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[Gmod-gbrowse] Re: further adventures installing CHADO
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From: Scott C. <ca...@cs...> - 2004-02-13 21:11:14
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Hi TD,
I sent this to the gmod-devel list, as this isn't directly gbrowse
related. Please trim the gbrowse list off future replies. On with the
fun (isn't it fun being a guinea pig: it is version 0.001 alpha, after
all :-) See my notes below:
On Fri, 2004-02-13 at 15:47, T.D. Houfek wrote:
> The anonymous CVS checkout did solve the problem I was having, although
> some of the sqlfairy install tests (17, 28-30) failed.
> I was able to proceed through the 'make' step. But then:
>
> % make load_schema
> bin/sh /usr/local/TGIanalysis/schema/chado/bin/test_load.sh chado
> DROP DATABASE
> CREATE DATABASE
> ERROR: language "plpgsql" does not exist
> database chado created
>
> I am unsure if that error will cause problems downstream...?
Not really unless you are going to use the microarray-related modules;
at any rate, I will add directions for adding plpgsql to template1 (the
template database that all databases are created from). Here are the
items added to the install doc:
* make it accept tcp/ip connections by adding this line to
postgresql.conf:
tcpip_socket = true
* create a database user with permission to drop and add databases:
psql> CREATE USER <username> WITH CREATDB;
* tell postgres that it can use the plpgsql language (either as user
postgres or as the user created above):
# /usr/bin/createlang plpgsql template1
These postgres directions will no doubt continue to grow as we figure
out what else we need to tell people.
>
> For users like me who are kinda new to PostgreSQL, the installation
> documentation might point out that to follow the CHADO install
> instructions as given, you may need to create a 'root' PG user. I
> su'd to username postgres and ran "make load_schema" as that user. But
> I then found that I had to open up the permissions of /chado/load/logs
> to make them writable by user postgres.
It is probably easier to give yourself permission to create databases as
above.
>
> There were a couple of NULL insert warnings when preparing the database:
>
> bash-2.05b$ make prepdb
> ./Build prepdb
> INSERT 22356 1
> INSERT 22357 1
> INSERT 22358 1
> INSERT 22359 1
> INSERT 22360 1
> INSERT 22361 1
> INSERT 22362 1
> INSERT 22363 1
> INSERT 22364 1
> INSERT 22365 1
> INSERT 22366 1
> INSERT 22367 1
> INSERT 22368 1
> INSERT 22369 1
> INSERT 22370 1
> INSERT 22371 1
> INSERT 22372 1
> INSERT 22373 1
> psql:/usr/local/TGIanalysis/schema/chado/load/etc/initialize.sql:29:
> ERROR: ExecInsert: Fail to add null value in not null attribute type_id
> psql:/usr/local/TGIanalysis/schema/chado/load/etc/initialize.sql:34:
> ERROR: ExecInsert: Fail to add null value in not null attribute type_id
> INSERT 22374 1
> INSERT 22375 1
> INSERT 22376 1
> INSERT 22377 1
> INSERT 22378 1
> INSERT 22379 1
> INSERT 22380 1
>
> ---- (end output) -----------------------------
>
> For the making of the ontologies, I again had to open up permissions to
> user postgres on /chado/_build/notes... But then I again ran into
> trouble:
>
>
> bash-2.05b$ make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Embryonic Mouse Anatomy Ontology
> [5] Mouse Anatomy Ontology
> [6] Mouse Pathology Ontology (Pathbase)
> [7] Cell Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4,5,6,7
> fetching files for Relationship Ontology
> +http://cvs.sf.net/viewcvs.py/obo/obo/ontology/OBO_REL/rel.definitions?rev=HEAD
> updated
> +http://cvs.sf.net/viewcvs.py/obo/obo/ontology/OBO_REL/rel.ontology?rev=HEAD
> updated
> loading...Ima::DBI connect('dbname=chado;port=5432;host=localhost','postgres',...) failed: could not connect to server: Connection refused at ./load/bin/gmod_load_ontology.pl line 87
> System call './load/bin/gmod_load_ontology.pl /tmp/chado_load/obo/OBO_REL/rel.ontology /tmp/chado_load/obo/OBO_REL/rel.definitions' failed: 65280
> Died at /usr/local/TGIanalysis/schema/chado/lib/Chado/Builder.pm line 285, <STDIN> line 1.
> make: *** [ontologies] Error 2
>
>
> ------ (end output) ------------------
>
> I was curious about why gmod_load_ontology.pl was failing, so I
> executed it with the same arguments, on its own, i.e.:
>
> bash-2.05b$ ./load/bin/gmod_load_ontology.pl /tmp/chado_load/obo/OBO_REL/rel.ontology /tmp/chado_load/obo/OBO_REL/rel.definitions
> Ima::DBI connect('dbname=chado;port=5432;host=localhost','postgres',...) failed:
> could not connect to server: Connection refused at ./load/bin/gmod_load_ontology.pl line 87
>
> As far as I can tell all the database connection parameters are
> correct, the postmaster is running, etc. Can anyone look at the
> outputs I have here and guess what the problem with loading the
> ontology info is?
These failures happened because postgres doesn't accept tcp/ip
connections by default (it's more secure that way). In order for it to
accept tcp/ip connections, see the note above.
Thanks for your perseverance,
Scott
>
> TD
>
>
> On Fri, 2004-02-13 at 11:39, Scott Cain wrote:
> > Hi TD,
> >
> > This is a known problem and fixed in the CVS repository for
> > SQL::Translator. You can check out the current CVS repository with the
> > following commands:
> >
> > cvs -d:pserver:ano...@cv...:/cvsroot/sqlfairy login
> > cvs -d:pserver:ano...@cv...:/cvsroot/sqlfairy co sqlfairy
> >
> > Be patient as the anonymous cvs server can be very slow.
> >
> > Scott
> >
> > On Fri, 2004-02-13 at 11:18, T.D. Houfek wrote:
> > > I have run into an issue installing CHADO. I do not know its import,
> > > but faithfully mention it. ;-)
> > >
> > > When I execute:
> > >
> > > [root@aether chado]% perl Makefile.PL
> > >
> > > I am asked a list of questions about my RDBMS and which
> > > schema extensions I am interested in installing. What I have found
> > > (under Red Hat 9.0 running on a Dell Latitude D800) is that if I try to
> > > install any of the extensions, my execution of Makefile.PL always fails
> > > with:
> > >
> > > Creating Class::DBI classes in
> > > '/usr/local/TGIanalysis/schema/chado/lib/Chado'
> > > (This could take a while) ...
> > >
> > > ERROR (line 20): Invalid statement: Was expecting create, or
> > > comment, or
> > > alter, or grant, or revoke, or drop, or insert,
> > > or
> > > connect, or update, or set
> > > -------- translate: Error with parser
> > > 'SQL::Translator::Parser::PostgreSQL': Parse failed.
> > > bin/pg2cdbi.pl failed, is SQL::Translator installed?
> > >
> > > --- (end of output) -----------------------------------------
> > >
> > > SQL::Translator is installed, and seems to be recent and to
> > > pass all of its self tests.
> > >
> > > Any ideas? Also, can anyone point me to documentation concerning the
> > > extensions?
> > >
> > > Thank you,
> > > TD
> > >
--
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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