Fixing error with bio reaction, fixing check for compounds in templat…

…e, setting failure testing to false, and fixing report

modelseedpy/core/msbuilder.py

@@ -13,6 +13,7 @@
 )
 from cobra.core import Gene, Metabolite, Model, Reaction, Group
 from modelseedpy.core import FBAHelper
+from modelseedpy.core.msmodel import MSModel
 from modelseedpy.fbapkg.mspackagemanager import MSPackageManager
 from modelseedpy.biochem.modelseed_biochem import ModelSEEDBiochem
 from modelseedpy.biochem.modelseed_to_cobra import modelseed_to_cobra_reaction
@@ -1078,7 +1079,8 @@ def build_full_template_model(template, model_id=None, index="0"):
                 bio.build_biomass(
                     model, index, classic=False, GC=0.5, add_to_model=True
                 )
-            model.objective = "bio1"
+            if "bio1" in model.reactions:
+                model.objective = "bio1"
 
         reactions_sinks = []
         for cpd_id in ["cpd02701_c0", "cpd11416_c0", "cpd15302_c0", "cpd03091_c0"]:

modelseedpy/core/msmodelreport.py

@@ -610,13 +610,13 @@ def build_report(self, output_path):
         with open(output_path, "w", encoding="utf-8") as f:
             f.write('<meta charset="UTF-8">')
             f.write("<h1>Model Summary</h1>")
-            f.write(model_summary_df_styled.render(escape=False))
+            f.write(model_summary_df_styled.to_html(escape=False))
             f.write("<br><br>")
             f.write("<h1>Gapfillings Analysis</h1>")
 
             # Check for Gapfillings Analysis data
             if not gapfillings_analysis_df.empty:
-                f.write(gapfillings_analysis_df_styled.render(escape=False))
+                f.write(gapfillings_analysis_df_styled.to_html(escape=False))
                 f.write(f"<br><br><h3>Legend:</h3>{annotations_text_gapfillings}")
             else:
                 f.write(
@@ -627,7 +627,7 @@ def build_report(self, output_path):
 
             # Check for ATP Analysis data
             if not atp_analysis_df.empty:
-                f.write(atp_analysis_df_styled.render(escape=False))
+                f.write(atp_analysis_df_styled.to_html(escape=False))
                 f.write(f"<br><br><h3>Legend:</h3>{annotations_text_atp_analysis}")
                 f.write(explanation_text_atp_analysis)
             else:

modelseedpy/core/msmodelutl.py

@@ -1375,7 +1375,7 @@ def apply_test_condition(self, condition, model=None):
         #    model.objective.direction = "min"
         pkgmgr.getpkg("KBaseMediaPkg").build_package(condition["media"])
 
-    def test_single_condition(self, condition, apply_condition=True, model=None,report_atp_loop_reactions=False,analyze_failures=True,rxn_list=[]):
+    def test_single_condition(self, condition, apply_condition=True, model=None,report_atp_loop_reactions=False,analyze_failures=False,rxn_list=[]):
         """Runs a single test condition to determine if objective value on set media exceeds threshold
 
         Parameters

modelseedpy/core/mstemplate.py

@@ -182,6 +182,10 @@ def to_metabolite(self, index="0", force=False):
 
         cpd_id = f"{self.id}{index}"
         compartment = f"{self.compartment}{index}"
+        if self.compound == None:
+            logger.critical(
+                f"Compound objective associated with [{cpd_id}] is missing from template"
+            )
         name = f"{self.compound.name} [{compartment}]"
         metabolite = Metabolite(cpd_id, self.formula, name, self.charge, compartment)
         metabolite.notes["modelseed_template_id"] = self.id