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Source code for galaxy.webapps.galaxy.services.history_contents
import datetime
import logging
import os
import re
from enum import Enum
from typing import (
Any,
Dict,
List,
Optional,
Set,
Union,
)
from pydantic import (
Extra,
Field,
)
from typing_extensions import Literal
from galaxy import (
exceptions,
)
from galaxy.managers import (
folders,
hdas,
hdcas,
histories,
history_contents
)
from galaxy.managers.base import (
ModelSerializer,
)
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.collections_util import (
api_payload_to_create_params,
dictify_dataset_collection_instance,
)
from galaxy.managers.jobs import (
fetch_job_states,
summarize_jobs_to_dict,
)
from galaxy.managers.library_datasets import LibraryDatasetsManager
from galaxy.model import (
History,
HistoryDatasetAssociation,
HistoryDatasetCollectionAssociation,
LibraryDataset,
)
from galaxy.model.security import GalaxyRBACAgent
from galaxy.schema import (
FilterQueryParams,
SerializationParams,
)
from galaxy.schema.fields import (
EncodedDatabaseIdField,
)
from galaxy.schema.schema import (
AnyHistoryContentItem,
AnyJobStateSummary,
ContentsNearResult,
ContentsNearStats,
CreateNewCollectionPayload,
DatasetAssociationRoles,
DeleteHistoryContentPayload,
DeleteHistoryContentResult,
HistoryContentsArchiveDryRunResult,
HistoryContentSource,
HistoryContentType,
JobSourceType,
Model,
UpdateDatasetPermissionsPayload,
UpdateHistoryContentsBatchPayload,
)
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.util.zipstream import ZipstreamWrapper
from galaxy.webapps.galaxy.api.common import parse_serialization_params
from galaxy.webapps.galaxy.services.base import ServiceBase
log = logging.getLogger(__name__)
DatasetDetailsType = Union[Set[EncodedDatabaseIdField], Literal['all']]
HistoryContentFilter = List[Any] # Lists with [attribute:str, operator:str, value:Any]
HistoryContentsFilterList = List[HistoryContentFilter]
[docs]class HistoryContentsIndexParams(Model):
"""Query parameters exclusively used by the *new version* of `index` operation."""
v: Optional[Literal['dev']]
dataset_details: Optional[DatasetDetailsType]
[docs]class LegacyHistoryContentsIndexParams(Model):
"""Query parameters exclusively used by the *legacy version* of `index` operation."""
ids: Optional[List[EncodedDatabaseIdField]]
types: List[HistoryContentType]
dataset_details: Optional[DatasetDetailsType]
deleted: Optional[bool]
visible: Optional[bool]
[docs]class HistoryContentsIndexJobsSummaryParams(Model):
"""Query parameters exclusively used by the `index_jobs_summary` operation."""
ids: List[EncodedDatabaseIdField] = []
types: List[JobSourceType] = []
[docs]class CreateHistoryContentPayloadBase(Model):
type: Optional[HistoryContentType] = Field(
HistoryContentType.dataset,
title="Type",
description="The type of content to be created in the history.",
)
[docs]class CreateHistoryContentPayloadFromCopy(CreateHistoryContentPayloadBase):
source: Optional[HistoryContentSource] = Field(
None,
title="Source",
description="The source of the content. Can be other history element to be copied or library elements.",
)
content: Optional[EncodedDatabaseIdField] = Field(
None,
title="Content",
description=(
"Depending on the `source` it can be:\n"
"- The encoded id from the library dataset\n"
"- The encoded id from the library folder\n"
"- The encoded id from the HDA\n"
"- The encoded id from the HDCA\n"
),
)
[docs]class CreateHistoryContentPayloadFromCollection(CreateHistoryContentPayloadFromCopy):
dbkey: Optional[str] = Field(
default=None,
title="DBKey",
description="TODO",
)
copy_elements: Optional[bool] = Field(
default=False,
title="Copy Elements",
description=(
"If the source is a collection, whether to 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."
),
)
[docs]class CreateHistoryContentPayload(CreateHistoryContentPayloadFromCollection, CreateNewCollectionPayload):
[docs]class HistoriesContentsService(ServiceBase):
"""Common interface/service logic for interactions with histories contents in the context of the API.
Provides the logic of the actions invoked by API controllers and uses type definitions
and pydantic models to declare its parameters and return types.
"""
[docs] def __init__(
self,
security: IdEncodingHelper,
history_manager: histories.HistoryManager,
history_contents_manager: history_contents.HistoryContentsManager,
hda_manager: hdas.HDAManager,
dataset_collection_manager: DatasetCollectionManager,
ldda_manager: LibraryDatasetsManager,
folder_manager: folders.FolderManager,
hda_serializer: hdas.HDASerializer,
hda_deserializer: hdas.HDADeserializer,
hdca_serializer: hdcas.HDCASerializer,
history_contents_filters: history_contents.HistoryContentsFilters,
):
super().__init__(security)
self.history_manager = history_manager
self.history_contents_manager = history_contents_manager
self.hda_manager = hda_manager
self.dataset_collection_manager = dataset_collection_manager
self.ldda_manager = ldda_manager
self.folder_manager = folder_manager
self.hda_serializer = hda_serializer
self.hda_deserializer = hda_deserializer
self.hdca_serializer = hdca_serializer
self.history_contents_filters = history_contents_filters
[docs] def index(
self,
trans,
history_id: EncodedDatabaseIdField,
params: HistoryContentsIndexParams,
legacy_params: LegacyHistoryContentsIndexParams,
serialization_params: SerializationParams,
filter_query_params: FilterQueryParams,
) -> List[AnyHistoryContentItem]:
"""
Return a list of contents (HDAs and HDCAs) for the history with the given ``ID``.
.. note:: Anonymous users are allowed to get their current history contents.
"""
if params.v == 'dev':
return self.__index_v2(
trans, history_id, params, serialization_params, filter_query_params
)
return self.__index_legacy(trans, history_id, legacy_params)
[docs] def show(
self,
trans,
id: EncodedDatabaseIdField,
serialization_params: SerializationParams,
contents_type: HistoryContentType,
fuzzy_count: Optional[int] = None,
) -> AnyHistoryContentItem:
"""
Return detailed information about an HDA or HDCA within a history
.. note:: Anonymous users are allowed to get their current history contents
:param id: the encoded id of the HDA or HDCA to return
:param contents_type: 'dataset' or 'dataset_collection'
:param serialization_params.view: 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'.
:param fuzzy_count: 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.
:returns: dictionary containing detailed HDA or HDCA information
"""
if contents_type == HistoryContentType.dataset:
return self.__show_dataset(trans, id, serialization_params)
elif contents_type == HistoryContentType.dataset_collection:
return self.__show_dataset_collection(trans, id, serialization_params, fuzzy_count)
raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
[docs] def index_jobs_summary(
self, trans,
params: HistoryContentsIndexJobsSummaryParams,
) -> List[AnyJobStateSummary]:
"""
Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations
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.
"""
ids = params.ids
types = params.types
if len(ids) != len(types):
raise exceptions.RequestParameterInvalidException(
f"The number of ids ({len(ids)}) and types ({len(types)}) must match."
)
decoded_ids = self.decode_ids(ids)
return [
self.encode_all_ids(job_state)
for job_state in fetch_job_states(trans.sa_session, decoded_ids, types)
]
[docs] def show_jobs_summary(
self, trans,
id: EncodedDatabaseIdField,
contents_type: HistoryContentType,
) -> AnyJobStateSummary:
"""
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.
:param id: the encoded id of the HDA or HDCA to return
:param contents_type: 'dataset' or 'dataset_collection'
:returns: dictionary containing jobs summary object
"""
# At most one of job or implicit_collection_jobs should be found.
job = None
implicit_collection_jobs = None
if contents_type == HistoryContentType.dataset:
hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
job = hda.creating_job
elif contents_type == HistoryContentType.dataset_collection:
dataset_collection_instance = self.__get_accessible_collection(trans, id)
job_source_type = dataset_collection_instance.job_source_type
if job_source_type == JobSourceType.Job:
job = dataset_collection_instance.job
elif job_source_type == JobSourceType.ImplicitCollectionJobs:
implicit_collection_jobs = dataset_collection_instance.implicit_collection_jobs
assert job is None or implicit_collection_jobs is None
return self.encode_all_ids(summarize_jobs_to_dict(trans.sa_session, job or implicit_collection_jobs))
[docs] def get_dataset_collection_archive_for_download(self, trans, id: EncodedDatabaseIdField):
"""
Download the content of a HistoryDatasetCollection as a tgz archive
while maintaining approximate collection structure.
:param id: encoded HistoryDatasetCollectionAssociation (HDCA) id
"""
try:
dataset_collection_instance = self.__get_accessible_collection(trans, id)
return self.__stream_dataset_collection(trans, dataset_collection_instance)
except Exception:
error_message = "Error in API while creating dataset collection archive"
log.exception(error_message)
raise exceptions.InternalServerError(error_message)
def __stream_dataset_collection(self, trans, dataset_collection_instance):
archive = hdcas.stream_dataset_collection(dataset_collection_instance=dataset_collection_instance, upstream_mod_zip=trans.app.config.upstream_mod_zip)
return archive
[docs] def create(
self, trans,
history_id: EncodedDatabaseIdField,
payload: CreateHistoryContentPayload,
serialization_params: SerializationParams,
) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
"""
Create a new HDA or HDCA.
..note:
Currently, a user can only copy an HDA from a history that the user owns.
"""
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
serialization_params.default_view = "detailed"
history_content_type = payload.type
if history_content_type == HistoryContentType.dataset:
source = payload.source
if source == HistoryContentSource.library_folder:
return self.__create_datasets_from_library_folder(trans, history, payload, serialization_params)
else:
return self.__create_dataset(trans, history, payload, serialization_params)
elif history_content_type == HistoryContentType.dataset_collection:
return self.__create_dataset_collection(trans, history, payload, serialization_params)
raise exceptions.UnknownContentsType(f'Unknown contents type: {payload.type}')
[docs] def update_permissions(
self, trans,
history_content_id: EncodedDatabaseIdField,
payload: UpdateDatasetPermissionsPayload,
) -> DatasetAssociationRoles:
"""
Set permissions of the given dataset to the given role ids.
:type payload: dict
:param payload: dictionary structure containing:
- action: (required) describes what action should be performed.
Available actions: make_private, remove_restrictions, set_permissions
- access_ids[]: list of Role.id defining roles that should have access permission on the dataset
- manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset
- modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item
:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
RequestParameterMissingException
"""
payload_dict = payload.dict(by_alias=True)
hda = self.hda_manager.get_owned(self.decode_id(history_content_id), trans.user, current_history=trans.history, trans=trans)
assert hda is not None
self.hda_manager.update_permissions(trans, hda, **payload_dict)
roles = self.hda_manager.serialize_dataset_association_roles(trans, hda)
return DatasetAssociationRoles.parse_obj(roles)
[docs] def update(
self, trans,
history_id: EncodedDatabaseIdField,
id: EncodedDatabaseIdField,
payload: Dict[str, Any],
serialization_params: SerializationParams,
contents_type: HistoryContentType,
):
"""
Updates the values for the history content item with the given ``id``
:param history_id: encoded id string of the items's History
:param id: the encoded id of the history item to update
:param payload: a dictionary containing any or all the fields for
HDA or HDCA with values different than the defaults
:returns: an error object if an error occurred or a dictionary containing
any values that were different from the original and, therefore, updated
"""
if contents_type == HistoryContentType.dataset:
return self.__update_dataset(trans, history_id, id, payload, serialization_params)
elif contents_type == HistoryContentType.dataset_collection:
return self.__update_dataset_collection(trans, id, payload)
else:
raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
[docs] def update_batch(
self, trans,
history_id: EncodedDatabaseIdField,
payload: UpdateHistoryContentsBatchPayload,
serialization_params: SerializationParams,
) -> List[AnyHistoryContentItem]:
"""
PUT /api/histories/{history_id}/contents
:type history_id: str
:param history_id: encoded id string of the history containing supplied items
: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
: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
"""
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
items = payload.items
hda_ids = []
hdca_ids = []
for item in items:
contents_type = item.history_content_type
if contents_type == HistoryContentType.dataset:
decoded_id = self.decode_id(item.id)
hda_ids.append(decoded_id)
else:
hdca_ids.append(item.id)
payload_dict = payload.dict(exclude_unset=True)
hdas = self.__datasets_for_update(trans, history, hda_ids, payload_dict)
rval = []
for hda in hdas:
self.__deserialize_dataset(trans, hda, payload_dict)
serialization_params.default_view = "summary"
rval.append(self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
))
for hdca_id in hdca_ids:
self.__update_dataset_collection(trans, hdca_id, payload.dict(exclude_defaults=True))
dataset_collection_instance = self.__get_accessible_collection(trans, hdca_id)
rval.append(self.__collection_dict(trans, dataset_collection_instance, view="summary"))
return rval
[docs] def validate(
self, trans,
history_id: EncodedDatabaseIdField,
history_content_id: EncodedDatabaseIdField
):
"""
Validates the metadata associated with a dataset within a History.
:type history_id: str
:param history_id: encoded id string of the items's History
:type id: str
:param id: the encoded id of the history item to validate
:rtype: dict
:returns: TODO
"""
decoded_id = self.decode_id(history_content_id)
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
hda = self.hda_manager.get_owned_ids([decoded_id], history=history)[0]
if hda:
self.hda_manager.set_metadata(trans, hda, overwrite=True, validate=True)
return {}
[docs] def delete(
self, trans,
id,
serialization_params: SerializationParams,
contents_type: HistoryContentType,
payload: DeleteHistoryContentPayload,
) -> DeleteHistoryContentResult:
"""
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.
"""
if contents_type == HistoryContentType.dataset:
return self.__delete_dataset(trans, id, payload.purge, serialization_params)
elif contents_type == HistoryContentType.dataset_collection:
self.dataset_collection_manager.delete(
trans, "history", id, recursive=payload.recursive, purge=payload.purge
)
return DeleteHistoryContentResult(id=id, deleted=True)
else:
raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
[docs] def archive(
self, trans,
history_id: EncodedDatabaseIdField,
filter_query_params: FilterQueryParams,
filename: Optional[str] = '',
dry_run: Optional[bool] = True,
) -> Union[HistoryContentsArchiveDryRunResult, ZipstreamWrapper]:
"""
Build and return a compressed archive of the selected history contents
:type filename: string
:param filename: (optional) archive name (defaults to history name)
:type dry_run: boolean
:param dry_run: (optional) if True, return the archive and file paths only
as json and not an archive file
:returns: archive file for download or json in `dry run` mode
"""
# roughly from: http://stackoverflow.com/a/31976060 (windows, linux)
invalid_filename_char_regex = re.compile(r'[:<>|\\\/\?\* "]')
# path format string - dot separator between id and name
id_name_format = '{}.{}'
def name_to_filename(name, max_length=150, replace_with='_'):
# TODO: seems like shortening unicode with [:] would cause unpredictable display strings
return invalid_filename_char_regex.sub(replace_with, name)[0:max_length]
# given a set of parents for a dataset (HDCAs, DC, DCEs, etc.) - build a directory structure that
# (roughly) recreates the nesting in the contents using the parent names and ids
def build_path_from_parents(parents):
parent_names = []
for parent in parents:
# an HDCA
if hasattr(parent, 'hid'):
name = name_to_filename(parent.name)
parent_names.append(id_name_format.format(parent.hid, name))
# a DCE
elif hasattr(parent, 'element_index'):
name = name_to_filename(parent.element_identifier)
parent_names.append(id_name_format.format(parent.element_index, name))
# NOTE: DCs are skipped and use the wrapping DCE info instead
return parent_names
# get the history used for the contents query and check for accessibility
history = self.history_manager.get_accessible(trans.security.decode_id(history_id), trans.user)
archive_base_name = filename or name_to_filename(history.name)
# this is the fn applied to each dataset contained in the query
paths_and_files = []
def build_archive_files_and_paths(content, *parents):
archive_path = archive_base_name
if not self.hda_manager.is_accessible(content, trans.user):
# if the underlying dataset is not accessible, skip it silently
return
content_container_id = content.hid
content_name = name_to_filename(content.name)
if parents:
if hasattr(parents[0], 'element_index'):
# if content is directly wrapped in a DCE, strip it from parents (and the resulting path)
# and instead replace the content id and name with the DCE index and identifier
parent_dce, parents = parents[0], parents[1:]
content_container_id = parent_dce.element_index
content_name = name_to_filename(parent_dce.element_identifier)
# reverse for path from parents: oldest parent first
archive_path = os.path.join(archive_path, *build_path_from_parents(parents)[::-1])
# TODO: this is brute force - building the path each time instead of re-using it
# possibly cache
# add the name as the last element in the archive path
content_id_and_name = id_name_format.format(content_container_id, content_name)
archive_path = os.path.join(archive_path, content_id_and_name)
# ---- for composite files, we use id and name for a directory and, inside that, ...
if self.hda_manager.is_composite(content):
# ...save the 'main' composite file (gen. html)
paths_and_files.append((content.file_name, os.path.join(archive_path, f"{content.name}.html")))
for extra_file in self.hda_manager.extra_files(content):
extra_file_basename = os.path.basename(extra_file)
archive_extra_file_path = os.path.join(archive_path, extra_file_basename)
# ...and one for each file in the composite
paths_and_files.append((extra_file, archive_extra_file_path))
# ---- for single files, we add the true extension to id and name and store that single filename
else:
# some dataset names can contain their original file extensions, don't repeat
if not archive_path.endswith(f".{content.extension}"):
archive_path += f".{content.extension}"
paths_and_files.append((content.file_name, archive_path))
# filter the contents that contain datasets using any filters possible from index above and map the datasets
filters = self.history_contents_filters.parse_query_filters(filter_query_params)
self.history_contents_manager.map_datasets(history, build_archive_files_and_paths, filters=filters)
# if dry_run, return the structure as json for debugging
if dry_run:
return HistoryContentsArchiveDryRunResult.parse_obj(paths_and_files)
# create the archive, add the dataset files, then stream the archive as a download
archive = ZipstreamWrapper(
archive_name=archive_base_name,
upstream_mod_zip=trans.app.config.upstream_mod_zip,
upstream_gzip=trans.app.config.upstream_gzip,
)
for file_path, archive_path in paths_and_files:
archive.write(file_path, archive_path)
return archive
[docs] def contents_near(
self, trans,
history_id: EncodedDatabaseIdField,
serialization_params: SerializationParams,
filter_params: HistoryContentsFilterList,
direction: DirectionOptions,
hid: int,
limit: int,
since: Optional[datetime.datetime] = None,
) -> Optional[ContentsNearResult]:
"""
Return {limit} history items "near" the {hid}. The {direction} determines what items
are selected:
- before: select items with hid < {hid}
- after: select items with hid > {hid}
- near: select items "around" {hid}, so that
n. items before <= limit // 2,
n. items after <= limit // 2 + 1
Additional counts provided in the HTTP headers.
"""
history: History = self.history_manager.get_accessible(
self.decode_id(history_id), trans.user, current_history=trans.history
)
# while polling, check to see if the history has changed
# if it hasn't then we can short-circuit the poll request
if since:
# sqlalchemy DateTime columns are not timezone aware, but `since` may be a timezone aware
# DateTime object if a timezone offset is provided (https://github.com/samuelcolvin/pydantic/blob/5ccbdcb5904f35834300b01432a665c75dc02296/pydantic/datetime_parse.py#L179).
# If a timezone is provided (since.tzinfo is not None) we convert to UTC and remove tzinfo so that comparison with history.update_time is correct.
since = since if since.tzinfo is None else since.astimezone(datetime.timezone.utc).replace(tzinfo=None)
if history.update_time <= since:
return None
order_by_dsc = self.build_order_by(self.history_contents_manager, 'hid-dsc')
order_by_asc = self.build_order_by(self.history_contents_manager, 'hid-asc')
min_hid, max_hid = self._get_filtered_extrema(history, filter_params, order_by_dsc, order_by_asc)
up_total_count, down_total_count = self._get_total_counts(history, filter_params, hid)
if direction == DirectionOptions.after: # seek up: contents > hid (newer)
_hid_params = self._hid_greater_than(hid)
matches = self._get_matches(history, filter_params, _hid_params, order_by_asc, limit, serialization_params)
expanded = self._expand_contents(trans, matches, serialization_params)
expanded.reverse()
item_counts = self._set_item_counts(
matches_up=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count)
elif direction == DirectionOptions.before: # seek down: contents <= hid (older)
_hid_params = self._hid_less_than(hid)
matches = self._get_matches(history, filter_params, _hid_params, order_by_dsc, limit, serialization_params)
expanded = self._expand_contents(trans, matches, serialization_params)
item_counts = self._set_item_counts(
matches_down=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count)
elif direction == DirectionOptions.near: # seek up, down; then reverse up, and combine
up_limit, down_limit = self._get_limits(limit)
_hid_params = self._hid_greater_than(hid)
up_matches = self._get_matches(history, filter_params, _hid_params, order_by_asc, up_limit, serialization_params)
up_expanded = self._expand_contents(trans, up_matches, serialization_params)
up_expanded.reverse()
_hid_params = self._hid_less_or_equal_than(hid) # note <=: we are including the item with hid == {hid}
down_matches = self._get_matches(history, filter_params, _hid_params, order_by_dsc, down_limit, serialization_params)
down_expanded = self._expand_contents(trans, down_matches, serialization_params)
expanded = up_expanded + down_expanded
item_counts = self._set_item_counts(
matches_up=len(up_matches), matches_down=len(down_matches), total_matches_up=up_total_count,
total_matches_down=down_total_count)
stats = ContentsNearStats(
max_hid=max_hid,
min_hid=min_hid,
history_size=history.disk_size,
history_empty=history.empty,
**item_counts,
)
return ContentsNearResult(contents=expanded, stats=stats)
def _get_limits(self, limit):
q, r = divmod(limit, 2)
return q, q + r
def _set_item_counts(self, *, matches_up=0, total_matches_up=0, matches_down=0, total_matches_down=0):
counts = {}
counts['matches'] = matches_up + matches_down
counts['matches_up'] = matches_up
counts['matches_down'] = matches_down
counts['total_matches'] = total_matches_up + total_matches_down + 1 # + 1 for hid == {hid}
counts['total_matches_up'] = total_matches_up
counts['total_matches_down'] = total_matches_down
return counts
def _hid_greater_than(self, hid: int) -> HistoryContentsFilterList:
return [["hid", "gt", hid]]
def _hid_less_than(self, hid: int) -> HistoryContentsFilterList:
return [["hid", "lt", hid]]
def _hid_less_or_equal_than(self, hid: int) -> HistoryContentsFilterList:
return [["hid", "le", hid]]
def _get_total_counts(self, history, filter_params, hid):
def get_count(params, hid_params):
params = params + hid_params
count_filters = self.history_contents_filters.parse_filters(params)
return self.history_contents_manager.contents_count(history, count_filters)
params = self._copy_excluding_update_time(filter_params)
total_up = get_count(params, self._hid_greater_than(hid))
total_down = get_count(params, self._hid_less_than(hid))
return total_up, total_down
def _get_matches(self, history, filter_params, hid_params, order_by, limit, serialization_params):
params = filter_params + hid_params
filters = self.history_contents_filters.parse_filters(params)
contents = self.history_contents_manager.contents(history,
filters=filters,
limit=limit,
offset=0,
order_by=order_by,
serialization_params=serialization_params)
return contents
def _copy_excluding_update_time(self, filter_params):
return [f for f in filter_params if f[0] != 'update_time']
# Adds subquery details to initial contents results, perhaps better realized
# as a proc or view.
def _expand_contents(self, trans, contents, serialization_params: SerializationParams):
rval = []
for content in contents:
if isinstance(content, HistoryDatasetAssociation):
dataset = self.hda_serializer.serialize_to_view(content,
user=trans.user, trans=trans, **serialization_params.dict())
rval.append(dataset)
elif isinstance(content, HistoryDatasetCollectionAssociation):
collection = self.hdca_serializer.serialize_to_view(content,
user=trans.user, trans=trans, **serialization_params.dict())
rval.append(collection)
return rval
def _get_filtered_extrema(self, history, filter_params, order_by_dsc, order_by_asc):
extrema_params = parse_serialization_params(keys='hid', default_view='summary')
extrema_filter_params = self._copy_excluding_update_time(filter_params)
extrema_filters = self.history_contents_filters.parse_filters(extrema_filter_params)
max_row_result = self.history_contents_manager.contents(history,
limit=1,
filters=extrema_filters,
order_by=order_by_dsc,
serialization_params=extrema_params)
max_row = max_row_result.pop() if len(max_row_result) else None
min_row_result = self.history_contents_manager.contents(history,
limit=1,
filters=extrema_filters,
order_by=order_by_asc,
serialization_params=extrema_params)
min_row = min_row_result.pop() if len(min_row_result) else None
max_hid = max_row.hid if max_row else None
min_hid = min_row.hid if min_row else None
return min_hid, max_hid
def __delete_dataset(
self, trans,
id: EncodedDatabaseIdField,
purge: bool,
serialization_params: SerializationParams
):
hda = self.hda_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
self.hda_manager.error_if_uploading(hda)
if purge:
self.hda_manager.purge(hda)
else:
self.hda_manager.delete(hda)
serialization_params.default_view = 'detailed'
return self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
)
def __update_dataset_collection(self, trans, id: EncodedDatabaseIdField, payload: Dict[str, Any]):
return self.dataset_collection_manager.update(trans, "history", id, payload)
def __update_dataset(
self, trans,
history_id: EncodedDatabaseIdField,
id: EncodedDatabaseIdField,
payload: Dict[str, Any],
serialization_params: SerializationParams
):
# anon user: ensure that history ids match up and the history is the current,
# check for uploading, and use only the subset of attribute keys manipulatable by anon users
decoded_id = self.decode_id(id)
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
hda = self.__datasets_for_update(trans, history, [decoded_id], payload)[0]
if hda:
self.__deserialize_dataset(trans, hda, payload)
serialization_params.default_view = 'detailed'
return self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
)
return {}
def __datasets_for_update(
self, trans,
history: History,
hda_ids: List[int],
payload: Dict[str, Any]
):
anonymous_user = not trans.user_is_admin and trans.user is None
if anonymous_user:
anon_allowed_payload = {}
if 'deleted' in payload:
anon_allowed_payload['deleted'] = payload['deleted']
if 'visible' in payload:
anon_allowed_payload['visible'] = payload['visible']
payload = anon_allowed_payload
hdas = self.hda_manager.get_owned_ids(hda_ids, history=history)
# only check_state if not deleting, otherwise cannot delete uploading files
check_state = not payload.get('deleted', False)
if check_state:
for hda in hdas:
hda = self.hda_manager.error_if_uploading(hda)
return hdas
def __deserialize_dataset(self, trans, hda, payload: Dict[str, Any]):
self.hda_deserializer.deserialize(hda, payload, user=trans.user, trans=trans)
# TODO: this should be an effect of deleting the hda
if payload.get('deleted', False):
self.hda_manager.stop_creating_job(hda)
def __index_legacy(
self, trans,
history_id: EncodedDatabaseIdField,
legacy_params: LegacyHistoryContentsIndexParams,
) -> List[AnyHistoryContentItem]:
"""Legacy implementation of the `index` action."""
history = self._get_history(trans, history_id)
legacy_params_dict = legacy_params.dict(exclude_defaults=True)
ids = legacy_params_dict.get("ids")
if ids:
legacy_params_dict["ids"] = self.decode_ids(ids)
contents = history.contents_iter(**legacy_params_dict)
return [
self._serialize_legacy_content_item(trans, content, legacy_params_dict.get("dataset_details"))
for content in contents
]
def __index_v2(
self,
trans,
history_id: EncodedDatabaseIdField,
params: HistoryContentsIndexParams,
serialization_params: SerializationParams,
filter_query_params: FilterQueryParams,
) -> List[AnyHistoryContentItem]:
"""
Latests implementation of the `index` action.
Allows additional filtering of contents and custom serialization.
"""
history = self._get_history(trans, history_id)
filters = self.history_contents_filters.parse_query_filters(filter_query_params)
filter_query_params.order = filter_query_params.order or "hid-asc"
order_by = self.build_order_by(self.history_contents_manager, filter_query_params.order)
contents = self.history_contents_manager.contents(
history,
filters=filters,
limit=filter_query_params.limit,
offset=filter_query_params.offset,
order_by=order_by,
serialization_params=serialization_params
)
return [
self._serialize_content_item(
trans, content,
dataset_details=params.dataset_details,
serialization_params=serialization_params,
)
for content in contents
]
def _serialize_legacy_content_item(
self,
trans,
content,
dataset_details: Optional[DatasetDetailsType] = None,
):
encoded_content_id = self.encode_id(content.id)
detailed = dataset_details and (dataset_details == 'all' or (encoded_content_id in dataset_details))
if isinstance(content, HistoryDatasetAssociation):
view = 'detailed' if detailed else 'summary'
return self.hda_serializer.serialize_to_view(content, view=view, user=trans.user, trans=trans)
elif isinstance(content, HistoryDatasetCollectionAssociation):
view = 'element' if detailed else 'collection'
return self.__collection_dict(trans, content, view=view)
def _serialize_content_item(
self,
trans,
content,
dataset_details: Optional[DatasetDetailsType],
serialization_params: SerializationParams,
default_view: str = "summary",
):
"""
Returns a dictionary with the appropriate values depending on the
serialization parameters provided.
"""
serialization_params_dict = serialization_params.dict()
view = serialization_params_dict.pop("view", default_view) or default_view
serializer: Optional[ModelSerializer] = None
if isinstance(content, HistoryDatasetAssociation):
serializer = self.hda_serializer
if dataset_details and (dataset_details == 'all' or self.encode_id(content.id) in dataset_details):
view = "detailed"
elif isinstance(content, HistoryDatasetCollectionAssociation):
serializer = self.hdca_serializer
if serializer is None:
raise exceptions.UnknownContentsType(f'Unknown contents type: {content.content_type}')
rval = serializer.serialize_to_view(
content, user=trans.user, trans=trans, view=view, **serialization_params_dict
)
# Override URL generation to use UrlBuilder
if trans.url_builder:
if rval.get("url"):
rval["url"] = trans.url_builder('history_content_typed',
history_id=rval["history_id"], id=rval["id"], type=rval["history_content_type"]
)
if rval.get("contents_url"):
rval["contents_url"] = trans.url_builder('contents_dataset_collection',
hdca_id=rval["id"],
parent_id=self.encode_id(content.collection_id)
)
return rval
def __collection_dict(self, trans, dataset_collection_instance, **kwds):
return dictify_dataset_collection_instance(
dataset_collection_instance,
security=trans.security,
url_builder=trans.url_builder,
parent=dataset_collection_instance.history,
**kwds
)
def _get_history(self, trans, history_id: EncodedDatabaseIdField) -> History:
"""Retrieves the History with the given ID or raises an error if the current user cannot access it."""
history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
return history
def __show_dataset(
self, trans,
id: EncodedDatabaseIdField,
serialization_params: SerializationParams,
):
serialization_params.default_view = "detailed"
hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
return self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
)
def __show_dataset_collection(
self, trans,
id: EncodedDatabaseIdField,
serialization_params: SerializationParams,
fuzzy_count: Optional[int] = None,
):
dataset_collection_instance = self.__get_accessible_collection(trans, id)
view = serialization_params.view or "element"
return self.__collection_dict(trans, dataset_collection_instance, view=view, fuzzy_count=fuzzy_count)
def __get_accessible_collection(self, trans, id: EncodedDatabaseIdField):
return self.dataset_collection_manager.get_dataset_collection_instance(
trans=trans, instance_type="history", id=id,
)
def __create_datasets_from_library_folder(
self, trans,
history: History,
payload: CreateHistoryContentPayloadFromCopy,
serialization_params: SerializationParams,
):
rval = []
source = payload.source
if source == HistoryContentSource.library_folder:
content = payload.content
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of lda or hda is missing")
folder_id = self.folder_manager.cut_and_decode(trans, content)
folder = self.folder_manager.get(trans, folder_id)
current_user_roles = trans.get_current_user_roles()
security_agent: GalaxyRBACAgent = trans.app.security_agent
def traverse(folder):
admin = trans.user_is_admin
rval = []
for subfolder in folder.active_folders:
if not admin:
can_access, folder_ids = security_agent.check_folder_contents(trans.user, current_user_roles, subfolder)
if (admin or can_access) and not subfolder.deleted:
rval.extend(traverse(subfolder))
for ld in folder.datasets:
if not admin:
can_access = security_agent.can_access_dataset(
current_user_roles,
ld.library_dataset_dataset_association.dataset
)
if (admin or can_access) and not ld.deleted:
rval.append(ld)
return rval
for ld in traverse(folder):
hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
hda_dict = self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
)
rval.append(hda_dict)
else:
message = f"Invalid 'source' parameter in request: {source}"
raise exceptions.RequestParameterInvalidException(message)
trans.sa_session.flush()
return rval
def __create_dataset(
self, trans,
history: History,
payload: CreateHistoryContentPayloadFromCopy,
serialization_params: SerializationParams,
):
source = payload.source
if source not in (HistoryContentSource.library, HistoryContentSource.hda):
raise exceptions.RequestParameterInvalidException(
f"'source' must be either 'library' or 'hda': {source}")
content = payload.content
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of lda or hda is missing")
hda = None
if source == HistoryContentSource.library:
hda = self.__create_hda_from_ldda(trans, history, content)
elif source == HistoryContentSource.hda:
hda = self.__create_hda_from_copy(trans, history, content)
if hda is None:
return None
trans.sa_session.flush()
return self.hda_serializer.serialize_to_view(
hda, user=trans.user, trans=trans, **serialization_params.dict()
)
def __create_hda_from_ldda(self, trans, history: History, ldda_id: EncodedDatabaseIdField):
decoded_ldda_id = self.decode_id(ldda_id)
ld = self.ldda_manager.get(trans, decoded_ldda_id)
if type(ld) is not LibraryDataset:
raise exceptions.RequestParameterInvalidException(
f"Library content id ( {ldda_id} ) is not a dataset")
hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
return hda
def __create_hda_from_copy(self, trans, history: History, original_hda_id: EncodedDatabaseIdField):
unencoded_hda_id = self.decode_id(original_hda_id)
original = self.hda_manager.get_accessible(unencoded_hda_id, trans.user)
# check for access on history that contains the original hda as well
self.history_manager.error_unless_accessible(original.history, trans.user, current_history=trans.history)
hda = self.hda_manager.copy(original, history=history)
return hda
def __create_dataset_collection(
self, trans,
history: History,
payload: CreateHistoryContentPayloadFromCollection,
serialization_params: SerializationParams,
):
"""Create hdca in a history from the list of element identifiers
:param history: history the new hdca should be added to
:param source: whether to create a new collection or copy existing one
:type source: str
:param payload: dictionary structure containing:
:param collection_type: type (and depth) of the new collection
:type name: str
:param element_identifiers: list of elements that should be in the new collection
:param element: one member of the collection
:param name: name of the element
:type name: str
:param src: source of the element (hda/ldda)
:type src: str
:param id: identifier
:type id: str
:param id: tags
:type id: list
:type element: dict
:type name: list
:param name: name of the collection
:type name: str
:param hide_source_items: whether to mark the original hdas as hidden
:type name: bool
:param copy_elements: whether to copy HDAs when creating collection
:type name: bool
:type payload: dict
.. note:: Elements may be nested depending on the collection_type
:returns: dataset collection information
:rtype: dict
:raises: RequestParameterInvalidException, RequestParameterMissingException
"""
source = payload.source or HistoryContentSource.new_collection
dataset_collection_manager = self.dataset_collection_manager
if source == HistoryContentSource.new_collection:
create_params = api_payload_to_create_params(payload.dict())
dataset_collection_instance = dataset_collection_manager.create(
trans,
parent=history,
history=history,
**create_params
)
elif source == HistoryContentSource.hdca:
content = payload.content
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of target to copy is missing")
dbkey = payload.dbkey
copy_required = dbkey is not None
copy_elements = payload.copy_elements or copy_required
if copy_required and not copy_elements:
raise exceptions.RequestParameterMissingException("copy_elements passed as 'false' but it is required to change specified attributes")
dataset_instance_attributes = {}
if dbkey is not None:
dataset_instance_attributes["dbkey"] = dbkey
dataset_collection_instance = dataset_collection_manager.copy(
trans=trans,
parent=history,
source=source,
encoded_source_id=content,
copy_elements=copy_elements,
dataset_instance_attributes=dataset_instance_attributes,
)
else:
message = f"Invalid 'source' parameter in request: {source}"
raise exceptions.RequestParameterInvalidException(message)
# if the consumer specified keys or view, use the secondary serializer
if serialization_params.view or serialization_params.keys:
return self.hdca_serializer.serialize_to_view(
dataset_collection_instance, user=trans.user, trans=trans, **serialization_params.dict()
)
return self.__collection_dict(trans, dataset_collection_instance, view="element")