Fixes #28

pyenzyme/enzymeml/core/enzymemldocument.py

@@ -14,6 +14,7 @@
 import re
 import ast
 import json
+from tkinter import TRUE
 import yaml
 import logging
 import pandas as pd
@@ -551,7 +552,7 @@ def exportMeasurementData(
         self,
         measurement_ids: Union[str, List[str]] = "all",
         species_ids: Union[str, List[str]] = "all",
-        proteins: bool = False,
+        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'
@@ -564,6 +565,11 @@ def exportMeasurementData(
             Dict[str, Dict[str, Union[tuple, pd.DataFrame]]]: The data corresponding to the specified options. The dictionary will still distinguish between meassuremnts.
         """
 
+        if proteins is False and reactants is False:
+            raise ValueError(
+                "Export of data needs at least one of 'protein' and 'reactants' specified. Otherwise no data can be exported."
+            )
+
         if isinstance(measurement_ids, str):
             measurement_ids = [measurement_ids]
         if isinstance(species_ids, str):
@@ -577,15 +583,20 @@ def exportMeasurementData(
                 data = measurement.exportData(species_ids=species_ids)
 
                 # Initialize the data dict that will be returned
-                measurement_data = {}
+                df = {}
+                init_conc = {}
 
                 if reactants:
-                    measurement_data.update(data["reactants"])
+                    df.update(data["reactants"]["data"].to_dict())
+                    init_conc.update(data["reactants"]["initConc"])
                 if proteins:
-                    measurement_data.update(data["proteins"])
+                    df.update(data["proteins"]["data"].to_dict())
+                    init_conc.update(data["proteins"]["initConc"])
 
-                if measurement_data["data"] is not None:
-                    replicate_data[measurement_id] = measurement_data
+                replicate_data[measurement_id] = {
+                    "data": pd.DataFrame(df),
+                    "initConc": init_conc,
+                }
 
         return replicate_data
 

tests/enzymeml/core/test_enzymemldocument.py

@@ -1,4 +1,5 @@
 import os
+import pytest
 
 from pyenzyme.enzymeml.core.enzymemldocument import EnzymeMLDocument
 from pyenzyme.enzymeml.core.abstract_classes import AbstractSpecies
@@ -152,3 +153,72 @@ def test_add_species(self):
 
         assert "p0" in enzmldoc.protein_dict
         assert species == enzmldoc.protein_dict["p0"]
+
+    def test_unit_change(self, enzmldoc):
+        """Tests whether units remain consistent when changed at run-time and are reloaded"""
+
+        # Change an arbitrary unit
+        species = enzmldoc.getReactant("s0")
+        species.unit = "umole / l"
+
+        # Write to file
+        enzmldoc.toFile("./tests/tmp/", name="Test_Unit_Change")
+
+        # Read file and check if the unit change is consistent
+        nu_enzmldoc = EnzymeMLDocument.fromFile("./tests/tmp/Test_Unit_Change.omex")
+        unit = enzmldoc.getReactant("s0").unit
+
+        assert unit == "umole / l"
+
+    def test_full_data_export(self, enzmldoc):
+        """Tests whether data is exported correctly"""
+
+        # Test all export of reactant/protein
+        data = enzmldoc.exportMeasurementData()
+
+        expected_conc = {"s0": (10.0, "mmole / l"), "p0": (10.0, "mmole / l")}
+        expected_data = {
+            "s0": {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0},
+            "time": {0: 1.0, 1: 2.0, 2: 3.0, 3: 4.0},
+            "p0": {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0},
+        }
+
+        assert "m0" in data
+        assert data["m0"]["data"].to_dict() == expected_data
+        assert data["m0"]["initConc"] == expected_conc
+
+        # Test case of no specification
+        with pytest.raises(ValueError) as exc_info:
+            enzmldoc.exportMeasurementData(proteins=False, reactants=False)
+
+    def test_protein_data_export(self, enzmldoc):
+        """Tests whether data is exported correctly"""
+
+        # Test all export of reactant/protein
+        data = enzmldoc.exportMeasurementData(reactants=False)
+
+        expected_conc = {"p0": (10.0, "mmole / l")}
+        expected_data = {
+            "time": {0: 1.0, 1: 2.0, 2: 3.0, 3: 4.0},
+            "p0": {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0},
+        }
+
+        assert "m0" in data
+        assert data["m0"]["data"].to_dict() == expected_data
+        assert data["m0"]["initConc"] == expected_conc
+
+    def test_reactant_data_export(self, enzmldoc):
+        """Tests whether data is exported correctly"""
+
+        # Test all export of reactant/protein
+        data = enzmldoc.exportMeasurementData(proteins=False)
+
+        expected_conc = {"s0": (10.0, "mmole / l")}
+        expected_data = {
+            "time": {0: 1.0, 1: 2.0, 2: 3.0, 3: 4.0},
+            "s0": {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0},
+        }
+
+        assert "m0" in data
+        assert data["m0"]["data"].to_dict() == expected_data
+        assert data["m0"]["initConc"] == expected_conc