remove logfile

Author: karlnyr

configExample.json

@@ -21,8 +21,6 @@
     "results": "/tmp/MLST/results/",
     "_comment": "Report collection folder",
     "reports": "/tmp/MLST/reports/",
-    "_comment": "Log file position and name",
-    "log_file": "/tmp/microsalt.log",
     "_comment": "Root folder for input fasta sequencing data",
     "seqdata": "/tmp/projects/",
     "_comment": "ST profiles. Each ST profile file under 'profiles' have an identicial folder under references",

microSALT/cli.py

@@ -22,6 +22,7 @@
     initialize_database,
 )
 from microSALT.utils.job_creator import Job_Creator
+from microSALT.utils.pubmlst.get_credentials import main as get_bigsdb_credentials_main
 from microSALT.utils.referencer import Referencer
 from microSALT.utils.reporter import Reporter
 from microSALT.utils.scraper import Scraper
@@ -99,12 +100,6 @@ def _ensure_directories(config: MicroSALTConfig) -> None:
             click.echo("ERROR - Database writing failed! Invalid user access detected!")
             sys.exit(-1)
 
-    log_dir = os.path.dirname(config.folders.log_file)
-    if log_dir and not pathlib.Path(log_dir).exists():
-        os.makedirs(log_dir)
-    proc = subprocess.Popen(f"touch {config.folders.log_file}".split(), stdout=subprocess.PIPE)
-    proc.communicate()
-
     folder_paths = [
         config.folders.results,
         config.folders.reports,
@@ -470,6 +465,15 @@ def report(config: MicroSALTConfig, sampleinfo_file, email, type, output, collec
     done()
 
 
+@utils.command("get-bigsdb-credentials")
+@click.argument("service", type=click.Choice(["pubmlst", "pasteur"]))
+@click.option("--species", default=None, help="Species name (required for the 'pasteur' service)")
+@pass_config
+def get_bigsdb_credentials(config: MicroSALTConfig, service, species):
+    """Obtain and store BIGSdb OAuth credentials for SERVICE (pubmlst or pasteur)"""
+    get_bigsdb_credentials_main(service, config, species)
+
+
 @utils.command()
 @click.option("--input", help="Full path to project folder", default=os.getcwd())
 @click.pass_context

microSALT/config.py

@@ -23,7 +23,6 @@ class Regex(BaseModel):
 class Folders(BaseModel):
     results: str
     reports: str
-    log_file: str
     seqdata: str
     profiles: str
     references: str

microSALT/utils/job_creator.py

@@ -742,7 +742,7 @@ def finish_job(self, joblist, single_sample=False):
             f"-A {self.slurm_header.project} -p core -n 1 -t 6:00:00 "
             f"-J {self.slurm_header.job_prefix}_{self.name}_MAILJOB "
             f"--qos {self.slurm_header.qos} --open-mode append "
-            f"--dependency=afterany:{final} --output {self.folders.log_file}"
+            f"--dependency=afterany:{final} --output {self.finishdir}/mailjob.out"
         )
         bash_cmd = f"sbatch {head} {mailfile}"
         mailproc = subprocess.Popen(bash_cmd.split(), stdout=subprocess.PIPE)

microSALT/utils/pubmlst/get_credentials.py

@@ -1,14 +1,9 @@
 import os
 import sys
-from argparse import ArgumentParser
 
 from requests_oauthlib import OAuth1Session
 
 from microSALT.config import (
-    Folders,
-    PasteurCredentials,
-    PubMLSTCredentials,
-    load_config,
     MicroSALTConfig,
 )
 from microSALT.utils.pubmlst.constants import CREDENTIALS_KEY
@@ -118,28 +113,3 @@ def main(service: str, config: MicroSALTConfig, species: str | None = None):
     except Exception as e:
         print(f"Error: {e}")
         sys.exit(1)
-
-
-if __name__ == "__main__":
-    parser = ArgumentParser(description="Get PubMLST or Pasteur credentials.")
-    parser.add_argument(
-        "-s",
-        "--service",
-        type=str,
-        default="pubmlst",
-        help="Service name (default: pubmlst)",
-    )
-    parser.add_argument(
-        "--species",
-        type=str,
-        help="Species name (required for the 'pasteur' service)",
-    )
-    parser.add_argument(
-        "--config",
-        type=str,
-        required=True,
-        help="Path to the microSALT configuration JSON file.",
-    )
-    args = parser.parse_args()
-    cfg = load_config(args.config)
-    main(args.service, cfg, args.species)

tests/conftest.py

@@ -39,7 +39,6 @@ def config(tmp_path_factory: pytest.TempPathFactory) -> MicroSALTConfig:
     for d in (results, reports, seqdata, profiles, references, resistances, genomes, credentials):
         d.mkdir(parents=True, exist_ok=True)
 
-    log_file = base / "microsalt.log"
     db_path = base / "microsalt.db"
 
     cfg = MicroSALTConfig(
@@ -59,7 +58,6 @@ def config(tmp_path_factory: pytest.TempPathFactory) -> MicroSALTConfig:
         folders=Folders(
             results=str(results),
             reports=str(reports),
-            log_file=str(log_file),
             seqdata=str(seqdata),
             profiles=str(profiles),
             references=str(references),
@@ -130,7 +128,6 @@ def exp_config():
         "folders": {
             "results",
             "reports",
-            "log_file",
             "seqdata",
             "profiles",
             "references",

tests/test_cli.py

@@ -51,7 +51,6 @@ def setup_config(tmp_path: Path) -> MicroSALTConfig:
         folders=Folders(
             results=str(base / "results"),
             reports=str(base / "reports"),
-            log_file=str(base / "microsalt.log"),
             seqdata=str(base / "seqdata"),
             profiles=str(base / "profiles"),
             references=str(base / "references"),

tests/test_config.py

@@ -46,7 +46,6 @@ def test_folders_fields():
     cfg = load_config(CONFIGEXAMPLE)
     assert cfg.folders.results
     assert cfg.folders.reports
-    assert cfg.folders.log_file
     assert cfg.folders.seqdata
     assert cfg.folders.profiles
     assert cfg.folders.references