We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
In some cases a pending metric that raises a ValueError fails to end the job and wrap up.
This causes infinitely pending metric calculation.
ondemand | 03-18 23:26:49 [ DEBUG ] ondemand.providers.squidpy_provider:172: Computed feature value of 14: lesion 0_2, 1.0 ondemand | /usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/workflow/common/squidpy.py:158: UserWarning: All phenotypes provided had identical values. Only one cluster could be made. ondemand | warn('All phenotypes provided had identical values. Only one cluster could be made.') ondemand | 03-18 23:26:51 [ DEBUG ] ondemand.providers.squidpy_provider:172: Computed feature value of 14: lesion 0_3, 1.0 ondemand | Exception in thread Thread-11 (have_feature_computed): ondemand | Traceback (most recent call last): ondemand | File "/usr/local/lib/python3.11/threading.py", line 1045, in _bootstrap_inner ondemand | self.run() ondemand | File "/usr/local/lib/python3.11/threading.py", line 982, in run ondemand | self._target(*self._args, **self._kwargs) ondemand | File "/usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/ondemand/providers/squidpy_provider.py", line 163, in have_feature_computed ondemand | value = compute_squidpy_metric_for_one_sample( ondemand | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ondemand | File "/usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/workflow/common/squidpy.py", line 69, in compute_squidpy_metric_for_one_sample ondemand | return _summarize_ripley(_ripley(adata)) ondemand | ^^^^^^^^^^^^^^ ondemand | File "/usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/workflow/common/squidpy.py", line 186, in _ripley ondemand | result = ripley(adata, 'cluster', copy=True) ondemand | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ondemand | File "/usr/local/lib/python3.11/site-packages/squidpy/gr/_ripley.py", line 143, in ripley ondemand | distances, _ = tree_c.kneighbors(random, n_neighbors=n_neigh) ondemand | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ondemand | File "/usr/local/lib/python3.11/site-packages/sklearn/neighbors/_base.py", line 810, in kneighbors ondemand | raise ValueError( ondemand | ValueError: Expected n_neighbors <= n_samples, but n_samples = 1, n_neighbors = 2 apiserver | 03-18 23:26:52 [ DEBUG ] ondemand.service_client:204: Host and port (with service "squidpy"): ('fast-counts-server', 8016) ondemand | 03-18 23:26:52 [ INFO ] ondemand.request_handler: Request: b'ripley\x1dMelanoma intralesional IL2\x1dSOX10\x1dCD20\x1eCD3\x1eCD4\x1eCD8\x1eFOXP3' ondemand | 03-18 23:26:52 [ DEBUG ] ondemand.request_handler:228: ['Melanoma intralesional IL2', 'SOX10', 'CD20\x1eCD3\x1eCD4\x1eCD8\x1eFOXP3'] ondemand | 03-18 23:26:52 [ DEBUG ] ondemand.providers.pending_provider:29: Requesting computation. ondemand | 03-18 23:26:52 [ DEBUG ] ondemand.providers.pending_provider:99: Number of values possible to be computed: 7 ondemand | 03-18 23:26:52 [ DEBUG ] ondemand.providers.pending_provider:128: Actual number computed: 3 ondemand | 03-18 23:26:52 [ DEBUG ] ondemand.providers.pending_provider:42: Already pending.
The text was updated successfully, but these errors were encountered:
Related, there are times when a lightly-caught exception in the ondemand service is mishandled by the API service:
Host and port (with service "squidpy"): ('fast-counts-server', 8016) ondemand | 03-18 23:33:34 [ INFO ] ondemand.request_handler: Request: b'co-occurrence\x1dMelanoma intralesional IL2\x1dCD3\x1eCD4\x1dCD20\x1eCD56\x1eCD8\x1eFOXP3\x1eSOX10\x1d100.0' ondemand | 03-18 23:33:34 [ DEBUG ] ondemand.request_handler:228: ['Melanoma intralesional IL2', 'CD3\x1eCD4', 'CD20\x1eCD56\x1eCD8\x1eFOXP3\x1eSOX10', '100.0'] ondemand | 03-18 23:33:34 [ INFO ] ondemand.request_handler: Query to on-demand computation service could not be handled. apiserver | INFO: 172.18.0.1:38940 - "GET /request-spatial-metrics-computation-custom-phenotype/?negative_marker=CD20&negative_marker=CD56&negative_marker=CD8&negative_marker=FOXP3&negative_marker=SOX10&positive_marker=CD3&positive_marker=CD4&study=Melanoma+intralesional+IL2&feature_class=co-occurrence&radius=100 HTTP/1.1" 500 Internal Server Error apiserver | ERROR: Exception in ASGI application apiserver | Traceback (most recent call last): apiserver | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 108, in __call__ apiserver | response = await self.dispatch_func(request, call_next) apiserver | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ... ... apiserver | | File "/usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/apiserver/app/main.py", line 286, in get_squidpy_metrics apiserver | | metrics = requester.get_squidpy_metrics( apiserver | | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ apiserver | | File "/usr/local/lib/python3.11/site-packages/spatialprofilingtoolbox/ondemand/service_client.py", line 169, in get_squidpy_metrics apiserver | | values=response['metrics'], apiserver | | ~~~~~~~~^^^^^^^^^^^ apiserver | | KeyError: 'metrics' apiserver | +------------------------------------
Sorry, something went wrong.
No branches or pull requests
In some cases a pending metric that raises a ValueError fails to end the job and wrap up.
This causes infinitely pending metric calculation.
The text was updated successfully, but these errors were encountered: