added initial biocypher functions

networkcommons/_data/network/biocypher.py

@@ -0,0 +1,103 @@
+from biocypher import BioCypher
+import pandas as pd
+from networkcommons._utils import network_from_df
+import yaml
+
+def update_config(file_path, changes):
+    """
+    Update the YAML configuration file with the provided changes.
+
+    Args:
+        file_path (str): Path to the YAML configuration file.
+        changes (dict): Changes to apply to the configuration. Keys are dot-separated paths to the config values to update.
+
+    Returns:
+        None
+    """
+    try:
+        with open(file_path, 'r') as file:
+            config = yaml.safe_load(file)
+    except FileNotFoundError:
+        print(f"File {file_path} not found.")
+        return
+    except yaml.YAMLError as exc:
+        print(f"Error in configuration file: {exc}")
+        return
+
+    for key, value in changes.items():
+        keys = key.split('.')
+        d = config
+        for k in keys[:-1]:
+            d = d.setdefault(k, {})
+        d[keys[-1]] = value
+
+    with open(file_path, 'w') as file:
+        yaml.safe_dump(config, file)
+
+# Example usage:
+config_changes = {
+    'biocypher.dbms': 'postgres',
+    'biocypher.offline': False,
+    'biocypher.debug': True,
+    'biocypher.output_directory': 'new-output-directory'
+}
+
+update_config('path/to/your/config.yaml', config_changes)
+
+
+def get_config_options(file_path):
+    """
+    Retrieve all available options from the YAML configuration file.
+
+    Args:
+        file_path (str): Path to the YAML configuration file.
+
+    Returns:
+        dict: A dictionary containing the configuration options.
+    """
+    try:
+        with open(file_path, 'r') as file:
+            config = yaml.safe_load(file)
+        return config
+    except FileNotFoundError:
+        print(f"File {file_path} not found.")
+        return {}
+    except yaml.YAMLError as exc:
+        print(f"Error in configuration file: {exc}")
+        return {}
+
+
+def init_biocypher(dbms: Optional[str] = 'neo4j', 
+                   offline: Optional[bool] = True,
+                   strict_mode: Optional[bool] = False,
+                   db_name: Optional[str] = None):
+    bc = BioCypher(dbms=dbms,
+                   offline=offline,
+                   strict_mode=strict_mode,
+                   db_name=db_name)
+
+    return bc
+
+def biocypher_to_graph(bc_obj):
+    """
+    Convert a BioCypher object to a networkx graph.
+
+    Args:
+        bc_obj (BioCypher): The BioCypher object to convert.
+
+    Returns:
+        nx.DiGraph: The networkx graph representation of the BioCypher object.
+    """
+    network_df = bc_obj.to_df()
+    network = network_from_df(network_df,
+                              source_col='source',
+                              target_col='target',
+                              directed=True)
+    return network
+
+
+from bccb.ppi_adapter import get_ppi_edges
+
+
+
+