February 2014 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] Defunct services
by Shane Canon 25 Feb '14

25 Feb '14

I will look through the nginx logs to verify. I don't know if we have them in an easy-to-access spot yet. --Shane On Feb 25, 2014, at 2:11 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > It would be handy if we had an URL for the server logs—maybe I will request that as a feature. > In the meantime, how can I access the server logs? > Nomi > > On Feb 25, 2014, at 1:51 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> I don't know if we have one. >> >> On Feb 25, 2014, at 3:27 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Good point, Bob. Can you remind me of the URL for checking the server logs? >>> >>> >>> On Tue, Feb 25, 2014 at 1:24 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>> Have we checked the server logs to see if there are any users of these? >>> >>> On Feb 25, 2014, at 3:07 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: >>>> feature_selection (fizzy) >>>> file_type_service >>>> genotype_phenotype >>>> experiment >>>> prom_service >>>> communities_qc >>>> regulation (regprecise) >>>> >>>> On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>>> >>>>> >>>>> So ERDB may still be needed by translation and trees. >>>>> >>>>> --Shane >>>>> >>>>> root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* >>>>> experiment/DEPENDENCIES:erdb_service >>>>> prom_service/DEPENDENCIES:erdb_service >>>>> translation/DEPENDENCIES:erdb_service >>>>> trees/DEPENDENCIES:erdb_service >>>>> >>>>> On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: >>>>> >>>>>> I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. >>>>>> >>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>> >>>>>> >>>>>> Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>>> >>>>>> Sure. We can follow up on it during tomorrow's devel call if needed. >>>>>> >>>>>> >>>>>> On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: >>>>>> >>>>>> This is very helpful. Should we notify the devel list as well? >>>>>> >>>>>> --Shane >>>>>> >>>>>> >>>>>> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>>> >>>>>> > I believe the following services are not currently supported and can be shut down (if they haven’t been already): >>>>>> > >>>>>> > feature_selection (fizzy) >>>>>> > file_type_services >>>>>> > genotype_phenotype >>>>>> > experiment >>>>>> > prom_service >>>>>> > communities_qc >>>>>> > regulation (regprecise) >>>>>> > erdb_service >>>>>> > >>>>>> > Ccing the release team in case they have any adjustments to that list. >>>>>> > >>>>>> > Nomi >>>>>> > >>>>>> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>>>>> > >>>>>> >> >>>>>> >> So we can retire this service? Are there other services we can shutdown? >>>>>> >> >>>>>> >> Shane >>>>>> >> >>>>>> >> Sent from my iPhone >>>>>> >> >>>>>> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>>> >>> >>>>>> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>>>>> >>> Nomi >>>>>> >>> >>>>>> >>> Begin forwarded message: >>>>>> >>> >>>>>> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >>>>>> >>>> Subject: Re: Genotype/Phenotype service repo? >>>>>> >>>> Date: February 18, 2014 at 2:59:58 PM PST >>>>>> >>>> To: Nomi Harris <nlharris(a)gmail.com> >>>>>> >>>> >>>>>> >>>> Yes. Thanks. >>>>>> >>>> Ranjan >>>>>> >>>> >>>>>> >>>> >>>>>> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: >>>>>> >>>>> >>>>>> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>>>> >>>>> Nomi >>>>>> >>>>> >>>>>> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: >>>>>> >>>>>> >>>>>> >>>>>> Hi Nomi, >>>>>> >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>>>> >>>>>> I will request them to be deleted in few weeks. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Ranjan >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ________________________________________ >>>>>> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >>>>>> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>>>> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >>>>>> >>>>>> Cc: release-team(a)kbase.us >>>>>> >>>>>> Subject: Genotype/Phenotype service repo? >>>>>> >>>>>> >>>>>> >>>>>> Hi Ranjan, >>>>>> >>>>>> What is the correct repo for the Genotype/Phenotype service? >>>>>> >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>>>> >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>>>> >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>>>> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> 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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Empty or obsolete git repos--can we get rid of some of them?
by Nomi Harris 25 Feb '14

25 Feb '14

By the way, while we’re talking about defunct services, there are some repos that we could probably get rid of. Here are repos that are empty: Empty: prinseq.git support%40kbase.us Empty: coexpression.git gang.fang%40yale.edu Empty: fat_cat.git dave.dineen%40gmail.com Empty: kmer_annotation_function.git olson%40mcs.anl.gov Empty: kbtypedef_common_proposals.git msneddon%40lbl.gov Empty: fbaModelData.git support%40kbase.us Empty: kbtyped_obj_service.git msneddon%40lbl.gov And here are some repos that haven’t been touched in 7 months or more (see https://git.kbase.us/?o=age) and may no longer be needed: structured_assertions.git repo for structured assertions... psdehal(a)lbl.gov 7 months ago genome_data_browser.git a kbase lab project to browse... wjriehl(a)lbl.gov 8 months ago registry.git "service registry" brettin(a)anl.gov 8 months ago seq_search.git sequence search nconrad(a)mcs.anl.gov 8 months ago # erdb_service.git service to query cs via erdb... gaprice(a)lbl.gov 9 months ago # erdb_service is apparently still in use user_page.git repo for a user page wjriehl(a)lbl.gov 9 months ago askkb.git natural language interface... disz 9 months ago data_scatter_plot.git js for displaying data in... psdehal(a)lbl.gov 9 months ago strep_repeats.git Unnamed repository; edit this... olson(a)mcs.anl.gov 9 months ago plant.git repository for all things... shiran(a)cshl.edu 10 months ago adapters.git adapters repo brettin(a)mcs.anl.gov 10 months ago network_viewer.git browser for networks jmchandonia(a)lbl.gov 11 months ago otu_correlation.git generate correlations between... wjriehl(a)lbl.gov 11 months ago exchange_format_specs.git data exchange formats for... disz(a)mcs.anl.gov 11 months ago regprecise.git things related to regulons... psnovichkov(a)lbl.gov 12 months ago prinseq.git one of Rob Edwards services support(a)kbase.us 13 months ago core_model.git old code for gui nconrad(a)mcs.anl.gov 13 months ago fbaModelData.git "new module for storing fba... support(a)kbase.us 13 months ago

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Re: [Release-team] Defunct services
by Nomi Harris 25 Feb '14

25 Feb '14

It would be handy if we had an URL for the server logs—maybe I will request that as a feature. In the meantime, how can I access the server logs? Nomi On Feb 25, 2014, at 1:51 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > I don't know if we have one. > > On Feb 25, 2014, at 3:27 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Good point, Bob. Can you remind me of the URL for checking the server logs? >> >> >> On Tue, Feb 25, 2014 at 1:24 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >> Have we checked the server logs to see if there are any users of these? >> >> On Feb 25, 2014, at 3:07 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: >>> feature_selection (fizzy) >>> file_type_service >>> genotype_phenotype >>> experiment >>> prom_service >>> communities_qc >>> regulation (regprecise) >>> >>> On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>> >>>> >>>> So ERDB may still be needed by translation and trees. >>>> >>>> --Shane >>>> >>>> root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* >>>> experiment/DEPENDENCIES:erdb_service >>>> prom_service/DEPENDENCIES:erdb_service >>>> translation/DEPENDENCIES:erdb_service >>>> trees/DEPENDENCIES:erdb_service >>>> >>>> On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: >>>> >>>>> I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. >>>>> >>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>> >>>>> >>>>> Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>> >>>>> Sure. We can follow up on it during tomorrow's devel call if needed. >>>>> >>>>> >>>>> On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: >>>>> >>>>> This is very helpful. Should we notify the devel list as well? >>>>> >>>>> --Shane >>>>> >>>>> >>>>> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>> >>>>> > I believe the following services are not currently supported and can be shut down (if they haven’t been already): >>>>> > >>>>> > feature_selection (fizzy) >>>>> > file_type_services >>>>> > genotype_phenotype >>>>> > experiment >>>>> > prom_service >>>>> > communities_qc >>>>> > regulation (regprecise) >>>>> > erdb_service >>>>> > >>>>> > Ccing the release team in case they have any adjustments to that list. >>>>> > >>>>> > Nomi >>>>> > >>>>> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>>>> > >>>>> >> >>>>> >> So we can retire this service? Are there other services we can shutdown? >>>>> >> >>>>> >> Shane >>>>> >> >>>>> >> Sent from my iPhone >>>>> >> >>>>> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>> >>> >>>>> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>>>> >>> Nomi >>>>> >>> >>>>> >>> Begin forwarded message: >>>>> >>> >>>>> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >>>>> >>>> Subject: Re: Genotype/Phenotype service repo? >>>>> >>>> Date: February 18, 2014 at 2:59:58 PM PST >>>>> >>>> To: Nomi Harris <nlharris(a)gmail.com> >>>>> >>>> >>>>> >>>> Yes. Thanks. >>>>> >>>> Ranjan >>>>> >>>> >>>>> >>>> >>>>> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: >>>>> >>>>> >>>>> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>>> >>>>> Nomi >>>>> >>>>> >>>>> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: >>>>> >>>>>> >>>>> >>>>>> Hi Nomi, >>>>> >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>>> >>>>>> I will request them to be deleted in few weeks. >>>>> >>>>>> Thanks >>>>> >>>>>> Ranjan >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> ________________________________________ >>>>> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >>>>> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>>> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >>>>> >>>>>> Cc: release-team(a)kbase.us >>>>> >>>>>> Subject: Genotype/Phenotype service repo? >>>>> >>>>>> >>>>> >>>>>> Hi Ranjan, >>>>> >>>>>> What is the correct repo for the Genotype/Phenotype service? >>>>> >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>>> >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>>> >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>>> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>>> >>>>>> Thanks, >>>>> >>>>>> Nomi >>>>> > >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> 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] Defunct services
by Robert Olson 25 Feb '14

25 Feb '14

I don't know if we have one. On Feb 25, 2014, at 3:27 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Good point, Bob. Can you remind me of the URL for checking the server logs? > > > On Tue, Feb 25, 2014 at 1:24 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > Have we checked the server logs to see if there are any users of these? > > On Feb 25, 2014, at 3:07 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: >> feature_selection (fizzy) >> file_type_service >> genotype_phenotype >> experiment >> prom_service >> communities_qc >> regulation (regprecise) >> >> On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> >>> So ERDB may still be needed by translation and trees. >>> >>> --Shane >>> >>> root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* >>> experiment/DEPENDENCIES:erdb_service >>> prom_service/DEPENDENCIES:erdb_service >>> translation/DEPENDENCIES:erdb_service >>> trees/DEPENDENCIES:erdb_service >>> >>> On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: >>> >>>> I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. >>>> >>>> Sent from my Verizon Wireless 4G LTE DROID >>>> >>>> >>>> Nomi Harris <nlharris(a)lbl.gov> wrote: >>>> >>>> Sure. We can follow up on it during tomorrow's devel call if needed. >>>> >>>> >>>> On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: >>>> >>>> This is very helpful. Should we notify the devel list as well? >>>> >>>> --Shane >>>> >>>> >>>> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>> >>>> > I believe the following services are not currently supported and can be shut down (if they haven’t been already): >>>> > >>>> > feature_selection (fizzy) >>>> > file_type_services >>>> > genotype_phenotype >>>> > experiment >>>> > prom_service >>>> > communities_qc >>>> > regulation (regprecise) >>>> > erdb_service >>>> > >>>> > Ccing the release team in case they have any adjustments to that list. >>>> > >>>> > Nomi >>>> > >>>> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>>> > >>>> >> >>>> >> So we can retire this service? Are there other services we can shutdown? >>>> >> >>>> >> Shane >>>> >> >>>> >> Sent from my iPhone >>>> >> >>>> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>> >>> >>>> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>>> >>> Nomi >>>> >>> >>>> >>> Begin forwarded message: >>>> >>> >>>> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >>>> >>>> Subject: Re: Genotype/Phenotype service repo? >>>> >>>> Date: February 18, 2014 at 2:59:58 PM PST >>>> >>>> To: Nomi Harris <nlharris(a)gmail.com> >>>> >>>> >>>> >>>> Yes. Thanks. >>>> >>>> Ranjan >>>> >>>> >>>> >>>> >>>> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: >>>> >>>>> >>>> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>> >>>>> Nomi >>>> >>>>> >>>> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: >>>> >>>>>> >>>> >>>>>> Hi Nomi, >>>> >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>> >>>>>> I will request them to be deleted in few weeks. >>>> >>>>>> Thanks >>>> >>>>>> Ranjan >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> ________________________________________ >>>> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >>>> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >>>> >>>>>> Cc: release-team(a)kbase.us >>>> >>>>>> Subject: Genotype/Phenotype service repo? >>>> >>>>>> >>>> >>>>>> Hi Ranjan, >>>> >>>>>> What is the correct repo for the Genotype/Phenotype service? >>>> >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>> >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>> >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>> >>>>>> Thanks, >>>> >>>>>> Nomi >>>> > >>>> >>>> >>> >> >> _______________________________________________ >> 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] Defunct services
by Nomi Harris 25 Feb '14

25 Feb '14

Good point, Bob. Can you remind me of the URL for checking the server logs? On Tue, Feb 25, 2014 at 1:24 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > Have we checked the server logs to see if there are any users of these? > > On Feb 25, 2014, at 3:07 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > Ok, thanks for checking. Sounds like ERDB is still needed. So the revised > list of services that can go is: > feature_selection (fizzy) > file_type_service > genotype_phenotype > experiment > prom_service > communities_qc > regulation (regprecise) > > On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > > So ERDB may still be needed by translation and trees. > > --Shane > > root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i > erdb */DEP* > experiment/DEPENDENCIES:erdb_service > prom_service/DEPENDENCIES:erdb_service > translation/DEPENDENCIES:erdb_service > trees/DEPENDENCIES:erdb_service > > On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> > wrote: > > I think the list is accurate. The only exception might be ERDB service. > A recursive grep might be needed for that one. > > *Sent from my Verizon Wireless 4G LTE DROID* > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > Sure. We can follow up on it during tomorrow's devel call if needed. > > > On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> This is very helpful. Should we notify the devel list as well? >> >> --Shane >> >> >> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> > I believe the following services are not currently supported and can be >> shut down (if they haven't been already): >> > >> > feature_selection (fizzy) >> > file_type_services >> > genotype_phenotype >> > experiment >> > prom_service >> > communities_qc >> > regulation (regprecise) >> > erdb_service >> > >> > Ccing the release team in case they have any adjustments to that list. >> > >> > Nomi >> > >> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> > >> >> >> >> So we can retire this service? Are there other services we can >> shutdown? >> >> >> >> Shane >> >> >> >> Sent from my iPhone >> >> >> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> >> >>> I forgot to forward this to you. Ranjan says to leave the >> genotype/phenotype service out of this release. >> >>> Nomi >> >>> >> >>> Begin forwarded message: >> >>> >> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >> >>>> Subject: Re: Genotype/Phenotype service repo? >> >>>> Date: February 18, 2014 at 2:59:58 PM PST >> >>>> To: Nomi Harris <nlharris(a)gmail.com> >> >>>> >> >>>> Yes. Thanks. >> >>>> Ranjan >> >>>> >> >>>> >> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> >> wrote: >> >>>>> >> >>>>> Ok--so the release of IRIS we're doing this week should not include >> Genotype/Phenotype commands, and I should remove it from the Services web >> page? >> >>>>> Nomi >> >>>>> >> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> >> wrote: >> >>>>>> >> >>>>>> Hi Nomi, >> >>>>>> Both these services are obsolete and their functionality are being >> incorporated into gwas service. >> >>>>>> I will request them to be deleted in few weeks. >> >>>>>> Thanks >> >>>>>> Ranjan >> >>>>>> >> >>>>>> >> >>>>>> ________________________________________ >> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >> >>>>>> Cc: release-team(a)kbase.us >> >>>>>> Subject: Genotype/Phenotype service repo? >> >>>>>> >> >>>>>> Hi Ranjan, >> >>>>>> What is the correct repo for the Genotype/Phenotype service? >> >>>>>> There's a repo called genotype_phenotype, which hasn't been >> updated since Sept. >> >>>>>> There's one called genotype_phenotype_api, which I think is the >> current repo. >> >>>>>> The Master tab of the Services repo ( >> https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) >> claims that the repo is called geno_pheno_service, which I guess is just >> wrong. >> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest >> deleting genotype_phenotype to avoid confusion. >> >>>>>> Thanks, >> >>>>>> Nomi >> > >> >> > > > _______________________________________________ > 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] Defunct services
by Robert Olson 25 Feb '14

25 Feb '14

Have we checked the server logs to see if there are any users of these? On Feb 25, 2014, at 3:07 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: > feature_selection (fizzy) > file_type_service > genotype_phenotype > experiment > prom_service > communities_qc > regulation (regprecise) > > On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> So ERDB may still be needed by translation and trees. >> >> --Shane >> >> root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* >> experiment/DEPENDENCIES:erdb_service >> prom_service/DEPENDENCIES:erdb_service >> translation/DEPENDENCIES:erdb_service >> trees/DEPENDENCIES:erdb_service >> >> On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: >> >>> I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. >>> >>> Sent from my Verizon Wireless 4G LTE DROID >>> >>> >>> Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> Sure. We can follow up on it during tomorrow's devel call if needed. >>> >>> >>> On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: >>> >>> This is very helpful. Should we notify the devel list as well? >>> >>> --Shane >>> >>> >>> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> > I believe the following services are not currently supported and can be shut down (if they haven’t been already): >>> > >>> > feature_selection (fizzy) >>> > file_type_services >>> > genotype_phenotype >>> > experiment >>> > prom_service >>> > communities_qc >>> > regulation (regprecise) >>> > erdb_service >>> > >>> > Ccing the release team in case they have any adjustments to that list. >>> > >>> > Nomi >>> > >>> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >>> > >>> >> >>> >> So we can retire this service? Are there other services we can shutdown? >>> >> >>> >> Shane >>> >> >>> >> Sent from my iPhone >>> >> >>> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> >>> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>> >>> Nomi >>> >>> >>> >>> Begin forwarded message: >>> >>> >>> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >>> >>>> Subject: Re: Genotype/Phenotype service repo? >>> >>>> Date: February 18, 2014 at 2:59:58 PM PST >>> >>>> To: Nomi Harris <nlharris(a)gmail.com> >>> >>>> >>> >>>> Yes. Thanks. >>> >>>> Ranjan >>> >>>> >>> >>>> >>> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: >>> >>>>> >>> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>> >>>>> Nomi >>> >>>>> >>> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: >>> >>>>>> >>> >>>>>> Hi Nomi, >>> >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>> >>>>>> I will request them to be deleted in few weeks. >>> >>>>>> Thanks >>> >>>>>> Ranjan >>> >>>>>> >>> >>>>>> >>> >>>>>> ________________________________________ >>> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >>> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >>> >>>>>> Cc: release-team(a)kbase.us >>> >>>>>> Subject: Genotype/Phenotype service repo? >>> >>>>>> >>> >>>>>> Hi Ranjan, >>> >>>>>> What is the correct repo for the Genotype/Phenotype service? >>> >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>> >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>> >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>> >>>>>> Thanks, >>> >>>>>> Nomi >>> > >>> >>> >> > > _______________________________________________ > 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] Defunct services
by Nomi Harris 25 Feb '14

25 Feb '14

Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: feature_selection (fizzy) file_type_service genotype_phenotype experiment prom_service communities_qc regulation (regprecise) On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > So ERDB may still be needed by translation and trees. > > --Shane > > root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* > experiment/DEPENDENCIES:erdb_service > prom_service/DEPENDENCIES:erdb_service > translation/DEPENDENCIES:erdb_service > trees/DEPENDENCIES:erdb_service > > On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: > >> I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. >> >> Sent from my Verizon Wireless 4G LTE DROID >> >> >> Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> Sure. We can follow up on it during tomorrow's devel call if needed. >> >> >> On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: >> >> This is very helpful. Should we notify the devel list as well? >> >> --Shane >> >> >> On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> > I believe the following services are not currently supported and can be shut down (if they haven’t been already): >> > >> > feature_selection (fizzy) >> > file_type_services >> > genotype_phenotype >> > experiment >> > prom_service >> > communities_qc >> > regulation (regprecise) >> > erdb_service >> > >> > Ccing the release team in case they have any adjustments to that list. >> > >> > Nomi >> > >> > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> > >> >> >> >> So we can retire this service? Are there other services we can shutdown? >> >> >> >> Shane >> >> >> >> Sent from my iPhone >> >> >> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> >> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >> >>> Nomi >> >>> >> >>> Begin forwarded message: >> >>> >> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> >> >>>> Subject: Re: Genotype/Phenotype service repo? >> >>>> Date: February 18, 2014 at 2:59:58 PM PST >> >>>> To: Nomi Harris <nlharris(a)gmail.com> >> >>>> >> >>>> Yes. Thanks. >> >>>> Ranjan >> >>>> >> >>>> >> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: >> >>>>> >> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >> >>>>> Nomi >> >>>>> >> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: >> >>>>>> >> >>>>>> Hi Nomi, >> >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >> >>>>>> I will request them to be deleted in few weeks. >> >>>>>> Thanks >> >>>>>> Ranjan >> >>>>>> >> >>>>>> >> >>>>>> ________________________________________ >> >>>>>> From: Nomi Harris [nlharris(a)gmail.com] >> >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >> >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya >> >>>>>> Cc: release-team(a)kbase.us >> >>>>>> Subject: Genotype/Phenotype service repo? >> >>>>>> >> >>>>>> Hi Ranjan, >> >>>>>> What is the correct repo for the Genotype/Phenotype service? >> >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >> >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >> >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >> >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >> >>>>>> Thanks, >> >>>>>> Nomi >> > >> >> >

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Re: [Release-team] Defunct services
by Shane Canon 25 Feb '14

25 Feb '14

So ERDB may still be needed by translation and trees. --Shane root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* experiment/DEPENDENCIES:erdb_service prom_service/DEPENDENCIES:erdb_service translation/DEPENDENCIES:erdb_service trees/DEPENDENCIES:erdb_service On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov> wrote: > I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > Sure. We can follow up on it during tomorrow's devel call if needed. > > > On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > This is very helpful. Should we notify the devel list as well? > > --Shane > > > On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > > I believe the following services are not currently supported and can be shut down (if they haven’t been already): > > > > feature_selection (fizzy) > > file_type_services > > genotype_phenotype > > experiment > > prom_service > > communities_qc > > regulation (regprecise) > > erdb_service > > > > Ccing the release team in case they have any adjustments to that list. > > > > Nomi > > > > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > > >> > >> So we can retire this service? Are there other services we can shutdown? > >> > >> Shane > >> > >> Sent from my iPhone > >> > >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >>> > >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. > >>> Nomi > >>> > >>> Begin forwarded message: > >>> > >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> > >>>> Subject: Re: Genotype/Phenotype service repo? > >>>> Date: February 18, 2014 at 2:59:58 PM PST > >>>> To: Nomi Harris <nlharris(a)gmail.com> > >>>> > >>>> Yes. Thanks. > >>>> Ranjan > >>>> > >>>> > >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> wrote: > >>>>> > >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? > >>>>> Nomi > >>>>> > >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> wrote: > >>>>>> > >>>>>> Hi Nomi, > >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. > >>>>>> I will request them to be deleted in few weeks. > >>>>>> Thanks > >>>>>> Ranjan > >>>>>> > >>>>>> > >>>>>> ________________________________________ > >>>>>> From: Nomi Harris [nlharris(a)gmail.com] > >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM > >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya > >>>>>> Cc: release-team(a)kbase.us > >>>>>> Subject: Genotype/Phenotype service repo? > >>>>>> > >>>>>> Hi Ranjan, > >>>>>> What is the correct repo for the Genotype/Phenotype service? > >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. > >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. > >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. > >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. > >>>>>> Thanks, > >>>>>> Nomi > > > >

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Re: [Release-team] Defunct services
by Brettin, Thomas S. 25 Feb '14

25 Feb '14

I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov> wrote: Sure. We can follow up on it during tomorrow's devel call if needed. On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: This is very helpful. Should we notify the devel list as well? --Shane On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > I believe the following services are not currently supported and can be shut down (if they haven’t been already): > > feature_selection (fizzy) > file_type_services > genotype_phenotype > experiment > prom_service > communities_qc > regulation (regprecise) > erdb_service > > Ccing the release team in case they have any adjustments to that list. > > Nomi > > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: > >> >> So we can retire this service? Are there other services we can shutdown? >> >> Shane >> >> Sent from my iPhone >> >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: >>> >>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>> Nomi >>> >>> Begin forwarded message: >>> >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu<mailto:[email protected]>> >>>> Subject: Re: Genotype/Phenotype service repo? >>>> Date: February 18, 2014 at 2:59:58 PM PST >>>> To: Nomi Harris <nlharris(a)gmail.com<mailto:[email protected]>> >>>> >>>> Yes. Thanks. >>>> Ranjan >>>> >>>> >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com<mailto:[email protected]>> wrote: >>>>> >>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>>> Nomi >>>>> >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu<mailto:[email protected]>> wrote: >>>>>> >>>>>> Hi Nomi, >>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>>>> I will request them to be deleted in few weeks. >>>>>> Thanks >>>>>> Ranjan >>>>>> >>>>>> >>>>>> ________________________________________ >>>>>> From: Nomi Harris [nlharris(a)gmail.com<mailto:[email protected]>] >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>>>> To: pranjan77(a)gmail.com<mailto:[email protected]>; Ranjan, Priya >>>>>> Cc: release-team(a)kbase.us<mailto:[email protected]> >>>>>> Subject: Genotype/Phenotype service repo? >>>>>> >>>>>> Hi Ranjan, >>>>>> What is the correct repo for the Genotype/Phenotype service? >>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>>>> Thanks, >>>>>> Nomi >

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Re: [Release-team] Defunct services
by Nomi Harris 25 Feb '14

25 Feb '14

Sure. We can follow up on it during tomorrow's devel call if needed. On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > This is very helpful. Should we notify the devel list as well? > > --Shane > > > On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > > I believe the following services are not currently supported and can be > shut down (if they haven't been already): > > > > feature_selection (fizzy) > > file_type_services > > genotype_phenotype > > experiment > > prom_service > > communities_qc > > regulation (regprecise) > > erdb_service > > > > Ccing the release team in case they have any adjustments to that list. > > > > Nomi > > > > On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > > >> > >> So we can retire this service? Are there other services we can > shutdown? > >> > >> Shane > >> > >> Sent from my iPhone > >> > >>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >>> > >>> I forgot to forward this to you. Ranjan says to leave the > genotype/phenotype service out of this release. > >>> Nomi > >>> > >>> Begin forwarded message: > >>> > >>>> From: "Ranjan, Priya" <pranjan(a)utk.edu> > >>>> Subject: Re: Genotype/Phenotype service repo? > >>>> Date: February 18, 2014 at 2:59:58 PM PST > >>>> To: Nomi Harris <nlharris(a)gmail.com> > >>>> > >>>> Yes. Thanks. > >>>> Ranjan > >>>> > >>>> > >>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com> > wrote: > >>>>> > >>>>> Ok--so the release of IRIS we're doing this week should not include > Genotype/Phenotype commands, and I should remove it from the Services web > page? > >>>>> Nomi > >>>>> > >>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu> > wrote: > >>>>>> > >>>>>> Hi Nomi, > >>>>>> Both these services are obsolete and their functionality are being > incorporated into gwas service. > >>>>>> I will request them to be deleted in few weeks. > >>>>>> Thanks > >>>>>> Ranjan > >>>>>> > >>>>>> > >>>>>> ________________________________________ > >>>>>> From: Nomi Harris [nlharris(a)gmail.com] > >>>>>> Sent: Tuesday, February 18, 2014 3:00 PM > >>>>>> To: pranjan77(a)gmail.com; Ranjan, Priya > >>>>>> Cc: release-team(a)kbase.us > >>>>>> Subject: Genotype/Phenotype service repo? > >>>>>> > >>>>>> Hi Ranjan, > >>>>>> What is the correct repo for the Genotype/Phenotype service? > >>>>>> There's a repo called genotype_phenotype, which hasn't been updated > since Sept. > >>>>>> There's one called genotype_phenotype_api, which I think is the > current repo. > >>>>>> The Master tab of the Services repo ( > https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) > claims that the repo is called geno_pheno_service, which I guess is just > wrong. > >>>>>> If genotype_phenotype_api is the live repo, then I would suggest > deleting genotype_phenotype to avoid confusion. > >>>>>> Thanks, > >>>>>> Nomi > > > >

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