Traits and Cofactors correlation error

[ckliethermes]

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 
Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

  GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92  http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/init.py", line 293, in load return loads(fp.read(), File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/init.py", line 346, in loads return _default_decoder.decode(s) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

[zsloan]

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.***> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init*.py", line 346, in loads return _default_decoder.decode(s) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

— Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

[zsloan]

This issue is apparently being caused by recently added code caching trait metadata for the correlation results (though I'm not sure what the specific issue is yet).

For the time being I disabled using the cache for phenotype datasets, so it should work.

On Wed, Mar 2, 2022 at 2:14 PM Zachary Sloan @.***> wrote:

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.***> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init*.py", line 346, in loads return _default_decoder.decode(s) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

— Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

[ckliethermes]

Thanks Zachary! It's working fine on my side now. I have some student using this for an assignment, and there was a flurry of panicked emails this morning... Chris

From: zsloan @.> Sent: Wednesday, March 2, 2022 3:46 PM To: genenetwork/genenetwork2 @.> Cc: Chris Kliethermes @.>; Author @.> Subject: Re: [genenetwork/genenetwork2] Traits and Cofactors correlation error (Issue #677)

This Email is from an EXTERNAL source. Ensure you trust this sender before clicking on any links or attachments. This issue is apparently being caused by recently added code caching trait metadata for the correlation results (though I'm not sure what the specific issue is yet).

For the time being I disabled using the cache for phenotype datasets, so it should work.

On Wed, Mar 2, 2022 at 2:14 PM Zachary Sloan @.<mailto:@.>> wrote:

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.<mailto:@.>> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init*.py", line 346, in loads return _default_decoder.decode(s) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

- Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.<mailto:@.>>

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgenenetwork%2Fgenenetwork2%2Fissues%2F677%23issuecomment-1057423340&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zTTGl5kUS6nSOBUgWoQzTow%2FjD0LBuiAEhjUmGLUJac%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYBBADZIUGVDIMAK7HKFGPDU57OP3ANCNFSM5PYKRGHQ&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9pg1aZbLIfbhodrMvI2XRCpVU0Esj959GCSLZxSYo8k%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NKX7Cm4Kr8NhQ0jWWLhGWSwxsIUfDIU%2FmAVRDFEngA0%3D&reserved=0 or Androidhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CZy%2BvpIKXLdGNChQ275ArAh5UNB7rVkH33xVxNWm4Rk%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.**@.>>

[BonfaceKilz]

ckliethermes @.***> anaandika:

Thanks Zachary! It's working fine on my side now. I have some student using this for an assignment, and there was a flurry of panicked emails this morning...

@Alexanderlacuna or @zsloan, best to add a test (or work out how to) when fixing this. Ideally, the steps for adding a test against a bug are:

• Try to reproduce the error above; without even writing any code.

• Reproduce that error in code as a test. Let tests fail: we call this a red.

• Fix the failing test in code and submit a PR.

• Close this issue automatically by adding the issue number: #677, as part of the subject or body.

Should you run into any problems let me know. Happy Hacking!

[ckliethermes]

We're having a new problem as of this afternoon (3-7) - we're getting a 502 Bad Gateway error when trying to access the site. I've tried multiple machines on multiple networks but the result is the same. Chris

From: zsloan @.> Sent: Wednesday, March 2, 2022 3:46 PM To: genenetwork/genenetwork2 @.> Cc: Chris Kliethermes @.>; Author @.> Subject: Re: [genenetwork/genenetwork2] Traits and Cofactors correlation error (Issue #677)

This Email is from an EXTERNAL source. Ensure you trust this sender before clicking on any links or attachments. This issue is apparently being caused by recently added code caching trait metadata for the correlation results (though I'm not sure what the specific issue is yet).

For the time being I disabled using the cache for phenotype datasets, so it should work.

On Wed, Mar 2, 2022 at 2:14 PM Zachary Sloan @.<mailto:@.>> wrote:

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.<mailto:@.>> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init*.py", line 346, in loads return _default_decoder.decode(s) File "/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

- Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.<mailto:@.>>

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgenenetwork%2Fgenenetwork2%2Fissues%2F677%23issuecomment-1057423340&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zTTGl5kUS6nSOBUgWoQzTow%2FjD0LBuiAEhjUmGLUJac%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYBBADZIUGVDIMAK7HKFGPDU57OP3ANCNFSM5PYKRGHQ&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9pg1aZbLIfbhodrMvI2XRCpVU0Esj959GCSLZxSYo8k%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NKX7Cm4Kr8NhQ0jWWLhGWSwxsIUfDIU%2FmAVRDFEngA0%3D&reserved=0 or Androidhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CZy%2BvpIKXLdGNChQ275ArAh5UNB7rVkH33xVxNWm4Rk%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.**@.>>

[robwwilliams]

Sorry Chris,

Zach and team trying to fix. Should be up soon. Holding me up too. Problems is being diagnosed.

On Mon, Mar 7, 2022 at 20:27 ckliethermes @.***> wrote:

We're having a new problem as of this afternoon (3-7) - we're getting a 502 Bad Gateway error when trying to access the site. I've tried multiple machines on multiple networks but the result is the same. Chris

From: zsloan @.> Sent: Wednesday, March 2, 2022 3:46 PM To: genenetwork/genenetwork2 @.> Cc: Chris Kliethermes @.>; Author @.> Subject: Re: [genenetwork/genenetwork2] Traits and Cofactors correlation error (Issue #677)

This Email is from an EXTERNAL source. Ensure you trust this sender before clicking on any links or attachments. This issue is apparently being caused by recently added code caching trait metadata for the correlation results (though I'm not sure what the specific issue is yet).

For the time being I disabled using the cache for phenotype datasets, so it should work.

On Wed, Mar 2, 2022 at 2:14 PM Zachary Sloan @.<mailto: @.>> wrote:

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.<mailto: @.>> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 346, in loads return _default_decoder.decode(s) File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

- Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

or Android < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub .

You are receiving this because you are subscribed to this thread.Message ID: @.<mailto:@.>>

- Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgenenetwork%2Fgenenetwork2%2Fissues%2F677%23issuecomment-1057423340&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zTTGl5kUS6nSOBUgWoQzTow%2FjD0LBuiAEhjUmGLUJac%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYBBADZIUGVDIMAK7HKFGPDU57OP3ANCNFSM5PYKRGHQ&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9pg1aZbLIfbhodrMvI2XRCpVU0Esj959GCSLZxSYo8k%3D&reserved=0

. Triage notifications on the go with GitHub Mobile for iOS< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NKX7Cm4Kr8NhQ0jWWLhGWSwxsIUfDIU%2FmAVRDFEngA0%3D&reserved=0> or Android< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CZy%2BvpIKXLdGNChQ275ArAh5UNB7rVkH33xVxNWm4Rk%3D&reserved=0 . You are receiving this because you authored the thread.Message ID: @.**@.>>

— Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677#issuecomment-1061341693, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC55V7F36KM6PYKZULYICVDU623I5ANCNFSM5PYKRGHQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Rob

Robert W Williams PhD Department of Genetics, Genomics and Informatics 71 S Manassas St, Memphis TN 38163 University of Tennessee Health Science Center, TSRB 405 Cell: 901 604 4752 EMAIL: @.*** Zoom: https://tennesseehipaa.zoom.us/j/9492269658

[zsloan]

This seems to be because of an issue where mapping of a particular dataset is causing the server to crash. I restarted it, so it should be working now.

On Mon, Mar 7, 2022 at 8:27 PM ckliethermes @.***> wrote:

We're having a new problem as of this afternoon (3-7) - we're getting a 502 Bad Gateway error when trying to access the site. I've tried multiple machines on multiple networks but the result is the same. Chris

From: zsloan @.> Sent: Wednesday, March 2, 2022 3:46 PM To: genenetwork/genenetwork2 @.> Cc: Chris Kliethermes @.>; Author @.> Subject: Re: [genenetwork/genenetwork2] Traits and Cofactors correlation error (Issue #677)

This Email is from an EXTERNAL source. Ensure you trust this sender before clicking on any links or attachments. This issue is apparently being caused by recently added code caching trait metadata for the correlation results (though I'm not sure what the specific issue is yet).

For the time being I disabled using the cache for phenotype datasets, so it should work.

On Wed, Mar 2, 2022 at 2:14 PM Zachary Sloan @.<mailto: @.>> wrote:

Thank you for pointing this out! Taking a look at it now.

On Wed, Mar 2, 2022 at 1:02 PM ckliethermes @.<mailto: @.>> wrote:

I received the error below when trying to identify traits that correlate with phenotypes in the Traits and Cofactors database (Trait Data And Analysis Page: Calculate Correlations > BXD Published phenotypes). None of the expression databases give this error; the list of top correlated traits generates as expected.

Copied from error screen:

(GeneNetwork error: Extra data: line 1 column 6765450 (char 6765449))

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 Extra data: line 1 column 6765450 (char 6765449) (error)

To check if this already a known issue, search the issue tracker.

GeneNetwork tux01:gene:2.11-rc2-testing-c71218d92 http://www.genenetwork.org/corr_compute ( 6:54PM UTC Mar 02, 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 949, 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 96, in correlation_json_for_table (file_path, dataset_metadata) = fetch_all_cached_metadata( File "/home/gn2/production/gene/wqflask/wqflask/correlation/pre_computes.py", line 18, in fetch_all_cached_metadata dataset_metadata = json.load(file_handler) File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 293, in load return loads(fp.read(), File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/ init.py", line 346, in loads return _default_decoder.decode(s) File

"/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode raise JSONDecodeError("Extra data", s, end) json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)

- Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AANQJGDO2JR4VIEDZEK375DU563NXANCNFSM5PYKRGHQ

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

or Android < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub .

You are receiving this because you are subscribed to this thread.Message ID: @.<mailto:@.>>

- Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgenenetwork%2Fgenenetwork2%2Fissues%2F677%23issuecomment-1057423340&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zTTGl5kUS6nSOBUgWoQzTow%2FjD0LBuiAEhjUmGLUJac%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYBBADZIUGVDIMAK7HKFGPDU57OP3ANCNFSM5PYKRGHQ&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9pg1aZbLIfbhodrMvI2XRCpVU0Esj959GCSLZxSYo8k%3D&reserved=0

. Triage notifications on the go with GitHub Mobile for iOS< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NKX7Cm4Kr8NhQ0jWWLhGWSwxsIUfDIU%2FmAVRDFEngA0%3D&reserved=0> or Android< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cchristopher.kliethermes%40drake.edu%7C07a926eacdc3416147d008d9fc95fb25%7C6f028129009c4b33b633bbfc58bbd960%7C0%7C0%7C637818543377646692%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CZy%2BvpIKXLdGNChQ275ArAh5UNB7rVkH33xVxNWm4Rk%3D&reserved=0 . You are receiving this because you authored the thread.Message ID: @.**@.>>

— Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677#issuecomment-1061341693, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGAEDESLAZ74LBU6YALU623I5ANCNFSM5PYKRGHQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

[fredmanglis]

@ckliethermes @zsloan Is this still an issue? May I close this issue as complete?

[zsloan]

The initial issue should be fixed, yeah (the correlation caching stuff).

The issue mentioned later is caused by GEMMA and I don't think is resolved yet, but Pjotr is looking into it. Since it's a completely different issue it should be okay to close this one.

On Tue, Mar 22, 2022, 5:16 AM Muriithi Frederick Muriuki < @.***> wrote:

Reopened #677 https://github.com/genenetwork/genenetwork2/issues/677.

— Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/677#event-6282354556, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGHGYAQWK2CO63BBVYTVBGMXJANCNFSM5PYKRGHQ . You are receiving this because you were mentioned.Message ID: @.***>

[fredmanglis]

@zsloan Okay then, do the following:

• [ ] extract what is not completed into a new issue in the gemtext issue tracker
• [ ] Add a link in the new gemtext issue pointing to this issue.
• [ ] Add a link to this issue pointing to the new gemtext issue
• [ ] close this issue

Tick the steps above as you finish them to ensure you do not miss any.

Also, you can tag me once you are done, and I'll have a look at the new gemtext issue.