seqr export upload

[evamar22]

I am unable to upload this week’s application export into seqr. I have tried refreshing the page and I waited a day to see if there was a difference. It doesn’t seem to be an issue with the file itself but rather seqr as the error it gives me is the following (when the error lies in the file, the message is different):

Link to page(s) where bug is occurring

(Applicable to GRU)

[hanars]

Hello, please always report bugs by filling out the full bug issue template: https://github.com/broadinstitute/seqr/issues/new?assignees=&labels=bug&projects=&template=bug_report.md&title=

This ticket is missing and can not be addressed without the following:

• Link to page(s) where bug is occurring
• Scope of the bug
• Screenshots

[evamar22]

GRU Project

https://seqr.broadinstitute.org/project/R0594_rare_genomes_project_gen/project_page

[hanars]

Any ticket related to file upload issues requires you to attach the file as well. Usually, files will be uploaded under the "links" section In general, if a ticket does not include enough detail and context for me to be able to do the exact same thing you did that caused the bug, then I am unable to fix it

[evamar22]

Understood! The file contains PHI. What is the best way for me to send you the file I am attempting to upload?

[evamar22]

I have attached the file I am attempting to upload. For clarification, it is the redacted NON-PHI version of the original file. The redacted versions are always uploaded to seqr, and we have not been uploading files with PHI to seqr. I thought it would be helpful to include the original file I redacted but understand this is not appropriate/necessary. Let me know if you have other questions.

WeeklySurveySummaryReportV2 - redacted and uploaded (11.04.2024).csv

[hanars]

@sjahl or @bpblanken this particular file upload is being blocked by ingress-nginx because of its high "anomaly score". Any idea how to identify what exactly is anomalous about this file thats causing this issue?

2024/11/06 16:06:48 [error] 890#890: *16027219 [client 10.44.3.4] ModSecurity: Access denied with code 403 (phase 2). Matched "Operator `Ge' with parameter `5' against variable `TX:ANOMALY_SCORE' (Value: `5' ) [file "/etc/nginx/owasp-modsecurity-crs/rules/REQUEST-949-BLOCKING-EVALUATION.conf"] [line "80"] [id "949110"] [rev ""] [msg "Inbound Anomaly Score Exceeded (Total Score: 5)"] [data ""] [severity "2"] [ver "OWASP_CRS/3.3.2"] [maturity "0"] [accuracy "0"] [tag "application-multi"] [tag "language-multi"] [tag "platform-multi"] [tag "attack-generic"] [hostname "10.44.3.4"] [uri "/api/project/R0594_rare_genomes_project_gen/upload_individuals_table"] [unique_id "1730909208"] [ref ""], client: 10.44.3.4, server: seqr.broadinstitute.org, request: "POST /api/project/R0594_rare_genomes_project_gen/upload_individuals_table HTTP/2.0", host: "seqr.broadinstitute.org", referrer: "https://seqr.broadinstitute.org/project/R0594_rare_genomes_project_gen/project_page"

[bpblanken]

@hanars I was able to eventually get this figured. There's a '\n' in front of a 'once' that's triggering the blocking. (Also one in front of a "much"... but this one makes less sense to me...).

I did enable additional logging in nginx in dev to debug this, and it works, but that process was much less effective than binary search through the file to find the bad character.

[hanars]

@evamar22 I have slacked you an updated version of the file that will load without issues (github was giving me trouble updating it). It looks like some of the user-generated info had an unsupported character in it that was being flagged as suspicious

[evamar22]

I see! It's difficult to catch all the unsupported characters sometimes. I uploaded the updated file with no issues. Thank you everyone for your help!