diff --git a/gisaid_cli/fluCLI/fluCLI b/gisaid_cli/fluCLI/fluCLI deleted file mode 100644 index e69de29..0000000 diff --git a/seqsender.py b/seqsender.py index cf15dd2..82fba53 100755 --- a/seqsender.py +++ b/seqsender.py @@ -173,7 +173,7 @@ def main(): elif command == "test_data": setup.create_test_data(organism=args.organism, database=database, submission_dir=submission_dir) elif command == "version": - print("Version: {VERSION}", file=sys.stdout) + print(f"Version: {VERSION}", file=sys.stdout) elif command == "update_biosample": print("Updating BioSample requirements.", file=sys.stdout) setup.download_biosample_xml_list() diff --git a/settings.py b/settings.py index 096ff3d..b49d6e6 100755 --- a/settings.py +++ b/settings.py @@ -12,7 +12,7 @@ PROG_DIR: str = os.path.dirname(os.path.abspath(__file__)) # SeqSender version -VERSION: str = "1.1.0 (Beta)" +VERSION: str = "1.2.1 (Beta)" # Organism options with unique submission options ORGANISM_CHOICES: List[str] = ["FLU", "COV", "POX", "ARBO", "OTHER"] diff --git a/submission_log.csv b/submission_log.csv deleted file mode 100755 index dd29dfc..0000000 --- a/submission_log.csv +++ /dev/null @@ -1,9 +0,0 @@ -Submission_Name,Organism,Database,Submission_Type,Submission_Date,Submission_Status,Submission_ID,Submission_Directory,Config_File,Update_Date -COV_TEST_DATA,COV,BIOSAMPLE,TEST,2024-08-05,PROCESSED,SUB921446,/scicomp/home-pure/psv4/seqsender_dev/seqsender/COV_TEST_DATA/submission_files/BIOSAMPLE,/scicomp/home-pure/psv4/seqsender_dev/seqsender/COV_TEST_DATA/config.yaml,2024-08-05 -COV_TEST_DATA,COV,GENBANK-FTP,TEST,2024-08-05,PROCESSED,SUB921490,/scicomp/home-pure/psv4/seqsender_dev/seqsender/COV_TEST_DATA/submission_files/GENBANK,/scicomp/home-pure/psv4/seqsender_dev/seqsender/COV_TEST_DATA/config.yaml,2024-08-06 -FLU_TEST_DATA,FLU,BIOSAMPLE,TEST,2024-08-05,PROCESSED,SUB921448,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/submission_files/BIOSAMPLE,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/config.yaml,2024-08-05 -FLU_TEST_DATA,FLU,SRA,TEST,2024-08-05,ERROR,SUB921447,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/submission_files/SRA,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/config.yaml,2024-08-06 -FLU_TEST_DATA,FLU,GENBANK-FTP,TEST,2024-08-06,FAILED,PENDING,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/submission_files/GENBANK,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/config.yaml,2024-08-06 -FLU_TEST_DATA,FLU,GENBANK-TBL2ASN,TEST,2024-08-06,PROCESSED,PENDING,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/submission_files/GENBANK,/scicomp/home-pure/psv4/seqsender_dev/seqsender/FLU_TEST_DATA/config.yaml,2024-08-06 -COV_TEST_DATA,COV,GISAID,PRODUCTION,2024-09-10,WAITING,PENDING,/scicomp/home-pure/psv4/seqsender_v1.2.1/seqsender/COV_TEST_DATA/submission_files/GISAID,/scicomp/home-pure/psv4/seqsender_v1.2.1/seqsender/COV_TEST_DATA/config.yaml,2024-09-10 -COV_TEST_DATA,COV,GISAID,TEST,2024-09-10,ERROR,PENDING,/scicomp/home-pure/psv4/seqsender_v1.2.1/seqsender/COV_TEST_DATA/submission_files/GISAID,/scicomp/home-pure/psv4/seqsender_v1.2.1/seqsender/COV_TEST_DATA/config.yaml,2024-09-10