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

Redeploy sim_service
by Nomi Harris 08 Aug '13

08 Aug '13

sim_service has been updated and needs to be redeployed. Thanks, Nomi

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Re: [Release-team] Status of initial tech doc testing
by Shane Canon 08 Aug '13

08 Aug '13

I've re-generated the nginx config. The only difference I saw was the addition of the microbes_model_builder which looks like a lab (versus a service) and doesn't have any typical service documentation. Was there anything else missing? I've fixed the broken links for all but FBA. FBA doesn't appeared to be deployed. I wasn't sure if there was a reason for that. --Shane On Aug 7, 2013, at 9:14 PM, Thomas Brettin <brettin(a)mcs.anl.gov> 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: > http://www.lbl.gov/cyber/services/suspicious-links.html > -------- > > Can someone on the sys admin team fix this? > > Thanks, > Tom > > > On Aug 7, 2013, at 6:58 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > >> Nearly all of the services that have been deployed passed the initial doc testing. >> >> The two exceptions are 'sim_service', which is not deploying API docs at all (needs to add the proper doc generation and deployment code to its Makefile), and 'search', which was deployed to a test VM that I couldn't find (not available from t1 by ssh search ??), and has no docs appearing here: http://140.221.84.191/services/docs/search/ >> >> In addition, several modules do have proper documentation that seems to be properly deployed, but is not appearing here: http://140.221.84.191/services/docs . It's probably just a proxy issue, but here is the list of those modules: >> >> auth_service >> cluster_service >> expression >> KBaseFBAModeling >> plant_expression_service >> >> >> _______________________________________________ >> 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] Status of release notes
by Nomi Harris 08 Aug '13

08 Aug '13

Thanks, Bob! Nomi On Aug 8, 2013, at 9:58 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > I added release notes for phispy as well. > > On Aug 7, 2013, at 7:47 PM, Michael Sneddon wrote: > >> I manually looked at the release notes for each of the modules that are deployed, and here is an updated report. Roughly the same results as the automated test though. I think just one or two differences from what Nomi compiled. >> >> Release Notes Not Found At All >> genome_annotation >> kb_seed >> matR >> phispy >> registry >> sim_service >> >> Release Notes File Found, but not up-to-date >> auth_service >> cluster_service >> KBaseFBAModeling >> id_server >> communities_qc >> typecomp >> workspace_service >> >> Release Notes are good >> auth >> expression >> plant_expression >> probabilistic_annotation >> protein_info_service >> trees >> >> >> >> On Wed, Aug 7, 2013 at 7:25 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> Only 7 out of the 27 services in this Build have up-to-date release notes (or it's possible that they put their release notes in an unexpected place or gave it a name that didn't include *rel* or *REL*). >> genome_annotation: None >> assembly: Out of date >> auth: good >> auth_service: out of date >> aux_store: none >> kb_seed: none >> cluster_service: out of date >> communities_api: none >> expression: none >> KBaseFBAModeling: out of date >> functional_ortholog_predictor: good >> idserver: out of date >> invocation: good >> kb_model_seed: none >> matR: none >> microbes_model_builder: none >> phispy: none >> plant_expression_service: good >> probabilistic_annotation: good >> protein_info_service: good >> communities_qc: out of date >> registry: none >> sim_service: none >> trees: good >> typecomp: out of date (and rudimentary) >> workspace_service: out of date >> >> Nomi >> _______________________________________________ >> 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] Status of release notes
by Robert Olson 08 Aug '13

08 Aug '13

I added release notes for phispy as well. On Aug 7, 2013, at 7:47 PM, Michael Sneddon wrote: > I manually looked at the release notes for each of the modules that are deployed, and here is an updated report. Roughly the same results as the automated test though. I think just one or two differences from what Nomi compiled. > > Release Notes Not Found At All > genome_annotation > kb_seed > matR > phispy > registry > sim_service > > Release Notes File Found, but not up-to-date > auth_service > cluster_service > KBaseFBAModeling > id_server > communities_qc > typecomp > workspace_service > > Release Notes are good > auth > expression > plant_expression > probabilistic_annotation > protein_info_service > trees > > > > On Wed, Aug 7, 2013 at 7:25 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Only 7 out of the 27 services in this Build have up-to-date release notes (or it's possible that they put their release notes in an unexpected place or gave it a name that didn't include *rel* or *REL*). > genome_annotation: None > assembly: Out of date > auth: good > auth_service: out of date > aux_store: none > kb_seed: none > cluster_service: out of date > communities_api: none > expression: none > KBaseFBAModeling: out of date > functional_ortholog_predictor: good > idserver: out of date > invocation: good > kb_model_seed: none > matR: none > microbes_model_builder: none > phispy: none > plant_expression_service: good > probabilistic_annotation: good > protein_info_service: good > communities_qc: out of date > registry: none > sim_service: none > trees: good > typecomp: out of date (and rudimentary) > workspace_service: out of date > > Nomi > _______________________________________________ > 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] Status of initial tech doc testing
by Thomas Brettin 07 Aug '13

07 Aug '13

Can someone on the sys admin team fix this? Thanks, Tom On Aug 7, 2013, at 6:58 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > Nearly all of the services that have been deployed passed the initial doc testing. > > The two exceptions are 'sim_service', which is not deploying API docs at all (needs to add the proper doc generation and deployment code to its Makefile), and 'search', which was deployed to a test VM that I couldn't find (not available from t1 by ssh search ??), and has no docs appearing here: http://140.221.84.191/services/docs/search/ > > In addition, several modules do have proper documentation that seems to be properly deployed, but is not appearing here: http://140.221.84.191/services/docs . It's probably just a proxy issue, but here is the list of those modules: > > auth_service > cluster_service > expression > KBaseFBAModeling > plant_expression_service > > > _______________________________________________ > 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] Status of release notes
by Thomas Brettin 07 Aug '13

07 Aug '13

Mike, Did you communicate this to module owners? Tom On Aug 7, 2013, at 6:47 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > I manually looked at the release notes for each of the modules that are deployed, and here is an updated report. Roughly the same results as the automated test though. I think just one or two differences from what Nomi compiled. > > Release Notes Not Found At All > genome_annotation > kb_seed > matR > phispy > registry > sim_service > > Release Notes File Found, but not up-to-date > auth_service > cluster_service > KBaseFBAModeling > id_server > communities_qc > typecomp > workspace_service > > Release Notes are good > auth > expression > plant_expression > probabilistic_annotation > protein_info_service > trees > > > > On Wed, Aug 7, 2013 at 7:25 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Only 7 out of the 27 services in this Build have up-to-date release notes (or it's possible that they put their release notes in an unexpected place or gave it a name that didn't include *rel* or *REL*). > genome_annotation: None > assembly: Out of date > auth: good > auth_service: out of date > aux_store: none > kb_seed: none > cluster_service: out of date > communities_api: none > expression: none > KBaseFBAModeling: out of date > functional_ortholog_predictor: good > idserver: out of date > invocation: good > kb_model_seed: none > matR: none > microbes_model_builder: none > phispy: none > plant_expression_service: good > probabilistic_annotation: good > protein_info_service: good > communities_qc: out of date > registry: none > sim_service: none > trees: good > typecomp: out of date (and rudimentary) > workspace_service: out of date > > Nomi > _______________________________________________ > 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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Status of initial tech doc testing
by Michael Sneddon 07 Aug '13

07 Aug '13

Nearly all of the services that have been deployed passed the initial doc testing. The two exceptions are 'sim_service', which is not deploying API docs at all (needs to add the proper doc generation and deployment code to its Makefile), and 'search', which was deployed to a test VM that I couldn't find (not available from t1 by ssh search ??), and has no docs appearing here: http://140.221.84.191/services/docs/search/ In addition, several modules do have proper documentation that seems to be properly deployed, but is not appearing here: http://140.221.84.191/services/docs . It's probably just a proxy issue, but here is the list of those modules: auth_service cluster_service expression KBaseFBAModeling plant_expression_service

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Re: [Release-team] Status of release notes
by Michael Sneddon 07 Aug '13

07 Aug '13

I manually looked at the release notes for each of the modules that are deployed, and here is an updated report. Roughly the same results as the automated test though. I think just one or two differences from what Nomi compiled. *Release Notes Not Found At All* genome_annotation kb_seed matR phispy registry sim_service *Release Notes File Found, but not up-to-date* auth_service cluster_service KBaseFBAModeling id_server communities_qc typecomp workspace_service *Release Notes are good* auth expression plant_expression probabilistic_annotation protein_info_service trees On Wed, Aug 7, 2013 at 7:25 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Only 7 out of the 27 services in this Build have up-to-date release notes > (or it's possible that they put their release notes in an unexpected place > or gave it a name that didn't include *rel* or *REL*). > genome_annotation: None > assembly: Out of date > auth: good > auth_service: out of date > aux_store: none > kb_seed: none > cluster_service: out of date > communities_api: none > expression: none > KBaseFBAModeling: out of date > functional_ortholog_predictor: good > idserver: out of date > invocation: good > kb_model_seed: none > matR: none > microbes_model_builder: none > phispy: none > plant_expression_service: good > probabilistic_annotation: good > protein_info_service: good > communities_qc: out of date > registry: none > sim_service: none > trees: good > typecomp: out of date (and rudimentary) > workspace_service: out of date > > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

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Status of release notes
by Nomi Harris 07 Aug '13

07 Aug '13

Only 7 out of the 27 services in this Build have up-to-date release notes (or it's possible that they put their release notes in an unexpected place or gave it a name that didn't include *rel* or *REL*). genome_annotation: None assembly: Out of date auth: good auth_service: out of date aux_store: none kb_seed: none cluster_service: out of date communities_api: none expression: none KBaseFBAModeling: out of date functional_ortholog_predictor: good idserver: out of date invocation: good kb_model_seed: none matR: none microbes_model_builder: none phispy: none plant_expression_service: good probabilistic_annotation: good protein_info_service: good communities_qc: out of date registry: none sim_service: none trees: good typecomp: out of date (and rudimentary) workspace_service: out of date Nomi

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Re: [Release-team] bool is now a reserved word
by Robert Olson 04 Aug '13

04 Aug '13

If y'all aren't interested in the updates then just tag typecomp at the last stable, doesn't matter to me. ----- Original Message ----- > > > > There's not too many, so I think we should change it ourselves if > roll out this change. > > But... I'm still not sure the bool type is ready to be rolled out. It > works in Perl, but I'm not sure that all client server language > combinations will work. I know for sure we will need some changes to > the python code, if Gavin hasn't made them this weekend yet. The > encoding to bool type in json I think is also handled differently in > Perl and java right now. It would have been nice to use a more > formal process for rolling out and testing these types of core > changes. > > I'm about to get on a plane so I'll be offline for most of the day, > but I'll try to test and see what issues come up en route. > > On Aug 4, 2013 10:19 AM, "Nomi Harris" < nlharris(a)lbl.gov > wrote: > > > Tom wrote: > > Check your type spec for bool typedefs. Remove those. > > > > typedef int bool > > > > bool is now a reserved word > > I found "typedef int bool" in several services: > > grep "typedef int bool" */*spec */*/*spec > KBaseFBAModeling/fbaModelServices.spec: typedef int bool; > experiment/experiment.spec: typedef int boolean; > probabilistic_annotation/ProbabilisticAnnotation.spec: typedef int > bool; > prom_service/PROM.spec: typedef int bool; > structured_assertions/SAL.spec: typedef int boolean; > trees/Tree.spec: typedef int boolean; > workspace_deluxe/workspace.spec: typedef int boolean; > kb_seed/lib/CDMI-API.spec: typedef int boolean; > > > Should we tell the developers or just fix it ourselves? (I can do > it.) > > Nomi > _______________________________________________ > 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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