From: Pablo C. <pc...@cn...> - 2018-03-09 15:39:44
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Excellent! Just keep us on the loop if you struggle with something. On 09/03/18 14:00, Kyle Douglass wrote: > > Dear Pablo and Jose Miguel, > > Thank you very much for your help. The ability to generate a project > and workflow based on a JSON template is exactly what I was looking > for. I should furthermore be able to figure out the Python API from > the .py files you mentioned. > > Cheers, > > Kyle > > > On 03/09/2018 01:40 PM, Pablo Conesa wrote: >> >> Thanks Jose....additionally you can have a look to this: >> >> https://github.com/I2PC/scipion/wiki/Streaming-Processing#kicking-off-scipion-in-your-pipeline >> >> I've just added today since I had to explain this to a facilitiy >> manager that had the same /similar question >> >> Feel free to ask...this is that first version and it can be more >> clear., may be?. >> >> >> On 09/03/18 10:40, Jose Miguel de la Rosa Trevin wrote: >>> Hi Kyle, >>> >>> Unfortunately we haven't documented the API that well...this is a >>> pending task. >>> Nonetheless you have some developers documentation here: >>> https://github.com/I2PC/scipion/wiki/Developers-Page >>> I would recommend to take a look at the "How to create a protocol page": >>> https://github.com/I2PC/scipion/wiki/Creating-a-Protocol >>> >>> I will recommend to look at the Python code, specially the following: >>> - Object (basic wrapper around Python types that can be >>> stored/retrieved), pyworkflow/object.py >>> - Protocol (basic execution unit:Manager (to deal we projects): >>> pyworkflow/protocol/protocol.py >>> - Project (managing a given project) pyworkflow/project.py >>> - Manager: pyworkflow/manager.py >>> >>> Feel free to provide any feedback, >>> Best, >>> Jose Miguel >>> >>> >>> On Fri, Mar 9, 2018 at 11:15 AM, Kyle Douglass >>> <kyl...@ep... <mailto:kyl...@ep...>> wrote: >>> >>> Hi Jose Miguel, >>> >>> >>> On 03/09/2018 09:23 AM, Jose Miguel de la Rosa Trevin wrote: >>> >>>> You can easily do what you want in a Python script via our API. >>>> Basically you will need to create a new project and then load the >>>> given .json file. Take a look at the following example here: >>>> >>>> https://github.com/delarosatrevin/scipion-session/blob/f2ac1934f24ebcf0c3da205e9878eca86e4d80a4/aarhus/new-session-aarhus.py#L60 >>>> <https://github.com/delarosatrevin/scipion-session/blob/f2ac1934f24ebcf0c3da205e9878eca86e4d80a4/aarhus/new-session-aarhus.py#L60> >>>> >>> >>> Thanks for the swift response! Indeed, I think that this is the >>> solution I am looking for. >>> >>> Is the Python API documented anywhere, or should I focus on >>> extracting the main functions by looking at the Python code itself? >>> >>> Thanks again, >>> >>> Kyle >>> >>> -- >>> Kyle M. Douglass, PhD >>> Post-doctoral researcher >>> The Laboratory of Experimental Biophysics >>> EPFL, Lausanne, Switzerland >>> http://kmdouglass.github.io >>> http://leb.epfl.ch >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Kyle M. Douglass, PhD > Post-doctoral researcher > The Laboratory of Experimental Biophysics > EPFL, Lausanne, Switzerland > http://kmdouglass.github.io > http://leb.epfl.ch > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |