biocypher 0.5.28__py3-none-any.whl → 0.5.31__py3-none-any.whl

biocypher/_config/biocypher_config.yaml

@@ -30,21 +30,21 @@ biocypher:
     root_node: entity
 
   ### Optional parameters ###
-  ## Logging granularity
-  ## Set debug to true if more granular logging is desired
 
-  debug: true
+  ## Logging
+  # Write log to disk
+  log_to_disk: true
 
-  ## Set to change the log directory
+  # Activate more granular logging
+  debug: true
 
+  # Change the log directory
   # log_directory: biocypher-log
 
-  ## Set to change the output directory
-
+  ## Data output directory
   # output_directory: biocypher-out
 
-  ## Set to change the cache directory
-
+  ## Resource cache directory
   # cache_directory: .cache
 
   ## Optional tail ontologies

biocypher/_core.py

@@ -181,7 +181,7 @@ class BioCypher:
         """
 
         if not self._schema_config_path:
-            return None
+            self._ontology_mapping = OntologyMapping()
 
         if not self._ontology_mapping:
             self._ontology_mapping = OntologyMapping(

biocypher/_logger.py

@@ -60,11 +60,27 @@ def get_logger(name: str = "biocypher") -> logging.Logger:
         now = datetime.now()
         date_time = now.strftime("%Y%m%d-%H%M%S")
 
-        logdir = (
-            _config.config("biocypher").get("log_directory") or "biocypher-log"
-        )
-        os.makedirs(logdir, exist_ok=True)
-        logfile = os.path.join(logdir, f"biocypher-{date_time}.log")
+        log_to_disk = _config.config("biocypher").get("log_to_disk")
+
+        if log_to_disk:
+            logdir = (
+                _config.config("biocypher").get("log_directory")
+                or "biocypher-log"
+            )
+            os.makedirs(logdir, exist_ok=True)
+            logfile = os.path.join(logdir, f"biocypher-{date_time}.log")
+
+            # file handler
+            file_handler = logging.FileHandler(logfile)
+
+            if _config.config("biocypher").get("debug"):
+                file_handler.setLevel(logging.DEBUG)
+            else:
+                file_handler.setLevel(logging.INFO)
+
+            file_handler.setFormatter(file_formatter)
+
+            logger.addHandler(file_handler)
 
         # handlers
         # stream handler
@@ -72,23 +88,15 @@ def get_logger(name: str = "biocypher") -> logging.Logger:
         stdout_handler.setLevel(logging.INFO)
         stdout_handler.setFormatter(stdout_formatter)
 
-        # file handler
-        file_handler = logging.FileHandler(logfile)
-
-        if _config.config("biocypher").get("debug"):
-            file_handler.setLevel(logging.DEBUG)
-        else:
-            file_handler.setLevel(logging.INFO)
-
-        file_handler.setFormatter(file_formatter)
-
         # add handlers
-        logger.addHandler(file_handler)
         logger.addHandler(stdout_handler)
 
         # startup message
         logger.info(f"This is BioCypher v{__version__}.")
-        logger.info(f"Logging into `{logfile}`.")
+        if log_to_disk:
+            logger.info(f"Logging into `{logfile}`.")
+        else:
+            logger.info("Logging into stdout.")
 
     return logging.getLogger(name)
 

biocypher/_mapping.py

@@ -40,7 +40,7 @@ class OntologyMapping:
         Read the configuration file and store the ontology mapping and extensions.
         """
         if config_file is None:
-            schema_config = _config.module_data("schema_config")
+            schema_config = {}
 
         # load yaml file from web
         elif config_file.startswith("http"):

biocypher/_metadata.py

@@ -19,7 +19,7 @@ import importlib.metadata
 
 import toml
 
-_VERSION = "0.5.28"
+_VERSION = "0.5.31"
 
 
 def get_metadata():

biocypher/_ontology.py

@@ -96,16 +96,7 @@ class OntologyAdapter:
         )
 
     def _rdf_to_nx(self, g, root_label, switch_id_and_label=True):
-        # Loop through all labels in the ontology
-        for s, _, o in g.triples((None, rdflib.RDFS.label, None)):
-            # If the label is the root label, set the root node to the subject of the label
-            if o.eq(root_label):
-                root = s
-                break
-        else:
-            raise ValueError(
-                f"Could not find root node with label {root_label}"
-            )
+        root = self._find_root_label(g, root_label)
 
         # Create a directed graph to represent the ontology as a tree
         G = nx.DiGraph()
@@ -177,6 +168,21 @@ class OntologyAdapter:
 
         return G
 
+    def _find_root_label(self, g, root_label):
+        # Loop through all labels in the ontology
+        for label_subject, _, label_in_ontology in g.triples(
+            (None, rdflib.RDFS.label, None)
+        ):
+            # If the label is the root label, set the root node to the label's subject
+            if str(label_in_ontology) == root_label:
+                root = label_subject
+                break
+        else:
+            raise ValueError(
+                f"Could not find root node with label {root_label}"
+            )
+        return root
+
     def _remove_prefix(self, uri: str) -> str:
         """
         Remove the prefix of a URI. URIs can contain either "#" or "/" as a
@@ -565,7 +571,7 @@ class Ontology:
         else:
             msg = f"Showing ontology structure based on {len(self._tail_ontology_meta)+1} ontologies: "
 
-        print(msg)
+        logger.info(msg)
 
         if not full:
             # set of leaves and their intermediate parents up to the root
@@ -594,7 +600,7 @@ class Ontology:
                         f"{self.mapping.extended_schema[node].get('synonym_for')}"
                     )
 
-            tree.show()
+            logger.info(f"\n{tree}")
 
             return tree
 

{biocypher-0.5.28.dist-info → biocypher-0.5.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.5.28
+Version: 0.5.31
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT

{biocypher-0.5.28.dist-info → biocypher-0.5.31.dist-info}/RECORD

@@ -1,24 +1,24 @@
 biocypher/__init__.py,sha256=ejNY53vH_pE3ZbIN8G_ZBYxxPG9aERovRLD0XhDvt4k,942
 biocypher/_config/__init__.py,sha256=fFHRFYxE2MtDAQWL6upe--MJ1vw3Z8CwIPhF2gW8cRU,3698
-biocypher/_config/biocypher_config.yaml,sha256=rPH0h1aQRPGkYQnoE-v-DJA6b01YuN5byPRbw_G7dUg,2430
+biocypher/_config/biocypher_config.yaml,sha256=H0TKBJun7pQmIfIAgEiMkDDgE3kKoCElBuMt8lkkQcU,2404
 biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
 biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
 biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
 biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
 biocypher/_connect.py,sha256=0oSyO6CEIlKL8rHo-HHE7y0FzGfSi4vnEXSDy1TnIUE,12456
-biocypher/_core.py,sha256=xDMIdpDXffUzUygC8B3GzXTGLvFH6dqTs39ele68VFE,22270
+biocypher/_core.py,sha256=2o3hhhM6kfaZI6TU3ZmzoBJc-RJgFFGWGe0MZW-oA3U,22301
 biocypher/_create.py,sha256=vpUchUdEpWupZi1LgFLxAWMtqoBwnWbP7PwEDUCBS4A,10202
 biocypher/_deduplicate.py,sha256=BBvfpXzu6L5YDY5FdtXxnf8YlsbJpbCE8RdUoKsm0n0,4949
 biocypher/_get.py,sha256=HrJuBm_i9zfi_Mzzi1s5kp0OyPh_oKQk0wwyYsxg0qA,9189
-biocypher/_logger.py,sha256=soYtz1DiduLFw3XrMnphWWUxeuJqvSof4AYhlafxl08,2933
-biocypher/_mapping.py,sha256=XJZjmXTPnXVkyub1ZU0h3EKXQ2YROaGaJOaGyPMqgy4,9338
-biocypher/_metadata.py,sha256=pE1NUSdNABIhMjx_2yUuRcA098xXDyGzEm018cv55Tg,1658
+biocypher/_logger.py,sha256=rEn_-ESh9cPxk6vdWZ1a25escCWHBWX4D1gtpNowyvI,3186
+biocypher/_mapping.py,sha256=ERSNH2Bg19145KytxbFE4BInPaiP-LWW7osOBot29Eo,9304
+biocypher/_metadata.py,sha256=kpXUxF5Umh3tsT9xxcrntbPWxL38kATPLhgrqRNV1cs,1658
 biocypher/_misc.py,sha256=wsjGVOqBDVM5hxbE_TEaZ69u1kJc8HXwRAtQHUgE8XQ,4545
-biocypher/_ontology.py,sha256=5TA4W0vcMyvFLtzuMLt_pFKXZmeLvgdyCHV4vMGrvmk,22794
+biocypher/_ontology.py,sha256=lIEHtdUGPFVbj7jrojwHNmP2-KJlXSET8bqVLRam3vI,23010
 biocypher/_pandas.py,sha256=GVCFM68J7yBjh40MpkNVgD8qT1RFMrrIjMOtD3iKsf4,3040
 biocypher/_translate.py,sha256=nj4Y60F0U3JBH36N2dh5pFcC8Ot86rskJ2ChJwje9dI,16494
 biocypher/_write.py,sha256=nvb75OwElu8fLUp0FjEBqQ1VNpx6iRrk-t7v_TOlDhg,68165
-biocypher-0.5.28.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
-biocypher-0.5.28.dist-info/WHEEL,sha256=vxFmldFsRN_Hx10GDvsdv1wroKq8r5Lzvjp6GZ4OO8c,88
-biocypher-0.5.28.dist-info/METADATA,sha256=APFsO_i3awV_7XdjE_kvSuWyKLUsc2yRC8Hn7QRHTVU,10274
-biocypher-0.5.28.dist-info/RECORD,,
+biocypher-0.5.31.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
+biocypher-0.5.31.dist-info/METADATA,sha256=Kzl2LeK_Y4Ul8bzzfPzYv7aXEjAohoQqfRJO_GdFhXs,10274
+biocypher-0.5.31.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
+biocypher-0.5.31.dist-info/RECORD,,

{biocypher-0.5.28.dist-info → biocypher-0.5.31.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.3.2
+Generator: poetry-core 1.6.1
 Root-Is-Purelib: true
 Tag: py3-none-any