diff options
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index 6183cef..09be0a0 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -17,6 +17,50 @@ The bug appears to occur in the rust correlation tool, so I'm not sure how to de subprocess.CalledProcessError: Command '['/usr/local/guix-profiles/gn-latest-20220820/bin/correlation_rust', '/home/zas1024/gn2-zach/tmp/gn2/correlation/IoaglmTgDJ.json', '/home/zas1024/gn2-zach/tmp/gn2']' died with <Signals.SIGSEGV: 11>. ``` +---- + +After fixing the issues with the interactions with the rust correlations code, I am now running into the following error when I run a correlation against the "Hippocampus Consortium M430v2 (Jun06) PDNN" dataset with the same trait from the URI above: +``` +Traceback (most recent call last): + File "/home/frederick/opt/gn_profiles/gn2_latest/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request + rv = self.dispatch_request() + File "/home/frederick/opt/gn_profiles/gn2_latest/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/frederick/genenetwork/genenetwork2/wqflask/wqflask/views.py", line 820, in corr_compute_page + correlation_results = set_template_vars(request.form, correlation_results) + File "/home/frederick/genenetwork/genenetwork2/wqflask/wqflask/correlation/show_corr_results.py", line 54, in set_template_vars + table_json = correlation_json_for_table(correlation_data, + File "/home/frederick/genenetwork/genenetwork2/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/frederick/genenetwork/genenetwork2/wqflask/base/trait.py", line 44, in create_trait + the_trait = retrieve_trait_info( + File "/home/frederick/genenetwork/genenetwork2/wqflask/base/trait.py", line 599, in retrieve_trait_info + raise KeyError(repr(trait.name) +KeyError: "'1' information is not found in the database." +``` + +I also run into the following error when I run the mechanical-rob tests + +``` +ERROR:wqflask:http://localhost:5033/corr_compute ( 4:26AM UTC Oct 03, 2022) +Traceback (most recent call last): + File "/home/frederick/opt/gn_profiles/gn2_latest/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request + rv = self.dispatch_request() + File "/home/frederick/opt/gn_profiles/gn2_latest/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/frederick/genenetwork/genenetwork2/wqflask/wqflask/views.py", line 818, in corr_compute_page + correlation_results = compute_correlation(request.form, compute_all=True) + File "/home/frederick/genenetwork/genenetwork2/wqflask/wqflask/correlation/correlation_gn3_api.py", line 199, in compute_correlation + return compute_correlation_rust( + File "/home/frederick/genenetwork/genenetwork2/wqflask/wqflask/correlation/rust_correlation.py", line 326, in compute_correlation_rust + results = corr_type_fns[corr_type]( + File "/home/frederick/genenetwork/genenetwork2/wqflask/wqflask/correlation/rust_correlation.py", line 299, in __compute_lit_corr__ + (this_trait_geneid, geneid_dict, species) = do_lit_correlation( + File "/home/frederick/genenetwork/genenetwork2/wqflask/wqflask/correlation/correlation_gn3_api.py", line 237, in do_lit_correlation + geneid_dict = this_dataset.retrieve_genes("GeneId") +AttributeError: 'PhenotypeDataSet' object has no attribute 'retrieve_genes' +``` + ## Tags * assigned: alexm, fredm, zsloan * type: bug |