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Allow access to invocation via shared or published history
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mvdbeek committed Aug 15, 2024
1 parent ccfb0bf commit 157c70d
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Showing 5 changed files with 55 additions and 17 deletions.
2 changes: 2 additions & 0 deletions lib/galaxy/managers/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,8 @@ def security_check(trans, item, check_ownership=False, check_accessible=False):
raise exceptions.ItemOwnershipException(
f"{item.__class__.__name__} is not owned by the current user", type="error"
)
# no need to check accessibility if we're the owner
return item

# Verify accessible:
# if it's part of a lib - can they access via security
Expand Down
4 changes: 3 additions & 1 deletion lib/galaxy/managers/markdown_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,9 @@ def _remap(container, line):
url = trans.app.config.organization_url
rval = self.handle_instance_organization_link(line, title, url)
elif container == "invocation_time":
invocation = workflow_manager.get_invocation(trans, object_id)
invocation = workflow_manager.get_invocation(
trans, object_id, check_ownership=False, check_accessible=True
)
rval = self.handle_invocation_time(line, invocation)
elif container == "visualization":
rval = None
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39 changes: 27 additions & 12 deletions lib/galaxy/managers/workflows.py
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,10 @@
deletable,
sharable,
)
from galaxy.managers.base import decode_id
from galaxy.managers.base import (
decode_id,
security_check,
)
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.executables import artifact_class
from galaxy.model import (
Expand Down Expand Up @@ -347,10 +350,10 @@ def check_security(self, trans, has_workflow, check_ownership=True, check_access
if isinstance(has_workflow, model.WorkflowInvocation):
# We use the owner of the history that is associated to the invocation as a proxy
# for the owner of the invocation.
if trans.user != has_workflow.history.user and not trans.user_is_admin:
raise exceptions.ItemOwnershipException()
else:
return True
security_check(
trans, has_workflow.history, check_ownership=check_ownership, check_accessible=check_accessible
)
return True

# stored workflow contains security stuff - follow that workflow to
# that unless given a stored workflow.
Expand Down Expand Up @@ -404,20 +407,26 @@ def _workflow_to_svg_canvas(self, trans, workflow, for_embed=False):
workflow_canvas.add_steps()
return workflow_canvas.finish(for_embed=for_embed)

def get_invocation(self, trans, decoded_invocation_id: int, eager=False) -> WorkflowInvocation:
def get_invocation(
self, trans, decoded_invocation_id: int, eager=False, check_ownership=True, check_accessible=True
) -> WorkflowInvocation:
workflow_invocation = _get_invocation(trans.sa_session, eager, decoded_invocation_id)
if not workflow_invocation:
encoded_wfi_id = trans.security.encode_id(decoded_invocation_id)
message = f"'{encoded_wfi_id}' is not a valid workflow invocation id"
raise exceptions.ObjectNotFound(message)
self.check_security(trans, workflow_invocation, check_ownership=True, check_accessible=False)
self.check_security(
trans, workflow_invocation, check_ownership=check_accessible, check_accessible=check_accessible
)
return workflow_invocation

def get_invocation_report(self, trans, invocation_id, **kwd):
decoded_workflow_invocation_id = (
trans.security.decode_id(invocation_id) if isinstance(invocation_id, str) else invocation_id
)
workflow_invocation = self.get_invocation(trans, decoded_workflow_invocation_id)
workflow_invocation = self.get_invocation(
trans, decoded_workflow_invocation_id, check_ownership=False, check_accessible=True
)
generator_plugin_type = kwd.get("generator_plugin_type")
runtime_report_config_json = kwd.get("runtime_report_config_json")
invocation_markdown = kwd.get("invocation_markdown", None)
Expand All @@ -433,7 +442,7 @@ def get_invocation_report(self, trans, invocation_id, **kwd):
)

def request_invocation_cancellation(self, trans, decoded_invocation_id: int):
workflow_invocation = self.get_invocation(trans, decoded_invocation_id)
workflow_invocation = self.get_invocation(trans, decoded_invocation_id, check_ownership=True)
cancelled = workflow_invocation.cancel()

if cancelled:
Expand All @@ -445,13 +454,18 @@ def request_invocation_cancellation(self, trans, decoded_invocation_id: int):

return workflow_invocation

def get_invocation_step(self, trans, decoded_workflow_invocation_step_id):
def get_invocation_step(
self, trans, decoded_workflow_invocation_step_id, check_ownership=True, check_accessible=True
):
try:
workflow_invocation_step = trans.sa_session.get(WorkflowInvocationStep, decoded_workflow_invocation_step_id)
except Exception:
raise exceptions.ObjectNotFound()
self.check_security(
trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False
trans,
workflow_invocation_step.workflow_invocation,
check_ownership=check_ownership,
check_accessible=check_accessible,
)
return workflow_invocation_step

Expand Down Expand Up @@ -490,6 +504,7 @@ def build_invocations_query(
sort_by=None,
sort_desc=None,
include_nested_invocations=True,
check_ownership=True,
) -> Tuple[List, int]:
"""Get invocations owned by the current user."""

Expand Down Expand Up @@ -536,7 +551,7 @@ def build_invocations_query(
invocations = [
inv
for inv in trans.sa_session.scalars(stmt)
if self.check_security(trans, inv, check_ownership=True, check_accessible=False)
if self.check_security(trans, inv, check_ownership=check_ownership, check_accessible=True)
]
return invocations, total_matches

Expand Down
17 changes: 13 additions & 4 deletions lib/galaxy/webapps/galaxy/services/invocations.py
Original file line number Diff line number Diff line change
Expand Up @@ -122,12 +122,15 @@ def index(
sort_by=invocation_payload.sort_by,
sort_desc=invocation_payload.sort_desc,
include_nested_invocations=invocation_payload.include_nested_invocations,
check_ownership=False,
)
invocation_dict = self.serialize_workflow_invocations(invocations, serialization_params)
return invocation_dict, total_matches

def show(self, trans, invocation_id, serialization_params, eager=False):
wfi = self._workflows_manager.get_invocation(trans, invocation_id, eager)
wfi = self._workflows_manager.get_invocation(
trans, invocation_id, eager, check_ownership=False, check_accessible=True
)
return self.serialize_workflow_invocation(wfi, serialization_params)

def cancel(self, trans, invocation_id, serialization_params):
Expand All @@ -139,7 +142,9 @@ def show_invocation_report(self, trans, invocation_id, format="json"):
return wfi_report

def show_invocation_step(self, trans, step_id) -> InvocationStep:
wfi_step = self._workflows_manager.get_invocation_step(trans, step_id)
wfi_step = self._workflows_manager.get_invocation_step(
trans, step_id, check_ownership=False, check_accessible=True
)
return self.serialize_workflow_invocation_step(wfi_step)

def update_invocation_step(self, trans, step_id, action):
Expand All @@ -164,7 +169,9 @@ def prepare_store_download(
) -> AsyncFile:
ensure_celery_tasks_enabled(trans.app.config)
model_store_format = payload.model_store_format
workflow_invocation = self._workflows_manager.get_invocation(trans, invocation_id, eager=True)
workflow_invocation = self._workflows_manager.get_invocation(
trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
)
if not workflow_invocation:
raise ObjectNotFound()
try:
Expand All @@ -190,7 +197,9 @@ def write_store(
self, trans, invocation_id: DecodedDatabaseIdField, payload: WriteInvocationStoreToPayload
) -> AsyncTaskResultSummary:
ensure_celery_tasks_enabled(trans.app.config)
workflow_invocation = self._workflows_manager.get_invocation(trans, invocation_id, eager=True)
workflow_invocation = self._workflows_manager.get_invocation(
trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
)
if not workflow_invocation:
raise ObjectNotFound()
request = WriteInvocationTo(
Expand Down
10 changes: 10 additions & 0 deletions lib/galaxy_test/api/test_workflows.py
Original file line number Diff line number Diff line change
Expand Up @@ -3069,6 +3069,16 @@ def test_workflow_invocation_report_1(self):
assert "## Workflow Outputs" in markdown_content
assert "## Workflow Inputs" in markdown_content
assert "## About This Report" not in markdown_content
with self._different_user():
exception_raised = False
try:
self.workflow_populator.workflow_report_json(workflow_id, invocation_id)
except AssertionError as e:
if "Request status code (403)" in str(e):
exception_raised = True
assert exception_raised, "Expected workflow report request to fail, but it didn't"
self.dataset_populator.make_public(history_id)
self.workflow_populator.workflow_report_json(workflow_id, invocation_id)

@skip_without_tool("cat")
def test_workflow_invocation_report_custom(self):
Expand Down

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