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2.0 9.0 0.0 13.24 MB

Data extraction, transformation and loading pipeline for the Princess Maxima Center

License: MIT License

Python 97.95% Shell 2.05%
luigi transmart cbioportal

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alepev avatar ewelinagr avatar forus avatar gijskant avatar jankanis avatar jochemb avatar spayralbe avatar wardweistra avatar wibo-pipping avatar

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pmc-conversion's Issues

Can't run individual task because of input signal file

@forus What is the purpose of comparing the input signal file with done file? A pipeline can run sequentially even without input signal files and without a requirement function. To check if a task has completed, the task itself can return a success.

To run the entire pipeline, we use python -m luigi --module scripts LoadDataFromNewFilesTask

If we remove the dependency of input signal files, we can run individual tasks, such as python -m luigi --module scripts CbioportalDataValidation without an error. This is also useful for unit testing, right?

This is the error I receive now when I only run CbioportalDataValidation

DEBUG: No input signal file specified. Create done signal file in the current directory.
ERROR: [pid 18307] Worker Worker(salt=127452127, workers=1, host=Sanders-MacBook-Pro.local, username=sander, pid=18307) failed    CbioportalDataValidation()
Traceback (most recent call last):
  File "/Users/sander/anaconda/envs/Python36/lib/python3.6/site-packages/luigi/worker.py", line 204, in run
    expl = self.task.on_success()
  File "/Users/sander/Data/Project_Princess/05_Pipeline/scripts/luigi_commons.py", line 107, in on_success
    f.write(self.calc_done_signal())
  File "/Users/sander/Data/Project_Princess/05_Pipeline/scripts/luigi_commons.py", line 92, in calc_done_signal
    input_signal_file = self.input_signal_file[0]
IndexError: list index out of range
DEBUG: 1 running tasks, waiting for next task to finish
INFO: Informed scheduler that task   CbioportalDataValidation__99914b932b   has status   FAILED

Pipeline succeeds when loading to cBioPortal fails

When the data loading step for cBioPortal fails, the data loading task still succeeds. Probably this is due to the concatenation of commands in https://github.com/thehyve/pmc-conversion/blob/master/luigi-pipeline/main.py#L280, https://github.com/thehyve/pmc-conversion/blob/master/luigi-pipeline/main.py#L287. When the last command is successful (restarting the service), the concatenation succeeds as well.
This is probably fixed by replacing ; by &&.

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