Updated EnzymeML Template Example

EnzymeML · Mar 9, 2022 · 0032552 · 0032552
1 parent 7f70906
commit 0032552
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/pyenzyme/enzymeml/tools/templatereader.py b/pyenzyme/enzymeml/tools/templatereader.py
@@ -1,5 +1,4 @@
 import pandas as pd
-import numpy as np
 import re
 
 from typing import List, Dict
@@ -28,7 +27,7 @@ def read_template(path: str, enzmldoc):
 
     params = dict(
         name=general_info.iloc[0, 1],
-        created=str(general_info.iloc[1, 1]),
+        created=str(general_info.iloc[1, 1].date()),
         doi=None,
         pubmedid=general_info.iloc[3, 1],
         url=general_info.iloc[4, 1],
@@ -66,6 +65,7 @@ def read_template(path: str, enzmldoc):
 
     # Reactants
     reactants = pd.read_excel(path, sheet_name="Reactants", skiprows=2)
+
     instances = get_instances(reactants, Reactant, enzmldoc)
 
     for instance in instances:
@@ -202,7 +202,6 @@ def get_template_map(obj) -> dict:
 
 
 def extract_values(sheet: pd.DataFrame, mapping: Dict[str, str]) -> list:
-    sheet = sheet.replace(r"^\s*$", np.nan, regex=True)
     sheet = sheet.dropna(thresh=len(mapping))
     records = sheet.to_dict(orient="records")
 
@@ -309,7 +308,7 @@ def parse_reaction_element(elements):
     if repr(elements) == "nan":
         return []
 
-    return elements.split(";")
+    return elements.split(",")
 
 
 def add_instances(fun, elements, enzmldoc) -> None:

diff --git a/tests/fixtures/EnzymeML_Template_Example.xlsm b/tests/fixtures/EnzymeML_Template_Example.xlsm