Re: [Release-team] Deploying meme, cmonkey, bambi and inferelator

3 Feb 2014


      No, that's what I was saying in my response to Tom. You'd have to get the
types manually, one by one, and have the owners go through the approval
process on the test server and redo the uploads if you want to duplicate
the prod db. There are short cuts possible, though. I need to deal with
some moving stuff now so I'll outline those when I get in.

-g
Sent from my Cray XT30
On Feb 3, 2014 9:10 AM, "Shane Canon" <[email protected]> wrote:
...
I think a dump from prod of the types and load to test makes sense.  This
allows us to at least be somewhat in sync with the production environment.
 I don't think it is feasible
to have all the data, but it is reasonable to have the types and maybe
some sample data.
Gavin: Do APIs and commands presently exist to do this?
--Shane
On Feb 2, 2014, at 7:56 PM, Gavin Price <[email protected]> wrote:
Sent from my Cray XT30
On Feb 2, 2014 5:07 PM, "Brettin, Thomas S." <[email protected]> wrote:
...
--------
WARNING: At least one of the links in the message below goes to an IP
address (e.g.10.1.1.1), which could be malicious. To learn how to protect
yourself, please go here: https://commons.lbl.gov/x/_591B
...
--------
We need a two step process. Dump all types in prod. Load onto test.
That's not going to happen in the next couple weeks.
...
Seems backwards.
It'll do for now. How we manage types in kbase needs an overall rethink,
as we discussed.
-g
...
Sent from my Verizon Wireless 4G LTE DROID
Gavin Price <[email protected]> wrote:
You don't need to review them, and the mechanics of approving a type (or
a set of types) takes a couple seconds. I would just say that if a type
is available in the prod server it should be available in the test
server, and the prod server can act as the list of approved types. All
the test team needs to do is see if the requester owns the type in the
prod server and if so, approve it on the test server. This could
probably be scripted easily.
...
Why is type registration a risky operation?
Giving all users admin privileges on the test workspace service is what
I was saying seems dangerous.
-g
On 2/2/2014 12:19 PM, Murphy-Olson, Daniel E. wrote:
...
--------
WARNING: At least one of the links in the message below goes to an IP
address (e.g. 10.1.1.1), which could be malicious. To learn how to protect
yourself, please go here: https://commons.lbl.gov/x/_591B
...
...
--------
I don't think the test team has the bandwidth to review and approve
types. I wouldn't even know where to start with criteria.
Why is type registration a risky operation?
--Dan
...
On Feb 2, 2014, at 12:04 PM, "Gavin Price"<[email protected]>  wrote:
Firstly, you may want to check out
http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#transl...
...
http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#transl...
...
These will allow you to translate type names between services even if
the types were not loaded in the same order. Generally I'd recommend
services use the MD5 style type in their code/settings and translate them
to human readable types on startup.
...
There are a few options that are possible:
1) The test team works with each module author to get the appropriate
types installed in the test workspace. That means the module author needs
to request the module name on the test server and a test team rep needs to
approve that request via the admin interface. Then the module author is
free to upload types as necessary.
...
2) The test team sets up a ws admin account and provides the
credentials to testers and module authors, who can then approve their own
modules. This seems a bit dangerous and I probably wouldn't recommend it
...
3) The test team owns all the modules in the test ws and installs any
necessary types for testing themselves.
...
-g
...
On 2/2/2014 8:57 AM, Shane Canon wrote:
Alexey,
You raise some interesting issues.  I hadn't appreciated some of
these complexities.  I'm glad you included Gavin in the chain.  I'm hoping
he has
...
...
some ideas.  For testing purposes perhaps we could upload a snapshot
of the production types into the test workspace.
--Shane
...
On Feb 1, 2014, at 9:20 PM, Alexey Kazakov<[email protected]>
wrote:
Hi all,
workspace service 0.1.x that we use now has several big differences
from the previous workspace version. In particular, it requires
registration of object types for every module to enable the objects to be
saved in workspace, and only module's owner can register typespec for the
module. Thus, several actions must be performed before workspace will be
populated with data:
1. Module's owner requests an authorship of the module
(Workspace.request_module_ownership function).
2. Workspace administrator approves the request (workspace service
WILL NOT notify module's owner about it). This step prevents implementation
of the whole process as a single script.
3. Module's owner registers typespec file and defines a list of
types that will be available in workspace (Workspace.register_typespec
function). At this step, typespec from another workspace can be copied by
Workspace.register_typespec_copy function.
4. Module's owner releases module for general use of its type
(Workspace.release_module).
These four steps can be performed once, as a preparation of a new
workspace installation for data loading. But version numbers for all
registered data types will be 1.0, and I anticipate a potential source of
problems here for modules that use previous versions of data types. I do
not use hard-coded version numbers in meme, cmonkey and inferelator
services, but some other modules may be affected.
If execution of a module depends on other modules or their data
types, their typespec files must be registered too. For instance, meme
module depends on types from KBaseSequences, cmonkey depends on types from
MEME, KBaseExpression, KBaseGenomes, KBaseNetworks typespecs, and
inferelator depends on types from Cmonkey, KBaseGenomes and KBaseExpression
typespecs.
Ideally, deployment of workspace 0.1.x in test environment should
include requests of authorship for all modules currently registered in
production workspace, with subsequent import of all typespecs (including
all versions of typespec) in a proper order from production workspace. This
will re-create all versions of data types from production workspace to
ensure identical behavior of modules in test and production environments.
What you think about it?
Best,
Alexey
...
On 2/1/2014 11:41 AM, Shane Canon wrote:
I'm adding the release-team to the thread so they are in the loop.
The test workspace is a standard deployment in the test
infrastructure.  The only difference is it isn't populated with the data
that is in the production
instance.  In general, it would be best if the tests could assume
that there isn't any data pre-loaded into a data store.  So if it requires
some data in
the workspace, it should populate it as part of the test.
In looking through the modules I see that there are various
references to host in 140.84.*.* and 140.85.*.*.  Are these "production"
services?
I'm worried that what we are deploying is actually contacting test
services on Magellan.  Also, we would prefer that  URLs not be hard coded
in the source code, but instead be read from the deployment
configuration file.  Right now it appears that all of this information is
hard-coded
in the java files, and we would need to recompile and redeploy if
we needed to change a URL.
By the way, my workaround for the type compiler issue is that I
have add the dev branch of the type compiler as a submodule.  This isn't
ideal but
at least provides a way for us to move forward.  I will try to
create a branch with these changes so that you can review them and merge
them in
if they seem reasonable.  Another option would be for you to add
the generated code to the module repo and only run the type comp when it
is necessary (i.e. a major change in the type compiler or an API
change).
--Shane
...
On Jan 31, 2014, at 5:26 PM, Alexey Kazakov<[email protected]>
wrote:
Hi Shane,
cmonkey and inferelator tests should pass because these services
call AWE client which is doing all calculations. Tests of three functions
of meme that call AWE client passed too. I am trying to figure out how to
deal with other meme functions that run MEME locally. How the workspace
service was configured for testing environment? Were modules and object
types from production WS made available for the testing WS, or this is only
a new clean installation?
Thank you,
Alexey
...
On 1/31/2014 4:48 PM, Shane Canon wrote:
Pavel,
Thanks for pointing me to Alexey.  I apologize that I keep
forgetting who was working on this.
BTW, I have inferelator up and running.  It seemed to pass the
tests easily.  There doesn't
appear to be any code in bambi (just a spec file).  So there
isn't anything to deploy there yet.
So the only one that we need to figure out is meme.  This
appears to just be due to testing
against a workspace service that isn't the production one.  So
it is probably missing some
objects that are used in the test.  I would like to have a test
I can run in the test environment
just for completeness.  But I think we are close.
--Shane
...
On Jan 31, 2014, at 2:50 PM, Pavel Novichkov<
[email protected]>    wrote:
Hi Shane,
Alexey (cc-ed) was the primary developer of meme, cmnokey and
inferelator services. Please talk to Alexey.
Thanks,
P.
...
On Jan 31, 2014, at 1:01 PM, Shane Canon<[email protected]>
wrote:
Pavel,
I'm working through the services.  I have cmonkey and meme
deployed.  I've noticed a few things that we will need to fix, but I'm
working around for
now.  Some of these are artifacts due to we no longer install
into /kb/deployment.  So if the code or tests assume that, then it can
cause problems.
We also install as a non-root user.  So this can sometime lead
to problems too.  If you or Roman grep through the code and look for
references
to /kb/deployment, then you will see what needs to be
addressed.  I also noticed that the tests have hard coded references for a
magellan host.
So that needs to be fixed.
After deploying meme, I am seeing the following failures when
I run make test.  I could use some help to understand how to deal with
these.
For now, I will work on bambi and inferelator.
--Shane
ubuntu@t46:/kbase/deployments/20140109-prod/dev_container/modules/meme$
make test
../../tools/Makefile.common.rules:36: warning: overriding
commands for target `deploy-libs'
Makefile:47: warning: ignoring old commands for target
`deploy-libs'
# run each test
/kbase/runtimes/20140109-prod/bin/perl
test/script_tests-command-line.t ; \
       if [ $? -ne 0 ] ; then \
               exit 1 ; \
       fi \
1..24
ok 1 - creating Test::Cmd object for
find_motifs_with_meme_from_ws
not ok 2 - Running find_motifs_with_meme_from_ws
#   Failed test 'Running find_motifs_with_meme_from_ws'
#   at test/script_tests-command-line.t line 32.
MemeRunResult ID:
{"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id
cannot be null or the empty
string","error":"us.kbase.common.service.ServerException: id cannot be null
or the empty string\n\tat
us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat
us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat
us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat
us.kbase.meme.MemeServerImpl.findMotifsWithMemeJobFromWs(MemeServerImpl.java:594)\n\tat
us.kbase.meme.MemeServerImpl.findMotifsWithMemeFromWs(MemeServerImpl.java:559)\n\tat
us.kbase.meme.MemeServerCaller.findMotifsWithMemeFromWs(MemeServerCaller.java:60)\n\tat
us.kbase.meme.MEMEServer.findMotifsWithMemeFromWs(MEMEServer.java:103)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat
...
...
...
n.reflect.Deleg
...
...
...
...
...
...
...
atingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat
java.lang.reflect.Method.invoke(Method.java:606)\n\tat
us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat
org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat
org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat
org.apache.catalina.connector.CoyoteA
 da
pter.service(Coy
...
oteAdapter.java:231)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat
com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat
com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat
com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat
com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat
com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat
com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat
com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat
com.sun.griz
 zl
y.SelectionKeyCo
ntextTask.call(SelectionKeyContextTask.java:59)\n\tat
com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat
java.lang.Thread.run(Thread.java:744)\n"},"id":"995521465406405"}
not ok 3 - MEME run successfuly
#   Failed test 'MEME run successfuly'
#   at test/script_tests-command-line.t line 35.
ok 4 - creating Test::Cmd object for
find_motifs_with_meme_job_from_ws
ok 5 - Running find_motifs_with_meme_job_from_ws
Job ID: 52ebf83ee4b0b278264a5393
ok 6 - MEME run successfuly
ok 7 - creating Test::Cmd object for
get_pspm_collection_from_meme_result_from_ws
not ok 8 - Running get_pspm_collection_from_meme_result_from_ws
#   Failed test 'Running
get_pspm_collection_from_meme_result_from_ws'
#   at test/script_tests-command-line.t line 50.
MemePSPMCollection ID:
{"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id
cannot be null or the empty
string","error":"us.kbase.common.service.ServerException: id cannot be null
or the empty string\n\tat
us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat
us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat
us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat
us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeJobResultFromWs(MemeServerImpl.java:917)\n\tat
us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeResultFromWs(MemeServerImpl.java:882)\n\tat
us.kbase.meme.MemeServerCaller.getPspmCollectionFromMemeResultFromWs(MemeServerCaller.java:488)\n\tat
us.kbase.meme.MEMEServer.getPspmCollectionFromMemeResultFromWs(MEMEServer.java:338)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat
sun.reflect.NativeMethodAccesso
 rI
mpl.invoke(Nati
veMethodAccessorImpl.java:57)\n\tat
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat
java.lang.reflect.Method.invoke(Method.java:606)\n\tat
us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat
org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat
org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.
 ja
va:331)\n\tat or
g.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat
com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat
com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat
com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat
com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat
com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat
com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat
com.sun.grizzly.ProtocolChainContextTask.doCall
 (P
rotocolChainCont
...
extTask.java:54)\n\tat
com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat
com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat
java.lang.Thread.run(Thread.java:744)\n"},"id":"633289031774389"}
not ok 9 - MEME PSPM collection generated successfuly
#   Failed test 'MEME PSPM collection generated successfuly'
#   at test/script_tests-command-line.t line 53.
ok 10 - creating Test::Cmd object for
get_pspm_collection_from_meme_result_job_from_ws
not ok 11 - Running
get_pspm_collection_from_meme_result_job_from_ws
#   Failed test 'Running
get_pspm_collection_from_meme_result_job_from_ws'
#   at test/script_tests-command-line.t line 59.
Job ID:
{"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"MemeRunResult
download error","error":"java.lang.Exception: MemeRunResult download
error\n\tat
us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeJobResultFromWs(MemeServerImpl.java:919)\n\tat
us.kbase.meme.MemeServerCaller.getPspmCollectionFromMemeResultJobFromWs(MemeServerCaller.java:502)\n\tat
us.kbase.meme.MEMEServer.getPspmCollectionFromMemeResultJobFromWs(MEMEServer.java:358)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat
java.lang.reflect.Method.invoke(Method.java:606)\n\tat
us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:77
su
 0)
...
...
\n\tat org.apac
...
...
...
...
...
...
...
he.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat
org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat
com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat
com.sun.grizzly.http.ProcessorTask
 .d
oProcess(Process
...
orTask.java:757)\n\tat
com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat
com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat
com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat
com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat
com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat
com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat
com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat
java.lang.Thread.run(Thread.java:744)\n"},"id":"6
 56
565433923738"}
ok 12 - MEME PSPM collection generated successfuly
ok 13 - creating Test::Cmd object for
compare_motifs_with_tomtom_by_collection_from_ws
not ok 14 - Running
compare_motifs_with_tomtom_by_collection_from_ws
#   Failed test 'Running
compare_motifs_with_tomtom_by_collection_from_ws'
#   at test/script_tests-command-line.t line 69.
TomtomRunResult ID:     Failed to acquire token: Failed to get
auth token: Failed to query Globus Online: 500 read timeout at
/kbase/deployments/20140109-prod//lib/Bio/KBase/AuthToken.pm line 574.
not ok 15 - TOMTOM run successfuly
#   Failed test 'TOMTOM run successfuly'
#   at test/script_tests-command-line.t line 72.
ok 16 - creating Test::Cmd object for
compare_motifs_with_tomtom_job_by_collection_from_ws
ok 17 - Running
compare_motifs_with_tomtom_job_by_collection_from_ws
Job ID: 52ebf85be4b0b278264a5395
ok 18 - TOMTOM run successfuly
ok 19 - creating Test::Cmd object for
find_sites_with_mast_by_collection_from_ws
not ok 20 - Running find_sites_with_mast_by_collection_from_ws
#   Failed test 'Running
find_sites_with_mast_by_collection_from_ws'
#   at test/script_tests-command-line.t line 87.
MastRunResult ID:
{"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id
cannot be null or the empty
string","error":"us.kbase.common.service.ServerException: id cannot be null
or the empty string\n\tat
us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat
us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat
us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat
us.kbase.meme.MemeServerImpl.findSitesWithMastJobByCollectionFromWs(MemeServerImpl.java:1298)\n\tat
us.kbase.meme.MemeServerImpl.findSitesWithMastByCollectionFromWs(MemeServerImpl.java:1260)\n\tat
us.kbase.meme.MemeServerCaller.findSitesWithMastByCollectionFromWs(MemeServerCaller.java:287)\n\tat
us.kbase.meme.MEMEServer.findSitesWithMastByCollectionFromWs(MEMEServer.java:279)\n\tat
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat
sun.reflect.NativeMethodAccessorImpl.
 in
voke(NativeMeth
odAccessorImpl.java:57)\n\tat
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat
java.lang.reflect.Method.invoke(Method.java:606)\n\tat
us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat
javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat
org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat
org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:3
 31
)\n\tat org.apac
he.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat
com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat
com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat
com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat
com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat
com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat
com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat
com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat
com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat
com.sun.grizzly.ProtocolChainContextTask.doCall(Proto
 co
lChainContextTas
...
k.java:54)\n\tat
com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat
com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat
com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat
java.lang.Thread.run(Thread.java:744)\n"},"id":"125399939805853"}
not ok 21 - MAST run successfuly
#   Failed test 'MAST run successfuly'
#   at test/script_tests-command-line.t line 90.
ok 22 - creating Test::Cmd object for
find_sites_with_mast_job_by_collection_from_ws
ok 23 - Running find_sites_with_mast_job_by_collection_from_ws
Job ID: 52ebf86ce4b0b278264a5396
ok 24 - MAST run successfuly
# Looks like you failed 9 tests of 24.
make: *** [test-scripts] Error 1

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Release-team mailing list
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Gavin Price

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