Can't duplicate sample_name

[nsheff]

If I have a sample sheet with sample but not sample_name columns, I should be able to:

pep_version: "2.0.0"
sample_table: "samplesheet_test.csv"

sample_modifiers:
  duplicate:
    sample: sample_name

But this leads to:

Traceback (most recent call last):
  File "/home/nsheff/.local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2895, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'sample_name'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/nsheff/.local/bin/eido", line 8, in <module>
    sys.exit(main())
  File "/home/nsheff/.local/lib/python3.8/site-packages/eido/eido.py", line 352, in main
    inspect_project(p, args.sample_name, args.attr_limit)
  File "/home/nsheff/.local/lib/python3.8/site-packages/eido/eido.py", line 302, in inspect_project
    print(p)
  File "/home/nsheff/.local/lib/python3.8/site-packages/peppy/project.py", line 581, in __str__
    sample_names = list(self[SAMPLE_DF_KEY][self.sample_name_colname])
  File "/home/nsheff/.local/lib/python3.8/site-packages/pandas/core/frame.py", line 2902, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/home/nsheff/.local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc
    raise KeyError(key) from err
KeyError: 'sample_name'

I think it may check for sample_name too early.

[stolarczyk]

I seem to be able to instantiate such a peppy.Project object. What did you actually execute? Maybe that's actually a problem in eido or looper? I see some eido code in the traceback.

[stolarczyk]

I got the same result when ran:

eido inspect <cfg>

I'm transferring this to eido

[stolarczyk]

that's an issue in peppy.Project.__str__, that's why it was pronounced only in eido inspect. Moving back to peppy...