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kbaseattic / KBaseFBAModeling

Flux balance modeling service. Deploys both the client and service codes.
MIT License
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Error: JSONRPCError: No equal sign in [reaction]! #59

Open Ghabry opened 7 years ago

Ghabry commented 7 years ago

This happens when I'm using a KBase Narrative and import a FBA model (I hope this is the correct place to report issues in the Kbase?)

Model I use: http://bigg.ucsd.edu/models/iJN678 Also fails with other models e.g.: http://bigg.ucsd.edu/models/iMM904

How to reproduce: I do [+] -> Import -> FBA Model -> [Next]

[Model from SBML] -> "IJN678.xml" (from the BIGG page)

Name: Whatever Genome: [Empty] Biomass: R_BIOMASS_SC5_notrace

[Import]

About the Biomass: When I keep this field empty and import I get

Error: JSONRPCError: Biomass bio1 not found! at /kb/module/bin/../lib/Bio/KBase/ObjectAPI/utilities.pm line 291.

Why doesn't the importer automatically determine the biomass function through the fbc:listOfObjectives list instead of failing? Is a bit user unfriendly imo.

Assuming the Biomass function is set to R_BIOMASS_Ec_SynHetero the import is still failing with:

Error: JSONRPCError: No equal sign in R_BIOMASS_Ec_SynHetero! at /kb/module/bin/../lib/Bio/KBase/ObjectAPI/utilities.pm line 291.
    Bio::KBase::ObjectAPI::utilities::error('No equal sign in R_BIOMASS_Ec_SynHetero!') called at /kb/module/bin/../lib/Bio/KBase/ObjectAPI/KBaseFBA/FBAModel.pm line 554
Bio::KBase::ObjectAPI::KBaseFBA::FBAModel::LoadExternalReactionEquation('Bio::KBase::ObjectAPI::KBaseFBA::FBAModel=HASH(0x13b521c0)', 'HASH(0x174682e0)') called at /kb/module/bin/../lib/Bio/KBase/ObjectAPI/KBaseFBA/FBAModel.pm line 278
    Bio::KBase::ObjectAPI::KBaseFBA::FBAModel::adjustBiomassReaction('Bio::KBase::ObjectAPI::KBaseFBA::FBAModel=HASH(0x13b521c0)', 'HASH(0x174683e8)') called at /kb/module/bin/../lib/Bio/KBase/ObjectAPI/functions.pm line 2936
    Bio::KBase::ObjectAPI::functions::func_importmodel('HASH(0x4b68320)') called at /kb/module/bin/../lib/fba_tools/fba_toolsImpl.pm line 1964
    fba_tools::fba_toolsImpl::sbml_file_to_model('fba_tools::fba_toolsImpl=HASH(0x44fe7b0)', 'HASH(0x3e...

No idea what the problem is, I guess "equal sign" is some kind of implementation detail that doesn't really help to find the error :/

meghandrake commented 7 years ago

Hi there! I work on KBase. We have a Help Board where users post their questions, and can view other users' questions and answers from developers! We would love to chat with you more there- this is the link to sign up: http://kbase.us/contact-us/