remove logmuse. See #29

bbconf/__init__.py

@@ -1,9 +1,6 @@
-import logmuse
-
 from bbconf._version import __version__
 from bbconf.bbconf import *
 from bbconf.const import *
 
 __all__ = ["BedBaseConf", "get_bedbase_cfg"]
 
-logmuse.init_logger("bbconf")

bbconf/bbconf.py

@@ -53,6 +53,8 @@
 _LOGGER = getLogger(PKG_NAME)
 
 DRS_ACCESS_URL = "{server_url}/objects/{object_id}/access/{access_id}"
+
+
 class BedBaseConf:
     """
     This class standardizes reporting of bedstat and bedbuncher results.
@@ -602,25 +604,29 @@ def get_bed_drs_metadata(object_id: str) -> dict:
             "size": bed_metadata["file_size"],
             "created_time": bed_metadata["created_time"],
             "checksums": object_id,
-            "access_methods": []
+            "access_methods": [],
         }
         # add access method for each remote class
         for access_id in keys(self.config[CFG_REMOTE_KEY]):
             access_dict = {
-                    "type": "https",
-                    "access_id": access_id,
-                    "access_url": DRS_ACCESS_URL.format(
-                        server_url=self.config["access_methods"][access_id]["server_url"],
-                        object_id=object_id,
-                        access_id=access_id)
-                }
-            access_dict["region"] = self.config["access_methods"][access_id]["region"] or None
+                "type": "https",
+                "access_id": access_id,
+                "access_url": DRS_ACCESS_URL.format(
+                    server_url=self.config["access_methods"][access_id]["server_url"],
+                    object_id=object_id,
+                    access_id=access_id,
+                ),
+            }
+            access_dict["region"] = (
+                self.config["access_methods"][access_id]["region"] or None
+            )
             drs_dict["access_methods"].append(access_dict)
         return drs_dict
-    
+
     def get_bed_url(object_id: str, access_id: str) -> str:
         access_url = DRS_ACCESS_URL.format(
             server_url=self.config["access_methods"][access_id]["server_url"],
             object_id=object_id,
-            access_id=access_id)
+            access_id=access_id,
+        )
         return access_url

interactive_testing.py

@@ -0,0 +1,19 @@
+from bbconf import BedBaseConf
+
+import logging
+import sys
+
+log = logging.getLogger()
+log.setLevel(logging.DEBUG)
+stream = logging.StreamHandler(sys.stdout)
+stream.setLevel(logging.DEBUG)
+log.addHandler(stream)
+logging.getLogger("bbconf").setLevel(logging.DEBUG)
+
+bbc = BedBaseConf("bedbase.org/config/bedbase2.yaml")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", "bedfile")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", result_identifier="bedfile")

requirements/requirements-all.txt

@@ -1,4 +1,3 @@
-logmuse
 yacman>=0.9.1
 pipestat>=0.6.0a2
 #pipestat @ git+https://github.com/pepkit/pipestat@dev#egg=pipestat