From hlapp at gnf.org Sun Oct 3 02:54:00 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Sun Oct 3 02:53:28 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: Message-ID: <01686134-1509-11D9-A1FE-000A959EB4C4@gnf.org> A year later, but I finally managed to add them to the repository. Would you test them as I don't have an HSQLDB running? Also, would you be willing to maintain them? I'm trying to catch up with the changes driven by Biojava at the end of last year (which led to issues this year again), and so I have already added the term_relationship_term table and foreign key constraints. (I'm also adding this to the other RDBMS's versions and will commit when I tested them.) -hilmar On Tuesday, October 21, 2003, at 07:58 PM, Len Trigg wrote: > Hilmar Lapp wrote: > > Sounds reasonable to me. Also, would be consistent with the other 2 > > supported platforms. > > This reminds me, I ported the BioSQL schema to support HSQLDB, and > added the neccessary support to BioJava's BioSQL binding. We use > HSQLDB in our BioSQL unit tests, and I have seen references to other > people making use of it. I have attached the appropriate schema files, > if you wish include them as part of the BioSQL project (in which case > BioSQL CVS can become the canonical location). > > > Cheers, > Len. > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From len at reeltwo.com Tue Oct 5 17:10:37 2004 From: len at reeltwo.com (Len Trigg) Date: Tue Oct 5 17:10:28 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: <01686134-1509-11D9-A1FE-000A959EB4C4@gnf.org> References: <01686134-1509-11D9-A1FE-000A959EB4C4@gnf.org> Message-ID: Hilmar Lapp wrote: > A year later, but I finally managed to add them to the repository. > > Would you test them as I don't have an HSQLDB running? Also, would you > be willing to maintain them? I'm trying to catch up with the changes > driven by Biojava at the end of last year (which led to issues this > year again), and so I have already added the term_relationship_term > table and foreign key constraints. I'm sure either me or someone else among the BioJava people will be happy to maintain it -- it's used in the BioJava unit tests. (I haven't had the opportunity to do much BioJava work recently.) There was an updated version of the schema posted to the BioJava mailing list a month or so ago, but I haven't looked at it in detail. Cheers, Len. > > (I'm also adding this to the other RDBMS's versions and will commit > when I tested them.) > > -hilmar > > On Tuesday, October 21, 2003, at 07:58 PM, Len Trigg wrote: > > > Hilmar Lapp wrote: > > > Sounds reasonable to me. Also, would be consistent with the other 2 > > > supported platforms. > > > > This reminds me, I ported the BioSQL schema to support HSQLDB, and > > added the neccessary support to BioJava's BioSQL binding. We use > > HSQLDB in our BioSQL unit tests, and I have seen references to other > > people making use of it. I have attached the appropriate schema files, > > if you wish include them as part of the BioSQL project (in which case > > BioSQL CVS can become the canonical location). > > > > > > Cheers, > > Len. > > > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > From hlapp at gnf.org Wed Oct 6 12:22:42 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Oct 6 12:22:10 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: Message-ID: On Tuesday, October 5, 2004, at 02:10 PM, Len Trigg wrote: > There was an updated version of the schema posted to the BioJava > mailing list a month or so ago, but I haven't looked at it in detail. > Could somebody point me to the respective email in the archives, or at least provide either of subject or author? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From len at reeltwo.com Wed Oct 6 14:30:56 2004 From: len at reeltwo.com (Len Trigg) Date: Wed Oct 6 14:30:37 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: References: Message-ID: At Wed, 6 Oct 2004 09:22:42 -0700, Hilmar Lapp wrote: > > > On Tuesday, October 5, 2004, at 02:10 PM, Len Trigg wrote: > > > There was an updated version of the schema posted to the BioJava > > mailing list a month or so ago, but I haven't looked at it in detail. > > > > Could somebody point me to the respective email in the archives, or at > least provide either of subject or author? http://www.biojava.org/pipermail/biojava-dev/2004-August/001950.html I think the only additions were adding primary key statements. I can have another look when I get to work. Cheers, Len. From alexsc at rge.fmrp.usp.br Sun Oct 10 16:40:46 2004 From: alexsc at rge.fmrp.usp.br (Alexandre dos Santos Cristino) Date: Tue Oct 12 09:56:32 2004 Subject: [BioSQL-l] problems with schema loading. Message-ID: <20041010142957.G17847-100000@rge.fmrp.usp.br> Hello biosqlers, I've tried to load the biosql schema for postgres in a debian linux, but there was some errors: bash$ psql bioseqdb < biosqldb-pg.sql . . . ERROR: parser: parse error at or near "volatile" ERROR: parser: parse error at or near "volatile" is this a real problem, because some initial load tests with python has worked with genbank files. thank you! cheers, alex -- Alexandre dos Santos Cristino|- _ -| Depto. Gen?tica - FMRP-USP alexsc@rge.fmrp.usp.br |_ = _ - _| http://www.ime.usp.br/~alexsc -. .-. .-. .-. .-. .-. .-. .-|_ _ _ = _|-. .-. .-. .-. .-. .-. .-. .-. .- X X X X X X X |- - _ - -| X X X X X X X X -' '-' '-' '-' '-' '-' '-' '-|=_=___=_=|-' '-' '-' '-' '-' '-' '-' '-' '- From hlapp at gmx.net Sun Oct 17 00:39:35 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun Oct 17 10:09:43 2004 Subject: [BioSQL-l] problems with schema loading. In-Reply-To: <20041010142957.G17847-100000@rge.fmrp.usp.br> Message-ID: <8BCDB4D8-1FF6-11D9-8CC1-000A959EB4C4@gmx.net> Which version of PostgreSQL are you using? I've tested the schema DDL against 7.3.4 and there is no problem. You don't necessarily need the two functions unless want to load the NCBI taxonomy database using load_ncbi_taxonomy.pl. And even then the script will run if you don't have them, it will just be very slow. -hilmar On Sunday, October 10, 2004, at 01:40 PM, Alexandre dos Santos Cristino wrote: > > > ?Hello biosqlers, > > ?I've tried to load the biosql schema for postgres in a debian linux, > but > there was some errors: > > bash$ psql bioseqdb < biosqldb-pg.sql > > . > . > . > ERROR:? parser: parse error at or near "volatile" > ERROR:? parser: parse error at or near "volatile" > > ?is this a real problem, because some initial load tests with python > has > worked with genbank files. > > ?thank you! > > ?cheers, > ?alex > > > -- > Alexandre dos Santos Cristino|-?? _?? -| Depto. Gen?tica - FMRP-USP > ?? alexsc@rge.fmrp.usp.br??? |_ = _ - _| http://www.ime.usp.br/~alexsc > -. .-. .-. .-. .-. .-. .-. .-|_ _ _ = _|-. .-. .-. .-. .-. .-. .-. .-. > .- > ? X?? X?? X?? X?? X?? X?? X? |- - _ - -|? X?? X?? X?? X?? X?? X?? X?? X > -' '-' '-' '-' '-' '-' '-' '-|=_=___=_=|-' '-' '-' '-' '-' '-' '-' '-' > '- > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Sun Oct 17 19:28:16 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Sun Oct 17 19:27:25 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: Message-ID: <389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org> I added the primary key constraints. Could somebody who has a functional HSQLDB server test the DDL script to weed out any possible typos and syntax errors? -hilmar On Wednesday, October 6, 2004, at 11:30 AM, Len Trigg wrote: > At Wed, 6 Oct 2004 09:22:42 -0700, > Hilmar Lapp wrote: > > > > > > On Tuesday, October 5, 2004, at 02:10? PM, Len Trigg wrote: > > > > > There was an updated version of the schema posted to the BioJava > > > mailing list a month or so ago, but I haven't looked at it in > detail. > > > > > > > Could somebody point me to the respective email in the archives, or > at > > least provide either of subject or author? > > http://www.biojava.org/pipermail/biojava-dev/2004-August/001950.html > > I think the only additions were adding primary key statements. I can > have another look when I get to work. > > Cheers, > Len. > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From len at reeltwo.com Tue Oct 19 23:18:57 2004 From: len at reeltwo.com (Len Trigg) Date: Tue Oct 19 23:42:45 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: <389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org> References: <389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org> Message-ID: Hilmar Lapp wrote: > I added the primary key constraints. Could somebody who has a > functional HSQLDB server test the DDL script to weed out any possible > typos and syntax errors? I plugged the version from BioSQL CVS into the BioJava unit tests and wiggled with them until they worked (other than the couple of known problems with the BioJava BioSQL support). biosqldb-hsqldb.sql is checked in with windows line endings. Other than that, the name field of the term_synonym table was incorrect (patch attached). I also updated the drop-biosqldb-hsqldb.sql. Cheers, Len. -------------- next part -------------- A non-text attachment was scrubbed... Name: biosqldb-hsqldb.sql.patch Type: application/octet-stream Size: 645 bytes Desc: not available Url : http://open-bio.org/pipermail/biosql-l/attachments/20041020/bf56d9b0/biosqldb-hsqldb.sql.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: drop-biosqldb-hsqldb.sql.patch Type: application/octet-stream Size: 5585 bytes Desc: not available Url : http://open-bio.org/pipermail/biosql-l/attachments/20041020/bf56d9b0/drop-biosqldb-hsqldb.sql.obj From hlapp at gnf.org Wed Oct 20 02:15:47 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Oct 20 02:15:07 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: Message-ID: <7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org> On Tuesday, October 19, 2004, at 08:18 PM, Len Trigg wrote: > I plugged the version from BioSQL CVS into the BioJava unit tests and > wiggled with them until they worked (other than the couple of known > problems with the BioJava BioSQL support). Thanks a lot for your help. I greatly appreciate it. > > biosqldb-hsqldb.sql is checked in with windows line endings. Fixed. > Other than that, the name field of the term_synonym table was > incorrect > (patch attached). Fixed. However, doesn't that mean that this column name needs to be changed in the PostgreSQL version as well? Or does Biojava revert to 'synonym' then? > > I also updated the drop-biosqldb-hsqldb.sql. Thanks, a applied this too. Cheers, -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From len at reeltwo.com Wed Oct 20 16:20:04 2004 From: len at reeltwo.com (Len Trigg) Date: Wed Oct 20 16:18:47 2004 Subject: [BioSQL-l] Re: HSQLDB support... In-Reply-To: <7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org> References: <7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org> Message-ID: Hilmar Lapp wrote: > > Other than that, the name field of the term_synonym table was > > incorrect > > (patch attached). > > Fixed. However, doesn't that mean that this column name needs to be > changed in the PostgreSQL version as well? Or does Biojava revert to > 'synonym' then? Actually the term_synonym table doesn't appear to be used at all in BioJava :-). The field name should probably be changed in the other schemas as well (it's mentioned in the BioSQL README). Cheers, Len. From hlapp at gmx.net Mon Oct 25 12:28:35 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon Oct 25 13:41:23 2004 Subject: [BioSQL-l] Re: Bioperl-DB question In-Reply-To: Message-ID: Michael, the location of the error suggests that a statement handle was returned undef and hence failed to prepare. Is it the very first term that fails or do several terms succeed until one fails? If you supply --printerror as a command-line argument a preceding DBI error should become visible. If so, please copy&paste verbatim and post it. When you say you instantiated the Oracle schema and view, does this mean you instantiated the view-based API for strict Biosql compliance, or did you install the alias-based API? I.e., did you run BS-create-Biosql-API.sql (alias-based) or BS-create-Biosql-API2.sql (view-based). Bioperl-db can't deal with the view-based yet due to column naming. If that is the API you need though (instead of the alias-based) then it is relatively easy to add; it will become another driver. Alternatively, as an immediate fix install the alias-based API under a different user, after prefixing the referenced tables with the schema owner (and of course then you need to grant access to the tables which is not pretty). If you instantiated the alias-based API and --printerror does not cause a preceding DBI error to be printed, supply --debug, capture the output (extensive!) in a file, and send it to me. Also, please use the unaltered distribution for this. -hilmar On Monday, October 25, 2004, at 07:55 AM, michael.g.moore@gsk.com wrote: > > Hi, > > We've instantiated the Oracle schema and view for the BioPerl-DB tree > (latest CVS checkout ~1 week old and using ) and I am having some > problems > > I've managed to get the NCBI taxonomy to load. > > When I try the Gene Ontology data I use the following program > > ./load_ontology --dbname USTST240 --driver=Oracle --dbuser=biosql > --dbpass=biosql --safe --updobsolete --namespace "Gene Ontology" > --format go --fmtargs "-def_file,GO.defs" function.ontology > component.ontology process.ontology > > I get a > > 'Cant call method 'bind_param" on an undefined value at > /blah-blah-blah/BasePersistenceAdaptor.pm line (in mine its 948 but I > added some debugging so I think its around 942 in the original code) > > One of the pieces of SQL that is being constructed from this part of > the module does not seem to make sense > > select > term.term_oid,term.indetifier,term.name,term,definition,term.is_obsolet > e,term.ont_oid > from term > where indentifier = ? > > The reason that this seems wrong is that the columns names are from > the SYMGENE schema and should not be available to the biosql view that > was constructed ?on the SYMGENE schema. > > Any help would be appreciated. > > Mike > > > > > Mike Moore > > BioInformatics Engineering and Integration > GlaxoSmithKline -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 -------------------------------------------------------------