refactor: use refactored antismash downloader module in `PODPDownload…

…er` class (#138)

* create `podp_download_and_extract_antismash_data` function which uses `antismash_downloader` function

* rename `_resolve_genome_id_data` to `_resolve_refseq_access_id`

* rename `best_id` as `raw_genome_id`

* rename `resolved_id` as `resolved_refseq_id`

* add `download_and_extract_antismash_data` to the refactored `podp_download_and_extract_antismash_data`

* add tests for podp_antismash_downloader.py

* add/improve doc strings in podp_antismash_downloader.py

* add type hints in podp_antismash_downloader.py

* fix prospector errors in podp_antismash_downloader.py

---------

Co-authored-by: Cunliang Geng <c.geng@esciencecenter.nl>

src/nplinker/pairedomics/__init__.py

@@ -1 +1,10 @@
+import logging
 from .podp_antismash_downloader import download_antismash_data
+from .podp_antismash_downloader import podp_download_and_extract_antismash_data
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+__all__ = [
+	"download_antismash_data",
+	"podp_download_and_extract_antismash_data"
+]

src/nplinker/pairedomics/downloader.py

@@ -26,7 +26,7 @@
 from nplinker.metabolomics.gnps.gnps_extractor import GNPSExtractor
 from nplinker.strain_collection import StrainCollection
 from nplinker.strains import Strain
-from . import download_antismash_data
+from . import podp_download_and_extract_antismash_data
 from .runbigscape import run_bigscape
 
 logger = LogConfig.getLogger(__name__)
@@ -152,7 +152,7 @@ def get(self, do_bigscape, extra_bigscape_parameters, use_mibig,
 
         self._download_metabolomics_zipfile(self.gnps_task_id)
 
-        download_antismash_data(self.project_json['genomes'],
+        podp_download_and_extract_antismash_data(self.project_json['genomes'],
                                 self.project_download_cache,
                                 self.project_file_cache)