genex-dev — GeneX developers

Re: [GeneX-dev] Jas Igues this is the same problem:

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

"Ron Ophir" <Ls...@wi...> writes:

> We tried to download Experiment set and this is what we 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.\ Thanks, Ron

Hey Ron,

You shouldn't be seeing that.

I'm really confused, now. I need some help. Can you show me the output
of your 'GeneX Status' page? It should be located at something like:

http://your.machine.edu/cgi-bin/genex/samples/status.pl

You can navigate to it from the main GeneX HTML page on your machine:

http://your.machine.edu/genex/

and then choosing any of the links, i.e. 'Background'. The navigation
bar that appears on those pages has an 'Installation Status'
link. Choose it and send the output.

provider_con_fk is correct. We renamed all the ambiguous foreign keys
to the contact table so that the role name was part of the column name
of the key, i.e role = provider, table = contact ==> provider_con_fk.

db2xml is complaining because the version of the DB you are talking to
*does not* have those changes in the schema. How did you create that
DB? Did you use the init-db.pl script as I suggested?

Thanks,
jas.

[GeneX-dev] Jas Igues this is the same problem:

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

Jas Igues this is the same problem:
We tried to download Experiment set and this is what we 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.\
Thanks,
Ron

[GeneX-dev] Browser problem

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

Hi All,
I load data and and then use the browser to look at them (The query works =
fine). Ichecked every radiobutton and this is wht I got :

TABLE NAME: AM_Factor
SOFTWARE ERROR: Bio::Genex::AM_FactorValues::get_objects: must set =
'pkey_link' for linking class at /usr/local/genex/perl5/Bio/Genex/AM_Factor=
Values.pm line 144.

TABLE NAME:AM_SuspectSpots
SOFTWARE ERROR:Bio::Genex::AM_SuspectSpots::get_objects: must set =
'pkey_link' for linking class at /usr/local/genex/perl5/Bio/Genex/AM_Suspec=
tSpots.pm line 141.

TABLE NAME:GroupLink
SOFTWARE ERROR:Bio::Genex::GroupLink::get_objects: must set 'pkey_link' =
for linking class at /usr/local/genex/perl5/Bio/Genex/GroupLink.pm line =
141.

TABLE NAME:HotSpots
SOFTWARE ERROR:Bio::Genex::HotSpots::get_objects: must set 'pkey_link' for =
linking class at /usr/local/genex/perl5/Bio/Genex/HotSpots.pm line 144.

TABLE NAME:SampleProtocols
SOFTWARE ERROR:Bio::Genex::SampleProtocols::get_objects: must set =
'pkey_link' for linking class at /usr/local/genex/perl5/Bio/Genex/SamplePro=
tocols.pm line 144.

TABLE NAME:SpotLink=20
SOFTWARE ERROR:Bio::Genex::SpotLink::get_objects: must set 'pkey_link' for =
linking class at /usr/local/genex/perl5/Bio/Genex/SpotLink.pm line 141.

TABLE NAME:TL_Factor
SOFTWARE ERROR:Bio::Genex::TL_FactorValues::get_objects: must set =
'pkey_link' for linking class at /usr/local/genex/perl5/Bio/Genex/TL_Factor=
Values.pm line 147.

TABLE NAME:Treatment_AMs
SOFTWARE ERROR:Bio::Genex::Treatment_AMs::get_objects: must set 'pkey_link'=
 for linking class at /usr/local/genex/perl5/Bio/Genex/Treatment_AMs.pm =
line 141.

TABLE NAME:UserSequenceFeature
SOFTWARE ERROR:Can't locate object method "putative_csf_fk" via package =
"Bio::Genex::UserSequenceFeature" (perhaps you forgot to load "Bio::Genex::=
UserSequenceFeature"?) at /usr/local/genex/perl5/Bio/Genex/UserSequenceFeat=
ure.pm line 350.

TABLE NAME:USF_ExternalDBLink
SOFTWARE ERROR:Bio::Genex::USF_ExternalDBLink::get_objects: must set =
'pkey_link' for linking class at /usr/local/genex/perl5/Bio/Genex/USF_Exter=
nalDBLink.pm line 144.

***************************************************************************=
*****TABLE NAME:UserCanonicalLink
ERROR:UserCanonicalLink not found, please try a different table

TABLE NAME:CitationLink
ERROR:CitationLink not found, please try a different table

TABLE NAME:BlastHits
ERROR:Sorry this table has no values

Do you know where are these eeror come from?
Thanks,
Ron

Re: [GeneX-dev] Re: Starting from a scratch

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

"Ron Ophir" <Ls...@wi...> writes:

> "Ron Ophir" <ls...@wi...> writes:
> 
> >> I'm trying to upload data from a scratch. I empty the entire genex
> >> database by TRUNCATE for all tables. Then I used the cml file of the
> >> control bundle you provided as a start (from the disk) and
> >> remove/add record in contact, softaware etc... lisCo ntactts. In the
> >> XML2DB step I got the following error ": SELECT con_pk from Contact
> >> where contact_person = 'genex' AND at ../../bin/xml2db.pl line
> >> 1650."  What do you think is the best way for starting from the
> >> scratch?  
> 
> >Ouch. Hey Ron.
> 
> No Ouch. I have a backup, however I do think that MEta data is
> something that should be editable.

Hey Ron,

If you look in the GeneX/scripts directory in the installer, you will
notice a number of (potentially) useful scripts. Look especially at
the *_insert.pl ones. They are for editing XML versions of the GeneX
metadata and inserting/updating your GeneX DB. Also notice CV_check.pl
for ensuring that you are properly setting controlled vocabulary
fields in your DB.

Some of these are better documented than others, I'll be happy to
answer questions.

Now, in terms of editing the metadata associated with an experiment,
that was to be the role of the curation tool. As far as I know,
however, todd and others, have not solved the issue of updates.

My goal was to develop WWW based tools that enable you to modify the
metadata for your own experiment. The MGED programming jamboree in
Sept will be working on this problem, and the tools we develop will be
very useful for GeneX. The issue right now is funding. If I receive
funding to continue this work it will get done soon.

> >There is a quick and simple way to start from scratch:
> 
> >* drop your DB using dropdb
> >* re-create your DB using createdb
> >* get the starting genex-init Pg dump which you may already, if not
> >  you can download it from the genex-server download at genex.ncgr.org
> >* load the dump into the DB (su to user postgres and run:
>    'gunzip --stdout path_to_dump_file.gz |psql genex_db_name'
> 
> >Or if you want, just run the init-dump.pl script (it lives in the
> >top-level directory of the GeneX-Server installation package) as user
> >postgres. It automates the whole process I listed above.

Were you able to recreate the DB?

> >> Would you care of organize a workshop on GeneX?  
> 
> >That's a wonderful idea. I'm hoping we can do just that at the
> >upcoming O'Reilly Open Source Bioinformatics conference (Jan 2002, in
> >Tucson Arizona). I'm including Jennifer Weller on this reply, she is a
> >co-organizer of the conference, as well as having been the GeneX
> >project leader while she was at NCGR, so I'm sure she'll look
> >favorably on your request.
> 
> >If Tucson is too far to travel from Israel, you can always invite me
> >to the Weizmann Institute for a visit. 
> 
> I'll try that, but the problem as always is money not the distance
> so I'm not promises anything. In any case, I would like very much to
> be informed about any workshop you give on GeneX.

If you would like to see a GeneX workshop, please email Jennifer and
request it from her (jew...@vt...). She can't do anything until
it's requested by someone else.

> You so well documented GeneX.pm and other tools. What about XML2DB
> and DB2XML?  

Well...

I didn't write xml2db. so all bets are off.

I did write db2xml, and there is documentation. Trying runing:
'pod2text db2xml.pl' or pod2man db2xml.pl on the command line from
within the GeneX/scripts directory in the installer directory.

Also, in the GeneX/html directory you should have db2xml.html which is
an html version of the same thing. This page should be installed in
your WWW server directory alongside all the other Genex.pm html pages.

And yes, the documentation should be better. Suggestions on what to
add would be appreciated.

jas.

[GeneX-dev] Re: Starting from a scratch

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

"Ron Ophir" <ls...@wi...> writes:

>> I'm trying to upload data from a scratch. I empty the entire genex
>> database by TRUNCATE for all tables. Then I used the cml file of the
>> control bundle you provided as a start (from the disk) and
>> remove/add record in contact, softaware etc... lisCo ntactts. In the
>> XML2DB step I got the following error ": SELECT con_pk from Contact
>> where contact_person =3D 'genex' AND at ../../bin/xml2db.pl line
>> 1650."  What do you think is the best way for starting from the
>> scratch? =20

>Ouch. Hey Ron.

No Ouch. I have a backup, however I do think that MEta data is something =
that should be editable.

>A significant part of the initial data set we include with GeneX are
>all of the control information that you need to use the DB, for
>example the contents of all the controlled vocabulary tables. By
>truncating them, you've thrown away necessary information. So the
>error above indicates that to make a valid SQL query, it was looking
>for extra information and didn't get it (hence the trailing 'AND ...'
>at the end of the SELECT.

>There is a quick and simple way to start from scratch:

>* drop your DB using dropdb
>* re-create your DB using createdb
>* get the starting genex-init Pg dump which you may already, if not
>  you can download it from the genex-server download at genex.ncgr.org
>* load the dump into the DB (su to user postgres and run:
   'gunzip --stdout path_to_dump_file.gz |psql genex_db_name'

>Or if you want, just run the init-dump.pl script (it lives in the
>top-level directory of the GeneX-Server installation package) as user
>postgres. It automates the whole process I listed above.

>> Would you care of organize a workshop on GeneX? =20

>That's a wonderful idea. I'm hoping we can do just that at the
>upcoming O'Reilly Open Source Bioinformatics conference (Jan 2002, in
>Tucson Arizona). I'm including Jennifer Weller on this reply, she is a
>co-organizer of the conference, as well as having been the GeneX
>project leader while she was at NCGR, so I'm sure she'll look
>favorably on your request.

>If Tucson is too far to travel from Israel, you can always invite me
>to the Weizmann Institute for a visit.=20

I'll try that, but the problem as always is money not the distance so I'm =
not promises anything. In any case, I would like very much to be informed =
about any workshop you give on GeneX.=20

>I'm no longer an employee of
>NCGR, and I do contract support work for GeneX, and I could help
>organize something there. I'll also be at the EBI in early December,
>perhaps you could convince Alvis Brazma to organize a Gene Expression
>DB workshop then?

>jas.

DearJas,
You so well documented GeneX.pm and other tools. What about XML2DB and =
DB2XML?
Ron

Re: [GeneX-dev] Starting from a scratch

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

"Ron Ophir" <ls...@wi...> writes:

> I'm trying to upload data from a scratch. I empty the entire genex
> database by TRUNCATE for all tables. Then I used the cml file of the
> control bundle you provided as a start (from the disk) and
> remove/add record in contact, softaware etc... lisCo ntactts. In the
> XML2DB step I got the following error ": SELECT con_pk from Contact
> where contact_person = 'genex' AND at ../../bin/xml2db.pl line
> 1650."  What do you think is the best way for starting from the
> scratch?  

Ouch. Hey Ron.

A significant part of the initial data set we include with GeneX are
all of the control information that you need to use the DB, for
example the contents of all the controlled vocabulary tables. By
truncating them, you've thrown away necessary information. So the
error above indicates that to make a valid SQL query, it was looking
for extra information and didn't get it (hence the trailing 'AND ...'
at the end of the SELECT.

There is a quick and simple way to start from scratch:

* drop your DB using dropdb
* re-create your DB using createdb
* get the starting genex-init Pg dump which you may already, if not
  you can download it from the genex-server download at genex.ncgr.org
* load the dump into the DB (su to user postgres and run:
   'gunzip --stdout path_to_dump_file.gz |psql genex_db_name'

Or if you want, just run the init-dump.pl script (it lives in the
top-level directory of the GeneX-Server installation package) as user
postgres. It automates the whole process I listed above.

> Would you care of organize a workshop on GeneX?  

That's a wonderful idea. I'm hoping we can do just that at the
upcoming O'Reilly Open Source Bioinformatics conference (Jan 2002, in
Tucson Arizona). I'm including Jennifer Weller on this reply, she is a
co-organizer of the conference, as well as having been the GeneX
project leader while she was at NCGR, so I'm sure she'll look
favorably on your request.

If Tucson is too far to travel from Israel, you can always invite me
to the Weizmann Institute for a visit. I'm no longer an employee of
NCGR, and I do contract support work for GeneX, and I could help
organize something there. I'll also be at the EBI in early December,
perhaps you could convince Alvis Brazma to organize a Gene Expression
DB workshop then?

jas.

[GeneX-dev] Starting from a scratch

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

Hi All,
I'm trying to upload data from a scratch. I empty the entire genex =
database by TRUNCATE for all tables. Then I used the cml file of the =
control bundle you provided as a start (from the disk) and remove/add =
record in contact, softaware etc... lisCo ntactts. In the XML2DB step I =
got the following error ": SELECT con_pk from Contact where contact_person =
=3D 'genex' AND   at ../../bin/xml2db.pl line 1650."
What do you think is the best way for starting from the scratch?
Would you care of organize a workshop on GeneX?=20
Thanks,
Ron

Re: [GeneX-dev] Re: GeneX

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

"Harry Mangalam" <man...@ho...> writes:

> > The main problem with the current state of gene expression array
> > experiments is that there is no agreed-upon standard data
> > structure. Thus, I have less enthusiasm for putting effort into a
> > database unless I know that the data is in a format that can be
> > used by me and others, and that the data produced by others can be
> > accessed by our lab in a useful way.
> 
> This is an excellent point and one that we're quite concerned about.
> You're right in that there is no standard currently, but a draft
> standard has been published and there will shortly be a programming
> jamboree in Toronto to develop tools to support it. As it happens,
> Jason Stewart, the chief developer for the GeneX project, has been
> one of the leads in working with the MGED and OMG organizations on
> just this issue and may shortly be hired directly by them to produce
> the software tools that are required for this to take place.  His
> development platform is GeneX so GeneX will probably be one of the
> first databases to support the MGED /MIAME standards.

I'm glad that someone else made this point, not having a standard
format has slowed things down. I'm happy to say that we now appear to
have a standard format. You can check out more details at:

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

and

   http://mged.sourceforge.net/

The data model is called MAGE-OM (MicroArray Gene Expression Object
Model), and the XML exchange format is MAGE-ML. We are starting to
develop Perl/Java/C++ implementations of these, and the ArrayExpress
group at EBI has already developed a relation DB schema based on
MAGE-OM. 

jas.

[GeneX-dev] Re: GeneX

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

> Date: Mon, 27 Aug 2001 09:56:23 -0700
> From: Daniel E Sabath <dsabath@u.washington.edu>
> To: Honghui Wan <hw...@nc...>
> Mime-Version: 1.0 (Apple Message framework v388)
> Subject: Re: GeneX
> 
> Dear Dr. Wan,
> 
> I was playing around with GeneX for two reasons: 1) we are doing
> gene expression experiments to study patterns of gene expression in
> low grade lymphomas. The platform we are using is spotted cDNA
> microarrays prepared by the UW Center for Expression Arrays, a core
> facility, and 2) I'm exploring the Unix capabilities of MacOS X, so
> I was interested to see if I could actually get GeneX to work on
> MacOS X (I was successful!).

And we're grateful for your efforts!  Incidentally, you may already know of this, but the latest version of R plus all the goodies for MacOSX was recently announced as being available at:

http://www.stat.ucla.edu/~deleeuw/R/


> For unrelated reasons, I wound up reinstalling MacOS X on my
> computer, so I haven't had a chance to reinstall GeneX. One of the
> things that I didn't like about GeneX (at least at the time I
> installed it) was that there was no obvious way to put our own data
> into the database. At the time, it appeared to be more of a
> demonstration project than anything, and it came with some sample
> databases.

This is largely true.  The method for getting data into GeneX is the least effective certainly.  We make a Java application available called the Curation tool which requires the Java 1.3 JVM (and I'm
not sure it's available for the Mac..?)
However, after a long delay (the lead developer was quite ill), an improved version (much faster, much reduced memory requirements) has been made available and that was announced to the listserv when
it happened.
We are also working on a server side data loader written in perl, but because of the reorganization at NCGR, its progress has slowed.  Neither I nor Jason are working for NCGR anymore so we're working
on GeneX but at a much-reduced pace.

> The main problem with the current state of gene expression array
> experiments is that there is no agreed-upon standard data
> structure. Thus, I have less enthusiasm for putting effort into a
> database unless I know that the data is in a format that can be
> used by me and others, and that the data produced by others can be
> accessed by our lab in a useful way.

This is an excellent point and one that we're quite concerned about.  You're right in that there is no standard currently, but a draft standard has been published and there will shortly be a
programming jamboree in Toronto to develop tools to support it. As it happens, Jason Stewart, the chief developer for the GeneX project, has been one of the leads in working with the MGED and OMG
organizations on just this issue and may shortly be hired directly by them to produce the software tools that are required for this to take place.  His development platform is GeneX so GeneX will
probably be one of the first databases to support the MGED /MIAME standards.

> The primary goal of my work is to develop an array with a limited
> number of genes that can be used as a diagnostic tool for
> lymphomas. Most of the preliminary data have been generated at this
> point. Now we're looking for an array maker to create a prototype
> array.
> 
> I've attached the feedback for you sent. I'm not sure how much help
> I can be in your attempt at getting funding, but please feel free
> to contact me if I can help in some way.

Thanks for the feedback.  GeneX is an OSS project, with the strengths and weaknesses that entails.  It's only with effort and feedback such as yours that it moves forward.

Thanks for helping out!

-- 
Cheers, Harry

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

[GeneX-dev] Re: CyberT installation problem

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

Dr. Calogero,

You can respond to the request for where the xcluster executable is with =
any path.  The installation program will fail to find it, announce it's e=
xasperation, and will then let you enter a path to
where you know it to be (which can be an imaginary path - say /usr/local/=
genex/bin/xcluster).  The installation should continue after another warn=
ing, allowing that 'false' path to remain in the
installation setup.  After you obtain the xcluster program and compile it=
, you can then place it in that path (/usr/local/genex/bin/xcluster) and =
everyone will be happy.

xcluster is not necessary for the use of CyberT, and CyberT itself should=
 be installed via the general GeneX installation script.  I agree this is=
 an onerous requirement and I'm currently modifying
the installation script to have an option to install only the analytical =
tools rather than the database as well.

Cheers
harry



raffaele calogero wrote:
> =

> Dear Sir,
> I downloaded the Genex Web interface and I installed all the required
> tools before running the install-all.pl. However, although in the help
> file the xcluster is considered optional the install-all.pl script ask
> be for it. I tryed to get the code by Sherlock since july but I did not=

> received any news from him. There is some way to skip the request of
> xcluster during the installation? Is it essential for the use of
> cyberT?  If not, do I escape the need of the xcluster if I use the old
> cyberT script present in the download to install it ?
> Thank you for your help
> Yours sincerely
> Raffaele
> =

> --
> Prof. Raffaele A. Calogero
> Dipartimento di Scienze Cliniche e Biologiche
> Universit=E0 di Torino, Ospedale S. Luigi
> Regione Gonzole 10, Orbassano TO-10043 (Italy)
> Tel ++39 0116708110
> Fax ++39 0119038639
> Mobile Phone ++39 3333827080
> email raf...@un...

-- =

Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... =

         [plain text appreciated, if possible]

[GeneX-dev] Re: GeneX

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

"Honghui Wan" <hw...@nc...> writes:

> FYI.
> ------------- Begin Forwarded Message -------------
> 
> From: "Robert Stuart, M.D." <ros...@uc...>
> To: "Honghui Wan" <hw...@nc...>
> Subject: Re: GeneX
> Date: Mon, 27 Aug 2001 12:54:47 -0700
> MIME-Version: 1.0
> Content-Transfer-Encoding: 7bit
> X-Priority: 3
> X-MSMail-Priority: Normal
> X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400
> 
> Yes, I continue to be interested in GeneX and would be able to write a
> letter of support. We work primarily with Affymetrix arrays and use a
> variety of generally available and custom software tools for analysis. I am
> somewhat responsible for perhaps 1000 chip's worth of data per year (no
> kidding). I will be storing *all* the relevant data including the original
> dat files. As you know, some custom software (including some of my own)
> allows one to delve into cel and dat files.
> 
> I have not yet invested the effort to set up GeneX in its entirety. I've
> simply used the CyberT program and think it pretty useful. My question is
> whether GeneX has the facility to store everything relevant to an instance
> of GeneChip data: PI/owner, experimental parameters, DAT, CEL, AvDiff text
> output, results of re-scanning a chip, etc.

Hi Robert,

The short answer is 'Yes' the GeneX-1.0 data model enables you to
'associate' all the information in the DB. I say associate, because we
believed that the supporting files (DAT, CEL, images, etc) should be
stored external to the DB (on disk or on tape) and their locations
should be stored in the DB. All of the other parameters: PI/owner,
experimental parameters (experimental design, protocols, detailed
sequence, clone, and organism info), and results of scanning and
re-scanning can all be stored directly in the DB.

If you are interested in GeneX, I would contact Michael Pear
(mic...@ho...), also at UCSD, who is currently developing
GeneX for an Array facility there.

Cheers,
jas.

Re: [GeneX-dev] Problem Running xml2db.pl

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

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

> I was trying to run xml2db.pl. I was at the dirctory:
> 
> /usr/local/src/ct150_usrunix/data/expsets/draft/gwhatfield_ecoli_ihf
> 
> I typed:
> 
> /usr/local/src/GeneX-Server-1.0.4/xml2db/xml2db.pl -S Postgres -D genex -H
> localhost -p 5432 -U genex -P yeastecol1 -f gwhatfield_ecoli_ihf.xml

This assumes that 'genex' is your user account (which seems correct)
and 'yeastecol1' is your password (which I have no idea whether that
is correct or not, but you probably don't want to be telling us).

see if you can login to the DB using psql from the command line:

psql -U genex genex_db_name

where you substitute in the name of your DB for 'genex_db_name'

jas.

[GeneX-dev] Problem Running xml2db.pl

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

I was trying to run xml2db.pl. I was at the dirctory:

/usr/local/src/ct150_usrunix/data/expsets/draft/gwhatfield_ecoli_ihf

I typed:

/usr/local/src/GeneX-Server-1.0.4/xml2db/xml2db.pl -S Postgres -D genex -H
localhost -p 5432 -U genex -P yeastecol1 -f gwhatfield_ecoli_ihf.xml

then I got the message:

DBI->connect(dbname=5432;host=localhost;port=5432) failed: PQconnectPoll()
-- connect() failed: Connection refused at
/usr/local/src/GeneX-Server-1.0.4/xml2db/xml2db.pl line 111
DB connect failed

I was running Postmaster on the background while I ran xml2db.pl
so what should I do to fix the problem? Please give me some suggestions.
Thank you


Shih-Hsiu Lin
3:06pm
8/24/2001

Re: [GeneX-dev] Question about GeneX Setting

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

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

> How can I change the setting that I did during the GeneX
> installation such as the name of the server?  

Good question. We made it extremely easy to modify parameters of your
installation. All you need to do is re-run the install-all.pl
script. Tell it you want to run in 'Prompting' mode when it asks. That
way you can review each of your choices and change them when
needed.

jas.

Re: [GeneX-dev] Question aobut xml2db.pl

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

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

> Do I need to run xml2db.pl manually to upload the data set in XML
> format into the database?

Yes. Submitting the data via the curation tool just stores it on the
server and sends an email to the curator. Because the XML can have
mistakes, we didn't want to automate it.

jas.

Re: [GeneX-dev] Question aobut xml2db.pl

[Jiaye Z. <ze...@in...>]

Hi,


 The correct syntex for using the program is as describe by the usage:

./xml2db.pl -S Postgres -D [name of your database] -H [name of db server]
-p [port number if the host is running on different one than 5432] -U
[uid] -P [passwd] -f [name of your xml file]

if xml2db.pl is in your path, you cna ignore the './' in front of it.

jiaye


On Fri, 24 Aug 2001, Shih-hsiu Lin wrote:

> Do I need to run xml2db.pl manually to upload the data set in XML format
> into the database?
> 
> 
> Shih-Hsiu Lin
> 11:04am
> 8/24/2001
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 

[GeneX-dev] Question about GeneX Setting

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

How can I change the setting that I did during the GeneX installation such
as the name of the server?
Thank you


Shih-Hsiu Lin
11:16am
8/24/2001

[GeneX-dev] Question aobut xml2db.pl

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

Do I need to run xml2db.pl manually to upload the data set in XML format
into the database?


Shih-Hsiu Lin
11:04am
8/24/2001

Re: [GeneX-dev] [Bioperl-l] Public Release of the Xobjects gene expression package

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

"Harry Mangalam" <man...@ho...> writes:

> Saw this as I was punting around.  Of interest?  Dunno yet..but it looks like it might be...
> 
> http://bioperl.org/pipermail/bioperl-l/2001-July/006037.html

I think that this could be very useful. Too bad fiveprime.com, the
site hosting the modules, has been off the net for a couple of days.

jas.

Re: [GeneX-dev] Question about Curation Tool

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

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

> I couldn't find any files in /usr/local/genex/cache/exp, but I found XML
> files in /usr/local/src/ct150_usrunix/data/expsets. I have few questions:
> 
> 1. what is the difference between db2xml.pl and xml2db.pl?

db2xml: takes data from the db and exports it as GeneXML
xml2db: takes GeneXML and imports it into the DB

> 2. After I followed the Curation Tool Tutorial to upload the E. coli data
> into the database, why can't I see the E. coli data from a client
> computer using the Curation Tool? 

Probably because the CGI scripts that help the curation tool talk to
the DB are out of sync with the current version of the curation tool. 

> 3. How can I open a web query that can access my local database? 

Ah.. Very important question

You need to know what CGI root you specified during genex
installation, but the default is just 'cgi-bin/genex'.

So if you didn't change that it should be:

http://your.host.edu/cgi-bin/genex/gxquery/query-intro.pl

If you have trouble, you can always navigate there by going to the
main GeneX page on your installation:

http://your.host.edu/genex/

Clicking on the 'Analysis/Query' link will take you to the 'GeneX
Analysis Tools' page. 

Clicking on the 'Database Query' link will take you to the query page.

HTH,
jas.

[GeneX-dev] Question about Curation Tool

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

I couldn't find any files in /usr/local/genex/cache/exp, but I found XML
files in /usr/local/src/ct150_usrunix/data/expsets. I have few questions:

1. what is the difference between db2xml.pl and xml2db.pl?
2. After I followed the Curation Tool Tutorial to upload the E. coli data
into the database, why can't I see the E. coli data from a client
computer using the Curation Tool? 
3. How can I open a web query that can access my local database? 

thank you 


Shih-Hsiu Lin
1:32pm
8/23/2001

[GeneX-dev] [Bioperl-l] Public Release of the Xobjects gene expression package

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

Saw this as I was punting around.  Of interest?  Dunno yet..but it looks like it might be...

http://bioperl.org/pipermail/bioperl-l/2001-July/006037.html

-- 
Cheers, Harry

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

Re: [GeneX-dev] Question about Using Curation Tool

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

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
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 

[GeneX-dev] Question about Using Curation Tool

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

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

Re: [GeneX-dev] Re: Question about GeneX

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

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.

By the way, were you able to install the Postgres database successfully?

Greg Colello
NCGR, GeneX developer

>From: Shih-hsiu Lin <ma...@jh...>
>To: "Todd F. Peterson" <tf...@nc...>
>Cc: gen...@li...
>MIME-version: 1.0
>Subject: [GeneX-dev] Re: Question about GeneX
>Date: Wed, 22 Aug 2001 13:36:21 -0400
>
>
>I followed the Curation Tool Tutorial to create a E. coli experimental
>data set. Do I need to run xml2db.pl by myself or the system uploads the
>data to postgres already?
>
>
>Shih-Hsiu Lin
>1:34pm
>8/22/2001
>
>
>_______________________________________________
>Genex-dev mailing list
>Gen...@li...
>http://lists.sourceforge.net/lists/listinfo/genex-dev