Fix exits and pre-commit config

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
             types-tabulate,
           ]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "3.0.3"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python

scripts/novaseq_run_recipe_generator.py

@@ -104,7 +104,7 @@ def main(lims, args):
         with open(f"{log_id}_{fc_name}_Error.log", "w") as f:
             f.write("\n".join(log))
         sys.stderr.write("Errors were met, check the log.")
-        sys.exit(1)
+        sys.exit(2)
 
 
 if __name__ == "__main__":

scripts/ont_calc_volumes.py

@@ -165,6 +165,6 @@ def main(lims, args):
     lims.check_version()
     try:
         main(lims, args)
-    except BaseException as e:
+    except Exception as e:
         sys.stderr.write(str(e))
         sys.exit(2)

scripts/ont_generate_samplesheet.py

@@ -104,7 +104,7 @@ def main(lims, args):
 
     except AssertionError as e:
         sys.stderr.write(str(e))
-        sys.exit()
+        sys.exit(2)
 
 
 def minknow_samplesheet_default(currentStep):
@@ -510,6 +510,6 @@ def get_kit_string(currentStep):
     lims.check_version()
     try:
         main(lims, args)
-    except BaseException as e:
+    except Exception as e:
         sys.stderr.write(str(e))
-        sys.exit()
+        sys.exit(2)

scripts/ont_pool.py

@@ -143,7 +143,7 @@ def main(lims, args):
                     lims.request_session.delete(f.uri)
                 lims.upload_new_file(out, log_filename)
 
-    except BaseException as e:
+    except Exception as e:
         sys.stderr.write(str(e))
         sys.exit(2)
 

scripts/ont_suggest_ports.py

@@ -84,7 +84,7 @@ def main(lims, args):
 
     except AssertionError as e:
         sys.stderr.write(str(e))
-        sys.exit(1)
+        sys.exit(2)
 
 
 if __name__ == "__main__":

scripts/ont_update_amount.py

@@ -113,7 +113,7 @@ def main(lims, args):
                     lims.request_session.delete(f.uri)
                 lims.upload_new_file(out, log_filename)
 
-    except BaseException as e:
+    except Exception as e:
         sys.stderr.write(str(e))
         sys.exit(2)
 

scripts/parse_ba_results.py

@@ -14,9 +14,9 @@
 from epp_utils import udf_tools
 from scilifelab_epps.epp import get_well_number
 
-DESC = """This script parses the Agilent BioAnalyzer XML report. 
+DESC = """This script parses the Agilent BioAnalyzer XML report.
 
-It is written to replace the current Illumina-supplied sfdcript consisting of compiled 
+It is written to replace the current Illumina-supplied sfdcript consisting of compiled
 Java which does not as of 2023-08-25 populate the measurement UDFs of interest.
 """
 
@@ -164,13 +164,13 @@ def main(lims, args):
 
             if any("ERROR" in entry for entry in log):
                 sys.stderr.write("Some samples were skipped, please check the Log file")
-                sys.exit(1)
+                sys.exit(2)
 
             if any("WARNING" in entry for entry in log):
                 sys.stderr.write(
                     "Some samples generated warnings, please check the Log file"
                 )
-                sys.exit(1)
+                sys.exit(2)
 
 
 def get_ba_output_file(currentStep, log):
@@ -201,6 +201,6 @@ def get_ba_output_file(currentStep, log):
     lims.check_version()
     try:
         main(lims, args)
-    except BaseException as e:
+    except Exception as e:
         sys.stderr.write(str(e))
         sys.exit(2)

scripts/samplesheet_generator.py

@@ -850,7 +850,7 @@ def main(lims, args):
                     f.write("\n".join(log))
 
                 sys.stderr.write("Errors were met, check the log.")
-                sys.exit(1)
+                sys.exit(2)
 
         else:
             print(content)

scripts/tecan_parser.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import csv
 import re
 import sys

scripts/write_notes_to_couchdb.py

@@ -28,7 +28,7 @@ def write_note_to_couch(pid, timestamp, note, lims):
             ),
             note["email"],
         )
-        sys.exit(1)
+        sys.exit(2)
 
     url_string = "https://{}:{}@{}".format(
         config["statusdb"].get("username"),