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

Updating services web page
by Nomi Harris 27 Feb '14

27 Feb '14

Miriam asked for the Services web page (http://kbase.us/developer-zone/services/) to be updated (see https://atlassian.kbase.us/browse/KBASE-635) I have been working on a private copy of the Services page (http://kbase.us/dev/services — you probably have to be signed into Concrete5 to see it) for a month or so but have been waiting to make the new version public because IRIS hadn’t been updated, so the new services (e.g., cMonkey) were not yet visible to the public. Now they are visible, but there are still various problems with them. Also, there are obsolete or temporarily out-of-order services that still appear in IRIS (but that I took off of the updated Services page). Finally, the API docs for the new services (e.g., http://kbase.us/services/docs/cmonkey/cmonkey.html) are up but have not had the kbase.us style applied to them yet. (Tom Brown has been asked to do this.) (Actually, I notice that cMonkey API doc has another formatting problem: the newlines in the description have been lost, so the lines all run together. There are newlines in the spec that the API doc was generated from. I don’t know if this is a deficiency in the script that converts the typespec to the API doc.) Anyway…it seems like it may take a while to get all the service issues (e.g., with workspaces and FBA modeling) straightened out in IRIS, but should I go ahead and make the updated services page public? Nomi

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Re: [Release-team] Some commands not working in IRIS
by Murphy-Olson, Daniel E. 26 Feb '14

26 Feb '14

Create a ticket for each issue you find, and assign them to me. I'll work through them and determine if they are a deployment issue, or code issue, and reassign as appropriate. ---- Daniel Murphy-Olson Sr. Systems Administrator Computing, Environment and Life Sciences Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Nomi Harris [nlharris(a)lbl.gov] Sent: Wednesday, February 26, 2014 7:46 PM To: release-team(a)kbase.us Subject: [Release-team] Some commands not working in IRIS So I’m trying some commands in IRIS (for commands whose —help output supplies an example) and running into various errors, for example: >/ fop-rank-pgene --wgene "kb|g.3899.locus.6994" --pgenes "kb|g.3907.locus.19887,kb|g.3907.locus.24709" --ndatasets "kb|netdataset.plant.fn.25" ",'kb|netdataset.plant.fn.27'" Return code from fop-rank-pgene: 111Error invoking method rank_pgene HTTP status: 500 Can't connect to localhost:7082 (Connection refused) Function invoked: rank_pgene Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/FunctionalOrthologPredictor/Client.pm line 147 Bio::KBase::FunctionalOrthologPredictor::Client::rank_pgene('Bio::KBase::FunctionalOrthologPredictor::Client=HASH(0x1f83908)', 'kb|g.3899.locus.6994', 'ARRAY(0x1f6b3d0)', 'ARRAY(0x1f6b400)') called at /kbase/deployments/20140109-prod/plbin/fop-rank-pgene.pl line 102 >/ qc-get-drisee-compute -id "kb|mg.1" Return code from qc-get-drisee-compute: 255Error invoking method kbase_ids_to_external_ids HTTP status: 301 Moved Permanently Function invoked: kbase_ids_to_external_ids Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/IDServer/Client.pm line 133 Bio::KBase::IDServer::Client::kbase_ids_to_external_ids('Bio::KBase::IDServer::Client=HASH(0x21eef40)', 'ARRAY(0x21e6920)') called at /kbase/deployments/20140109-prod/plbin/qc-get-drisee-compute.pl line 105 Should I create individual JIRA tickets for these, or are all they all just symptoms of some overall problem that you’re working on? 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] Some commands not working in IRIS
by Robert Olson 26 Feb '14

26 Feb '14

Looks like two issues. First is a module that doesn't do a recompile before install to get the proper default service URL in place. Second is one that has the wrong URL for the ID server; possibly another instance of the first problem in the client deployment of the ID server. I also wonder exactly what that service is using the ID server for. --bob On Feb 26, 2014, at 7:46 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > So I’m trying some commands in IRIS (for commands whose —help output supplies an example) and running into various errors, for example: > >> / fop-rank-pgene --wgene "kb|g.3899.locus.6994" --pgenes "kb|g.3907.locus.19887,kb|g.3907.locus.24709" --ndatasets "kb|netdataset.plant.fn.25" ",'kb|netdataset.plant.fn.27'" > Return code from fop-rank-pgene: 111Error invoking method rank_pgene > HTTP status: 500 Can't connect to localhost:7082 (Connection refused) > Function invoked: rank_pgene > Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/FunctionalOrthologPredictor/Client.pm line 147 > Bio::KBase::FunctionalOrthologPredictor::Client::rank_pgene('Bio::KBase::FunctionalOrthologPredictor::Client=HASH(0x1f83908)', 'kb|g.3899.locus.6994', 'ARRAY(0x1f6b3d0)', 'ARRAY(0x1f6b400)') called at /kbase/deployments/20140109-prod/plbin/fop-rank-pgene.pl line 102 > >> / qc-get-drisee-compute -id "kb|mg.1" > Return code from qc-get-drisee-compute: 255Error invoking method kbase_ids_to_external_ids > HTTP status: 301 Moved Permanently > Function invoked: kbase_ids_to_external_ids > > Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/IDServer/Client.pm line 133 > Bio::KBase::IDServer::Client::kbase_ids_to_external_ids('Bio::KBase::IDServer::Client=HASH(0x21eef40)', 'ARRAY(0x21e6920)') called at /kbase/deployments/20140109-prod/plbin/qc-get-drisee-compute.pl line 105 > > > Should I create individual JIRA tickets for these, or are all they all just symptoms of some overall problem that you’re working on? > > Thanks, > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Some commands not working in IRIS
by Nomi Harris 26 Feb '14

26 Feb '14

So I’m trying some commands in IRIS (for commands whose —help output supplies an example) and running into various errors, for example: >/ fop-rank-pgene --wgene "kb|g.3899.locus.6994" --pgenes "kb|g.3907.locus.19887,kb|g.3907.locus.24709" --ndatasets "kb|netdataset.plant.fn.25" ",'kb|netdataset.plant.fn.27'" Return code from fop-rank-pgene: 111Error invoking method rank_pgene HTTP status: 500 Can't connect to localhost:7082 (Connection refused) Function invoked: rank_pgene Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/FunctionalOrthologPredictor/Client.pm line 147 Bio::KBase::FunctionalOrthologPredictor::Client::rank_pgene('Bio::KBase::FunctionalOrthologPredictor::Client=HASH(0x1f83908)', 'kb|g.3899.locus.6994', 'ARRAY(0x1f6b3d0)', 'ARRAY(0x1f6b400)') called at /kbase/deployments/20140109-prod/plbin/fop-rank-pgene.pl line 102 >/ qc-get-drisee-compute -id "kb|mg.1" Return code from qc-get-drisee-compute: 255Error invoking method kbase_ids_to_external_ids HTTP status: 301 Moved Permanently Function invoked: kbase_ids_to_external_ids Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/IDServer/Client.pm line 133 Bio::KBase::IDServer::Client::kbase_ids_to_external_ids('Bio::KBase::IDServer::Client=HASH(0x21eef40)', 'ARRAY(0x21e6920)') called at /kbase/deployments/20140109-prod/plbin/qc-get-drisee-compute.pl line 105 Should I create individual JIRA tickets for these, or are all they all just symptoms of some overall problem that you’re working on? Thanks, Nomi

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Looking at service logs
by Nomi Harris 26 Feb '14

26 Feb '14

I can’t seem to see anything at https://kbase.us/servicelogs. It let me log in with the user/pass you listed; I end up at https://kbase.us/servicelogs/en-US/app/launcher/home, which shows nothing interested. If I try to click on any of the interesting-sounding links (e.g., “Search activity overview”) it says “Authentication required”, and won’t accept the kbasedev credentials. Nomi On Feb 25, 2014, at 3:20 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > Thanks. I couldn't recall which logs were being captured by this. I assumed the nginx logs were, but I didn't want to presume. > > --Shane > > > On Feb 25, 2014, at 2:33 PM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > >> They are all at https://kbase.us/servicelogs >> >> User: kbasedev >> Pass: kbase4me2! >> >> I sent this out to the devel list a while ago, and went over it on the call. >> >> ---- >> Daniel Murphy-Olson >> Sr. Systems Administrator >> Computing, Environment and Life Sciences Division >> Argonne National Laboratory >> 630-252-0055 >> From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Shane Canon [scanon(a)lbl.gov] >> Sent: Tuesday, February 25, 2014 4:23 PM >> To: Nomi Harris >> Cc: release-team(a)kbase.us >> Subject: Re: [Release-team] Defunct services >> >> >> 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

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Re: [Release-team] Defunct services
by Land, Miriam L. 26 Feb '14

26 Feb '14

Nomi, Andreas has been working on JIRA tickets this week for communities_qc and feature_selection. He may not consider them defunct. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Tuesday, February 25, 2014 4:07 PM To: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: Re: [Release-team] Defunct services 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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] Possible narrative demo tomorrow during SAC meeting
by Nomi Harris 25 Feb '14

25 Feb '14

Also probably best to avoid destabilizing IRIS or any of the services during that time period. Thanks, Nomi On Tue, Feb 25, 2014 at 5:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Adam and Rick have a phone meeting with the SAC tomorrow morning from > 9-10:30am PT. They will be talking about the new Narrative interface and > may want to demo it. Adam requests that the Narrative Interface be kept > stable during that period. That also means that it's not a good time to > change the featured narratives. > Thanks, > Nomi >

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

25 Feb '14

Thanks. I couldn't recall which logs were being captured by this. I assumed the nginx logs were, but I didn't want to presume. --Shane On Feb 25, 2014, at 2:33 PM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > They are all at https://kbase.us/servicelogs > > User: kbasedev > Pass: kbase4me2! > > I sent this out to the devel list a while ago, and went over it on the call. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Computing, Environment and Life Sciences Division > Argonne National Laboratory > 630-252-0055 > From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Shane Canon [scanon(a)lbl.gov] > Sent: Tuesday, February 25, 2014 4:23 PM > To: Nomi Harris > Cc: release-team(a)kbase.us > Subject: Re: [Release-team] Defunct services > > > 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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Re: [Release-team] Empty or obsolete git repos--can we get rid of some of them?
by Robert Olson 25 Feb '14

25 Feb '14

strep_repeats is untouched because it is stable and working. On Feb 25, 2014, at 4:20 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > 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 > _______________________________________________ > 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 Murphy-Olson, Daniel E. 25 Feb '14

25 Feb '14

They are all at https://kbase.us/servicelogs User: kbasedev Pass: kbase4me2! I sent this out to the devel list a while ago, and went over it on the call. ---- Daniel Murphy-Olson Sr. Systems Administrator Computing, Environment and Life Sciences Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Shane Canon [scanon(a)lbl.gov] Sent: Tuesday, February 25, 2014 4:23 PM To: Nomi Harris Cc: release-team(a)kbase.us Subject: Re: [Release-team] Defunct services 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<mailto:[email protected]>> 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<mailto:[email protected]>> wrote: I don't know if we have one. On Feb 25, 2014, at 3:27 PM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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<mailto:[email protected]>> 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 > _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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