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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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gdc_loadfile does not observe or respect datestamps properly #57

Closed noblem closed 6 years ago

noblem commented 6 years ago

Today (2017_09_11) I tried make test_loadfile from a directory tree in which I had not done test_mirror and test_dice since 2017_07_19:

ls sandbox/mirror/TCGA/TCGA-ACC/metadata/ 2017_07_19

But, instead of gdc_loadfile discovering the 2017_07_09 data and using it, it complained that there was no 2017_09_11 data instead!


2017-09-11 18:33:46,245[ERROR]: Create Loadfile FAILED:
Traceback (most recent call last):
  File "../gdctools/gdc_loadfile.py", line 321, in execute
    (projects, annotations) = self.inspect_data()
  File "../gdctools/gdc_loadfile.py", line 113, in inspect_data
    metapath = get_diced_metadata(projname, projpath, self.datestamp)
  File "../gdctools/gdc_loadfile.py", line 357, in get_diced_metadata
    raise ValueError("Could not find dice metadata for " + project + " on " + datestamp)
ValueError: Could not find dice metadata for TCGA-ACC on 2017_09_11```
noblem commented 6 years ago

This is related to #47

noblem commented 6 years ago

Fixed in v0.2.5, commit https://github.com/broadinstitute/gdctools/commit/df437aba5baf8d4204a45577d4968ba6bf4e15fe