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Sage-Bionetworks / Genie

Validation and processing of GENIE files
https://genie.synapse.org/
MIT License
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[GEN-177] HOTFIX - Lock down pandas version #482

Closed thomasyu888 closed 1 year ago

thomasyu888 commented 1 year ago

The latest pandas version is not backwards compatible and causes an error like:

  Traceback (most recent call last):
    File "/root/Genie/bin/input_to_database.py", line 190, in <module>
      main(
    File "/root/Genie/bin/input_to_database.py", line 118, in main
      input_to_database.center_input_to_database(
    File "/root/Genie/genie/input_to_database.py", line 854, in center_input_to_database
      processfiles(
    File "/root/Genie/genie/input_to_database.py", line 360, in processfiles
      processor.process(
    File "/root/Genie/genie/example_filetype_format.py", line 152, in process
      preprocess_args = self.preprocess(kwargs.get("newPath"))
    File "/root/Genie/genie_registry/clinical.py", line 394, in preprocess
      clinicalTemplate = pd.DataFrame(columns=set(patient_cols + sample_cols))
    File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 639, in __init__
      raise ValueError("columns cannot be a set")
  ValueError: columns cannot be a set

This is a temporary remediation to the problem...