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OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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Using DataWarrior #385

Open drc007 opened 8 years ago

drc007 commented 8 years ago

DataWarrior (http://www.openmolecules.org/datawarrior/) is a free cheminformatics visualisation program. At the moment getting data into this program is a little tedious, but DataWarrior does have a scripting/macro interface. If anyone has any experience in using this facility it might be very useful if they could use it to provide a way to seamlessly import the latest OSM directly into DataWarrior.

drc007 commented 8 years ago

If it helps I've written an iPython notebook to access the data http://www.macinchem.org/reviews/osm/osmipython.php and a script for Vortex http://www.macinchem.org/reviews/vortex/tut26/scripting_vortex26.php

neilfws commented 8 years ago

By "seamlessly import", do you mean directly from the online Google spreadsheet?

I looked at DataWarrior and I don't think there is a way to import from online tabular data sources. The best I could do was export the Google document as TSV and open that from disk, which seemed to work well. I don't see how macros could improve that process.

drc007 commented 8 years ago

Ideally it would be simply clicking a button or selecting a menu item like the Vortex script. I don't know enough about DataWarrior to know if this is possible.

MFernflower commented 8 years ago

Perhaps ask the datawarrior people to add an import from google spreadsheet button? As datawarrior is made in java this be a trivial task

thsa commented 8 years ago

Loading the data into DataWarrior currently it involves these steps:

For the upcoming version of DataWarrior, which is due in a few weeks, there will be a task to load data directly from any URL. Then, you can configure this task with above URL, put it into a small macro, and save the macro file in the DataWarrior/macros folder. In this case the DataWarrior menu would contain an item to directly retrieve and open the data from the GoogleDoc site.

drc007 commented 8 years ago

@thsa Thanks for the news about the update, sounds perfect.

mattodd commented 8 years ago

This sounds very useful, yes, thanks for the info @thsa. Chris it'd be nice to alert people to this possibility quickly on the 24th (#386) if there's time. Sounds like the kind of thing you were describing.

On 14 May 2016 at 07:03, Chris Swain notifications@github.com wrote:

@thsa https://github.com/thsa Thanks for the news about the update, sounds perfect.

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drc007 commented 8 years ago

@mattodd I agree and it perfectly underlines process of asking a question in an open forum and getting an answer!

MFernflower commented 8 years ago

I had a play with datawarrior myself - It's quite a solid bit of kit and im looking forward to having the OSTB/OSM series in a single .dwar