import logging
import os
from urllib.parse import (
quote_plus,
unquote_plus,
)
import paste.httpexceptions
from galaxy import (
util,
web,
)
from galaxy.datatypes.data import DatatypeConverterNotFoundException
from galaxy.datatypes.display_applications.util import (
decode_dataset_user,
encode_dataset_user,
)
from galaxy.datatypes.sniff import guess_ext
from galaxy.exceptions import (
InsufficientPermissionsException,
MessageException,
RequestParameterInvalidException,
)
from galaxy.managers.hdas import (
HDADeserializer,
HDAManager,
)
from galaxy.managers.histories import HistoryManager
from galaxy.model import (
Dataset,
HistoryDatasetAssociation,
)
from galaxy.model.db.role import get_private_role_user_emails_dict
from galaxy.model.item_attrs import (
UsesAnnotations,
UsesItemRatings,
)
from galaxy.structured_app import StructuredApp
from galaxy.util import sanitize_text
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.zipstream import ZipstreamWrapper
from galaxy.web import form_builder
from galaxy.webapps.base.controller import (
BaseUIController,
UsesExtendedMetadataMixin,
)
from galaxy.webapps.galaxy.services.datasets import DatasetsService
from ..api import depends
log = logging.getLogger(__name__)
comptypes = []
try:
import zlib # noqa: F401
comptypes.append("zip")
except ImportError:
pass
[docs]
class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesExtendedMetadataMixin):
history_manager: HistoryManager = depends(HistoryManager)
hda_manager: HDAManager = depends(HDAManager)
hda_deserializer: HDADeserializer = depends(HDADeserializer)
service: DatasetsService = depends(DatasetsService)
[docs]
def __init__(self, app: StructuredApp):
super().__init__(app)
def _can_access_dataset(self, trans, dataset_association, allow_admin=True, additional_roles=None):
roles = trans.get_current_user_roles()
if additional_roles:
roles = roles + additional_roles
return (allow_admin and trans.user_is_admin) or trans.app.security_agent.can_access_dataset(
roles, dataset_association.dataset
)
[docs]
@web.expose
def default(self, trans, dataset_id=None, **kwd):
return "This link may not be followed from within Galaxy."
def _check_dataset(self, trans, hda_id):
# DEPRECATION: We still support unencoded ids for backward compatibility
try:
data = trans.sa_session.query(HistoryDatasetAssociation).get(self.decode_id(hda_id))
if data is None:
raise ValueError(f"Invalid reference dataset id: {hda_id}.")
except Exception:
try:
data = trans.sa_session.query(HistoryDatasetAssociation).get(int(hda_id))
except Exception:
data = None
if not data:
raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
if not self._can_access_dataset(trans, data):
raise InsufficientPermissionsException("You are not allowed to access this dataset")
self.app.hda_manager.ensure_dataset_on_disk(trans, data)
return data
[docs]
@web.expose
def display(
self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd
):
data = self._check_dataset(trans, dataset_id)
if "hdca" in kwd:
raise RequestParameterInvalidException("Invalid request parameter 'hdca' encountered.")
if hdca_id := kwd.get("hdca_id", None):
hdca = self.app.dataset_collection_manager.get_dataset_collection_instance(trans, "history", hdca_id)
del kwd["hdca_id"]
kwd["hdca"] = hdca
# Ensure offset is an integer before passing through to datatypes.
if offset:
offset = int(offset)
# Ensure ck_size is an integer before passing through to datatypes.
if ck_size:
ck_size = int(ck_size)
kwd.pop("dataset", None)
# `dataset` in kwd would interfere with positional dataset argument of `display_data` method.
display_data, headers = data.datatype.display_data(
trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd
)
if isinstance(display_data, ZipstreamWrapper):
trans.response.headers.update(headers)
return display_data.response()
trans.response.headers.update(headers)
return display_data
[docs]
@web.expose_api_anonymous
def get_edit(self, trans, dataset_id=None, **kwd):
"""Produces the input definitions available to modify dataset attributes"""
status = None
data, message = self._get_dataset_for_edit(trans, dataset_id)
if message:
return message
if self._can_access_dataset(trans, data):
if data.state == Dataset.states.UPLOAD:
raise MessageException(
"Please wait until this dataset finishes uploading before attempting to edit its metadata."
)
# let's not overwrite the imported datatypes module with the variable datatypes?
# the built-in 'id' is overwritten in lots of places as well
ldatatypes = [
(dtype_name, dtype_name)
for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.items()
if dtype_value.is_datatype_change_allowed()
]
ldatatypes.sort()
data_metadata = list(data.metadata.spec.items())
converters_collection = [(key, value.name) for key, value in data.get_converter_types().items()]
# attribute editing
attribute_inputs = [
{"name": "name", "type": "text", "label": "Name", "value": data.get_display_name()},
{"name": "info", "type": "text", "area": True, "label": "Info", "value": data.info},
{
"name": "annotation",
"type": "text",
"area": True,
"label": "Annotation",
"optional": True,
"value": self.get_item_annotation_str(trans.sa_session, trans.user, data),
"help": "Add an annotation or notes to a dataset; annotations are available when a history is viewed.",
},
]
for name, spec in data_metadata:
if spec.visible:
attributes = data.metadata.get_metadata_parameter(name, trans=trans)
if type(attributes) is form_builder.SelectField:
attribute_inputs.append(
{
"type": "select",
"multiple": attributes.multiple,
"optional": spec.get("optional"),
"name": name,
"label": spec.desc,
"options": attributes.options,
"value": attributes.value,
}
)
elif type(attributes) is form_builder.TextField:
attribute_inputs.append(
{
"type": "text",
"name": name,
"label": spec.desc,
"value": attributes.value,
"readonly": spec.get("readonly"),
}
)
if data.missing_meta():
message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
status = "warning"
metadata_disable = data.state not in [
Dataset.states.OK,
Dataset.states.FAILED_METADATA,
]
# datatype conversion
conversion_options = [
(f"{convert_id} (using '{convert_name}')", convert_id)
for convert_id, convert_name in converters_collection
]
conversion_disable = len(conversion_options) == 0
conversion_inputs = [
{
"type": "select",
"name": "target_type",
"label": "Target datatype",
"help": "This will create a new dataset with the contents of this dataset converted to a new format.",
"options": conversion_options,
}
]
# datatype changing
datatype_options = [(ext_name, ext_id) for ext_id, ext_name in ldatatypes]
datatype_disable = len(datatype_options) == 0
datatype_input_default_value = None
current_datatype = trans.app.datatypes_registry.datatypes_by_extension.get(data.ext)
if current_datatype and current_datatype.is_datatype_change_allowed():
datatype_input_default_value = data.ext
datatype_inputs = [
{
"type": "select",
"name": "datatype",
"label": "New Type",
"options": datatype_options,
"value": datatype_input_default_value,
"help": "This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.",
}
]
# permissions
permission_disable = True
permission_inputs = []
if trans.user:
if not data.dataset.shareable:
permission_message = "The dataset is stored on private storage to you and cannot be shared."
permission_inputs.append(
{"name": "not_shareable", "type": "hidden", "label": permission_message, "readonly": True}
)
elif data.dataset.actions:
can_manage_dataset = trans.app.security_agent.can_manage_dataset(
trans.get_current_user_roles(), data.dataset
)
legitimate_roles = trans.app.security_agent.get_legitimate_roles(trans, data.dataset, "root")
legitimate_role_ids = {role.id for role in legitimate_roles}
private_role_emails = get_private_role_user_emails_dict(
trans.sa_session, role_ids=legitimate_role_ids
)
role_tuples = [
(private_role_emails.get(role.id, role.name), trans.security.encode_id(role.id))
for role in legitimate_roles
]
in_roles = {}
for action, roles in trans.app.security_agent.get_permissions(data.dataset).items():
in_roles[action.action] = [trans.security.encode_id(role.id) for role in roles]
for index, action in Dataset.permitted_actions.items():
if action == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
help_text = f"{action.description}<br/>NOTE: Users must have every role associated with this dataset in order to access it."
else:
help_text = action.description
permission_inputs.append(
{
"type": "select",
"multiple": True,
"optional": True,
"name": index,
"label": action.action,
"help": help_text,
"options": role_tuples,
"value": in_roles.get(action.action),
"readonly": not can_manage_dataset,
}
)
permission_disable = not can_manage_dataset
else:
permission_inputs.append(
{
"name": "access_public",
"type": "hidden",
"label": "This dataset is accessible by everyone (it is public).",
"readonly": True,
}
)
else:
permission_inputs.append(
{
"name": "no_access",
"type": "hidden",
"label": "Permissions not available (not logged in).",
"readonly": True,
}
)
return {
"display_name": data.get_display_name(),
"message": message,
"status": status,
"dataset_id": dataset_id,
"metadata_disable": metadata_disable,
"attribute_inputs": attribute_inputs,
"conversion_inputs": conversion_inputs,
"conversion_disable": conversion_disable,
"datatype_inputs": datatype_inputs,
"datatype_disable": datatype_disable,
"permission_inputs": permission_inputs,
"permission_disable": permission_disable,
}
else:
raise MessageException(
"You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
)
[docs]
@web.expose_api_anonymous
def set_edit(self, trans, payload=None, **kwd):
"""Allows user to modify parameters of an HDA."""
status = "success"
operation = payload.get("operation")
dataset_id = payload.get("dataset_id")
data, message = self._get_dataset_for_edit(trans, dataset_id)
if message:
return message
if operation == "attributes":
# The user clicked the Save button on the 'Edit Attributes' form
data.name = payload.get("name")
data.info = payload.get("info")
if data.ok_to_edit_metadata():
# The following for loop will save all metadata_spec items
for name, spec in data.datatype.metadata_spec.items():
if not spec.get("readonly"):
setattr(data.metadata, name, spec.unwrap(payload.get(name) or None))
data.datatype.after_setting_metadata(data)
# Sanitize annotation before adding it.
if payload.get("annotation"):
annotation = sanitize_html(payload.get("annotation"))
self.add_item_annotation(trans.sa_session, trans.get_user(), data, annotation)
# if setting metadata previously failed and all required elements have now been set, clear the failed state.
if data.state == Dataset.states.FAILED_METADATA and not data.missing_meta():
data.set_metadata_success_state()
message = f"Attributes updated. {message}" if message else "Attributes updated."
else:
message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata."
status = "warning"
trans.sa_session.commit()
elif operation == "datatype":
# The user clicked the Save button on the 'Change data type' form
datatype = payload.get("datatype")
self.hda_deserializer.deserialize(data, {"datatype": datatype}, trans=trans)
message = f"Changed the type to {datatype}."
elif operation == "datatype_detect":
# The user clicked the 'Detect datatype' button on the 'Change data type' form
if data.datatype.is_datatype_change_allowed():
# prevent modifying datatype when dataset is queued or running as input/output
if not data.ok_to_edit_metadata():
raise MessageException(
"This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them."
)
else:
# we can't detect datatype if the dataset is not on disk
self.hda_manager.ensure_dataset_on_disk(trans, data)
path = data.dataset.get_file_name()
datatype = guess_ext(path, trans.app.datatypes_registry.sniff_order)
trans.app.datatypes_registry.change_datatype(data, datatype)
trans.sa_session.commit()
job, *_ = trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
trans.app.datatypes_registry.set_external_metadata_tool,
trans,
incoming={"input1": data},
)
trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
message = f"Detection was finished and changed the datatype to {datatype}."
else:
raise MessageException(f'Changing datatype "{data.extension}" is not allowed.')
elif operation == "autodetect":
# The user clicked the Auto-detect button on the 'Edit Attributes' form
self.hda_manager.set_metadata(trans, data, overwrite=True)
message = "Auto-detect operation successfully submitted."
elif operation == "conversion":
target_type = payload.get("target_type")
if target_type:
try:
message = data.datatype.convert_dataset(trans, data, target_type)
except DatatypeConverterNotFoundException as e:
raise MessageException(str(e))
elif operation == "permission":
# Adapt form request to API - style.
payload_permissions = {}
for key, value in {"DATASET_MANAGE_PERMISSIONS": "manage_ids", "DATASET_ACCESS": "access_ids"}.items():
role_ids = util.listify(payload.get(key))
decoded_role_ids = list(map(self.decode_id, role_ids))
payload_permissions[f"{value}[]"] = decoded_role_ids
self.hda_manager.update_permissions(
trans,
data,
action="set_permissions",
**payload_permissions,
)
message = "Your changes completed successfully."
else:
raise MessageException(f"Invalid operation identifier ({operation}).")
return {"status": status, "message": sanitize_text(message)}
def _get_dataset_for_edit(self, trans, dataset_id):
if dataset_id is not None:
id = self.decode_id(dataset_id)
data = trans.sa_session.query(HistoryDatasetAssociation).get(id)
else:
trans.log_event("dataset_id is None, cannot load a dataset to edit.")
return None, self.message_exception(trans, "You must provide a dataset id to edit attributes.")
if data is None:
trans.log_event(f"Problem retrieving dataset id ({dataset_id}).")
return None, self.message_exception(trans, "The dataset id is invalid.")
if dataset_id is not None and data.user and data.user != trans.user:
trans.log_event(f"User attempted to edit a dataset they do not own (encoded: {dataset_id}, decoded: {id}).")
return None, self.message_exception(trans, "The dataset id is invalid.")
if data.history.user and not data.dataset.has_manage_permissions_roles(trans.app.security_agent):
# Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
# so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
# permission. In this case, we'll reset this permission to the hda user's private role.
manage_permissions_action = trans.app.security_agent.get_action(
trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action
)
permissions = {manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.user)]}
trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
return data, None
[docs]
@web.expose
def display_at(self, trans, dataset_id, filename=None, **kwd):
"""Sets up a dataset permissions so it is viewable at an external site"""
if not trans.app.config.enable_old_display_applications:
return trans.show_error_message(
"This method of accessing external display applications has been disabled by a Galaxy administrator."
)
site = filename
data = trans.sa_session.query(HistoryDatasetAssociation).get(dataset_id)
if not data:
raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(
f"Invalid reference dataset id: {str(dataset_id)}."
)
if "display_url" not in kwd or "redirect_url" not in kwd:
return trans.show_error_message(
'Invalid parameters specified for "display at" link, please contact a Galaxy administrator'
)
try:
redirect_url = kwd["redirect_url"] % quote_plus(kwd["display_url"])
except Exception:
redirect_url = kwd["redirect_url"] # not all will need custom text
if trans.app.security_agent.dataset_is_public(data.dataset):
return trans.response.send_redirect(redirect_url) # anon access already permitted by rbac
if self._can_access_dataset(trans, data):
trans.app.host_security_agent.set_dataset_permissions(data, trans.user, site)
return trans.response.send_redirect(redirect_url)
else:
return trans.show_error_message(
"You are not allowed to view this dataset at external sites. Please contact your Galaxy administrator to acquire management permissions for this dataset."
)
[docs]
@web.expose
@web.do_not_cache
def display_application(
self,
trans,
dataset_id=None,
user_id=None,
app_name=None,
link_name=None,
app_action=None,
action_param=None,
action_param_extra=None,
**kwds,
):
"""Access to external display applications"""
if None in [app_name, link_name]:
return trans.show_error_message("A display application name and link name must be provided.")
app_name = unquote_plus(app_name)
link_name = unquote_plus(link_name)
# Build list of parameters to pass in to display application logic (app_kwds)
app_kwds = {}
for name, value in dict(kwds).items(): # clone kwds because we remove stuff as we go.
if name.startswith("app_"):
app_kwds[name[len("app_") :]] = value
del kwds[name]
if kwds:
log.debug(f"Unexpected Keywords passed to display_application: {kwds}") # route memory?
# decode ids
data, user = decode_dataset_user(trans, dataset_id, user_id)
if not data:
raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(
f"Invalid reference dataset id: {str(dataset_id)}."
)
if user is None:
user = trans.user
if user:
user_roles = user.all_roles()
else:
user_roles = []
# Decode application name and link name
if self._can_access_dataset(trans, data, additional_roles=user_roles):
msg = []
display_app = trans.app.datatypes_registry.display_applications.get(app_name)
if not display_app:
log.debug("Unknown display application has been requested: %s", app_name)
return paste.httpexceptions.HTTPNotFound(
f"The requested display application ({app_name}) is not available."
)
dataset_hash, user_hash = encode_dataset_user(trans, data, user)
try:
display_link = display_app.get_link(link_name, data, dataset_hash, user_hash, trans, app_kwds)
except Exception as e:
log.debug("Error generating display_link: %s", e)
# User can sometimes recover from, e.g. conversion errors by fixing input metadata, so use conflict
return paste.httpexceptions.HTTPConflict(f"Error generating display_link: {e}")
if not display_link:
log.debug("Unknown display link has been requested: %s", link_name)
return paste.httpexceptions.HTTPNotFound(f"Unknown display link has been requested: {link_name}")
if data.state == data.states.ERROR:
msg.append(
(
"This dataset is in an error state, you cannot view it at an external display application.",
"error",
)
)
elif data.deleted:
msg.append(
("This dataset has been deleted, you cannot view it at an external display application.", "error")
)
elif data.state != data.states.OK:
msg.append(
(
"You must wait for this dataset to be created before you can view it at an external display application.",
"info",
)
)
else:
# We have permissions, dataset is not deleted and is in OK state, allow access
if display_link.display_ready():
if app_action in ["data", "param"]:
assert action_param, "An action param must be provided for a data or param action"
# data is used for things with filenames that could be passed off to a proxy
# in case some display app wants all files to be in the same 'directory',
# data can be forced to param, but not the other way (no filename for other direction)
# get param name from url param name
try:
action_param = display_link.get_param_name_by_url(action_param)
except ValueError as e:
log.debug(e)
return paste.httpexceptions.HTTPNotFound(util.unicodify(e))
value = display_link.get_param_value(action_param)
assert value, f"An invalid parameter name was provided: {action_param}"
assert value.parameter.viewable, "This parameter is not viewable."
if value.parameter.type == "data":
try:
if action_param_extra:
assert (
value.parameter.allow_extra_files_access
), f"Extra file content requested ({action_param_extra}), but allow_extra_files_access is False."
file_name = os.path.join(value.extra_files_path, action_param_extra)
else:
file_name = value.get_file_name()
content_length = os.path.getsize(file_name)
rval = open(file_name, "rb")
except OSError as e:
log.debug("Unable to access requested file in display application: %s", e)
return paste.httpexceptions.HTTPNotFound("This file is no longer available.")
else:
rval = str(value)
content_length = len(rval)
# Set Access-Control-Allow-Origin as specified in GEDA
if value.parameter.allow_cors:
trans.set_cors_origin()
trans.set_cors_allow()
trans.response.set_content_type(value.mime_type(action_param_extra=action_param_extra))
trans.response.headers["Content-Length"] = str(content_length)
return rval
elif app_action is None:
# redirect user to url generated by display link
return trans.response.send_redirect(display_link.display_url())
else:
msg.append((f"Invalid action provided: {app_action}", "error"))
else:
if app_action is None:
msg.append(
(
"Launching this display application requires additional datasets to be generated.",
"info",
)
)
else:
return trans.show_error_message(
f"Attempted a view action ({app_action}) on a non-ready display application"
)
return dict(msg=msg)
return trans.show_error_message(
"You do not have permission to view this dataset at an external display application."
)