ExportData now has species_id headers

EnzymeML · Jan 27, 2022 · c38e2cc · c38e2cc
1 parent 3250848
commit c38e2cc
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/pyenzyme/enzymeml/core/enzymemldocument.py b/pyenzyme/enzymeml/core/enzymemldocument.py
@@ -359,7 +359,9 @@ def unifyMeasurementUnits(
     def exportMeasurementData(
         self,
         measurement_ids: Union[str, list[str]] = "all",
-        species_ids: Union[str, list[str]] = "all"
+        species_ids: Union[str, list[str]] = "all",
+        proteins: bool = True,
+        reactants: bool = True,
     ) -> dict[str, dict[str, Union[tuple, pd.DataFrame]]]:
         """Exports either all replicates present in any measurement or the ones specified via 'species_ids' or 'measurement_ids'
 
@@ -381,14 +383,17 @@ def exportMeasurementData(
 
         for measurement_id, measurement in self.measurement_dict.items():
             if measurement_id in measurement_ids or measurement_ids == ["all"]:
-                measurement_data = measurement.exportData(
+                data = measurement.exportData(
                     species_ids=species_ids
                 )
 
-                measurement_data = {
-                    **measurement_data["proteins"],
-                    **measurement_data["reactants"]
-                }
+                # Initialize the data dict that will be returned
+                measurement_data = {}
+
+                if reactants:
+                    measurement_data.update(data["reactants"])
+                if proteins:
+                    measurement_data.update(data["proteins"])
 
                 if measurement_data["data"] is not None:
                     replicate_data[measurement_id] = measurement_data

diff --git a/pyenzyme/enzymeml/core/measurement.py b/pyenzyme/enzymeml/core/measurement.py
@@ -180,7 +180,7 @@ def _combineReplicates(
         if isinstance(species_ids, str):
             species_ids = [species_ids]
 
-        columns = {f"time|{self.global_time_unit}": self.global_time}
+        columns = {"time": self.global_time}
         initial_concentration = {}
 
         # Iterate over measurementData to fill columns
@@ -191,8 +191,7 @@ def _combineReplicates(
                 # Fetch replicate data
                 for replicate in data.getReplicates():
 
-                    header = f"{replicate.getReplica()}|{species_id}|{replicate.getDataUnit()}"
-                    columns[header] = replicate.data
+                    columns[species_id] = replicate.data
 
                     # Fetch initial concentration
                     initial_concentration[species_id] = (