket. If not provided, Galaxy sends all the datasets belonging the specified history.
- overwrite_existing: [Optional; default: False]
- A boolean value. If set to “True”, and an object with same name of the dataset to be sent already exist in the bucket, Galaxy replaces the existing object with the dataset to be sent. If set to “False”, Galaxy appends datetime to the dataset name to prevent overwriting an existing object.
- kwargs –
Return type: dictionary
Returns: Information about the (un)successfully submitted dataset send jobs, containing the following keys:
- bucket_name: The name of bucket to which the listed datasets are queued
to be sent.
sent_dataset_labels: A list of JSON objects with the following key-value pair: ** object: The name of object is queued to be created. ** job_id: The id of the queued send job.
- failed_dataset_labels: A list of JSON objects with the following key-value pair
representing the datasets Galaxy failed to create (and queue) send job for:
** object: The name of object is queued to be created. ** error: A descriptive error message.
-
galaxy.webapps.galaxy.api.configuration module¶
API operations allowing clients to determine Galaxy instance’s capabilities and configuration settings.
-
class
galaxy.webapps.galaxy.api.configuration.
ConfigurationController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
whoami
(trans, *args, **kwargs)[source]¶ GET /api/whoami Return information about the current authenticated user.
Returns: dictionary with user information Return type: dict
-
index
(trans, *args, **kwargs)[source]¶ GET /api/configuration Return an object containing exposable configuration settings.
Note: a more complete list is returned if the user is an admin.
-
version
(trans, *args, **kwargs)[source]¶ GET /api/version Return a description of the major version of Galaxy (e.g. 15.03).
Return type: dict Returns: dictionary with major version keyed on ‘version_major’
-
get_config_dict
(trans, return_admin=False, view=None, keys=None, default_view='all')[source]¶ Return a dictionary with (a subset of) current Galaxy settings.
If return_admin also include a subset of more sensitive keys. Pass in view (String) and comma seperated list of keys to control which configuration settings are returned.
-
galaxy.webapps.galaxy.api.dataset_collections module¶
-
class
galaxy.webapps.galaxy.api.dataset_collections.
DatasetCollectionsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixinItems
-
create
(trans, *args, **kwargs)[source]¶ - POST /api/dataset_collections:
- create a new dataset collection instance.
Parameters: payload (dict) – (optional) dictionary structure containing: * collection_type: dataset colltion type to create. * instance_type: Instance type - ‘history’ or ‘library’. * name: the new dataset collections’s name * datasets: object describing datasets for collection Return type: dict Returns: element view of new dataset collection
-
galaxy.webapps.galaxy.api.datasets module¶
API operations on the contents of a history dataset.
-
class
galaxy.webapps.galaxy.api.datasets.
DatasetsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesVisualizationMixin
-
show
(trans, *args, **kwargs)[source]¶ GET /api/datasets/{encoded_dataset_id} Displays information about and/or content of a dataset.
-
update_permissions
(trans, *args, **kwargs)[source]¶ PUT /api/datasets/{encoded_dataset_id}/permissions Updates permissions of a dataset.
Return type: dict Returns: dictionary containing new permissions
-
extra_files
(trans, *args, **kwargs)[source]¶ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/extra_files Generate list of extra files.
-
display
(trans, *args, **kwargs)[source]¶ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays history content (dataset).
The query parameter ‘raw’ should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display (the defult if raw is unspecified or explicitly false.
-
converted
(self, trans, dataset_id, ext, **kwargs)[source]¶ - GET /api/datasets/{dataset_id}/converted/{ext}
- return information about datasets made by converting this dataset to a new format
Parameters: If there is no existing converted dataset for the format in ext, one will be created.
If ext is None, a dictionary will be returned of the form { <converted extension> : <converted id>, … } containing all the existing converted datasets.
- ..note: view and keys are also available to control the serialization
- of individual datasets. They have no effect when ext is None.
Return type: dict Returns: dictionary containing detailed HDA information or (if ext is None) an extension->dataset_id map
-
galaxy.webapps.galaxy.api.datatypes module¶
API operations allowing clients to determine datatype supported by Galaxy.
-
class
galaxy.webapps.galaxy.api.datatypes.
DatatypesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
index
(trans, *args, **kwargs)[source]¶ GET /api/datatypes Return an object containing upload datatypes.
-
galaxy.webapps.galaxy.api.extended_metadata module¶
API operations on annotations.
-
class
galaxy.webapps.galaxy.api.extended_metadata.
BaseExtendedMetadataController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesExtendedMetadataMixin
,galaxy.web.base.controller.UsesLibraryMixinItems
,galaxy.web.base.controller.UsesStoredWorkflowMixin
-
class
galaxy.webapps.galaxy.api.extended_metadata.
LibraryDatasetExtendMetadataController
(app)[source]¶ Bases:
galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController
-
controller_name
= 'library_dataset_extended_metadata'¶
-
exmeta_item_id
= 'library_content_id'¶
-
-
class
galaxy.webapps.galaxy.api.extended_metadata.
HistoryDatasetExtendMetadataController
(app)[source]¶ Bases:
galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController
-
controller_name
= 'history_dataset_extended_metadata'¶
-
exmeta_item_id
= 'history_content_id'¶
-
galaxy.webapps.galaxy.api.folder_contents module¶
API operations on the contents of a library folder.
-
class
galaxy.webapps.galaxy.api.folder_contents.
FolderContentsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixin
,galaxy.web.base.controller.UsesLibraryMixinItems
Class controls retrieval, creation and updating of folder contents.
-
index
(trans, *args, **kwargs)[source]¶ GET /api/folders/{encoded_folder_id}/contents
Displays a collection (list) of a folder’s contents (files and folders). Encoded folder ID is prepended with ‘F’ if it is a folder as opposed to a data set which does not have it. Full path is provided in response as a separate object providing data for breadcrumb path building.
Parameters: - folder_id (encoded string) – encoded ID of the folder which contents should be library_dataset_dict
- kwd (dict) – keyword dictionary with other params
Returns: dictionary containing all items and metadata
Type: dict
Raises: MalformedId, InconsistentDatabase, ObjectNotFound, InternalServerError
-
build_path
(trans, folder)[source]¶ Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes.
Parameters: - folder – current folder for navigating up
- type – Galaxy LibraryFolder
Returns: list consisting of full path to the library
Type: list
-
create
(trans, *args, **kwargs)[source]¶ - POST /api/folders/{encoded_id}/contents
- create a new library file from an HDA
Parameters: - encoded_folder_id (an encoded id string) – the encoded id of the folder to import dataset(s) to
- payload (dict) – dictionary structure containing: :param from_hda_id: (optional) the id of an accessible HDA to copy into the library :type from_hda_id: encoded id :param from_hdca_id: (optional) the id of an accessible HDCA to copy into the library :type from_hdca_id: encoded id :param ldda_message: (optional) the new message attribute of the LDDA created :type ldda_message: str :param extended_metadata: (optional) dub-dictionary containing any extended metadata to associate with the item :type extended_metadata: dict
Returns: a dictionary describing the new item if
from_hda_id
is supplied or a list of such dictionaries describing the new items iffrom_hdca_id
is supplied.Return type: Raises: ObjectAttributeInvalidException, InsufficientPermissionsException, ItemAccessibilityException, InternalServerError
-
galaxy.webapps.galaxy.api.folders module¶
API operations on library folders.
-
class
galaxy.webapps.galaxy.api.folders.
FoldersController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixin
,galaxy.web.base.controller.UsesLibraryMixinItems
-
index
(trans, *args, **kwargs)[source]¶ *GET /api/folders/ This would normally display a list of folders. However, that would be across multiple libraries, so it’s not implemented.
-
show
(self, trans, id, **kwd)[source]¶ *GET /api/folders/{encoded_folder_id}
Displays information about a folder.
Parameters: id (an encoded id string (has to be prefixed by 'F')) – the folder’s encoded id (required) Returns: dictionary including details of the folder Return type: dict
-
create
(trans, *args, **kwargs)[source]¶ - *POST /api/folders/{encoded_parent_folder_id}
- Create a new folder object underneath the one specified in the parameters.
Parameters: - encoded_parent_folder_id (an encoded id string (should be prefixed by 'F')) – (required) the parent folder’s id
- payload – dictionary structure containing: :param name: (required) the name of the new folder :type name: str :param description: the description of the new folder :type description: str
:type dictionary :returns: information about newly created folder, notably including ID :rtype: dictionary :raises: RequestParameterMissingException
-
get_permissions
(trans, *args, **kwargs)[source]¶ - GET /api/folders/{id}/permissions
Load all permissions for the given folder id and return it.
Parameters: - encoded_folder_id (an encoded id string) – the encoded id of the folder
- scope (string) – either ‘current’ or ‘available’
Returns: dictionary with all applicable permissions’ values
Return type: dictionary
Raises: InsufficientPermissionsException
-
set_permissions
(trans, *args, **kwargs)[source]¶ - *POST /api/folders/{encoded_folder_id}/permissions
- Set permissions of the given folder to the given role ids.
Parameters: - encoded_folder_id (an encoded id string) – the encoded id of the folder to set the permissions of
- payload – dictionary structure containing: :param action: (required) describes what action should be performed :type action: string :param add_ids[]: list of Role.id defining roles that should have add item permission on the folder :type add_ids[]: string or list :param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder :type manage_ids[]: string or list :param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder :type modify_ids[]: string or list
:type dictionary :returns: dict of current roles for all available permission types. :rtype: dictionary :raises: RequestParameterInvalidException, InsufficientPermissionsException, RequestParameterMissingException
-
delete
(self, trans, encoded_folder_id, **kwd)[source]¶ - 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)
Note
Currently, only admin users can un/delete folders.
Parameters: - encoded_folder_id (an encoded id string) – the encoded id of the folder to un/delete
- undelete (bool) – (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
Returns: detailed folder information
Return type: dictionary
-
update
(trans, *args, **kwargs)[source]¶ - 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
-
galaxy.webapps.galaxy.api.forms module¶
API operations on FormDefinition objects.
-
class
galaxy.webapps.galaxy.api.forms.
FormDefinitionAPIController
(app)[source]¶
galaxy.webapps.galaxy.api.genomes module¶
-
class
galaxy.webapps.galaxy.api.genomes.
GenomesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTful controller for interactions with genome data.
galaxy.webapps.galaxy.api.group_roles module¶
API operations on Group objects.
-
class
galaxy.webapps.galaxy.api.group_roles.
GroupRolesAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
index
(trans, *args, **kwargs)[source]¶ GET /api/groups/{encoded_group_id}/roles Displays a collection (list) of groups.
-
show
(trans, *args, **kwargs)[source]¶ GET /api/groups/{encoded_group_id}/roles/{encoded_role_id} Displays information about a group role.
-
galaxy.webapps.galaxy.api.group_users module¶
API operations on Group objects.
-
class
galaxy.webapps.galaxy.api.group_users.
GroupUsersAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
index
(trans, *args, **kwargs)[source]¶ GET /api/groups/{encoded_group_id}/users Displays a collection (list) of groups.
-
show
(trans, *args, **kwargs)[source]¶ GET /api/groups/{encoded_group_id}/users/{encoded_user_id} Displays information about a group user.
-
galaxy.webapps.galaxy.api.groups module¶
API operations on Group objects.
-
class
galaxy.webapps.galaxy.api.groups.
GroupAPIController
(app)[source]¶
galaxy.webapps.galaxy.api.histories module¶
API operations on a history.
See also
-
class
galaxy.webapps.galaxy.api.histories.
HistoriesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.ExportsHistoryMixin
,galaxy.web.base.controller.ImportsHistoryMixin
,galaxy.web.base.controller.SharableMixin
-
index
(trans, deleted='False')[source]¶ - GET /api/histories:
- return undeleted histories for the current user
- GET /api/histories/deleted:
- return deleted histories for the current user
Note
Anonymous users are allowed to get their current history
Parameters: deleted (boolean) – if True, show only deleted histories, if False, non-deleted Return type: list Returns: list of dictionaries containing summary history information - The following are optional parameters:
- view: string, one of (‘summary’,’detailed’), defaults to ‘summary’
- controls which set of properties to return
- keys: comma separated strings, unused by default
- keys/names of individual properties to return
If neither keys or views are sent, the default view (set of keys) is returned. If both a view and keys are sent, the key list and the view’s keys are combined. If keys are send and no view, only those properties in keys are returned.
- For which properties are available see:
- galaxy/managers/histories/HistorySerializer
- The list returned can be filtered by using two optional parameters:
- q: string, generally a property name to filter by followed
- by an (often optional) hyphen and operator string.
qv: string, the value to filter by
- ..example:
To filter the list to only those created after 2015-01-29, the query string would look like:
‘?q=create_time-gt&qv=2015-01-29’- Multiple filters can be sent in using multiple q/qv pairs:
- ‘?q=create_time-gt&qv=2015-01-29&q=tag-has&qv=experiment-1’
- The list returned can be paginated using two optional parameters:
- limit: integer, defaults to no value and no limit (return all)
- how many items to return
- offset: integer, defaults to 0 and starts at the beginning
- skip the first ( offset - 1 ) items and begin returning at the Nth item
- ..example:
- limit and offset can be combined. Skip the first two and return five:
- ‘?limit=5&offset=3’
- The list returned can be ordered using the optional parameter:
- order: string containing one of the valid ordering attributes followed
- (optionally) by ‘-asc’ or ‘-dsc’ for ascending and descending order respectively. Orders can be stacked as a comma- separated list of values.
- ..example:
- To sort by name descending then create time descending:
- ‘?order=name-dsc,create_time’
- The ordering attributes and their default orders are:
- create_time defaults to ‘create_time-dsc’ update_time defaults to ‘update_time-dsc’ name defaults to ‘name-asc’
‘order’ defaults to ‘create_time-dsc’
-
show
(trans, id, deleted='False')[source]¶ - GET /api/histories/{id}:
- return the history with
id
- GET /api/histories/deleted/{id}:
- return the deleted history with
id
- GET /api/histories/most_recently_used:
- return the most recently used history
Parameters: - id (an encoded id string) – the encoded id of the history to query or the string ‘most_recently_used’
- deleted (boolean) – if True, allow information on a deleted history to be shown.
- keys – same as the use of keys in the index function above
- view – same as the use of view in the index function above
Return type: dictionary
Returns: detailed history information
-
published
(trans, *args, **kwargs)[source]¶ published( self, trans, **kwd ): * GET /api/histories/published:
return all histories that are publishedReturn type: list Returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above.
- GET /api/histories/shared_with_me:
- return all histories that are shared with the current user
Return type: list Returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above.
-
create
(trans, payload)[source]¶ - POST /api/histories:
- create a new history
Parameters: - payload (dict) – (optional) dictionary structure containing: * name: the new history’s name * history_id: the id of the history to copy * all_datasets: copy deleted hdas/hdcas? ‘True’ or ‘False’, defaults to True * archive_source: the url that will generate the archive to import * archive_type: ‘url’ (default)
- keys – same as the use of keys in the index function above
- view – same as the use of view in the index function above
Return type: Returns: element view of new history
-
delete
(self, trans, id, **kwd)[source]¶ - DELETE /api/histories/{id}
- delete the history with the given
id
Note
Stops all active jobs in the history if purge is set.
Parameters: You can purge a history, removing all it’s datasets from disk (if unshared), by passing in
purge=True
in the url.Parameters: - keys – same as the use of keys in the index function above
- view – same as the use of view in the index function above
Return type: Returns: the deleted or purged history
-
undelete
(self, trans, id, **kwd)[source]¶ - POST /api/histories/deleted/{id}/undelete:
- undelete history (that hasn’t been purged) with the given
id
Parameters: - id (str) – the encoded id of the history to undelete
- keys – same as the use of keys in the index function above
- view – same as the use of view in the index function above
Return type: Returns: ‘OK’ if the history was undeleted
-
update
(self, trans, id, payload, **kwd)[source]¶ - PUT /api/histories/{id}
- updates the values for the history with the given
id
Parameters: - id (str) – the encoded id of the history to update
- payload (dict) –
a dictionary containing any or all the fields in
galaxy.model.History.to_dict()
and/or the following:- annotation: an annotation for the history
- keys – same as the use of keys in the index function above
- view – same as the use of view in the index function above
Return type: Returns: an error object if an error occurred or a dictionary containing any values that were different from the original and, therefore, updated
-
archive_export
(trans, *args, **kwargs)[source]¶ export_archive( self, trans, id, payload ) * PUT /api/histories/{id}/exports:
start job (if needed) to create history export for corresponding history.Parameters: id (str) – the encoded id of the history to export Return type: dict Returns: object containing url to fetch export from.
-
archive_download
(trans, *args, **kwargs)[source]¶ export_download( self, trans, id, jeha_id ) * GET /api/histories/{id}/exports/{jeha_id}:
If ready and available, return raw contents of exported history. Use/poll “PUT /api/histories/{id}/exports” to initiate the creation of such an export - when ready that route will return 200 status code (instead of 202) with a JSON dictionary containing a download_url.
-
galaxy.webapps.galaxy.api.history_contents module¶
API operations on the contents of a history.
-
class
galaxy.webapps.galaxy.api.history_contents.
HistoryContentsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixin
,galaxy.web.base.controller.UsesLibraryMixinItems
,galaxy.web.base.controller.UsesTagsMixin
-
index
(self, trans, history_id, ids=None, **kwd)[source]¶ - GET /api/histories/{history_id}/contents
- return a list of HDA data for the history with the given
id
Note
Anonymous users are allowed to get their current history contents
If Ids is not given, index returns a list of summary objects for every HDA associated with the given history_id.
If ids is given, index returns a more complete json object for each HDA in the ids list.
Parameters: Return type: Returns: dictionaries containing summary or detailed HDA information
-
show
(trans, *args, **kwargs)[source]¶ - GET /api/histories/{history_id}/contents/{id}
- GET /api/histories/{history_id}/contents/{type}/{id}
- return detailed information about an HDA or HDCA within a history
Note
Anonymous users are allowed to get their current history contents
Parameters: - id (str) – the encoded id of the HDA or HDCA to return
- id – ‘dataset’ or ‘dataset_collection’
- history_id (str) – encoded id string of the HDA’s or HDCA’s History
- view (str) – if fetching a dataset collection - the view style of the dataset collection to produce. ‘collection’ returns no element information, ‘element’ returns detailed element information for all datasets, ‘element-reference’ returns a minimal set of information about datasets (for instance id, type, and state but not metadata, peek, info, or name). The default is ‘element’.
- fuzzy_count (int) – this value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be “a bit” more than this number or “a lot” less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a “balanced” concept of the “start” of large collections at every depth of the collection.
Return type: Returns: dictionary containing detailed HDA or HDCA information
-
index_jobs_summary
(trans, *args, **kwargs)[source]¶ - GET /api/histories/{history_id}/jobs_summary
- return detailed information about an HDA or HDCAs jobs
Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn’t considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible.
Parameters: - history_id (str) – encoded id string of the HDA’s or the HDCA’s History
- ids (str[]) – the encoded ids of job summary objects to return - if ids is specified types must also be specified and have same length.
- types (str[]) – type of object represented by elements in the ids array - either Job or ImplicitCollectionJob.
Return type: dict[]
Returns: an array of job summary object dictionaries.
-
show_jobs_summary
(trans, *args, **kwargs)[source]¶ - GET /api/histories/{history_id}/contents/{type}/{id}/jobs_summary
- return detailed information about an HDA or HDCAs jobs
Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn’t considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible.
Parameters: Return type: Returns: dictionary containing jobs summary object
-
download_dataset_collection
(trans, *args, **kwargs)[source]¶ - GET /api/histories/{history_id}/contents/{id}/download
- GET /api/dataset_collection/{id}/download
Download the content of a HistoryDatasetCollection as a tgz archive while maintaining approximate collection structure.
Parameters: - id – encoded HistoryDatasetCollectionAssociation (HDCA) id
- history_id – encoded id string of the HDCA’s History
-
create
(self, trans, history_id, payload, **kwd)[source]¶ - POST /api/histories/{history_id}/contents/{type}s
- POST /api/histories/{history_id}/contents
- create a new HDA or HDCA
Parameters: - history_id (str) – encoded id string of the new HDA’s History
- type (str) – Type of history content - ‘dataset’ (default) or ‘dataset_collection’. This can be passed in via payload or parsed from the route.
- payload (dict) –
dictionary structure containing:: copy from library (for type ‘dataset’): ‘source’ = ‘library’ ‘content’ = [the encoded id from the library dataset]
copy from library folder ‘source’ = ‘library_folder’ ‘content’ = [the encoded id from the library folder]
copy from history dataset (for type ‘dataset’): ‘source’ = ‘hda’ ‘content’ = [the encoded id from the HDA]
copy from history dataset collection (for type ‘dataset_collection’) ‘source’ = ‘hdca’ ‘content’ = [the encoded id from the HDCA] ‘copy_elements’ = Copy child HDAs into the target history as well,
defaults to False but this is less than ideal and may be changed in future releases.create new history dataset collection (for type ‘dataset_collection’) ‘source’ = ‘new_collection’ (default ‘source’ if type is
’dataset_collection’ - no need to specify this)’collection_type’ = For example, “list”, “paired”, “list:paired”. ‘copy_elements’ = Copy child HDAs when creating new collection,
defaults to False in the API but is set to True in the UI, so that we can modify HDAs with tags when creating collections.’name’ = Name of new dataset collection. ‘element_identifiers’ = Recursive list structure defining collection.
Each element must have ‘src’ which can be ‘hda’, ‘ldda’, ‘hdca’, or ‘new_collection’, as well as a ‘name’ which is the name of element (e.g. “forward” or “reverse” for paired datasets, or arbitrary sample names for instance for lists). For all src’s except ‘new_collection’ - a encoded ‘id’ attribute must be included wiht element as well. ‘new_collection’ sources must defined a ‘collection_type’ and their own list of (potentially) nested ‘element_identifiers’.
- ..note:
- Currently, a user can only copy an HDA from a history that the user owns.
Return type: dict Returns: dictionary containing detailed information for the new HDA
-
show_roles
(trans, *args, **kwargs)[source]¶ Display information about current or available roles for a given dataset permission.
- GET /api/histories/{history_id}/contents/datasets/{encoded_dataset_id}/permissions
Parameters: encoded_dataset_id (an encoded id string) – the encoded id of the dataset to query Returns: either dict of current roles for all permission types or dict of available roles to choose from (is the same for any permission type) Return type: dictionary Raises: InsufficientPermissionsException
-
update_permissions
(trans, *args, **kwargs)[source]¶ Set permissions of the given library dataset to the given role ids.
- PUT /api/histories/{history_id}/contents/datasets/{encoded_dataset_id}/permissions
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the dataset to update permissions of
- payload –
dictionary structure containing: :param action: (required) describes what action should be performed
available actions: make_private, remove_restrictions, set_permissionstype action: string param access_ids[]: list of Role.id defining roles that should have access permission on the dataset type access_ids[]: string or list param manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset type manage_ids[]: string or list param modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item type modify_ids[]: string or list
Type: dictionary
Returns: dict of current roles for all available permission types
Return type: dictionary
Raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError RequestParameterMissingException
-
update
(self, trans, history_id, id, payload, **kwd)[source]¶ - PUT /api/histories/{history_id}/contents/{id}
- updates the values for the HDA with the given
id
Parameters: - history_id (str) – encoded id string of the HDA’s History
- id (str) – the encoded id of the history to update
- payload (dict) –
a dictionary containing any or all the fields in
galaxy.model.HistoryDatasetAssociation.to_dict()
and/or the following:- annotation: an annotation for the HDA
Return type: Returns: an error object if an error occurred or a dictionary containing any values that were different from the original and, therefore, updated
-
delete
(self, trans, history_id, id, **kwd)[source]¶ - DELETE /api/histories/{history_id}/contents/{id}
- DELETE /api/histories/{history_id}/contents/{type}s/{id}
- delete the history content with the given
id
and specified type (defaults to dataset)
Note
Currently does not stop any active jobs for which this dataset is an output.
Parameters: - id (str) – the encoded id of the history to delete
- recursive (bool) – if True, and deleted an HDCA also delete containing HDAs
- purge (bool) – if True, purge the target HDA or child HDAs of the target HDCA
- kwd (dict) –
(optional) dictionary structure containing:
- payload: a dictionary itself containing:
- purge: if True, purge the HDA
- recursive: if True, see above.
Note
that payload optionally can be placed in the query string of the request. This allows clients that strip the request body to still purge the dataset.
Return type: dict Returns: an error object if an error occurred or a dictionary containing: * id: the encoded id of the history, * deleted: if the history was marked as deleted, * purged: if the history was purged
-
archive
(self, trans, history_id, filename='', format='tgz', dry_run=True, **kwd)[source]¶ - GET /api/histories/{history_id}/contents/archive/{id}
- GET /api/histories/{history_id}/contents/archive/{filename}.{format}
- build and return a compressed archive of the selected history contents
Parameters: - filename (string) – (optional) archive name (defaults to history name)
- dry_run (boolean) – (optional) if True, return the archive and file paths only as json and not an archive file
Returns: archive file for download
Note
this is a volatile endpoint and settings and behavior may change.
-
galaxy.webapps.galaxy.api.item_tags module¶
API operations related to tagging items.
galaxy.webapps.galaxy.api.job_files module¶
API for asynchronous job running mechanisms can use to fetch or put files related to running and queued jobs.
-
class
galaxy.webapps.galaxy.api.job_files.
JobFilesAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
This job files controller allows remote job running mechanisms to read and modify the current state of files for queued and running jobs. It is certainly not meant to represent part of Galaxy’s stable, user facing API.
Furthermore, even if a user key corresponds to the user running the job, it should not be accepted for authorization - this API allows access to low-level unfiltered files and such authorization would break Galaxy’s security model for tool execution.
-
index
(self, trans, job_id, **kwargs)[source]¶ - GET /api/jobs/{job_id}/files
- Get a file required to staging a job (proper datasets, extra inputs, task-split inputs, working directory files).
Parameters: - ..note:
- This API method is intended only for consumption by job runners, not end users.
Return type: binary Returns: contents of file
-
create
(self, trans, job_id, payload, **kwargs)[source]¶ - POST /api/jobs/{job_id}/files
- Populate an output file (formal dataset, task split part, working directory file (such as those related to metadata)). This should be a multipart post with a ‘file’ parameter containing the contents of the actual file to create.
Parameters: - ..note:
- This API method is intended only for consumption by job runners, not end users.
Return type: dict Returns: an okay message
-
galaxy.webapps.galaxy.api.jobs module¶
API operations on a jobs.
See also
galaxy.model.Jobs
-
class
galaxy.webapps.galaxy.api.jobs.
JobController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixinItems
-
index
(trans, state=None, tool_id=None, history_id=None, date_range_min=None, date_range_max=None, user_details=False)[source]¶ - GET /api/jobs:
return jobs for current user
- !! if user is admin and user_details is True, then
return jobs for all galaxy users based on filtering - this is an extended service
Parameters: state (string or list) – limit listing of jobs to those that match one of the included states. If none, all are returned. - Valid Galaxy job states include:
- ‘new’, ‘upload’, ‘waiting’, ‘queued’, ‘running’, ‘ok’, ‘error’, ‘paused’, ‘deleted’, ‘deleted_new’
Parameters: - tool_id (string or list) – limit listing of jobs to those that match one of the included tool_ids. If none, all are returned.
- user_details (boolean) – if true, and requestor is an admin, will return external job id and user email.
- date_range_min (string '2014-01-01') – limit the listing of jobs to those updated on or after requested date
- date_range_max (string '2014-12-31') – limit the listing of jobs to those updated on or before requested date
- history_id (string) – limit listing of jobs to those that match the history_id. If none, all are returned.
Return type: Returns: list of dictionaries containing summary job information
-
show
(trans, id)[source]¶ - GET /api/jobs/{id}:
- return jobs for current user
Parameters: - id (string) – Specific job id
- full (boolean) – whether to return extra information
Return type: dictionary
Returns: dictionary containing full description of job data
-
inputs
(trans, *args, **kwargs)[source]¶ show( trans, id ) * GET /api/jobs/{id}/inputs
returns input datasets created by jobParameters: id (string) – Encoded job id Return type: dictionary Returns: dictionary containing input dataset associations
-
outputs
(trans, id)[source]¶ - GET /api/jobs/{id}/outputs
- returns output datasets created by job
Parameters: id (string) – Encoded job id Return type: dictionary Returns: dictionary containing output dataset associations
-
delete
(trans, id)[source]¶ - Delete /api/jobs/{id}
- cancels specified job
Parameters: id (string) – Encoded job id
-
resume
(trans, *args, **kwargs)[source]¶ - PUT /api/jobs/{id}/resume
- Resumes a paused job
Parameters: id (string) – Encoded job id Return type: dictionary Returns: dictionary containing output dataset associations
-
build_for_rerun
(trans, *args, **kwargs)[source]¶ - GET /api/jobs/{id}/build_for_rerun
- returns a tool input/param template prepopulated with this job’s information, suitable for rerunning or rendering parameters of the job.
Parameters: id (string) – Encoded job id Return type: dictionary Returns: dictionary containing output dataset associations
-
search
(trans, payload)[source]¶ - POST /api/jobs/search:
- return jobs for current user
Parameters: payload (dict) – Dictionary containing description of requested job. This is in the same format as a request to POST /apt/tools would take to initiate a job Return type: list Returns: list of dictionaries containing summary job information of the jobs that match the requested job run This method is designed to scan the list of previously run jobs and find records of jobs that had the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply recycle the old results.
-
galaxy.webapps.galaxy.api.libraries module¶
API operations on a data library.
-
class
galaxy.webapps.galaxy.api.libraries.
LibrariesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
index
(self, trans, **kwd)[source]¶ - GET /api/libraries:
- Returns a list of summary data for all libraries.
Parameters: deleted (boolean (optional)) – if True, show only deleted
libraries, if False show onlynon-deleted
Returns: list of dictionaries containing library information Return type: list
-
show
(self, trans, id, deleted='False', **kwd)[source]¶ - GET /api/libraries/{encoded_id}:
- returns detailed information about a library
- GET /api/libraries/deleted/{encoded_id}:
- returns detailed information about a
deleted
library
Parameters: - id (an encoded id string) – the encoded id of the library
- deleted (boolean) – if True, allow information on a
deleted
library
Returns: detailed library information
Return type: dictionary
Raises: MalformedId, ObjectNotFound
-
create
(trans, *args, **kwargs)[source]¶ - POST /api/libraries:
- Creates a new library.
Note
Currently, only admin users can create libraries.
Parameters: payload (dict) – dictionary structure containing:: :param name: (required) the new library’s name :type name: str :param description: the new library’s description :type description: str :param synopsis: the new library’s synopsis :type synopsis: str Returns: detailed library information Return type: dict Raises: RequestParameterMissingException
-
update
(trans, *args, **kwargs)[source]¶ - PATCH /api/libraries/{encoded_id}
- Updates the library defined by an
encoded_id
with the data in the payload.
Note
Currently, only admin users can update libraries. Also the library must not be deleted.
param id: the encoded id of the library type id: an encoded id string param payload: dictionary structure containing:: :param name: new library’s name, cannot be empty :type name: str :param description: new library’s description :type description: str :param synopsis: new library’s synopsis :type synopsis: str type payload: dict returns: detailed library information rtype: dict raises: RequestParameterMissingException
-
delete
(trans, *args, **kwargs)[source]¶ - DELETE /api/libraries/{id}
- marks the library with the given
id
as deleted (or removes the deleted mark if the undelete param is true)
Note
Currently, only admin users can un/delete libraries.
Parameters: - id (an encoded id string) – the encoded id of the library to un/delete
- payload – dictionary structure containing: :param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false: :type undelete: bool
Type: dictionary
Returns: detailed library information
Return type: dictionary
-
get_permissions
(trans, *args, **kwargs)[source]¶ - GET /api/libraries/{id}/permissions
Load all permissions for the given library id and return it.
Parameters: Returns: dictionary with all applicable permissions’ values
Return type: dictionary
Raises: InsufficientPermissionsException
-
set_permissions
(trans, *args, **kwargs)[source]¶ - *POST /api/libraries/{encoded_library_id}/permissions
- Set permissions of the given library to the given role ids.
Parameters: - encoded_library_id (an encoded id string) – the encoded id of the library to set the permissions of
- payload –
dictionary structure containing: :param action: (required) describes what action should be performed
available actions: remove_restrictions, set_permissionstype action: str param access_ids[]: list of Role.id defining roles that should have access permission on the library type access_ids[]: string or list param add_ids[]: list of Role.id defining roles that should have add item permission on the library type add_ids[]: string or list param manage_ids[]: list of Role.id defining roles that should have manage permission on the library type manage_ids[]: string or list param modify_ids[]: list of Role.id defining roles that should have modify permission on the library type modify_ids[]: string or list
Type: dictionary
Returns: dict of current roles for all available permission types
Return type: dictionary
Raises: RequestParameterInvalidException, InsufficientPermissionsException, InternalServerError RequestParameterMissingException
-
galaxy.webapps.galaxy.api.library_contents module¶
API operations on the contents of a data library.
-
class
galaxy.webapps.galaxy.api.library_contents.
LibraryContentsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesLibraryMixin
,galaxy.web.base.controller.UsesLibraryMixinItems
,galaxy.web.base.controller.UsesFormDefinitionsMixin
,galaxy.actions.library.LibraryActions
-
index
(self, trans, library_id, **kwd)[source]¶ - GET /api/libraries/{library_id}/contents:
- Returns a list of library files and folders.
Note
May be slow! Returns all content traversing recursively through all folders.
See also
galaxy.webapps.galaxy.api.FolderContentsController.index
for a non-recursive solutionParameters: library_id (str) – the encoded id of the library Returns: list of dictionaries of the form: * id: the encoded id of the library item * name: the ‘library path’ or relationship of the library item to the root- type: ‘file’ or ‘folder’
- url: the url to get detailed information on the library item
Return type: list Raises: MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError
-
show
(self, trans, id, library_id, **kwd)[source]¶ - GET /api/libraries/{library_id}/contents/{id}
- Returns information about library file or folder.
Parameters: Returns: detailed library item information
Return type:
-
create
(self, trans, library_id, payload, **kwd)[source]¶ - 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 infrom_hda_id
(and optionallyldda_message
).To copy an HDCA into a library send
create_type
of ‘file’ and the HDCA’s encoded id infrom_hdca_id
(and optionallyldda_message
).Parameters: - library_id (str) – the encoded id of the library where to create the new item
- payload (dict) –
dictionary structure containing:
- folder_id: the encoded id of the parent folder of the new item
- create_type: the type of item to create (‘file’, ‘folder’ or ‘collection’)
- from_hda_id: (optional, only if create_type is ‘file’) the
- encoded id of an accessible HDA to copy into the library
- ldda_message: (optional) the new message attribute of the LDDA created
- extended_metadata: (optional) sub-dictionary containing any extended
- metadata to associate with the item
- upload_option: (optional) one of ‘upload_file’ (default), ‘upload_directory’ or ‘upload_paths’
- server_dir: (optional, only if upload_option is
- ’upload_directory’) relative path of the subdirectory of Galaxy
library_import_dir
(if admin) oruser_library_import_dir
(if non-admin) to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded.
- filesystem_paths: (optional, only if upload_option is
- ’upload_paths’ and the user is an admin) file paths on the Galaxy server to upload to the library, one file per line
- link_data_only: (optional, only when upload_option is
- ’upload_directory’ or ‘upload_paths’) either ‘copy_files’ (default) or ‘link_to_files’. Setting to ‘link_to_files’ symlinks instead of copying the files
- name: (optional, only if create_type is ‘folder’) name of the
- folder to create
- description: (optional, only if create_type is ‘folder’)
- description of the folder to create
- tag_using_filename: (optional)
- create tags on datasets using the file’s original name
Returns: a dictionary describing the new item unless
from_hdca_id
is supplied, in that case a list of such dictionaries is returned.Return type:
-
update
(self, trans, id, library_id, payload, **kwd)[source]¶ - PUT /api/libraries/{library_id}/contents/{id}
- create a ImplicitlyConvertedDatasetAssociation
Parameters: Return type: Returns: None
-
delete
(self, trans, library_id, id, **kwd)[source]¶ - DELETE /api/libraries/{library_id}/contents/{id}
- delete the LibraryDataset with the given
id
Parameters: Return type: Returns: an error object if an error occurred or a dictionary containing: * id: the encoded id of the library dataset, * deleted: if the library dataset was marked as deleted, * purged: if the library dataset was purged
-
galaxy.webapps.galaxy.api.library_datasets module¶
API operations on the library datasets.
-
class
galaxy.webapps.galaxy.api.library_datasets.
LibraryDatasetsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesVisualizationMixin
,galaxy.actions.library.LibraryActions
-
show
(trans, *args, **kwargs)[source]¶ Show the details of a library dataset.
- GET /api/libraries/datasets/{encoded_dataset_id}
Parameters: id (an encoded id string) – the encoded id of the library dataset to query Returns: detailed library dataset information Return type: dictionary
-
show_version
(trans, *args, **kwargs)[source]¶ Display a specific version of a library dataset (i.e. ldda).
- GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the related library dataset
- encoded_ldda_id (an encoded id string) – the encoded id of the ldda to query
Returns: dict of ldda’s details
Return type: dictionary
Raises: ObjectNotFound
-
show_roles
(trans, *args, **kwargs)[source]¶ Display information about current or available roles for a given dataset permission.
- GET /api/libraries/datasets/{encoded_dataset_id}/permissions
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the dataset to query
- scope (string) – either ‘current’ or ‘available’
Returns: either dict of current roles for all permission types or dict of available roles to choose from (is the same for any permission type)
Return type: dictionary
Raises: InsufficientPermissionsException
-
update
(trans, *args, **kwargs)[source]¶ Update the given library dataset (the latest linked ldda).
- PATCH /api/libraries/datasets/{encoded_dataset_id}
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the library dataset to update
- payload (dict) – dictionary structure containing:: :param name: new ld’s name, must be longer than 0 :type name: str :param misc_info: new ld’s misc info :type misc_info: str :param file_ext: new ld’s extension, must exist in the Galaxy registry :type file_ext: str :param genome_build: new ld’s genome build :type genome_build: str
Returns: detailed library dataset information
Return type: dictionary
-
update_permissions
(trans, *args, **kwargs)[source]¶ Set permissions of the given library dataset to the given role ids.
*POST /api/libraries/datasets/{encoded_dataset_id}/permissions
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the dataset to update permissions of
- payload –
dictionary structure containing: :param action: (required) describes what action should be performed
available actions: make_private, remove_restrictions, set_permissionstype action: string param access_ids[]: list of Role.id defining roles that should have access permission on the dataset type access_ids[]: string or list param manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset type manage_ids[]: string or list param modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item type modify_ids[]: string or list
Type: dictionary
Returns: dict of current roles for all available permission types
Return type: dictionary
Raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError RequestParameterMissingException
-
delete
(trans, *args, **kwargs)[source]¶ Mark the dataset deleted or undeleted.
- DELETE /api/libraries/datasets/{encoded_dataset_id}
Parameters: - encoded_dataset_id (an encoded id string) – the encoded id of the dataset to change
- undelete (bool) – flag whether to undeleted instead of deleting
Returns: dict containing information about the dataset
Return type: dictionary
-
load
(trans, *args, **kwargs)[source]¶ Load dataset(s) from the given source into the library.
- POST /api/libraries/datasets
Parameters: payload – dictionary structure containing: :param encoded_folder_id: the encoded id of the folder to import dataset(s) to :type encoded_folder_id: an encoded id string :param source: source the datasets should be loaded from
- Source can be:
- user directory - root folder specified in galaxy.ini as “$user_library_import_dir”
- example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here} the folder with the user login has to be created beforehand
- (admin)import directory - root folder specified in galaxy ini as “$library_import_dir”
- example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}
(admin)any absolute or relative path - option allowed with “allow_library_path_paste” in galaxy.ini
type source: str param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy while linking is set to True all symlinks will be resolved _once_ type link_data: bool param preserve_dirs: flag whether to preserve the directory structure when importing dir if False only datasets will be imported type preserve_dirs: bool param file_type: file type of the loaded datasets, defaults to ‘auto’ (autodetect) type file_type: str param dbkey: dbkey of the loaded genome, defaults to ‘?’ (unknown) type dbkey: str param tag_using_filenames: flag whether to generate dataset tags from filenames type tag_using_filenames: bool :type dictionary
Returns: dict containing information about the created upload job Return type: dictionary Raises: RequestParameterMissingException, AdminRequiredException, ConfigDoesNotAllowException, RequestParameterInvalidException InsufficientPermissionsException, ObjectNotFound
-
download
(trans, format, **kwd)[source]¶ Download requested datasets (identified by encoded IDs) in requested format.
- GET /api/libraries/datasets/download/{format}
- POST /api/libraries/datasets/download/{format}
example:
GET localhost:8080/api/libraries/datasets/download/tbz?ld_ids%255B%255D=a0d84b45643a2678&ld_ids%255B%255D=fe38c84dcd46c828
Note
supported format values are: ‘zip’, ‘tgz’, ‘tbz’, ‘uncompressed’
Parameters: - format (string) – string representing requested archive format
- ld_ids[] (an array) – an array of encoded dataset ids
- folder_ids[] (an array) – an array of encoded folder ids
Returns: either archive with the requested datasets packed inside or a single uncompressed dataset
Return type: Raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound
-
galaxy.webapps.galaxy.api.metrics module¶
API operations for for querying and recording user metrics from some client (typically a user’s browser).
-
class
galaxy.webapps.galaxy.api.metrics.
MetricsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
debugging
= None¶ set to true to send additional debugging info to the log
-
create
(trans, payload)[source]¶ - POST /api/metrics:
- record any metrics sent and return some status object
Note
Anonymous users can post metrics
Parameters: payload (dict) – (optional) dictionary structure containing: * metrics: a list containing dictionaries of the form:
** namespace: label indicating the source of the metric ** time: isoformat datetime when the metric was recorded ** level: an integer representing the metric’s log level ** args: a json string containing an array of extra dataReturn type: dict Returns: status object
-
galaxy.webapps.galaxy.api.page_revisions module¶
API for updating Galaxy Pages
-
class
galaxy.webapps.galaxy.api.page_revisions.
PageRevisionsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.SharableItemSecurityMixin
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.web.base.controller.SharableMixin
-
index
(self, trans, page_id, **kwd)[source]¶ - GET /api/pages/{page_id}/revisions
- return a list of Page revisions
Parameters: page_id – Display the revisions of Page with ID=page_id Return type: list Returns: dictionaries containing different revisions of the page
-
create
(self, trans, page_id, payload **kwd)[source]¶ - POST /api/pages/{page_id}/revisions
- Create a new revision for a page
Parameters: - page_id – Add revision to Page with ID=page_id
- payload – A dictionary containing:: ‘title’ = New title of the page ‘content’ = New content of the page
Return type: dictionary
Returns: Dictionary with ‘success’ or ‘error’ element to indicate the result of the request
-
galaxy.webapps.galaxy.api.pages module¶
API for updating Galaxy Pages
-
class
galaxy.webapps.galaxy.api.pages.
PagesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.SharableItemSecurityMixin
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.web.base.controller.SharableMixin
RESTful controller for interactions with pages.
-
index
(self, trans, deleted=False, **kwd)[source]¶ - GET /api/pages
- return a list of Pages viewable by the user
Parameters: deleted – Display deleted pages Return type: list Returns: dictionaries containing summary or detailed Page information
-
create
(self, trans, payload, **kwd)[source]¶ - POST /api/pages
- Create a page and return dictionary containing Page summary
Parameters: payload – dictionary structure containing:: ‘slug’ = The title slug for the page URL, must be unique ‘title’ = Title of the page ‘content’ = HTML contents of the page ‘annotation’ = Annotation that will be attached to the page Return type: dict Returns: Dictionary return of the Page.to_dict call
-
galaxy.webapps.galaxy.api.plugins module¶
Plugins resource control over the API.
-
class
galaxy.webapps.galaxy.api.plugins.
PluginsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTful controller for interactions with plugins.
galaxy.webapps.galaxy.api.provenance module¶
API operations provenance
galaxy.webapps.galaxy.api.quotas module¶
API operations on Quota objects.
-
class
galaxy.webapps.galaxy.api.quotas.
QuotaAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.actions.admin.AdminActions
,galaxy.web.base.controller.UsesQuotaMixin
,galaxy.web.params.QuotaParamParser
-
index
(trans, *args, **kwargs)[source]¶ GET /api/quotas GET /api/quotas/deleted Displays a collection (list) of quotas.
-
galaxy.webapps.galaxy.api.remote_files module¶
API operations on remote files.
-
class
galaxy.webapps.galaxy.api.remote_files.
RemoteFilesAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
index
(trans, *args, **kwargs)[source]¶ GET /api/remote_files/
Displays remote files.
Parameters: - target (str) – target to load available datasets from, defaults to ftp possible values: ftp, userdir, importdir
- format – requested format of data, defaults to flat possible values: flat, jstree, ajax
Returns: list of available files
Return type:
-
galaxy.webapps.galaxy.api.roles module¶
API operations on Role objects.
-
class
galaxy.webapps.galaxy.api.roles.
RoleAPIController
(app)[source]¶
galaxy.webapps.galaxy.api.search module¶
API for searching Galaxy Datasets
-
class
galaxy.webapps.galaxy.api.search.
SearchController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.SharableItemSecurityMixin
galaxy.webapps.galaxy.api.tool_data module¶
-
class
galaxy.webapps.galaxy.api.tool_data.
ToolData
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTful controller for interactions with tool data
-
delete
(trans, *args, **kwargs)[source]¶ DELETE /api/tool_data/{id} Removes an item from a data table
Parameters:
-
galaxy.webapps.galaxy.api.tool_dependencies module¶
API operations allowing clients to manage tool dependencies.
-
class
galaxy.webapps.galaxy.api.tool_dependencies.
ToolDependenciesAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
-
update
(trans, *args, **kwargs)[source]¶ PUT /api/dependency_resolvers
Reload tool dependency resolution configuration.
-
resolver_dependency
(trans, *args, **kwargs)[source]¶ GET /api/dependency_resolvers/{index}/dependency
Resolve described requirement against specified dependency resolver.
Parameters: - index (int) – index of the dependency resolver
- kwds (dict) – dictionary structure containing extra parameters
- name (str) – name of the requirement to find a dependency for (required)
- version (str) – version of the requirement to find a dependency for (required)
- exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).
Return type: Returns: a dictified description of the dependency, with attribute
dependency_type: None
if no match was found.
-
install_dependency
(trans, *args, **kwargs)[source]¶ POST /api/dependency_resolvers/{index}/dependency
Install described requirement against specified dependency resolver.
Parameters: - index (int) – index of the dependency resolver
- kwds (dict) – dictionary structure containing extra parameters
- name (str) – name of the requirement to find a dependency for (required)
- version (str) – version of the requirement to find a dependency for (required)
- exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).
Return type: Returns: a dictified description of the dependency, with attribute
dependency_type: None
if no match was found.
-
manager_dependency
(trans, *args, **kwargs)[source]¶ GET /api/dependency_resolvers/dependency
Resolve described requirement against all dependency resolvers, returning the match with highest priority.
Parameters: - index (int) – index of the dependency resolver
- kwds (dict) – dictionary structure containing extra parameters
- name (str) – name of the requirement to find a dependency for (required)
- version (str) – version of the requirement to find a dependency for (required)
- exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).
Return type: Returns: a dictified description of the dependency, with type: None if no match was found.
-
resolver_requirements
(trans, *args, **kwargs)[source]¶ GET /api/dependency_resolvers/{index}/requirements
Find all “simple” requirements that could be resolved “exactly” by this dependency resolver. The dependency resolver must implement ListDependencyResolver.
Parameters: index (int) – index of the dependency resolver Return type: dict Returns: a dictified description of the requirement that could be resolved.
-
manager_requirements
(trans, *args, **kwargs)[source]¶ GET /api/dependency_resolvers/requirements
Find all “simple” requirements that could be resolved “exactly” by all dependency resolvers that support this operation.
Parameters: index (int) – index of the dependency resolver Return type: dict Returns: a dictified description of the requirement that could be resolved (keyed on ‘requirement’) and the index of the corresponding resolver (keyed on ‘index’).
-
clean
(trans, *args, **kwargs)[source]¶ POST /api/dependency_resolvers/{index}/clean
Cleans up intermediate files created by resolvers during the dependency installation.
Parameters: index (int) – index of the dependency resolver Return type: dict Returns: a dictified description of the requirement that could be resolved (keyed on ‘requirement’) and the index of the corresponding resolver (keyed on ‘index’).
-
galaxy.webapps.galaxy.api.tool_shed_repositories module¶
-
class
galaxy.webapps.galaxy.api.tool_shed_repositories.
ToolShedRepositoriesController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTful controller for interactions with tool shed repositories.
-
check_for_updates
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/check_for_updates Check for updates to the specified repository, or all installed repositories.
Parameters: - key – the current Galaxy admin user’s API key
- id – the galaxy-side encoded repository ID
-
exported_workflows
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/exported_workflows
Display a list of dictionaries containing information about this tool shed repository’s exported workflows.
Parameters: id – the encoded id of the ToolShedRepository object
-
get_latest_installable_revision
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/get_latest_installable_revision Get the latest installable revision of a specified repository from a specified Tool Shed.
Parameters: key – the current Galaxy admin user’s API key The following parameters are included in the payload. :param tool_shed_url (required): the base URL of the Tool Shed from which to retrieve the Repository revision. :param name (required): the name of the Repository :param owner (required): the owner of the Repository
-
shed_category
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/shed_category
Display a list of repositories in the selected category.
Parameters: - tool_shed_url – the url of the toolshed to get repositories from
- category_id – the category to get repositories from
-
shed_repository
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/shed_repository
Get details about the specified repository from its shed.
Parameters: - tsr_id – the tool_shed_repository_id
- tsr_id – str
- tool_shed_url – the URL of the toolshed whence to retrieve repository details
- tool_shed_url – str
- tool_ids – (optional) comma-separated list of tool IDs
- tool_ids – str
-
shed_search
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/shed_search
Search for a specific repository in the toolshed.
Parameters: - q – the query string to search for
- q – str
- tool_shed_url – the URL of the toolshed to search
- tool_shed_url – str
-
import_workflow
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/import_workflow
Import the specified exported workflow contained in the specified installed tool shed repository into Galaxy.
Parameters: - key – the API key of the Galaxy user with which the imported workflow will be associated.
- id – the encoded id of the ToolShedRepository object
The following parameters are included in the payload. :param index: the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository
-
import_workflows
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/import_workflows
Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy.
Parameters: - key – the API key of the Galaxy user with which the imported workflows will be associated.
- id – the encoded id of the ToolShedRepository object
-
index
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories Display a list of dictionaries containing information about installed tool shed repositories.
-
install
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/install Initiate the installation of a repository.
Parameters: - install_resolver_dependencies – True to install resolvable dependencies.
- install_tool_dependencies – True to install tool dependencies.
- install_repository_dependencies – True to install repository dependencies.
- tool_panel_section_id – The unique identifier for an existing tool panel section
- new_tool_panel_section_label – Create a new tool panel section with this label
- shed_tool_conf – The shed tool config file to use for this installation
- tool_shed_url – The URL for the toolshed whence this repository is being installed
- changeset – The changeset to update to after cloning the repository
-
install_repository_revision
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/install_repository_revision Install a specified repository revision from a specified tool shed into Galaxy.
Parameters: key – the current Galaxy admin user’s API key The following parameters are included in the payload. :param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository :param name (required): the name of the Repository :param owner (required): the owner of the Repository :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository :param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load
tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string or both must be an empty string (both cannot be used simultaneously).Parameters: - (optional) (shed_tool_conf) – id of the Galaxy tool panel section in which to load tools contained in the Repository. If this parameter is an empty string and the above new_tool_panel_section_label parameter is an empty string, tools will be loaded outside of any sections in the tool panel. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string of both must be an empty string (both cannot be used simultaneously).
- (optional) – Set to True if you want to install repository dependencies defined for the specified repository being installed. The default setting is False.
- (optional) – Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False.
- (optional) – The shed-related tool panel configuration file configured in the “tool_config_file” setting in the Galaxy config file (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path=”database/shed_tools”>). If this parameter is not set, a shed-related tool panel configuration file will be selected automatically.
-
install_repository_revisions
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/install_repository_revisions Install one or more specified repository revisions from one or more specified tool sheds into Galaxy. The received parameters must be ordered lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.
It’s questionable whether this method is needed as the above method for installing a single repository can probably cover all desired scenarios. We’ll keep this one around just in case…
Parameters: key – the current Galaxy admin user’s API key The following parameters are included in the payload. :param tool_shed_urls: the base URLs of the Tool Sheds from which to install a specified Repository :param names: the names of the Repositories to be installed :param owners: the owners of the Repositories to be installed :param changeset_revisions: the changeset_revisions of each RepositoryMetadata object associated with each Repository to be installed :param new_tool_panel_section_label: optional label of a new section to be added to the Galaxy tool panel in which to load
tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, as both cannot be used.Parameters: - tool_panel_section_id – optional id of the Galaxy tool panel section in which to load tools contained in the Repository. If not set, tools will be loaded outside of any sections in the tool panel. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, as both cannot be used.
- (optional) (shed_tool_conf) – Set to True if you want to install repository dependencies defined for the specified repository being installed. The default setting is False.
- (optional) – Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False.
- (optional) – The shed-related tool panel configuration file configured in the “tool_config_file” setting in the Galaxy config file (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path=”database/shed_tools”>). If this parameter is not set, a shed-related tool panel configuration file will be selected automatically.
-
uninstall_repository
(trans, *args, **kwargs)[source]¶ DELETE /api/tool_shed_repositories/id DELETE /api/tool_shed_repositories/
Parameters: - id – encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied
- kwd –
- ‘remove_from_disk’ : Remove repository from disk or deactivate repository.
- Defaults to True (= remove repository from disk).
’name’ : Repository name ‘owner’ : Repository owner ‘changeset_revision’: Changeset revision to uninstall ‘tool_shed_url’ : Tool Shed URL
-
repair_repository_revision
(trans, *args, **kwargs)[source]¶ POST /api/tool_shed_repositories/repair_repository_revision Repair a specified repository revision previously installed into Galaxy.
Parameters: key – the current Galaxy admin user’s API key The following parameters are included in the payload. :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed :param name (required): the name of the Repository :param owner (required): the owner of the Repository :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
-
reset_metadata_on_installed_repositories
(trans, *args, **kwargs)[source]¶ PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories
Resets all metadata on all repositories installed into Galaxy in an “orderly fashion”.
Parameters: key – the API key of the Galaxy admin user.
-
galaxy.webapps.galaxy.api.tools module¶
-
class
galaxy.webapps.galaxy.api.tools.
ToolsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesVisualizationMixin
RESTful controller for interactions with tools.
-
index
(trans, *args, **kwargs)[source]¶ GET /api/tools: returns a list of tools defined by parameters:
parameters: in_panel - if true, tools are returned in panel structure, including sections and labels trackster - if true, only tools that are compatible with Trackster are returned q - if present search on the given query will be performed tool_id - if present the given tool_id will be searched for all installed versions
-
show
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}
Returns tool information
parameters:
io_details - if true, parameters and inputs are returned link_details - if true, hyperlink to the tool is returned tool_version - if provided return this tool version
-
build
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/build Returns a tool model including dynamic parameters and updated values, repeats block etc.
-
test_data_path
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version}
-
test_data_download
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename}
-
tests_summary
(trans, *args, **kwargs)[source]¶ GET /api/tools/tests_summary
Fetch summary information for each tool and version combination with tool tests defined. This summary information currently includes tool name and a count of the tests.
Fetch complete test data for each tool with /api/tools/{tool_id}/test_data?tool_version=<tool_version>
-
test_data
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/test_data?tool_version={tool_version}
This API endpoint is unstable and experimental. In particular the format of the response has not been entirely nailed down (it exposes too many Galaxy internals/Pythonisms in a rough way). If this endpoint is being used from outside of scripts shipped with Galaxy let us know and please be prepared for the response from this API to change its format in some ways.
-
all_requirements
(trans, *args, **kwargs)[source]¶ GET /api/tools/all_requirements Return list of unique requirements for all tools.
-
requirements
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/requirements Return the resolver status for a specific tool id. [{“status”: “installed”, “name”: “hisat2”, “versionless”: false, “resolver_type”: “conda”, “version”: “2.0.3”, “type”: “package”}]
-
install_dependencies
(trans, *args, **kwargs)[source]¶ POST /api/tools/{tool_id}/dependencies
This endpoint is also available through POST /api/tools/{tool_id}/install_dependencies, but will be deprecated in the future.
Attempts to install requirements via the dependency resolver
- parameters:
- index: index of dependency resolver to use when installing dependency.
- Defaults to using the highest ranking resolver
resolver_type: Use the dependency resolver of this resolver_type to install dependency. build_dependency_cache: If true, attempts to cache dependencies for this tool force_rebuild: If true and cache dir exists, attempts to delete cache dir
-
uninstall_dependencies
(trans, *args, **kwargs)[source]¶ DELETE /api/tools/{tool_id}/dependencies Attempts to uninstall requirements via the dependency resolver
- parameters:
- index: index of dependency resolver to use when installing dependency.
- Defaults to using the highest ranking resolver
resolver_type: Use the dependency resolver of this resolver_type to install dependency
-
build_dependency_cache
(trans, *args, **kwargs)[source]¶ POST /api/tools/{tool_id}/build_dependency_cache Attempts to cache installed dependencies.
- parameters:
- force_rebuild: If true and chache dir exists, attempts to delete cache dir
-
diagnostics
(trans, *args, **kwargs)[source]¶ GET /api/tools/{tool_id}/diagnostics Return diagnostic information to help debug panel and dependency related problems.
-
galaxy.webapps.galaxy.api.toolshed module¶
-
class
galaxy.webapps.galaxy.api.toolshed.
ToolShedController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
RESTful controller for interactions with tool sheds.
-
index
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed Interact with this galaxy instance’s toolshed registry.
-
status
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/{id}/status Display a dictionary containing information about a specified repository’s installation status and a list of its dependencies and the status of each.
Parameters: id – the repository’s encoded id
-
tool_json
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed_repositories/shed_tool_json
Get the tool form JSON for a tool in a toolshed repository.
Parameters: - guid – the GUID of the tool
- guid – str
- tsr_id – the ID of the repository
- tsr_id – str
- changeset – the changeset at which to load the tool json
- changeset – str
- tool_shed_url – the URL of the toolshed to load from
- tool_shed_url – str
-
show
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed/contents
Display a list of categories in the selected toolshed.
Parameters: tool_shed_url – the url of the toolshed to get categories from
-
category
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed/category
Display a list of repositories in the selected category.
Parameters: - tool_shed_url – the url of the toolshed to get repositories from
- category_id – the category to get repositories from
-
repository
(trans, *args, **kwargs)[source]¶ GET /api/tool_shed/repository
Get details about the specified repository from its shed.
Parameters: - repository_id – the tool_shed_repository_id
- repository_id – str
- tool_shed_url – the URL of the toolshed whence to retrieve repository details
- tool_shed_url – str
- tool_ids – (optional) comma-separated list of tool IDs
- tool_ids – str
-
galaxy.webapps.galaxy.api.tours module¶
API Controller providing Galaxy Tours
-
class
galaxy.webapps.galaxy.api.tours.
ToursController
(app)[source]¶
galaxy.webapps.galaxy.api.uploads module¶
API operations for uploaded files in storage.
galaxy.webapps.galaxy.api.users module¶
API operations on User objects.
-
class
galaxy.webapps.galaxy.api.users.
UserAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesTagsMixin
,galaxy.web.base.controller.CreatesUsersMixin
,galaxy.web.base.controller.CreatesApiKeysMixin
,galaxy.web.base.controller.BaseUIController
,galaxy.web.base.controller.UsesFormDefinitionsMixin
-
index
(trans, *args, **kwargs)[source]¶ GET /api/users GET /api/users/deleted Displays a collection (list) of users.
Parameters: - deleted (bool) – (optional) If true, show deleted users
- f_email (str) – (optional) An email address to filter on. (Non-admin
users can only use this if
expose_user_email
isTrue
in galaxy.ini) - f_name (str) – (optional) A username to filter on. (Non-admin users
can only use this if
expose_user_name
isTrue
in galaxy.ini) - f_any (str) – (optional) Filter on username OR email. (Non-admin users
can use this, the email filter and username filter will
only be active if their corresponding
expose_user_*
isTrue
in galaxy.ini)
-
show
(trans, *args, **kwargs)[source]¶ GET /api/users/{encoded_id} GET /api/users/deleted/{encoded_id} GET /api/users/current Displays information about a user.
-
update
(self, trans, id, payload, **kwd)[source]¶ - PUT /api/users/{id}
- updates the values for the item with the given
id
Parameters: Return type: Returns: an error object if an error occurred or a dictionary containing the serialized item after any changes
-
delete
(trans, *args, **kwargs)[source]¶ DELETE /api/users/{id} delete the user with the given
id
Parameters:
-
anon_user_api_value
(trans)[source]¶ Return data for an anonymous user, truncated to only usage and quota_percent
-
get_information
(trans, *args, **kwargs)[source]¶ GET /api/users/{id}/information/inputs Return user details such as username, email, addresses etc.
Parameters: id (str) – the encoded id of the user
-
set_information
(trans, *args, **kwargs)[source]¶ PUT /api/users/{id}/information/inputs Save a user’s email, username, addresses etc.
Parameters:
-
send_verification_email
(trans, email, username)[source]¶ Send the verification email containing the activation link to the user’s email.
-
get_activation_token
(trans, email)[source]¶ Check for the activation token. Create new activation token and store it in the database if no token found.
-
get_permissions
(trans, *args, **kwargs)[source]¶ Get the user’s default permissions for the new histories
-
set_permissions
(trans, *args, **kwargs)[source]¶ Set the user’s default permissions for the new histories
-
get_toolbox_filters
(trans, *args, **kwargs)[source]¶ API call for fetching toolbox filters data. Toolbox filters are specified in galaxy.ini. The user can activate them and the choice is stored in user_preferences.
-
set_communication
(trans, *args, **kwargs)[source]¶ Allows the user to activate/deactivate the communication server.
-
get_custom_builds
(trans, *args, **kwargs)[source]¶ GET /api/users/{id}/custom_builds Returns collection of custom builds.
Parameters: id (str) – the encoded id of the user
-
galaxy.webapps.galaxy.api.visualizations module¶
Visualizations resource control over the API.
NOTE!: this is a work in progress and functionality and data structures may change often.
-
class
galaxy.webapps.galaxy.api.visualizations.
VisualizationsController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesVisualizationMixin
,galaxy.web.base.controller.SharableMixin
,galaxy.model.item_attrs.UsesAnnotations
RESTful controller for interactions with visualizations.
galaxy.webapps.galaxy.api.webhooks module¶
API Controller providing Galaxy Webhooks
galaxy.webapps.galaxy.api.workflows module¶
API operations for Workflows
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class
galaxy.webapps.galaxy.api.workflows.
WorkflowsAPIController
(app)[source]¶ Bases:
galaxy.web.base.controller.BaseAPIController
,galaxy.web.base.controller.UsesStoredWorkflowMixin
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.web.base.controller.SharableMixin
Get workflows present in the tools panel GET /api/workflows/menu
Save workflow menu to be shown in the tool panel PUT /api/workflows/menu
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get_workflows_list
(trans, kwd)[source]¶ Displays a collection of workflows.
Parameters: - show_published (boolean) – if True, show also published workflows
- missing_tools (boolean) – if True, include a list of missing tools per workflow
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show
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{encoded_workflow_id}
Displays information needed to run a workflow from the command line.
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show_versions
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{encoded_workflow_id}/versions
Lists all versions of this workflow.
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create
(trans, *args, **kwargs)[source]¶ POST /api/workflows
Run or create workflows from the api.
If installed_repository_file or from_history_id is specified a new workflow will be created for this user. Otherwise, workflow_id must be specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified :type installed_repository_file str
Parameters: - workflow_id (str) – An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
- parameters (dict) – If workflow_id is set - see _update_step_parameters()
- ds_map (dict) – If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: ‘src’ (which can be ‘ldda’, ‘ld’ or ‘hda’) and ‘id’ (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
- no_add_to_history (str) – If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
- history (str) – If workflow_id is set - optional history where to run the workflow, either the name of a new history or “hist_id=HIST_ID” where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
- replacement_params (dict) – If workflow_id is set - an optional dictionary used when renaming datasets
- from_history_id (str) – Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
- job_ids (str) – If from_history_id is set - optional list of jobs to include when extracting a workflow from history
- dataset_ids (str) – If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history
- dataset_collection_ids (str) – If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history
- workflow_name (str) – If from_history_id is set - name of the workflow to create when extracting a workflow from history
- allow_tool_state_corrections (bool) – If set to True, any Tool parameter changes will not prevent running workflow, defaults to False
- use_cached_job – If set to True galaxy will attempt to find previously executed steps for all workflow steps with the exact same parameter combinations and will copy the outputs of the previously executed step.
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workflow_dict
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary.
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delete
(trans, *args, **kwargs)[source]¶ DELETE /api/workflows/{encoded_workflow_id} Deletes a specified workflow Author: rpark
copied from galaxy.web.controllers.workflows.py (delete)
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import_new_workflow_deprecated
(trans, *args, **kwargs)[source]¶ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark
# currently assumes payload[‘workflow’] is a json representation of a workflow to be inserted into the database
Deprecated in favor to POST /api/workflows with encoded ‘workflow’ in payload the same way.
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update
(trans, *args, **kwargs)[source]¶ - PUT /api/workflows/{id}
- updates the workflow stored with
id
Parameters: - id (str) – the encoded id of the workflow to update
- payload (dict) –
a dictionary containing any or all the * workflow the json description of the workflow as would be
produced by GET workflows/<id>/download or given to POST workflowsThe workflow contents will be updated to target this.
- name optional string name for the workflow, if not present in payload,
- name defaults to existing name
- annotation optional string annotation for the workflow, if not present in payload,
- annotation defaults to existing annotation
- menu_entry optional boolean marking if the workflow should appear in the user’s menu,
- if not present, workflow menu entries are not modified
Return type: Returns: serialized version of the workflow
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build_module
(trans, *args, **kwargs)[source]¶ POST /api/workflows/build_module Builds module models for the workflow editor.
POST /api/workflows/import Import a workflow shared by other users.
Parameters: workflow_id (str) – the workflow id (required) Raises: exceptions.MessageException, exceptions.ObjectNotFound
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invoke
(trans, *args, **kwargs)[source]¶ POST /api/workflows/{encoded_workflow_id}/invocations
Schedule the workflow specified by workflow_id to run.
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index_invocations
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{workflow_id}/invocations GET /api/invocations
Get the list of a user’s workflow invocations. If workflow_id is supplied (either via URL or query parameter) it should be an encoded StoredWorkflow id and returned invocations will be restricted to that workflow. history_id (an encoded History id) can be used to further restrict the query. If neither a workflow_id or history_id is supplied, all the current user’s workflow invocations will be indexed (as determined by the invocation being executed on one of the user’s histories).
Parameters: - workflow_id (str) – an encoded stored workflow id to restrict query to
- history_id (str) – an encoded history id to restrict query to
- view (str) – level of detail to return per invocation ‘element’ or ‘collection’.
- step_details (bool) – If ‘view’ is ‘element’, also include details on individual steps.
Raises: exceptions.MessageException, exceptions.ObjectNotFound
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show_invocation
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{workflow_id}/invocations/{invocation_id} Get detailed description of workflow invocation
Parameters: - workflow_id (str) – the workflow id (required)
- invocation_id (str) – the invocation id (required)
- step_details (bool) – fetch details about individual invocation steps and populate a steps attribute in the resulting dictionary. Defaults to false.
- legacy_job_state (bool) – If step_details is true, and this is set to true populate the invocation step state with the job state instead of the invocation step state. This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections. Partially scheduled steps may provide incomplete information and the listed steps outputs are the mapped over step outputs but the individual job outputs when this is set - at least for now.
Raises: exceptions.MessageException, exceptions.ObjectNotFound
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cancel_invocation
(trans, *args, **kwargs)[source]¶ DELETE /api/workflows/{workflow_id}/invocations/{invocation_id} Cancel the specified workflow invocation.
Parameters: Raises: exceptions.MessageException, exceptions.ObjectNotFound
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invocation_step
(trans, *args, **kwargs)[source]¶ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}
Parameters: Raises: exceptions.MessageException, exceptions.ObjectNotFound
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update_invocation_step
(trans, *args, **kwargs)[source]¶ PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc….
Parameters: Raises: exceptions.MessageException, exceptions.ObjectNotFound