genex-dev — GeneX developers

[GeneX-dev] Re: GeneX Enhancement Request

[Greg D. C. <gd...@nc...>]

The Canonical Sequence Features table was originally part of the schema, but is 
no longer, although there are miscellaneous nonfunctional references to it that 
we have not cleaned out yet, as you discovered. The idea was that a user has 
their name for a sequence feature, and then NCGR provides a master list of 
"canonical" names that can be tied to the user feature. These canonical names 
were supposed to be some sort of master reference for something like a gene. 
This idea was abandoned when NCGR discovered we did not have the resources 
available to maintain the Canonical table.

Greg Colello
NCGR Software Developer

>Date: Mon, 24 Sep 2001 13:58:03 -0600 (MDT)
>To: ge...@nc...
>From: rre...@in... (Dick Repasky)
>Cc: rre...@in... (Dick Repasky)
>Subject: GeneX Enhancement Request
>Mime-Version: 1.0
>
>Below is the result of your feedback form.  It was submitted by:
>    Dick Repasky (rre...@in...)
>    on Monday, September 24, 2001 at 13:58:03
>---------------------------------------------------------------------------
>
>subject: GeneX Enhancement Request
>
>realname: Dick Repasky
>
>email: rre...@in...
>
>Organization: Indiana Univ
>
>Location: Bloomington, IN
>
>Country: USA
>
>Operatingsys: Solaris
>
>Otheropsys: request for document enhancement
>
>Enhancement: The background web page that explains the database schema mentions 
UserSequenceFeature and CanonicalSequenceFeture.  UserSequenceFeature is 
described in the schema.pdf file, but CanonicalSequenceFeture is not.  For us it 
is necessary to know what's in the CanonicalSequenceFeature in order to decide 
whether genex meets our
>needs.
>
>Thanks,
>
>Dick Repasky
>
>P.S. This input box is really tiny on netscape.                                                                   
>                                                                   
>                                           
>                                                                   
>                                           
>                                    
>
>---------------------------------------------------------------------------
>

[GeneX-dev] (no subject)

[Ron O. <Ls...@wi...>]

Hi Jas and Todd,
I reinstalled the database the messages when install GeneX.pm runs fast, =
However I' ve catch part of it

Can't use an undefined value as an ARRAY reference at t/TestDB.pm line =
114.
BEGIN failed--compilation aborted at t/TestDB.pm line 162.
Compilation failed in require at t/XMLUtils.t line 16.
BEGIN failed--compilation aborted at t/XMLUtils.t line 16.
t/XMLUtils..........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-31
        Failed 31/31 tests, 0.00% okay
Failed Test    Status Wstat Total Fail  Failed  List of Failed
---------------------------------------------------------------------------=
-----
t/Chromosome.t     2   512     5    5 100.00%  1-5
t/Citation.t       2   512     5    5 100.00%  1-5
t/Contact.t        2   512     5    5 100.00%  1-5
t/DBUtils.t        2   512    21   21 100.00%  1-21
t/Genex.t          2   512    14   14 100.00%  1-14
t/GroupLink.t      2   512     4    4 100.00%  1-4
t/GroupSec.t       2   512     5    5 100.00%  1-5
t/HTMLUtils.t      2   512     4    4 100.00%  1-4
t/Protocol.t       2   512     2    2 100.00%  1-2
t/Sample.t         2   512     5    5 100.00%  1-5
t/Scanner.t        2   512     2    2 100.00%  1-2
t/Software.t       2   512     5    5 100.00%  1-5
t/Species.t        2   512     9    9 100.00%  1-9
t/Spotter.t        2   512     2    2 100.00%  1-2
t/UserSec.t        2   512     5    5 100.00%  1-5
t/XMLUtils.t       2   512    31   31 100.00%  1-31
Failed 16/36 test scripts, 55.56% okay. 124/196 subtests failed, 36.73% =
okay.
make: *** [test_dynamic] Error 2

maybe that is why I can't download expset?
 Ron

[GeneX-dev] Re: GeneX Enhancement Request

[Todd F. P. <tf...@nc...>]

Dear Mr. Repasky:

We have eliminated canonical sequence features from the schema (and any
references to them). The web page that you refer to needs to be rewritten
to reflect this. Thank you for pointing this out. Let us know if you have
more questions about features or how we can meet your needs.

Note that I have cc'd this message to the open-source list on source
forge. More GeneX experts monitor that list.

Sincerely,
Todd Peterson
Software Developer
NCGR

On Mon, 24 Sep 2001, Dick Repasky wrote:

> Below is the result of your feedback form.  It was submitted by:
>     Dick Repasky (rre...@in...)
>     on Monday, September 24, 2001 at 13:58:03
> ---------------------------------------------------------------------------
> 
> subject: GeneX Enhancement Request
> 
> realname: Dick Repasky
> 
> email: rre...@in...
> 
> Organization: Indiana Univ
> 
> Location: Bloomington, IN
> 
> Country: USA
> 
> Operatingsys: Solaris
> 
> Otheropsys: request for document enhancement
> 
> Enhancement: The background web page that explains the database schema mentions UserSequenceFeature and CanonicalSequenceFeture.  UserSequenceFeature is described in the schema.pdf file, but CanonicalSequenceFeture is not.  For us it is necessary to know what's in the CanonicalSequenceFeature in order to decide whether genex meets our
> needs.
> 
> Thanks,
> 
> Dick Repasky
> 
> P.S. This input box is really tiny on netscape.                                                                   
>                                                                    
>                                            
>                                                                    
>                                            
>                                     
> 
> ---------------------------------------------------------------------------
> 
> 

[GeneX-dev] Re: Genex

[Harry M. <man...@ho...>]

This means that:

EITHER the directory mentioned wasn't created properly in the course 
  of the run (does it exist?) 

OR that your 'tar' command isn't in the right place 
  (does `which tar` return  /bin/tar ? )  This should have been detected
  in the installation procedure, but you can tell the installation script that
  you'll fix it later.

OR that NONE of the xcluster files mentioned were created in the course of 
  the xcluster run (which might mean that your xcluster application either 
  isn't working or might not be named 'xcluster'?)

Any of these the case?

hjm



Yue Wang wrote:
> I am still working on the installation of Genex. I met
> another problem. When I run xcluster on the web. I got
> an error message:"Couldn't complete the command: cd
> /tmp/genex/xcl126321001106472; /bin/tar -czf
> xcluster.tar.gz xcluster*.[acegf]* ) ".
> Do you have some suggestion about it?
-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]

[GeneX-dev] Re:

[Harry M. <man...@ho...>]

Yue Wang wrote:

> Thank you very much. I will check DB.
> But I have one more question. I have not installed
> xcluster. Does it will effect it?

No, if you don't have xcluster installed, the installation procedure will detect it and complain a bit, but will allow you to continue.

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
         [plain text appreciated, if possible]

[GeneX-dev] Re:

[Harry M. <man...@ho...>]

Yue Wang wrote:
> Thank you very much for your email. I have finished
> that part. But I met other problem. I set up all
> stuffs. But when I went to the web, clicked on all the
> windows. Two windows don't work. They are "Database
> Query and Browse Database". The error message for both
> of them is "Couldn't connect to genex1.0.2: FATAL 1:
> at /usr/local/genex/perl5/Bio/Genex.pm line 664." Then
> I checked the files I downloaded from your web. The
> version is geneX1.0.4. Does it will effect it? Could
> you give me some suggestions? (I am working on Linux.)

It would be best if you had the latest version (1.0.4) and in fact it will detect that you have previously installed GeneX and take the same settings if you wish.

That said, it sounds like the DB is non-functional or the server is refusing connections.  Is the Postgres postmaster running? Can you connect to the DB via the postgres shell 'psql'?
Is the DB running on the same machine as the web server? I seem to remember that there was an issue with it if you were running on different physical servers.

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
         [plain text appreciated, if possible]

Re: [GeneX-dev] Re: GeneX database

[Harry M. <man...@ho...>]

Hi Jodi,

The place to get these packages is not from SOurceforge (Sourceforge is undergoing another, hopefully final, re-org of its download services.  For now, you can pull the latest versions from:

http://genex.ncgr.org

read the Release notes and the INSTALL doc to see what needs to be installed and in what order.  If you have questions about how to do any of this, Please post to this listserv as Greg mentioned:  

gen...@li...

hjm


"Greg D. Colello" wrote:
> 
> Jodi:
> 
> Sorry for the delayed response. I was out of town last week stranded in Houston
> by the airline shutdown.
> 
> You should send messages like this to gen...@li..., which I
> took the liberty of copying this email in on. You will get more prompt replies.
> Besides I am not involved in GeneX support anymore. Generally speaking Todd
> Peterson answers questions like this for NCGR, although many times Jason Stewart
> and Harry mangalam also answer as interested open source parties.
> 
> Good luck...
> 
> Greg Colello
> 
> >Date: Mon, 10 Sep 2001 09:08:50 -0400
> >From: Default User <de...@uv...>
> >X-Accept-Language: en
> >MIME-Version: 1.0
> >To: gd...@nc...
> >Subject: GeneX database
> >Content-Transfer-Encoding: 7bit
> >
> >Dear Dr. Colello:
> >My name is Jodi Kanter and I am a database administrator working at the
> >University of Virginia.  We are working toward installing a version of
> >the GeneX database locally, and I was hoping that you might be able to
> >offer some assistance.
> >
> >The following are are the items that I believe we need to download from
> >the SourceForge page:
> >
> >1)    GeneX DB Intialization
> >2)    GeneX Server
> >3)    GeneX Perl API
> >4)    GeneX Curation Tool (Linux)
> >
> >I would appreciate it if you could please let me know if I am missing
> >anything.
> >
> >We currently have or plan to have the following installed:
> >1)    Apache Web Server
> >2)    PostgreSQL
> >3)    R
> >4)    DBI.pm
> >5)    CGI.pm
> >
> >Can you tell me if there is a particular order in which the downloads
> >need to be installed? I have not been able to find any specific
> >installation instructions on your web site. Does the GeneXML come with
> >these downloads or does it need to be downloaded seperately?
> >Also, can you tell me if NCGR has any test data available?
> >
> >Thanks so much for your assistance. If there is someone else that I
> >should be contacting for help in this area please let me know.
> >
> >Sincerely,
> >Jodi Kanter, M.S.
> >(804) 924-2846
> >jk...@vi...
> >
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
         [plain text appreciated, if possible]

[GeneX-dev] Re: GeneX database

[Greg D. C. <gd...@nc...>]

Jodi:

Sorry for the delayed response. I was out of town last week stranded in Houston 
by the airline shutdown.

You should send messages like this to gen...@li..., which I 
took the liberty of copying this email in on. You will get more prompt replies. 
Besides I am not involved in GeneX support anymore. Generally speaking Todd 
Peterson answers questions like this for NCGR, although many times Jason Stewart 
and Harry mangalam also answer as interested open source parties.

Good luck...

Greg Colello

>Date: Mon, 10 Sep 2001 09:08:50 -0400
>From: Default User <de...@uv...>
>X-Accept-Language: en
>MIME-Version: 1.0
>To: gd...@nc...
>Subject: GeneX database
>Content-Transfer-Encoding: 7bit
>
>Dear Dr. Colello:
>My name is Jodi Kanter and I am a database administrator working at the
>University of Virginia.  We are working toward installing a version of
>the GeneX database locally, and I was hoping that you might be able to
>offer some assistance.
>
>The following are are the items that I believe we need to download from
>the SourceForge page:
>
>1)    GeneX DB Intialization
>2)    GeneX Server
>3)    GeneX Perl API
>4)    GeneX Curation Tool (Linux)
>
>I would appreciate it if you could please let me know if I am missing
>anything.
>
>We currently have or plan to have the following installed:
>1)    Apache Web Server
>2)    PostgreSQL
>3)    R
>4)    DBI.pm
>5)    CGI.pm
>
>Can you tell me if there is a particular order in which the downloads
>need to be installed? I have not been able to find any specific
>installation instructions on your web site. Does the GeneXML come with
>these downloads or does it need to be downloaded seperately?
>Also, can you tell me if NCGR has any test data available?
>
>Thanks so much for your assistance. If there is someone else that I
>should be contacting for help in this area please let me know.
>
>Sincerely,
>Jodi Kanter, M.S.
>(804) 924-2846
>jk...@vi...
>

Re: [GeneX-dev] DB2XML problem

[Todd F. P. <tf...@nc...>]

What procedure did you use to add the new user? Did you check that the
attributes are actually in the database?

todd

On Mon, 17 Sep 2001, Ron Ophir wrote:

> Hi Jas,
> I checked the output of db2xml and from some reason the last person don't get the following attribute
> <contact last_updated="2001-09-03 17:37:34+03"
>               type="experiment_set_provider"
>               id="Contact:522:NCGR">
> only the persons above.
> try to add a new user and see whether it is a local problem?
> thanks,
> Ron
> 

[GeneX-dev] DB2XML problem

[Ron O. <Ls...@wi...>]

Hi Jas,
I checked the output of db2xml and from some reason the last person don't =
get the following attribute
<contact last_updated=3D"2001-09-03 17:37:34+03"
              type=3D"experiment_set_provider"
              id=3D"Contact:522:NCGR">
only the persons above.
try to add a new user and see whether it is a local problem?
thanks,
Ron

Re: [GeneX-dev] Downloader

[<ja...@op...>]

"Todd F. Peterson" <tf...@nc...> writes:

> We will probably be converting the entire GeneX to the MAGE standard
> which is in the process of being approved. See
> http://www.ebi.ac.uk/microarray/MGED/index.html 

To find out more about MAGE see:

http://www.geml.org/omg.htm

and for software associated with MAGE:

http://mged.sf.net/

> Currently, there is a programming jamboree taking place in
> Toronto. Much of the groundwork is taking place there to implement
> the key pieces of this new standard. The newsgroup for this
> discussion is: http://bfx.kribb.re.kr/microarray/

That is badly out of date. For a slightly less badly out of date
archive, see: 

http://industry.ebi.ac.uk/~alan/maf/thread.htm

> I personally will be converting the GeneX system to use this new
> standard.  I am thinking that the downloader needs to be able to
> handle more than Postgres. Oracle is my first choice as an
> alternative. Sybase could be another. Maybe even MySQL, too. Anyway,
> if you would like to contribute, this would be something to
> consider.

I'm glad to hear that NCGR wants to prioritize this. I will also point
out that it is not a matter of just 'converting'. It will mean an
almost total re-write of major parts of the system. 

Also, which DBMS is used as a back-end, is an orthogonal issue. The
pieces to support multiple back-ends already exist, we've just never
tried using it.

Greg, if you're interested in helping, the EBI is planning a second
jamboree to be held in the UK during the first week of Dec. During
that time we will be developing Annotation tools and Data loading
tools. If you'd like to help out then, that would be a great
contribution. 

jas.

Re: [GeneX-dev] Downloader

[Todd F. P. <tf...@nc...>]

We will probably be converting the entire GeneX to the MAGE standard which
is in the process of being approved. See
http://www.ebi.ac.uk/microarray/MGED/index.html
Currently, there is a programming jamboree taking place in Toronto. Much
of the groundwork is taking place there to implement the key pieces of
this new standard. The newsgroup for this discussion is:
http://bfx.kribb.re.kr/microarray/

I personally will be converting the GeneX system to use this new standard.
I am thinking that the downloader needs to be able to handle more than
Postgres. Oracle is my first choice as an alternative. Sybase could be
another. Maybe even MySQL, too. Anyway, if you would like to contribute,
this would be something to consider.

Todd Peterson
Software Developer
NCGR

On Sun, 16 Sep 2001, Greg Riddick wrote:

> I'm interested in working on the Downloader project that uses perl for server-side data curation.  Any pointers to people or resources involved with this project?
> 
> Thanks,
> Greg Riddick
> 

[GeneX-dev] Downloader

[Greg R. <gr...@vi...>]

I'm interested in working on the Downloader project that uses perl for =
server-side data curation.  Any pointers to people or resources involved =
with this project?

Thanks,
Greg Riddick

Re: [GeneX-dev] Problem with XML2DB.pl

[<ja...@op...>]

"Shih-hsiu Lin" <ma...@jh...> writes:

> I have changed DBI->connect() in xml2db.pl to
> Genex->get_current_connection(). However, it is still not working, and I
> got the following error message:
> 
> Can't locate object method "get_current_connection" via package "Genex" at
> xml2db.pl line 113.

First, the method is Genex::current_connection() if I mistyped it in
my message I appologize. 

If you invoke a perl class method using the ClassName->method()
syntax, perl will include 'ClassName' as the first argument of
method. If you invoke it using ClassName::method() you are using the
fully resolve name of method, it it will *not* pass the classname.

So the proper way is to use:

Genex::current_connection() 

Hope this helps,
jas.

Re: [GeneX-dev] Re: Installation GeneX

[Harry M. <man...@ho...>]

> On Wed, 12 Sep 2001, YUEWANG wrote:
> 
> > Hi;
> >
> > I am trying to install GeneX. But I am stalled at "Perl & Using the CPAN shell to install Modules". As Ron Ophir noted, I met some problems at installing 'Bundle::libnet'. Could you tell me how to bug or retry installation this part?

Hi Yue,

I'm assuming that you're using Linux or a Unix variant.

You'll have to be a bit more specific in describing 'some problems'.  

- Do you have Perl installed?  ( does 'perl --version' return anything? )
- Can you start the CPAN shell? (does 'perl -MCPAN -e shell' get you into the shell?)
- Does the shell hang indefinitely?

etc, etc.  

Be happy to respond to more specific questions.

Harry




-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
         [plain text appreciated, if possible]

[GeneX-dev] Problem with XML2DB.pl

[Shih-hsiu L. <ma...@jh...>]

I have changed DBI->connect() in xml2db.pl to
Genex->get_current_connection(). However, it is still not working, and I
got the following error message:

Can't locate object method "get_current_connection" via package "Genex" at
xml2db.pl line 113.

Can you give me more suggestions what I can do to fix the problem? Thank
you


Shih-Hsiu Lin
10:39am
9/14/2001

[GeneX-dev] Re: Installation GeneX

[Todd F. P. <tf...@nc...>]

Dear Yue Wang:

I have CC'd this message to gen...@li... since more
experts subscribe to that list.

What platform are you installing the server on? What sort of problems are
you having? Did you sucessfullly install Perl itself? Unless you have root
privileges on the machine, the module install will fail since it needs to
write to a privileged directory.

A way around this is to do a Perl installation in your home directory and
then install the required modules there. See "How do I manually install a
module in a private/non-standard directory?" at
http://www.perl.com/pub/a/CPAN/misc/cpan-faq.html.

Please let us know if that doesn't help you.

Todd Peterson
Software Developer
NCGR

On Wed, 12 Sep 2001, YUEWANG wrote:

> Hi;
> 
> I am trying to install GeneX. But I am stalled at "Perl & Using the CPAN shell to install Modules". As Ron Ophir noted, I met some problems at installing 'Bundle::libnet'. Could you tell me how to bug or retry installation this part?
> 
> Thank you very much.
> 
> Yue Wang
>     
> 

Re: [GeneX-dev] Downloading experiment set

[<ja...@op...>]

"Todd F. Peterson" <tf...@nc...> writes:

> > > > The download bundele creation failed. The output of the XML writer program is:\
> > > > Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\'
> > not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > > > DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not
> > found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > 
> > Maybe I am working on the wrong version of the database. I
> > downloaded it from you site a week ago.  The status.pl result is
> > 
> > GeneX Server Installation Status Page
> > GeneX Server Information
> > VersionDate of VersionInstallation DateInstalled By
> > 1.0.22001-05-02 09:39:47 -07002001-09-12 11:31:52 +030...@we...

Hey Ron, Todd,

Something is very wrong with that DB dump if Ron is not getting the
provider_con_fk in the ExperimentSet table. According to CVS that was
added on 22 Jan 2001. Let me download the dump and check.

jas.

Re: [GeneX-dev] Downloading experiment set

[Todd F. P. <tf...@nc...>]

I will take a look at this problem. Could you send the .xar file which you
used to load the experiment set?

Todd

On Thu, 13 Sep 2001, Ron Ophir wrote:

> Dear Todd,
> Here is what I did:
> >genex=# select es_pk from experimentset;
> and got
>        es_pk
>       -------
>            8
>           17
>           28
>       (3 rows)
> 28 is of course the additional experiment.
> Then I queried the experimentset table for all fields and I noticed that columns us_fk is 0 and gs_fk is null. I checked the key of user Michael Steiner and found that it is 60, therefore I update us_fk in experimentset table to 60 by SQL. Now, I am seeing the Michael Steiner experiment set at the combo box but no "see text" (I guess that is because the gs_fk field is null. However when I tried retriev the set by db2xml or equivalently through the web I still get
> 
>      > > The download bundele creation failed. The output of the XML writer program is:\
>      > > Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\'
>      not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
>      > > DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not
>      found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> 
> Maybe I am working on the wrong version of the database. I downloaded it from you site a week ago.
> The status.pl result is 
> 
> GeneX Server Installation Status Page
> GeneX Server Information
> VersionDate of VersionInstallation DateInstalled By
> 1.0.22001-05-02 09:39:47 -07002001-09-12 11:31:52 +030...@we...
> 
> GeneX Database Information
> VersionDate of VersionInstallation DateInstalled ByDescription
> 
> Perl Information
> Path to InterpreterVersion
> /usr/bin/perl5.6.1
> 
> Perl Module Information
> Module NameVersion
> Bio::Genex2.6.1
> Class::ObjectTemplate0.4
> Class::ObjectTemplate::DB0.23
> CGI2.76
> DBI1.19
> DBD::Pg1.01
> XML::DOM1.30
> Term::ReadKey2.14
> 
> 
> as you see the genex database information is not available and from a small survey I made the reason for this is that I don't have the GeneXAdmin table.
> What do you say?
> Thanks,
> Ron
> 
> 
> 
> >>> "Todd F. Peterson" <tf...@nc...> 09/12/01 05:30PM >>>
> Ron
> 
> Here is a previous message from the gen...@li...
> regarding this problem. Let me know if this doesn't help you.
> 
> Todd Peterson
> Software Developer
> NCGR
> 
>   Mailing Lists
>       SourceForge
>           genex-dev - 
> Archive
> 2001 (554 msgs)
> 
>       
> 
> Thread: [GeneX-dev] Question about Using Curation Tool
> Print | Monitor This List | Reply To Author 
> 
> Message: 6459987 
> FROM: Todd F. PetersonDATE: 08/22/2001 14:53:27SUBJECT: RE:  [GeneX-dev]
> Question about Using Curation Tool I believe the server caches the
> experiment sets in
> /usr/local/genex/cache/db2xml/exp (actual path defined at server install
> and hard-coded in db2xml.pl around line 17.
> 
> To run db2xml.pl manually, type perl db2xml.pl to get a list of the
> command line parameters.
> 
> it looks like it wants 
> 
> perl --exp=17,8 --directory=~/
> 
> this should put the results in my home directory (--directory=~/)
> 
> where the --exp=17,8 parameter comes from the database itself (you could
> use psql as follows to find out the experiment set id's in your database):
> 
> [tfp@genebox bin]$ psql -U genex
> Welcome to psql, the PostgreSQL interactive terminal.
> 
> Type:  \copyright for distribution terms
>        \h for help with SQL commands
>        \? for help on internal slash commands
>        \g or terminate with semicolon to execute query
>        \q to quit
> 
> genex=# select es_pk from experimentset;
> es_pk
> -------
>      8
>     17
> (2 rows)
> 
> genex=#
> 
> Let me know if this doesn't help.
> 
> Todd
> 
> On Wed, 22 Aug 2001, Shih-hsiu Lin wrote:
> 
> > 
> > I have created a E. coli experimental data set in the local database
> > (following the Curation Tool Tutorial). Now, I am tring to use Curation
> > Tool on a client computer (windows system) to view the E. coli data. I
> > have changed the URL under File->Properties to my server
> > (http://genex.jhu.edu/cgi-bin.genex/curation-tool/expset-login.pl).
> > However, when I clicked the DOWNLOAD EXP SET button and login as
> > test/test, I didn't see the E. coli data in the database. Please give me
> > some pointers where I did wrong.
> > 
> > 
> > Shih-Hsiu Lin
> > 3:58pm
> > 8/22/2001
> > 
> > 
> > 
> > _______________________________________________
> > Genex-dev mailing list
> > <EMAIL: PROTECTED>
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> > 
> 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> <EMAIL: PROTECTED>
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 
> 
> 
> 
> 
> 
> 
> 
> On Wed, 12 Sep 2001, Ron Ophir wrote:
> 
> > Hi Jas,
> > I drop the database and re-install it. Then I insert a user through the creatLogin.pl script, download the control-bundel, create a new experiment using the curation tool and uploaded it. I can see it in the Query screen and analyze it. However, if I want to download the experiment set using the curation tool I get only Pat's and Hatfield's experiment sets in the combobox list. Where did the new experiment has gone? When I choose one of the experiments That what I got:
> > The download bundele creation failed. The output of the XML writer program is:\
> > Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > 
> > 
> > Maybe I can't see thw new experiment becase it ain't public? Although, I loged in using the new provider user ID.
> > Accession NumberAnalysis DescriptionArchive Bundle ReferenceBiology DescriptionData ProviderExperiment NameGroupGroup Can UpdateIs PublicLocal Accession NumberOwnerPrimary CitationQuantity Series TypeRelease DateSubmission DateTreatment Type8see textunknownWes Hatfield E. coli study Hatfield-Ecoli-K12-IHFWes Hatfield group, UCI(1)01 Not Available(1)0 2000-04-24 09:00:00+032000-04-24 09:00:00+03multidimentional17see text02Pat Brown Yeast Metabolism Study, Diauxic Shift Brown-Yeast-diauxicshiftPat Brown Lab, Stanford(2)01 Not Available(2)1quantity_series_nutrient1997-12-01 09:00:00+022000-04-24 09:00:00+03time_series28  ? Michael Steiner 00 0 0001-09-12 00:00
> > 
> > 
> > Thanks and hope for better day,
> > Ron
> > 
> 

Re: [GeneX-dev] Downloading experiment set

[<ja...@op...>]

Todd's reply is correct.

In order to speed up db2xml, I began to implement caching. At the
time, there was no way to indicate that the DB state had been
changed. 

jas.

"Todd F. Peterson" <tf...@nc...> writes:

> Here is a previous message from the gen...@li...
> regarding this problem. Let me know if this doesn't help you.
> 
> Todd Peterson
> Software Developer
> NCGR
> 
>   Mailing Lists
>       SourceForge
>           genex-dev - 
>  Archive
>  2001 (554 msgs)
>  
>       
> 
> Thread: [GeneX-dev] Question about Using Curation Tool
> Print | Monitor This List | Reply To Author 
> 
> Message: 6459987 
> FROM: Todd F. PetersonDATE: 08/22/2001 14:53:27SUBJECT: RE:  [GeneX-dev]
> Question about Using Curation Tool I believe the server caches the
> experiment sets in
> /usr/local/genex/cache/db2xml/exp (actual path defined at server install
> and hard-coded in db2xml.pl around line 17.
> 
> To run db2xml.pl manually, type perl db2xml.pl to get a list of the
> command line parameters.
> 
> it looks like it wants 
> 
> perl --exp=17,8 --directory=~/
> 
> this should put the results in my home directory (--directory=~/)
> 
> where the --exp=17,8 parameter comes from the database itself (you could
> use psql as follows to find out the experiment set id's in your database):
> 
> [tfp@genebox bin]$ psql -U genex
> Welcome to psql, the PostgreSQL interactive terminal.
> 
> Type:  \copyright for distribution terms
>        \h for help with SQL commands
>        \? for help on internal slash commands
>        \g or terminate with semicolon to execute query
>        \q to quit
> 
> genex=# select es_pk from experimentset;
>  es_pk
> -------
>      8
>     17
> (2 rows)
> 
> genex=#
> 
> Let me know if this doesn't help.
> 
> Todd
> 
> On Wed, 22 Aug 2001, Shih-hsiu Lin wrote:
> 
> > 
> > I have created a E. coli experimental data set in the local database
> > (following the Curation Tool Tutorial). Now, I am tring to use Curation
> > Tool on a client computer (windows system) to view the E. coli data. I
> > have changed the URL under File->Properties to my server
> > (http://genex.jhu.edu/cgi-bin.genex/curation-tool/expset-login.pl).
> > However, when I clicked the DOWNLOAD EXP SET button and login as
> > test/test, I didn't see the E. coli data in the database. Please give me
> > some pointers where I did wrong.
> > 
> > 
> > Shih-Hsiu Lin
> > 3:58pm
> > 8/22/2001
> > 
> > 
> > 
> > _______________________________________________
> > Genex-dev mailing list
> > <EMAIL: PROTECTED>
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> > 
> 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> <EMAIL: PROTECTED>
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 
> 
>  
>  
> 
>  
> 
> 
> On Wed, 12 Sep 2001, Ron Ophir wrote:
> 
> > Hi Jas,
> > I drop the database and re-install it. Then I insert a user through the creatLogin.pl script, download the control-bundel, create a new experiment using the curation tool and uploaded it. I can see it in the Query screen and analyze it. However, if I want to download the experiment set using the curation tool I get only Pat's and Hatfield's experiment sets in the combobox list. Where did the new experiment has gone? When I choose one of the experiments That what I got:
> > The download bundele creation failed. The output of the XML writer program is:\
> > Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> > 
> > 
> > Maybe I can't see thw new experiment becase it ain't public? Although, I loged in using the new provider user ID.
> > Accession NumberAnalysis DescriptionArchive Bundle ReferenceBiology DescriptionData ProviderExperiment NameGroupGroup Can UpdateIs PublicLocal Accession NumberOwnerPrimary CitationQuantity Series TypeRelease DateSubmission DateTreatment Type8see textunknownWes Hatfield E. coli study Hatfield-Ecoli-K12-IHFWes Hatfield group, UCI(1)01 Not Available(1)0 2000-04-24 09:00:00+032000-04-24 09:00:00+03multidimentional17see text02Pat Brown Yeast Metabolism Study, Diauxic Shift Brown-Yeast-diauxicshiftPat Brown Lab, Stanford(2)01 Not Available(2)1quantity_series_nutrient1997-12-01 09:00:00+022000-04-24 09:00:00+03time_series28  ? Michael Steiner 00 0 0001-09-12 00:00
> > 
> > 
> > Thanks and hope for better day,
> > Ron
> > 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Downloading experiment set

[Todd F. P. <tf...@nc...>]

Ron

Here is a previous message from the gen...@li...
regarding this problem. Let me know if this doesn't help you.

Todd Peterson
Software Developer
NCGR

  Mailing Lists
      SourceForge
          genex-dev - 
 Archive
 2001 (554 msgs)
 
      

Thread: [GeneX-dev] Question about Using Curation Tool
Print | Monitor This List | Reply To Author 

Message: 6459987 
FROM: Todd F. PetersonDATE: 08/22/2001 14:53:27SUBJECT: RE:  [GeneX-dev]
Question about Using Curation Tool I believe the server caches the
experiment sets in
/usr/local/genex/cache/db2xml/exp (actual path defined at server install
and hard-coded in db2xml.pl around line 17.

To run db2xml.pl manually, type perl db2xml.pl to get a list of the
command line parameters.

it looks like it wants 

perl --exp=17,8 --directory=~/

this should put the results in my home directory (--directory=~/)

where the --exp=17,8 parameter comes from the database itself (you could
use psql as follows to find out the experiment set id's in your database):

[tfp@genebox bin]$ psql -U genex
Welcome to psql, the PostgreSQL interactive terminal.

Type:  \copyright for distribution terms
       \h for help with SQL commands
       \? for help on internal slash commands
       \g or terminate with semicolon to execute query
       \q to quit

genex=# select es_pk from experimentset;
 es_pk
-------
     8
    17
(2 rows)

genex=#

Let me know if this doesn't help.

Todd

On Wed, 22 Aug 2001, Shih-hsiu Lin wrote:

> 
> I have created a E. coli experimental data set in the local database
> (following the Curation Tool Tutorial). Now, I am tring to use Curation
> Tool on a client computer (windows system) to view the E. coli data. I
> have changed the URL under File->Properties to my server
> (http://genex.jhu.edu/cgi-bin.genex/curation-tool/expset-login.pl).
> However, when I clicked the DOWNLOAD EXP SET button and login as
> test/test, I didn't see the E. coli data in the database. Please give me
> some pointers where I did wrong.
> 
> 
> Shih-Hsiu Lin
> 3:58pm
> 8/22/2001
> 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> <EMAIL: PROTECTED>
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 



_______________________________________________
Genex-dev mailing list
<EMAIL: PROTECTED>
http://lists.sourceforge.net/lists/listinfo/genex-dev


 
 

 


On Wed, 12 Sep 2001, Ron Ophir wrote:

> Hi Jas,
> I drop the database and re-install it. Then I insert a user through the creatLogin.pl script, download the control-bundel, create a new experiment using the curation tool and uploaded it. I can see it in the Query screen and analyze it. However, if I want to download the experiment set using the curation tool I get only Pat's and Hatfield's experiment sets in the combobox list. Where did the new experiment has gone? When I choose one of the experiments That what I got:
> The download bundele creation failed. The output of the XML writer program is:\
> Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\
> 
> 
> Maybe I can't see thw new experiment becase it ain't public? Although, I loged in using the new provider user ID.
> Accession NumberAnalysis DescriptionArchive Bundle ReferenceBiology DescriptionData ProviderExperiment NameGroupGroup Can UpdateIs PublicLocal Accession NumberOwnerPrimary CitationQuantity Series TypeRelease DateSubmission DateTreatment Type8see textunknownWes Hatfield E. coli study Hatfield-Ecoli-K12-IHFWes Hatfield group, UCI(1)01 Not Available(1)0 2000-04-24 09:00:00+032000-04-24 09:00:00+03multidimentional17see text02Pat Brown Yeast Metabolism Study, Diauxic Shift Brown-Yeast-diauxicshiftPat Brown Lab, Stanford(2)01 Not Available(2)1quantity_series_nutrient1997-12-01 09:00:00+022000-04-24 09:00:00+03time_series28  ? Michael Steiner 00 0 0001-09-12 00:00
> 
> 
> Thanks and hope for better day,
> Ron
> 

[GeneX-dev] Downloading experiment set

[Ron O. <Ls...@wi...>]

Hi Jas,
I drop the database and re-install it. Then I insert a user through the =
creatLogin.pl script, download the control-bundel, create a new experiment =
using the curation tool and uploaded it. I can see it in the Query screen =
and analyze it. However, if I want to download the experiment set using =
the curation tool I get only Pat's and Hatfield's experiment sets in the =
combobox list. Where did the new experiment has gone? When I choose one of =
the experiments That what I got:
The download bundele creation failed. The output of the XML writer program =
is:\
Bio::Genex::ExperimentSet::initialize: ERROR:  Attribute \'provider_con_fk\=
' not found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line =
486.\
DBD::Pg::st execute failed: ERROR:  Attribute \'provider_con_fk\' not =
found at /usr/local/genex/perl5/Bio/Genex/ExperimentSet.pm line 486.\


Maybe I can't see thw new experiment becase it ain't public? Although, I =
loged in using the new provider user ID.
Accession NumberAnalysis DescriptionArchive Bundle ReferenceBiology =
DescriptionData ProviderExperiment NameGroupGroup Can UpdateIs PublicLocal =
Accession NumberOwnerPrimary CitationQuantity Series TypeRelease DateSubmis=
sion DateTreatment Type8see textunknownWes Hatfield E. coli study =
Hatfield-Ecoli-K12-IHFWes Hatfield group, UCI(1)01 Not Available(1)0 =
2000-04-24 09:00:00+032000-04-24 09:00:00+03multidimentional17see =
text02Pat Brown Yeast Metabolism Study, Diauxic Shift Brown-Yeast-diauxicsh=
iftPat Brown Lab, Stanford(2)01 Not Available(2)1quantity_series_nutrient19=
97-12-01 09:00:00+022000-04-24 09:00:00+03time_series28  ? Michael Steiner =
00 0 0001-09-12 00:00


Thanks and hope for better day,
Ron

[GeneX-dev] Re: [microarray-format] Mapping of Affy data to GeneX

[<ja...@op...>]

"Eric F. Tsung" <ef...@ch...> writes:

> I have been looking at the database that you help develop, GeneX,
> and will probably implement the Postgres part of it to store results
> we get from collaberators that my orginization analyzes.  I have set
> up GeneX on one of our servers.

Hey Eric,

I think that it's great that you're using GeneX. You may want to ask
for help or post information on the primary development list:

   gen...@li...

That way you'll get more attention.

Also I'm not sure what you mean by 'implement the Postgres part of
it'. The current GeneX schema is already a Postgres schema. Are you
talking about implementing a MAGE schema in Postgres? If so, that
would be great, but you would have to re-work all the tools, because
they are currently very schema-specific.

> Since GeneX first stored Affymetrix data, do you have a specific mapping
> of columns that come from Affy's .CHP and .CEL files into columns of the
> GeneX database.  I know that in general AM_Spots coorespond to the .CEL
> file and ArrayMeasurement, to the .CHP.

GeneX has been used to store Affy data, but only after analysis and
derivation. It wasn't until recently that I saw my first .CEL or .CHP
files, so I'm sorry but I don't have a mapping to give you.

I am currently seeking funding from a number of sources to build an
Open Source Affy data loader (as well as a spotted microarray
loader). We haven't heard back on the proposals yet, but we are
hopeful. In my mind the lack of an automateable loader is GeneX's
biggest weakness.

> Also, since I'm here in Boston, I'm very interested in attending
> MGED-4.  I'll keep checking the web site for updates.

Great! Let us know of your successes (or issues) with GeneX.

jas.

Re: [GeneX-dev] Curation Tool XML & xml2db versions

[<ja...@op...>]

"Joe Roden" <ro...@ai...> writes:

> On 08/22/2001 Greg D. Colello wrote:
> 
> I have worked through the curation tool tutorial, submitted the tutorial 
> experiment to my own genex site, and tried xml2db on the xml.  Like Ron, I 
> also got an error:
> 
>   DBD::Pg::st execute failed: ERROR:  parser: parse error at or near "" at
>   /tmp/xml2db.pl line 1650.
>   7Contact: SELECT con_pk from Contact where contact_person = 'genex' AND   at 
>   /tmp/xml2db.pl line 1650.
> 
> Is this error a symptom of the xml version issue Greg mentioned
> above?

No, it's because the author of xml2db didn't want to use the Genex.pm
API that I had written. No one writing Genex code should call
DBI::connect() directly. There is a wrapper method
Genex::get_current_connection() that caches the DB handle that should
be used instead. Re-writing of xml2db is never going to happen,
though. So you should make whatever local changes you feel you need to
make.

In the devel version of GeneX, the monolithic applications db2xml and
xml2db where made object oriented, so that every DB object has its own
db2xml() and xml2db() methods. So the applications just call xml2db()
or db2xml() on the root object.

jas.

[GeneX-dev] Curation Tool XML & xml2db versions

[Joe R. <ro...@ai...>]

On 08/22/2001 Greg D. Colello wrote:

> You need to run xml2db.pl yourself. There may be a problem depending on what 
> version of the Curation Tool and xml2db you have. The XML created by some 
> versions of the Curation Tool was not readable by some versions of xml2db.
> 
> Unfortunately that is probably the case with the latest version of the Curation 
> Tool. I have been out sick for 1 month and have not had a chance to try xml2db 
> on the latest Curation Tool XML output. I will be doing that soon.

I have worked through the curation tool tutorial, submitted the tutorial 
experiment to my own genex site, and tried xml2db on the xml.  Like Ron, I 
also got an error:

  DBD::Pg::st execute failed: ERROR:  parser: parse error at or near "" at
  /tmp/xml2db.pl line 1650.
  7Contact: SELECT con_pk from Contact where contact_person = 'genex' AND   at 
  /tmp/xml2db.pl line 1650.

Is this error a symptom of the xml version issue Greg mentioned above?

Perhaps unrelated, I made a /tmp copy of xml2db to get around a login issue, 
probably because we disabled tcp connections to postgres during earlier 
DBI connections debugging.

  Using directory:
  /usr/software/genex/1.0.4/submission/hatield_ecoli_ihf-857883546.5300/.
  DBI->connect(dbname=genex;host=localhost;port=5432) failed: PQconnectPoll() --
  connect() failed: Connection refused at ./xml2db.pl line 112
  DB connect failed

In my /tmp copy I simply changed connectString from:

  my $connectString = "dbi:Pg:dbname=$database;host=$host;port=$port";

to 

  my $connectString = "dbi:Pg:dbname=$database ";

and connected after setting PGUSER=genex, which I think will use unix 
domain sockets to the localhost.  So permissions should be equivalent.

Thanks for your help!

Joe