Fix a number of issues to make more uniform and simpler for imports and uploads by cjmyers · Pull Request #479 · MyersResearchGroup/SynBioSuite

cjmyers · 2026-08-28T14:39:52Z

Closes #470
Closes #471
Closes #472
Closes #461
Closes #475
Closes #469
Closes #480
Closes #474
Closes #464
Closes #481
Closes #482

…nd uploads

github-actions · 2026-08-28T14:42:45Z

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github-actions · 2026-08-30T21:33:47Z

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Gonza10V · 2026-09-01T21:00:03Z

@codex review

chatgpt-codex-connector · 2026-09-01T21:00:18Z

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-01T21:04:27.048609Z	`113f887`	Manual request

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Copilot

Pull request overview

This PR refactors SynBioSuite’s import/upload workflow to be more uniform across object types, removing legacy “uploads” directories, improving spreadsheet import behavior, and expanding explorer context-menu actions (upload/open/rename) while tightening uploaded-state tracking.

Changes:

Update object type handling so Resources/Strains/SampleDesigns are spreadsheet-based and support import/upload/update with “single sheet” constraints.
Rework explorer/import/upload flows to store files alongside their sidecars (no per-type uploads/), add rename/open actions, and use upload snapshots for “uploaded” state.
Backend upload endpoints now return subCollectionUrl and add plate-reader outputs as SynBioHub attachments; SBOL upload also computes a top-level URI for easier navigation.

Reviewed changes

Copilot reviewed 14 out of 16 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
frontend/src/redux/hooks/workingDirectoryHooks.js	Add optional `addToStore` control when creating files.
frontend/src/redux/hooks/panelsHooks.js	Resolve experiment panels against `.xdc` backing files for spreadsheet handles.
frontend/src/panels.js	Route metadata spreadsheets to Experiment panel; block opening certain spreadsheet types.
frontend/src/objectTypes.js	Shift several object types to spreadsheet-based matching; add update/limit-one flags; remove Assays object type entry.
frontend/src/components/WelcomeScreen.jsx	Update product naming in UI text.
frontend/src/components/panels/xdc/CollectionWizard.jsx	Normalize stored file IDs; record uploaded snapshot fields (results/plateOutput) and use `subCollectionUrl`.
frontend/src/components/BrowserCompatibilityCatch.jsx	Update product naming in UI text.
frontend/src/components/activities/explorer/ImportFile.jsx	Remove `uploads/` directory usage; add “upload now” path; create assay workflow on metadata import.
frontend/src/components/activities/explorer/ExplorerListItem.jsx	Add rename modal and context commands; compute uploaded-state from upload snapshots; gate delete/open accordingly.
frontend/src/components/activities/explorer/ExplorerList.jsx	Adjust study access error handling; split Import vs Upload actions; enforce limit-one behavior.
frontend/src/commands.js	Add FileRename/FileOpen; adjust delete/upload/update logic for new sidecar locations; update autosave backing file handling.
frontend/src/API.js	Remove unused `upload_sbs`; make SBML attachment reading more tolerant.
frontend/src/activities.js	Remove Assays from listed activity object types.
backend/sbs_server/app/utils.py	Add helper to find root SBOL ComponentDefinitions.
backend/sbs_server/app/synbiohubUpload.py	Return sub-collection URL from SynBioHub submit flow.
backend/sbs_server/app/route.py	Return `subCollectionUrl` in responses; attach plate-reader outputs; compute top-level URI for SBOL uploads.

Suppressed comments (3)

frontend/src/components/activities/explorer/ExplorerListItem.jsx:63

When the current file does not match the latest upload snapshot for a given .xdc, the code sets uploadInfo to null and returns immediately. This prevents checking the remaining .xdc files, so a file that is uploaded in a different assay can incorrectly appear deletable/not-uploaded.

                                if (!metadataMatches && !plateMatches && !resultsMatches) {
                                    setUploadInfo(null)
                                } else {
                                    setUploadInfo(xdc.uploads[xdc.uploads.length - 1])
                                }
                                return

frontend/src/components/activities/explorer/ExplorerListItem.jsx:67

If a .xdc has no uploads, the loop returns immediately, which again prevents checking other .xdc files that may contain an upload record for this file. This can incorrectly allow deleting uploaded plate-reader/results/metadata files.

                            } else {
                                setUploadInfo(null)
                                return
                            }

frontend/src/commands.js:968

updateFileReferences updates top-level file/metadata/plateOutput/results, but does not update references inside uploads[]. Since uploaded-state coloring and delete restrictions now key off the latest upload snapshot, renaming a file can orphan those snapshot references and make uploaded files appear not uploaded/deletable.

                // XDC results reference(s)
                if (Array.isArray(json.results)) {
                    const updated = json.results.map(replaceReference)

                    if (updated.some((value, i) =>
                        value !== json.results[i])) {
                        json.results = updated
                        changed = true
                    }
                } else if (json.results !== undefined) {
                    const updated = replaceReference(json.results)

                    if (updated !== json.results) {
                        json.results = updated
                        changed = true
                    }
                }

                if (changed) {
                    const writable = await entry.createWritable()
                    await writable.write(JSON.stringify(json, null, 2))
                    await writable.close()
                }

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github-actions · 2026-09-03T22:58:19Z

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github-actions · 2026-09-03T23:00:39Z

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Gonza10V

Tested #470, #471, #472, #461 (works fur now you MUST have a Fj account to upload xlsx document I could not added as other, which I think should be relaxed). #475 Sample designs lost the options after uploading a template, just can recover by deleting the template. Tested and all of them loose the options after uploading a template. #469 , #480 , #474 , #464 (color is lost after renaming on metadata but not on resources, link is lost on metadata), #481 , #482 .

github-actions · 2026-09-03T23:16:13Z

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cjmyers · 2026-09-03T23:17:45Z

@Gonza10V

Need for FJ account is definitely a bug. Is this for Assay or any spreadsheet?

Losing options on upload is by design, since you are only allowed one resource, strain, and sample design sheet.

Color lost on renaming metadata is a bug. I may have fixed that one when fixing @Kerem-G 's issues, but will re-test.

cjmyers · 2026-09-03T23:21:53Z

@Gonza10V
Correct about color being lost. It is not updating the file name in the XDC file.

Could not reproduce the need for FJ account for resources. Is this only for Assay? Did you create the study with a Flapjack study at the beginning?

cjmyers · 2026-09-04T19:38:27Z

@Gonza10V Fixed the issue with color being lost on rename for Assays.

Cannot reproduce your other issue.

github-actions · 2026-09-04T19:41:52Z

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Gonza10V · 2026-09-04T21:03:28Z

Need for FJ account is definitely a bug. Is this for Assay or any spreadsheet?

This is just for Assay. The Study didnt had an Fj accoun connected at the begining and couldnt connect it afterwards.

cjmyers · 2026-09-04T21:06:47Z

Got it. Basically, this happens if you try to upload Plate Reader files with no Flapjack.

cjmyers · 2026-09-04T21:09:30Z

That is fixed. Just one simple check. It will now add plate files as attachments in SBH but not try to use Flapjack if no repo is associated with the study. Good check.

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Gonza10V

bugs fixed and functions clarified

github-actions · 2026-09-05T01:37:31Z

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Fix a number of issues to make more uniform and simpler for imports a…

107d8d2

…nd uploads

github-code-quality Bot found potential problems Aug 28, 2026

View reviewed changes

Updates to right-click commands and new open in SynBioHub feature

5575b8c

github-code-quality Bot found potential problems Aug 28, 2026

View reviewed changes

Comment thread frontend/src/components/activities/explorer/ExplorerList.jsx Fixed

Add plate reader files as attachments in SynBioHub

375e2da

github-advanced-security Bot found potential problems Aug 28, 2026

View reviewed changes

Comment thread backend/sbs_server/app/route.py Dismissed

Support opening SBOL objects on SynBioHub

a280792

Implement Rename

e4f5bc0

github-code-quality Bot found potential problems Aug 28, 2026

View reviewed changes

Comment thread frontend/src/commands.js Fixed

Comment thread frontend/src/commands.js Fixed

Remove unused

2e95ac0

Fix assay update

c4151ff

Restrict delete to before upload

113f887

cjmyers requested review from Gonza10V and Kerem-G September 1, 2026 20:55

Kerem-G requested a lite review from Copilot September 1, 2026 20:55

Copilot started reviewing on behalf of Kerem-G September 1, 2026 20:56 View session

Copilot AI reviewed Sep 1, 2026

View reviewed changes

Comment thread frontend/src/commands.js Outdated

Comment thread frontend/src/components/activities/explorer/ExplorerListItem.jsx Outdated

chatgpt-codex-connector Bot reviewed Sep 1, 2026

View reviewed changes

Comment thread frontend/src/commands.js Outdated

Comment thread frontend/src/commands.js

Comment thread frontend/src/components/activities/explorer/ImportFile.jsx Outdated

Comment thread frontend/src/components/activities/explorer/ExplorerListItem.jsx Outdated

cjmyers and others added 2 commits September 2, 2026 10:21

Potential fix for pull request finding

9e034b8

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Potential fix for pull request finding

25f98a8

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cjmyers added 2 commits September 3, 2026 16:54

Fix bugs in update overwriting with JSON file

3074a92

small bug

a5a529c

Gonza10V requested changes Sep 3, 2026

View reviewed changes

Swapped Open and View

e80d70c

Fix issue with metadata upload not being updated on rename

48b4bdd

github-code-quality Bot found potential problems Sep 4, 2026

View reviewed changes

Comment thread frontend/src/components/activities/explorer/ExplorerListItem.jsx Fixed

Remove unused

f973c5d

Do not ask for FJ login when no FJ repo associatd with study

98f5a7c

Open in the appropriate SynBioHub

e9ad51a

Fix issue uploading SBML for devices

9dc2972

Gonza10V self-requested a review September 5, 2026 01:12

Gonza10V approved these changes Sep 5, 2026

View reviewed changes

Fix issue with URI returned

aec45b7

cjmyers merged commit be4e023 into master Sep 5, 2026
8 checks passed

cjmyers deleted the uniformFrontend branch September 5, 2026 01:38

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