genex-dev — GeneX developers

[GeneX-dev] Try this URL

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

Hi All,

Thanks to Hongui for the suggestion/reminder:

Try this

http://genex.ncgr.org/cgi-bin/anlgform.pl

You only have hits if you count them....

-- 
Cheers,
Harry

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

[GeneX-dev] [genex2] API complete

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

Hey All,

I'm happy to announce that the API is now complete for genex2. This
means that I am able to succesfully run the make_classes.pl and
automatically generate syntactically correct modules for each table
(and now views as well) in the DB.

This does *not* necessarily mean that the modules are functional (I'll
have to test that later), it just means that I can load the modules
into a perl script without the compiler complaining.

Whew!

Since there is still only minimal data in the DB (Contact and
ContactType) it is hard for me to run the regression tests. I'll
insert some more data now and run some of the regression tests. Once
it seems like the base modules work (Contact, ContactType,
ContactOwner, Security, UserSec, GroupSec, GroupLink). I'll check the
code in to CVS.

jas.

Re: [GeneX-dev] Looking for LIMITs..

[Michael P. <mic...@ho...>]

Hi Jason,

This turns out to be a "never mind" relative to the database API.
It is a limit in the number of rows printed in the embperl pages
I am working with. I've found how to adjust that limit, so problem
goes away.

Getting started too early on Monday morning!!

Regards,

Michael Pear
 

----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Monday, March 19, 2001 8:34 AM
Subject: Re: [GeneX-dev] Looking for LIMITs..


> "Michael Pear" <mic...@ho...> writes:
> 
> > I'm using the Bio:Genex API to access V1 DB to retrieve
> > arraymeasurements for an experimentset with 262 arrays in it. I"m
> > hitting a limit of 100 arraymeasurement entries retrieved from the
> > database through Bio::Genex::ArrayMeasurement->get_all_objects, but
> > I've not set the LIMIT variable. Even if I set the LIMIT variable
> > explicitly to "1000", I'm still getting only 100 objects returned.
> 
> Hey Michael,
> 
> Sounds irritating... I checked the code, and the only places that
> LIMIT could be creeping into the picture is in Genex::undefined()
> (Genex.pm) or in ArrayMeasurement::get_all_objects(). In each case
> it's prefaced with an 'if defined $LIMIT', so if $LIMIT is not set, it
> shouldn't affect you....
> 
> What version of Genex.pm are you using?
> 
> $ perl -I/var/lib/genex/perl5 -MBio::Genex -e 'print $Bio::Genex::VERSION\n'
> 2.6.1
> 
> Can you send me a piece of the code that is doing the access?
> 
> Sorry I can't be more informative,
> jas.
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Looking for LIMITs..

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

"Michael Pear" <mic...@ho...> writes:

> I'm using the Bio:Genex API to access V1 DB to retrieve
> arraymeasurements for an experimentset with 262 arrays in it. I"m
> hitting a limit of 100 arraymeasurement entries retrieved from the
> database through Bio::Genex::ArrayMeasurement->get_all_objects, but
> I've not set the LIMIT variable. Even if I set the LIMIT variable
> explicitly to "1000", I'm still getting only 100 objects returned.

Hey Michael,

Sounds irritating... I checked the code, and the only places that
LIMIT could be creeping into the picture is in Genex::undefined()
(Genex.pm) or in ArrayMeasurement::get_all_objects(). In each case
it's prefaced with an 'if defined $LIMIT', so if $LIMIT is not set, it
shouldn't affect you....

What version of Genex.pm are you using?

$ perl -I/var/lib/genex/perl5 -MBio::Genex -e 'print $Bio::Genex::VERSION\n'
2.6.1

Can you send me a piece of the code that is doing the access?

Sorry I can't be more informative,
jas.

[GeneX-dev] Looking for LIMITs..

[Michael P. <mic...@ho...>]

I'm using the Bio:Genex API to access V1 DB to retrieve =
arraymeasurements
for an experimentset with 262 arrays in it. I"m hitting  a limit of 100 =
arraymeasurement
entries retrieved from the database through  =
Bio::Genex::ArrayMeasurement->get_all_objects, but I've not set the =
LIMIT variable. Even if I set the LIMIT variable
explicitly to "1000", I'm still getting only 100 objects returned.

Ideas on where to look?

Regards,

Michael Pear

[GeneX-dev] [Genex2]: Success!!

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

Hey all,

So I've finally got enough of the API working with the new genex2
schema that I can run the contact-insertion scripts:

genex2=# select * from contacttype;
 con_fk | type  
--------+-------
     15 | login
     16 | login
(2 rows)

genex2=# select * from contact;
 con_pk |   modification_date    | modified_by |     creation_date      | created_by | organization | contact_person | contact_person_phone | contact_person_email | org_phone | org_email | org_mail_address | org_toll_free_phone | org_fax |          url           
--------+------------------------+-------------+------------------------+------------+--------------+----------------+----------------------+----------------------+-----------+-----------+------------------+---------------------+---------+------------------------
     15 | 2001-03-18 11:20:51-07 |             | 2001-03-18 11:20:51-07 |            | test         | test           | test                 | test                 | test      | test      | test             | test                | test    | http://genex.ncgr.org/
     16 | 2001-03-18 11:20:51-07 |             | 2001-03-18 11:20:51-07 |            |              | genex          |                      |                      |           |           |                  |                     |         | 
(2 rows)

Yeah!!!

Now I'll begin to add the Security information. Once that's done, all
the new API features should be added...

jas.

[GeneX-dev] Re: Curation Tool Release 1.0

[Harry J. M. <hj...@nc...>]

Hi Lonnie,

On Sat, 17 Mar 2001, Lonny Montoya wrote:

> The reason for the framemaker files is that our(NCGR) people who maintain
> the help screens use framemaker for this.  They needed (or at least wanted)
> the original framemaker files to be able to make any changes to the help
> screens in the future.  I think the framemaker files should be removed if
> one of two things happen:

That's fine - we can keep them in the CVS tree I guess, but shouldn't we
remove them from the tarball? 

> 1) We decide not to maintain the help screens (which are terribly out of
> date now anyway) internally.

Possibility I guess, but not too high on the admin's priority list, I'd
imagine.

> 2) Someone outside ncgr (yes, this is a solicitaion to any out there who is
> interested) decides to update the help files using the html files directly
> rather than frammaker.
>
> Number two, of course would be preferred.

Agreed.
 

> There used to be a README.txt inside the download directory.  We decided to
> remove it for just the reason you mentioned here (and to make it a tiny bit
> easier for us to post to the download directory).  We decided that expanding
> a .tar.gz or an exe package is a no brainer.  The README.txt now appears at
> the root level of the download package after they expand it, where we think
> it belongs.

Ahhh yes, I seem to remember now about making that argument... Oh well, like
I said - never satisfied... cuz he can't remember what he wanted.

Harry 'mr. alzheimer' Mangalam

[GeneX-dev] Re: Curation Tool Release 1.0

[Lonny M. <lon...@st...>]

Hi Harry,

----- Original Message -----
From: "Harry J. Mangalam" <hj...@nc...>
To: "Lonny Montoya" <lon...@st...>
Cc: <gen...@nc...>; <gen...@so...>
Sent: Saturday, March 17, 2001 6:53 PM
Subject: Re: Curation Tool Release 1.0


> Hey, Great!! - good job, Lonnie & Todd,
>
> one thing tho - what's the point of including the FrameMaker files?  Could
a
> user (or developer) actually use them for anything?  Would we want them
to?
>
> Only reason I ask is that they take up ~ 13MB of disk..
>

The reason for the framemaker files is that our(NCGR) people who maintain
the help screens use framemaker for this.  They needed (or at least wanted)
the original framemaker files to be able to make any changes to the help
screens in the future.  I think the framemaker files should be removed if
one of two things happen:

1) We decide not to maintain the help screens (which are terribly out of
date now anyway) internally.

2) Someone outside ncgr (yes, this is a solicitaion to any out there who is
interested) decides to update the help files using the html files directly
rather than frammaker.

Number two, of course would be preferred.

> Also, we should have a README for the 1.0 release in the download dir.
>
> Also, the typical thing for unix-type archives is to assume that they know
> how to unpack an tarball and have the instructions inside the tarball as a
> README.  If they can't do that, they probably shouldn't be playing with
this
> stuff anyway.
>

There used to be a README.txt inside the download directory.  We decided to
remove it for just the reason you mentioned here (and to make it a tiny bit
easier for us to post to the download directory).  We decided that expanding
a .tar.gz or an exe package is a no brainer.  The README.txt now appears at
the root level of the download package after they expand it, where we think
it belongs.

That said, I don't feel very strongly one way or the other and I don't think
anyone else does either.  We can put a copy in the download directory if
anyone thinks it is necessary.I

> ..ok - that was 3 things...
>
> Harry 'never satisfied' Mangalam
>
>

Lonny

>
> On Sat, 17 Mar 2001, Lonny Montoya wrote:
>
> > Hello All,
> >
> > The Genex Curation Tool (Release 1.0) is now available for download on
the
> > Genex website:
> >
> > http://genex.ncgr.org/genex/download/curation_tool/
> >
> > This release has a few new features and several new bug fixes.  Please
try
> > the download and report any problems you may have installing or using it
to:
> >
> > gen...@nc...
> >
> > Thank You,
> >
> > Lonny Montoya
> > Genex Developer
> >
> >
>

[GeneX-dev] Re: Curation Tool Release 1.0

[Harry J. M. <hj...@nc...>]

Hey, Great!! - good job, Lonnie & Todd,

one thing tho - what's the point of including the FrameMaker files?  Could a
user (or developer) actually use them for anything?  Would we want them to?

Only reason I ask is that they take up ~ 13MB of disk..

Also, we should have a README for the 1.0 release in the download dir.

Also, the typical thing for unix-type archives is to assume that they know
how to unpack an tarball and have the instructions inside the tarball as a
README.  If they can't do that, they probably shouldn't be playing with this
stuff anyway.

..ok - that was 3 things...

Harry 'never satisfied' Mangalam




On Sat, 17 Mar 2001, Lonny Montoya wrote:

> Hello All,
> 
> The Genex Curation Tool (Release 1.0) is now available for download on the
> Genex website:
> 
> http://genex.ncgr.org/genex/download/curation_tool/
> 
> This release has a few new features and several new bug fixes.  Please try
> the download and report any problems you may have installing or using it to:
> 
> gen...@nc...
> 
> Thank You,
> 
> Lonny Montoya
> Genex Developer
> 
> 

[GeneX-dev] Curation Tool Release 1.0

[Lonny M. <lon...@st...>]

Hello All,

The Genex Curation Tool (Release 1.0) is now available for download on the
Genex website:

http://genex.ncgr.org/genex/download/curation_tool/

This release has a few new features and several new bug fixes.  Please try
the download and report any problems you may have installing or using it to:

gen...@nc...

Thank You,

Lonny Montoya
Genex Developer

[GeneX-dev] GeneX-Server-1.0.0

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

Hey All,

I'm happy to announce the version 1.0.0 of the GeneX-Server is finally
released and can be downloaded from:

http://genex.ncgr.org/genex/download/genex-server/GeneX-Server-1.0.0.tar.gz

There are only minor changes since release candidate 11 (such as
installation of the API documentation into the HTML tree).

Enjoy,
jas.

[GeneX-dev] New Genex CVS available with new machine!

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

Hi All,

After some initial DNS confuscation, things seem to have settled down, with the new server now renamed to genex.ncgr.org.  It has a new hompage and we've installed the new CVS tree (and bugzilla) to
go with it.

FYI, the new server is an HP Kayak, 2x866MHz PIII, 2 GB Rambus RAM ~ $10K brand new.  I personally would  have bought a cheaper machine [and did - 2x733MHz PIII, 0.5 GB PC133 ECC RAM (for $900)], but
it IS a very fast machine.  try it out for a sample of what the DB will do on a not-even-the-state-of-the-art machine.

To pull down the latest CVS code, please follow the instructions at:

http://genex.ncgr.org/CVS.note

(and please try it out to see that it does indeed work).

the new GeneX home page is at:
http://genex.ncgr.org

& the new GeneX demo site is:
http://genex.ncgr.org/genex

The Xwindows demos are currently enabled altho they may be turned off if too many sessions become a problem).

-- 
Cheers,
Harry

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

Re: [GeneX-dev] Re: Some Installation Problems

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

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

> I think that this indicates that your DB is installed mostly OK,
> with the exception that some of the html help files may not have
> installed correctly and I think that Jason has fixed this bug in the
> meantime (Jason, is this the case?)  Or is it a version problem with
> the >> perlSGML.2001Jan23.tar.gz << ?

Rian, I really have no idea why you're seeing this error. The only
thing that is wrong are the html'ized dtd files the other 99.9% of the
installation worked fine. My only guess is that there is another
version of dtd.pl on your system. Could you please send me your
/usr/local/lib/perl/dtd.pl? I want to check it. Also, do a 'locate
dtd.pl' and see if you have more than one. If you do it may be finding
the incorrect one (not likely).

> I wonder if I could ask a(nother) favor - could you do an anonymous
> CVS checkout of the code to:

This is still a good idea.

jas.

[GeneX-dev] Re: Some Installation Problems

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

Hi Rian,

I was tooling around the country so I didn't see this until today.

I think that this indicates that your DB is installed mostly OK, with the exception that some of the html help files may not have installed correctly and I think that Jason has fixed this bug in the
meantime (Jason, is this the case?)  Or is it a version problem with the >> perlSGML.2001Jan23.tar.gz << ?

Have you tried to connect with your GeneX DB?  The  install-all.pl script should have finished with some text that told you where to point your browser. Did it work?

I wonder if I could ask a(nother) favor - could you do an anonymous CVS checkout of the code to:

a) see if the CVS checkout works for someone unrelated to the project?

b) update your system with the very latest code to see if it does indeed address this problem.

If you can do this, it'll address whether the fix works.

It's really pretty easy.  Just follow the instructions in:

http://genex.ncgr.org/CVS.note

which is mainly just cutting and pasting into a terminal if you already have a version of CVS installed.  If you don't, then don't bother unless you really want to try it.

Cheers
Harry

rian wrote:
> 
> Hi Harry,
> 
> After making sure all the requirement software were installed, I decided
> to make a fresh install, & I use GeneX-Server-1.0.0-pre9 package. However
> luck was not on my side :(
> 
> I ran this command to do installation:
> 
> $ sudo /usr/bin/perl-5.005 install-all.pl
> 
> during installation I found these error messages:
> 
> -----------Err Messages start here---------------------------
>         Running dtd2html on genexml.dtd ...
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus"
> 
> !! System Error:  @ line: 2113  (/usr/local/bin/dtd2html  -tree  -all
> genexml-all.html  -dtd genexml  -home genexml-home.html  -out
> /usr/local/lib/dtd/genexml-html  -top genexml-top.html  --treefile
> genexml-tree.html  /usr/local/lib/dtd/genexml.dtd)
>         Running dtd2html on ams.dtd ...
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus"
> 
> !! System Error:  @ line: 2124  (/usr/local/bin/dtd2html  -tree  -all
> ams-all.html  -dtd ams  -home ams-home.html  -out
> /usr/local/lib/dtd/genexml-html  -top ams-top.html  --treefile
> ams-tree.html  /usr/local/lib/dtd/ams.dtd)
>         Running dtd2html on als.dtd ...
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus"
> 
> !! System Error:  @ line: 2135  (/usr/local/bin/dtd2html  -tree  -all
> als-all.html  -dtd als  -home als-home.html  -out
> /usr/local/lib/dtd/genexml-html  -top als-top.html  --treefile
> als-tree.html  /usr/local/lib/dtd/als.dtd)
>         Running dtd2html on usf.dtd ...
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> 1475, within pattern
>         (Missing operator before ?)
> syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus"
> 
> !! System Error:  @ line: 2146  (/usr/local/bin/dtd2html  -tree  -all
> usf-all.html  -dtd usf  -home usf-home.html  -out
> /usr/local/lib/dtd/genexml-html  -top usf-top.html  --treefile
> usf-tree.html  /usr/local/lib/dtd/usf.dtd)
> 
> -----------------Err Messages end here ---------------------------------
> 
> I notice the systax error messages on one of dtd's modules. The DTD2HTML
> package that I used is perlSGML.2001Jan23.tar.gz. Is the the correct
> version?
> 
> I've also attached 3 files that you may require for troubleshooting:
> 1. Option.Reminders
> 2. genex-errors.txt
> 3. install-all.pl
> 
> Thanks in advance
> 
> Rian
> 
> On Wed, 7 Mar 2001, Harry Mangalam wrote:
> 
> > Hi All,
> >
> > This just in from Rian (cc:ed to keep him in the loop), who's trying to install GeneX locally to try it out.
> >
> > Jason, it looks like this is due to a dtd2html or (more likely) installation-of-it bug...?
> >
> > It also sounds like he's probably be better off to just download the lastest V1. rc tarball and start again.  He should probably be able to just untar it and run taking the params from the previous
> > installation, no?  Since it checks for the existance of config.pm?
> >
> > He sent me the original install-all script which I can pass on if it turns out we need it, but I held it back to keep down the bandwidth.
> >
> > hjm
> >
> >
> > -------- Original Message --------
> > Subject: Re: Some Installation Problems (fwd)
> > Date: Tue, 6 Mar 2001 11:26:44 +1100 (EST)
> > From: rian <bud...@en...>
> > To: Harry Mangalam <man...@ho...>
> >
> >   This message is in MIME format.  The first part should be readable text,
> >   while the remaining parts are likely unreadable without MIME-aware tools.
> >   Send mail to mi...@do... for more info.
> >
> > ---1463785174-1683262881-983838404=:656
> > Content-Type: TEXT/PLAIN; charset=US-ASCII
> >
> > > Ugh. Unfortunately, you've caught a documentation mismatch.
> > > That means we owe you a beer :).
> >
> > Hi Harry, sorry about the late reply. I was unwell for few days + the work
> > was building up during my absent. so a beer would help :)
> >
> > > We recently updated the approach to install the database (automated thru the install-all script) so that's no longer required and the script will automatically go and get the file you mention below.
> >
> > This is great news. Thanks, I will try again using the new approach.
> >
> > > >
> > > > I've attached the genex-errors.txt and Option.Reminders to this email.
> > >
> > > THANK YOU!!  this is helpful, but I wonder if you can also send us a copy of the install-all.pl that you used.  (I realized that we didn't write out the version information of the script, even tho we
> > > set it) OK... another beer.
> >
> > I've attached the requested file. I hope it helps. & thanks for the beer
> > :))
> >
> > > >From the genex-errors.txt file it looks like there is a dir or
> > permissions problem on your system (how can you tell if a SA doesn't know
> > what the problem is...?)
> > >
> > > OR that the /usr/local/bin/dtd2html did not get installed correctly.  The Option.reminders file indicates that it either got installed or that you told the script you'd install it in that dir.  Is it
> > > installed there?
> >
> > hammerhead@hammerhead:/$ ls -l /usr/local/bin/dtd2html
> > -rwxr-xr-x    1 root     staff       33471 Feb 26 14:53
> >
> > This is the output when it's run:
> >
> > dtd2html
> > Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> > 1475, within pattern
> >         (Missing operator before ?)
> > Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line
> > 1475, within pattern
> >         (Missing operator before ?)
> > syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus"
> >
> > >
> > > Did the dir: '/usr/local/genex/lib/dtd/'  get made OK and is set to be writable?
> >
> > It seems that it made ok & it's writable only to root though. Do I need to
> > change it be group writeable?
> >
> > hammerhead@hammerhead:/$ ls -ld /usr/local/genex/lib/dtd
> > drwxr-sr-x    3 root     staff        4096 Feb 26 17:30
> > /usr/local/genex/lib/dtd
> > hammerhead@hammerhead:/$ ls -l /usr/local/genex/lib/dtd
> > total 56
> > -rw-r--r--    1 root     staff        1772 Feb 26 17:30 als.dtd
> > -rw-r--r--    1 root     staff        2024 Feb 26 17:30 ams.dtd
> > -rw-r--r--    1 root     staff        1633 Feb 26 17:30 csf.dtd
> > lrwxrwxrwx    1 root     staff          24 Feb 26 17:30 dtd ->
> > /usr/local/genex/lib/dtd
> > drwxr-sr-x    2 root     staff        4096 Feb 26 16:21 genexml-html
> > -rw-r--r--    1 root     staff       34788 Feb 26 17:30 genexml.dtd
> > -rw-r--r--    1 root     staff        3199 Feb 26 17:30 usf.dtd
> >
> >
> > > The only other thing I can suggest but would NOT recommend (b/c of all kinds of security/privacy issues) is to allow one of us to log into a non-root account to see what we can discover.  BUt don't
> > > even consider this until all else has been exhausted.
> >
> > This won't be possible, the network is protected by a firewall besides
> > the ipaddress of the machine is not routable (private ip)
> >
> >
> > Thanks again for your help & insights. I do appriciate it heaps, not to
> > mention the beers :)
> >
> > Cheers,
> > Rian
> >
> 
>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>                        Name: Option.Reminders
>    Option.Reminders    Type: Plain Text (TEXT/PLAIN)
>                    Encoding: BASE64
> 
>                        Name: genex-errors.txt
>    genex-errors.txt    Type: Plain Text (TEXT/PLAIN)
>                    Encoding: BASE64
> 
>                      Name: install-all.pl
>    install-all.pl    Type: Perl Program (APPLICATION/X-PERL)
>                  Encoding: BASE64

-- 
Cheers,
Harry

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

[GeneX-dev] [Fwd: Perl.com Newsletter: Embperl (03/13/2001)]

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

FYI - see the link on embperl; also check out axkit ( http://axkit.org )

hjm


-------- Original Message --------
Subject: Perl.com Newsletter: Embperl (03/13/2001)
Date: Wed, 14 Mar 2001 17:14:51 -0800
From: Perl Newsletter <eli...@or...>
To: "Perl Newsletter" <pe...@pa...>


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is my honor and pleasure to bring you the latest www.perl.com
newsletter. So, without further ado, here's what's new in the world
of Perl.

* Perl at large.

The big buzz in Perl today is a Slashdot post to the effect that a
couple of high school sophmores attracted the attention of their
school administrators, and eventually even the police, all thanks to
a little confusion over the difference between scalar and list
contexts in perl.

    # Scalar context assignment: Store the entire output of the well-known
    #     UNIX fortune(1) program.

    my $f   = `fortune`;

    ... is not the same as ...

    # List context assignment, with one element on the left side: Store
    #    *just the first line* of the output of fortune(1).

    my ($f) = `fortune`;

Apparently, the lad in question used the latter code to generate
random quotes on his webpage, rather than the former scala context
code, which is probably what he wanted. When school administrators
viewed the site, they got a page containing, among other things,
just the first line of a William Gibson quote mentioning smuggling
firearms, totally out of context and without attribution. The rest
of the story isn't hard to imagine, but you can read all about it at:

    http://slashdot.org/article.pl?sid=01/03/13/208259

The article concludes by quoting from the Camel 3: "You will be
miserable until you learn the difference between scalar and list
context." Yeah, no kidding.

* What's new on www.perl.com?

This week, www.perl.com introduces Neil Gunton with an article on
using Embperl to simplify web site construction and maintenance.
Embperl, as you may be aware, is a web application platform written
in perl, that's typically run in concert with Apache and mod_perl.
Gunton details the implementation and use of EmbperlObject to produce
reusable web page objects which can greatly aid the development of
modular web sites of all sizes.

Once again, and as always, Simon Cozens returns with his truly
smashing perl5-porters digest. This week, come on down, and listen as
Simon spins wild yarns of Plain Old Documentation issues, undocumented
CV flags, the mysterious sub x { sub {} } memory leak, and testing
features that even Schwern doesn't understand.

Until next week, noble Perl hackers! We now return you to your
regularly scheduled e-mail.

SDE


====================================================================
ONLamp.com: O'Reilly Network's site for high-performance web serving.

ONLamp.com helps you optimize your use of the open source
web platform. Whether you use some or all of the LAMP
technologies-- Linux, Apache, MySQL, Perl/PHP/Python and much
more--you'll learn from informative articles, insightful
interviews, and helpful resources, with the experience and
quality you expect from O'Reilly.  http://onlamp.com

====================================================================

Article: Creating Modular Web Pages With EmbPerl
http://www.perl.com/pub/2001/03/embperl.html?wwwrrr_20010313.txt
If you have ever wished for an "include" HTML tag to reuse large
chunks of HTML, you are in luck. Neil Gunton explains how
Embperl solves the problem.


Article: Writing GUI Applications in Perl/Tk
http://www.perl.com/pub/2001/03/gui.html?wwwrrr_20010313.txt
Nick Temple shows how to program a graphical Point-of-Sale
application in Perl, complete with credit card processing.


Article: DBIx::Recordset VS DBI
http://www.perl.com/pub/2001/02/dbix.html?wwwrrr_20010313.txt
Terrance Brannon explains why DBI is the standard database
interface for Perl but should not be the interface for most Perl
applications requiring database functionality.


Article: The e-smith Server and Gateway: a Perl Case Study
http://www.perl.com/pub/2001/02/esmith.html?wwwrrr_20010313.txt
Kirrily "Skud" Robert explains the Perl behind the web-based
administrator for the e-smith server.


============================================================
Sponsored by Thawte
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Get the free Thawte Apache SSL Guide and find the answers to
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[GeneX-dev] URGENT: genex-server CVS moved to genebox

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

Hey All,

If you've checked out the genex-server code from CVS on harwin, this
affects you. If you haven't checked it out, you can ignore the rest of
the message.

I have moved the CVS repository to genebox. 

The old repository was:

your_harwin_user@24.1.175.29:/home/opengenex

The new repository will be:

you...@ge...:/home/cvsroot/opengenex


This will take effect tomorrow, and Harry will send out an email. In
the meantime I am including a perl script that will help you migrate
your already checked out code over to the new repository. If you don'y
already have a CVS account on genebox, Harry or I will need to get you
one for this to work.

Once you have an account on genebox, run the cvs-fix.pl script from
the top-level of your genex-server directory, and it will recursively
descend looking for 'Root' files. It will substitute in the new cvs
root in each such file.

jas.

[GeneX-dev] Re: [genex2]: CVS checkin of tdscripts, API changes

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

"Michael Pear" <mic...@ho...> writes:

> I see that the type used for created_by and modified_by is
> "name". What value do you envision going there? Is it a refrence to
> the UserSec entry (corresponding to a con_pk as well)?

Ummm. White man askem heap big question ;-)

But, seriously, this is a question that I don't have an answer for,
and I'd appreciate some help solving it. 

The example trigger I saw used the 'name' type to store the value
returned by the getpgusername(), but if we're not giving each GeneX
user a Postgres user account, the getpgusername() will just return
'readonly' or 'genex' which isn't highly useful. 

I'd like to know how we could use your Embperl scripts login
information to set this information automatically in a trigger or some
such...

jas.

Re: [GeneX-dev] [genex2]: CVS checkin of tdscripts, API changes

[Michael P. <mic...@ho...>]

Hi Jason,
  I see that the type used for created_by and modified_by is "name". What value
do you envision going there? Is it a refrence to the UserSec entry (corresponding to
a con_pk as well)?

Regards,

Michael Pear

----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Tuesday, March 13, 2001 1:34 PM
Subject: [GeneX-dev] [genex2]: CVS checkin of tdscripts, API changes


> Hey all,
> 
> So after Harry and I looked at the Stanford SMD schema yesterday with
> the UNM group, I noticed that all (or almost all) their tables had
> four columns for tracking changes:
> 
> creation_date
> modification_date
> created_by
> modified_by
> 
> I standardized our use of these terms using SMD's convention. 
> 
> jas.
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] [genex2]: CVS checkin of tdscripts, API changes

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

Hey all,

So after Harry and I looked at the Stanford SMD schema yesterday with
the UNM group, I noticed that all (or almost all) their tables had
four columns for tracking changes:

creation_date
modification_date
created_by
modified_by

I standardized our use of these terms using SMD's convention. 

jas.

Re: [GeneX-dev] Re: Checked in table changes...

[Michael P. <mic...@ho...>]

[Following applies to the "genex2" branch, not version 1]

Jason,

 I remember our conversation about that. You are right..it can go either way.
The current definition of SequenceFeature includes clone, clone provider, a (possible) sample
reference that are much more specific than a reference, for example, to a
gene (e.g., two different clones could contain the same gene). If we decide
to consolidate all that information in AL_Spots, then we should move those fields
as well.

One advantage that I see to keeping SequenceFeature associated with specific
plates, wells, clones, etc. is that a site can establish SequenceFeatures once
for their particular libraries, and various array layouts representing different
combinations of spotting plates could refer to them.  If the info is consolidated
in AL_Spots, then it will be repeated for each array layout.

The disadvantage I see is the one you point out...the lack of a higher level Reporter
entity that ties together related sequence features.

I'm wondering if others on the GeneX list have thoughts on this.

Regards,

Michael Pear
>
> Here was my original desire:
> * The info in AL_Spots describes *exactly* what is on the array, cDNA,
>   oligo, PCR product, etc.
> * the SF table would represent the higher level entity that the spot
>   is attempting to measure, which corresponds to the 'Reporter' notion
>   or our old CSF notion.
>
> This way entries in the AL_Spots table are specific to each layout
> (and thus would want plate, row, and column), and the SF table could
> be shared among different layouts.
>
> On the other hand, we could also put the information about what is in
> each spot in the SF table, the only drawback is that it would get
> pretty redundant with multiple layouts having to potentially re-enter
> the same information multiple times.
>
> That said, I don't see any drawbacks with either approach. Can you see
> any drawbacks with re-utilizing the SF entries with multiple layouts?
> If you can, we should use the approach you checked in. If you don't
> forsee any re-use issues, I'd like to move those columns into
> AL_Spots.
>
> jas.
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Extra Species in the Database

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

"Greg D. Colello" <gd...@nc...> writes:

> >Before anyone can add an array-layout into the DB the species for all
> >their USF must first exist in the DB. 
> >
> >I have no problem removing species without SF, and especially those
> >that we never will, like Red Kangaroo. They were put there to help the
> >CT folks test out the organism table.
> 
> Hmmm. I thought the point of the species table being rather thorough was to 
> avoid having to add species all the time as new dtasets appeared. Also looks 
> more professional. I though Carol vetted the list to be those species most 
> likely to succeed?

No, they were chosen so that one species from each
general_classification appeared in the pull-down menu in the CT.

> And, while we're talking about species, let's go the other direction
> towards more species. These species, which are not in our species
> table, have spots on the Stanford microarrays (they also have Homo
> sapiens, Escheria coli, and of course Arabidopsis thaliana):
> 
> Streptomyces hygroscopicus
> Bacillus thuringiensis
> Aequorea victoria
> Photinus pyralis
> 
> Can't load the data properly until these are in the species table
> and appear in the Control Bundle. In the short run I was thinking of
> taking an old Control Bundle and patching it by hand to include
> these new species, but I gotta fake the species id. Do we need to
> talk Jason?

That would be yes. The template XML file for adding a new species is
in CVS. 

On genebox that would be:

setenv CVSROOT gdc@genebox:/home/cvsroot/opengenex
cvs co analysis_scripts_install/Genex/data/db_tables/species.xml

Provide an XML file in that format, and it will be entered into the
DB.

jas.

Re: [GeneX-dev] Extra Species in the Database

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

"Harry J. Mangalam" <hj...@nc...> writes:

> On 9 Mar 2001, Jason E. Stewart wrote:
> 
> > I'm not sure what you mean by 'that they don't work'. The annoyance
> > that I'm aware of just has to do with the list being very long. So
> > when there's a select list, you have to scroll forever. 
> 
> I meant that there's no experiments that match them so a user could be
> clicking and getting the 'Sorry, no experiments matched your query' response
> for a long time.  We don;t have to remvoe all of them but we should remove
> those that we'll not support for a long time (like purple wombat, red kanga,
> blue shark, variagated plover, etc).

Hey what's wrong with plovers? I think they're cute...

I see. I forgot the query page also used the. There's a better way of
doing that for the Query Page. We should only be displaying Species
for which there exist Experiments in the DB that have SequenceFeatures
of that species. 

There is in fact a utility function in the DB fetch_es_species() that
does the necessary JOIN and returns the (single) species object for
each Experiment in the DB.

So instead of this code (from query-intro.pl.in):

my $species_names_sql = create_select_sql($dbh,COLUMNS=>['spc_pk',
							 'common_names'], 
					  FROM=>['Species']);
my @species_names;
if ($array_ref = $dbh->selectall_arrayref($species_names_sql)) {
  foreach (@{$array_ref}) {
    push(@species_names,$_);
  }
} else {
  die "Couldn't get Species names";
}

we want:
my @species_names;
foreach (@exp_set_names) {
  my $spc_obj = fetch_es_species($_->[0]);
  push(@species_names,[$spc_obj->spc_pk,$spc_obj->primary_scientific_name]);
}

I've just checked this code into CVS.

jas.


> > > What's the effort in removing the unsupported Species names in the
> > > Db for now and adding them back only when there's SF support for
> > > them?  Or (he said, demonstrating his lack of attention to the SF
> > > area) are they required for client-side-loading of SF data?
> > 
> > Before anyone can add an array-layout into the DB the species for all
> > their USF must first exist in the DB. 
> 
> OK - so we should keep things like Arab. thaliana, mouse, but remove some of
> the more exotic species.
> 
> 
> What say ye, others?
> 
> hjm
> 
> 
> > I have no problem removing species without SF, and especially those
> > that we never will, like Red Kangaroo. They were put there to help the
> > CT folks test out the organism table.
> > 
> > jas.
> > 
> > 
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> > 
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Extra Species in the Database

[Harry J. M. <hj...@nc...>]

Yes, that would be a better idea (asking the DB which species to display). 
Shouldn;t be too bad to do either.  I'll stab at it next week.

hjm

On Fri, 9 Mar 2001, Greg D. Colello wrote:

> Harry:
> 
> Ok. Now I understand the problem you are talking about. I think there is better 
> way to solve this than putting the Species table on a diet. There are two uses 
> of the table:
> 
> 1. To allow selection of data related to a given species.
> 
> 2. To allow the data loader routines to check the usage of species names.
> 
> I think the first problem should be solved by writing a program which only 
> displays those species that are actually in use in the database. I don't know 
> how to do this. It may be a dirty job, but wouldn't you have to do this anyway 
> to determine which species can be safely removed from the species table?
> 
> Greg
> 
> >From: "Harry J. Mangalam" <hj...@nc...>
> >X-Sender: hjm@cleveland
> >To: gen...@li...
> >Subject: Re: [GeneX-dev] Extra Species in the Database
> >MIME-Version: 1.0
> >Date: Fri, 9 Mar 2001 11:42:41 -0700 (MST)
> >
> >
> >
> >On 9 Mar 2001, Jason E. Stewart wrote:
> >
> >> I'm not sure what you mean by 'that they don't work'. The annoyance
> >> that I'm aware of just has to do with the list being very long. So
> >> when there's a select list, you have to scroll forever. 
> >
> >I meant that there's no experiments that match them so a user could be
> >clicking and getting the 'Sorry, no experiments matched your query' response
> >for a long time.  We don;t have to remvoe all of them but we should remove
> >those that we'll not support for a long time (like purple wombat, red kanga,
> >blue shark, variagated plover, etc).
> >
> >> > What's the effort in removing the unsupported Species names in the
> >> > Db for now and adding them back only when there's SF support for
> >> > them?  Or (he said, demonstrating his lack of attention to the SF
> >> > area) are they required for client-side-loading of SF data?
> >> 
> >> Before anyone can add an array-layout into the DB the species for all
> >> their USF must first exist in the DB. 
> >
> >OK - so we should keep things like Arab. thaliana, mouse, but remove some of
> >the more exotic species.
> >
> >
> >What say ye, others?
> >
> >hjm
> >
> >
> >> I have no problem removing species without SF, and especially those
> >> that we never will, like Red Kangaroo. They were put there to help the
> >> CT folks test out the organism table.
> >> 
> >> jas.
> >> 
> >> 
> >> _______________________________________________
> >> Genex-dev mailing list
> >> Gen...@li...
> >> http://lists.sourceforge.net/lists/listinfo/genex-dev
> >> 
> >
> >
> >_______________________________________________
> >Genex-dev mailing list
> >Gen...@li...
> >http://lists.sourceforge.net/lists/listinfo/genex-dev
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 

Re: [GeneX-dev] Extra Species in the Database

[Harry J. M. <hj...@nc...>]

If we need to have more species cuz we NEED more species then by all means -
add them - I'm thinking about all those angry notes we'll be getting about
'why can't I get any data for the green woggly fork-tongued stickleback -
it's listed as being in your DB'

hjm


On Fri, 9 Mar 2001, Greg D. Colello wrote:

> >Before anyone can add an array-layout into the DB the species for all
> >their USF must first exist in the DB. 
> >
> >I have no problem removing species without SF, and especially those
> >that we never will, like Red Kangaroo. They were put there to help the
> >CT folks test out the organism table.
> 
> Hmmm. I thought the point of the species table being rather thorough was to 
> avoid having to add species all the time as new dtasets appeared. Also looks 
> more professional. I though Carol vetted the list to be those species most 
> likely to succeed?
> 
> And, while we're talking about species, let's go the other direction towards 
> more species. These species, which are not in our species table, have spots on 
> the Stanford microarrays (they also have Homo sapiens, Escheria coli, and of 
> course Arabidopsis thaliana):
> 
> Streptomyces hygroscopicus
> Bacillus thuringiensis
> Aequorea victoria
> Photinus pyralis
> 
> Can't load the data properly until these are in the species table and appear in 
> the Control Bundle. In the short run I was thinking of taking an old Control 
> Bundle and patching it by hand to include these new species, but I gotta fake 
> the species id. Do we need to talk Jason?
> 
> Greg
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 

Re: [GeneX-dev] Extra Species in the Database

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

Harry:

Ok. Now I understand the problem you are talking about. I think there is better 
way to solve this than putting the Species table on a diet. There are two uses 
of the table:

1. To allow selection of data related to a given species.

2. To allow the data loader routines to check the usage of species names.

I think the first problem should be solved by writing a program which only 
displays those species that are actually in use in the database. I don't know 
how to do this. It may be a dirty job, but wouldn't you have to do this anyway 
to determine which species can be safely removed from the species table?

Greg

>From: "Harry J. Mangalam" <hj...@nc...>
>X-Sender: hjm@cleveland
>To: gen...@li...
>Subject: Re: [GeneX-dev] Extra Species in the Database
>MIME-Version: 1.0
>Date: Fri, 9 Mar 2001 11:42:41 -0700 (MST)
>
>
>
>On 9 Mar 2001, Jason E. Stewart wrote:
>
>> I'm not sure what you mean by 'that they don't work'. The annoyance
>> that I'm aware of just has to do with the list being very long. So
>> when there's a select list, you have to scroll forever. 
>
>I meant that there's no experiments that match them so a user could be
>clicking and getting the 'Sorry, no experiments matched your query' response
>for a long time.  We don;t have to remvoe all of them but we should remove
>those that we'll not support for a long time (like purple wombat, red kanga,
>blue shark, variagated plover, etc).
>
>> > What's the effort in removing the unsupported Species names in the
>> > Db for now and adding them back only when there's SF support for
>> > them?  Or (he said, demonstrating his lack of attention to the SF
>> > area) are they required for client-side-loading of SF data?
>> 
>> Before anyone can add an array-layout into the DB the species for all
>> their USF must first exist in the DB. 
>
>OK - so we should keep things like Arab. thaliana, mouse, but remove some of
>the more exotic species.
>
>
>What say ye, others?
>
>hjm
>
>
>> I have no problem removing species without SF, and especially those
>> that we never will, like Red Kangaroo. They were put there to help the
>> CT folks test out the organism table.
>> 
>> jas.
>> 
>> 
>> _______________________________________________
>> Genex-dev mailing list
>> Gen...@li...
>> http://lists.sourceforge.net/lists/listinfo/genex-dev
>> 
>
>
>_______________________________________________
>Genex-dev mailing list
>Gen...@li...
>http://lists.sourceforge.net/lists/listinfo/genex-dev