MetaboFBAPkg example

import sys
import cobra
import cplex
import cobrakbase
#Put the path to ModelSEEDpy on your machine here
sys.path.append("/Users/chenry/code/ModelSEEDpy")
#import modelseedpy.fbapkg
from modelseedpy import GapfillingPkg, KBaseMediaPkg, MetaboFBAPkg
from modelseedpy import FBAHelper

cobrakbase 0.2.7

kbase_api = cobrakbase.KBaseAPI()
model = kbase_api.get_from_ws("test_model",18528)
pickaxe_model = kbase_api.get_from_ws("MMSyn3Expansion",29280)
model.solver = 'optlang-cplex'
template = kbase_api.get_from_ws("GramNegModelTemplateV3","NewKBaseModelTemplates")
media = kbase_api.get_from_ws("Carbon-D-Glucose","KBaseMedia")
metabolome = kbase_api.get_from_ws("JCVI_Syn3_metabolomics",29280)
FBAHelper.set_objective_from_target_reaction(model,"bio1")
copy_model = cobra.io.json.from_json(cobra.io.json.to_json(model))
gfp = GapfillingPkg(copy_model)
gfp.build_package({
    "default_gapfill_models":[pickaxe_model]
    "default_gapfill_templates":[template],
    "gapfill_all_indecies_with_default_templates":1,
    "minimum_obj":0.01,
    "set_objective":0
})
kmp = KBaseMediaPkg(copy_model)
kmp.build_package(media)
mfp = MetaboFBAPkg(copy_model)
mfp.build_package({"peaks":metabolome.build_peaks_data(),"set_objective":1})
sol=model.optimize()
with open('MetaboFBA.lp', 'w') as out:
    out.write(str(model.solver))
#Next minimize active reactions
model.summary()

cobra.io.save_json_model(model,filename)

  File "<ipython-input-1-9c96e9aed238>", line 18
    mfp.build_package({"peaks":[{"id":"peak.1","inchi":,"set_objective":1})
                                                       ^
SyntaxError: invalid syntax