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Harmonize user configuration #146

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afaulconbridge opened this issue Oct 2, 2018 · 4 comments

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commented Oct 2, 2018

When running various parts of the pipeline (e.g. data_pipeline, evidence_datasource_parsers etc) some things users want to customise are command line arguments, some are environment variables, and some are ini files (and still some are by editing the code directly).

We should bring all of these together, and use a single system to manage them e.g. https://github.com/bw2/ConfigArgParse This will make it easier for ourselves to run and maintain, and easier for users to run too.

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commented Dec 6, 2018

@Docproc will take a look at the DATASOURCE_TO_DATATYPE_MAPPING in Setting.py

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commented Jan 24, 2019

90% of this is done as part of opentargets/data_pipeline#444

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commented Feb 5, 2019

Last few bits will have to roll over into 19.04, updating this ticket.

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commented Apr 1, 2019

Closing this ticket in favour of #532 which details the remaining elasticsearch configuration.

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