[SYNPY-1760] Add ability to link Grid to CurationTask by andrewelamb · Pull Request #1383 · Sage-Bionetworks/synapsePythonClient

andrewelamb · 2026-05-18T17:31:25Z

Problem:

Python Client users could not link a Grid session to a CurationTask
Curator Extension Docs were out of date

Solution:

Added these methods to CurationTask:

get_status
update_status
set_active_grid_session
set_task_state_async
create_grid_session_async

Added owner_principal_id to Grid

Separated Curator docs into one for data managers and one for contributors

Testing:

All new methods have unit and integration tests

thomasyu888 · 2026-05-29T18:19:42Z

+                "taskProperties was not found in the Synapse response for this CurationTask. "
+                "This means it is likely an older CurationTask from before taskProperties was added. "
+                "It is recommended that this task be deleted: task.delete(delete_source=False)"


Add to the message to recreate the task with the existing source entity

thomasyu888 · 2026-05-29T18:34:10Z

+            await self.set_active_grid_session_async(
+                active_session_id=grid.session_id, synapse_client=synapse_client
+            )
+        except Exception:


This should probably be the one that catches the 412 error. Should we have a "finally" clause to delete the grid sesison for all other errors on this active grid session command?

thomasyu888 · 2026-05-29T18:38:41Z

+        try:
+            await self.set_active_grid_session_async(
+                active_session_id=grid.session_id, synapse_client=synapse_client
+            )
+        except Exception:
+            try:
+                await grid.delete_async(synapse_client=synapse_client)
+            except Exception:
+                Synapse.get_client(synapse_client=synapse_client).logger.warning(
+                    "Failed to delete orphan grid session %s after status "
+                    "update failure; manual cleanup may be required.",
+                    grid.session_id,
+                )
+            raise


Add a comment

There can only be one grid session that is active, but there can be multiple grid sessions. So multiple users running this command may run into the 412 error.

thomasyu888

🔥 LGTM! just some minor comments, and will defer to @BryanFauble for a final pass next sprint for the code and @cconrad8 on the documentation.

cconrad8 · 2026-06-01T02:38:26Z

+
+### Step 5: Upsert your edits back into the grid
+
+`import_csv` upserts rows into the grid based on the `upsert_keys` the administrator configured on the curation task. Existing rows matching on those keys are updated; new rows are inserted.


I think the task has the upsert key as a property?

BryanFauble · 2026-06-03T17:37:30Z



+@dataclass
+class TaskExecutionDetails(ABC):


Although Synapse is representing this with inheritance and a base class, we do not have to follow this pattern exactly. In fact this would be the first usage of an abstract base class in the python code. Ideally - If possible I would rather this not exist.

If there is a case to be said that there are going to be many more of these, then that would be a reason to keep this. If this is all we will have, then I do not think we need to have this extra layer.

John has mentioned that they plan on having more of these, but I don't have any firm timeline. I'm happy to keep or change this.

BryanFauble · 2026-06-03T17:49:35Z

+            )
+            grid = Grid(
+                initial_query=Query(
+                    sql=f"SELECT * FROM {self.task_properties.file_view_id}"


Are there cases where this should be user controlled to set the query to something like, like SELECT col_1, col_2, col_3 ...?

From a product perspective, this is not supported within the UI flow when people "Open Curator" from a task. opening curator from a task will always select * on the underlying source id (recordset and/or fileview)

BryanFauble · 2026-06-03T17:59:59Z

+            await self.set_active_grid_session_async(
+                active_session_id=grid.session_id, synapse_client=synapse_client
+            )
+        except Exception:


Exception is way too wide to catch here for this logic. You need to catch for the specific exception (I assume an HTTP type exception), and inspect the message for the specific one that you care about. That should be the only case where you clean this up automatically.

Wouldn't we want to clean up this grid everytime Synapse was unable to set it as the active grid on the CurationTask?

does it make any sense for the Grid created during this process to stay under any circumstances? If no, then keep as is. If yes, change the behavior.

I don't think so. In my opinion, the user would be trying to create a grid and attach it with one method. If the attachment didn't work, they would probably try to call this method again, which would leave the grid from the first try.

BryanFauble

Thanks for the changes.

Approving, however please look to at least address #1383 (comment) before merge.

andrewelamb added 30 commits March 5, 2026 07:50

added examples for getting data into a grid

3175175

clarified todo comment

2199893

un-number examples

3620e39

remove redundant sentence

163e24b

change exmaple to annotate two files

fa74a18

fix example script comment

fc02a36

fix c+p error

dbddb31

changed example to biospecimen, added example csv

81dee71

added example csv

15f2bfd

fixed typo

649837c

randomize entity names

1ba8b79

added print statements for all entities created

eaa7147

Merge branch 'develop' into SYNPY-1786

d0b678f

update examples to add data directly into grid

3e26692

split doc into curation and contribution

173a345

Merge branch 'develop' into SYNPY-1786

f3f2772

added not about upcoming assign_to_me param

1ae27ee

various fixes

2e48c35

removed some examples

8efc6b1

rearange doc

21144dd

remove section

b4610ed

rename files

11b9c2b

fix links

df37556

fixed consistency issues

ea4aea1

remove grid creation

110e099

added back grid output

88f657b

some cleanup

3ad6b29

fix Grid session wording

666dfc8

added validation step

e089637

fixed typo

344d9d0

andrewelamb added 3 commits May 26, 2026 10:38

simplified tests

b521989

reverted TestGrid class

5f9221f

added principal owner id

760b02f

andrewelamb commented May 26, 2026

View reviewed changes

Comment thread synapseclient/models/curation.py

thomasyu888 reviewed May 28, 2026

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Comment thread docs/guides/extensions/curator/metadata_contribution.md

thomasyu888 reviewed May 28, 2026

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Comment thread docs/guides/extensions/curator/metadata_curation.md

thomasyu888 reviewed May 29, 2026

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thomasyu888 approved these changes May 29, 2026

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Toms suggestions

d43666f

cconrad8 suggested changes Jun 1, 2026

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BryanFauble reviewed Jun 3, 2026

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Comment thread synapseclient/models/curation.py Outdated

BryanFauble reviewed Jun 3, 2026

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Comment thread synapseclient/models/curation.py Outdated

BryanFauble reviewed Jun 3, 2026

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address PR comment

0ce7882

BryanFauble approved these changes Jun 3, 2026

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Edit docs

7a4d909

thomasyu888 reviewed Jun 3, 2026

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Comment thread docs/guides/extensions/curator/metadata_curation.md

thomasyu888 reviewed Jun 3, 2026

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Comment thread docs/guides/extensions/curator/metadata_curation.md

andrewelamb added 4 commits June 4, 2026 08:14

Chistinas suggestion

0dc4baa

stripped redundant dict.get(x, None)

2f5060d

removed uneeded imports from docstring examples

2db50df

Merge branch 'develop' into SYNPY-1760

586983f

andrewelamb requested a review from cconrad8 June 4, 2026 15:28

cconrad8 approved these changes Jun 4, 2026

View reviewed changes

andrewelamb merged commit 2243452 into develop Jun 4, 2026
20 of 23 checks passed

andrewelamb deleted the SYNPY-1760 branch June 4, 2026 18:29


		### Step 5: Upsert your edits back into the grid

		`import_csv` upserts rows into the grid based on the `upsert_keys` the administrator configured on the curation task. Existing rows matching on those keys are updated; new rows are inserted.

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andrewelamb commented May 18, 2026 •

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