Bug fixes for dependencies #85

minor bug fixes
draeger-lab · Sep 27, 2023 · cf8b6e7 · cf8b6e7
1 parent 6e3edc2
commit cf8b6e7
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diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
 </p>
 
 # refineGEMs
-`refineGEMs` is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
+`refineGEMs` is a python package intended to help with the curation of genome-scale metabolic models (GEMS).
 
 ## Documentation
 The docs can be found [here](https://refinegems.readthedocs.io/en/latest/).

diff --git a/main.py b/main.py
@@ -80,7 +80,7 @@ def main(configpath=None):
     if (config['single']):        
         try:    
             model_cobra, errors = cobra.io.sbml.validate_sbml_model(config['model'])
-            logging.info(errors)
+            #logging.info(errors)
         except (OSError):
             model_cobra = None
             logging.info('No or no valid model given, please enter a valid path in the model field in the config file.')
@@ -162,14 +162,19 @@ def main(configpath=None):
         if any(mods):
             if config['model_out'] == 'stdout':   
                 config['model_out'] = config['out_path'] + model_libsbml.getId() + '_modified_' + str(today) + '.xml'
-
-            rg.io.write_to_file(model_libsbml, config['model_out'])
+
+            try:
+                rg.io.write_to_file(model_libsbml, config['model_out'])
+            except (OSError) as e:
+                logging.info(e)
+                logging.info("Model could not be saved...")
 
             if model_cobra is not None:                                          
                 try:    
                     model_cobra, errors = cobra.io.sbml.validate_sbml_model(config['model_out'])
                     logging.info(errors)
-                except (OSError):
+                except (OSError) as e:
+                    logging.info(e)
                     model_cobra = None
                     logging.info('Model was invalidated during curation steps.')
 

diff --git a/refinegems/growth.py b/refinegems/growth.py
@@ -306,7 +306,7 @@ def get_growth_selected_media(model: cobraModel, media: list[str], basis: str, a
             growth_one = growth_one_medium_from_default(model, medium_df, anaerobic)
         elif (basis == 'minimal_uptake'):
             growth_one = growth_one_medium_from_minimal(model, medium_df, anaerobic)
-        growth = growth.append(growth_one, ignore_index=True)
+        growth = pd.concat([growth, growth_one], ignore_index=True) # pd.append is deprecated
     return growth
 
 

diff --git a/refinegems/investigate.py b/refinegems/investigate.py
@@ -251,7 +251,7 @@ def get_egc(model: cobraModel) -> pd.DataFrame:
                 rxn = Reaction(row['type'])
                 rxn.name = 'Test ' + row['type'] + ' dissipation reaction'
                 rxn.add_metabolites(met_atp)
-                model.add_reaction(rxn)
+                model.add_reactions([rxn]) # add_reactions instead of add_reaction -> needs list of reactions
             except(KeyError):
                 dissipation_rxns.drop(dissipation_rxns[dissipation_rxns['type'] == row['type']].index, inplace=True)
 

diff --git a/refinegems/io.py b/refinegems/io.py
@@ -111,7 +111,7 @@ def load_medium_from_db(mediumname: str) -> pd.DataFrame:
     Returns:
         pd.DataFrame: Table containing composition for one medium with metabs added as BiGG_EX exchange reactions
     """
-    medium_query = f"SELECT * FROM media m JOIN media_compositions mc ON m.id = mc.medium_id WHERE m.medium = '{mediumname}'" 
+    medium_query = f"SELECT * FROM media m JOIN media_compositions mc ON m.id = mc.medium_id WHERE m.medium = '{mediumname}'"
     medium = load_a_table_from_database(medium_query)
     medium = medium[['medium', 'medium_description', 'BiGG', 'substance']]
     medium['BiGG_R'] = 'R_EX_' + medium['BiGG'] + '_e'
@@ -168,7 +168,7 @@ def load_a_table_from_database(table_name_or_query: str) -> pd.DataFrame:
     engine = sqlalchemy.create_engine(sqlalchemy_engine_input)
     open_con = engine.connect()
 
-    db_table = pd.read_sql(table_name_or_query, open_con)
+    db_table = pd.read_sql(sqlalchemy.text(table_name_or_query), open_con)
 
     open_con.close()
     return db_table
@@ -220,9 +220,12 @@ def write_to_file(model: libModel, new_filename: str):
         - model (libModel): Model loaded with libSBML
         - new_filename (str): Filename|Path for modified model
     """
-    new_document = model.getSBMLDocument()
-    writeSBMLToFile(new_document, new_filename)
-    logging.info("Modified model written to " + new_filename)
+    try:
+        new_document = model.getSBMLDocument()
+        writeSBMLToFile(new_document, new_filename)
+        logging.info("Modified model written to " + new_filename)
+    except (OSError) as e:
+        print("Could not write to file. Wrong path?")
 
 
 def write_report(dataframe: pd.DataFrame, filepath: str):

diff --git a/setup.py b/setup.py
@@ -14,27 +14,27 @@
       url='https://github.com/draeger-lab/refinegems',
       license='MIT',
       packages=['refinegems'],
-      python_requires ='>=3.8, <3.10',
+      python_requires ='>=3.8, <3.11',
       install_requires = [
-            "cobra==0.22.0",
-            "biopython==1.79",
+            "cobra>=0.26.0", # cobra changed model.add_reaction to model.add_reactions -> important in investigate.py
+            "biopython>=1.79",
             "bioregistry",
             "bioservices",
             "importlib-resources<=5.13.0",
-            "memote==0.13.0",
-            "pandas==1.2.4",
-            "numpy==1.20.3",
-            "gffutils==0.10.1",
-            "markupsafe==2.0.1", 
-            "depinfo==1.7.0",
-            "sortedcontainers==2.4.0",
-            "libchebipy==1.0.10",
-            "ratelimit==2.2.1",
-            "sqlalchemy==1.4.43",
-            "venn==0.1.3",
-            "ols-client==0.1.3",
-            "seaborn==0.12.2",
-            "click==8.1.3"
+            "memote>=0.13.0",
+            "pandas>=1.2.4",
+            "numpy>=1.20.3",
+            "gffutils>=0.10.1",
+            "markupsafe>=2.0.1", 
+            "depinfo>=1.7.0",
+            "sortedcontainers>=2.4.0",
+            "libchebipy>=1.0.10",
+            "ratelimit>=2.2.1",
+            "sqlalchemy>=1.4.43",
+            "venn>=0.1.3",
+            "ols-client>=0.1.3",
+            "seaborn>=0.12.2",
+            "click>=8.1.3"
             ],
       zip_safe=False,
       include_package_data=True,