swap referencer with db manipulator for checking ref_lock

Author: karlnyr

microSALT/cli.py

@@ -2,7 +2,6 @@
 By: Isak Sylvin, @sylvinite"""
 
 #!/usr/bin/env python
-
 import json
 import logging
 import os
@@ -21,8 +20,9 @@
     get_scoped_session_registry,
     initialize_database,
 )
+from microSALT.store.db_manipulator import DB_Manipulator
 from microSALT.utils.job_creator import Job_Creator
-from microSALT.utils.pubmlst.get_credentials import main as get_bigsdb_credentials_main
+from microSALT.utils.pubmlst.get_credentials import get_bigsdb_access_token
 from microSALT.utils.referencer import Referencer
 from microSALT.utils.reporter import Reporter
 from microSALT.utils.scraper import Scraper
@@ -298,9 +298,7 @@ def refer(ctx):
 )
 @click.option("--output", help="Report output folder", default="")
 @pass_config
-def finish(
-    config: MicroSALTConfig, sampleinfo_file, input, track, dry, email, skip_update, report, output
-):
+def finish(config: MicroSALTConfig, sampleinfo_file, input, track, dry, email, report, output):
     """Sequence analysis, typing and resistance identification"""
     pool = []
     if email:
@@ -316,31 +314,12 @@ def finish(
             pool.append(subfolder)
 
     sampleinfo = review_sampleinfo(sampleinfo_file)
-    ext_refs = Referencer(
-        log=logger,
-        folders=config.folders,
-        threshold=config.threshold,
-        pubmlst=config.pubmlst,
-        pasteur=config.pasteur,
-        singularity=config.singularity,
-        containers=config.containers,
-        sampleinfo=sampleinfo,
-    )
+    db_manipulator = DB_Manipulator(log=logger, folders=config.folders, threshold=config.threshold)
     try:
-        ext_refs.db_access.check_ref_lock()
+        db_manipulator.check_ref_lock()
     except RefUpdateLockError as e:
-        click.echo("ERROR - {}".format(e))
+        click.echo(f"ERROR - {e}")
         click.Abort()
-    click.echo("INFO - Checking versions of references..")
-    try:
-        if not skip_update:
-            ext_refs.identify_new(project=True)
-            ext_refs.update_refs()
-            click.echo("INFO - Version check done. Creating sbatch jobs")
-        else:
-            click.echo("INFO - Skipping version check.")
-    except Exception as e:
-        click.echo(f"{e}")
 
     res_scraper = Scraper(
         log=logger,
@@ -463,7 +442,7 @@ def report(config: MicroSALTConfig, sampleinfo_file, email, type, output, collec
 @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)
+    get_bigsdb_access_token(service, config, species)
 
 
 @utils.command()

microSALT/utils/pubmlst/get_credentials.py

@@ -77,7 +77,7 @@ def save_to_credentials_py(
     print(f"Tokens saved to {credentials_file}")
 
 
-def main(service: str, config: MicroSALTConfig, species: str | None = None):
+def get_bigsdb_access_token(service: str, config: MicroSALTConfig, species: str | None = None):
     try:
         service_config = get_service_config(service, pubmlst=config.pubmlst, pasteur=config.pasteur)
         bigsd_config = service_config["config"]

microSALT/utils/referencer.py

@@ -464,6 +464,7 @@ def add_pubmlst(self, organism: str):
         """Checks pubmlst for references of given organism and downloads them"""
         # Organism must be in binomial format and only resolve to one hit
         errorg = organism
+        self.db_access.check_ref_lock()
         try:
             organism = organism.lower().replace(".", " ")
             if organism.replace(" ", "_") in self.organisms and not self.force:

microSALT/utils/reporter.py

@@ -27,7 +27,17 @@
 
 
 class Reporter:
-    def __init__(self, log, folders: Folders, threshold: Threshold, regex: Regex, sampleinfo={}, name="", output="", collection=False):
+    def __init__(
+        self,
+        log,
+        folders: Folders,
+        threshold: Threshold,
+        regex: Regex,
+        sampleinfo={},
+        name="",
+        output="",
+        collection=False,
+    ):
         self.folders = folders
         self.threshold = threshold
         self.regex = regex
@@ -69,6 +79,7 @@ def create_subfolders(self):
         os.makedirs(f"{self.folders.reports}/analysis", exist_ok=True)
 
     def report(self, type="default", customer="all"):
+        self.db_pusher.check_ref_lock()
         self.create_subfolders()
         if type in ["default", "typing", "qc"]:
             # Only typing and qc reports are version controlled
@@ -152,7 +163,12 @@ def gen_typing(self, silent=False):
             self.logger.error(f"Project {self.name} does not exist")
             sys.exit(-1)
         try:
-            content = typing_page(self.name, "all", threshold=self.threshold, verified_organisms=self.regex.verified_organisms)
+            content = typing_page(
+                self.name,
+                "all",
+                threshold=self.threshold,
+                verified_organisms=self.regex.verified_organisms,
+            )
             outfile = f"{self.sample.get('Customer_ID_project')}_Typing_{last_version}.html"
             local = f"{self.output}/{outfile}"
             output = f"{self.folders.reports}/analysis/{outfile}"