fix: type error

[JaeAeich]

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fix type error caused by mishandling path type.

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Summary by Sourcery

Update the WES endpoint URL and fix a type error in the workflow run document.

Bug Fixes:

• Fixed a type error when setting the work_dir field by converting the Path object to a string.

Enhancements:

• Updated the WES endpoint URL from https://csc-wes-noauth.rahtiapp.fi to https://wes-na.cloud.e-infra.cz to use a working endpoint.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request fixes a type error by changing the type of the work_dir field in the DbDocument model from Path to str. It also updates the WES endpoint URL.

Class diagram showing updated DbDocument model

classDiagram
    class DbDocument {
        +RunLog run_log
        +Optional[str] task_id
        +Optional[str] user_id
        +Optional[str] work_dir
        +Optional[WesEndpoint] wes_endpoint
    }
    note for DbDocument "Changed work_dir type from Path to str"

    class RunLog {
    }

    class WesEndpoint {
        +str host
    }

    DbDocument --> RunLog
    DbDocument --> WesEndpoint

Loading

File-Level Changes

Change	Details	Files
Changed the type of work_dir from Path to str.	Modified the type annotation of the work_dir field in the DbDocument model. Updated the assignment of the work_dir field to convert the Path object to a string.	pro_wes/ga4gh/wes/models.py pro_wes/ga4gh/wes/workflow_runs.py
Updated the WES endpoint URL.	Changed the host value from https://csc-wes-noauth.rahtiapp.fi to https://wes-na.cloud.e-infra.cz.	pro_wes/ga4gh/wes/workflow_runs.py

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[sourcery-ai]

Hey @JaeAeich - I've reviewed your changes - here's some feedback:

Overall Comments:

• The WES endpoint URL should be configurable rather than hardcoded. Consider moving this to a configuration file or environment variable.
• Please explain why the work_dir type needed to be changed from Path to str. If there were issues with the Path type, we should understand and possibly fix the root cause.

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[uniqueg]

Can you please make 2 PRs out of this? Especially with changes like changing defaults, they should have good visibility.

[JaeAeich]

@uniqueg maybe lets leave changing the url altogether, lets keep that implicit.

[uniqueg]

Looks good, but please make sure the PR description is up to date (check whether the issues are still addressed, check that only the type change is described, make sure that the template is either filled out properly or delete it)

[JaeAeich]

yeah it doesn't I have changes the description.