Draft
Conversation
jmillanacosta
commented
Feb 4, 2026
| return await datasource_service.get_available_sources() | ||
|
|
||
|
|
||
| @router.get("/{set_id}/annotations", response_model=DataSourceProcessingResponse) |
Collaborator
Author
There was a problem hiding this comment.
Avoid loading the annotations result in browser, which led to quota errors even with moderate sizes
jmillanacosta
commented
Feb 4, 2026
| pygraph, error = GraphService.create_pygraph(annotations, graph_dir) | ||
| if error: | ||
| return None, f"Graph error: {error}" | ||
| try: |
Collaborator
Author
There was a problem hiding this comment.
Some more exception catching
jmillanacosta
commented
Feb 4, 2026
| ) | ||
| dataframes.append(pubchem_assay_df) | ||
| metadata.append(pubchem_assay_metadata) | ||
| # Clean up pubchem cache file created by pyBiodatafuse |
Collaborator
Author
There was a problem hiding this comment.
I saw some tmp files persist in memory. This is one of them, maybe this is intended, so we can undo this.
jmillanacosta
commented
Feb 4, 2026
| } catch (e) { | ||
| error.value = 'Failed to parse annotation results.' | ||
| console.error("JSON parse error:", e) | ||
| onMounted(async () => { |
Collaborator
Author
There was a problem hiding this comment.
Applying the API call to get the annotations as stored. Not sure about when (if at all) they should be removed from db.
jmillanacosta
commented
Feb 4, 2026
| @@ -1,4 +1,4 @@ | |||
| pyBiodatafuse | |||
| pyBiodatafuse==1.3.0 | |||
Collaborator
Author
There was a problem hiding this comment.
We should hardcode versions
jmillanacosta
commented
Feb 4, 2026
| # Remove external port exposure - backend only accessible internally | ||
| volumes: | ||
| - ./backend:/app | ||
| - ./data:/app/data |
Collaborator
Author
There was a problem hiding this comment.
Not sure about this: it's needed for e.g. the cytoscape styles download, but was it left out for a reason?
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
QuotaExceededErrorduring /process #25 (done with 8ef726c)