Isotope parsing fails when multiple isotopes are separated with a command and a space: e.g. [13C6, 15N3]

[lparsons]

BUG DESCRIPTION

Problem

Tracers with multiple Isotopes separated with a command and space (,) instead of just a a comma with no space (,) result in and IsotopeParsingError

Steps to reproduce

1. Attempt to load the following study sheet: col013a_tracebase_studydoc.xlsx

   python manage.py load_protocols --infile "col013a_tracebase_studydoc.xlsx"
   

Current behavior

Importing animals and samples...
Traceback (most recent call last):
  File "/var/www/tracebase/manage.py", line 22, in <module>
    main()
  File "/var/www/tracebase/manage.py", line 18, in main
    execute_from_command_line(sys.argv)
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/core/management/__init__.py", line 442, in execute_from_command_line
    utility.execute()
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/core/management/__init__.py", line 436, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/core/management/base.py", line 412, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/core/management/base.py", line 458, in execute
    output = self.handle(*args, **options)
  File "/var/www/tracebase/DataRepo/models/maintained_model.py", line 1232, in wrapper
    fn(*args, **kwargs)
  File "/var/www/tracebase/DataRepo/management/commands/load_animals_and_samples.py", line 192, in handle
    loader.load_sample_table(
  File "/var/www/tracebase/DataRepo/models/maintained_model.py", line 1232, in wrapper
    fn(*args, **kwargs)
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 253, in load_sample_table
    raise e
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 237, in load_sample_table
    self._load_data(data)
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 288, in _load_data
    infusate_rec = self.get_or_create_infusate(rownum, row)
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 496, in get_or_create_infusate
    infusate_data_object = parse_infusate_name(infusate_str, tracer_concs)
  File "/var/www/tracebase/DataRepo/utils/infusate_name_parser.py", line 102, in parse_infusate_name
    "tracer": parse_tracer_string(tracer_string),
  File "/var/www/tracebase/DataRepo/utils/infusate_name_parser.py", line 124, in parse_tracer_string
    tracer_data["isotopes"] = parse_isotope_string(match.group("isotopes").strip())
  File "/var/www/tracebase/DataRepo/utils/infusate_name_parser.py", line 176, in parse_isotope_string
    raise IsotopeParsingError(
DataRepo.utils.infusate_name_parser.IsotopeParsingError: One or more encoded isotopes in [13C6, 15N3] could not be parsed. Only the following were parsed: [13C6,15N3].

Expected behavior

The tracer would be parsed and loaded correctly.

Suggested Change

None provided

Comment

None

---

ISSUE OWNER SECTION

Assumptions

1. List of assumptions made WRT the code
2. E.g. We will assume input is correct (explaining why there is no validation)

Limitations

1. A list of things this work will specifically not do
2. E.g. This feature will only handle the most frequent use case X

Affected Components

• change: File path or DB table ...
• add: Environment variable or server setting
• delete: External executable or cron job

Requirements

• [ ] 1. List of numbered conditions to be met for the feature
• [ ] 2. E.g. Every column/row must display a value, i.e. cannot be empty
• [ ] 3. Numbers for reference & checkboxes for progress tracking

DESIGN

GUI Change description

None provided

Code Change Description

None provided

Tests

• [ ] 1. A description of at least one test for each requirement above.
• [ ] 2. E.g. Test for req 2 that there's an exception when display value is ''
• [ ] 3. Numbers for reference & checkboxes for progress tracking