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

Re: [Release-team] plant ontolog, . expression, and co-expression networks in IRIS
by Thomas Brettin 15 Feb '13

15 Feb '13

Also, for the plant_expression service, you will need to pull changes to the dev_container out of the kbase.us git repo before doing the make. On Feb 15, 2013, at 2:56 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Hey Guys, I've been working with Shinjae. Here is where we stand (sorry if you already know this): > > 1) redeploy ontology_service immediately > 2) redeploy networks immediately > 3) redeploy plant_expression on Shinjae's command > > Shinjae needs to verify a few more things on plant_expression service. > > Tom > > > > > On Feb 15, 2013, at 10:43 AM, Sergei Maslov <maslov(a)bnl.gov> wrote: > >> Tom, >> >> I just wanted to confirm that these services will be available in IRIS. >> My understanding is that if it will pass all the tests it will start being deployed next Tuesday. >> >> I may be showing a video demo walking through these steps >> https://docs.google.com/document/d/1kIBk19jjWsegApoG4QNAKEZ48eBNae8jXQW8EFq… >> at the Bethesda meeting and I would like to record it using the IRIS interface. >> Shinjae promised to help with recording. >> >> Sergei >> >> -- >> Dr. Sergei Maslov, >> Department of Biology, >> Brookhaven National Laboratory, >> Upton, New York, 11973 >> Tel: (631) 344-3742; >> FAX: (631) 344-3407 >> E@mail: maslov(a)bnl.gov >> WWW: http://www.cmth.bnl.gov/~maslov >> > > Thomas Brettin > 865-603-7760 (cell) > brettin(a)mcs.anl.gov > > > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] plant ontolog, . expression, and co-expression networks in IRIS
by Thomas Brettin 15 Feb '13

15 Feb '13

Hey Guys, I've been working with Shinjae. Here is where we stand (sorry if you already know this): 1) redeploy ontology_service immediately 2) redeploy networks immediately 3) redeploy plant_expression on Shinjae's command Shinjae needs to verify a few more things on plant_expression service. Tom On Feb 15, 2013, at 10:43 AM, Sergei Maslov <maslov(a)bnl.gov> wrote: > Tom, > > I just wanted to confirm that these services will be available in IRIS. > My understanding is that if it will pass all the tests it will start being deployed next Tuesday. > > I may be showing a video demo walking through these steps > https://docs.google.com/document/d/1kIBk19jjWsegApoG4QNAKEZ48eBNae8jXQW8EFq… > at the Bethesda meeting and I would like to record it using the IRIS interface. > Shinjae promised to help with recording. > > Sergei > > -- > Dr. Sergei Maslov, > Department of Biology, > Brookhaven National Laboratory, > Upton, New York, 11973 > Tel: (631) 344-3742; > FAX: (631) 344-3407 > E@mail: maslov(a)bnl.gov > WWW: http://www.cmth.bnl.gov/~maslov > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] redeploy phispy
by Shane Canon 14 Feb '13

14 Feb '13

Ready. --S On Feb 14, 2013, at 9:15 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > I'll mark phispy for redeploy. > > Miriam > > On 2/14/13 12:14 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > >> Thanks, >> >> fixed server-tests >> >> tom >> >> >> Thomas Brettin >> 865-603-7760 (cell) >> brettin(a)mcs.anl.gov >> >> >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team > > _______________________________________________ > 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] redeploy phispy
by Land, Miriam L. 14 Feb '13

14 Feb '13

I'll mark phispy for redeploy. Miriam On 2/14/13 12:14 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >Thanks, > >fixed server-tests > >tom > > >Thomas Brettin >865-603-7760 (cell) >brettin(a)mcs.anl.gov > > > >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

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redeploy phispy
by Thomas Brettin 14 Feb '13

14 Feb '13

Thanks, fixed server-tests tom Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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redeploy phispy requested
by Thomas Brettin 14 Feb '13

14 Feb '13

mods to make file mods to runtime added client tests tom Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] Fwd: API doc for regprecise
by Dan Olson 13 Feb '13

13 Feb '13

I've redeployed this. It gets a startup error, which it seems to have always had.. It doesn't look like it affects deployment, but I'm going to bring it up with the owner. -- root@t21:~# ./deploy.rsc Service is regprecise No pid file /kb/deployment/services/cdmi_api/service.pid found for service cdmi_api No pid file /kb/deployment/services/idserver/service.pid found for service idserver Waiting for the domain to stop ..... Command stop-domain executed successfully. - Cloning dev_container - Cloning kb_seed - Cloning kbapi_common - Cloning typecomp - Cloning auth - Cloning idserver Running Make in dev_container Running Make deploy in dev_container ==== Deploying regprecise - Cloning regprecise * Using 20130213-test for regprecise - Processing dependencies for regprecise Starting bootstrap at /kb/dev_container Running make Running make deploy root@t21:~# There is a process already using the admin port 4848 -- it probably is another instance of a GlassFish server. Command start-domain failed. ----- Original Message ----- > From: "Miriam L. Land" <landml(a)ornl.gov> > To: "Nomi Harris" <nlharris(a)lbl.gov>, release-team(a)lists.kbase.us > Sent: Wednesday, February 13, 2013 10:29:48 AM > Subject: Re: [Release-team] Fwd: API doc for regprecise > > Nomi, > > I've marked the spreadsheet for redeploy of regprecise. > > Miriam > > From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> > Date: Wednesday, February 13, 2013 10:26 AM > To: "release-team(a)lists.kbase.us<mailto:[email protected]>" > <release-team(a)lists.kbase.us<mailto:[email protected]>> > Subject: [Release-team] Fwd: API doc for regprecise [was Re: Initial > tech doc results for your module (Full Build, Feb 4, 2013)] > > Dear Deploy team, > Can you re-deploy regprecise? > Thanks, > Nomi > > Begin forwarded message: > > From: "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> > Subject: Re: API doc for regprecise [was Re: Initial tech doc results > for your module (Full Build, Feb 4, 2013)] > Date: February 13, 2013 12:51:00 AM PST > To: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> > Cc: Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> > > > Nomi, > > Your suggested changes is in place now: > > root@ntest:/kb/dev_container/modules/regprecise# ls -al > /kb/deployment/services/Regulation/webroot/ > total 40 > drwxr-xr-x 2 root root 4096 2013-02-13 08:48 . > drwxr-xr-x 3 root root 4096 2013-02-13 08:48 .. > -rw-r--r-- 1 root root 32716 2013-02-13 08:48 Regulation.html > root@ntest:/kb/dev_container/modules/regprecise# > > Please let me know if you have any other issues with Makefile. > > Thanks, > -SJ > > On Feb 13, 2013, at 3:41 AM, Shinjae Yoo wrote: > > Thanks Nomi, > > Two things: > > 1) deploy-docs target fixed last week > It seems the Makefile is old version > > 2) If you want just empty folder as web root, I can make changes to > deploy-dir target to have empty webroot folder to copy it. > I'll make this change now and test it on my test VM. > > -SJ > > On Feb 12, 2013, at 5:46 PM, Nomi Harris wrote: > > (Sorry, forgot to cc you, Shinjae.) > Nomi > > Begin forwarded message: > > From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> > Subject: API doc for regprecise [was Re: Initial tech doc results for > your module (Full Build, Feb 4, 2013)] > Date: February 12, 2013 11:55:19 AM PST > To: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]>> > Cc: "Tom S. Brettin" > <Brettin(a)mcs.anl.gov<mailto:[email protected]>>, Shane Canon > <scanon(a)lbl.gov<mailto:[email protected]>>, Nomi Harris > <NLHarris(a)lbl.gov<mailto:[email protected]>> > > Hi Pavel, > The "deploy-docs" target in your Makefile is still copying docs to > the wrong directory; furthermore, by copying docs/*html it copies an > index.html that is a Glassfish default page, which then hides the > actual API doc (Regulation.html) from being visible in > http://140.221.84.191/services/docs/Regulation/ . (If you look there > now, you can see Regulation.html only because Shane manually moved > index.html to index2.html.) > > Your Makefile has: > deploy-docs: build-docs > cp docs/*.html $(TARGET)/services/$(SERVICE_NAME)/webroot/docroot/ > > It should say (I think--I did not actually test this): > deploy-docs: build-docs > mkdir -p $(TARGET)/services/$(SERVICE_NAME)/webroot > cp docs/Regulation.html $(TARGET)/services/$(SERVICE_NAME)/webroot > > Please let us know when you've made that change so we can redeploy > regprecise and make sure the API doc ends up in the correct place so > that we can clear your module for production release. > > Thanks, > Nomi > > > On Feb 5, 2013, at 9:44 AM, Nomi Harris > <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > > Dear KBase Module Owner, > > Modules are required to have API docs deployed to the appropriate > webroot directory in order to be included in the release. For this > release, API docs should be visibile in > http://140.221.84.191/services/docs/ > > If your module's Makefile conforms to the KBase standard Makefile, > “make deploy” will have run “make deploy-docs”, which should make > the html documents and copy them to webroot: > ($(TARGET)/services/$(SERVICE)/webroot/ where $(TARGET) is typically > /kb/deployment and $(SERVICE) is the name of your service--so, for > example, /kb/deployment/services/idserver/webroot). These docs are > normally generated from the comments in the typespec. > > RESULTS OF TECH DOC CHECK (Full release, week of 2/4/2013) > MODULE NAME: regprecise > AUTHOR(S): psnovichkov(a)lbl.gov<mailto:[email protected]> > DIRECTORY FOR API DOCS: > http://140.221.84.191/services/docs/Regulation > API DOCS PRESENT AT THAT URL? No--your "deploy-docs" target is > copying the docs to the wrong directory. Please change to conform to > the standard Makefile, > https://git.kbase.us/dev_container.git/blob/HEAD:/doc/module.Makefile > for more info. > API DOCS COMPLETE? yes (but in wrong dir) > > _______________________________________________ > 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] Fwd: API doc for regprecise
by Land, Miriam L. 13 Feb '13

13 Feb '13

Nomi, I've marked the spreadsheet for redeploy of regprecise. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Wednesday, February 13, 2013 10:26 AM To: "release-team(a)lists.kbase.us<mailto:[email protected]>" <release-team(a)lists.kbase.us<mailto:[email protected]>> Subject: [Release-team] Fwd: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)] Dear Deploy team, Can you re-deploy regprecise? Thanks, Nomi Begin forwarded message: From: "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> Subject: Re: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)] Date: February 13, 2013 12:51:00 AM PST To: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Cc: Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> Nomi, Your suggested changes is in place now: root@ntest:/kb/dev_container/modules/regprecise# ls -al /kb/deployment/services/Regulation/webroot/ total 40 drwxr-xr-x 2 root root 4096 2013-02-13 08:48 . drwxr-xr-x 3 root root 4096 2013-02-13 08:48 .. -rw-r--r-- 1 root root 32716 2013-02-13 08:48 Regulation.html root@ntest:/kb/dev_container/modules/regprecise# Please let me know if you have any other issues with Makefile. Thanks, -SJ On Feb 13, 2013, at 3:41 AM, Shinjae Yoo wrote: Thanks Nomi, Two things: 1) deploy-docs target fixed last week It seems the Makefile is old version 2) If you want just empty folder as web root, I can make changes to deploy-dir target to have empty webroot folder to copy it. I'll make this change now and test it on my test VM. -SJ On Feb 12, 2013, at 5:46 PM, Nomi Harris wrote: (Sorry, forgot to cc you, Shinjae.) Nomi Begin forwarded message: From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Subject: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)] Date: February 12, 2013 11:55:19 AM PST To: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]>> Cc: "Tom S. Brettin" <Brettin(a)mcs.anl.gov<mailto:[email protected]>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>>, Nomi Harris <NLHarris(a)lbl.gov<mailto:[email protected]>> Hi Pavel, The "deploy-docs" target in your Makefile is still copying docs to the wrong directory; furthermore, by copying docs/*html it copies an index.html that is a Glassfish default page, which then hides the actual API doc (Regulation.html) from being visible in http://140.221.84.191/services/docs/Regulation/ . (If you look there now, you can see Regulation.html only because Shane manually moved index.html to index2.html.) Your Makefile has: deploy-docs: build-docs cp docs/*.html $(TARGET)/services/$(SERVICE_NAME)/webroot/docroot/ It should say (I think--I did not actually test this): deploy-docs: build-docs mkdir -p $(TARGET)/services/$(SERVICE_NAME)/webroot cp docs/Regulation.html $(TARGET)/services/$(SERVICE_NAME)/webroot Please let us know when you've made that change so we can redeploy regprecise and make sure the API doc ends up in the correct place so that we can clear your module for production release. Thanks, Nomi On Feb 5, 2013, at 9:44 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: Dear KBase Module Owner, Modules are required to have API docs deployed to the appropriate webroot directory in order to be included in the release. For this release, API docs should be visibile in http://140.221.84.191/services/docs/ If your module's Makefile conforms to the KBase standard Makefile, “make deploy” will have run “make deploy-docs”, which should make the html documents and copy them to webroot: ($(TARGET)/services/$(SERVICE)/webroot/ where $(TARGET) is typically /kb/deployment and $(SERVICE) is the name of your service--so, for example, /kb/deployment/services/idserver/webroot). These docs are normally generated from the comments in the typespec. RESULTS OF TECH DOC CHECK (Full release, week of 2/4/2013) MODULE NAME: regprecise AUTHOR(S): psnovichkov(a)lbl.gov<mailto:[email protected]> DIRECTORY FOR API DOCS: http://140.221.84.191/services/docs/Regulation API DOCS PRESENT AT THAT URL? No--your "deploy-docs" target is copying the docs to the wrong directory. Please change to conform to the standard Makefile, https://git.kbase.us/dev_container.git/blob/HEAD:/doc/module.Makefile for more info. API DOCS COMPLETE? yes (but in wrong dir)

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Fwd: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)]
by Nomi Harris 13 Feb '13

13 Feb '13

Dear Deploy team, Can you re-deploy regprecise? Thanks, Nomi Begin forwarded message: > From: "Yoo, Shinjae" <sjyoo(a)bnl.gov> > Subject: Re: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)] > Date: February 13, 2013 12:51:00 AM PST > To: Nomi Harris <nlharris(a)lbl.gov> > Cc: Pavel Novichkov <psnovichkov(a)lbl.gov> > > Nomi, > > > Your suggested changes is in place now: > > root@ntest:/kb/dev_container/modules/regprecise# ls -al /kb/deployment/services/Regulation/webroot/ > total 40 > drwxr-xr-x 2 root root 4096 2013-02-13 08:48 . > drwxr-xr-x 3 root root 4096 2013-02-13 08:48 .. > -rw-r--r-- 1 root root 32716 2013-02-13 08:48 Regulation.html > root@ntest:/kb/dev_container/modules/regprecise# > > Please let me know if you have any other issues with Makefile. > > Thanks, > -SJ > > On Feb 13, 2013, at 3:41 AM, Shinjae Yoo wrote: > >> Thanks Nomi, >> >> Two things: >> >> 1) deploy-docs target fixed last week >> It seems the Makefile is old version >> >> 2) If you want just empty folder as web root, I can make changes to deploy-dir target to have empty webroot folder to copy it. >> I'll make this change now and test it on my test VM. >> >> -SJ >> >> On Feb 12, 2013, at 5:46 PM, Nomi Harris wrote: >> >>> (Sorry, forgot to cc you, Shinjae.) >>> Nomi >>> >>> Begin forwarded message: >>> >>>> From: Nomi Harris <nlharris(a)lbl.gov> >>>> Subject: API doc for regprecise [was Re: Initial tech doc results for your module (Full Build, Feb 4, 2013)] >>>> Date: February 12, 2013 11:55:19 AM PST >>>> To: Pavel Novichkov <PSNovichkov(a)lbl.gov> >>>> Cc: "Tom S. Brettin" <Brettin(a)mcs.anl.gov>, Shane Canon <scanon(a)lbl.gov>, Nomi Harris <NLHarris(a)lbl.gov> >>>> >>>> Hi Pavel, >>>> The "deploy-docs" target in your Makefile is still copying docs to the wrong directory; furthermore, by copying docs/*html it copies an index.html that is a Glassfish default page, which then hides the actual API doc (Regulation.html) from being visible in http://140.221.84.191/services/docs/Regulation/ . (If you look there now, you can see Regulation.html only because Shane manually moved index.html to index2.html.) >>>> >>>> Your Makefile has: >>>> deploy-docs: build-docs >>>> cp docs/*.html $(TARGET)/services/$(SERVICE_NAME)/webroot/docroot/ >>>> >>>> It should say (I think--I did not actually test this): >>>> deploy-docs: build-docs >>>> mkdir -p $(TARGET)/services/$(SERVICE_NAME)/webroot >>>> cp docs/Regulation.html $(TARGET)/services/$(SERVICE_NAME)/webroot >>>> >>>> Please let us know when you've made that change so we can redeploy regprecise and make sure the API doc ends up in the correct place so that we can clear your module for production release. >>>> >>>> Thanks, >>>> Nomi >>>> >>>> >>>> On Feb 5, 2013, at 9:44 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>> >>>>> Dear KBase Module Owner, >>>>> >>>>> Modules are required to have API docs deployed to the appropriate webroot directory in order to be included in the release. For this release, API docs should be visibile in http://140.221.84.191/services/docs/ >>>>> >>>>> If your module's Makefile conforms to the KBase standard Makefile, “make deploy” will have run “make deploy-docs”, which should make the html documents and copy them to webroot: ($(TARGET)/services/$(SERVICE)/webroot/ where $(TARGET) is typically /kb/deployment and $(SERVICE) is the name of your service--so, for example, /kb/deployment/services/idserver/webroot). These docs are normally generated from the comments in the typespec. >>>>> >>>>> RESULTS OF TECH DOC CHECK (Full release, week of 2/4/2013) >>>>> MODULE NAME: regprecise >>>>> AUTHOR(S): psnovichkov(a)lbl.gov >>>>> DIRECTORY FOR API DOCS: http://140.221.84.191/services/docs/Regulation >>>>> API DOCS PRESENT AT THAT URL? No--your "deploy-docs" target is copying the docs to the wrong directory. Please change to conform to the standard Makefile, https://git.kbase.us/dev_container.git/blob/HEAD:/doc/module.Makefile for more info. >>>>> API DOCS COMPLETE? yes (but in wrong dir)

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Re: [Release-team] Deployments
by Dan Olson 11 Feb '13

11 Feb '13

Hey.. I'm just getting started with the redeployments today. I had to do some reconciling of where we're at. I did that earlier this morning and sent new, additional, notices to the developers we're waiting on items from. I don't think I need any help at the moment. They should all be redeployed within an hour. ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: "Shane Canon" <scanon(a)lbl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov> > Cc: release-team(a)lists.kbase.us > Sent: Monday, February 11, 2013 12:37:35 PM > Subject: Re: [Release-team] Deployments > > Hey guys, > > want me to do some deployments? > > Tom > > > On Feb 11, 2013, at 12:17 PM, "Land, Miriam L." <landml(a)ornl.gov> > wrote: > > > Will there be any deployments today? I haven't seen any changes > > since I added modules to be deployed on Friday morning. > > > > Miriam > > _______________________________________________ > > Release-team mailing list > > Release-team(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/release-team > > Thomas Brettin > 865-603-7760 (cell) > brettin(a)mcs.anl.gov > > > >

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