fix #23 - Replaced deprecated methods

EnzymeML · Feb 22, 2022 · 929b1b0 · 929b1b0
1 parent 7147deb
commit 929b1b0
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 15 deletions.
diff --git a/pyenzyme/enzymeml/core/measurement.py b/pyenzyme/enzymeml/core/measurement.py
@@ -249,10 +249,9 @@ def addReplicates(self, replicates: Union[List[Replicate], Replicate], enzmldoc,
                 if len(self.global_time) == 0:
 
                     # Add global time if this is the first replicate to be added
-                    self.global_time = replicate.getData(sep=True)[0]
-                    self.global_time_unit = (replicate.getTimeUnit())
-                    self._global_time_unit_id = enzmldoc._convertToUnitDef(
-                        replicate.getTimeUnit())
+                    self.global_time = replicate.time
+                    self.global_time_unit = replicate.time_unit
+                    self._global_time_unit_id = replicate._time_unit_id
 
                 # Log Replicate creation
                 if log:

diff --git a/pyenzyme/enzymeml/tools/enzymemlwriter.py b/pyenzyme/enzymeml/tools/enzymemlwriter.py
@@ -152,8 +152,8 @@ def toSBML(self, enzmldoc):
         doc.setLevelAndVersion(3, 2)
 
         model = doc.createModel()
-        model.setName(enzmldoc.getName())
-        model.setId(enzmldoc.getName())
+        model.setName(enzmldoc.name)
+        model.setId(enzmldoc.name)
 
         # Convert the SBML model to EnzymeML
         self.convertEnzymeMLToSBML(model, enzmldoc)
@@ -232,11 +232,11 @@ def _createArchive(self, enzmldoc, listofPaths, name: str = None):
 
         # Add files from fileDict
         tmpFolder = None
-        if enzmldoc.getFileDict() != {}:
+        if enzmldoc.file_dict:
             # create temporary directory for files
             tmpFolder = tempfile.mkdtemp()
 
-            for fileDict in enzmldoc.getFileDict().values():
+            for fileDict in enzmldoc.file_dict.values():
 
                 file_handler = fileDict["handler"]
                 file_name = fileDict["name"]
@@ -258,7 +258,7 @@ def _createArchive(self, enzmldoc, listofPaths, name: str = None):
         if name:
             out_file = f"{name.replace(' ', '_')}.omex"
         else:
-            out_file = f"{enzmldoc.getName().replace(' ', '_')}.omex"
+            out_file = f"{enzmldoc.name.replace(' ', '_')}.omex"
 
         out_path = os.path.join(self.path, out_file)
 
@@ -420,8 +420,8 @@ def _addUnits(self, model: libsbml.Model, unit_dict: Dict[str, UnitDef]) -> None
 
             unit = model.createUnitDefinition()
             unit.setId(unit_id)
-            unit.setMetaId(unit_def.getMetaid())
-            unit.setName(unit_def.getName())
+            unit.setMetaId(unit_def.meta_id)
+            unit.setName(unit_def.name)
 
             # TODO Add ontology
             # if unit_def.getOntology() != "NONE":
@@ -944,7 +944,7 @@ def _addData(
                 measurement_annot.addAttr('file', file_id)
 
             measurement_annot.addAttr('id', measurement_id)
-            measurement_annot.addAttr('name', measurement.getName())
+            measurement_annot.addAttr('name', measurement.name)
 
             # TODO find a sustainable way
             if measurement.temperature:
@@ -1083,7 +1083,7 @@ def appendReplicateData(
         replicates = [
             replicate
             for data in species.values()
-            for replicate in data.getReplicates()
+            for replicate in data.replicates
         ]
 
         for replicate in replicates:

diff --git a/pyenzyme/enzymeml/tools/unitcreator.py b/pyenzyme/enzymeml/tools/unitcreator.py
@@ -113,9 +113,9 @@ def getUnit(self, unit_string, enzmldoc) -> str:
         if self.__checkFootprints(enzmldoc, unitdef.getFootprint()) != "NEW":
             return self.__checkFootprints(enzmldoc, unitdef.getFootprint())
 
-        enzmldoc.getUnitDict()[unitdef.getId()] = unitdef
+        enzmldoc.unit_dict[unitdef.id] = unitdef
 
-        return unitdef.getId()
+        return unitdef.id
 
     def __checkFootprints(self, enzmldoc, footprint):