Menu
▾
▴
Re: [scipion-users] Creating a project and loading a workflow from the command line
|
From: Kyle D. <kyl...@ep...> - 2018-03-09 14:00:29
|
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 |
