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cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
MIT License
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document requirement of dpath for script/make_data.py #207

Closed turbomam closed 1 month ago

ddooley commented 3 years ago

More info on this, or close it?

turbomam commented 3 years ago

Normally I would say "add a requirements section to the README", but your README already has a god flow to it

You could make a one-line requirements.txt and assume people know how to use that with pip install -r

ddooley commented 2 years ago

Just to be clear, do you mean instructions for installing make_data.py so it can be run in any directory? If you have an exact requirements.txt line I should add I would appreciate that.

turbomam commented 2 years ago

My original intent was just to communicate that users have to install the dpath module.

The ability to run make_data.py from any template directory without specifying the "full relative" path would be nice, but I wasn't asking for that.

ddooley commented 2 years ago

Ah right! Ok, good, I'll add that requirements.txt into our repo too.

ddooley commented 2 years ago

I've merged your patch. Not sure a version needs to be mentioned for dpath - the script uses the basic dpath stuff.

cmrn-rhi commented 2 years ago

Might it be worth making a "Quick Start script/make_data.py" page in the wiki for new users?

turbomam commented 2 years ago

Might it be worth making a "Quick Start script/make_data.py" page in the wiki for new users?

Yeah. I can help with that if I have sufficient permission.

The requirement for dpath is semi-documented in the linkml-datastructure's requirements.txt now. We would just need to add the standard

Then the user would add their own template folder and LinkML source files and write a Makefile rule based on the provided samples.

Likewise,

ddooley commented 1 month ago

I will close this now. Our code has changed a bit since make_data.py; now it is called tabular_to_schema.py and is run in a particular schema folder (see https://github.com/cidgoh/DataHarmonizer/wiki/DataHarmonizer-Templates). Soon a change will be implemented so that people can work on templates independently of a DataHarmonizer source code installation.