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Diffstat (limited to 'issues')
| -rw-r--r-- | issues/error-when-fetching-snps.gmi | 54 |
1 files changed, 54 insertions, 0 deletions
diff --git a/issues/error-when-fetching-snps.gmi b/issues/error-when-fetching-snps.gmi new file mode 100644 index 0000000..68e70c2 --- /dev/null +++ b/issues/error-when-fetching-snps.gmi @@ -0,0 +1,54 @@ +# Error when fetching SNPs in a search page +Wed 28 Sep 2022 17:45:01 EAT + +* assigned: zachs, bonfacem +* tags: critical + +## Steps to reproduce + +* Consider this search page: + +=> https://genenetwork.org/show_trait?trait_id=1434280_at&dataset=HC_M2_0606_P + +=> https://github.com/genenetwork/gn-gemtext-threads/blob/main/pictures/trait-search-page-1427571_at.png + +* After clicking on "SNPs", this error is generated (full stack-trace): + +``` + GeneNetwork tux01:gene:2.11-rc2-HEAD-52318e03c http://genenetwork.org/snp_browser?first_run=true&species=mouse&gene_name=BG976607&limit_strains=on ( 2:42PM UTC Sep 28, 2022) +Traceback (most recent call last): + File "/usr/local/guix-profiles/gn-latest-20220122/lib/python3.9/site-packages/flask/app.py", line 1513, in full_dispatch_request + rv = self.dispatch_request() + File "/usr/local/guix-profiles/gn-latest-20220122/lib/python3.9/site-packages/flask/app.py", line 1499, 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 867, in snp_browser_page + template_vars = snp_browser.SnpBrowser(cursor, request.args) + File "/home/gn2/production/gene/wqflask/wqflask/snp_browser/snp_browser.py", line 14, in __init__ + self.initialize_parameters(start_vars) +TypeError: initialize_parameters() missing 1 required positional argument: 'start_vars' + +``` + +* If you are using the provided local database, you get an error because the "RatSnpPattern" table does not exist: + +``` +ERROR:wqflask:http://localhost:5004/snp_browser?first_run=true&species=mouse&gene_name=BG976607&limit_strains=on ( 2:11PM UTC Sep 28, 2022) +Traceback (most recent call last): + File "/home/bonface/opt/genenetwork2/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request + rv = self.dispatch_request() + File "/home/bonface/opt/genenetwork2/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/bonface/projects/oqo-genenetwork2/search/wqflask/wqflask/views.py", line 859, in snp_browser_page + template_vars = snp_browser.SnpBrowser(request.args) + File "/home/bonface/projects/oqo-genenetwork2/search/wqflask/wqflask/snp_browser/snp_browser.py", line 13, in __init__ + self.strain_lists = get_browser_sample_lists() + File "/home/bonface/projects/oqo-genenetwork2/search/wqflask/wqflask/snp_browser/snp_browser.py", line 672, in get_browser_sample_lists + cursor.execute("SHOW COLUMNS FROM RatSnpPattern") + File "/home/bonface/opt/genenetwork2/lib/python3.9/site-packages/MySQLdb/cursors.py", line 206, in execute + res = self._query(query) + File "/home/bonface/opt/genenetwork2/lib/python3.9/site-packages/MySQLdb/cursors.py", line 319, in _query + db.query(q) + File "/home/bonface/opt/genenetwork2/lib/python3.9/site-packages/MySQLdb/connections.py", line 259, in query + _mysql.connection.query(self, query) +MySQLdb._exceptions.ProgrammingError: (1146, "Table 'db_webqtl_s.RatSnpPattern' doesn't exist") +``` |