September 2013 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] IRIS updates
by Land, Miriam L. 28 Sep '13

28 Sep '13

I would vote in favor of leaving jnomics out of the dmg that we are building in order to get the dmg out. Per Tom, we will be doing another build in a couple of weeks. That gives us 2 weeks to fix the problem. Miriam From: Robert Olson <olson(a)mcs.anl.gov<mailto:[email protected]>> Date: Friday, September 27, 2013 5:10 PM To: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]>> Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Subject: Re: [Release-team] Build Status Sept. 27 Current status with the dmg: running into java issues with jnomics. its makefile hardcodes JAVA_HOME:=/kb/runtime/java ANT_HOME:=/kb/runtime/ant THRIFT_HOME:=/kb/runtime/thrift it also does the build on deploy instead of the build step, delaying the appearance of this problem until the dmg packaging pass is underway. --bob On Sep 27, 2013, at 10:58 AM, Thomas Brettin wrote: I do not know what the current status of the dmg is, but I suggested to bob he wait. He was leaning towards doing it anyways.

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Re: [Release-team] Build Status Sept. 27
by Robert Olson 27 Sep '13

27 Sep '13

Current status with the dmg: running into java issues with jnomics. its makefile hardcodes JAVA_HOME:=/kb/runtime/java ANT_HOME:=/kb/runtime/ant THRIFT_HOME:=/kb/runtime/thrift it also does the build on deploy instead of the build step, delaying the appearance of this problem until the dmg packaging pass is underway. --bob On Sep 27, 2013, at 10:58 AM, Thomas Brettin wrote: > I do not know what the current status of the dmg is, but I suggested to bob he wait. He was leaning towards doing it anyways.

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Re: [Release-team] Build Status Sept. 27
by Land, Miriam L. 27 Sep '13

27 Sep '13

I haven't seen a go ahead on FBA. There is invocation and probabilistic annotation. Miriam On 9/27/13 4:18 PM, "Shane Canon" <scanon(a)lbl.gov> wrote: > >Miriam et al, > >Is there anything waiting on a re-deploy? I see FBA, but I wasn't >certain if I needed to retag it or not. >Are there any others that are ready? If so, let me know if they need a >retag. > >--Shane > > >On Sep 27, 2013, at 10:50 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> Tom, >> >> Is it ready to retest? It still has a failed test. >> >> Miriam >> >> On 9/27/13 1:47 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >>> OK, thanks again. >>> >>> Miriam, I don't think we need to do a redeploy. The tag on the cbd repo >>> isn't changing. >>> >>> Tom >>> On Sep 27, 2013, at 12:46 PM, Stephen Chan <sychan(a)lbl.gov> wrote: >>> >>>> Only auth, I didn't want to monkey around with deploying other >>>> stuff when I don't know how the deployment team handles these things. >>>> >>>> Steve >>>> >>>> On Fri, Sep 27, 2013 at 10:34 AM, Thomas Brettin <brettin(a)mcs.anl.gov> >>>> wrote: >>>>> Thanks, >>>>> >>>>> did you deploy only auth, or did you do a full deploy that would have >>>>> included cbd? >>>>> >>>>> t >>>>> >>>>> >>>>> On Sep 27, 2013, at 12:32 PM, Stephen Chan <sychan(a)lbl.gov> wrote: >>>>> >>>>>> Hi Tom, >>>>>> I've tagged the repo as suggested, pulled it down and deployed it >>>>>> on cbd. The master branch of the auth repo passes all perl and >>>>>>python >>>>>> unit tests (we do the dev in other branches) so I believe it to be >>>>>>in >>>>>> a releasable state, inform me immediately if it is not. >>>>>> >>>>>> Miriam thought that there might be a stray space in the COMMANDS >>>>>> file, but I just checked and according to cat -t it is all tabs. If >>>>>> there's another issue with the COMMANDS file, let me know. >>>>>> >>>>>> root@t43:/kb/dev_container/modules/auth# python >>>>>> Python 2.7.2+ (default, Jul 20 2012, 22:15:08) >>>>>> [GCC 4.6.1] on linux2 >>>>>> Type "help", "copyright", "credits" or "license" for more >>>>>>information. >>>>>>>>> import biokbase.nexus >>>>>>>>> biokbase.nexus.__file__ >>>>>> '/kb/deployment/lib/biokbase/nexus/__init__.py' >>>>>>>>> >>>>>> root@t43:/kb/dev_container/modules/auth# cat -t COMMANDS >>>>>> #group-name^Iauth_client^IClient side scripts for authentication >>>>>> #command-set^Iscripts/(.*).pl^Iauth_client >>>>>> root@t43:/kb/dev_container/modules/auth# >>>>>> >>>>>> On Fri, Sep 27, 2013 at 10:00 AM, Thomas Brettin >>>>>> <brettin(a)mcs.anl.gov> wrote: >>>>>>> Yes, ok'd. >>>>>>> >>>>>>> Request you tag the proper commit hash with 20130927-test IF this >>>>>>> commit will work with all the other service modules to the best of >>>>>>> you knowledge. >>>>>>> >>>>>>> Thanks, >>>>>>> Tom >>>>>>> >>>>>>> >>>>>>> On Sep 27, 2013, at 11:56 AM, Stephen Chan <sychan(a)lbl.gov> wrote: >>>>>>> >>>>>>>> I see what the problem is. The makefile for deployment was updated >>>>>>>> on 8/16/2013 (I think it was actually in response to a trouble >>>>>>>> ticket >>>>>>>> from Mike). Prior to that there was a problem in the python >>>>>>>> deployment >>>>>>>> script (Python auth client wasn't fully supported for prod the >>>>>>>> time). >>>>>>>> >>>>>>>> The auth repo on cbd only has commits up to 8/12/2013, so it is >>>>>>>> missing all the subsequent fixes. I can pull down everything up to >>>>>>>> 9/26 and do a re-deploy if the release team okays it. >>>>>>>> >>>>>>>> Steve >>>>>>>> >>>>>>>> On Fri, Sep 27, 2013 at 9:50 AM, Thomas Brettin >>>>>>>> <brettin(a)mcs.anl.gov> wrote: >>>>>>>>> Steve, >>>>>>>>> >>>>>>>>> For what it's worth, auth should have been built off of the >>>>>>>>> 20130926-test tag. >>>>>>>>> >>>>>>>>> Tom >>>>>>>>> On Sep 27, 2013, at 11:43 AM, Stephen Chan <sychan(a)lbl.gov> >>>>>>>>>wrote: >>>>>>>>> >>>>>>>>>> Duh, sorry, my fault, I my coffee hasn't kicked in yet... >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 27, 2013 at 9:43 AM, Stephen Chan <sychan(a)lbl.gov> >>>>>>>>>> wrote: >>>>>>>>>>> Are you missing another ssh into a host like t2? This takes me >>>>>>>>>>>to >>>>>>>>>>> t1, which doesn't have a /kb/deployment directory >>>>>>>>>>> >>>>>>>>>>> Steve >>>>>>>>>>> >>>>>>>>>>> On Fri, Sep 27, 2013 at 9:36 AM, Mundy, Michael B. (Mike) >>>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>>> Steve, >>>>>>>>>>>> >>>>>>>>>>>> Here are the directions I got for accessing the test instance. >>>>>>>>>>>> >>>>>>>>>>>> You can replicate this by logging into the VM using: >>>>>>>>>>>> >>>>>>>>>>>> ssh 140.221.84.191<tel:140.221.84.191> >>>>>>>>>>>> sudo su >>>>>>>>>>>> ssh <module_name> >>>>>>>>>>>> source /kb/deployment/user-env.sh >>>>>>>>>>>> cd /kb/dev_container/modules/<module_name> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>>> mayoclinic.org >>>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 9/27/13 11:32 AM, "Stephen Chan" <sychan(a)lbl.gov> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> It should get created by "make deploy" from the auth repo. >>>>>>>>>>>>> However >>>>>>>>>>>>> the python libraries are only added to the deployment a month >>>>>>>>>>>>> or two >>>>>>>>>>>>> ago, so if we building under an auth repo tagged before those >>>>>>>>>>>>> changes, >>>>>>>>>>>>> it may not show up. You should be able to fix it by checking >>>>>>>>>>>>> out the >>>>>>>>>>>>> dev_container and auth repos and then doing the normal >>>>>>>>>>>>> deployment. >>>>>>>>>>>>> >>>>>>>>>>>>> Is there an magellan instance you want me to login to and >>>>>>>>>>>>>take >>>>>>>>>>>>> a look >>>>>>>>>>>>> at? >>>>>>>>>>>>> >>>>>>>>>>>>> Steve >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, Sep 27, 2013 at 9:28 AM, Mundy, Michael B. (Mike) >>>>>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>>>>> Steve, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Can you help us out here? On the test system for the CBD >>>>>>>>>>>>>> service, there >>>>>>>>>>>>>> is no /kb/deployment/lib/biokbase/nexus directory. The >>>>>>>>>>>>>> directory does >>>>>>>>>>>>>> exist on my development system but I'm not sure how it gets >>>>>>>>>>>>>> created. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>>>>> mayoclinic.org >>>>>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On 9/27/13 11:18 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Mike, we made sure to use the latest type compiler, because >>>>>>>>>>>>>>> of reference >>>>>>>>>>>>>>> to KBase-282. Can you tell us what commit to use for each >>>>>>>>>>>>>>> of Auth and >>>>>>>>>>>>>>> Type compiler? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Sep 27, 2013, at 11:13 AM, "Mundy, Michael B. (Mike)" >>>>>>>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> From the CBD server log file there is this error: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Traceback (most recent call last): >>>>>>>>>>>>>>>> File >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>"/kb/deployment/lib/biokbase/CompressionBasedDistance/Serve >>>>>>>>>>>>>>>>r. >>>>>>>>>>>>>>>> py", >>>>>>>>>>>>>>>> line 10, in <module> >>>>>>>>>>>>>>>> import biokbase.nexus >>>>>>>>>>>>>>>> ImportError: No module named nexus >>>>>>>>>>>>>>>> unable to load app 0 (mountpoint='') (callable not found >>>>>>>>>>>>>>>>or >>>>>>>>>>>>>>>> import >>>>>>>>>>>>>>>> error) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> and looking in /kb/deployment/lib/biokbase on the test >>>>>>>>>>>>>>>> machine there >>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>> no >>>>>>>>>>>>>>>> nexus directory. See Steve Chan's comment from Sep 9 in >>>>>>>>>>>>>>>> JIRA issue >>>>>>>>>>>>>>>> https://atlassian.kbase.us/browse/KBASE-292. I'm not sure >>>>>>>>>>>>>>>> if the auth >>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>> typecomp module is downlevel. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>>>>>>> mayoclinic.org >>>>>>>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On 9/27/13 10:40 AM, "Thomas Brettin" >>>>>>>>>>>>>>>><brettin(a)mcs.anl.gov> >>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We need to figure out what is going on with FBA and CBD. >>>>>>>>>>>>>>>>> I'd really >>>>>>>>>>>>>>>>> like >>>>>>>>>>>>>>>>> to see those included in Iris this week. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Chris, Mike, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Are you aware of what the problems are with these two? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> t >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Sep 27, 2013, at 10:05 AM, "Land, Miriam L." >>>>>>>>>>>>>>>>> <landml(a)ornl.gov> >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Tom, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Below is the build status according to the spreadsheet. >>>>>>>>>>>>>>>>>> If anyone >>>>>>>>>>>>>>>>>> has >>>>>>>>>>>>>>>>>> updates, please contact me or update the spreadsheet. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Typecomp Release Candidate. Deployed. Internal. >>>>>>>>>>>>>>>>>>Will >>>>>>>>>>>>>>>>>> not have >>>>>>>>>>>>>>>>>> testing, release notes, or documentation. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ID server Release Candidate. Added yesterday. >>>>>>>>>>>>>>>>>> Deployed, tested, >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> passed checks for scripts, documentation, and release >>>>>>>>>>>>>>>>>> notes. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> m5nr Waiting on Release Notes - passed deploy, >>>>>>>>>>>>>>>>>>testing, >>>>>>>>>>>>>>>>>> script >>>>>>>>>>>>>>>>>> standards and initial documentation check . Failed the >>>>>>>>>>>>>>>>>> check for >>>>>>>>>>>>>>>>>> release notes. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> communities_api Release Candidate. Passed deploy, >>>>>>>>>>>>>>>>>> testing, script >>>>>>>>>>>>>>>>>> standards, release notes and initial documentation >>>>>>>>>>>>>>>>>>check. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Invocation Waiting on developer - Failed 3rd round of >>>>>>>>>>>>>>>>>> testing >>>>>>>>>>>>>>>>>> (client >>>>>>>>>>>>>>>>>> tests but server tests failes) and there are not >>>>>>>>>>>>>>>>>>updates >>>>>>>>>>>>>>>>>> in the >>>>>>>>>>>>>>>>>> release >>>>>>>>>>>>>>>>>> notes. No report on initial documentation. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> FBAModeling Waiting on developer. Failed 2nd round of >>>>>>>>>>>>>>>>>> testing. >>>>>>>>>>>>>>>>>> Script testing is dependent on the problems found in >>>>>>>>>>>>>>>>>> testing and >>>>>>>>>>>>>>>>>> cannot >>>>>>>>>>>>>>>>>> be completed at this time. Release notes have not been >>>>>>>>>>>>>>>>>> updated. No >>>>>>>>>>>>>>>>>> report on initial documentation. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Compression Base Distance Tentative. One test failed >>>>>>>>>>>>>>>>>> because of >>>>>>>>>>>>>>>>>> problems with the shock module. Everything else has >>>>>>>>>>>>>>>>>> passed. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> shock_service Waiting on developer. Failed 2nd >>>>>>>>>>>>>>>>>>deploy. >>>>>>>>>>>>>>>>>> Failure >>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>> deploy this module will prevent another module from >>>>>>>>>>>>>>>>>> moving forward. >>>>>>>>>>>>>>>>>> Internal service and therefore has no scripts and has >>>>>>>>>>>>>>>>>> relaxed >>>>>>>>>>>>>>>>>> expectations for documentation and release notes. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> awe_service Waiting on developer. Failed 2nd deploy. >>>>>>>>>>>>>>>>>> Internal >>>>>>>>>>>>>>>>>> service and therefore has no scripts and has relaxed >>>>>>>>>>>>>>>>>> expectations >>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>> documentation and release notes. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Miriam >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >> > >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Build Status Sept. 27
by Shane Canon 27 Sep '13

27 Sep '13

Miriam et al, Is there anything waiting on a re-deploy? I see FBA, but I wasn't certain if I needed to retag it or not. Are there any others that are ready? If so, let me know if they need a retag. --Shane On Sep 27, 2013, at 10:50 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > Tom, > > Is it ready to retest? It still has a failed test. > > Miriam > > On 9/27/13 1:47 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > >> OK, thanks again. >> >> Miriam, I don't think we need to do a redeploy. The tag on the cbd repo >> isn't changing. >> >> Tom >> On Sep 27, 2013, at 12:46 PM, Stephen Chan <sychan(a)lbl.gov> wrote: >> >>> Only auth, I didn't want to monkey around with deploying other >>> stuff when I don't know how the deployment team handles these things. >>> >>> Steve >>> >>> On Fri, Sep 27, 2013 at 10:34 AM, Thomas Brettin <brettin(a)mcs.anl.gov> >>> wrote: >>>> Thanks, >>>> >>>> did you deploy only auth, or did you do a full deploy that would have >>>> included cbd? >>>> >>>> t >>>> >>>> >>>> On Sep 27, 2013, at 12:32 PM, Stephen Chan <sychan(a)lbl.gov> wrote: >>>> >>>>> Hi Tom, >>>>> I've tagged the repo as suggested, pulled it down and deployed it >>>>> on cbd. The master branch of the auth repo passes all perl and python >>>>> unit tests (we do the dev in other branches) so I believe it to be in >>>>> a releasable state, inform me immediately if it is not. >>>>> >>>>> Miriam thought that there might be a stray space in the COMMANDS >>>>> file, but I just checked and according to cat -t it is all tabs. If >>>>> there's another issue with the COMMANDS file, let me know. >>>>> >>>>> root@t43:/kb/dev_container/modules/auth# python >>>>> Python 2.7.2+ (default, Jul 20 2012, 22:15:08) >>>>> [GCC 4.6.1] on linux2 >>>>> Type "help", "copyright", "credits" or "license" for more information. >>>>>>>> import biokbase.nexus >>>>>>>> biokbase.nexus.__file__ >>>>> '/kb/deployment/lib/biokbase/nexus/__init__.py' >>>>>>>> >>>>> root@t43:/kb/dev_container/modules/auth# cat -t COMMANDS >>>>> #group-name^Iauth_client^IClient side scripts for authentication >>>>> #command-set^Iscripts/(.*).pl^Iauth_client >>>>> root@t43:/kb/dev_container/modules/auth# >>>>> >>>>> On Fri, Sep 27, 2013 at 10:00 AM, Thomas Brettin >>>>> <brettin(a)mcs.anl.gov> wrote: >>>>>> Yes, ok'd. >>>>>> >>>>>> Request you tag the proper commit hash with 20130927-test IF this >>>>>> commit will work with all the other service modules to the best of >>>>>> you knowledge. >>>>>> >>>>>> Thanks, >>>>>> Tom >>>>>> >>>>>> >>>>>> On Sep 27, 2013, at 11:56 AM, Stephen Chan <sychan(a)lbl.gov> wrote: >>>>>> >>>>>>> I see what the problem is. The makefile for deployment was updated >>>>>>> on 8/16/2013 (I think it was actually in response to a trouble >>>>>>> ticket >>>>>>> from Mike). Prior to that there was a problem in the python >>>>>>> deployment >>>>>>> script (Python auth client wasn't fully supported for prod the >>>>>>> time). >>>>>>> >>>>>>> The auth repo on cbd only has commits up to 8/12/2013, so it is >>>>>>> missing all the subsequent fixes. I can pull down everything up to >>>>>>> 9/26 and do a re-deploy if the release team okays it. >>>>>>> >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 27, 2013 at 9:50 AM, Thomas Brettin >>>>>>> <brettin(a)mcs.anl.gov> wrote: >>>>>>>> Steve, >>>>>>>> >>>>>>>> For what it's worth, auth should have been built off of the >>>>>>>> 20130926-test tag. >>>>>>>> >>>>>>>> Tom >>>>>>>> On Sep 27, 2013, at 11:43 AM, Stephen Chan <sychan(a)lbl.gov> wrote: >>>>>>>> >>>>>>>>> Duh, sorry, my fault, I my coffee hasn't kicked in yet... >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 27, 2013 at 9:43 AM, Stephen Chan <sychan(a)lbl.gov> >>>>>>>>> wrote: >>>>>>>>>> Are you missing another ssh into a host like t2? This takes me to >>>>>>>>>> t1, which doesn't have a /kb/deployment directory >>>>>>>>>> >>>>>>>>>> Steve >>>>>>>>>> >>>>>>>>>> On Fri, Sep 27, 2013 at 9:36 AM, Mundy, Michael B. (Mike) >>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>> Steve, >>>>>>>>>>> >>>>>>>>>>> Here are the directions I got for accessing the test instance. >>>>>>>>>>> >>>>>>>>>>> You can replicate this by logging into the VM using: >>>>>>>>>>> >>>>>>>>>>> ssh 140.221.84.191<tel:140.221.84.191> >>>>>>>>>>> sudo su >>>>>>>>>>> ssh <module_name> >>>>>>>>>>> source /kb/deployment/user-env.sh >>>>>>>>>>> cd /kb/dev_container/modules/<module_name> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>> mayoclinic.org >>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 9/27/13 11:32 AM, "Stephen Chan" <sychan(a)lbl.gov> wrote: >>>>>>>>>>> >>>>>>>>>>>> It should get created by "make deploy" from the auth repo. >>>>>>>>>>>> However >>>>>>>>>>>> the python libraries are only added to the deployment a month >>>>>>>>>>>> or two >>>>>>>>>>>> ago, so if we building under an auth repo tagged before those >>>>>>>>>>>> changes, >>>>>>>>>>>> it may not show up. You should be able to fix it by checking >>>>>>>>>>>> out the >>>>>>>>>>>> dev_container and auth repos and then doing the normal >>>>>>>>>>>> deployment. >>>>>>>>>>>> >>>>>>>>>>>> Is there an magellan instance you want me to login to and take >>>>>>>>>>>> a look >>>>>>>>>>>> at? >>>>>>>>>>>> >>>>>>>>>>>> Steve >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Sep 27, 2013 at 9:28 AM, Mundy, Michael B. (Mike) >>>>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>>>> Steve, >>>>>>>>>>>>> >>>>>>>>>>>>> Can you help us out here? On the test system for the CBD >>>>>>>>>>>>> service, there >>>>>>>>>>>>> is no /kb/deployment/lib/biokbase/nexus directory. The >>>>>>>>>>>>> directory does >>>>>>>>>>>>> exist on my development system but I'm not sure how it gets >>>>>>>>>>>>> created. >>>>>>>>>>>>> >>>>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>>>> mayoclinic.org >>>>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 9/27/13 11:18 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Mike, we made sure to use the latest type compiler, because >>>>>>>>>>>>>> of reference >>>>>>>>>>>>>> to KBase-282. Can you tell us what commit to use for each >>>>>>>>>>>>>> of Auth and >>>>>>>>>>>>>> Type compiler? >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Sep 27, 2013, at 11:13 AM, "Mundy, Michael B. (Mike)" >>>>>>>>>>>>>> <Mundy.Michael(a)mayo.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> From the CBD server log file there is this error: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Traceback (most recent call last): >>>>>>>>>>>>>>> File >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> "/kb/deployment/lib/biokbase/CompressionBasedDistance/Server. >>>>>>>>>>>>>>> py", >>>>>>>>>>>>>>> line 10, in <module> >>>>>>>>>>>>>>> import biokbase.nexus >>>>>>>>>>>>>>> ImportError: No module named nexus >>>>>>>>>>>>>>> unable to load app 0 (mountpoint='') (callable not found or >>>>>>>>>>>>>>> import >>>>>>>>>>>>>>> error) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> and looking in /kb/deployment/lib/biokbase on the test >>>>>>>>>>>>>>> machine there >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> no >>>>>>>>>>>>>>> nexus directory. See Steve Chan's comment from Sep 9 in >>>>>>>>>>>>>>> JIRA issue >>>>>>>>>>>>>>> https://atlassian.kbase.us/browse/KBASE-292. I'm not sure >>>>>>>>>>>>>>> if the auth >>>>>>>>>>>>>>> or >>>>>>>>>>>>>>> typecomp module is downlevel. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Mike Mundy | Senior Analyst Programmer | Bioinformatics >>>>>>>>>>>>>>> Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >>>>>>>>>>>>>>> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >>>>>>>>>>>>>>> mayoclinic.org >>>>>>>>>>>>>>> <http://www.mayoclinic.org> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 9/27/13 10:40 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> We need to figure out what is going on with FBA and CBD. >>>>>>>>>>>>>>>> I'd really >>>>>>>>>>>>>>>> like >>>>>>>>>>>>>>>> to see those included in Iris this week. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Chris, Mike, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Are you aware of what the problems are with these two? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> t >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Sep 27, 2013, at 10:05 AM, "Land, Miriam L." >>>>>>>>>>>>>>>> <landml(a)ornl.gov> >>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Tom, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Below is the build status according to the spreadsheet. >>>>>>>>>>>>>>>>> If anyone >>>>>>>>>>>>>>>>> has >>>>>>>>>>>>>>>>> updates, please contact me or update the spreadsheet. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Typecomp Release Candidate. Deployed. Internal. Will >>>>>>>>>>>>>>>>> not have >>>>>>>>>>>>>>>>> testing, release notes, or documentation. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ID server Release Candidate. Added yesterday. >>>>>>>>>>>>>>>>> Deployed, tested, >>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>> passed checks for scripts, documentation, and release >>>>>>>>>>>>>>>>> notes. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> m5nr Waiting on Release Notes - passed deploy, testing, >>>>>>>>>>>>>>>>> script >>>>>>>>>>>>>>>>> standards and initial documentation check . Failed the >>>>>>>>>>>>>>>>> check for >>>>>>>>>>>>>>>>> release notes. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> communities_api Release Candidate. Passed deploy, >>>>>>>>>>>>>>>>> testing, script >>>>>>>>>>>>>>>>> standards, release notes and initial documentation check. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Invocation Waiting on developer - Failed 3rd round of >>>>>>>>>>>>>>>>> testing >>>>>>>>>>>>>>>>> (client >>>>>>>>>>>>>>>>> tests but server tests failes) and there are not updates >>>>>>>>>>>>>>>>> in the >>>>>>>>>>>>>>>>> release >>>>>>>>>>>>>>>>> notes. No report on initial documentation. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> FBAModeling Waiting on developer. Failed 2nd round of >>>>>>>>>>>>>>>>> testing. >>>>>>>>>>>>>>>>> Script testing is dependent on the problems found in >>>>>>>>>>>>>>>>> testing and >>>>>>>>>>>>>>>>> cannot >>>>>>>>>>>>>>>>> be completed at this time. Release notes have not been >>>>>>>>>>>>>>>>> updated. No >>>>>>>>>>>>>>>>> report on initial documentation. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Compression Base Distance Tentative. One test failed >>>>>>>>>>>>>>>>> because of >>>>>>>>>>>>>>>>> problems with the shock module. Everything else has >>>>>>>>>>>>>>>>> passed. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> shock_service Waiting on developer. Failed 2nd deploy. >>>>>>>>>>>>>>>>> Failure >>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> deploy this module will prevent another module from >>>>>>>>>>>>>>>>> moving forward. >>>>>>>>>>>>>>>>> Internal service and therefore has no scripts and has >>>>>>>>>>>>>>>>> relaxed >>>>>>>>>>>>>>>>> expectations for documentation and release notes. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> awe_service Waiting on developer. Failed 2nd deploy. >>>>>>>>>>>>>>>>> Internal >>>>>>>>>>>>>>>>> service and therefore has no scripts and has relaxed >>>>>>>>>>>>>>>>> expectations >>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>> documentation and release notes. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Miriam >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>> >>>>>> >>>> >> >

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Re: [Release-team] Build Status Sept. 27
by Robert Olson 27 Sep '13

27 Sep '13

the DMG is currently waiting on the build mac to be brought back online. On Sep 27, 2013, at 10:58 AM, Thomas Brettin wrote: > I do not know what the current status of the dmg is, but I suggested to bob he wait. He was leaning towards doing it anyways. > > Right now, my priorities are to get a running invocation service. This depends on the other modules passing. I'll get to the release notes and service description text later, as it's not front and center on the critical path, though it's important to have next week. > > > On Sep 27, 2013, at 10:50 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> FBA is one of our most popular services. I hope it can be fixed. >> >> I don't see Compression Base Distance on the Master sheet either (https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8zN0…) (m5nr hasn't been added either.) Has maintaining the Services master sheet somehow become another one of *my* jobs? :-) I will fill it what I can but I don't have most of the info. >> >> What happened with Functional Ortholog Predictor? Should it be on our public Services web page even if it's not usable from Iris? >> >> Are we holding off on making and releasing a new dmg until we finish this mini-build? >> >> Nomi >> >> On Sep 27, 2013, at 8:40 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> We need to figure out what is going on with FBA and CBD. I'd really like to see those included in Iris this week. >>> >>> Chris, Mike, >>> >>> Are you aware of what the problems are with these two? >>> >>> t >>> >>> >>> On Sep 27, 2013, at 10:05 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >>> >>>> Tom, >>>> >>>> >>>> Below is the build status according to the spreadsheet. If anyone has updates, please contact me or update the spreadsheet. >>>> >>>> Typecomp – Release Candidate. Deployed. Internal. Will not have testing, release notes, or documentation. >>>> >>>> ID server – Release Candidate. Added yesterday. Deployed, tested, and passed checks for scripts, documentation, and release notes. >>>> >>>> m5nr – Waiting on Release Notes - passed deploy, testing, script standards and initial documentation check . Failed the check for release notes. >>>> >>>> communities_api – Release Candidate. Passed deploy, testing, script standards, release notes and initial documentation check. >>>> >>>> Invocation – Waiting on developer - Failed 3rd round of testing (client tests but server tests failes) and there are not updates in the release notes. No report on initial documentation. >>>> >>>> FBAModeling – Waiting on developer. Failed 2nd round of testing. Script testing is dependent on the problems found in testing and cannot be completed at this time. Release notes have not been updated. No report on initial documentation. >>>> >>>> Compression Base Distance – Tentative. One test failed because of problems with the shock module. Everything else has passed. >>>> >>>> shock_service – Waiting on developer. Failed 2nd deploy. Failure to deploy this module will prevent another module from moving forward. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >>>> >>>> awe_service – Waiting on developer. Failed 2nd deploy. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >>>> >>>> >>>> >>>> Miriam >>> >> > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Build Status Sept. 27
by Land, Miriam L. 27 Sep '13

27 Sep '13

I've added these to the Master tab but I don't know the description, domain, etc. Miriam On 9/27/13 11:50 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >I don't see Compression Base Distance on the Master sheet either >(https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8z >N0Y3Vm5YM095aWc#gid=15). (m5nr hasn't been added either.) Has maintaining >the Services master sheet somehow become another one of *my* jobs? :-) I >will fill it what I can but I don't have most of the info.

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Re: [Release-team] Build Status Sept. 27
by Thomas Brettin 27 Sep '13

27 Sep '13

I do not know what the current status of the dmg is, but I suggested to bob he wait. He was leaning towards doing it anyways. Right now, my priorities are to get a running invocation service. This depends on the other modules passing. I'll get to the release notes and service description text later, as it's not front and center on the critical path, though it's important to have next week. On Sep 27, 2013, at 10:50 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > FBA is one of our most popular services. I hope it can be fixed. > > I don't see Compression Base Distance on the Master sheet either (https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8zN0…) (m5nr hasn't been added either.) Has maintaining the Services master sheet somehow become another one of *my* jobs? :-) I will fill it what I can but I don't have most of the info. > > What happened with Functional Ortholog Predictor? Should it be on our public Services web page even if it's not usable from Iris? > > Are we holding off on making and releasing a new dmg until we finish this mini-build? > > Nomi > > On Sep 27, 2013, at 8:40 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> We need to figure out what is going on with FBA and CBD. I'd really like to see those included in Iris this week. >> >> Chris, Mike, >> >> Are you aware of what the problems are with these two? >> >> t >> >> >> On Sep 27, 2013, at 10:05 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >> >>> Tom, >>> >>> >>> Below is the build status according to the spreadsheet. If anyone has updates, please contact me or update the spreadsheet. >>> >>> Typecomp – Release Candidate. Deployed. Internal. Will not have testing, release notes, or documentation. >>> >>> ID server – Release Candidate. Added yesterday. Deployed, tested, and passed checks for scripts, documentation, and release notes. >>> >>> m5nr – Waiting on Release Notes - passed deploy, testing, script standards and initial documentation check . Failed the check for release notes. >>> >>> communities_api – Release Candidate. Passed deploy, testing, script standards, release notes and initial documentation check. >>> >>> Invocation – Waiting on developer - Failed 3rd round of testing (client tests but server tests failes) and there are not updates in the release notes. No report on initial documentation. >>> >>> FBAModeling – Waiting on developer. Failed 2nd round of testing. Script testing is dependent on the problems found in testing and cannot be completed at this time. Release notes have not been updated. No report on initial documentation. >>> >>> Compression Base Distance – Tentative. One test failed because of problems with the shock module. Everything else has passed. >>> >>> shock_service – Waiting on developer. Failed 2nd deploy. Failure to deploy this module will prevent another module from moving forward. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >>> >>> awe_service – Waiting on developer. Failed 2nd deploy. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >>> >>> >>> >>> Miriam >> >

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Re: [Release-team] Build Status Sept. 27
by Nomi Harris 27 Sep '13

27 Sep '13

FBA is one of our most popular services. I hope it can be fixed. I don't see Compression Base Distance on the Master sheet either (https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8zN0…) (m5nr hasn't been added either.) Has maintaining the Services master sheet somehow become another one of *my* jobs? :-) I will fill it what I can but I don't have most of the info. What happened with Functional Ortholog Predictor? Should it be on our public Services web page even if it's not usable from Iris? Are we holding off on making and releasing a new dmg until we finish this mini-build? Nomi On Sep 27, 2013, at 8:40 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > We need to figure out what is going on with FBA and CBD. I'd really like to see those included in Iris this week. > > Chris, Mike, > > Are you aware of what the problems are with these two? > > t > > > On Sep 27, 2013, at 10:05 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> Tom, >> >> >> Below is the build status according to the spreadsheet. If anyone has updates, please contact me or update the spreadsheet. >> >> Typecomp – Release Candidate. Deployed. Internal. Will not have testing, release notes, or documentation. >> >> ID server – Release Candidate. Added yesterday. Deployed, tested, and passed checks for scripts, documentation, and release notes. >> >> m5nr – Waiting on Release Notes - passed deploy, testing, script standards and initial documentation check . Failed the check for release notes. >> >> communities_api – Release Candidate. Passed deploy, testing, script standards, release notes and initial documentation check. >> >> Invocation – Waiting on developer - Failed 3rd round of testing (client tests but server tests failes) and there are not updates in the release notes. No report on initial documentation. >> >> FBAModeling – Waiting on developer. Failed 2nd round of testing. Script testing is dependent on the problems found in testing and cannot be completed at this time. Release notes have not been updated. No report on initial documentation. >> >> Compression Base Distance – Tentative. One test failed because of problems with the shock module. Everything else has passed. >> >> shock_service – Waiting on developer. Failed 2nd deploy. Failure to deploy this module will prevent another module from moving forward. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >> >> awe_service – Waiting on developer. Failed 2nd deploy. Internal service and therefore has no scripts and has relaxed expectations for documentation and release notes. >> >> >> >> Miriam >

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Re: [Release-team] When will IRIS be updated?
by Shane Canon 26 Sep '13

26 Sep '13

Dan straightened me out. We still need to figure out how to integrate this into deployment. But I was able to move forward. --Shane On Sep 26, 2013, at 1:33 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > On Sep 25, 2013, at 8:58 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > >> This is the deploy.cfg service list from invocation: >> >> deploy-client = ontology_service, communities_api, communities_qc, trees, networks, genome_annotation, invocation, kb_seed, kbapi_common, sim_service, typecomp, idserver, genotype_phenotype_api, KBaseFBAModeling, workspace_service, phispy, plant_expression_service, translation, assembly >> deploy-service = invocation, genome_annotation, phispy >> deploy-master = auth >> >> The IRIS candidate column is not populated in the release spreadsheet, so I'm not sure what I should >> compare this list to. >> >> Maybe Tom or Nomi have an idea of all the services that should be present in Iris? > > This is not something I have at hand. Jim, do you have a list? And how do you decide whether new services (e.g. Functional Ortholog Predictor) should be added to Iris? > > For now, since it looks like FOP will not be available to users, should I take it off the Services page? (We can always add it in the future.) > > Nomi > >> >> >> ----- Original Message ----- >>> From: "Shane Canon" <scanon(a)lbl.gov> >>> To: "Dan Olson" <dolson(a)mcs.anl.gov> >>> Cc: release-team(a)kbase.us >>> Sent: Wednesday, September 25, 2013 10:28:33 AM >>> Subject: Re: [Release-team] When will IRIS be updated? >>> >>> >>> Are there any other new ones that we overlooked? >>> >>> --Shane >>> >>> On Sep 25, 2013, at 6:19 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >>> >>>> I think this didn't get deployed onto the production, or test iris >>>> instances because it >>>> didn't make it into the deploy.cfg file for either of them, it also >>>> didn't make it into >>>> the config file for the VM. >>>> >>>> It looks like we're still ironing out the details of adding modules >>>> to our process. >>>> >>>> I'll get this one into the config file, and I can attempt to deploy >>>> onto production. >>>> >>>> Jim, can you document what is needed to deploy an additional module >>>> onto a running IRIS >>>> deployment? For example, what command is needed to rebuild the >>>> whitelist, and if a new >>>> js client build is needed..etc. >>>> >>>> ----- Original Message ----- >>>>> From: "Miriam L. Land" <landml(a)ornl.gov> >>>>> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>>> Cc: "James Thomason" <thomason(a)cshl.edu>, release-team(a)kbase.us, >>>>> "Nomi Harris" <nlharris(a)lbl.gov> >>>>> Sent: Wednesday, September 25, 2013 6:45:03 AM >>>>> Subject: Re: [Release-team] When will IRIS be updated? >>>>> >>>>> Yes. >>>>> >>>>> On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >>>>> >>>>>> Did Functional Ortholog make it through the Aug Build? >>>>>> >>>>>> >>>>>> On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> >>>>>> wrote: >>>>>> >>>>>>> Invocation is one of the modules in the current mini build. >>>>>>> >>>>>>> Miriam >>>>>>> >>>>>>> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >>>>>>> >>>>>>>> Dear Release Team, >>>>>>>> >>>>>>>> I just checked IRIS to see if the one (!?) script for >>>>>>>> Functional >>>>>>>> Ortholog >>>>>>>> Predictor was there, and it was not. I don't see any way to see >>>>>>>> when >>>>>>>> IRIS >>>>>>>> was last updated. (I filed a new JIRA ticket about this.) >>>>>>>> >>>>>>>> Does anyone know when IRIS will be updated? Is this something >>>>>>>> that has >>>>>>>> to >>>>>>>> be done manually? >>>>>>>> >>>>>>>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, >>>>>>>> then be >>>>>>>> accessible from IRIS? It should be, right? >>>>>>>> >>>>>>>> I am asking because the updated Services page (which includes >>>>>>>> the >>>>>>>> new >>>>>>>> service, Functional Ortholog Predictor) is basically ready to >>>>>>>> push to >>>>>>>> the >>>>>>>> public site but I don't want to push it out until the release >>>>>>>> is >>>>>>>> complete. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Nomi >>>>>>>> _ > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] When will IRIS be updated?
by Nomi Harris 26 Sep '13

26 Sep '13

On Sep 25, 2013, at 8:58 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > This is the deploy.cfg service list from invocation: > > deploy-client = ontology_service, communities_api, communities_qc, trees, networks, genome_annotation, invocation, kb_seed, kbapi_common, sim_service, typecomp, idserver, genotype_phenotype_api, KBaseFBAModeling, workspace_service, phispy, plant_expression_service, translation, assembly > deploy-service = invocation, genome_annotation, phispy > deploy-master = auth > > The IRIS candidate column is not populated in the release spreadsheet, so I'm not sure what I should > compare this list to. > > Maybe Tom or Nomi have an idea of all the services that should be present in Iris? This is not something I have at hand. Jim, do you have a list? And how do you decide whether new services (e.g. Functional Ortholog Predictor) should be added to Iris? For now, since it looks like FOP will not be available to users, should I take it off the Services page? (We can always add it in the future.) Nomi > > > ----- Original Message ----- >> From: "Shane Canon" <scanon(a)lbl.gov> >> To: "Dan Olson" <dolson(a)mcs.anl.gov> >> Cc: release-team(a)kbase.us >> Sent: Wednesday, September 25, 2013 10:28:33 AM >> Subject: Re: [Release-team] When will IRIS be updated? >> >> >> Are there any other new ones that we overlooked? >> >> --Shane >> >> On Sep 25, 2013, at 6:19 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >> >>> I think this didn't get deployed onto the production, or test iris >>> instances because it >>> didn't make it into the deploy.cfg file for either of them, it also >>> didn't make it into >>> the config file for the VM. >>> >>> It looks like we're still ironing out the details of adding modules >>> to our process. >>> >>> I'll get this one into the config file, and I can attempt to deploy >>> onto production. >>> >>> Jim, can you document what is needed to deploy an additional module >>> onto a running IRIS >>> deployment? For example, what command is needed to rebuild the >>> whitelist, and if a new >>> js client build is needed..etc. >>> >>> ----- Original Message ----- >>>> From: "Miriam L. Land" <landml(a)ornl.gov> >>>> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>> Cc: "James Thomason" <thomason(a)cshl.edu>, release-team(a)kbase.us, >>>> "Nomi Harris" <nlharris(a)lbl.gov> >>>> Sent: Wednesday, September 25, 2013 6:45:03 AM >>>> Subject: Re: [Release-team] When will IRIS be updated? >>>> >>>> Yes. >>>> >>>> On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >>>> >>>>> Did Functional Ortholog make it through the Aug Build? >>>>> >>>>> >>>>> On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> >>>>> wrote: >>>>> >>>>>> Invocation is one of the modules in the current mini build. >>>>>> >>>>>> Miriam >>>>>> >>>>>> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >>>>>> >>>>>>> Dear Release Team, >>>>>>> >>>>>>> I just checked IRIS to see if the one (!?) script for >>>>>>> Functional >>>>>>> Ortholog >>>>>>> Predictor was there, and it was not. I don't see any way to see >>>>>>> when >>>>>>> IRIS >>>>>>> was last updated. (I filed a new JIRA ticket about this.) >>>>>>> >>>>>>> Does anyone know when IRIS will be updated? Is this something >>>>>>> that has >>>>>>> to >>>>>>> be done manually? >>>>>>> >>>>>>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, >>>>>>> then be >>>>>>> accessible from IRIS? It should be, right? >>>>>>> >>>>>>> I am asking because the updated Services page (which includes >>>>>>> the >>>>>>> new >>>>>>> service, Functional Ortholog Predictor) is basically ready to >>>>>>> push to >>>>>>> the >>>>>>> public site but I don't want to push it out until the release >>>>>>> is >>>>>>> complete. >>>>>>> >>>>>>> Thanks, >>>>>>> Nomi >>>>>>> _

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