Initial implementation of a central logger (#159) (#278)

* Add get_logger * start simplifying * revert nopen * don't check py version any more * minor * use logger * update annoreader_base * update idtogos_reader * update find_enrichment * update go_enrichment.py * update obo_optional_attributes * minor formatting
tanghaibao · Sep 28, 2023 · 2a12d66 · 2a12d66
1 parent eff7681
commit 2a12d66
Show file tree

Hide file tree

Showing 8 changed files with 163 additions and 155 deletions.
diff --git a/goatools/anno/annoreader_base.py b/goatools/anno/annoreader_base.py
@@ -6,10 +6,11 @@
 import collections as cx
 import logging
 
-from goatools.evidence_codes import EvidenceCodes
-from goatools.anno.opts import AnnoOptions
-from goatools.godag.consts import NAMESPACE2NS
-from goatools.gosubdag.go_tasks import get_go2parents_go2obj
+from ..anno.opts import AnnoOptions
+from ..base import logger
+from ..evidence_codes import EvidenceCodes
+from ..godag.consts import NAMESPACE2NS
+from ..gosubdag.go_tasks import get_go2parents_go2obj
 
 __copyright__ = (
     "Copyright (C) 2016-present, DV Klopfenstein, H Tang. All rights reserved."
@@ -148,13 +149,12 @@ def _get_1ns_assn(self, namespace_usr):
         if len(self.namespaces) == 1:
             nspc = next(iter(self.namespaces))
             if namespace_usr is not None and nspc != namespace_usr:
-                print(f"**WARNING: IGNORING {namespace_usr}; ONLY {nspc} WAS LOADED")
+                logger.warning("IGNORING %s; ONLY %s WAS LOADED", namespace_usr, nspc)
             return nspc, self.associations
         if namespace_usr is None:
-            print(
-                "**ERROR get_id2gos: GODAG NOT LOADED. USING: {NSs}".format(
-                    NSs=" ".join(sorted(self.namespaces))
-                )
+            logger.error(
+                "get_id2gos: GODAG NOT LOADED. USING: %s",
+                " ".join(sorted(self.namespaces)),
             )
         return namespace_usr, self.associations
 

diff --git a/goatools/anno/idtogos_reader.py b/goatools/anno/idtogos_reader.py
@@ -1,8 +1,10 @@
 """Reads a Annotation File in text format with data in id2gos line"""
 
 import sys
-from goatools.anno.annoreader_base import AnnoReaderBase
-from goatools.anno.init.reader_idtogos import InitAssc
+
+from ..base import logger
+from .annoreader_base import AnnoReaderBase
+from .init.reader_idtogos import InitAssc
 
 __copyright__ = "Copyright (C) 2016-2019, DV Klopfenstein, H Tang. All rights reserved."
 __author__ = "DV Klopfenstein"
@@ -35,7 +37,7 @@ def wr_id2gos(fout_txt, id2gos):
 
     def prt_summary_anno2ev(self, prt=sys.stdout):
         """Print a summary of all Evidence Codes seen in annotations"""
-        prt.write(f"**NOTE: No evidence codes in associations: {self.filename}\n")
+        logger.info("No evidence codes in associations: %s", self.filename)
 
     # pylint: disable=unused-argument
     def reduce_annotations(self, associations, options):

diff --git a/goatools/anno/init/reader_idtogos.py b/goatools/anno/init/reader_idtogos.py
@@ -1,10 +1,11 @@
 """Reads a Annotation File in text format with data in id2gos line"""
 
-from sys import stdout
 import timeit
 import datetime
 import collections as cx
-from goatools.godag.consts import NAMESPACE2NS
+
+from ...base import logger
+from ...godag.consts import NAMESPACE2NS
 
 __copyright__ = (
     "Copyright (C) 2016-present, DV Klopfenstein, H Tang. All rights reserved."
@@ -39,7 +40,7 @@ def init_associations(self, namespaces):
         if self.godag is None:
             if namespaces is not None:
                 # pylint: disable=superfluous-parens
-                print(f"**WARNING: GODAG NOT LOADED. IGNORING namespaces={namespaces}")
+                logger.warning("GODAG NOT LOADED. IGNORING namespaces=%s", namespaces)
             return nts
         if namespaces == {"BP", "MF", "CC"}:
             return nts
@@ -56,7 +57,7 @@ def _init_dflt(self):
                 nts.append(ntobj(DB_ID=itemid, GO_ID=goid))
         return nts
 
-    def _init_w_godag(self, prt=stdout):
+    def _init_w_godag(self):
         """Get a list of namedtuples, one for each annotation."""
         nts = []
         ntobj = cx.namedtuple("ntanno", self.flds + ["NS"])
@@ -65,12 +66,12 @@ def _init_w_godag(self, prt=stdout):
             to_add = set()
             for goid in gos:
                 if goid not in s_godag:
-                    prt.write(f"**WARNING: {goid} NOT FOUND IN DAG\n")
+                    logger.warning("%s NOT FOUND IN DAG", goid)
                     continue
                 goobj = s_godag[goid]
                 if goobj.is_obsolete:
                     if self.obsolete == "keep":
-                        prt.write(f"**WARNING: {goid} obsolete in DAG, kept\n")
+                        logger.warning("%s obsolete in DAG, kept", goid)
                         to_add.add(goid)
                     elif self.obsolete == "replace":
                         to_replace = set()
@@ -79,16 +80,14 @@ def _init_w_godag(self, prt=stdout):
                         if "consider" in goobj.__dict__ and goobj.consider:
                             to_replace |= goobj.consider
                         if to_replace:
-                            prt.write(
-                                f"**WARNING: {goid} obsolete in DAG, replaced by {to_replace}\n"
+                            logger.warning(
+                                "%s obsolete in DAG, replaced by %s", goid, to_replace
                             )
                         else:
-                            prt.write(
-                                f"**WARNING: {goid} obsolete in DAG, no replacement\n"
-                            )
+                            logger.warning("%s obsolete in DAG, no replacement", goid)
                         to_add |= to_replace
                     elif self.obsolete == "skip":
-                        prt.write(f"**WARNING: {goid} obsolete in DAG, skipped\n")
+                        logger.warning("%s obsolete in DAG, skipped", goid)
                 else:
                     to_add.add(goid)
             for goid in to_add: