fix: use correct logging setup

GenomicMedLab · Jul 2, 2024 · f0d4448 · f0d4448
1 parent ec6cced
commit f0d4448
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Showing 11 changed files with 71 additions and 80 deletions.
diff --git a/src/cool_seq_tool/__init__.py b/src/cool_seq_tool/__init__.py
@@ -1,12 +1 @@
 """The cool_seq_tool package"""
-
-import logging
-
-logging.basicConfig(
-    filename="cool_seq_tool.log",
-    format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s",
-)
-logger = logging.getLogger("cool_seq_tool")
-logger.setLevel(logging.DEBUG)
-
-LOG_FN = "cool_seq_tool.log"
diff --git a/src/cool_seq_tool/app.py b/src/cool_seq_tool/app.py
@@ -17,7 +17,7 @@
 from cool_seq_tool.sources.transcript_mappings import TranscriptMappings
 from cool_seq_tool.sources.uta_database import UTA_DB_URL, UtaDatabase
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 class CoolSeqTool:

diff --git a/src/cool_seq_tool/handlers/seqrepo_access.py b/src/cool_seq_tool/handlers/seqrepo_access.py
@@ -11,7 +11,7 @@
 from cool_seq_tool.schemas import ResidueMode
 from cool_seq_tool.utils import get_inter_residue_pos
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 SEQREPO_ROOT_DIR = environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
@@ -66,7 +66,7 @@ def get_reference_sequence(
             sequence = self.sr.fetch(ac, start=start, end=end)
         except KeyError:
             msg = f"Accession, {ac}, not found in SeqRepo"
-            logger.warning(msg)
+            _logger.warning(msg)
             return "", msg
         except ValueError as e:
             error = str(e)
@@ -80,7 +80,7 @@ def get_reference_sequence(
                 )
             else:
                 msg = f"{e}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return "", msg
         else:
             # If start is valid, but end is invalid, SeqRepo still returns
@@ -118,7 +118,7 @@ def translate_identifier(
             )
         except KeyError:
             msg = f"SeqRepo unable to get translated identifiers for {ac}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return [], msg
         else:
             return ga4gh_identifiers, None
@@ -133,7 +133,7 @@ def translate_alias(self, input_str: str) -> tuple[list[str | None], str | None]
             return self.sr.translate_alias(input_str), None
         except KeyError:
             msg = f"SeqRepo could not translate alias {input_str}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return [], msg
 
     def chromosome_to_acs(self, chromosome: str) -> tuple[list[str] | None, str | None]:

diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -23,7 +23,7 @@
     "CoordinatesResponseType", GenomicDataResponse, TranscriptExonDataResponse
 )
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 class ExonGenomicCoordsMapper:
@@ -80,7 +80,7 @@ def _return_warnings(
             ``genomic_data`` field is ``None``
         :return: Response object with warning message
         """
-        logger.warning(warning_msg)
+        _logger.warning(warning_msg)
         resp.warnings.append(warning_msg)
         return resp
 
@@ -436,7 +436,7 @@ async def _get_alt_ac_start_and_end(
         """
         if tx_exon_start is None and tx_exon_end is None:
             msg = "Must provide either `tx_exon_start` or `tx_exon_end` or both"
-            logger.warning(msg)
+            _logger.warning(msg)
             return None, msg
 
         alt_ac_data = {"start": None, "end": None}
@@ -462,7 +462,7 @@ async def _get_alt_ac_start_and_end(
                         error = "Genomic accession does not match"
                     else:
                         error = "Strand does not match"
-                    logger.warning(
+                    _logger.warning(
                         "%s: %s != %s",
                         error,
                         alt_ac_data["start"][i],
@@ -726,7 +726,7 @@ async def _set_mane_genomic_data(
             msg = f"Unable to find mane data for {alt_ac} with position {pos}"
             if gene:
                 msg += f" on gene {gene}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return msg
 
         params["gene"] = mane_data.gene
@@ -750,7 +750,7 @@ async def _set_mane_genomic_data(
                 f"{params['transcript']} with position {tx_pos} "
                 f"does not exist on exons: {tx_exons}"
             )
-            logger.warning(msg)
+            _logger.warning(msg)
             return msg
 
         strand_to_use = strand if strand is not None else mane_data.strand

diff --git a/src/cool_seq_tool/mappers/mane_transcript.py b/src/cool_seq_tool/mappers/mane_transcript.py
@@ -35,7 +35,7 @@
 )
 from cool_seq_tool.utils import get_inter_residue_pos
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 class EndAnnotationLayer(str, Enum):
@@ -168,10 +168,10 @@ async def _p_to_c(
                 elif ac.startswith("ENSP"):
                     ac = self.transcript_mappings.ensp_to_enst[ac]
                 else:
-                    logger.warning("Unable to find accession: %s", ac)
+                    _logger.warning("Unable to find accession: %s", ac)
                     return None
             except KeyError:
-                logger.warning("%s not found in transcript_mappings", ac)
+                _logger.warning("%s not found in transcript_mappings", ac)
                 return None
 
         pos = self._p_to_c_pos(start_pos, end_pos)
@@ -196,7 +196,7 @@ async def _c_to_g(self, ac: str, pos: tuple[int, int]) -> dict | None:
                     0
                 ]
             ):
-                logger.warning("Ensembl transcript not found: %s", ac)
+                _logger.warning("Ensembl transcript not found: %s", ac)
                 return None
 
             temp_ac = ac.split(".")[0]
@@ -206,7 +206,7 @@ async def _c_to_g(self, ac: str, pos: tuple[int, int]) -> dict | None:
         # c. coordinate does not contain cds start, so we need to add it
         cds_start_end = await self.uta_db.get_cds_start_end(temp_ac)
         if not cds_start_end:
-            logger.warning("Accession %s not found in UTA", temp_ac)
+            _logger.warning("Accession %s not found in UTA", temp_ac)
             return None
         coding_start_site = cds_start_end[0]
         pos = pos[0] + coding_start_site, pos[1] + coding_start_site
@@ -237,7 +237,7 @@ async def _get_and_validate_genomic_tx_data(
             tx_ac, pos, annotation_layer, alt_ac=alt_ac
         )
         if not genomic_tx_data:
-            logger.warning(
+            _logger.warning(
                 "Unable to find genomic_tx_data for %s at position %s on annotation layer %s",
                 alt_ac,
                 pos,
@@ -255,7 +255,7 @@ async def _get_and_validate_genomic_tx_data(
 
             # Validation check: Exon structure
             if og_alt_exon_id != liftover_alt_exon_id:
-                logger.warning(
+                _logger.warning(
                     "Original alt_exon_id %s does not match liftover alt_exon_id %s",
                     og_alt_exon_id,
                     liftover_alt_exon_id,
@@ -293,7 +293,7 @@ def _get_c_data(
         gt_cds_end = c_pos_change[1] > cds_end and c_pos_change[1] > cds_end
 
         if lt_cds_start or gt_cds_end:
-            logger.info(
+            _logger.info(
                 "%s with position %s is not within CDS start/end",
                 refseq_c_ac,
                 c_pos_change,
@@ -381,7 +381,7 @@ async def _g_to_c(
             )
 
             if not result:
-                logger.warning(
+                _logger.warning(
                     "Unable to find transcript, %s, position change", refseq_c_ac
                 )
                 return None
@@ -438,7 +438,7 @@ def _validate_reading_frames(
                 new_rf = self._get_reading_frame(transcript_data.pos[pos_index])
 
                 if og_rf != new_rf:
-                    logger.warning(
+                    _logger.warning(
                         "%s original reading frame (%s) does not match new %s, %s reading frame (%s)",
                         ac,
                         og_rf,
@@ -449,7 +449,7 @@ def _validate_reading_frames(
                     return False
             else:
                 if pos_index == 0:
-                    logger.warning("%s must having start position", ac)
+                    _logger.warning("%s must having start position", ac)
                     return False
         return True
 
@@ -503,18 +503,18 @@ def _validate_references(
                 residue_mode=residue_mode,
             )
             if not mane_ref:
-                logger.info("Unable to validate reference for MANE Transcript")
+                _logger.info("Unable to validate reference for MANE Transcript")
 
             if expected_ref != mane_ref:
-                logger.info(
+                _logger.info(
                     "Expected ref, %s, but got %s on MANE accession, %s",
                     expected_ref,
                     mane_ref,
                     mane_transcript.refseq,
                 )
 
         if expected_ref != ref:
-            logger.warning(
+            _logger.warning(
                 "Expected ref, %s, but got %s on accession, %s", expected_ref, ref, ac
             )
             return False
@@ -692,7 +692,7 @@ def _get_protein_rep(
             )
 
         if df.is_empty():
-            logger.warning("Unable to get transcripts from gene %s", gene)
+            _logger.warning("Unable to get transcripts from gene %s", gene)
             return lcr_result
 
         prioritized_tx_acs = self._get_prioritized_transcripts_from_gene(df)
@@ -814,7 +814,7 @@ def _get_protein_rep(
                 pos = lcr_result.pos
 
                 if not self._validate_index(ac, pos, coding_start_site):
-                    logger.warning(
+                    _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
                         pos,
                         ac,
@@ -841,7 +841,7 @@ def _get_protein_rep(
                 pos = lcr_result_dict[k]["pos"]
                 if not self._validate_index(ac, pos, cds):
                     valid = False
-                    logger.warning(
+                    _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
                         pos,
                         ac,
@@ -999,7 +999,7 @@ async def get_mane_transcript(
             return await self.g_to_mane_c(
                 ac, start_pos, end_pos, gene=gene, residue_mode=residue_mode
             )
-        logger.warning("Annotation layer not supported: %s", start_annotation_layer)
+        _logger.warning("Annotation layer not supported: %s", start_annotation_layer)
         return None
 
     async def g_to_grch38(self, ac: str, start_pos: int, end_pos: int) -> dict | None:
@@ -1025,7 +1025,7 @@ async def g_to_grch38(self, ac: str, start_pos: int, end_pos: int) -> dict | Non
 
         # Coordinate liftover
         if assembly < "GRCh37":
-            logger.warning("Liftover only supported for GRCh37")
+            _logger.warning("Liftover only supported for GRCh37")
             return None
 
         liftover_start_i = self.uta_db.get_liftover(
@@ -1130,7 +1130,7 @@ async def g_to_mane_c(
             )
 
         if not await self.uta_db.validate_genomic_ac(ac):
-            logger.warning("Genomic accession does not exist: %s", ac)
+            _logger.warning("Genomic accession does not exist: %s", ac)
             return None
 
         mane_data = self.mane_transcript_mappings.get_gene_mane_data(gene)
@@ -1156,7 +1156,7 @@ async def g_to_mane_c(
                 )
                 if not mane_tx_genomic_data:
                     continue
-                logger.info("Not using most recent assembly")
+                _logger.info("Not using most recent assembly")
 
             coding_start_site = mane_tx_genomic_data["coding_start_site"]
             coding_end_site = mane_tx_genomic_data["coding_end_site"]
@@ -1167,7 +1167,7 @@ async def g_to_mane_c(
             if not self._validate_index(
                 mane_c_ac, mane_c_pos_change, coding_start_site
             ):
-                logger.warning(
+                _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,
                     mane_c_ac,
@@ -1257,7 +1257,7 @@ async def grch38_to_mane_c_p(
             if not self._validate_index(
                 mane_c_ac, mane_c_pos_change, coding_start_site
             ):
-                logger.warning(
+                _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,
                     mane_c_ac,

diff --git a/src/cool_seq_tool/routers/default.py b/src/cool_seq_tool/routers/default.py
@@ -22,7 +22,7 @@
 )
 from cool_seq_tool.utils import service_meta
 
-logger = logging.getLogger("cool_seq_tool")
+_logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix=f"/{SERVICE_NAME}")
 
@@ -54,7 +54,9 @@ async def genomic_to_transcript_exon_coordinates(
             **request_body
         )
     except Exception as e:
-        logger.error("genomic_to_transcript_exon_coordinates unhandled exception %s", e)
+        _logger.error(
+            "genomic_to_transcript_exon_coordinates unhandled exception %s", e
+        )
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return response
@@ -89,7 +91,7 @@ async def transcript_to_genomic_coordinates(
             )
         )
     except Exception as e:
-        logger.error("transcript_to_genomic_coordinates unhandled exception %s", e)
+        _logger.error("transcript_to_genomic_coordinates unhandled exception %s", e)
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return response

diff --git a/src/cool_seq_tool/routers/mane.py b/src/cool_seq_tool/routers/mane.py
@@ -14,7 +14,7 @@
 from cool_seq_tool.schemas import AnnotationLayer, ManeDataService, ResidueMode
 from cool_seq_tool.utils import service_meta
 
-logger = logging.getLogger("cool_seq_tool")
+_logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix=f"/{SERVICE_NAME}/mane")
 
@@ -90,7 +90,7 @@ async def get_mane_data(
         if not mane_data:
             warnings.append("Unable to retrieve MANE data")
     except Exception as e:
-        logger.exception("get_mane_data unhandled exception %s", e)
+        _logger.exception("get_mane_data unhandled exception %s", e)
         warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return ManeDataService(