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Source code for galaxy.webapps.galaxy.api.histories

"""
API operations on a history.

.. seealso:: :class:`galaxy.model.History`
"""
import logging
from typing import (
    Any,
    List,
    Optional,
    Union,
)

from fastapi import (
    Body,
    Depends,
    Path,
    Query,
    Response,
    status,
)
from pydantic.fields import Field
from pydantic.main import BaseModel
from starlette.responses import FileResponse

from galaxy import (
    util
)
from galaxy.managers.context import (
    ProvidesHistoryContext,
    ProvidesUserContext,
)
from galaxy.schema import (
    FilterQueryParams,
    SerializationParams,
)
from galaxy.schema.fields import (
    EncodedDatabaseIdField,
    OrderParamField,
)
from galaxy.schema.schema import (
    AnyHistoryView,
    CreateHistoryPayload,
    CustomBuildsMetadataResponse,
    ExportHistoryArchivePayload,
    HistoryArchiveExportResult,
    JobExportHistoryArchiveCollection,
    JobImportHistoryResponse,
    SetSlugPayload,
    ShareWithPayload,
    ShareWithStatus,
    SharingStatus,
)
from galaxy.schema.types import LatestLiteral
from galaxy.util import (
    string_as_bool
)
from galaxy.web import (
    expose_api,
    expose_api_anonymous,
    expose_api_anonymous_and_sessionless,
    expose_api_raw_anonymous_and_sessionless,
)
from galaxy.webapps.galaxy.api.common import (
    parse_serialization_params,
    query_serialization_params,
)
from galaxy.webapps.galaxy.services.histories import HistoriesService
from . import (
    as_form,
    BaseGalaxyAPIController,
    depends,
    DependsOnTrans,
    Router,
    try_get_request_body_as_json
)

log = logging.getLogger(__name__)

router = Router(tags=['histories'])

HistoryIDPathParam: EncodedDatabaseIdField = Path(
    ...,
    title="History ID",
    description="The encoded database identifier of the History."
)

JehaIDPathParam: Union[EncodedDatabaseIdField, LatestLiteral] = Path(
    default="latest",
    title='Job Export History ID',
    description=(
        'The ID of the specific Job Export History Association or '
        '`latest` (default) to download the last generated archive.'
    ),
    example="latest"
)


[docs]class HistoryFilterQueryParams(FilterQueryParams): order: Optional[str] = OrderParamField(default_order="create_time-dsc")
[docs]class HistoryIndexParams(HistoryFilterQueryParams): all: Optional[bool] = False
[docs]class DeleteHistoryPayload(BaseModel): purge: bool = Field( default=False, title="Purge", description="Whether to definitely remove this history from disk." )
[docs]@as_form class CreateHistoryFormData(CreateHistoryPayload): """Uses Form data instead of JSON"""
[docs]@router.cbv class FastAPIHistories: service: HistoriesService = depends(HistoriesService)
[docs] @router.get( '/api/histories', summary='Returns histories for the current user.', ) def index( self, trans: ProvidesHistoryContext = DependsOnTrans, params: HistoryIndexParams = Depends(HistoryIndexParams), serialization_params: SerializationParams = Depends(query_serialization_params), deleted: bool = Query( # This is for backward compatibility but looks redundant default=False, title="Deleted Only", description="Whether to return only deleted items.", deprecated=True, # Marked as deprecated as it seems just like '/api/histories/deleted' ) ) -> List[AnyHistoryView]: return self.service.index(trans, serialization_params, params, deleted_only=deleted, all_histories=params.all)
[docs] @router.get( '/api/histories/deleted', summary='Returns deleted histories for the current user.', ) def index_deleted( self, trans: ProvidesHistoryContext = DependsOnTrans, params: HistoryIndexParams = Depends(HistoryIndexParams), serialization_params: SerializationParams = Depends(query_serialization_params), ) -> List[AnyHistoryView]: return self.service.index(trans, serialization_params, params, deleted_only=True, all_histories=params.all)
[docs] @router.get( '/api/histories/published', summary='Return all histories that are published.', ) def published( self, trans: ProvidesHistoryContext = DependsOnTrans, serialization_params: SerializationParams = Depends(query_serialization_params), filter_params: HistoryFilterQueryParams = Depends(HistoryFilterQueryParams), ) -> List[AnyHistoryView]: return self.service.published(trans, serialization_params, filter_params)
[docs] @router.get( '/api/histories/shared_with_me', summary='Return all histories that are shared with the current user.', ) def shared_with_me( self, trans: ProvidesHistoryContext = DependsOnTrans, serialization_params: SerializationParams = Depends(query_serialization_params), filter_params: HistoryFilterQueryParams = Depends(HistoryFilterQueryParams), ) -> List[AnyHistoryView]: return self.service.shared_with_me(trans, serialization_params, filter_params)
[docs] @router.get( '/api/histories/most_recently_used', summary='Returns the most recently used history of the user.', ) def show_recent( self, trans: ProvidesHistoryContext = DependsOnTrans, serialization_params: SerializationParams = Depends(query_serialization_params), ) -> AnyHistoryView: return self.service.show(trans, serialization_params)
[docs] @router.get( '/api/histories/{id}', name="history", summary='Returns the history with the given ID.', ) def show( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, serialization_params: SerializationParams = Depends(query_serialization_params), ) -> AnyHistoryView: return self.service.show(trans, serialization_params, id)
[docs] @router.get( '/api/histories/{id}/citations', summary='Return all the citations for the tools used to produce the datasets in the history.', ) def citations( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> List[Any]: return self.service.citations(trans, id)
[docs] @router.post( '/api/histories', summary='Creates a new history.', ) def create( self, trans: ProvidesHistoryContext = DependsOnTrans, payload: CreateHistoryPayload = Depends(CreateHistoryFormData.as_form), payload_as_json: Optional[Any] = Depends(try_get_request_body_as_json), serialization_params: SerializationParams = Depends(query_serialization_params), ) -> Union[JobImportHistoryResponse, AnyHistoryView]: """The new history can also be copied form a existing history or imported from an archive or URL.""" # This action needs to work both with json and x-www-form-urlencoded payloads. # The way to support different content types on the same path operation is reading # the request directly and parse it depending on the content type. # We will assume x-www-form-urlencoded (payload) by default to deal with possible file uploads # and if the content type is explicitly JSON, we will use payload_as_json instead. # See https://github.com/tiangolo/fastapi/issues/990#issuecomment-639615888 if payload_as_json: payload = CreateHistoryPayload.parse_obj(payload_as_json) return self.service.create(trans, payload, serialization_params)
[docs] @router.delete( '/api/histories/{id}', summary='Marks the history with the given ID as deleted.', ) def delete( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, serialization_params: SerializationParams = Depends(query_serialization_params), purge: bool = Query(default=False), payload: Optional[DeleteHistoryPayload] = Body(default=None) ) -> AnyHistoryView: if payload: purge = payload.purge return self.service.delete(trans, id, serialization_params, purge)
[docs] @router.post( '/api/histories/deleted/{id}/undelete', summary="Restores a deleted history with the given ID (that hasn't been purged).", ) def undelete( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, serialization_params: SerializationParams = Depends(query_serialization_params), ) -> AnyHistoryView: return self.service.undelete(trans, id, serialization_params)
[docs] @router.put( '/api/histories/{id}', summary="Updates the values for the history with the given ID.", ) def update( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, payload: Any = Body( ..., description="Object containing any of the editable fields of the history.", ), serialization_params: SerializationParams = Depends(query_serialization_params), ) -> AnyHistoryView: return self.service.update(trans, id, payload, serialization_params)
[docs] @router.get( '/api/histories/{id}/exports', summary=( "Get previous history exports (to links). Effectively returns serialized JEHA objects." ), ) def index_exports( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> JobExportHistoryArchiveCollection: exports = self.service.index_exports(trans, id) return JobExportHistoryArchiveCollection.parse_obj(exports)
[docs] @router.put( # PUT instead of POST because multiple requests should just result in one object being created. '/api/histories/{id}/exports', summary=( "Start job (if needed) to create history export for corresponding history." ), responses={ 200: { "description": "Object containing url to fetch export from.", }, 202: { "description": "The exported archive file is not ready yet.", } }, ) def archive_export( self, response: Response, trans=DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, payload: Optional[ExportHistoryArchivePayload] = Body(None), ) -> HistoryArchiveExportResult: """This will start a job to create a history export archive. Calling this endpoint multiple times will return the 202 status code until the archive has been completely generated and is ready to download. When ready, it will return the 200 status code along with the download link information. If the history will be exported to a `directory_uri`, instead of returning the download link information, the Job ID will be returned so it can be queried to determine when the file has been written. """ export_result, ready = self.service.archive_export(trans, id, payload) if not ready: response.status_code = status.HTTP_202_ACCEPTED return export_result
[docs] @router.get( '/api/histories/{id}/exports/{jeha_id}', name="history_archive_download", summary=( "If ready and available, return raw contents of exported history as a downloadable archive." ), response_class=FileResponse, responses={ 200: { "description": "The archive file containing the History.", } }, ) def archive_download( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, jeha_id: Union[EncodedDatabaseIdField, LatestLiteral] = JehaIDPathParam, ): """ See ``PUT /api/histories/{id}/exports`` to initiate the creation of the history export - when ready, that route will return 200 status code (instead of 202) and this route can be used to download the archive. """ jeha = self.service.get_ready_history_export(trans, id, jeha_id) media_type = self.service.get_archive_media_type(jeha) file_path = self.service.get_archive_download_path(trans, jeha) return FileResponse( path=file_path, media_type=media_type, filename=jeha.export_name, )
[docs] @router.get( '/api/histories/{id}/custom_builds_metadata', summary="Returns meta data for custom builds.", ) def get_custom_builds_metadata( self, trans: ProvidesHistoryContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> CustomBuildsMetadataResponse: return self.service.get_custom_builds_metadata(trans, id)
[docs] @router.get( '/api/histories/{id}/sharing', summary="Get the current sharing status of the given item.", ) def sharing( self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> SharingStatus: """Return the sharing status of the item.""" return self.service.shareable_service.sharing(trans, id)
[docs] @router.put( '/api/histories/{id}/publish', summary="Makes this item public and accessible by a URL link.", ) def publish( self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> SharingStatus: """Makes this item publicly available by a URL link and return the current sharing status.""" return self.service.shareable_service.publish(trans, id)
[docs] @router.put( '/api/histories/{id}/unpublish', summary="Removes this item from the published list.", ) def unpublish( self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, ) -> SharingStatus: """Removes this item from the published list and return the current sharing status.""" return self.service.shareable_service.unpublish(trans, id)
[docs] @router.put( '/api/histories/{id}/share_with_users', summary="Share this item with specific users.", ) def share_with_users( self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, payload: ShareWithPayload = Body(...) ) -> ShareWithStatus: """Shares this item with specific users and return the current sharing status.""" return self.service.shareable_service.share_with_users(trans, id, payload)
[docs] @router.put( '/api/histories/{id}/slug', summary="Set a new slug for this shared item.", status_code=status.HTTP_204_NO_CONTENT, ) def set_slug( self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = HistoryIDPathParam, payload: SetSlugPayload = Body(...), ): """Sets a new slug to access this item by URL. The new slug must be unique.""" self.service.shareable_service.set_slug(trans, id, payload) return Response(status_code=status.HTTP_204_NO_CONTENT)
[docs]class HistoriesController(BaseGalaxyAPIController): service: HistoriesService = depends(HistoriesService)
[docs] @expose_api_anonymous def index(self, trans, deleted='False', **kwd): """ 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 :type deleted: boolean :param deleted: if True, show only deleted histories, if False, non-deleted :rtype: 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 all: boolean, defaults to 'false', admin-only returns all histories, not just current user's 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' """ deleted_only = util.string_as_bool(deleted) all_histories = util.string_as_bool(kwd.get('all', False)) serialization_params = parse_serialization_params(**kwd) filter_parameters = HistoryFilterQueryParams(**kwd) return self.service.index(trans, serialization_params, filter_parameters, deleted_only, all_histories)
[docs] @expose_api_anonymous def show(self, trans, id, deleted='False', **kwd): """ show( trans, id, deleted='False' ) * 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 :type id: an encoded id string :param id: the encoded id of the history to query or the string 'most_recently_used' :type deleted: boolean :param deleted: if True, allow information on a deleted history to be shown. :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dictionary :returns: detailed history information """ history_id = id if history_id == "most_recently_used": history_id = None # Will default to the most recently used serialization_params = parse_serialization_params(**kwd) return self.service.show(trans, serialization_params, history_id)
[docs] @expose_api_anonymous def citations(self, trans, history_id, **kwd): """ GET /api/histories/{id}/citations Return all the citations for the tools used to produce the datasets in the history. """ return self.service.citations(trans, history_id)
[docs] @expose_api_anonymous_and_sessionless def published(self, trans, **kwd): """ GET /api/histories/published return all histories that are published :rtype: list :returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above. """ serialization_params = parse_serialization_params(**kwd) filter_parameters = HistoryFilterQueryParams(**kwd) return self.service.published(trans, serialization_params, filter_parameters)
[docs] @expose_api def shared_with_me(self, trans, **kwd): """ shared_with_me( self, trans, **kwd ) * GET /api/histories/shared_with_me: return all histories that are shared with the current user :rtype: list :returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above. """ serialization_params = parse_serialization_params(**kwd) filter_parameters = HistoryFilterQueryParams(**kwd) return self.service.shared_with_me(trans, serialization_params, filter_parameters)
[docs] @expose_api_anonymous def create(self, trans, payload, **kwd): """ create( trans, payload ) * POST /api/histories: create a new history :type payload: dict :param payload: (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) :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: element view of new history """ create_payload = CreateHistoryPayload(**payload) serialization_params = parse_serialization_params(**kwd) return self.service.create(trans, create_payload, serialization_params)
[docs] @expose_api def delete(self, trans, id, **kwd): """ DELETE /api/histories/{id} delete the history with the given ``id`` .. note:: Stops all active jobs in the history if purge is set. :type id: str :param id: the encoded id of the history to delete :type kwd: dict :param kwd: (optional) dictionary structure containing extra parameters You can purge a history, removing all it's datasets from disk (if unshared), by passing in ``purge=True`` in the url. :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: the deleted or purged history """ history_id = id # a request body is optional here purge = string_as_bool(kwd.get('purge', False)) # for backwards compat, keep the payload sub-dictionary if kwd.get('payload', None): purge = string_as_bool(kwd['payload'].get('purge', purge)) serialization_params = parse_serialization_params(**kwd) return self.service.delete(trans, history_id, serialization_params, purge)
[docs] @expose_api def undelete(self, trans, id, **kwd): """ undelete( self, trans, id, **kwd ) * POST /api/histories/deleted/{id}/undelete: undelete history (that hasn't been purged) with the given ``id`` :type id: str :param id: the encoded id of the history to undelete :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: str :returns: 'OK' if the history was undeleted """ serialization_params = parse_serialization_params(**kwd) return self.service.undelete(trans, id, serialization_params)
[docs] @expose_api def update(self, trans, id, payload, **kwd): """ update( self, trans, id, payload, **kwd ) * PUT /api/histories/{id} updates the values for the history with the given ``id`` :type id: str :param id: the encoded id of the history to update :type payload: dict :param payload: a dictionary containing any or all the fields in :func:`galaxy.model.History.to_dict` and/or the following: * annotation: an annotation for the history :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: an error object if an error occurred or a dictionary containing any values that were different from the original and, therefore, updated """ # TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) serialization_params = parse_serialization_params(**kwd) return self.service.update(trans, id, payload, serialization_params)
[docs] @expose_api def index_exports(self, trans, id): """ GET /api/histories/{id}/exports Get previous history exports (to links). Effectively returns serialized JEHA objects. """ return self.service.index_exports(trans, id)
[docs] @expose_api def archive_export(self, trans, id, payload=None, **kwds): """ PUT /api/histories/{id}/exports start job (if needed) to create history export for corresponding history. :type id: str :param id: the encoded id of the history to export :rtype: dict :returns: object containing url to fetch export from. """ # PUT instead of POST because multiple requests should just result # in one object being created. payload = payload or {} payload.update(kwds or {}) export_payload = ExportHistoryArchivePayload(**payload) export_result, ready = self.service.archive_export(trans, id, export_payload) if not ready: trans.response.status = 202 return export_result
[docs] @expose_api_raw_anonymous_and_sessionless def archive_download(self, trans, id, jeha_id, **kwds): """ 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``. """ # TODO: remove the HistoriesService.legacy_archive_download function when # removing this endpoint return self.service.legacy_archive_download(trans, id, jeha_id)
[docs] @expose_api def get_custom_builds_metadata(self, trans, id, payload=None, **kwd): """ GET /api/histories/{id}/custom_builds_metadata Returns meta data for custom builds. :param id: the encoded history id :type id: str """ return self.service.get_custom_builds_metadata(trans, id)
[docs] @expose_api def sharing(self, trans, id, **kwd): """ * GET /api/histories/{id}/sharing """ return self.service.shareable_service.sharing(trans, id)
[docs] @expose_api def publish(self, trans, id, **kwd): """ * PUT /api/histories/{id}/publish """ return self.service.shareable_service.publish(trans, id)
[docs] @expose_api def unpublish(self, trans, id, **kwd): """ * PUT /api/histories/{id}/unpublish """ return self.service.shareable_service.unpublish(trans, id)
[docs] @expose_api def share_with_users(self, trans, id, payload, **kwd): """ * PUT /api/histories/{id}/share_with_users """ payload = ShareWithPayload(**payload) return self.service.shareable_service.share_with_users(trans, id, payload)
[docs] @expose_api def set_slug(self, trans, id, payload, **kwd): """ * PUT /api/histories/{id}/slug """ payload = SetSlugPayload(**payload) self.service.shareable_service.set_slug(trans, id, payload)