Resource workflow v2

[Kerem-G]

Implements changes to the resources workflow which includes file structure changes and update functionality.

Closes #288 - File structure
Closes #301 - Updated resources, strains, and sample design workflow
Closes #303 - Implements an "update" button

[Copilot]

Pull request overview

This PR implements version 2 of the resources workflow, introducing a new file structure with separate uploads directories, automatic file naming collision resolution, and an update feature for resources, strains, and sample designs. The changes reorganize how workflow files are stored and tracked, moving from a flat structure to a hierarchical one with JSON metadata files and separate uploads subdirectories.

Changes:

• Moved upload functionality from ResourcesWizard to ImportFile component with integrated SynBioHub collection browser
• Implemented automatic file naming collision resolution that appends numeric suffixes to prevent overwrites
• Added FileUpdate command that allows updating previously uploaded resources while tracking upload history

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 7 comments.

File	Description
frontend/src/components/panels/resources-editor/ResourcesWizard.jsx	Removed upload button and handler; now displays upload history in reverse chronological order with visual distinction for older versions
frontend/src/components/activities/explorer/ImportFile.jsx	Added workflow subdirectory handling, file naming collision resolution, and integrated upload to SynBioHub during import
frontend/src/commands.js	Enhanced file deletion to handle uploads subdirectory, improved download to read from new file structure, and added comprehensive file update command with authentication

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 7 comments.

Comments suppressed due to low confidence (1)

frontend/src/API.js:70

• The upload_resource function in API.js no longer includes sbh_user and sbh_pass fields in its paramsObj. However, the backend (views.py, lines 71–77) still lists both sbh_user and sbh_pass in required_params and returns a 400 error if either is missing. This means every call to upload_resource from the updated frontend will receive a 400 Bad Request: Parameter sbh_user not found in request response. Either the backend's required_params must be updated to remove sbh_user and sbh_pass, or the frontend must restore sending them as null.

        const paramsObj = {
            sbh_url: sbh_url,
            sbh_token: sbh_token,
            fj_url: "charmmefj-api.synbiohub.org",
            fj_token: null,
            fj_user: null,
            fj_pass: null,
            sbh_collec: sbh_collec,
            sbh_collec_desc: sbh_collec_desc,
            sbh_overwrite: sbh_overwrite,
            fj_overwrite: 1,
            version: "",
            attachments: {}
        }

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 4 comments.

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[Kerem-G]

Note: current iterations still contains bugs with overwrite handling on update and writing to existing collections likely due to downstream issues with XDC.

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[Gonza10V]

@codex review this PR

[chatgpt-codex-connector]

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