Re: [Release-team] Build Status Sept. 27
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" <[email protected]> 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." <[email protected]> wrote:
Tom,
Is it ready to retest? It still has a failed test.
Miriam
On 9/27/13 1:47 PM, "Thomas Brettin" <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote:
Duh, sorry, my fault, I my coffee hasn't kicked in yet...
On Fri, Sep 27, 2013 at 9:43 AM, Stephen Chan <[email protected]> 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) <[email protected]> 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 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org <http://www.mayoclinic.org>
On 9/27/13 11:32 AM, "Stephen Chan" <[email protected]> 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) <[email protected]> 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 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org <http://www.mayoclinic.org>
On 9/27/13 11:18 AM, "Thomas Brettin" <[email protected]> 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)" <[email protected]> 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 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org <http://www.mayoclinic.org>
On 9/27/13 10:40 AM, "Thomas Brettin" <[email protected]> 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." <[email protected]> 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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Land, Miriam L.