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@trispera trispera commented Feb 28, 2025

  • nextflow and plugin nf-ga4gh were failing to parse the JSON fields in the response from the TES server.
  • Unrecognized field \"backend_parameters_strict\" was the error message.
  • The solution was to add the JSON fields to the TesResources.java class.

Summary by Sourcery

Bug Fixes:

  • Fixes an issue where the nextflow and nf-ga4gh plugins were failing to parse JSON fields in the response from the TES server.

- nextflow and plugin nf-ga4gh were failing to parse the JSON fields in the response from the TES server.
- `Unrecognized field \"backend_parameters_strict\"` was the error message.
- The solution was to add the JSON fields to the TesResources.java class.
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sourcery-ai bot commented Feb 28, 2025

Reviewer's Guide by Sourcery

This pull request modifies the TesResources class to include two new fields, backend_parameters and backend_parameters_strict. These fields are intended to map JSON fields from the TES server response, which were previously causing parsing errors. The JsonInclude annotation was added to the class to prevent null or default values from being serialized.

Updated class diagram for TesResources

classDiagram
  class TesResources {
    Long cpuCores
    Double ramGb
    Double diskGb
    List~String~ zones
    Map~String, String~ backendParameters
    Boolean backendParametersStrict
  }
  note for TesResources "Added backendParameters and backendParametersStrict fields"
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File-Level Changes

Change Details Files
Added new fields to the TesResources class to map JSON fields from the TES server response.
  • Added backendParameters field of type Map<String, String>.
  • Added backendParametersStrict field of type Boolean.
src/main/java/uk/ac/ebi/tsc/tesk/tes/model/TesResources.java

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@trispera trispera requested a review from lvarin February 28, 2025 08:25
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@sourcery-ai sourcery-ai bot left a comment

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

Overall Comments:

  • Consider adding a unit test to verify the serialization and deserialization of the new fields.
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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@lvarin lvarin left a comment

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LGTM

@lvarin lvarin merged commit 751d482 into master Feb 28, 2025
2 checks passed
@lvarin lvarin deleted the add-json-fields branch February 28, 2025 08:29
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3 participants