updated the converter.py

excel2sbol/excel2sbol/compiler.py

@@ -10,7 +10,53 @@
 
 # the homespace only works if the change is made to pysbol2 shown in https://github.com/SynBioDex/pySBOL2/pull/411/files
 
+def initialise_welcome(file_path_in):
+    init_info = pd.read_excel(file_path_in, sheet_name="Init",
+                              skiprows=9, index_col=0,
+                              engine='openpyxl')
+    init_info = init_info.applymap(lambda x: x.strip() if isinstance(x, str) else x).to_dict('index')
+
+    version_info = pd.read_excel(file_path_in, sheet_name="Init",
+                                 nrows=4, index_col=0, header=None,
+                                 engine='openpyxl')
+    version_info = version_info.applymap(lambda x: x.strip() if isinstance(x, str) else x).to_dict('index')
+    if 'Homespace' in version_info:
+        homespace = version_info['Homespace'][1]
+    else:
+        homespace = ""
+    version_info = version_info['SBOL Version'][1]
 
+    # For key in dict read in sheet,
+    # if sheet convert = true, add to convert list
+    compiled_sheets = {}
+    to_convert = []
+    for sheet_name, val in init_info.items():
+        # print(f"reading in {sheet_name}...")
+        # MY CODE
+        if sheet_name.lower() == "welcome":
+            print("Processing the welcome page...")
+            try:
+                welcome_metadata = pd.read_excel(file_path_in, sheet_name=sheet_name,
+                                                 index_col=0, engine='openpyxl').fillna("")
+                print("Welcome Page Metadata:")
+
+                dict = {}
+                for _, row in welcome_metadata.iterrows():
+                    if len(row) >= 2:
+                        key, value = row[0], row[1]
+                        if isinstance(key, str) and key.strip():
+                            dict[key.strip()] = value.strip() if isinstance(value, str) else value
+                for key, value in dict.items():
+                    print(f"{key}: {value}")
+                return dict
+
+            except Exception as e:
+                print(f"Error reading the welcome page: {e}")
+                return None
+
+        else:
+            return
+
 def initialise(file_path_in):
     init_info = pd.read_excel(file_path_in, sheet_name="Init",
                               skiprows=9, index_col=0,
@@ -33,6 +79,11 @@ def initialise(file_path_in):
     to_convert = []
     for sheet_name, val in init_info.items():
         # print(f"reading in {sheet_name}...")
+        # MY CODE
+        if sheet_name.lower() == "welcome":
+            continue
+		# MY CODE
+
         convert = val['Convert']
 
         if convert:
@@ -390,4 +441,4 @@ def column_parse(to_convert, compiled_sheets, sht_convert_dict, dict_of_objs,
     else:
         doc.write(file_path_out, file_format = file_format)
 
-    return
+    return

excel2sbol/excel2sbol/converter.py

@@ -1,16 +1,31 @@
 # from ensurepip import version
 import excel2sbol.compiler as e2s
+import os
+import json
+from datetime import datetime
 
-
-def converter(file_path_in, file_path_out, sbol_version=3, homespace="http://examples.org/", file_format=None):
+def converter(file_path_in, file_path_out, sbol_version=3, homespace="http://examples.org/", file_format=None,  username=None, password=None, url = None):
     """Convert a given excel file to SBOL
 
     Args:
         file_path_in (string): path to excel file
         file_path_out (string): desired path to sbol file
         sbol_version (int): sbol version number, defaults to 3
     """
+    if username is not None and password is not None and url is not None:
+        # print(username, password, url)
+        os.environ["SBOL_USERNAME"] = username
+        os.environ["SBOL_PASSWORD"] = password
+        os.environ["SBOL_URL"] = url
+
     col_read_df, to_convert, compiled_sheets, version_info, homespace2 = e2s.initialise(file_path_in)
+    dict = e2s.initialise_welcome(file_path_in)
+    for key, value in dict.items():
+        if isinstance(value, datetime):
+            dict[key] = value.isoformat()
+    if dict is not None:
+        os.environ["SBOL_DICTIONARY"] = json.dumps(dict)
+    # print(dict)
 
     if len(homespace2) > 0:
         homespace = homespace2
@@ -33,3 +48,5 @@ def converter(file_path_in, file_path_out, sbol_version=3, homespace="http://exa
     e2s.column_parse(to_convert, compiled_sheets, sht_convert_dict,
                      dict_of_objs, col_read_df, doc, file_path_out,
                      sbol_version=sbol_version, file_format=file_format)
+
+