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Princeton-LSI-ResearchComputing / tracebase

Mouse Metabolite Tracing Data Repository for the Rabinowitz Lab
MIT License
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Sample table error reporting throws an exception instead of reporting the missing record (e.g. missing tissue) #951

Closed lparsons closed 2 months ago

lparsons commented 2 months ago

BUG DESCRIPTION

Problem

The sample table loader error reporting can throw and exception attempting to format an error message.

  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 397, in get_tissue
    rownum=row.name + 2,
AttributeError: 'dict' object has no attribute 'name'

Steps to reproduce

  1. Attempt to load the following study doc: col013a_tracebase_studydoc.xlsx 
    python manage.py load_animals_and_samples --animal-and-sample-table-filename "col013a_tracebase_studydoc.xlsx"

Current behavior

Importing animals and samples...
Registering class Tracer as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.tracer.Tracer'>
Validating Tracer updater: {'update_function': '_name', 'update_field': 'name', 'parent_field': 'infusates', 'child_fields': [], 'update_label': 'name', 'generation': 2}
Inserting infusate histidine-[13C6,15N3]
Registering class Infusate as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.infusate.Infusate'>
Validating Infusate updater: {'update_function': '_name', 'update_field': 'name', 'parent_field': None, 'child_fields': [], 'update_label': 'name', 'generation': 0}
Adding propagation handler to Infusate.tracers.through
Registering class InfusateTracer as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.infusate_tracer.InfusateTracer'>
Validating InfusateTracer updater: {'update_function': '_name', 'update_field': None, 'parent_field': 'infusate', 'child_fields': [], 'update_label': 'name', 'generation': 1}
Registering class Animal as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.animal.Animal'>
Validating Animal updater: {'update_function': '_last_serum_sample', 'update_field': 'last_serum_sample', 'parent_field': None, 'child_fields': ['samples'], 'update_label': 'fcirc_calcs', 'generation': 0}
Adding propagation handler to Animal.studies.through
Getting cache Animal.389.tracers
Registering class Sample as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.sample.Sample'>
Validating Sample updater: {'update_function': '_is_serum_sample', 'update_field': 'is_serum_sample', 'parent_field': 'animal', 'child_fields': ['fcircs'], 'update_label': 'fcirc_calcs', 'generation': 1}
Registering class TracerLabel as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.tracer_label.TracerLabel'>
Validating TracerLabel updater: {'update_function': '_name', 'update_field': 'name', 'parent_field': 'tracer', 'child_fields': [], 'update_label': 'name', 'generation': 3}
Registering class FCirc as a MaintainedModel from _maintained_model_setup: <class 'DataRepo.models.fcirc.FCirc'>
Validating FCirc updater: {'update_function': 'is_last_serum_peak_group', 'update_field': 'is_last', 'parent_field': 'serum_sample', 'child_fields': [], 'update_label': 'fcirc_calcs', 'generation': 2}
Traceback (most recent call last):
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 391, in get_tissue
    tissue_rec = Tissue.objects.get(name=tissue_name)
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/db/models/manager.py", line 87, in manager_method
    return getattr(self.get_queryset(), name)(*args, **kwargs)
  File "/usr/local/tracebase/lib/python3.9/site-packages/django/db/models/query.py", line 637, in get
    raise self.model.DoesNotExist(
DataRepo.models.tissue.Tissue.DoesNotExist: Tissue matching query does not exist.

During handling of the above exception, another exception occurred:

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 283, in _load_data
    tissue_rec, is_blank = self.get_tissue(rownum, row)
  File "/var/www/tracebase/DataRepo/loaders/sample_table_loader.py", line 397, in get_tissue
    rownum=row.name + 2,
AttributeError: 'dict' object has no attribute 'name'

Expected behavior

The error regarding the missing tissue record would be reported and include at least the tissue in question.

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

Requirements

DESIGN

GUI Change description

None provided

Code Change Description

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Tests