Merge branch 'main' of https://github.com/ModelSEED/KB-ModelSEEDReconstruction

Author: Christopher Henry

lib/ModelSEEDReconstruction/modelseedrecon.py

@@ -16,7 +16,7 @@
 from modelseedpy.core.mstemplate import MSTemplateBuilder
 from modelseedpy.core.msgenome import normalize_role
 from kbbasemodules.basemodelingmodule import BaseModelingModule
-from modelseedpy.community.mscommunity import MSCommunity
+from mscommunity import MSCommunity
 
 logger = logging.getLogger(__name__)
 
@@ -481,10 +481,11 @@ def run_community_fba(self,params):
         species_list = []
         abundance_hash = {}
         comm_model = MSCommunity(
-            model=mdlutl,
-            names=species_list
+            model=mdlutl.model,
+            ids=species_list
         )
         comm_model.set_abundance(abundance_hash)
+        #TODO:  This code will need to be updated
         mdlutl.pkgmgr.getpkg("CommKineticPkg").build_package(float(params["kinetics_coef"]), comm_model)
         output = {}
         #Optimizing and constraining objective to fraction of optimum
@@ -606,4 +607,4 @@ def build_dataframe_report(self,table,model_objs=None):
         #Creating data table file
         json_str = '{"data":'+table.to_json(orient='records')+'}'
         with open(self.working_dir+"/html/data.json", 'w') as f:
-            f.write(json_str)
+            f.write(json_str)