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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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python3 test failing, due to code from methylation branch #60

Closed noblem closed 5 years ago

noblem commented 6 years ago

cd tests make test3

... snip ...

Test dice: on subset of cohorts, to show CLI args override config file set -o pipefail && env PYTHONPATH=.. /usr/local/bin/python3 ../gdctools/gdc_dice.py --config tcgaSmoketest.cfg --projects TCGA-ACC TCGA-SKCM TCGA-ESCA 2>&1 | tee test_dice.log | egrep "Dicing TCGA|date" 2017-09-15 23:48:27,330[INFO]: Mirror date: 2017_09_15 2017-09-15 23:48:27,331[INFO]: Dicing TCGA-ACC to sandbox/dice/TCGA/TCGA-ACC /Users/mnoble/src.local/gdctools/util/checkError.sh test_dice.log Traceback (most recent call last): File "../gdctools/gdc_dice.py", line 231, in execute File "../gdctools/gdc_dice.py", line 176, in dice File "../gdctools/gdc_dice.py", line 393, in dice_one File "../gdctools/gdc_dice.py", line 609, in usc_meth2magetab File "/Users/mnoble/src.local/gdctools/gdctools/lib/convert/tsv2magetab.py", line 41, in process writeCsvFile(filepath, csvfile_with_new_column_order) File "/Users/mnoble/src.local/gdctools/gdctools/lib/common.py", line 155, in writeCsvFile File "/Users/mnoble/src.local/gdctools/gdctools/lib/common.py", line 144, in rearrange_columns TypeError: object of type 'map' has no len() make[1]: [test_dice] Error 1 make: [test3] Error 2

noblem commented 5 years ago

The viability of Python3 testing has been re-established many times since this issue was first written, therefore marking closed.