thehyve / pmc-conversion Goto Github PK
View Code? Open in Web Editor NEWData extraction, transformation and loading pipeline for the Princess Maxima Center
License: MIT License
Data extraction, transformation and loading pipeline for the Princess Maxima Center
License: MIT License
@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
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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