Regarding the runtime images, I talked to the infrastructure group several times about creating new images, but they haven't had a chance (or it hasn't been a high enough priority). The last time runtime images were created for download was October 2013. I declared in May 2014 (see https://atlassian.kbase.us/browse/KBASE-760) that if there wasn't time/resources to create new images, then I would take down the downloads page, rather than offer out-of-date images that would only create confusion for users and hassle for us as users submitted bug reports. I took the downloads page down in July 2014. We can quickly put it back up whenever the release team has time to create new images.
In the meantime, the suggestion to create a script and then upload it to IRIS seems like the best advice. Is there any way for us to create a script for downloading metabolic models (even if the users needed to edit it a bit to get exactly what they wanted? We could perhaps give them a skeleton of a script?).
Nomi
On Aug 29, 2014, at 7:26 AM, Michael Mundy (JIRA) <help(a)kbase.us> wrote:
>
>
>
> Michael Mundy commented on KBASE-620
> Help Downloading Metabolic Models
> There is a way to script in IRIS but it is limited. You can save commands in a file and then run all of the commands from the file using "execute". Unfortunately there are no variables or control flow features in IRIS scripting. You could generate the file with your favorite scripting language on your computer and then upload the script to IRIS. Run "whatsnew" from the IRIS command line to get some details on the scripting support.
>
> Using the restful API or command line is difficult right now with no pre-built client image available. Building your own client image can be done but that is not in a very good state at the moment. The fba modeling service has dependencies on the typecomp, kb_seed, workspace_service, auth, idserver, kb_model_seed, probabilistic_annotation, and workspace_deluxe services. I'm pretty sure the workspace_service and auth repos are not moving to github so you can't build fba modeling unless you have a developer account. And you would still need to track down a runtime image and I don't think there is a current image that is publicly available.
>
> Do we know what language the user wants to use when accessing the restful API? With Python it might be possible to grab the Client.py file and get something to work. Also, what type of system is the user running on (Linux, Mac, etc.)?
>
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i’m ok with just sending it out.
On Aug 20, 2014, at 2:14 PM, Nomi Harris <nlharris(a)gmail.com> wrote:
> Dear Release Team,
> Erik and I are starting a review of all the service documentation (including API docs, release notes, and tutorials). In order to make sure our list of services is current and complete, we need to update the master Services spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) Erik had the good suggestion that we should add a column where the service owner can indicate that they have updated or verified the information for their service—I have added column H for this purpose.
>
> Should I go ahead and send a note to kbase-devel to ask people to update that spreadsheet (adding any missing services, striking out obsolete ones, changing info as needed), or do you guys want a chance to work on it before I send that out?
>
> Thanks,
> Nomi
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Dear Release Team,
Erik and I are starting a review of all the service documentation (including API docs, release notes, and tutorials). In order to make sure our list of services is current and complete, we need to update the master Services spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) Erik had the good suggestion that we should add a column where the service owner can indicate that they have updated or verified the information for their service—I have added column H for this purpose.
Should I go ahead and send a note to kbase-devel to ask people to update that spreadsheet (adding any missing services, striking out obsolete ones, changing info as needed), or do you guys want a chance to work on it before I send that out?
Thanks,
Nomi
