Add substances + specific fluxes to medium

#104 , #99
- function to add a substance from db to medium
- changes to media_config to allow adding substances
- small docs additions

refinegems/database/medium.py

@@ -74,12 +74,39 @@ def __init__(self, name:str, substance_table:pd.DataFrame=pd.DataFrame(columns=[
 
     # possible @TODO
     # ..............
-    # add compound
     # has compound
     # remove compound
     # set source of
     # ------------------------------------
 
+    def add_substance_from_db(self, name:str, flux:float=10.0):
+        """Add a substance from the database to the medium.
+
+        Args:
+            name (str): Name of the substance. Should be part of the database substance.name column.
+            flux (float, optional): Sets the flux value of the new substance. Defaults to 10.0.
+        """
+        # build connection to DB
+        connection = sqlite3.connect(PATH_TO_DB)
+        cursor = connection.cursor()
+        # fetch substance
+        result = cursor.execute(""" SELECT substance.name, substance.formula, substance2db.db_id, substance2db.db_type 
+                                    FROM substance, substance2db 
+                                    WHERE substance.name = ? AND substance.id = substance2db.substance_id""", (name,))
+        substance = result.fetchall()
+
+        # check if fetch was successful
+        if len(substance) == 0:
+            warnings.warn(f'Could not fetch substance {name} from DB.')
+            return
+
+        # add substance to table
+        substance_table = pd.DataFrame(substance, columns=['name','formula','db_id','db_type'])
+        substance_table.insert(2,'flux',flux)
+        substance_table.insert(3,'source',None)
+        self.substance_table = pd.concat([self.substance_table, substance_table], ignore_index=True)
+
+
     def get_source(self, element:str) -> list[str]:
         """Get the source of a given element for the medium.
 

refinegems/growth.py

@@ -355,7 +355,15 @@ def growth_sim_multi(models: cobraModel|list[cobraModel], media: medium.Medium|l
 # @IDEA: more options for fluxes
 # @TODO/@IDEA: validity check nefore parsing
 # @ASK: maybe something for the io module or does it fit here?
-def read_media_config(yaml_path:str):
+def read_media_config(yaml_path:str) -> tuple[list[medium.Medium],list[str,None]]:
+    """Read the information from a media configuration file.
+
+    Args:
+        yaml_path (str): The path to a media configuration file in YAML-format.
+
+    Returns:
+        tuple[list[medium.Medium],list[str,None]]: Tuple of A) list of the loaded media and B) list of supplement modes.
+    """
 
     media_list = []
     supplement_list = []
@@ -428,6 +436,36 @@ def read_media_config(yaml_path:str):
                 elif params and 'o2_percemt' in params.keys():
                     new_medium.set_oxygen_percentage(params['o2_percent'])
 
+                # add additional substances from DB
+                if p and 'add_substance' in p.keys():
+                    for s,f in p['add_substance'].items():
+                        # read in flux 
+                        if not f:
+                            if p and 'default_flux' in p.keys():
+                                f = p['default_flux']
+                            elif params and 'default_flux' in params.keys():
+                                f = params['default_flux']
+                        elif isinstance(f,str):
+                            if '%' in f:
+                                f = float(f[:f.index('%')])/100
+                                if p and 'default_flux' in p.keys():
+                                    f = f * p['default_flux']
+                                elif params and 'default_flux' in params.keys():
+                                    f = f * params['default_flux']
+                                else:
+                                    f = f * 10.0
+                            else:
+                                warn_string = f'Could not read in flux for {s}: {f}. \nWill be using default 10.0 instead.'
+                                warnings.warn(warn_string)
+                                f = 10.0
+                        # change medium
+                        if s in new_medium.substance_table['name'].tolist():
+                            # change fluxes only
+                            new_medium.substance_table.loc[new_medium.substance_table['name']==s,'flux'] = f
+                        else:
+                            # add substance to medium 
+                            new_medium.add_substance_from_db(s,f)
+
                 # supplement settings
                 if p and 'supplement' in p.keys():
                     supplement_list.append(p['supplement'])

refinegems/media_config.yml

@@ -57,6 +57,11 @@ params:
 #   supplement
 #   default_flux
 #   o2_percent
+#   add_substance: Null|float|str in format 'X.X%' with X being [0-9]*
+#            Add further substances to the medium and/or add specific fluxes to 
+#            to substances. Flux settings here overwrite all previously set fluxes.
+#            Null uses the most specific set default flux.
+#            When a percentage is set uses this percentage of the most specific set default flux.
 # --------------------------------------------------------------------
 
 media:
@@ -72,6 +77,10 @@ media:
 #    add: 
 #      - aa
 #      - SNM3
+    add_substance:
+      Glycine: Null
+      Glycerol: 0.87
+      Guanosine: '20%'
 #  PERS:
 #    external_base: link
 #    add_external: