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pepkit / pipestat

Pipeline results reporting package
https://pep.databio.org/pipestat/
BSD 2-Clause "Simplified" License
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Quickstart example does not work #153

Closed simeoncarstens closed 4 months ago

simeoncarstens commented 5 months ago

The quickstart example on https://pep.databio.org/pipestat/ does not work. After installing pipestat in a virtual environment, setting the environment variables and creating the output_schema.yaml file, running pipestat report -i result_name -v 1.1 makes pipestat yell at me:

$ pipestat report -i result_name -v 1.1
Could not locate config file.
Traceback (most recent call last):
  File "/home/simeon/projects/uva/pipestat/.venv/bin/pipestat", line 8, in <module>
    sys.exit(main())
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/cli.py", line 113, in main
    psm = PipestatManager(
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/pipestat.py", line 175, in __init__
    self.process_schema(schema_path)
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/pipestat.py", line 499, in process_schema
    parsed_schema = ParsedSchema(schema_to_read)
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/parsed_schema.py", line 140, in __init__
    raise SchemaError(
pipestat.exceptions.SchemaError: Could not find valid pipeline identifier (key 'pipeline_name') in given schema data

If I then add the following line:

pipeline_name: "my_pipeline"

to output_schema.yaml, this particular problem seems to be solved, but it then throws another error:

Could not locate config file.
Traceback (most recent call last):
  File "/home/simeon/projects/uva/pipestat/.venv/bin/pipestat", line 8, in <module>
    sys.exit(main())
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/cli.py", line 113, in main
    psm = PipestatManager(
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/pipestat.py", line 175, in __init__
    self.process_schema(schema_path)
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/pipestat.py", line 499, in process_schema
    parsed_schema = ParsedSchema(schema_to_read)
  File "/home/simeon/projects/uva/pipestat/.venv/lib/python3.10/site-packages/pipestat/parsed_schema.py", line 146, in __init__
    raise SchemaError("Neither sample-level nor project-level data items are declared.")
pipestat.exceptions.SchemaError: Neither sample-level nor project-level data items are declared.

at which point I gave up. So I guess this example would need to be updated :slightly_smiling_face:

donaldcampbelljr commented 5 months ago

Thanks for flagging this. I've merged the changes to dev! I've updated the README here in pipestat as well as at our new documentation page: https://pep.databio.org/pipestat/