Saving intermediate work

[wrcannon]

Hi,
I've got a parsed sbml model that includes all of my submodels. I then join all of the sub graphs but don't link any metabolites. I would like to save it as a sammi model so that I can come back to it later. But when I save as a sammi model in the Downloads menu, the model gets saved as JSON, but when I try to read it in later as a sammi or sbml model nothing shows up in the tool.

[schultzdre]

When you download the map are you downloading using the "Download SAMMI" option to save it as a JSON? Then when uploading it are you uploading it using the "Load SAMMI model" option? If so it seems to be working with the models I am trying out. If you are willing to share the model you are having trouble with I can try to help.

[wrcannon]

Hi Andre, Thanks for getting back to me. Great tool – thanks for making it. Yes, that is what I did. When I examine the file that is generated by “Download SAMMI”, it looks fine. But when I try to read it in using “Load SAMMI Model”, the new canvas appears but it is blank. If I try to search for any reaction/metabolite, nothing is found, so I don’t think that it is the case that the map if just off the canvas. I’ve attached the file that was generated using “Download SAMMI”. Strangely enough, if I initially read in the model without parsing, then I can export it as SAMMI and read in back in without a problem. Bill From: Andre Schultz <notifications@github.com> Reply-To: MD-Anderson-Bioinformatics/SAMMI <reply@reply.github.com> Date: Monday, July 27, 2020 at 6:42 PM To: MD-Anderson-Bioinformatics/SAMMI <SAMMI@noreply.github.com> Cc: "Cannon, William R" <William.Cannon@pnnl.gov>, Author <author@noreply.github.com> Subject: Re: [MD-Anderson-Bioinformatics/SAMMI] Saving intermediate work (#4) When you download the map are you downloading using the "Download SAMMI" option to save it as a JSON? Then when uploading it are you uploading it using the "Load SAMMI model" option? If so it seems to be working with the models I am trying out. If you are willing to share the model you are having trouble with I can try to help. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADTGAVDPRCRSYXM26WWQRKTR5YUF5ANCNFSM4PIEFXDA>.

[schultzdre]

Hi Bill,
For some reason rxncolorbreaks was exported as a null vector. That is currently breaking the code. Replace "rxncolorbreaks": [null,null] with "rxncolorbreaks": [-1,1] in your exported file and it should work. I will include a fix for this in upcoming versions.
Thanks again