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

Re: [Release-team] Aug 2013 Build - Workspace service failed initial testing
by Thomas Brettin 20 Aug '13

20 Aug '13

Hi Shane, I tagged it this am. I ran it in a developer test mode and it passed all tests. I talked to Chris, the dependency as declared in the deploy.cfg file is non-existent. We can comment out that line in deploy.cfg. I just spoke with Dan about a strategy to deploy. It might be the case that the three of us should sync. Can you do a google hangout now'ish? Tom On Aug 20, 2013, at 10:56 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > It looks like someone tagged it. > > How do we deploy msserver in kbase? What is it? > > --Shane > > > On Aug 20, 2013, at 5:18 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Chris sent an email on 8/7 requesting that the workspace service be re-tagged and re-deployed. >> >> The oldest test tag in git is 20130806-test. >> >> Also, workspace is now dependent on: >> >> mssserver-url=http://biologin-4.mcs.anl.gov:7050 >> >> which is not a deployable kbase service. >> >> >> 1) retag, redeploy and retest as per chris's request >> 2) make msserver deployable in kbase. >> >> >> On Aug 8, 2013, at 8:07 AM, "Moulton, Steve" <moultonsa(a)ornl.gov> wrote: >> >>> I'm on it. >>> >>> -s >>> >>> -- >>> Steve Moulton UNIX/Linux Systems Engineer >>> Cyber Operations & Research Integration (R&D Support), ITSD >>> Oak Ridge National Laboratory >>> Voice: 865-574-9609 Fax: 865-576-7605 moultonsa at ornl dot gov >>> >>> >>> -----Original Message----- >>> From: Land, Miriam L. >>> Sent: Thursday, August 08, 2013 8:37 AM >>> To: Moulton, Steve; Dantong Yu; Dan Olson >>> Cc: Thomas Brettin (brettin(a)mcs.anl.gov) Matt DeJongh; Christopher Henry >>> Subject: Re: Aug 2013 Build - Workspace service failed initial testing >>> >>> What does the deployment team think about this? The version on the test >>> VM has passed testing. >>> >>> Miriam >>> >>> On 8/7/13 7:32 PM, "Christopher Henry" <chrisshenry(a)gmail.com> wrote: >>> >>>> Can we update the workspace_service being deployed to the code I just >>>> committed to master (the latest master branch)? I just submitted a new >>>> function that allows us to pull multiple objects from the workspace at >>>> once. It's needed to clear up an outstanding ticket in JIRA. Tests all >>>> appear to be working. >>>> >>>> On Aug 7, 2013, at 1:18 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >>>> >>>>> I restarted the workspace_service and the tests all passed. >>>>> >>>>> Matt >>>>> >>>>> >>>>> On Wed, Aug 7, 2013 at 12:35 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >>>>> I restarted the localhost mongod process and the server tests pass now. >>>>> >>>>> Matt >>>>> >>>>> >>>>> On Tue, Aug 6, 2013 at 1:41 PM, Land, Miriam L. <landml(a)ornl.gov> wrote: >>>>> Chris and Matt, >>>>> >>>>> >>>>> >>>>> The module workspace service failed the Œmake test¹. It was run from >>>>> the experiment VM on Magellan. You can replicate this by logging into >>>>> the VM using: >>>>> >>>>> >>>>> >>>>> ssh 140.221.84.191 >>>>> >>>>> sudo su >>>>> >>>>> ssh <module_name> >>>>> >>>>> source /kb/deployment/user-env.sh >>>>> >>>>> cd /kb/dev_container/modules/<module_name> >>>>> >>>>> >>>>> >>>>> This info is also given in >>>>> https://trac.kbase.us/projects/kbase/wiki/TestingOverview. Some errors >>>>> could be due to the configuration, the actual tests, or dependencies. >>>>> Please work with the deployment team (Dan O., Dantong and Steve M.) if >>>>> you believe that the problems are out of your control. >>>>> >>>>> >>>>> >>>>> Warning: As root, you can make edits here but you will not be able to >>>>> commit changes to the git repo. >>>>> >>>>> >>>>> >>>>> Below is the error message that I got. >>>>> >>>>> >>>>> >>>>> Miriam >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------- >>>>> -------------- >>>>> >>>>> Summary of workspace service >>>>> >>>>> >>>>> >>>>> make test >>>>> >>>>> ../../tools/Makefile.common.rules:36: warning: overriding commands for >>>>> target `deploy-libs' >>>>> >>>>> Makefile:102: warning: ignoring old commands for target `deploy-libs' >>>>> >>>>> for t in server-tests/workspaceServiceImpl.t ; do \ >>>>> >>>>> if [ -f $t ] ; then \ >>>>> >>>>> /kb/runtime/bin/prove >>>>> $t ; \ >>>>> >>>>> if [ $? -ne 0 ] ; then \ >>>>> >>>>> exit 1 >>>>> ; \ >>>>> >>>>> fi \ >>>>> >>>>> fi \ >>>>> >>>>> done >>>>> >>>>> server-tests/workspaceServiceImpl.t .. ***Starting workspace service >>>>> with mongo parameters:*** >>>>> >>>>> Host: localhost >>>>> >>>>> Database: workspace_test >>>>> >>>>> User: >>>>> >>>>> Can't use string ("not master") as a HASH ref while "strict refs" in >>>>> use at >>>>> /kb/runtime/lib/perl5/site_perl/5.16.2/x86_64-linux/MongoDB/Collection.pm >>>>> line 424. >>>>> >>>>> server-tests/workspaceServiceImpl.t .. Dubious, test returned 255 >>>>> (wstat 65280, 0xff00) >>>>> >>>>> No subtests run >>>>> >>>>> >>>>> >>>>> Test Summary Report >>>>> >>>>> ------------------- >>>>> >>>>> server-tests/workspaceServiceImpl.t (Wstat: 65280 Tests: 0 Failed: 0) >>>>> >>>>> Non-zero exit status: 255 >>>>> >>>>> Parse errors: No plan found in TAP output >>>>> >>>>> Files=1, Tests=0, 3 wallclock secs ( 0.03 usr 0.01 sys + 0.46 cusr >>>>> 0.12 csys = 0.62 CPU) >>>>> >>>>> Result: FAIL >>>>> >>>>> make: *** [test-service] Error 1 >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Matt DeJongh, Ph.D. >>>>> Computer Science Department >>>>> Hope College, Holland, MI 49423 >>>>> (616) 395-7429 >>>>> >>>>> >>>>> >>>>> -- >>>>> Matt DeJongh, Ph.D. >>>>> Computer Science Department >>>>> Hope College, Holland, MI 49423 >>>>> (616) 395-7429 >>>> >>> >> >> _______________________________________________ >> 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] genome_annotaiton
by Shane Canon 20 Aug '13

20 Aug '13

I see it on row 3. Or did you add that recently? --Shane On Aug 20, 2013, at 6:31 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > I don't see this one listed in the kbase services spread sheet. What happened to this one at the build? > > thanks > t > > On Aug 20, 2013, at 8:19 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Hi Miriam, >> >> Running make test on genome annotation fails for me. Is there something particular that you are doing on this module? If I had to guess, I'd say that a server is not being started on the localhost. >> >> ok 1 - Did an object get defined >> ok 2 - Is it in the right class isa Bio::KBase::GenomeAnnotation::Client >> ok 3 - Bio::KBase::GenomeAnnotation::Client->can(...) >> ok 4 - Did an object get defined >> ok 5 - Is it in the right class isa Bio::KBase::GenomeAnnotation::Client >> ok 6 - Downloaded test data >> # Test the happy cases for annotation methods >> not ok 7 - Test call_CDSs >> # Failed test 'Test call_CDSs' >> # at t/client-tests/annotation.t line 68. >> not ok 8 - Test assign_functions_to_CDSs >> # Failed test 'Test assign_functions_to_CDSs' >> # at t/client-tests/annotation.t line 80. >> not ok 9 - Test annotate_genome >> # Failed test 'Test annotate_genome' >> # at t/client-tests/annotation.t line 80. >> 1..9 >> # Looks like you failed 3 tests of 9. >> make: *** [test] Error 1 > > _______________________________________________ > 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] Aug 2013 Build - Workspace service failed initial testing
by Shane Canon 20 Aug '13

20 Aug '13

It looks like someone tagged it. How do we deploy msserver in kbase? What is it? --Shane On Aug 20, 2013, at 5:18 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Chris sent an email on 8/7 requesting that the workspace service be re-tagged and re-deployed. > > The oldest test tag in git is 20130806-test. > > Also, workspace is now dependent on: > > mssserver-url=http://biologin-4.mcs.anl.gov:7050 > > which is not a deployable kbase service. > > > 1) retag, redeploy and retest as per chris's request > 2) make msserver deployable in kbase. > > > On Aug 8, 2013, at 8:07 AM, "Moulton, Steve" <moultonsa(a)ornl.gov> wrote: > >> I'm on it. >> >> -s >> >> -- >> Steve Moulton UNIX/Linux Systems Engineer >> Cyber Operations & Research Integration (R&D Support), ITSD >> Oak Ridge National Laboratory >> Voice: 865-574-9609 Fax: 865-576-7605 moultonsa at ornl dot gov >> >> >> -----Original Message----- >> From: Land, Miriam L. >> Sent: Thursday, August 08, 2013 8:37 AM >> To: Moulton, Steve; Dantong Yu; Dan Olson >> Cc: Thomas Brettin (brettin(a)mcs.anl.gov) Matt DeJongh; Christopher Henry >> Subject: Re: Aug 2013 Build - Workspace service failed initial testing >> >> What does the deployment team think about this? The version on the test >> VM has passed testing. >> >> Miriam >> >> On 8/7/13 7:32 PM, "Christopher Henry" <chrisshenry(a)gmail.com> wrote: >> >>> Can we update the workspace_service being deployed to the code I just >>> committed to master (the latest master branch)? I just submitted a new >>> function that allows us to pull multiple objects from the workspace at >>> once. It's needed to clear up an outstanding ticket in JIRA. Tests all >>> appear to be working. >>> >>> On Aug 7, 2013, at 1:18 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >>> >>>> I restarted the workspace_service and the tests all passed. >>>> >>>> Matt >>>> >>>> >>>> On Wed, Aug 7, 2013 at 12:35 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >>>> I restarted the localhost mongod process and the server tests pass now. >>>> >>>> Matt >>>> >>>> >>>> On Tue, Aug 6, 2013 at 1:41 PM, Land, Miriam L. <landml(a)ornl.gov> wrote: >>>> Chris and Matt, >>>> >>>> >>>> >>>> The module workspace service failed the Œmake test¹. It was run from >>>> the experiment VM on Magellan. You can replicate this by logging into >>>> the VM using: >>>> >>>> >>>> >>>> ssh 140.221.84.191 >>>> >>>> sudo su >>>> >>>> ssh <module_name> >>>> >>>> source /kb/deployment/user-env.sh >>>> >>>> cd /kb/dev_container/modules/<module_name> >>>> >>>> >>>> >>>> This info is also given in >>>> https://trac.kbase.us/projects/kbase/wiki/TestingOverview. Some errors >>>> could be due to the configuration, the actual tests, or dependencies. >>>> Please work with the deployment team (Dan O., Dantong and Steve M.) if >>>> you believe that the problems are out of your control. >>>> >>>> >>>> >>>> Warning: As root, you can make edits here but you will not be able to >>>> commit changes to the git repo. >>>> >>>> >>>> >>>> Below is the error message that I got. >>>> >>>> >>>> >>>> Miriam >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> -------------- >>>> >>>> Summary of workspace service >>>> >>>> >>>> >>>> make test >>>> >>>> ../../tools/Makefile.common.rules:36: warning: overriding commands for >>>> target `deploy-libs' >>>> >>>> Makefile:102: warning: ignoring old commands for target `deploy-libs' >>>> >>>> for t in server-tests/workspaceServiceImpl.t ; do \ >>>> >>>> if [ -f $t ] ; then \ >>>> >>>> /kb/runtime/bin/prove >>>> $t ; \ >>>> >>>> if [ $? -ne 0 ] ; then \ >>>> >>>> exit 1 >>>> ; \ >>>> >>>> fi \ >>>> >>>> fi \ >>>> >>>> done >>>> >>>> server-tests/workspaceServiceImpl.t .. ***Starting workspace service >>>> with mongo parameters:*** >>>> >>>> Host: localhost >>>> >>>> Database: workspace_test >>>> >>>> User: >>>> >>>> Can't use string ("not master") as a HASH ref while "strict refs" in >>>> use at >>>> /kb/runtime/lib/perl5/site_perl/5.16.2/x86_64-linux/MongoDB/Collection.pm >>>> line 424. >>>> >>>> server-tests/workspaceServiceImpl.t .. Dubious, test returned 255 >>>> (wstat 65280, 0xff00) >>>> >>>> No subtests run >>>> >>>> >>>> >>>> Test Summary Report >>>> >>>> ------------------- >>>> >>>> server-tests/workspaceServiceImpl.t (Wstat: 65280 Tests: 0 Failed: 0) >>>> >>>> Non-zero exit status: 255 >>>> >>>> Parse errors: No plan found in TAP output >>>> >>>> Files=1, Tests=0, 3 wallclock secs ( 0.03 usr 0.01 sys + 0.46 cusr >>>> 0.12 csys = 0.62 CPU) >>>> >>>> Result: FAIL >>>> >>>> make: *** [test-service] Error 1 >>>> >>>> >>>> >>>> >>>> -- >>>> Matt DeJongh, Ph.D. >>>> Computer Science Department >>>> Hope College, Holland, MI 49423 >>>> (616) 395-7429 >>>> >>>> >>>> >>>> -- >>>> Matt DeJongh, Ph.D. >>>> Computer Science Department >>>> Hope College, Holland, MI 49423 >>>> (616) 395-7429 >>> >> > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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genome_annotaiton
by Thomas Brettin 20 Aug '13

20 Aug '13

I don't see this one listed in the kbase services spread sheet. What happened to this one at the build? thanks t On Aug 20, 2013, at 8:19 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Hi Miriam, > > Running make test on genome annotation fails for me. Is there something particular that you are doing on this module? If I had to guess, I'd say that a server is not being started on the localhost. > > ok 1 - Did an object get defined > ok 2 - Is it in the right class isa Bio::KBase::GenomeAnnotation::Client > ok 3 - Bio::KBase::GenomeAnnotation::Client->can(...) > ok 4 - Did an object get defined > ok 5 - Is it in the right class isa Bio::KBase::GenomeAnnotation::Client > ok 6 - Downloaded test data > # Test the happy cases for annotation methods > not ok 7 - Test call_CDSs > # Failed test 'Test call_CDSs' > # at t/client-tests/annotation.t line 68. > not ok 8 - Test assign_functions_to_CDSs > # Failed test 'Test assign_functions_to_CDSs' > # at t/client-tests/annotation.t line 80. > not ok 9 - Test annotate_genome > # Failed test 'Test annotate_genome' > # at t/client-tests/annotation.t line 80. > 1..9 > # Looks like you failed 3 tests of 9. > make: *** [test] Error 1

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Re: [Release-team] Aug 2013 Build - Workspace service failed initial testing
by Thomas Brettin 20 Aug '13

20 Aug '13

Chris sent an email on 8/7 requesting that the workspace service be re-tagged and re-deployed. The oldest test tag in git is 20130806-test. Also, workspace is now dependent on: mssserver-url=http://biologin-4.mcs.anl.gov:7050 which is not a deployable kbase service. 1) retag, redeploy and retest as per chris's request 2) make msserver deployable in kbase. On Aug 8, 2013, at 8:07 AM, "Moulton, Steve" <moultonsa(a)ornl.gov> wrote: > I'm on it. > > -s > > -- > Steve Moulton UNIX/Linux Systems Engineer > Cyber Operations & Research Integration (R&D Support), ITSD > Oak Ridge National Laboratory > Voice: 865-574-9609 Fax: 865-576-7605 moultonsa at ornl dot gov > > > -----Original Message----- > From: Land, Miriam L. > Sent: Thursday, August 08, 2013 8:37 AM > To: Moulton, Steve; Dantong Yu; Dan Olson > Cc: Thomas Brettin (brettin(a)mcs.anl.gov) Matt DeJongh; Christopher Henry > Subject: Re: Aug 2013 Build - Workspace service failed initial testing > > What does the deployment team think about this? The version on the test > VM has passed testing. > > Miriam > > On 8/7/13 7:32 PM, "Christopher Henry" <chrisshenry(a)gmail.com> wrote: > >> Can we update the workspace_service being deployed to the code I just >> committed to master (the latest master branch)? I just submitted a new >> function that allows us to pull multiple objects from the workspace at >> once. It's needed to clear up an outstanding ticket in JIRA. Tests all >> appear to be working. >> >> On Aug 7, 2013, at 1:18 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >> >>> I restarted the workspace_service and the tests all passed. >>> >>> Matt >>> >>> >>> On Wed, Aug 7, 2013 at 12:35 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: >>> I restarted the localhost mongod process and the server tests pass now. >>> >>> Matt >>> >>> >>> On Tue, Aug 6, 2013 at 1:41 PM, Land, Miriam L. <landml(a)ornl.gov> wrote: >>> Chris and Matt, >>> >>> >>> >>> The module workspace service failed the Œmake test¹. It was run from >>> the experiment VM on Magellan. You can replicate this by logging into >>> the VM using: >>> >>> >>> >>> ssh 140.221.84.191 >>> >>> sudo su >>> >>> ssh <module_name> >>> >>> source /kb/deployment/user-env.sh >>> >>> cd /kb/dev_container/modules/<module_name> >>> >>> >>> >>> This info is also given in >>> https://trac.kbase.us/projects/kbase/wiki/TestingOverview. Some errors >>> could be due to the configuration, the actual tests, or dependencies. >>> Please work with the deployment team (Dan O., Dantong and Steve M.) if >>> you believe that the problems are out of your control. >>> >>> >>> >>> Warning: As root, you can make edits here but you will not be able to >>> commit changes to the git repo. >>> >>> >>> >>> Below is the error message that I got. >>> >>> >>> >>> Miriam >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> -------------- >>> >>> Summary of workspace service >>> >>> >>> >>> make test >>> >>> ../../tools/Makefile.common.rules:36: warning: overriding commands for >>> target `deploy-libs' >>> >>> Makefile:102: warning: ignoring old commands for target `deploy-libs' >>> >>> for t in server-tests/workspaceServiceImpl.t ; do \ >>> >>> if [ -f $t ] ; then \ >>> >>> /kb/runtime/bin/prove >>> $t ; \ >>> >>> if [ $? -ne 0 ] ; then \ >>> >>> exit 1 >>> ; \ >>> >>> fi \ >>> >>> fi \ >>> >>> done >>> >>> server-tests/workspaceServiceImpl.t .. ***Starting workspace service >>> with mongo parameters:*** >>> >>> Host: localhost >>> >>> Database: workspace_test >>> >>> User: >>> >>> Can't use string ("not master") as a HASH ref while "strict refs" in >>> use at >>> /kb/runtime/lib/perl5/site_perl/5.16.2/x86_64-linux/MongoDB/Collection.pm >>> line 424. >>> >>> server-tests/workspaceServiceImpl.t .. Dubious, test returned 255 >>> (wstat 65280, 0xff00) >>> >>> No subtests run >>> >>> >>> >>> Test Summary Report >>> >>> ------------------- >>> >>> server-tests/workspaceServiceImpl.t (Wstat: 65280 Tests: 0 Failed: 0) >>> >>> Non-zero exit status: 255 >>> >>> Parse errors: No plan found in TAP output >>> >>> Files=1, Tests=0, 3 wallclock secs ( 0.03 usr 0.01 sys + 0.46 cusr >>> 0.12 csys = 0.62 CPU) >>> >>> Result: FAIL >>> >>> make: *** [test-service] Error 1 >>> >>> >>> >>> >>> -- >>> Matt DeJongh, Ph.D. >>> Computer Science Department >>> Hope College, Holland, MI 49423 >>> (616) 395-7429 >>> >>> >>> >>> -- >>> Matt DeJongh, Ph.D. >>> Computer Science Department >>> Hope College, Holland, MI 49423 >>> (616) 395-7429 >> >

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Re: [Release-team] Release Team Telecon
by Land, Miriam L. 19 Aug '13

19 Aug '13

YEA!!! Auth_service passed testing. Miriam On 8/19/13 10:42 AM, "Shane Canon" <scanon(a)lbl.gov> wrote: > >Miriam, > >Can you try now? I think the errors were related to the testing of Mongo >replication. > >--Shane > > >On Aug 19, 2013, at 6:22 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> Shane, >> >> The 'make test' for auth_service still ends in 'FAILED'. Am I reading >>the >> results right? Am I doing something wrong? >> >> Miriam >> >> --------------------------------- >> make test >> Makefile:53: warning: overriding commands for target `build-docs' >> Makefile:49: warning: ignoring old commands for target `build-docs' >> cd authorization_server; \ >> ./manage.py test authorization_server >> No connection settings specified: 'Settings' object has no attribute >> 'MONGODB_CONN' >> Connection to mongodb.kbase.us by default. >> WARNING:root:MongoDB is a read-only instance, no roles can be created, >> updated or deleted >> Creating test database for alias 'default'... >> No connection settings specified: 'Settings' object has no attribute >> 'MONGODB_CONN' >> >> sNo connection settings specified: 'Settings' object has no attribute >> 'MONGODB_CONN' >> >> sNo connection settings specified: 'Settings' object has no attribute >> 'MONGODB_CONN' >> >> FNo connection settings specified: 'Settings' object has no attribute >> 'MONGODB_CONN' >> >> s >> ====================================================================== >> FAIL: testRead (authorization_server.tests.RoleHandlerTest) >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File >> >>"/kb/dev_container/modules/auth_service/authorization_server/authorizatio >>n_ >> server/tests.py", line 252, in testRead >> self.assertEqual(resp.status_code, 200, "Should accept queries from >> legit kbase test user") >> AssertionError: Should accept queries from legit kbase test user >> >> ---------------------------------------------------------------------- >> Ran 4 tests in 0.495s >> >> FAILED (failures=1, skipped=3) >> Destroying test database for alias 'default'... >> make: *** [test_django] Error 1 >> >> >> >> >> On 8/17/13 1:25 PM, "Shane Canon" <scanon(a)lbl.gov> wrote: >> >>> >>> Miriam, >>> >>> Shock is deployed now. It still has one minor fix that is required, >>>but >>> we can work through those during deployment. >>> >>> --Shane >>> >>> >> >

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Re: [Release-team] Release Team Telecon
by Shane Canon 19 Aug '13

19 Aug '13

Miriam, Can you try now? I think the errors were related to the testing of Mongo replication. --Shane On Aug 19, 2013, at 6:22 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > Shane, > > The 'make test' for auth_service still ends in 'FAILED'. Am I reading the > results right? Am I doing something wrong? > > Miriam > > --------------------------------- > make test > Makefile:53: warning: overriding commands for target `build-docs' > Makefile:49: warning: ignoring old commands for target `build-docs' > cd authorization_server; \ > ./manage.py test authorization_server > No connection settings specified: 'Settings' object has no attribute > 'MONGODB_CONN' > Connection to mongodb.kbase.us by default. > WARNING:root:MongoDB is a read-only instance, no roles can be created, > updated or deleted > Creating test database for alias 'default'... > No connection settings specified: 'Settings' object has no attribute > 'MONGODB_CONN' > > sNo connection settings specified: 'Settings' object has no attribute > 'MONGODB_CONN' > > sNo connection settings specified: 'Settings' object has no attribute > 'MONGODB_CONN' > > FNo connection settings specified: 'Settings' object has no attribute > 'MONGODB_CONN' > > s > ====================================================================== > FAIL: testRead (authorization_server.tests.RoleHandlerTest) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/kb/dev_container/modules/auth_service/authorization_server/authorization_ > server/tests.py", line 252, in testRead > self.assertEqual(resp.status_code, 200, "Should accept queries from > legit kbase test user") > AssertionError: Should accept queries from legit kbase test user > > ---------------------------------------------------------------------- > Ran 4 tests in 0.495s > > FAILED (failures=1, skipped=3) > Destroying test database for alias 'default'... > make: *** [test_django] Error 1 > > > > > On 8/17/13 1:25 PM, "Shane Canon" <scanon(a)lbl.gov> wrote: > >> >> Miriam, >> >> Shock is deployed now. It still has one minor fix that is required, but >> we can work through those during deployment. >> >> --Shane >> >> >

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Re: [Release-team] Documentation not showing up
by Dan Olson 19 Aug '13

19 Aug '13

Deployment. Someone did not run ./mkdoc, after deploy.rsc. ----- Original Message ----- > From: "Miriam L. Land" <landml(a)ornl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov> > Sent: Monday, August 19, 2013 9:20:44 AM > Subject: Documentation not showing up > > Dan, > > If a module, such as communities_qc (t5), has documentation in the > webroot dir: > > ls -l /kb/deployment/services/communities_qc/webroot > > -rw-r--r-- 1 root root 7634 2013-08-13 15:09 communitiesQC.html > -rw-r--r-- 1 root root 8242 2013-08-13 15:09 > communitiesQC-with-index.html > > But it is not showing up at the test web pages: > > http://140.221.84.191/services/docs/communities_qc/ > > Is this a problem for the developer, the web maintainer (Mr. Brown), > or deployment? > > Miriam >

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Re: [Release-team] Release Team Telecon
by Land, Miriam L. 19 Aug '13

19 Aug '13

Tom, My guess is: we are all waiting on someone to make the go/no-go decision on the modules so they can be deployed to production and tested there. In my opinion it was a hard call because auth and auth_service were among the modules that didn't pass testing during build week. It made it difficult to move forward without them. We have several modules that made improvements after the official end of the build week. It has been a form of build-creep. We are in better shape than we were a week ago. My 2 cents worth = I suggest that we push hard to get full compliance on some of the stragglers by COB Tues. (on any other deadline), do production deploy and test on Wed., create the products on Thurs. and test, then release and announce on Friday. Miriam On 8/18/13 8:22 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >where do we stand with our public release notices and products? > > >On Aug 16, 2013, at 7:46 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> In an ideal world, if we had the person-time available, then sure. As >>it is, I'm not sure who would take on the other responsibilities of the >>people who are working on releases AND other things (e.g., Dan, Shane, >>Mike). (I view Miriam as already fully committed to the release >>team--thank goodness for that!) >> Nomi >> >> On Aug 15, 2013, at 2:44 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> I'm beginning to think that the release team should be a team >>>dedicated to releases. >>> >>> Thoughts anyone? >>> >>> Tom >>> >>> >>> On Aug 13, 2013, at 2:57 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >>> >>>> Here are my issue modules: >>>> >>>> Assembly - developers claims that fixes have been made but these have >>>>not >>>> been retested. >>>> Auth client and service - Not passing testing >>>> Communities_api - minor problems with 3 commands (in scripts but not >>>>in >>>> deployment). Mostly okay as is. >>>> FBA modeling - failing due to workspace deployment problems >>>> Functional ortholog predictor - COMMANDS file has been added since >>>>testing >>>> but the command returns a non-zero value >>>> ID Server - Issues with the command-line commands have been fixed >>>>since >>>> testing. Needs new tag before deployment >>>> Probabilistic Annotation - still failing testing >>>> Communities QC - still failing testing >>>> SHOCK - never passed deployment - hence never tested >>>> >>>> Miriam >>>> >>>> On 8/13/13 3:41 PM, "Nomi L. Harris" <nlharris(a)lbl.gov> wrote: >>>> >>>>> I'm at lunch but Mike is the tech doc lead. Feel free to have the >>>>>meeting >>>>> without me. I pretty much said my piece in my email last night. >>>>> Nomi >>>>> >>>>> Sent from my iPhone >>>>> >>>>> On Aug 13, 2013, at 12:26 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >>>>> >>>>>> Ok.. I primarily wanted to make go over the outstanding issues. >>>>>>The >>>>>> cleared for production >>>>>> column is fairly empty. >>>>>> >>>>>> Nomi, when you get back, can you have a look. I think some may have >>>>>> been waiting on API doc checks? >>>>>> >>>>>> ----- Original Message ----- >>>>>>> From: "Miriam L. Land" <landml(a)ornl.gov> >>>>>>> To: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)kbase.us >>>>>>> Sent: Tuesday, August 13, 2013 2:23:58 PM >>>>>>> Subject: Re: [Release-team] Release Team Telecon >>>>>>> >>>>>>> Nomi went to lunch. >>>>>>> >>>>>>> >>>>>>> On 8/13/13 3:22 PM, "Dan Olson" <dolson(a)mcs.anl.gov> wrote: >>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I apologize, I had a meeting that backed up to this that ran >>>>>>>>long.. >>>>>>>> >>>>>>>> Can we regroup? >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Miriam L. Land" <landml(a)ornl.gov> >>>>>>>>> To: brettin(a)mcs.anl.gov, "Dan Olson" <dolson(a)mcs.anl.gov> >>>>>>>>> Sent: Tuesday, August 13, 2013 2:04:00 PM >>>>>>>>> Subject: Re: Release Team Telecon >>>>>>>>> >>>>>>>>> Who is leading this meeting? >>>>>>>>> >>>>>>>>> Nomi, Mike, and Miriam are in attendance. >>>>>>>>> >>>>>>>>> From: brettin(a)mcs.anl.gov<mailto:[email protected]> >>>>>>>>> When: 3:00 PM - 3:45 PM August 13, 2013 >>>>>>>>> Subject: Release Team Telecon >>>>>>>>> Location: 888-850-4523, passcode: 416791, leader passcode (Dan >>>>>>>>> only) >>>>>>>>> 4167913 >>>>>>>>> >>>>>>>>> >>>>>>>>> The following is a new meeting request: >>>>>>>>> Subject: Release Team Telecon >>>>>>>>> Organizer: brettin(a)mcs.anl.gov<mailto:[email protected]> >>>>>>>>> Sent By: "India S. Gordon" >>>>>>>>> <igordon(a)cels.anl.gov<mailto:[email protected]>> >>>>>>>>> Location: 888-850-4523, passcode: 416791, leader passcode >>>>>>>>> (Dan >>>>>>>>> only) 4167913 >>>>>>>>> Time: Tuesday, August 13, 2013, 2:00:00 PM - 2:45:00 PM GMT >>>>>>>>> -06:00 >>>>>>>>> US/Canada Central >>>>>>>>> Invitees: >>>>>>>>> release-team(a)kbase.us<mailto:[email protected]> >>>>>>>>> *~*~*~*~*~*~*~*~*~* >>>>>>>> _ >

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Re: [Release-team] Release Team Telecon
by Land, Miriam L. 19 Aug '13

19 Aug '13

Shane, The 'make test' for auth_service still ends in 'FAILED'. Am I reading the results right? Am I doing something wrong? Miriam --------------------------------- make test Makefile:53: warning: overriding commands for target `build-docs' Makefile:49: warning: ignoring old commands for target `build-docs' cd authorization_server; \ ./manage.py test authorization_server No connection settings specified: 'Settings' object has no attribute 'MONGODB_CONN' Connection to mongodb.kbase.us by default. WARNING:root:MongoDB is a read-only instance, no roles can be created, updated or deleted Creating test database for alias 'default'... No connection settings specified: 'Settings' object has no attribute 'MONGODB_CONN' sNo connection settings specified: 'Settings' object has no attribute 'MONGODB_CONN' sNo connection settings specified: 'Settings' object has no attribute 'MONGODB_CONN' FNo connection settings specified: 'Settings' object has no attribute 'MONGODB_CONN' s ====================================================================== FAIL: testRead (authorization_server.tests.RoleHandlerTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/kb/dev_container/modules/auth_service/authorization_server/authorization_ server/tests.py", line 252, in testRead self.assertEqual(resp.status_code, 200, "Should accept queries from legit kbase test user") AssertionError: Should accept queries from legit kbase test user ---------------------------------------------------------------------- Ran 4 tests in 0.495s FAILED (failures=1, skipped=3) Destroying test database for alias 'default'... make: *** [test_django] Error 1 On 8/17/13 1:25 PM, "Shane Canon" <scanon(a)lbl.gov> wrote: > >Miriam, > >Shock is deployed now. It still has one minor fix that is required, but >we can work through those during deployment. > >--Shane > >

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