The build should be completed this week and all deployed commands should be accessible in IRIS. If the communities API service had problems, you should be able to determine that by looking at the Services sheet (https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8zN0Y...) and/or checking with Miriam. Not sure why you would think Adam and Rick would have any info about that. Note that there's an open ticket https://atlassian.kbase.us/browse/KBASE-146 about communities_api Not sure if that got fixed.
I can see two reasons the scripts not being found in IRIS: All scripts are prefixed and have to follow a naming convention now. So get_metagenome.pl will be mg-get-metagenome. Did you try with the prefix? All commands will still work with their old command names for a while (months, at least).
Nomi On Sep 16, 2013, at 9:54 AM, Dylan Chivian <[email protected]> wrote:
Hi Andreas,
frankly I'm using the REST interface directly, not the Perl API nor IRIS. I was asking because I did go to IRIS just to check some of the Tree stuff and noticed that the Communities API methods are not in the list of modules nor do they show up when you run "commands". Perhaps they just haven't been deployed to the public site yet? What's the ETA on that?
Thanks, - Dylan
On Mon, Sep 16, 2013 at 6:56 AM, Andreas Wilke <[email protected]> wrote: Hi Dylan,
On Sep 13, 2013, at 9:44 PM, Dylan Chivian <[email protected]> wrote:
I'm not seeing the Communities API methods on the live IRIS. Where did it go?
The API is accessible via http or language specific libraries. The best way to use the libraries is starting your own VM with KBase runtime and do the following steps: ssh [email protected] sudo -u root -H bash # check out dev_container and setup dev environment # deployment is always from a dev_container cd /kb git clone [email protected]:dev_container.git cd dev_container ./bootstrap /kb/runtime source user-env.sh cd modules # check out all required modules git clone [email protected]:communities_api.git git clone [email protected]:idserver.git git clone [email protected]:typecomp.git git clone [email protected]:auth cd .. ./bootstrap /kb/runtime source user-env.sh # check the make output it will tell you if required modules/dependencies are missing make # deploy make deploy # now source the deployment environment and start using the scripts or APIs cd /kb/deployment source user-env.sh # execute scripts mg-get-metagenome-list --help # use libraries: use CommunitiesAPIClient; use Bio::KBase::Exceptions; my $client = new CommunitiesAPIClient($host);
The communities command line scripts will be accessible through IRIS after successful deployment and test. I don't know when IRIS gets updated with new scripts after a successful deployment. Despite this I can see two reasons the scripts not being found in IRIS: All scripts are prefixed and have to follow a naming convention now. So get_metagenome.pl will be mg-get-metagenome. Did you try with the prefix? As you know everything in KBase has to follow the deployment procedure and pass "make deploy" and "make test" automatically. If something went wrong there scripts won't be deployed either. In addition there is the COMMANDS file, only scripts matching the pattern in the COMMANDS file will be deployed in IRIS. I have to touch base with the deployment and testing team to get a report but I expect them to show up in IRIS this week.
Keep in mind that IRIS is a front-end and not suited for search/indexing tasks and that all KBase services/products have to have a Makefile following the deployment rules. It did cost me some time in the beginning to adapt and be compliant.
Andreas
Thanks, - Dylan
Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 240 , 4F8 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax)