From mira at lanl.gov Mon Feb 6 18:08:31 2012 From: mira at lanl.gov (mira) Date: Mon, 6 Feb 2012 16:08:31 -0700 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl Message-ID: Hello, I am interested in using your BioSQL schema for a project I am currently working on. I downloaded version 1.0.1 and found that the sql folder has no schema script for SQLite which I thought you were supporting now. Is that not true? I have no problems re-writing the schema file but after that I find myself trying to fix the Perl script that loads the NCBI taxonomy files... Can you tell me if BioSQL for SQLite is available and where I can find the package for download? Many thanks, Mira Dimitrijevic From rbuels at gmail.com Fri Feb 10 12:35:34 2012 From: rbuels at gmail.com (Robert Buels) Date: Fri, 10 Feb 2012 12:35:34 -0500 Subject: [BioSQL-l] Google Summer of Code project ideas Message-ID: <4F355566.3030503@gmail.com> Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From p.j.a.cock at googlemail.com Fri Feb 10 20:12:48 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 01:12:48 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References: Message-ID: On Monday, February 6, 2012, mira wrote: > Hello, > > I am interested in using your BioSQL schema for a project I am currently working on. I downloaded version 1.0.1 and > found that the sql folder has no schema script for SQLite which I thought you were supporting now. Is that not true? I > have no problems re-writing the schema file but after that I find myself trying to fix the Perl script that loads the NCBI > taxonomy files... > > Can you tell me if BioSQL for SQLite is available and where I can find the package for download? > > Many thanks, > Mira Dimitrijevic The latest release of BioSQL was before the SQLite3 schema. You can get the schema from BioSQL's GitHub repository. I'm not sure if BioPerl supports BioSQL in SQLite yet - Biopython does. Peter From hlapp at drycafe.net Sat Feb 11 17:15:45 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 17:15:45 -0500 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: Indeed. I was thinking that there is a 1.0.2 release that includes it, but apparently there isn't. It appears that bioperl-db (and thus BioPerl) does not support the SQlite schema (yet). -hilmar On Feb 10, 2012, at 8:12 PM, Peter Cock wrote: > On Monday, February 6, 2012, mira wrote: >> Hello, >> >> I am interested in using your BioSQL schema for a project I am currently > working on. I downloaded version 1.0.1 and >> found that the sql folder has no schema script for SQLite which I thought > you were supporting now. Is that not true? I >> have no problems re-writing the schema file but after that I find myself > trying to fix the Perl script that loads the NCBI >> taxonomy files... >> >> Can you tell me if BioSQL for SQLite is available and where I can find > the package for download? >> >> Many thanks, >> Mira Dimitrijevic > > The latest release of BioSQL was before the SQLite3 schema. > > You can get the schema from BioSQL's GitHub repository. > > I'm not sure if BioPerl supports BioSQL in SQLite yet - Biopython does. > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From p.j.a.cock at googlemail.com Sat Feb 11 18:08:43 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 23:08:43 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: > Indeed. I was thinking that there is a 1.0.2 release that > includes it, but apparently there isn't. > The schema itself should be ready - but what else is needed for BioSQL on SQLite to be ready for release? Assorted BioSQL Perl script updates like load_ncbi_taxonomy.pl might need work? > It appears that bioperl-db (and thus BioPerl) does not support > the SQlite schema (yet). > That would be good, but doesn't need to holdup a BioSQL release, does it? Peter From hlapp at drycafe.net Sat Feb 11 20:36:06 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 20:36:06 -0500 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: <958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> On Feb 11, 2012, at 6:08 PM, Peter Cock wrote: > On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: >> Indeed. I was thinking that there is a 1.0.2 release that >> includes it, but apparently there isn't. >> > > The schema itself should be ready - but what else is needed for > BioSQL on SQLite to be ready for release? Assorted BioSQL > Perl script updates like load_ncbi_taxonomy.pl might need work? Yes, at least testing. > >> It appears that bioperl-db (and thus BioPerl) does not support >> the SQlite schema (yet). >> > > That would be good, but doesn't need to holdup a BioSQL > release, does it? No, not at all. Just needs a disclaimer somewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sat Feb 11 23:03:58 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sun, 12 Feb 2012 04:03:58 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: <958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> References:

<958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> Message-ID: On Feb 11, 2012, at 7:36 PM, Hilmar Lapp wrote: > On Feb 11, 2012, at 6:08 PM, Peter Cock wrote: > >> On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: >>> Indeed. I was thinking that there is a 1.0.2 release that >>> includes it, but apparently there isn't. >>> >> >> The schema itself should be ready - but what else is needed for >> BioSQL on SQLite to be ready for release? Assorted BioSQL >> Perl script updates like load_ncbi_taxonomy.pl might need work? > > Yes, at least testing. > >>> It appears that bioperl-db (and thus BioPerl) does not support >>> the SQlite schema (yet). >>> >> >> That would be good, but doesn't need to holdup a BioSQL >> release, does it? > > > No, not at all. Just needs a disclaimer somewhere. > > -hilmar On a possibly related note, were the DBIx::Class-based BioSQL mappings ever developed? I think one holdup with SQLite was to see is a generic ORM level mapping could be implemented, then maybe add a BioPerl layer over that. chris From rbuels at gmail.com Mon Feb 27 11:22:52 2012 From: rbuels at gmail.com (Robert Buels) Date: Mon, 27 Feb 2012 11:22:52 -0500 Subject: [BioSQL-l] Update: call for Google Summer of Code project ideas Message-ID: <4F4BADDC.5020905@gmail.com> Hi all, As kindly pointed out by Reece Hart, the previous email I sent out calling for Google Summer of Code project ideas, had the wrong due date for project ideas in it. I actually want them to all be in place by Friday, March 2, which is this coming Friday. == Instructions for Wiki Editing == For each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. == end instructions == Again, please have the updates done by this Friday (March 2). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From mira at lanl.gov Mon Feb 13 11:42:37 2012 From: mira at lanl.gov (mira) Date: Mon, 13 Feb 2012 16:42:37 -0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: <8168AD28-46AA-461D-9A96-9353A421E2B1@lanl.gov> Thanks for your reply Peter - I'll look for the schema on GitHub. Also, the load_ncbi_taxonomy.pl script doesn't work with SQLite yet. Mira On Feb 11, 2012, at 4:08 PM, Peter Cock wrote: > On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: >> Indeed. I was thinking that there is a 1.0.2 release that >> includes it, but apparently there isn't. >> > > The schema itself should be ready - but what else is needed for > BioSQL on SQLite to be ready for release? Assorted BioSQL > Perl script updates like load_ncbi_taxonomy.pl might need work? > >> It appears that bioperl-db (and thus BioPerl) does not support >> the SQlite schema (yet). >> > > That would be good, but doesn't need to holdup a BioSQL > release, does it? > > Peter From mira at lanl.gov Mon Feb 6 23:08:31 2012 From: mira at lanl.gov (mira) Date: Mon, 6 Feb 2012 16:08:31 -0700 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl Message-ID: Hello, I am interested in using your BioSQL schema for a project I am currently working on. I downloaded version 1.0.1 and found that the sql folder has no schema script for SQLite which I thought you were supporting now. Is that not true? I have no problems re-writing the schema file but after that I find myself trying to fix the Perl script that loads the NCBI taxonomy files... Can you tell me if BioSQL for SQLite is available and where I can find the package for download? Many thanks, Mira Dimitrijevic From rbuels at gmail.com Fri Feb 10 17:35:34 2012 From: rbuels at gmail.com (Robert Buels) Date: Fri, 10 Feb 2012 12:35:34 -0500 Subject: [BioSQL-l] Google Summer of Code project ideas Message-ID: <4F355566.3030503@gmail.com> Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From p.j.a.cock at googlemail.com Sat Feb 11 01:12:48 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 01:12:48 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References: Message-ID: On Monday, February 6, 2012, mira wrote: > Hello, > > I am interested in using your BioSQL schema for a project I am currently working on. I downloaded version 1.0.1 and > found that the sql folder has no schema script for SQLite which I thought you were supporting now. Is that not true? I > have no problems re-writing the schema file but after that I find myself trying to fix the Perl script that loads the NCBI > taxonomy files... > > Can you tell me if BioSQL for SQLite is available and where I can find the package for download? > > Many thanks, > Mira Dimitrijevic The latest release of BioSQL was before the SQLite3 schema. You can get the schema from BioSQL's GitHub repository. I'm not sure if BioPerl supports BioSQL in SQLite yet - Biopython does. Peter From hlapp at drycafe.net Sat Feb 11 22:15:45 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 17:15:45 -0500 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: Indeed. I was thinking that there is a 1.0.2 release that includes it, but apparently there isn't. It appears that bioperl-db (and thus BioPerl) does not support the SQlite schema (yet). -hilmar On Feb 10, 2012, at 8:12 PM, Peter Cock wrote: > On Monday, February 6, 2012, mira wrote: >> Hello, >> >> I am interested in using your BioSQL schema for a project I am currently > working on. I downloaded version 1.0.1 and >> found that the sql folder has no schema script for SQLite which I thought > you were supporting now. Is that not true? I >> have no problems re-writing the schema file but after that I find myself > trying to fix the Perl script that loads the NCBI >> taxonomy files... >> >> Can you tell me if BioSQL for SQLite is available and where I can find > the package for download? >> >> Many thanks, >> Mira Dimitrijevic > > The latest release of BioSQL was before the SQLite3 schema. > > You can get the schema from BioSQL's GitHub repository. > > I'm not sure if BioPerl supports BioSQL in SQLite yet - Biopython does. > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From p.j.a.cock at googlemail.com Sat Feb 11 23:08:43 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 23:08:43 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: > Indeed. I was thinking that there is a 1.0.2 release that > includes it, but apparently there isn't. > The schema itself should be ready - but what else is needed for BioSQL on SQLite to be ready for release? Assorted BioSQL Perl script updates like load_ncbi_taxonomy.pl might need work? > It appears that bioperl-db (and thus BioPerl) does not support > the SQlite schema (yet). > That would be good, but doesn't need to holdup a BioSQL release, does it? Peter From hlapp at drycafe.net Sun Feb 12 01:36:06 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 20:36:06 -0500 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References:

Message-ID: <958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> On Feb 11, 2012, at 6:08 PM, Peter Cock wrote: > On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: >> Indeed. I was thinking that there is a 1.0.2 release that >> includes it, but apparently there isn't. >> > > The schema itself should be ready - but what else is needed for > BioSQL on SQLite to be ready for release? Assorted BioSQL > Perl script updates like load_ncbi_taxonomy.pl might need work? Yes, at least testing. > >> It appears that bioperl-db (and thus BioPerl) does not support >> the SQlite schema (yet). >> > > That would be good, but doesn't need to holdup a BioSQL > release, does it? No, not at all. Just needs a disclaimer somewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sun Feb 12 04:03:58 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sun, 12 Feb 2012 04:03:58 +0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: <958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> References:

<958EC33F-992B-4F3F-B12B-7225134CBEC1@drycafe.net> Message-ID: On Feb 11, 2012, at 7:36 PM, Hilmar Lapp wrote: > On Feb 11, 2012, at 6:08 PM, Peter Cock wrote: > >> On Sat, Feb 11, 2012 at 10:15 PM, Hilmar Lapp wrote: >>> Indeed. I was thinking that there is a 1.0.2 release that >>> includes it, but apparently there isn't. >>> >> >> The schema itself should be ready - but what else is needed for >> BioSQL on SQLite to be ready for release? Assorted BioSQL >> Perl script updates like load_ncbi_taxonomy.pl might need work? > > Yes, at least testing. > >>> It appears that bioperl-db (and thus BioPerl) does not support >>> the SQlite schema (yet). >>> >> >> That would be good, but doesn't need to holdup a BioSQL >> release, does it? > > > No, not at all. Just needs a disclaimer somewhere. > > -hilmar On a possibly related note, were the DBIx::Class-based BioSQL mappings ever developed? I think one holdup with SQLite was to see is a generic ORM level mapping could be implemented, then maybe add a BioPerl layer over that. chris From rbuels at gmail.com Mon Feb 27 16:22:52 2012 From: rbuels at gmail.com (Robert Buels) Date: Mon, 27 Feb 2012 11:22:52 -0500 Subject: [BioSQL-l] Update: call for Google Summer of Code project ideas Message-ID: <4F4BADDC.5020905@gmail.com> Hi all, As kindly pointed out by Reece Hart, the previous email I sent out calling for Google Summer of Code project ideas, had the wrong due date for project ideas in it. I actually want them to all be in place by Friday, March 2, which is this coming Friday. == Instructions for Wiki Editing == For each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. == end instructions == Again, please have the updates done by this Friday (March 2). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From mira at lanl.gov Mon Feb 13 16:42:37 2012 From: mira at lanl.gov (mira) Date: Mon, 13 Feb 2012 16:42:37 -0000 Subject: [BioSQL-l] Error in load_ncbi_taxonomy.pl In-Reply-To: References: