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authorFrederick Muriuki Muriithi2022-10-03 07:28:50 +0300
committerFrederick Muriuki Muriithi2022-10-03 07:28:50 +0300
commit6e554c1dae7f49bdd338c714c24b87ac6710de54 (patch)
tree919ea0892feefccc6057ec121962d6c8b45da5f6
parent3a585cf83ceb67f400a60b20a3b08971f15ebec1 (diff)
downloadgn-gemtext-6e554c1dae7f49bdd338c714c24b87ac6710de54.tar.gz
Issues (phenotype-correlation-error.gmi): Add new errors
* issues/phenotype-correlation-error.gmi: Add new errors arising after fixing the rust correlation issue.
-rw-r--r--issues/phenotype-correlation-error.gmi44
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