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

Re: [Release-team] Need downloadable KBase product for Windows
by Adam Arkin 27 Jan '13

27 Jan '13

The problem is that it is not windows-- it is THEIR version of corporate windows with NOTHING else installed. We can't use Cygwin or anything like it. We can't specify using Firefox. The web provides a way for them to use remote resources... if IRIS worked in Explorer 9 that would be awesome but I think we need to push back a little on this unless this is easy to do. I think if we get the web interface running -- meaning the search first and narrative thereafter we will be in good stead. I think if we can demo things on our computers over a 4G network we will be fine with them. For other Window's users we need to discuss the configuration requirements. Adam On Sun, Jan 27, 2013 at 4:36 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > On Jan 27, 2013, at 4:33 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > > Last I heard IRIS didn't run on IE. > > creating a windows equivalent to the dmg requires that we build the kbase > runtime on windows. > > > If that's what it takes, then someone (not me) needs to do this. We can't > just ignore Windows (much as I know we'd all like to), given that our > sponsors (DOE) use it. > > So, who can build the KBase runtime on Windows? > > Nomi > > > > On Jan 27, 2013, at 5:47 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > Hi all, > > During the meeting with our DOE program managers on Friday, they raised > the issue that currently our only downloadable KBase product is the Mac > dmg. People who work at DOE are forced to use Windows. Not only that--they > are forced to use very old versions of Windows (and therefore very old > versions of applications--which they are not allowed to update without > permission). They are currently on Windows XP but will soon be upgrading to > Windows 7. I forget which version of IE they said they had. A very old one, > anyway. > > So it is politically important to get something out in Feb that works on > Windows. We told them that IRIS works on any platform, and doesn't require > you to download any software, but now we need to check that IRIS actually > does run in some ancient version of IE on Windows XP or Windows 7. Do any > of you have access to an old PC? (Miriam, I know you switched to Mac fairly > recently--you don't happen to have an old PC lying around, do you?) Susan > said she can try out IRIS on her Windows machine, but we also need to be > able to test it, particularly if she has problems. (I'm a little worried > about some of the javascript stuff that we're talking about adding.) Maybe > someone can run old Windows VMs to test this stuff? > > It would also be good to make a Linux image available, but I think Windows > is actually more important. Lots of people (even scientists) still use > Windows. Linux users are generally power-users who are used to not being > able to download plug-and-play software. > > If it's not a huge hassle, it would be good if we could offer the > downloadable tarball, which theoretically should work on any OS, right? Was > there some reason to think it might not work on Windows, or were we just > reluctant to state that it would work fi we couldn't test it? > > Nomi Harris > Project Manager, KBase > > > -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov -------------------------------------

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Re: [Release-team] Need downloadable KBase product for Windows
by Thomas Brettin 27 Jan '13

27 Jan '13

How about Jason B. I noticed he is a windows power user. On Jan 27, 2013, at 6:36 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > On Jan 27, 2013, at 4:33 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Last I heard IRIS didn't run on IE. >> >> creating a windows equivalent to the dmg requires that we build the kbase runtime on windows. > > If that's what it takes, then someone (not me) needs to do this. We can't just ignore Windows (much as I know we'd all like to), given that our sponsors (DOE) use it. > > So, who can build the KBase runtime on Windows? > > Nomi > >> >> >> On Jan 27, 2013, at 5:47 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Hi all, >>> >>> During the meeting with our DOE program managers on Friday, they raised the issue that currently our only downloadable KBase product is the Mac dmg. People who work at DOE are forced to use Windows. Not only that--they are forced to use very old versions of Windows (and therefore very old versions of applications--which they are not allowed to update without permission). They are currently on Windows XP but will soon be upgrading to Windows 7. I forget which version of IE they said they had. A very old one, anyway. >>> >>> So it is politically important to get something out in Feb that works on Windows. We told them that IRIS works on any platform, and doesn't require you to download any software, but now we need to check that IRIS actually does run in some ancient version of IE on Windows XP or Windows 7. Do any of you have access to an old PC? (Miriam, I know you switched to Mac fairly recently--you don't happen to have an old PC lying around, do you?) Susan said she can try out IRIS on her Windows machine, but we also need to be able to test it, particularly if she has problems. (I'm a little worried about some of the javascript stuff that we're talking about adding.) Maybe someone can run old Windows VMs to test this stuff? >>> >>> It would also be good to make a Linux image available, but I think Windows is actually more important. Lots of people (even scientists) still use Windows. Linux users are generally power-users who are used to not being able to download plug-and-play software. >>> >>> If it's not a huge hassle, it would be good if we could offer the downloadable tarball, which theoretically should work on any OS, right? Was there some reason to think it might not work on Windows, or were we just reluctant to state that it would work fi we couldn't test it? >>> >>> Nomi Harris >>> Project Manager, KBase > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] Need downloadable KBase product for Windows
by Adam Arkin 27 Jan '13

27 Jan '13

Yeah-- I find this a hard pill to swallow. I think the leadership can see us demo our own system on our own machines... they are not going to be real users of the system in general. The important thing is to be able to demo the system off a 4G cell network. :) Not that I don't think Windows might one day be an important target... and not that I think we don't need to get most things working across platform to SOME degree. But this seems lower priority than other things. I don't see Todd or Sharlene really using IRIS. I will say- for them- the thing I worry about most is putting a good foot forward on search. Adam On Sun, Jan 27, 2013 at 4:33 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Last I heard IRIS didn't run on IE. > > creating a windows equivalent to the dmg requires that we build the kbase > runtime on windows. > > > > > On Jan 27, 2013, at 5:47 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > Hi all, > > During the meeting with our DOE program managers on Friday, they raised > the issue that currently our only downloadable KBase product is the Mac > dmg. People who work at DOE are forced to use Windows. Not only that--they > are forced to use very old versions of Windows (and therefore very old > versions of applications--which they are not allowed to update without > permission). They are currently on Windows XP but will soon be upgrading to > Windows 7. I forget which version of IE they said they had. A very old one, > anyway. > > So it is politically important to get something out in Feb that works on > Windows. We told them that IRIS works on any platform, and doesn't require > you to download any software, but now we need to check that IRIS actually > does run in some ancient version of IE on Windows XP or Windows 7. Do any > of you have access to an old PC? (Miriam, I know you switched to Mac fairly > recently--you don't happen to have an old PC lying around, do you?) Susan > said she can try out IRIS on her Windows machine, but we also need to be > able to test it, particularly if she has problems. (I'm a little worried > about some of the javascript stuff that we're talking about adding.) Maybe > someone can run old Windows VMs to test this stuff? > > It would also be good to make a Linux image available, but I think Windows > is actually more important. Lots of people (even scientists) still use > Windows. Linux users are generally power-users who are used to not being > able to download plug-and-play software. > > If it's not a huge hassle, it would be good if we could offer the > downloadable tarball, which theoretically should work on any OS, right? Was > there some reason to think it might not work on Windows, or were we just > reluctant to state that it would work fi we couldn't test it? > > Nomi Harris > Project Manager, KBase > > _______________________________________________ > 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 > > > > -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov -------------------------------------

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Re: [Release-team] Need downloadable KBase product for Windows
by Nomi Harris 27 Jan '13

27 Jan '13

On Jan 27, 2013, at 4:33 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Last I heard IRIS didn't run on IE. > > creating a windows equivalent to the dmg requires that we build the kbase runtime on windows. If that's what it takes, then someone (not me) needs to do this. We can't just ignore Windows (much as I know we'd all like to), given that our sponsors (DOE) use it. So, who can build the KBase runtime on Windows? Nomi > > > On Jan 27, 2013, at 5:47 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Hi all, >> >> During the meeting with our DOE program managers on Friday, they raised the issue that currently our only downloadable KBase product is the Mac dmg. People who work at DOE are forced to use Windows. Not only that--they are forced to use very old versions of Windows (and therefore very old versions of applications--which they are not allowed to update without permission). They are currently on Windows XP but will soon be upgrading to Windows 7. I forget which version of IE they said they had. A very old one, anyway. >> >> So it is politically important to get something out in Feb that works on Windows. We told them that IRIS works on any platform, and doesn't require you to download any software, but now we need to check that IRIS actually does run in some ancient version of IE on Windows XP or Windows 7. Do any of you have access to an old PC? (Miriam, I know you switched to Mac fairly recently--you don't happen to have an old PC lying around, do you?) Susan said she can try out IRIS on her Windows machine, but we also need to be able to test it, particularly if she has problems. (I'm a little worried about some of the javascript stuff that we're talking about adding.) Maybe someone can run old Windows VMs to test this stuff? >> >> It would also be good to make a Linux image available, but I think Windows is actually more important. Lots of people (even scientists) still use Windows. Linux users are generally power-users who are used to not being able to download plug-and-play software. >> >> If it's not a huge hassle, it would be good if we could offer the downloadable tarball, which theoretically should work on any OS, right? Was there some reason to think it might not work on Windows, or were we just reluctant to state that it would work fi we couldn't test it? >> >> Nomi Harris >> Project Manager, KBase

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Re: [Release-team] Need downloadable KBase product for Windows
by Thomas Brettin 27 Jan '13

27 Jan '13

Last I heard IRIS didn't run on IE. creating a windows equivalent to the dmg requires that we build the kbase runtime on windows. On Jan 27, 2013, at 5:47 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Hi all, > > During the meeting with our DOE program managers on Friday, they raised the issue that currently our only downloadable KBase product is the Mac dmg. People who work at DOE are forced to use Windows. Not only that--they are forced to use very old versions of Windows (and therefore very old versions of applications--which they are not allowed to update without permission). They are currently on Windows XP but will soon be upgrading to Windows 7. I forget which version of IE they said they had. A very old one, anyway. > > So it is politically important to get something out in Feb that works on Windows. We told them that IRIS works on any platform, and doesn't require you to download any software, but now we need to check that IRIS actually does run in some ancient version of IE on Windows XP or Windows 7. Do any of you have access to an old PC? (Miriam, I know you switched to Mac fairly recently--you don't happen to have an old PC lying around, do you?) Susan said she can try out IRIS on her Windows machine, but we also need to be able to test it, particularly if she has problems. (I'm a little worried about some of the javascript stuff that we're talking about adding.) Maybe someone can run old Windows VMs to test this stuff? > > It would also be good to make a Linux image available, but I think Windows is actually more important. Lots of people (even scientists) still use Windows. Linux users are generally power-users who are used to not being able to download plug-and-play software. > > If it's not a huge hassle, it would be good if we could offer the downloadable tarball, which theoretically should work on any OS, right? Was there some reason to think it might not work on Windows, or were we just reluctant to state that it would work fi we couldn't test it? > > Nomi Harris > Project Manager, KBase > > _______________________________________________ > 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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Need downloadable KBase product for Windows
by Nomi Harris 27 Jan '13

27 Jan '13

Hi all, During the meeting with our DOE program managers on Friday, they raised the issue that currently our only downloadable KBase product is the Mac dmg. People who work at DOE are forced to use Windows. Not only that--they are forced to use very old versions of Windows (and therefore very old versions of applications--which they are not allowed to update without permission). They are currently on Windows XP but will soon be upgrading to Windows 7. I forget which version of IE they said they had. A very old one, anyway. So it is politically important to get something out in Feb that works on Windows. We told them that IRIS works on any platform, and doesn't require you to download any software, but now we need to check that IRIS actually does run in some ancient version of IE on Windows XP or Windows 7. Do any of you have access to an old PC? (Miriam, I know you switched to Mac fairly recently--you don't happen to have an old PC lying around, do you?) Susan said she can try out IRIS on her Windows machine, but we also need to be able to test it, particularly if she has problems. (I'm a little worried about some of the javascript stuff that we're talking about adding.) Maybe someone can run old Windows VMs to test this stuff? It would also be good to make a Linux image available, but I think Windows is actually more important. Lots of people (even scientists) still use Windows. Linux users are generally power-users who are used to not being able to download plug-and-play software. If it's not a huge hassle, it would be good if we could offer the downloadable tarball, which theoretically should work on any OS, right? Was there some reason to think it might not work on Windows, or were we just reluctant to state that it would work fi we couldn't test it? Nomi Harris Project Manager, KBase

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new worksheet for this weeks release
by Thomas Brettin 27 Jan '13

27 Jan '13

I created a new worksheet as agreed during our call on Friday. It's the "Jan 28 2013 Minor" tab. Take a look. We can add more as needed. Tom Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] Are minor releases cumulative? [was Re: Redeploy testing summary]
by Thomas Brettin 27 Jan '13

27 Jan '13

Can we talk by phone? Email isn't working. Tom On Jan 27, 2013, at 12:29 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > On Jan 27, 2013, at 6:51 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> >> On Jan 26, 2013, at 4:42 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Thanks, Miriam. >>> Are minor releases cumulative? In other words, if we released a service last week (say, Ontology), is it included in this minor release as well? I'm guessing not, because there might have been new changes to the service that broke it. >> >> >> A module owner can have their module in the release cycle each week if they choose. I'm targeting that goal. >> >>> That means that I need to move the "Available Now" releases on http://www.kbase.us/developer-zone/services/ back to "Coming Soon", right? >>> If so, then I think we also need to list the services included in each dmg on the Downloads page (http://www.kbase.us/developer-zone/downloads/) >> >> Can someone think of how to auto-generate this? > > Although I'm pro-automation in many cases, this isn't one of them. The amount of effort required to automate this would exceed the (minor) amount of work it takes a human to make these adjustments for each release. > > But you didn't answer the questions: should I make the changes described? > There must be something that I am missing. I don't understand why this change is necessary, so I can't answer the question. I'm available to talk right now. If it has already been released, why would it be changed to coming soon? >>> because a new user might really want one of the services in the first Jan release and thus might want to download the older release instead of the newer one. But what if they want some of the services from the first minor release and some from the second? Is there any way to get both, or do they just have to wait a month for the full release? >> >> This is going to require some thought. The distinction between minor and major releases and how fine the versioning of all the independent parts should be thought through. Also, it needs lend itself to automation or our releases won't scale. Lets put this on the agenda for discussion at the Feb 4 release week. > > Fine, but I still need to know what to do for THIS release. Or are we not making this a release? Are we just waiting until the Feb 4 major build? I need to know that today, too. For this release, I would like to see updates to the dmg with the items that weren't released in the dmg last week and the javascript libraries should be released as well. > > Nomi > >> >> >>> Nomi >>> >>> On Jan 26, 2013, at 7:09 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >>> >>>> Release team, >>>> >>>> The list of modules that passed testing on either the 1st or redeploy and passed documents are: >>>> >>>> * communities_qc >>>> * erdb_service (private) >>>> * kb_seed >>>> * workspace_service >>>> * And the dependencies idserver, typecomp, cluster_service, kb_model_seed >>>> >>>> Just for completeness, the services that followed our procedure and failed are: >>>> >>>> * genome_annotation – failed make test on redeploy. It may work but until someone rewrites the tests, it fails the established procedure. >>>> * KBaseFBAModeling – failed make test on redeploy >>>> * matR – instructions for running demo (instead of make test) failed on redeploy >>>> * Translation – failed make test on redeploy >>>> * The dependency sim_service still is marked as having no documents but was in the last release. Therefore, it fails the established procedure. >>>> >>>> Miriam > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] Are minor releases cumulative? [was Re: Redeploy testing summary]
by Nomi Harris 27 Jan '13

27 Jan '13

On Jan 27, 2013, at 6:51 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > > On Jan 26, 2013, at 4:42 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Thanks, Miriam. >> Are minor releases cumulative? In other words, if we released a service last week (say, Ontology), is it included in this minor release as well? I'm guessing not, because there might have been new changes to the service that broke it. > > > A module owner can have their module in the release cycle each week if they choose. I'm targeting that goal. > >> That means that I need to move the "Available Now" releases on http://www.kbase.us/developer-zone/services/ back to "Coming Soon", right? >> If so, then I think we also need to list the services included in each dmg on the Downloads page (http://www.kbase.us/developer-zone/downloads/) > > Can someone think of how to auto-generate this? Although I'm pro-automation in many cases, this isn't one of them. The amount of effort required to automate this would exceed the (minor) amount of work it takes a human to make these adjustments for each release. But you didn't answer the questions: should I make the changes described? >> because a new user might really want one of the services in the first Jan release and thus might want to download the older release instead of the newer one. But what if they want some of the services from the first minor release and some from the second? Is there any way to get both, or do they just have to wait a month for the full release? > > This is going to require some thought. The distinction between minor and major releases and how fine the versioning of all the independent parts should be thought through. Also, it needs lend itself to automation or our releases won't scale. Lets put this on the agenda for discussion at the Feb 4 release week. Fine, but I still need to know what to do for THIS release. Or are we not making this a release? Are we just waiting until the Feb 4 major build? I need to know that today, too. Nomi > > >> Nomi >> >> On Jan 26, 2013, at 7:09 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >> >>> Release team, >>> >>> The list of modules that passed testing on either the 1st or redeploy and passed documents are: >>> >>> * communities_qc >>> * erdb_service (private) >>> * kb_seed >>> * workspace_service >>> * And the dependencies idserver, typecomp, cluster_service, kb_model_seed >>> >>> Just for completeness, the services that followed our procedure and failed are: >>> >>> * genome_annotation – failed make test on redeploy. It may work but until someone rewrites the tests, it fails the established procedure. >>> * KBaseFBAModeling – failed make test on redeploy >>> * matR – instructions for running demo (instead of make test) failed on redeploy >>> * Translation – failed make test on redeploy >>> * The dependency sim_service still is marked as having no documents but was in the last release. Therefore, it fails the established procedure. >>> >>> Miriam

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Final: release targets for Jan 28.
by Thomas Brettin 27 Jan '13

27 Jan '13

OK. I just added those services that failed last week based on the email Miriam sent on Saturday. here is the final list for tomorrow. > phi spy > plant_expression_service > genotype_phenotype_api > protein_info_service > prom_service > registry > genome_annotation – failed make test on redeploy. It may work but until someone rewrites the tests, it fails the established procedure. > KBaseFBAModeling – failed make test on redeploy > matR – instructions for running demo (instead of make test) failed on redeploy > translation – failed make test on redeploy > sim_service - still is marked as having no documents but was in the last release. Therefore, it fails the established procedure. On Jan 25, 2013, at 4:05 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Here are the targets thus far for the next release. We should add to it > > phi spy > plant_expression_service > genotype_phenotype_api > protein_info_service > prom_service > registry > > > > > > > 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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