Launch pipeline regex fails

[edmundmiller]

Describe the bug
When trying to launch a new workflow some of the regex check fail

But .csv Passes

To Reproduce
Steps to reproduce the behavior:

1. Go to Launch Pipeline for rnaseq
2. Add samplesheet.csv
3. Scroll down to launch
4. See error

Expected behavior
The regex passes because it ends in csv

Screenshots

Browser (please complete the following information):

• OS: NixOS 21.05
• Browser: Firefox
• Version 88.0.1

[edmundmiller]

I have a feeling it's either in

rnaseq/nextflow_schema.json

Line 18 in 7919c2d

"pattern": "\\.csv$",

Or in the way the site parses it. It also seems to fail with anything that starts with \\. so the gtf or .gtf.gz for the gtf file also fails similarly.

[mashehu]

Good catch! The problem is that the HTML form field wants the regex to match the whole string, therefore the pattern in the nextflow_schema.json needs to be updated. I guess \S*\.csv$ should be sufficient. Moving the issue to the RNAseq repo.

[drpatelh]

Thanks @mashehu ! Fancy giving the dev launcher a test-drive @emiller88 to double-check?

[edmundmiller]

Gave it a run and it works great!

[ewels]

@mashehu I think that this is a website bug, not a pipeline schema issue.

JSON schema patterns should match partial strings unless I'm mistaken..?

[mashehu]

Yes and no. We check for these by adding the regex into the pattern field for the respective input field. These are always checked against the whole string according to the HTML specs: https://developer.mozilla.org/en-US/docs/Web/HTML/Attributes/pattern#constraint_validation

[ewels]

Struggling to find the reference now, but I'm 90% sure I looked into this a few weeks ago when the same thing came up in the Tower launch interface..

[mashehu]

By already matching the full string in the regex it should now be okay in the json-schema and in the form, no?

[ewels]

http://json-schema.org/draft/2020-12/json-schema-core.html#rfc.section.6.4

Finally, implementations MUST NOT take regular expressions to be anchored, neither at the beginning nor at the end. This means, for instance, the pattern "es" matches "expression".

This is from a more recent schema version but I think it still holds true. The validation from the Java library that we use within the pipeline certainly seems to behave this way anyway.