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| author | Frederick Muriuki Muriithi | 2022-10-03 11:58:16 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-10-03 11:58:16 +0300 |
| commit | c505fd4795647dd3fb4008d38d0ad7c18585839d (patch) | |
| tree | 44f7c07d30a5a20ea3f4ed4c1534bff079844f38 | |
| parent | 6e554c1dae7f49bdd338c714c24b87ac6710de54 (diff) | |
| download | gn-gemtext-c505fd4795647dd3fb4008d38d0ad7c18585839d.tar.gz | |
Issues: Add information on debug progress
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index 09be0a0..1bea54e 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -39,6 +39,41 @@ Traceback (most recent call last): KeyError: "'1' information is not found in the database." ``` +The error above was caused by processing the data for output way too early. This has been fixed. + + +---- + +Running "Tissue" correlations on +=> https://genenetwork.org/show_trait?trait_id=1442370_at&dataset=HC_M2_0606_P +against the "BXD Published Phenotypes" database fails with the error: + +``` +Traceback (most recent call last): + File "/usr/local/guix-profiles/gn-latest-20220820/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request + rv = self.dispatch_request() + File "/usr/local/guix-profiles/gn-latest-20220820/lib/python3.9/site-packages/flask/app.py", line 1509, in dispatch_request + return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) + File "/home/gn2/production/gene/wqflask/wqflask/views.py", line 820, in corr_compute_page + correlation_results = set_template_vars(request.form, correlation_results) + File "/home/gn2/production/gene/wqflask/wqflask/correlation/show_corr_results.py", line 54, in set_template_vars + table_json = correlation_json_for_table(correlation_data, + File "/home/gn2/production/gene/wqflask/wqflask/correlation/show_corr_results.py", line 104, in correlation_json_for_table + target_trait_ob = create_trait(dataset=target_dataset_ob, + File "/home/gn2/production/gene/wqflask/base/trait.py", line 44, in create_trait + the_trait = retrieve_trait_info( + File "/home/gn2/production/gene/wqflask/base/trait.py", line 599, in retrieve_trait_info + raise KeyError(repr(trait.name) +KeyError: "'1422223_at' information is not found in the database." +``` + +so far, triangulated the issue to possibly being the fact that the "target_dataset" value is not used +=> https://github.com/genenetwork/genenetwork2/blob/53aa084fd2c9c930ac791ee43affffb3f788547c/wqflask/wqflask/correlation/rust_correlation.py#L271-L289 in this function. + +@zsloan and @alexm: any ideas? + +---- + I also run into the following error when I run the mechanical-rob tests ``` @@ -73,3 +108,4 @@ AttributeError: 'PhenotypeDataSet' object has no attribute 'retrieve_genes' * 2022-09-29: Successfully reproduced on production * 2022-09-29: Fix file format issues * 2022-09-30: Fix issues in rust correlation code +* 2022-10-03: Fix: avoid processing for output early |