Skip to content

Feature/antismash_api_jobs #312

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
wants to merge 35 commits into
base: dev
Choose a base branch
from
Open

Feature/antismash_api_jobs #312

wants to merge 35 commits into from

Conversation

@liannette
Copy link
Contributor

@liannette liannette commented Mar 19, 2025 •
edited
Loading

This pull request improves antiSMASH BGC data acquisition in PODP mode by adding new features for handling previously downloaded data and for automating job submissions via the antiSMASH API

Features:

  1. processing of previously downloaded antiSMASH data
  • checks if existing BGC data archives are extracted in the antismash directory
  • extracts unprocessed archives to ensure they are ready for use
  1. antiSMASH job submission and download of results
  • if BGC data for a genome is unavailable and cannot be downloaded from antiSMASH-DB, the corresponding refseq genome is retrieved from NCBI
  • the downloaded genome is submitted to the antiSMASH API
  • waits for the job to complete
  • downloads and extracts the results
liannette and others added 30 commits March 18, 2025 17:58
@liannette
Merge pull request #4 from NPLinker/dev
881e3eb 
Local strain mappings (NPLinker#310)
@liannette
Refactor: Simplify Path handling
2430868
@liannette
Refactor: Improve extract path handling to ensure that non-empty dirs…
1f07246 
… are not deleted
@liannette
Refactor: Extract file cleanup logic into a separate function for bet…
8d7238c 
…ter readability
@liannette
Refactor: Move extract_path preparation logic into a seperate functio…
d5e64eb 
…n for better readabiliy
@liannette
Refactor: Separate genome assembly resolution and antiSMASH data retr…
66f13d6 
…ieval into distinct functions for improved clarity
@liannette
Refactor: Improve genome ID handling and logging
706f841
@liannette
Refactor: Move logging for antiSMASH data retrieval errors and succes…
b25506e 
…s messages
@liannette
simplify comment
2ed8ac6
@liannette
Enhance logging messages in antiSMASH data retrieval
a1e4962
@liannette
test: adapt test to changed logging info message
e8dd391
@liannette
Feat: Add antiSMASH API functionality
ea159ca
@liannette
Feat: Add antiSMASH API functionality
a972a70
@liannette
Merge branch 'feature/antismash-jobs' of https://github.com/liannette…
0569976 
…/nplinker into feature/antismash-jobs
@liannette
fix: improve logging message for start of antiSMASH API process
f3a159f
@liannette
docs: improve docstring for download_and_extract_ncbi_genome function
da4da3c
@liannette
fix: update logging messages for antiSMASH data retrieval failures
af094e4
@liannette
add logging after antiSMASH job submission
99d99a2
@liannette
refactor: rename refseq_id to genome_assembly_acc
1c83934
@liannette
improve genome download process with validation and retry logic
496db38
@liannette
test: add unit tests for download_and_extract_ncbi_genome function
cc6573c
@liannette
refactor: rename verify_ncbi_dataset_md5_sums to _verify_ncbi_dataset…
51e4817 
…_md5_sums for consistency
@liannette
refactor: move _verify_ncbi_dataset_md5_sums function to a new locati…
6b564ea 
…on for better organization
@liannette
feat: handle already download antiSMASH results
7570852
@liannette
fix mistake in docstring
9881254
@liannette
fix: update return type of submit_antismash_job to str
0e1ec54
@liannette
fix: update return type of download_and_extract_ncbi_genome to Path
f53f1a7
@liannette
update submit_antismash_job to return job ID as string and improve er…
5e5b2bd 
…ror handling in antismash_job_is_done
@liannette
chore: add types-requests to development dependencies
909ca63
@liannette
fix: update return type of _verify_ncbi_dataset_md5_sums to None and …
252a177 
…remove return value documentation
@liannette liannette mentioned this pull request Mar 21, 2025
Open
@liannette liannette changed the title Feature/antismash jobs Feature/antismash_api_jobs Mar 21, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

1 participant

@liannette