Template selection during model reconstruction

[ctseto]

Having problems with model template selection during reconstruction.

This involves the params['template_model']. Despite my attempt to pass a custom parameter, it consistently defaults to /chenry/public/modelsupport/templates/GramNegative.modeltemplate . Even attempts to pass a different /chenry/ modeltemplate defaults to GramNegative.

[samseaver]

Do you still have this problem, I've used this successfully:

my $parameters = { genome => "/seaver/plantseed/Athaliana-TAIR10/genome",
                   templatemodel => "/plantseed/Data/plant.modeltemplate"}

[samseaver]

Actually, looking at what you wrote, you're using a hyphen in the parameter name.

[ctseto]

To clarify, I am using Mike Mundy's mackinac to reconstruct modelseed models. There, reconstruction is invoked by:

mackinac.reconstruct_modelseed_model('1679.26',template_reference='/mmundy/public/modelsupport/templates/MicrobialPositiveResolved.modeltemplate')

There's a few layers of abstraction between Mackinac and what gets sent to ModelSEED.

template_reference is specified in input, attached to a dict, which is then passed to ModelSEED.

    request_data = dict()
    request_data['method'] = self.name + '.' + method #where in our case, method is 'ModelReconstruction'
    request_data['params'] = params #in our case, params['template_model'] is a string corresponding to the location of the desired template
    request_data['version'] = '1.1'
    request_data['id'] = '1'

The server request is simply:
requests.post(self.url, data=json.dumps(request_data), headers=self.headers, timeout=timeout)

I was assuming that something broke in the chain between Mackinac and what is being passed to the server and back, but instead of failing verbosely it may just be defaulting, since template_reference being output is:

'template_ref': u'/chenry/public/modelsupport/templates/GramNegative.modeltemplate'

[samseaver]

I just tested this, by passing a separate template with the template_model parameter, and it worked for me, here's a summary of my output before and after:

seaver@twig:~$ ws-cat /seaver/plantseed/Athaliana-TAIR10/model --shock | perl -MJSON -lne 'use JSON;print to_json(from_json($_),{pretty=>1})' | grep template_ref
   "template_ref" : "/chenry/public/modelsupport/templates/plant.modeltemplate||",
seaver@twig:~$ ws-cat /seaver/plantseed/Athaliana-TAIR10/model --shock | perl -MJSON -lne 'use JSON;print to_json(from_json($_),{pretty=>1})' | grep template_ref
   "template_ref" : "/seaver/plantseed/Templates/plant.modeltemplate||"

By output, I was assuming that you're saying that you checked inside the resulting model.

I ran ModelReconstruction directly using ProbModelSEEDHelper.pm, are you able to write a piece of code that calls this directly, and confirm that it works for you?