Issue151 use json for genome status file (#157)

* re-format code

* remove deprecated methods and unused varaibles

* refactor class GenomeStatus

* remove private method `_get_genome_status_log`

instead you can use GenomeStatus.load_from_json.

* update GenomeStatus usage in podp antismash downloader

* Update __init__.py

* update GenomeStatus attribute names in tests

* remove tests for old GenomeStatus class

* fix GenomeUsage usage in tests

* add unit tests for GenomeStatus class

* rename method `load_from_json` to `read_json`

* rename method `save_to_json` to `to_json`

* change parameter `output_dir` to `file` for `to_json` method

* enable `to_json` return string when output file is None

* fix refseq id `None`

src/nplinker/genomics/antismash/antismash_downloader.py

@@ -7,14 +7,12 @@
 from nplinker.utils import list_dirs
 from nplinker.utils import list_files
 
+
 logger = LogConfig.getLogger(__name__)
 
 # urls to be given to download antismash data
-ANTISMASH_DB_PAGE_URL = 'https://antismash-db.secondarymetabolites.org/output/{}/'
 ANTISMASH_DB_DOWNLOAD_URL = 'https://antismash-db.secondarymetabolites.org/output/{}/{}'
-
 # The antiSMASH DBV2 is for the availability of the old version, better to keep it.
-ANTISMASH_DBV2_PAGE_URL = 'https://antismash-dbv2.secondarymetabolites.org/output/{}/'
 ANTISMASH_DBV2_DOWNLOAD_URL = 'https://antismash-dbv2.secondarymetabolites.org/output/{}/{}'
 
 
@@ -29,8 +27,8 @@ def download_and_extract_antismash_data(antismash_id: str,
 
     Args:
         antismash_id(str): The id used to download BGC archive from antiSMASH database.
-            If the id is versioned (e.g., "GCF_004339725.1") please be sure to 
-            specify the version as well. 
+            If the id is versioned (e.g., "GCF_004339725.1") please be sure to
+            specify the version as well.
         download_root(str | PathLike): Path to the directory to place downloaded archive in.
         extract_root(str | PathLike): Path to the directory data files will be extracted to.
             Note that an `antismash` directory will be created in the specified `extract_root` if

src/nplinker/pairedomics/__init__.py

@@ -1,10 +1,9 @@
 import logging
-from .podp_antismash_downloader import download_antismash_data
+from .podp_antismash_downloader import GENOME_STATUS_FILENAME
+from .podp_antismash_downloader import GenomeStatus
 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"
-]
+__all__ = ["GENOME_STATUS_FILENAME", "GenomeStatus", "podp_download_and_extract_antismash_data"]