Minor bug fixes; Improve debug loggin

BBQuercus · Jun 29, 2022 · 2e42659 · 2e42659
1 parent 9423d7c
commit 2e42659
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 6 deletions.
diff --git a/eFISHent/cli.py b/eFISHent/cli.py
@@ -146,9 +146,10 @@ def create_custom_config(args: argparse.Namespace, config_file: str) -> None:
 
 def set_logging_level(verbose: bool, debug: bool) -> logging.Logger:
     """Set the logging level of luigi and custom logger."""
-    LOG_FORMAT = "%(asctime)s %(levelname)-4s [%(name)s] %(message)s"
+    log_format = "%(asctime)s %(levelname)-4s %(message)s"
 
     if debug:
+        log_format = "%(asctime)s %(levelname)-4s [%(name)s] %(filename)s %(funcName)s %(lineno)d / %(thread)d - %(message)s"
         luigi_level = "DEBUG"
         custom_level = logging.DEBUG
         logfile = "eFISHent.log"
@@ -161,7 +162,7 @@ def set_logging_level(verbose: bool, debug: bool) -> logging.Logger:
         custom_level = logging.WARNING
         logfile = None
 
-    logging.basicConfig(filename=logfile,format=LOG_FORMAT, force=True)
+    logging.basicConfig(filename=logfile,format=log_format, force=True)
     logging.getLogger("luigi").setLevel(luigi_level)
     logging.getLogger("luigi-interface").setLevel(luigi_level)
     luigi.interface.core.log_level = luigi_level

diff --git a/eFISHent/prepare_sequence.py b/eFISHent/prepare_sequence.py
@@ -89,7 +89,7 @@ class BuildBlastDatabase(luigi.Task):
     def output(self):
         return [
             luigi.LocalTarget(f"{util.get_genome_name()}.{extension}")
-            for extension in ["ndb", "nhr", "nin", "not", "nsq", "ntf", "nto"]
+            for extension in ["nhr", "nin", "nsq"]
         ]
 
     def run(self):

diff --git a/eFISHent/util.py b/eFISHent/util.py
@@ -46,7 +46,7 @@ def get_gene_name(hashed: bool = True, config: luigi.Config = SequenceConfig) ->
     """Return the gene name without extension."""
     # Name based on gene fasta file
     sequence_file = config().sequence_file
-    if sequence_file is not None and os.path.isfile(sequence_file):
+    if sequence_file and os.path.isfile(sequence_file):
         basename = secure_filename(os.path.splitext(os.path.basename(sequence_file))[0])
     # Using Ensembl ID
     elif config().ensembl_id:

diff --git a/tests/test_util.py b/tests/test_util.py
@@ -59,7 +59,10 @@ def test_gene_name():
 
     # Gene file
     class Config(luigi.Config):
-        sequence_file = luigi.Parameter("./tests/renilla.fa")
+        sequence_file = luigi.Parameter("./tests/renilla.fasta")
+        ensembl_id = luigi.Parameter("")
+        gene_name = luigi.Parameter("")
+        organism_name = luigi.Parameter("")
 
     assert get_gene_name(config=Config).startswith("renilla")
     assert get_gene_name(hashed=False, config=Config) == "renilla"
@@ -68,6 +71,8 @@ class Config(luigi.Config):
     class Config(luigi.Config):
         sequence_file = luigi.Parameter("")
         ensembl_id = luigi.Parameter("ENSG00000026025")
+        gene_name = luigi.Parameter("")
+        organism_name = luigi.Parameter("")
 
     assert get_gene_name(config=Config).startswith("ENSG00000026025")
 
@@ -82,7 +87,7 @@ class Config(luigi.Config):
 
     # Gene file > NCBI
     class Config(luigi.Config):
-        sequence_file = luigi.Parameter("./tests/renilla.fa")
+        sequence_file = luigi.Parameter("./tests/renilla.fasta")
         ensembl_id = luigi.Parameter("")
         gene_name = luigi.Parameter("ACOOLGene123")
         organism_name = luigi.Parameter("Latin name")