pysodafair 0.1.67__tar.gz → 0.1.68__tar.gz

{pysodafair-0.1.67 → pysodafair-0.1.68}/PKG-INFO

@@ -1,17 +1,14 @@
 Metadata-Version: 2.4
 Name: pysodafair
-Version: 0.1.67
+Version: 0.1.68
 Summary: Pysoda package for Fairdataihub tools
 License: MIT
 License-File: LICENSE
 Author: Christopher Marroquin
 Author-email: cmarroquin@calmi2.org
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11

{pysodafair-0.1.67 → pysodafair-0.1.68}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pysodafair"
-version = "0.1.67"
+version = "0.1.68"
 description = "Pysoda package for Fairdataihub tools"
 authors = ["Christopher Marroquin <cmarroquin@calmi2.org>"]
 license = "MIT"
@@ -17,10 +17,10 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.6"
+python = ">=3.9"
 openpyxl = "*"
 
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core", "poetry==2.2.1"]
 build-backend = "poetry.core.masonry.api"

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/dataset_generation/upload.py

@@ -1,4 +1,5 @@
 
+from pysoda.utils.exceptions import PennsieveAgentRPCError
 from ...utils import (
     generate_options_set, generating_locally, generating_on_ps, 
     uploading_with_ps_account, uploading_to_existing_ps_dataset, 
@@ -2148,8 +2149,6 @@ def ps_upload_to_dataset(soda, ps, ds, resume=False):
                     my_bf_existing_files_name_with_extension,
                 ) = ps_get_existing_files_details(my_tracking_folder)
 
-                logger.info(f"Existing files in Pennsieve: {my_bf_existing_files_name_with_extension}")
-
                 list_local_files = []
                 list_projected_names = []
                 list_desired_names = []
@@ -2466,7 +2465,7 @@ def ps_upload_to_dataset(soda, ps, ds, resume=False):
                     relative_path,
                 )
 
-                logger.info(f"List of files to upload: {list_upload_files}")
+                logger.info(f"Amount of files to upload: {len(list_upload_files)} ")
 
 
                 # return and mark upload as completed if nothing is added to the manifest
@@ -3032,6 +3031,7 @@ def ps_upload_to_dataset(soda, ps, ds, resume=False):
         end = timer()
         logger.info(f"Time for ps_upload_to_dataset function: {timedelta(seconds=end - start)}")
     except Exception as e:
+        logger.error(f"An error occurred in ps_upload_to_dataset function: {str(e)}")
         # reset the total bytes uploaded for any file that has not been fully uploaded
         ums.set_main_total_generate_dataset_size(main_total_generate_dataset_size)
         ums.set_total_files_to_upload(total_files)
@@ -3056,6 +3056,7 @@ renaming_files_flow = False
 elapsed_time = None
 manifest_id = None 
 origin_manifest_id = None
+curation_error_message = ""
 
 
 
@@ -3557,6 +3558,7 @@ def reset_upload_session_environment(resume):
     global generated_dataset_id
     global bytes_file_path_dict
     global renaming_files_flow
+    global curation_error_message
 
     start_generate = 0
     myds = ""
@@ -3571,6 +3573,7 @@ def reset_upload_session_environment(resume):
     main_curation_uploaded_files = 0
     uploaded_folder_counter = 0
     generated_dataset_id = None
+    curation_error_message = ""
 
     main_curate_status = "Curating"
     main_curate_progress_message = "Starting dataset curation"
@@ -3599,6 +3602,7 @@ def main_curate_function(soda, resume):
     global manifest_id 
     global origin_manifest_id
     global total_files
+    global curation_error_message
 
     logger.info("Starting generating selected dataset")
     logger.info(f"Generating dataset metadata generate-options={soda['generate-dataset']}")
@@ -3624,7 +3628,9 @@ def main_curate_function(soda, resume):
             ps = connect_pennsieve_client(accountname)
             generate_dataset(soda, resume, ps)
     except Exception as e:
+        logger.error(f"An error occurred in main_curate_function function: {str(e)}")
         main_curate_status = "Done"
+        curation_error_message = str(e)
         raise e
 
     main_curate_status = "Done"
@@ -3662,6 +3668,7 @@ def main_curate_function_progress():
     global renaming_files_flow
     global ums 
     global elapsed_time
+    global curation_error_message
 
 
     prior_elapsed_time = ums.get_elapsed_time()
@@ -3688,6 +3695,7 @@ def main_curate_function_progress():
         "total_files_uploaded": main_curation_uploaded_files,
         "generated_dataset_id": myds["content"]["id"] if myds != "" else None, # when a new dataset gets generated log its id to our analytics
         "generated_dataset_int_id": myds["content"]["intId"] if myds != "" else None,
+        "curation_error_message": curation_error_message,
     }
 
 

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/code_description.py

@@ -1,6 +1,6 @@
 from .constants import METADATA_UPLOAD_PS_PATH, TEMPLATE_PATH, SDS_FILE_CODE_DESCRIPTION, SCHEMA_NAME_CODE_DESCRIPTION
 from .excel_utils import rename_headers, excel_columns
-from openpyxl.styles import PatternFill
+from openpyxl.styles import PatternFill, Font
 from os.path import join, getsize
 from openpyxl import load_workbook
 import shutil
@@ -53,27 +53,47 @@ def populate_input_output_information(ws1, soda):
 
     excel_ascii = excel_columns(start_index=3)[0]
     ws1[excel_ascii + str(row)] = input_output_information["number_of_inputs"]
+    ws1[excel_ascii + str(row)].font = Font(bold=False, size=11, name="Arial")
 
     for input, column in zip(input_output_information["inputs"], excel_columns(start_index=3)):
         row = 28
         ws1[column + str(row)] = input["input_parameter_name"]
+        ws1[column + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 1)] = input["input parameter type"]
+        ws1[column + str(row + 1)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 2)] = input["input_parameter_description"]
+        ws1[column + str(row + 2)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 3)] = input["input_units"]
+        ws1[column + str(row + 3)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 4)] = input["input_default_value"]
+        ws1[column + str(row + 4)].font = Font(bold=False, size=11, name="Arial")
 
     # populate number of outputs into row 34
     row = 34
     ws1[excel_ascii + str(row)] = input_output_information["number_of_outputs"]
+    ws1[excel_ascii + str(row)].font = Font(bold=False, size=11, name="Arial")
 
     # populate the outputs from row 35 - 39
     for output, column in zip(input_output_information["outputs"], excel_columns(start_index=3)):
         row = 35
         ws1[column + str(row)] = output["output_parameter_name"]
+        ws1[column + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 1)] = output["output_parameter_type"]
+        ws1[column + str(row + 1)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 2)] = output["output_parameter_description"]
+        ws1[column + str(row + 2)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 3)] = output["output_units"]
+        ws1[column + str(row + 3)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 4)] = output["output_default_value"]
+        ws1[column + str(row + 4)].font = Font(bold=False, size=11, name="Arial")
 
 
 def populate_basic_information(ws1, soda):
@@ -83,9 +103,16 @@ def populate_basic_information(ws1, soda):
     row = 2
     for info, column in zip(basic_information, excel_columns(start_index=3)):
         ws1[column + str(row)] = info["RRID_term"]
+        ws1[column + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 1)] = info["RRID_identifier"]
+        ws1[column + str(row + 1)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 2)] = info["ontology_term"]
+        ws1[column + str(row + 2)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[column + str(row + 3)] = info["ontology_identifier"]
+        ws1[column + str(row + 3)].font = Font(bold=False, size=11, name="Arial")
 
 
 def populate_ten_simple_rules(ws1, soda):
@@ -94,10 +121,19 @@ def populate_ten_simple_rules(ws1, soda):
     ascii_cols = excel_columns(start_index=3)
     for _, rule in ten_simple_rules.items():
         ws1[ascii_cols[0] + str(row)] = rule.get("Link", "")
+        ws1[ascii_cols[0] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_cols[1] + str(row)] = rule.get("Rating", "")
+        ws1[ascii_cols[1] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_cols[2] + str(row)] = rule.get("Target", "")
+        ws1[ascii_cols[2] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_cols[3] + str(row)] = rule.get("Target Justification", "")
+        ws1[ascii_cols[3] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_cols[4] + str(row)] = rule.get("Text", "")
+        ws1[ascii_cols[4] + str(row)].font = Font(bold=False, size=11, name="Arial")
         row += 1
 
 

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/dataset_description.py

@@ -146,7 +146,9 @@ def populate_contributor_info(workbook, soda):
         workbook[column + "28"] = contributor.get("contributor_name", "")
         workbook[column + "29"] = contributor.get("contributor_orcid_id", "")
         workbook[column + "30"] = contributor.get("contributor_affiliation", "")
-        workbook[column + "31"] = contributor.get("contributor_role", "")
+        roles = contributor.get("contributor_roles", [])
+        roles_str = ", ".join(roles) if roles else ""
+        workbook[column + "31"] = roles_str
     # Return the length of the contributor array, or 1 if empty
     return max(1, len(contributor_info))
 

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/performances.py

@@ -1,6 +1,6 @@
 from .constants import METADATA_UPLOAD_PS_PATH, TEMPLATE_PATH, SDS_FILE_PERFORMANCES, SCHEMA_NAME_PERFORMANCES
 from .excel_utils import rename_headers, excel_columns
-from openpyxl.styles import PatternFill
+from openpyxl.styles import PatternFill, Font
 from os.path import join, getsize
 from openpyxl import load_workbook
 import shutil
@@ -26,13 +26,26 @@ def create_excel(soda, upload_boolean, local_destination):
     ascii_headers = excel_columns(start_index=0)
     for performance in performances: 
         ws1[ascii_headers[0] + str(row)] = performance.get("performance_id", "")
+        ws1[ascii_headers[0] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[1] + str(row)] = performance.get("protocol_url_or_doi", "")
+        ws1[ascii_headers[1] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[2] + str(row)] = performance.get("date", "")
+        ws1[ascii_headers[2] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[3] + str(row)] = performance.get("start_datetime", "")
+        ws1[ascii_headers[3] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[4] + str(row)] = performance.get("end_datetime", "")
+        ws1[ascii_headers[4] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         participants = " ".join(performance.get("participants", []))
         ws1[ascii_headers[5] + str(row)] = participants
+        ws1[ascii_headers[5] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[6] + str(row)] = performance.get("additional_metadata", "")
+        ws1[ascii_headers[6] + str(row)].font = Font(bold=False, size=11, name="Arial")
         row += 1
 
     wb.save(destination)

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/resources.py

@@ -1,6 +1,6 @@
 from .constants import METADATA_UPLOAD_PS_PATH, TEMPLATE_PATH, SDS_FILE_RESOURCES, SCHEMA_NAME_RESOURCES
 from .excel_utils import rename_headers, excel_columns
-from openpyxl.styles import PatternFill
+from openpyxl.styles import PatternFill, Font
 from os.path import join, getsize
 from openpyxl import load_workbook
 import shutil
@@ -27,13 +27,28 @@ def create_excel(soda, upload_boolean, local_destination):
     ascii_headers = excel_columns(start_index=0)
     for resource in resources: 
         ws1[ascii_headers[0] + str(row)] = resource.get("rrid", "")
+        ws1[ascii_headers[0] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[1] + str(row)] = resource.get("type", "")
+        ws1[ascii_headers[1] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[2] + str(row)] = resource.get("name", "")
+        ws1[ascii_headers[2] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[3] + str(row)] = resource.get("url", "")
+        ws1[ascii_headers[3] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[4] + str(row)] = resource.get("vendor", "")
+        ws1[ascii_headers[4] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[5] + str(row)] = resource.get("version", "")
+        ws1[ascii_headers[5] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[6] + str(row)] = resource.get("id_in_protocol", "")
+        ws1[ascii_headers[6] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[7] + str(row)] = resource.get("additional_metadata", "")
+        ws1[ascii_headers[7] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
         row += 1
 

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/samples.py

@@ -49,7 +49,7 @@ def create_excel(soda, upload_boolean, local_destination):
         ws1[ascii_headers[5] + str(row)] = sample.get("sample_type", "")
         ws1[ascii_headers[5] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[6] + str(row)] = sample.get("sample_anatomical_location", "")
+        ws1[ascii_headers[6] + str(row)] = handle_anatomical_location_field(sample)
         ws1[ascii_headers[6] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
         ws1[ascii_headers[7] + str(row)] = sample.get("also_in_dataset", "")
@@ -61,36 +61,39 @@ def create_excel(soda, upload_boolean, local_destination):
         ws1[ascii_headers[9] + str(row)] = sample.get("metadata_only", "")
         ws1[ascii_headers[9] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[10] + str(row)] = sample.get("laboratory_internal_id", "")
+        ws1[ascii_headers[10] + str(row)] = sample.get("number_of_directly_derived_samples", "")
         ws1[ascii_headers[10] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[11] + str(row)] = sample.get("date_of_derivation", "")
+        ws1[ascii_headers[11] + str(row)] = sample.get("laboratory_internal_id", "")
         ws1[ascii_headers[11] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[12] + str(row)] = sample.get("experimental_log_file_path", "")
+        ws1[ascii_headers[12] + str(row)] = sample.get("date_of_derivation", "")
         ws1[ascii_headers[12] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[13] + str(row)] = sample.get("reference_atlas", "")
+        ws1[ascii_headers[13] + str(row)] = sample.get("experimental_log_file_path", "")
         ws1[ascii_headers[13] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[14] + str(row)] = sample.get("pathology", "")
+        ws1[ascii_headers[14] + str(row)] = sample.get("reference_atlas", "")
         ws1[ascii_headers[14] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[15] + str(row)] = sample.get("laterality", "")
+        ws1[ascii_headers[15] + str(row)] = sample.get("pathology", "")
         ws1[ascii_headers[15] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[16] + str(row)] = sample.get("cell_type", "")
+        ws1[ascii_headers[16] + str(row)] = sample.get("laterality", "")
         ws1[ascii_headers[16] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[17] + str(row)] = sample.get("plane_of_section", "")
+        ws1[ascii_headers[17] + str(row)] = sample.get("cell_type", "")
         ws1[ascii_headers[17] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[18] + str(row)] = sample.get("protocol_title", "")
+        ws1[ascii_headers[18] + str(row)] = sample.get("plane_of_section", "")
         ws1[ascii_headers[18] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[19] + str(row)] = sample.get("protocol_url_or_doi", "")
+        ws1[ascii_headers[19] + str(row)] = sample.get("protocol_title", "")
         ws1[ascii_headers[19] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
+        ws1[ascii_headers[20] + str(row)] = sample.get("protocol_url_or_doi", "")
+        ws1[ascii_headers[20] + str(row)].font = Font(bold=False, size=11, name="Arial")
+
         # Handle custom fields
         for field_name, field in sample.items():
             if field_name in sds_headers:
@@ -102,14 +105,14 @@ def create_excel(soda, upload_boolean, local_destination):
 
                 # Create the column header in the Excel file
                 offset_from_final_sds_header = custom_headers_to_column[field_name]
-                ws1[ascii_headers[19 + offset_from_final_sds_header] + "1"] = field_name
-                ws1[ascii_headers[19 + offset_from_final_sds_header] + "1"].fill = orangeFill
-                ws1[ascii_headers[19 + offset_from_final_sds_header] + "1"].font = Font(bold=True, size=12, name="Calibri")
+                ws1[ascii_headers[20 + offset_from_final_sds_header] + "1"] = field_name
+                ws1[ascii_headers[20 + offset_from_final_sds_header] + "1"].fill = orangeFill
+                ws1[ascii_headers[20 + offset_from_final_sds_header] + "1"].font = Font(bold=True, size=12, name="Calibri")
 
             # Add the field value to the corresponding cell in the Excel file
             offset_from_final_sds_header = custom_headers_to_column[field_name]
-            ws1[ascii_headers[19 + offset_from_final_sds_header] + str(row)] = field
-            ws1[ascii_headers[19 + offset_from_final_sds_header] + str(row)].font = Font(bold=False, size=11, name="Arial")
+            ws1[ascii_headers[20 + offset_from_final_sds_header] + str(row)] = field
+            ws1[ascii_headers[20 + offset_from_final_sds_header] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
         row += 1
 
@@ -124,61 +127,9 @@ def create_excel(soda, upload_boolean, local_destination):
     return size
 
 
-# soda = {
-#     "dataset_metadata": {
-#         "samples": [
-#             {
-#                 "sample_id": "sample_1",
-#                 "subject_id": "subject_1",
-#                 "was_derived_from": "derived_from_1",
-#                 "pool_id": "pool_1",
-#                 "sample_experimental_group": "experimental_group_1",
-#                 "sample_type": "type_1",
-#                 "sample_anatomical_location": "location_1",
-#                 "also_in_dataset": "dataset_1",
-#                 "member_of": "member_1",
-#                 "metadata_only": "False",
-#                 "laboratory_internal_id": "internal_id_1",
-#                 "date_of_derivation": "2023-01-01",
-#                 "experimental_log_file_path": "/path/to/log/file",
-#                 "reference_atlas": "/path/to/atlas",
-#                 "pathology": "pathology_1",
-#                 "laterality": "left",
-#                 "cell_type": "cell_type_1",
-#                 "plane_of_section": "plane_1",
-#                 "protocol_title": "protocol_title_1",
-#                 "protocol_url_or_doi": "/path/to/protocol",
-#                 "custom_field_1": "custom_value_1",
-#             },
-#             {
-#                 "sample_id": "sample_2",
-#                 "subject_id": "subject_2",
-#                 "was_derived_from": "derived_from_2",
-#                 "pool_id": "pool_2",
-#                 "sample_experimental_group": "experimental_group_2",
-#                 "sample_type": "type_2",
-#                 "sample_anatomical_location": "location_2",
-#                 "also_in_dataset": "dataset_2",
-#                 "member_of": "member_2",
-#                 "metadata_only": "True",
-#                 "laboratory_internal_id": "internal_id_2",
-#                 "date_of_derivation": "2023-02-01",
-#                 "experimental_log_file_path": "/path/to/log/file2",
-#                 "reference_atlas": "/path/to/atlas2",
-#                 "pathology": "pathology_2",
-#                 "laterality": "right",
-#                 "cell_type": "cell_type_2",
-#                 "plane_of_section": "plane_2",
-#                 "protocol_title": "protocol_title_2",
-#                 "protocol_url_or_doi": "/path/to/protocol2",
-#                 "custom_field_1": "custom_value_12",
-
-#             }
-#         ]
-#     }
-# }
-
-# try:
-#     create_excel(soda, False, "samples.xlsx")
-# except Exception as e:
-#     print(f"An error occurred: {e}")
+
+def handle_anatomical_location_field(sample):
+    anatomical_location = sample.get("sample_anatomical_location", "")
+    if isinstance(anatomical_location, list):
+        return " ".join(anatomical_location)
+    return anatomical_location

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/sites.py

@@ -1,6 +1,6 @@
 from .constants import METADATA_UPLOAD_PS_PATH, TEMPLATE_PATH, SDS_FILE_SITES, SCHEMA_NAME_SITES
 from .excel_utils import rename_headers, excel_columns
-from openpyxl.styles import PatternFill
+from openpyxl.styles import PatternFill, Font
 from os.path import join, getsize
 from openpyxl import load_workbook
 import shutil
@@ -27,12 +27,25 @@ def create_excel(soda, upload_boolean, local_destination):
     ascii_headers = excel_columns(start_index=0)
     for performance in sites: 
         ws1[ascii_headers[0] + str(row)] = performance.get("site_id", "")
+        ws1[ascii_headers[0] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[1] + str(row)] = performance.get("specimen_id", "")
+        ws1[ascii_headers[1] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[2] + str(row)] = performance.get("site_type", "")
+        ws1[ascii_headers[2] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[3] + str(row)] = performance.get("laboratory_internal_id", "")
+        ws1[ascii_headers[3] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[4] + str(row)] = performance.get("coordinate_system", "")
+        ws1[ascii_headers[4] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[5] + str(row)] = performance.get("coordinate_system_position", "")
+        ws1[ascii_headers[5] + str(row)].font = Font(bold=False, size=11, name="Arial")
+        
         ws1[ascii_headers[6] + str(row)] = performance.get("more...", "")
+        ws1[ascii_headers[6] + str(row)].font = Font(bold=False, size=11, name="Arial")
         row += 1
 
     wb.save(destination)

{pysodafair-0.1.67 → pysodafair-0.1.68}/pysoda/core/metadata/subjects.py

@@ -84,54 +84,57 @@ def create_excel(soda, upload_boolean, local_destination):
         ws1[ascii_headers[11] + str(row)] = subject.get("metadata_only", "")
         ws1[ascii_headers[11] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[12] + str(row)] = subject.get("laboratory_internal_id", "")
+        ws1[ascii_headers[12] + str(row)] = subject.get("number_of_directly_derived_samples", "")
         ws1[ascii_headers[12] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[13] + str(row)] = subject.get("date_of_birth", "")
+        ws1[ascii_headers[13] + str(row)] = subject.get("laboratory_internal_id", "")
         ws1[ascii_headers[13] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[14] + str(row)] = subject.get("age_range_min", "")
+        ws1[ascii_headers[14] + str(row)] = subject.get("date_of_birth", "")
         ws1[ascii_headers[14] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[15] + str(row)] = subject.get("age_range_max", "")
+        ws1[ascii_headers[15] + str(row)] = subject.get("age_range_min", "")
         ws1[ascii_headers[15] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[16] + str(row)] = subject.get("body_mass", "")
+        ws1[ascii_headers[16] + str(row)] = subject.get("age_range_max", "")
         ws1[ascii_headers[16] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[17] + str(row)] = subject.get("genotype", "")
+        ws1[ascii_headers[17] + str(row)] = normalize_body_mass(subject.get("body_mass", ""))
         ws1[ascii_headers[17] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[18] + str(row)] = subject.get("phenotype", "")
+        ws1[ascii_headers[18] + str(row)] = subject.get("genotype", "")
         ws1[ascii_headers[18] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[19] + str(row)] = subject.get("handedness", "")
+        ws1[ascii_headers[19] + str(row)] = subject.get("phenotype", "")
         ws1[ascii_headers[19] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[20] + str(row)] = subject.get("reference_atlas", "")
+        ws1[ascii_headers[20] + str(row)] = subject.get("handedness", "")
         ws1[ascii_headers[20] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[21] + str(row)] = subject.get("experimental_log_file_path", "")
+        ws1[ascii_headers[21] + str(row)] = subject.get("reference_atlas", "")
         ws1[ascii_headers[21] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[22] + str(row)] = subject.get("experiment_date", "")
+        ws1[ascii_headers[22] + str(row)] = subject.get("experimental_log_file_path", "")
         ws1[ascii_headers[22] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[23] + str(row)] = subject.get("disease_or_disorder", "")
+        ws1[ascii_headers[23] + str(row)] = subject.get("experiment_date", "")
         ws1[ascii_headers[23] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[24] + str(row)] = subject.get("intervention", "")
+        ws1[ascii_headers[24] + str(row)] = subject.get("disease", "")
         ws1[ascii_headers[24] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[25] + str(row)] = subject.get("disease_model", "")
+        ws1[ascii_headers[25] + str(row)] = subject.get("intervention", "")
         ws1[ascii_headers[25] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[26] + str(row)] = subject.get("protocol_title", "")
+        ws1[ascii_headers[26] + str(row)] = subject.get("disease_model", "")
         ws1[ascii_headers[26] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
-        ws1[ascii_headers[27] + str(row)] = subject.get("protocol_url_or_doi", "")
+        ws1[ascii_headers[27] + str(row)] = subject.get("protocol_title", "")
         ws1[ascii_headers[27] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
+        ws1[ascii_headers[28] + str(row)] = subject.get("protocol_url_or_doi", "")
+        ws1[ascii_headers[28] + str(row)].font = Font(bold=False, size=11, name="Arial")
+
         # handle custom fields
         for field_name, field in subject.items():
             if field_name in sds_headers:
@@ -146,17 +149,17 @@ def create_excel(soda, upload_boolean, local_destination):
 
                 # create the column header in the excel file
                 offset_from_final_sds_header = custom_headers_to_column[field_name]
-                ws1[ascii_headers[27 + offset_from_final_sds_header] + "1"] = field_name
-                ws1[ascii_headers[27 + offset_from_final_sds_header] + "1"].fill = orangeFill
-                ws1[ascii_headers[27 + offset_from_final_sds_header] + "1"].font = Font(bold=True, size=12, name="Calibri")
+                ws1[ascii_headers[28 + offset_from_final_sds_header] + "1"] = field_name
+                ws1[ascii_headers[28 + offset_from_final_sds_header] + "1"].fill = orangeFill
+                ws1[ascii_headers[28 + offset_from_final_sds_header] + "1"].font = Font(bold=True, size=12, name="Calibri")
 
 
 
             # add the field value to the corresponding cell in the excel file
             offset_from_final_sds_header = custom_headers_to_column[field_name]
 
-            ws1[ascii_headers[27 + offset_from_final_sds_header] + str(row)] = field
-            ws1[ascii_headers[27 + offset_from_final_sds_header] + str(row)].font = Font(bold=False, size=11, name="Arial")
+            ws1[ascii_headers[28 + offset_from_final_sds_header] + str(row)] = field
+            ws1[ascii_headers[28 + offset_from_final_sds_header] + str(row)].font = Font(bold=False, size=11, name="Arial")
 
 
         row += 1
@@ -169,4 +172,30 @@ def create_excel(soda, upload_boolean, local_destination):
     if upload_boolean:
         upload_metadata_file(SDS_FILE_SUBJECTS, soda, destination, True)
 
-    return {size: size}
+    return {size: size}
+
+
+
+def normalize_body_mass(body_mass_value):
+    """
+    Ensures that a body_mass value is normalized to a string for Excel export.
+    Handles cases where 'body_mass' is a string, number, or an object with 'value' and 'unit'.
+    """
+    # If already a string or empty, leave as is
+    if isinstance(body_mass_value, str):
+        return body_mass_value
+    # If a number, convert to string
+    if isinstance(body_mass_value, (int, float)):
+        return str(body_mass_value)
+    # If an object with value and unit
+    if isinstance(body_mass_value, dict):
+            value = body_mass_value.get("value")
+            unit = body_mass_value.get("unit")
+            if value is not None and unit:
+                return f"{value} {unit}"
+            elif value is not None:
+                return str(value)
+            else:
+                return ""
+    else:
+        return ""

pysodafair-0.1.68/pysoda/core/metadata_templates/.dss

@@ -0,0 +1 @@
+(sds 3.0.1)