added error handling when retrieving the user

CHANGELOG.md

@@ -4,6 +4,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## Unreleased - [2024-08-20]
+
+### `Fixed`
+
+- Added error handling to `getpass.getuser()` when to prevent throwing an error when there is no user UID such as when running the container in docker. [PR 37](https://github.com/phac-nml/locidex/pull/37)
+
+- Removed print debug statement from `report.py`. [PR 37](https://github.com/phac-nml/locidex/pull/37)
 
 ## v0.2.2 - [2024-08-01]
 

locidex/build.py

@@ -10,7 +10,7 @@
 from locidex.constants import DBConfig, MetadataFields, raise_file_not_found_e
 from locidex.classes.blast import BlastMakeDB
 from locidex.manifest import DBData
-import getpass
+from locidex.utils import get_user
 import errno
 import logging
 import sys
@@ -129,7 +129,7 @@ def add_args(parser=None):
     parser.add_argument('-i','--input_file', type=str, required=True,help='Input tsv formated for locidex')
     parser.add_argument('-o', '--outdir', type=str, required=True, help='Output directory to put results')
     parser.add_argument('-n', '--name', type=str, required=True, help='Database name',default='Locidex Database')
-    parser.add_argument('-a', '--author', type=str, required=False, help='Author Name for Locidex Database. Default: {}'.format(getpass.getuser()),default=getpass.getuser())
+    parser.add_argument('-a', '--author', type=str, required=False, help='Author Name for Locidex Database. Default: {}'.format(get_user()),default=get_user())
     parser.add_argument('-c', '--db_ver', type=str, required=False, help='Version code for locidex db: {}'.format(default_version),
                         default=default_version)
     parser.add_argument('-e', '--db_desc',type=str, required=False, help='Version code for locidex db',

locidex/report.py

@@ -254,8 +254,6 @@ def allele_assignment(self,dbtype):
 
         hit_loci_names = self.get_hit_locinames()
         loci_lookup = self.get_loci_to_query_map(hit_loci_names,dbtype)
-        print("loci names", hit_loci_names)
-
         for locus in loci_lookup:
             loci_lookup[locus] = list(set(loci_lookup[locus]) - self.failed_seqids)
 

locidex/utils.py

@@ -5,6 +5,7 @@
 import argparse
 import logging
 import errno
+import getpass
 from collections import Counter
 from pathlib import Path
 from locidex.manifest import ManifestItem
@@ -14,6 +15,17 @@
 import locidex.manifest as manifest 
 
 
+def get_user() -> str:
+    """
+    Return the user login or a default value if it cannot be determined
+    """
+    output: str = "No Author"
+    try:
+        output = getpass.getuser()
+    except KeyError:
+        pass
+    return output 
+
 def slots(annotations: Dict[str, object]) -> FrozenSet[str]:
     """
     Thank you for this: https://stackoverflow.com/a/63658478
@@ -191,4 +203,4 @@ def check_utilities(logger: logging.Logger, utilities: List[str]):
             logger.critical("Missing: {}".format(output))
 
     if missing_utilities:
-        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), ",".join(missing_utilities))
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), ",".join(missing_utilities))