genex-dev — GeneX developers

Re: [GeneX-dev] Installation experience..

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

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

> > 
> > I'm happy to add XML::Parser first. What is the failed test there?
> > 
> There isn't a failure when everything is installed correctly, but this
> is the module that uses the expat library. Given the dependency
> external to Perl, it would be good to make absolutely certain
> that it is installed correctly first. Tesitng this alone results in
> a manageable amount of output whereass testing XML::DOM doesn't.

OK. Thanks.

jas.

[GeneX-dev] patch for display-error.pl

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

Hey Michael,

Here is the corresponding patch for display-error.pl.

jas.

Index: curation-tool/display-error.pl.in
===================================================================
RCS file: /home/opengenex/analysis_scripts_install/curation-tool/display-error.pl.in,v
retrieving revision 1.3
diff -b -B -u -r1.3 display-error.pl.in
--- curation-tool/display-error.pl.in	2001/01/22 22:37:47	1.3
+++ curation-tool/display-error.pl.in	2001/01/26 05:38:11
@@ -22,8 +22,9 @@
 $ENV{PATH} = "/bin:/usr/bin";
 delete @ENV{ 'IFS','CDPATH','ENV','BASH_ENV' };
 
-#print "Content-type: text/html\n\n";
-#print "\n<br>************Starting Auth-Login.pl!!!!!!!!<br>\n";
+# we need to escape any '@' for string interpolation
+my $contact_email = '%%CONTACT_EMAIL%%';
+$contact_email =~ s/\@/\\\@/;
 
 # Get the CGI parameters
 # The error message is passed as the first command line argument
@@ -49,7 +50,7 @@
 <p>Please include this information in any bug reports.</p>
 Sorry for the trouble. Please try again.<br>
 <hr>
-You can notify <a href=mailto:%%CONTACT_EMAIL%%>%%CONTACT_EMAIL%%</a> about this problem.<br></div>
+You can notify <a href=mailto:$contact_email>$contact_email</a> about this problem.<br></div>
 </body></html>
 EofHTML
 

[GeneX-dev] Patch for LoginUtil.pm.in

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

Hey Michael,

Here is the patch to get CONTACT_EMAIL working properly.

HTH,
jas.

Index: curation-tool/LoginUtil.pm.in
===================================================================
RCS file: /home/opengenex/analysis_scripts_install/curation-tool/LoginUtil.pm.in,v
retrieving revision 1.3
diff -b -B -u -r1.3 LoginUtil.pm.in
--- curation-tool/LoginUtil.pm.in	2001/01/22 22:36:53	1.3
+++ curation-tool/LoginUtil.pm.in	2001/01/26 05:32:13
@@ -24,6 +24,10 @@
 my $base_job_dir = "%%CGITMPDIR%%/$base_job";
 my $basesubmitdir = "%%GENEX_SUBMISSION_HOME%%";
 
+# we need to escape any '@' for string interpolation
+my $contact_email = '%%CONTACT_EMAIL%%';
+$contact_email =~ s/\@/\\\@/;
+
 # -----------------------------------Subroutine create_checksum()
 #
 # This subroutine takes a string parameter, combines it with our shared secret 
@@ -392,7 +396,7 @@
 <q>$error</q><br>
 Sorry for the trouble. Please try again.<br>
 <hr>
-You can notify <a href=mailto:%%CONTACT_EMAIL%%>%%CONTACT_EMAIL%%</a> about this problem.<br></div>
+You can notify <a href=mailto:$contact_email>$contact_email</a> about this problem.<br></div>
 </body></html>
 EofHTML
 

[GeneX-dev] Re: Missed Genex:: -> Bio::Genex:: in DBUtils.pm.in

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

Yes, I suspected as much.

I'd really rather keep the *_EMAIL pure and simple if I could. I think
it should be straightforward to just do: '$email =~ s/\@/\\\@/;'
before we use it...

jas.

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

> Its a little more complicated than that...the @ is in the
> supplied "CONTACT_EMAIL". I don't know if simply
> changing "CONTACT_EMAIL" to have \@ will not break something
> somewhere else. 
> 
> mpear
> ----- Original Message ----- 
> From: "Jason E. Stewart" <ja...@op...>
> To: "Michael Pear" <mic...@ho...>
> Sent: Thursday, January 25, 2001 4:48 PM
> Subject: Re: Missed Genex:: -> Bio::Genex:: in DBUtils.pm.in
> 
> 
> > "Michael Pear" <mic...@ho...> writes:
> > 
> > > line 569
> > 
> > right in the middle of check_password(), nice. 
> > 
> > > Also, I manually changed LoginUtil.pm to \@ in the e-mail address
> > > and got past that.  Does that need to be added in when processing
> > > the e-mail addresses?
> > 
> > Hmmm... That seems like a smart idea, I suppose it's complaining
> > without it?
> > 
> > jas.

Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing...

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

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

> I missed the Release Notes for the DB...I see them on sourceforge
> now.

Not your fault, since the changes were in the Genex.pm API, I should
have indicated it there. I have just started using release notes for
the Server, though, so I'm just learning how I should do it.

> I did a quick check by doing an rgrep on the install tree and there
> are still a lot of references to CanonicalSequenceFeature in xml2db.pl
> as well, so even if the curation tool can handle it, having nothing there
> may break submission using xml2db.pl

Yes, Jiaye just found this out yesterday when he and I worked on the
XML API. He will have that fixed in a day or two.

I have removed the references to CSF in db2xml, and it prints out, but
I've found a rather troubling bug in the USF_ExternalDBLink class that
looks like another nasty linking table bug (did I mention that linking
tables give me gas??). I'm working to crack that one right now.

The good news is, as soon as I fix this, you will only need to update
your Genex.pm installation. As a stand-alone perl module, it uses your
already installed Config.pm to configure and install itself, so the
upgrade should be easy. 

I hope to post it later tonight to sourceforge.

Your a great help, Michael, and a good sport,
jas.

Re: [GeneX-dev] Installation experience..

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

One thing, all.  
I just realized that if we're going to make this list usable, we should trim as much multiply appended email bitrot as possible and NOT (like me) send huge (marginally) humorous text barrages to it.  

By all means send such to everyone, but keep that off the SF list.  Like I said, I'm a frequent offender and I'll try to reform..

Now returning you to your normal programming.

Aha!  OK - 'cluster' is such a common name that I arbitrarily changed it to xcluster (documented nowhere) and then required everyone to use that name.  But... it's as good as any other, and it is
closer to the Stanford release name..  I didn't want to call it Xcluster as that implies an X11 app which it isn't.

So I'll just document that in the INSTALL file.

Thanks again.

hjm


Michael Pear wrote:
> 
> >   # *Looking for xcluster in path, but executable by default  from stanford
> >   # is cluster in xcluster directory.
> >
> > ?? I don't understand this. Could you rephrase?
> 
> My turn for confusing phrases... I meant that you are looking for
> an xcluster executable file, but the executable file is named cluster that
> results from the makefile that comes with the distribution from Stanford.
> 

-- 
Cheers,
Harry

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

Re: [GeneX-dev] Installation experience..

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

>   # *Looking for xcluster in path, but executable by default  from stanford
>   # is cluster in xcluster directory.
>
> ?? I don't understand this. Could you rephrase?

My turn for confusing phrases... I meant that you are looking for
an xcluster executable file, but the executable file is named cluster that
results from the makefile that comes with the distribution from Stanford.

M. Pear

----- Original Message -----
From: "Harry Mangalam" <man...@ho...>
To: <gen...@li...>
Sent: Thursday, January 25, 2001 9:14 AM
Subject: Re: [GeneX-dev] Installation experience..


> Hi Michael,
>
> Can you tell Outlook to do text only mail?  Your mail come thru in a way that it doesn't get
picked up when I try to reply (anyone else have that problem?)
>
> Here are my comments on your (welcome) comments.  I have things just about cleared away so I can
help Jason patch / test these today..
>
> hjm
>
>
>   #
>   # Hi Jason,
>   #
>   # Here is some feedback regarding pre6...it is looking really good. There
>   # is only one problem that really should be addressed in your script:
>   # make sure that when an executable is supplied that it REALLY is an
>   # executable file instead of a directory.
>   #
>   # Other than that, many of the other things are fine tuning or
>   # documentation in the INSTALL doc.
>   #
>   # Great work! I know you'll be glad when this is over.
>   #
>   # Regards,
>   #
>   # Michael Pear
>   #
>   # -----------------------------------
>   #
>   # ****It is possible to enter a directory name as a substitute for an
>   # executable in the section asking program names, and it is particularly
>   # sticky once this is done. After installing dtd2html in my local
>   # directory not in the path, I accidentally entered /var/genex/local/bin
>   # without pointing all the way to the executable. After that, the only
>   # way I could recover was to edit the Bio/Genex/Config.pm file directly.
>   # Even when I ask to answer the installation questions again, it appears
>   # that it is checking the location of the executables rather than asking,
>   # so it keeps finding the directory. I think this is the most critical
>   # issue left in the installation, for those of us prone to making
>   # mistakes.
>
> OK - Adding a check for -f and -x would cure this, no?
>
>   # ***Perl modules are still one of the  most difficult to get right. I
>   # suggest you recommend XML::Parser and XML::DOM to make sure that parser
>   # works right before other tests. The problem with the XQL tests throws
>   # a wrinkle in because those problems are acceptable, but ones with the
>   # XML:Parser for example aren't. Harry noted that Class::ObjectTemplate
>   # isn't brought in automagically through dependency when installing
>   # Class::ObjectTemplate::DB, so you need to make those separate.
>
> And we should still automate this as much as possible.  I had volunteered
> to check into rolling the automatic install ofperl modules into the
> installation, bt I dropped the ball here.  We would have to careful about
> which modules were completely auto-installable and which had to be manually
> configured to ge the right params..
>
>   # **Rcluster queue_master gets mentioned, but I didn't need to start it
>   # before to get Rcluster to work....why not? ***Also, what happens on
>   # system reboot?
>
> The original rcluster installation code automatically started a
> queue-master regardless of how many were already running (so after several
> passes of installation tests I was running 15 copies).  Instead of fixing
> it at the time to detect this I  just commented out the code to allow me
> to fix what I was after.
>
> Jason remedied this but it still needs to be added to a genex init script,
> which DOES need to be installed as root in /etc/[rc.d]/init.d and
> symlinked into the appro startup.  Because the different Linux distro's
> put their scripts in different places, we could try to detect which distro
> (I think Jason already added this code) and put it in the appro place (or
> we could just write the script and have root install it where they want).
> The script will fail on Solaris unless we do some more testing, I think.
>
>   # **Installation itself completing  with no errors depends on dtd2html,
>   # it appears, so you might as well check earlier and kick things out if
>   # the it isn't installed.
>
> Also, looking at the .subst-cache on genomics I also noted that several
> apps were NOT detected (like sendmail below), but these errors
> were not caught at runtime or reported by the error reporting at the end.
>
>   # **Question reusing cached values vs. setting new values is confusing.
>   # Currently, the formatting always throws  me...I never quite know until
>   # I read the question several times what enter will do. I suggest
>   # changing this to a yes/no question with yes as default. "Enter/No"
>   # isn't really a common way people look at answering questions.
>
> Good point - there are a few of these inthe script - please tell us of
> others that seem oddly phrased (says the chief odd-phrase maker...).
>
>   # *Looks like all doc mods are made to INSTALL....README is out of date
>   # and probably should be removed or changed to refer installer to INSTALL
>   # file.
>
> Yes - I think both Jason and I have been adding to INSTALL.
>
>   # *Java dependency should be noted for Jpython. Jpythonc is part of
>   # Jpython1.1. Direct installer to look for JPython1.1 rather than
>   # jpythonc. It isn't clear what this is used for on the server, anyways.
>   # Can it be left out? I thought this was more of a development issue for
>   # the dendogram applet. (It will be nice to get rid of this in a future
>   # release, python may be a great scripting language, but you have plenty
>   # of languages to go around at the moment in GeneX!)
>
> My fault (being Java-ignorant, I thought the class file had to be built for
> each installation as APD has a jpythonc build line in his makefile).
> This should not be the case for the distro and in fact that line should be
> removed from the rcluster build if we're distibuting the class file (which
> we are, I think..)
>
>   # *Xgobi directory requested...why? Xgobi/xgvis are requested later on
>   # independent of this request. Also, it sort of throws me off in the flow
>   # because my first instinct when it asks for xgobi again is to enter a
>   # directory, not the executable.
>
> This is required to set the env variable XGOBID to point to the xgobi
> help files which are typically in a different place than the executables.
> If xgobi is installed in the genex directory, this could be more automated,
> but I thought it would be so variable that I'd ask for it.
>
>   # */usr/sbin/sendmail not detected, although it is a common location
>   # often not in  non-root user's path.
>
> Yup.  Hmmm.  It's typically on root's PATH, but not on users's....
> we could try a `locate bin/sendmail | wc, check to see if there's more than
> one and then ask which one it was if so...?  I'll play with this
>
>   # *Looking for xcluster in path, but executable by default  from stanford
>   # is cluster in xcluster directory.
>
> ?? I don't understand this. Could you rephrase?
>
>   # *Missed picking up existing tmp file definition in rerun of install.
>   # Most values are picked up and presented as defaults, but tmp file
>   # definition is not for some reason.
>
> ?!  Odd.  I'll check.
>
>
> --
> Cheers,
> Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Installation experience..

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

> 
> I'm happy to add XML::Parser first. What is the failed test there?
> 
There isn't a failure when everything is installed correctly, but this
is the module that uses the expat library. Given the dependency
external to Perl, it would be good to make absolutely certain
that it is installed correctly first. Tesitng this alone results in
a manageable amount of output whereass testing XML::DOM doesn't.


----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Thursday, January 25, 2001 1:40 PM
Subject: Re: [GeneX-dev] Installation experience..


> "Harry Mangalam" <man...@ho...> writes:
> 
> >   "Michael Pear" <mic...@ho...> writes:
> >   #
> >   # Here is some feedback regarding pre6...it is looking really
> >   # good. 
> 
> Oh, I'm blushing ;-)
> 
> Make sure Lonny and Greg hear that, don't want them thinking I've
> gotten lazy ...
> 
> >   # There is only one problem that really should be addressed in
> >   # your script: make sure that when an executable is supplied that
> >   # it REALLY is an executable file instead of a directory.
> 
> Nuts, thought I'd settled that one...
> 
> >   # ****It is possible to enter a directory name as a substitute for an
> >   # executable in the section asking program names, and it is particularly
> >   # sticky once this is done. After installing dtd2html in my local
> >   # directory not in the path, I accidentally entered /var/genex/local/bin
> >   # without pointing all the way to the executable. After that, the only
> >   # way I could recover was to edit the Bio/Genex/Config.pm file directly.
> >   # Even when I ask to answer the installation questions again, it appears
> >   # that it is checking the location of the executables rather than asking,
> >   # so it keeps finding the directory. I think this is the most critical
> >   # issue left in the installation, for those of us prone to making
> >   # mistakes.
> > 
> > OK - Adding a check for -f and -x would cure this, no?
> 
> This is two problems. First I think we want -x && !-d, so that it's
> executable but not a directory (I don't know how -f handles funny
> files). 
> 
> The other problem is that if you re-run the installer after your
> installation, and tell it *not* to auto-accept what's in Config.pm,
> it doesn't stop on any of the applications...
> 
> >   # ***Perl modules are still one of the  most difficult to get right. I
> >   # suggest you recommend XML::Parser and XML::DOM to make sure that parser
> >   # works right before other tests. The problem with the XQL tests throws 
> >   # a wrinkle in because those problems are acceptable, but ones with the
> >   # XML:Parser for example aren't. Harry noted that Class::ObjectTemplate
> >   # isn't brought in automagically through dependency when installing
> >   # Class::ObjectTemplate::DB, so you need to make those separate.
> 
> The Class::ObjectTemplate was my fault. I hoped CPAN would calculate
> the dependancy automagically, and I didn't test it (I already have
> them both installed :-( 
> 
> I'm happy to add XML::Parser first. What is the failed test there?
> 
> > And we should still automate this as much as possible.  
> 
> Harry and I talked about this, and I think it is problematic for us to
> automate cpan. Automation works fine once CPAN is configured, but if
> they haven't preconfigured CPAN, the interactive mode sets in to
> select a CPAN site...
> 
> >   # **Rcluster queue_master gets mentioned, but I didn't need to start it
> >   # before to get Rcluster to work....why not? ***Also, what happens on
> >   # system reboot? 
> > 
> > Jason remedied this but it still needs to be added to a genex init script,
> > which DOES need to be installed as root in /etc/[rc.d]/init.d and
> > symlinked into the appro startup.  Because the different Linux distro's
> > put their scripts in different places, we could try to detect which distro
> > (I think Jason already added this code) and put it in the appro place (or
> > we could just write the script and have root install it where they want). 
> > The script will fail on Solaris unless we do some more testing, I
> > think. 
> 
> Good point. We need to put together a genex init script. queuemaster
> is the only one right now, but there are likely to be others.
> 
> >   # **Installation itself completing  with no errors depends on dtd2html,
> >   # it appears, so you might as well check earlier and kick things out if
> >   # the it isn't installed.
> > 
> > Also, looking at the .subst-cache on genomics I also noted that several
> > apps were NOT detected (like sendmail below), but these errors 
> > were not caught at runtime or reported by the error reporting at the
> > end.
> 
> Yes, not locating apps does not trigger an error. We need to indicate
> which apps are critical, important, and optional, and based on that,
> die() if critical, cause an error if important, or just a warning if
> optional. 
> 
> >   # *Looks like all doc mods are made to INSTALL....README is out of date
> >   # and probably should be removed or changed to refer installer to INSTALL
> >   # file.
> 
> Hmmm... I just updated README, so it is very current. If you don't
> like it could you suggest why? I thought it would be good to have a
> general "This is GeneX" document, that talks at a high level, and then
> points to INSTALL for the details. Perhaps there are too many install
> details in README and they could be moved over.
> 
> >   # *Java dependency should be noted for Jpython. Jpythonc is part of
> >   # Jpython1.1. Direct installer to look for JPython1.1 rather than
> >   # jpythonc. It isn't clear what this is used for on the server, anyways.
> >   # Can it be left out? I thought this was more of a development issue for
> >   # the dendogram applet. (It will be nice to get rid of this in a future
> >   # release, python may be a great scripting language, but you have plenty
> >   # of languages to go around at the moment in GeneX!)
> > 
> > My fault (being Java-ignorant, I thought the class file had to be built for
> > each installation as APD has a jpythonc build line in his makefile).  
> > This should not be the case for the distro and in fact that line should be
> > removed from the rcluster build if we're distibuting the class file (which
> > we are, I think..)
> 
> This would be great to remove. I assumed that once we had the dendro.jar
> we didn't need jpythonc, but I didn't want to change it. Which is why
> I left the .jar file in CVS.
> 
> Harry if you can remove that I would be sooooooo happy!!!
> 
> >   # */usr/sbin/sendmail not detected, although it is a common location
> >   # often not in  non-root user's path.
> > 
> > Yup.  Hmmm.  It's typically on root's PATH, but not on users's....
> > we could try a `locate bin/sendmail | wc, check to see if there's more than
> > one and then ask which one it was if so...?  I'll play with this
> 
> Harry, once upon a time there was a PATH configuration question. It
> never gets executed anymore. It seems to auto-accept the PATH. I think
> instead of reading in the users PATH, we should set it to a minimal
> subset: /bin:/usr/bin:/usr/sbin:/usr/local/bin
> 
> And prompt the user for ones we missed. Would this be better, Michael?
> 
> >   # *Looking for xcluster in path, but executable by default  from stanford
> >   # is cluster in xcluster directory.
> > 
> > ?? I don't understand this. Could you rephrase?
> 
> I think the script is picking up the xcluster directory
> 
> >   # *Missed picking up existing tmp file definition in rerun of install.
> >   # Most values are picked up and presented as defaults, but tmp file
> >   # definition is not for some reason. 
> > 
> > ?!  Odd.  I'll check.
> 
> Nah, it's not that odd, we prompt for a 1,2,3 from the user, we need
> to order the list and put the default at the top. I never wrote the
> code for it.
> 
> 
> Thanks again Michael,
> jas.
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing...

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

I missed the Release Notes for the DB...I see them on sourceforge
now.

I did a quick check by doing an rgrep on the install tree and there
are still a lot of references to CanonicalSequenceFeature in xml2db.pl
as well, so even if the curation tool can handle it, having nothing there
may break submission using xml2db.pl

Regards,

Michael Pear

----- Original Message -----
From: "Jason E. Stewart" <ja...@op...>
To: "Michael Pear" <mic...@ho...>
Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou" <ze...@in...>;
<gen...@li...>
Sent: Thursday, January 25, 2001 6:56 PM
Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing...


> "Michael Pear" <mic...@ho...> writes:
>
> > I tried to download a control bundle on my new installation, but
> > db2xml.pl failed because it couldn't find
> > CanonicalSequenceFeature.pm. I don't see it or anything in
> > Genex/CanonicalSequenceFeature in the install tree. I no longer find
> > this table in the database either. What's up?
>
> This was in the Release Notes for DB v0.8.1, but for some reason, I
> didn't include it in the Server install notes:
>
> From the release notes:
>
> * All tables related to Canonical Sequence Features were removed
>   (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink,
>   RelatedCSF)
> * the two CSF related columns in UserSequenceFeature were removed
>   (putative_csf_fk, nonunique_flag)
>
> And it looks like *I* didn't debug things enough :-(
>
> CSF was supposed to go away a month ago, it has always been an
> unsupported feature, and since it was never really broken, it never
> made it high enough on my priority to remove. I did it last release.
>
> Todd and/or Lonny. Will the CT break without CSF in the control
> bundle? Should I just output a blank CSF section for now?
>
> Mea culpa, mea culpa,
> jas.
>
>
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] Re: CanonicalSequenceFeature is missing...

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

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

> I tried to download a control bundle on my new installation, but
> db2xml.pl failed because it couldn't find
> CanonicalSequenceFeature.pm. I don't see it or anything in
> Genex/CanonicalSequenceFeature in the install tree. I no longer find
> this table in the database either. What's up?

This was in the Release Notes for DB v0.8.1, but for some reason, I
didn't include it in the Server install notes:

From the release notes:

* All tables related to Canonical Sequence Features were removed
  (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink,
  RelatedCSF) 
* the two CSF related columns in UserSequenceFeature were removed
  (putative_csf_fk, nonunique_flag)

And it looks like *I* didn't debug things enough :-(

CSF was supposed to go away a month ago, it has always been an
unsupported feature, and since it was never really broken, it never
made it high enough on my priority to remove. I did it last release.

Todd and/or Lonny. Will the CT break without CSF in the control
bundle? Should I just output a blank CSF section for now?

Mea culpa, mea culpa,
jas.

[GeneX-dev] CanonicalSequenceFeature is missing...

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

Jason and Jiaye,

I tried to download a control bundle on my new installation, but =
db2xml.pl failed because it couldn't find
CanonicalSequenceFeature.pm. I don't see it or anything in =
Genex/CanonicalSequenceFeature
in the install tree. I no longer find this table in the database either. =
What's up?=20

Regards,

Michael Pear

[GeneX-dev] XML API

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

Hey, 

Yesterday Jiaye and I designed the framework for the XML API. This
critical piece had been postponed in order to get something working
quickly ==> xml2db.pl and db2xml.pl. 

Luckily Jiaye and I designed those two applications modularily with
the intent of eventually moving all their code into a general XML
API. Yesterday we tried out that concept for the first time. 

In good XP style, we first wrote some tests. Then we implemented
Bio::Genex::Chromosome::db2xml() and Bio::Genex::Species::db2xml(), by
pretty much just copying do_chromosome() and do_species() directly
from db2xml.pl. These methods take a DB object and convert them into a
XML::DOM node hierarchy (which can create XML by calling the toString()
method). 

And it worked... Yahoo!!!

The code is now in CVS on harwin.

The plan is now for me to move enough of the db2xml.pl code into
XMLUtils.pm so that DB updates are possible through GeneXML. This will
be a huge improvement for all of us so that whenever we make updates
to the core NCGR curated data, users will not have to install their DB
from scratch (which is currently the case).

This leaves the task of converting db2xml.pl over to the new API as it
becomes ready.

The next phase is to finish the API by design the inverse functions:
xml2db (given a XML::DOM node, convert it into a DB object), and
convert xml2db.pl to use the API.

jas.

[GeneX-dev] executable not directory, fixed

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

Hey All,

I've just committed the change to the installer so that it won't
accept directories for any apps.

I think we want to re-write GetOrSet() and GetOrSetGNU() to be the
same methods. The code is nearly identical, it's just the the GNU apps
have an extra --version check.

jas.

Re: [GeneX-dev] extra gibberish at top of list messages?

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

Ah, yes, but at least Emacs' CVS mode won't allow me to commit files
that have conflicts ;-)

jas.


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

> But we all know (and I quote Linus Torvalds)
> 
> "Emacs is just plain evil."
> 
> as it's name implies:
> 
> Escape-Meta-Alt-Control-Shift

[snip]

Re: [GeneX-dev] extra gibberish at top of list messages?

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

But we all know (and I quote Linus Torvalds)

"Emacs is just plain evil."

as it's name implies:

Escape-Meta-Alt-Control-Shift
Eight Megabytes And Constantly Swapping
Even a Master of Arts Comes Simpler
Emacs Manuals Are Cryptic and Surreal
Energetic Merchants Always Cultivate Sales
Each Manual's Audience is Completely Stupified
Emacs Means A Crappy Screen
Eventually Munches All Computer Storage
Even My Aunt Crashes the System
Eradication of Memory Accomplished with Complete Simplicity
Elsewhere Maybe Alternative Civilizations Survive
Egregious Managers Actively Court Stallman
Esoteric Malleability Always Considered Silly
Emacs Manuals Always Cause Senility
Easily Maintained with the Assistance of Chemical Solutions
Edwardian Manifestation of All Colonial Sins
Extended Macros Are Considered Superfluous
Every Mode Accelerates Creation of Software
Elsewhere Maybe All Commands are Simple
Emacs May Allow Customised Screwups
Excellent Manuals Are Clearly Suppressed
Emetic Macros Assault Core and Segmentation
Embarrassed Manual-Writer Accused of Communist Subversion
Extensibility and Modifiability Aggravate Confirmed Simpletons
Emacs May Annihilate Command Structures
Easily Mangles, Aborts, Crashes and Stupifies
Extraneous Macros And Commands Stink
Exceptionally Mediocre Algorithm for Computer Scientists
EMACS Makes no Allowances Considering its Stiff price
Equine Mammals Are Considerably Smaller
Embarrassingly Mundane Advertising Cuts Sales
Every Moron Assumes CCA is Superior
Exceptionally Mediocre Autocratic Control System
EMACS May Alienate Clients and Supporters
Excavating Mayan Architecture Comes Simpler
Erasing Minds Allows Complete Submission
Emacs Makers Are Crazy Sickos
Eenie-Meenie-Miney-Mo- Macros Are Completely Slow
Experience the Mildest Ad Campaign ever Seen
Emacs Makefiles Annihilate C- Shells
Eradication of Memory Accomplished with Complete Simplicity
Emetic Macros Assault Core and Segmentation
Epileptic MLisp Aggravates Compiler Seizures
Evenings, Mornings, And a Couple of Saturdays
Emacs Makes All Computing Simple
Emacs Masquerades As Comfortable Shell
Emacs: My Alternative Computer Story
Emacs Made Almost Completely Screwed
Each Mail A Continued Surprise
Every Mode Acknowledges Customized Strokes 
Eating Memory And Cycle-Sucking
Everyday Material Almost Compiled Successfully
Elvis Masterminds All Computer Software
Emacs Makes A Computer Slow
etc

"Jason E. Stewart" wrote:
> 
> If you're an emacs person, Gnus is excellent. And it works well over a
> standar tty (off a command-line prompt).
> 
> jas.

-- 
Cheers,
Harry

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

Re: [GeneX-dev] extra gibberish at top of list messages?

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

If you're an emacs person, Gnus is excellent. And it works well over a
standar tty (off a command-line prompt).

jas.

"Jiaye Zhou" <ze...@in...> writes:

> Hi Lonny,
> 
>   Try pine (way over featured) or mutt (both support MIME mails filtering). 
> There's also elm of course. But I believe that both Pine and Mutt use pico mode 
> of editing.
> 
> jiaye
> 
> Quoting Lonny Montoya <lx...@nc...>:
> 
> > Harry,
> > 
> > I'm stuck with accessing my e-mail through an ssh login so I get the
> > standard command prompt mail used by Solaris.  By the way, I hate VI for
> > sending e-mail, you wouldn't happen to know of an alternative to this
> > that I
> > can use that will work through the firewall would you?  I can't recieve
> > attachments, html, or links from home.
> > 
> > Lonny
> > 
> > ----- Original Message -----
> > From: Harry Mangalam <man...@ho...>
> > To: <gen...@li...>
> > Sent: Thursday, January 25, 2001 10:22 AM
> > Subject: Re: [GeneX-dev] extra gibberish at top of list messages?
> > 
> > 
> > > What are youse guys using as mailers?
> > >
> > > Netscape Messenger (what I use) has a configurable header filter, so I
> > don;t see anything odd.  Michael, living on the edge of safety and
> > sanity,
> > uses Outlook, ands also doesn;t see anything odd.
> > >
> > > hjm
> > >
> > >
> > > "Greg D. Colello" wrote:
> > > >
> > > > This is what it looks like to me. Since I did a REPLY TO I assume
> > your
> > filter
> > > > will not recognize the lines anymore. The header you see in my REPLY
> > copy should
> > > > have 17 lines. I have enclosed this area with two dashed lines.
> > > >
> > > > By the way there is another odd behavior. When I do a REPLY TO ALL
> > with
> > my
> > > > mailer the group address (gen...@li...) appears
> > twice.
> > > >
> > > > Another strange thing I haven't analyzed is when Jason sends mail to
> > this list,
> > > > I get two copies of his email. I don't believe this has happened
> > with
> > anyone
> > > > else.
> > > >
> > > > Greg
> > > >
> > > > ----------------------------------
> > > > >From: Harry Mangalam <man...@ho...>
> > > > >X-Accept-Language: en
> > > > >MIME-Version: 1.0
> > > > >To: genexdev at SF <gen...@li...>
> > > > >Content-Transfer-Encoding: 7bit
> > > > >Subject: [GeneX-dev] extra gibberish at top of list messages?
> > > > >X-BeenThere: gen...@li...
> > > > >X-Mailman-Version: 2.0
> > > > >List-Help:
> > <mailto:gen...@li...?subject=help>
> > > > >List-Post: <mailto:gen...@li...>
> > > > >List-Subscribe:
> > <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > > <mailto:gen...@li...?subject=subscribe>
> > > > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> > > > >List-Unsubscribe:
> > <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > > <mailto:gen...@li...?subject=unsubscribe>
> > > > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> > > > >Date: Wed, 24 Jan 2001 17:14:17 -0800
> > > > ----------------------------------
> > > > >
> > > > >Hi All,
> > > > >
> > > > >Greg says that there are several extra lines at the top of things
> > that
> > get sent
> > > > to the SF genex list (ie this message).  I don't see them (using
> > Netscape mail);
> > > > does anyone else?  could be they escape
> > > > >the header filter for Greg's mail reader?
> > > > >--
> > > > >Cheers,
> > > > >Harry
> > > > >
> > > > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> > man...@ho...
> > > > >
> > > > >_______________________________________________
> > > > >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
> > >
> > > --
> > > Cheers,
> > > Harry
> > >
> > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> > man...@ho...
> > >
> > > _______________________________________________
> > > 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] Installation experience..

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

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

>   "Michael Pear" <mic...@ho...> writes:
>   #
>   # Here is some feedback regarding pre6...it is looking really
>   # good. 

Oh, I'm blushing ;-)

Make sure Lonny and Greg hear that, don't want them thinking I've
gotten lazy ...

>   # There is only one problem that really should be addressed in
>   # your script: make sure that when an executable is supplied that
>   # it REALLY is an executable file instead of a directory.

Nuts, thought I'd settled that one...

>   # ****It is possible to enter a directory name as a substitute for an
>   # executable in the section asking program names, and it is particularly
>   # sticky once this is done. After installing dtd2html in my local
>   # directory not in the path, I accidentally entered /var/genex/local/bin
>   # without pointing all the way to the executable. After that, the only
>   # way I could recover was to edit the Bio/Genex/Config.pm file directly.
>   # Even when I ask to answer the installation questions again, it appears
>   # that it is checking the location of the executables rather than asking,
>   # so it keeps finding the directory. I think this is the most critical
>   # issue left in the installation, for those of us prone to making
>   # mistakes.
> 
> OK - Adding a check for -f and -x would cure this, no?

This is two problems. First I think we want -x && !-d, so that it's
executable but not a directory (I don't know how -f handles funny
files). 

The other problem is that if you re-run the installer after your
installation, and tell it *not* to auto-accept what's in Config.pm,
it doesn't stop on any of the applications...

>   # ***Perl modules are still one of the  most difficult to get right. I
>   # suggest you recommend XML::Parser and XML::DOM to make sure that parser
>   # works right before other tests. The problem with the XQL tests throws 
>   # a wrinkle in because those problems are acceptable, but ones with the
>   # XML:Parser for example aren't. Harry noted that Class::ObjectTemplate
>   # isn't brought in automagically through dependency when installing
>   # Class::ObjectTemplate::DB, so you need to make those separate.

The Class::ObjectTemplate was my fault. I hoped CPAN would calculate
the dependancy automagically, and I didn't test it (I already have
them both installed :-( 

I'm happy to add XML::Parser first. What is the failed test there?

> And we should still automate this as much as possible.  

Harry and I talked about this, and I think it is problematic for us to
automate cpan. Automation works fine once CPAN is configured, but if
they haven't preconfigured CPAN, the interactive mode sets in to
select a CPAN site...

>   # **Rcluster queue_master gets mentioned, but I didn't need to start it
>   # before to get Rcluster to work....why not? ***Also, what happens on
>   # system reboot? 
> 
> Jason remedied this but it still needs to be added to a genex init script,
> which DOES need to be installed as root in /etc/[rc.d]/init.d and
> symlinked into the appro startup.  Because the different Linux distro's
> put their scripts in different places, we could try to detect which distro
> (I think Jason already added this code) and put it in the appro place (or
> we could just write the script and have root install it where they want). 
> The script will fail on Solaris unless we do some more testing, I
> think. 

Good point. We need to put together a genex init script. queuemaster
is the only one right now, but there are likely to be others.

>   # **Installation itself completing  with no errors depends on dtd2html,
>   # it appears, so you might as well check earlier and kick things out if
>   # the it isn't installed.
> 
> Also, looking at the .subst-cache on genomics I also noted that several
> apps were NOT detected (like sendmail below), but these errors 
> were not caught at runtime or reported by the error reporting at the
> end.

Yes, not locating apps does not trigger an error. We need to indicate
which apps are critical, important, and optional, and based on that,
die() if critical, cause an error if important, or just a warning if
optional. 

>   # *Looks like all doc mods are made to INSTALL....README is out of date
>   # and probably should be removed or changed to refer installer to INSTALL
>   # file.

Hmmm... I just updated README, so it is very current. If you don't
like it could you suggest why? I thought it would be good to have a
general "This is GeneX" document, that talks at a high level, and then
points to INSTALL for the details. Perhaps there are too many install
details in README and they could be moved over.

>   # *Java dependency should be noted for Jpython. Jpythonc is part of
>   # Jpython1.1. Direct installer to look for JPython1.1 rather than
>   # jpythonc. It isn't clear what this is used for on the server, anyways.
>   # Can it be left out? I thought this was more of a development issue for
>   # the dendogram applet. (It will be nice to get rid of this in a future
>   # release, python may be a great scripting language, but you have plenty
>   # of languages to go around at the moment in GeneX!)
> 
> My fault (being Java-ignorant, I thought the class file had to be built for
> each installation as APD has a jpythonc build line in his makefile).  
> This should not be the case for the distro and in fact that line should be
> removed from the rcluster build if we're distibuting the class file (which
> we are, I think..)

This would be great to remove. I assumed that once we had the dendro.jar
we didn't need jpythonc, but I didn't want to change it. Which is why
I left the .jar file in CVS.

Harry if you can remove that I would be sooooooo happy!!!

>   # */usr/sbin/sendmail not detected, although it is a common location
>   # often not in  non-root user's path.
> 
> Yup.  Hmmm.  It's typically on root's PATH, but not on users's....
> we could try a `locate bin/sendmail | wc, check to see if there's more than
> one and then ask which one it was if so...?  I'll play with this

Harry, once upon a time there was a PATH configuration question. It
never gets executed anymore. It seems to auto-accept the PATH. I think
instead of reading in the users PATH, we should set it to a minimal
subset: /bin:/usr/bin:/usr/sbin:/usr/local/bin

And prompt the user for ones we missed. Would this be better, Michael?

>   # *Looking for xcluster in path, but executable by default  from stanford
>   # is cluster in xcluster directory.
> 
> ?? I don't understand this. Could you rephrase?

I think the script is picking up the xcluster directory

>   # *Missed picking up existing tmp file definition in rerun of install.
>   # Most values are picked up and presented as defaults, but tmp file
>   # definition is not for some reason. 
> 
> ?!  Odd.  I'll check.

Nah, it's not that odd, we prompt for a 1,2,3 from the user, we need
to order the list and put the default at the top. I never wrote the
code for it.


Thanks again Michael,
jas.

Re: [GeneX-dev] extra gibberish at top of list messages?

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

Hi Lonny,

  Try pine (way over featured) or mutt (both support MIME mails filtering). 
There's also elm of course. But I believe that both Pine and Mutt use pico mode 
of editing.

jiaye

Quoting Lonny Montoya <lx...@nc...>:

> Harry,
> 
> I'm stuck with accessing my e-mail through an ssh login so I get the
> standard command prompt mail used by Solaris.  By the way, I hate VI for
> sending e-mail, you wouldn't happen to know of an alternative to this
> that I
> can use that will work through the firewall would you?  I can't recieve
> attachments, html, or links from home.
> 
> Lonny
> 
> ----- Original Message -----
> From: Harry Mangalam <man...@ho...>
> To: <gen...@li...>
> Sent: Thursday, January 25, 2001 10:22 AM
> Subject: Re: [GeneX-dev] extra gibberish at top of list messages?
> 
> 
> > What are youse guys using as mailers?
> >
> > Netscape Messenger (what I use) has a configurable header filter, so I
> don;t see anything odd.  Michael, living on the edge of safety and
> sanity,
> uses Outlook, ands also doesn;t see anything odd.
> >
> > hjm
> >
> >
> > "Greg D. Colello" wrote:
> > >
> > > This is what it looks like to me. Since I did a REPLY TO I assume
> your
> filter
> > > will not recognize the lines anymore. The header you see in my REPLY
> copy should
> > > have 17 lines. I have enclosed this area with two dashed lines.
> > >
> > > By the way there is another odd behavior. When I do a REPLY TO ALL
> with
> my
> > > mailer the group address (gen...@li...) appears
> twice.
> > >
> > > Another strange thing I haven't analyzed is when Jason sends mail to
> this list,
> > > I get two copies of his email. I don't believe this has happened
> with
> anyone
> > > else.
> > >
> > > Greg
> > >
> > > ----------------------------------
> > > >From: Harry Mangalam <man...@ho...>
> > > >X-Accept-Language: en
> > > >MIME-Version: 1.0
> > > >To: genexdev at SF <gen...@li...>
> > > >Content-Transfer-Encoding: 7bit
> > > >Subject: [GeneX-dev] extra gibberish at top of list messages?
> > > >X-BeenThere: gen...@li...
> > > >X-Mailman-Version: 2.0
> > > >List-Help:
> <mailto:gen...@li...?subject=help>
> > > >List-Post: <mailto:gen...@li...>
> > > >List-Subscribe:
> <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > <mailto:gen...@li...?subject=subscribe>
> > > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> > > >List-Unsubscribe:
> <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > <mailto:gen...@li...?subject=unsubscribe>
> > > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> > > >Date: Wed, 24 Jan 2001 17:14:17 -0800
> > > ----------------------------------
> > > >
> > > >Hi All,
> > > >
> > > >Greg says that there are several extra lines at the top of things
> that
> get sent
> > > to the SF genex list (ie this message).  I don't see them (using
> Netscape mail);
> > > does anyone else?  could be they escape
> > > >the header filter for Greg's mail reader?
> > > >--
> > > >Cheers,
> > > >Harry
> > > >
> > > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> man...@ho...
> > > >
> > > >_______________________________________________
> > > >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
> >
> > --
> > Cheers,
> > Harry
> >
> > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> man...@ho...
> >
> > _______________________________________________
> > 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 gibberish at top of list messages?

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

I'm using a home grown webbased mail client talking to IMAP. No problem here 
either...

jiaye

Quoting "Jason E. Stewart" <ja...@op...>:

> I use an Emacs mail client, gnus, which also handles those headers
> just fine.
> 
> I would say that the verdict is:
>   Sun's mail tool is the cause
> 
> jas.
> 
> "Harry Mangalam" <man...@ho...> writes:
> 
> > What are youse guys using as mailers?
> > 
> > Netscape Messenger (what I use) has a configurable header filter, so I
> don;t see anything odd.  Michael, living on the edge of safety and
> sanity, uses Outlook, ands also doesn;t see anything odd.
> > 
> > hjm
> > 
> > 
> > "Greg D. Colello" wrote:
> > > 
> > > This is what it looks like to me. Since I did a REPLY TO I assume
> your filter
> > > will not recognize the lines anymore. The header you see in my REPLY
> copy should
> > > have 17 lines. I have enclosed this area with two dashed lines.
> > > 
> > > By the way there is another odd behavior. When I do a REPLY TO ALL
> with my
> > > mailer the group address (gen...@li...) appears
> twice.
> > > 
> > > Another strange thing I haven't analyzed is when Jason sends mail to
> this list,
> > > I get two copies of his email. I don't believe this has happened
> with anyone
> > > else.
> > > 
> > > Greg
> > > 
> > > ----------------------------------
> > > >From: Harry Mangalam <man...@ho...>
> > > >X-Accept-Language: en
> > > >MIME-Version: 1.0
> > > >To: genexdev at SF <gen...@li...>
> > > >Content-Transfer-Encoding: 7bit
> > > >Subject: [GeneX-dev] extra gibberish at top of list messages?
> > > >X-BeenThere: gen...@li...
> > > >X-Mailman-Version: 2.0
> > > >List-Help:
> <mailto:gen...@li...?subject=help>
> > > >List-Post: <mailto:gen...@li...>
> > > >List-Subscribe:
> <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > <mailto:gen...@li...?subject=subscribe>
> > > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> > > >List-Unsubscribe:
> <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > > <mailto:gen...@li...?subject=unsubscribe>
> > > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> > > >Date: Wed, 24 Jan 2001 17:14:17 -0800
> > > ----------------------------------
> > > >
> > > >Hi All,
> > > >
> > > >Greg says that there are several extra lines at the top of things
> that get sent
> > > to the SF genex list (ie this message).  I don't see them (using
> Netscape mail);
> > > does anyone else?  could be they escape
> > > >the header filter for Greg's mail reader?
> > > >--
> > > >Cheers,
> > > >Harry
> > > >
> > > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> man...@ho...
> > > >
> > > >_______________________________________________
> > > >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
> > 
> > -- 
> > Cheers,
> > Harry
> > 
> > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> man...@ho...
> > 
> > _______________________________________________
> > 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 gibberish at top of list messages?

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

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

> I am using Sun's DT mail.
> 
> Frankly I don't understand all this email filtering stuff. I have
> never really had a significant enough email problem that required me
> to even worry about filtering.

Uhh... I remember a few times when you indicated you were getting a
bit too much email. 

I moderate one mailing list. I want to know when I get email to be
approved. 

I am on around 10 other mailing lists. Many I just browse once every
couple of days. 

I like to have all my email pre-sorted into folders based on whether
they're are from one of the mailing lists, or personally to me, etc.

Makes my life easier.

However, this is not about filter.

> SourceForge email is the first case I've seen, where lots of extra
> lines appear in my header. That makes me think that something needs
> to be turned off at the "Source".

If you every look at all the headers that are in normal email, there
are many, many, many. Most of them are pointless to your email reading
program. It's job is to not show them. It should be configurable to
allow you to set which headers appear and which do not. 

If to many of the sourceforge headers show up, it is because your
email program thinks you want to see them. So find a way to tell it
not to.

It has nothing to do with sourceforge. The internet email RFP enables
mail servers and mail programs to add any headers they feel like (most
of these start with 'X-' by convention). It's up to the mail client to
do something useful with the headers.

jas.

Re: [GeneX-dev] extra gibberish at top of list messages?

[Lonny M. <lx...@nc...>]

Harry,

I'm stuck with accessing my e-mail through an ssh login so I get the
standard command prompt mail used by Solaris.  By the way, I hate VI for
sending e-mail, you wouldn't happen to know of an alternative to this that I
can use that will work through the firewall would you?  I can't recieve
attachments, html, or links from home.

Lonny

----- Original Message -----
From: Harry Mangalam <man...@ho...>
To: <gen...@li...>
Sent: Thursday, January 25, 2001 10:22 AM
Subject: Re: [GeneX-dev] extra gibberish at top of list messages?


> What are youse guys using as mailers?
>
> Netscape Messenger (what I use) has a configurable header filter, so I
don;t see anything odd.  Michael, living on the edge of safety and sanity,
uses Outlook, ands also doesn;t see anything odd.
>
> hjm
>
>
> "Greg D. Colello" wrote:
> >
> > This is what it looks like to me. Since I did a REPLY TO I assume your
filter
> > will not recognize the lines anymore. The header you see in my REPLY
copy should
> > have 17 lines. I have enclosed this area with two dashed lines.
> >
> > By the way there is another odd behavior. When I do a REPLY TO ALL with
my
> > mailer the group address (gen...@li...) appears
twice.
> >
> > Another strange thing I haven't analyzed is when Jason sends mail to
this list,
> > I get two copies of his email. I don't believe this has happened with
anyone
> > else.
> >
> > Greg
> >
> > ----------------------------------
> > >From: Harry Mangalam <man...@ho...>
> > >X-Accept-Language: en
> > >MIME-Version: 1.0
> > >To: genexdev at SF <gen...@li...>
> > >Content-Transfer-Encoding: 7bit
> > >Subject: [GeneX-dev] extra gibberish at top of list messages?
> > >X-BeenThere: gen...@li...
> > >X-Mailman-Version: 2.0
> > >List-Help:
<mailto:gen...@li...?subject=help>
> > >List-Post: <mailto:gen...@li...>
> > >List-Subscribe:
<http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > <mailto:gen...@li...?subject=subscribe>
> > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> > >List-Unsubscribe:
<http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > <mailto:gen...@li...?subject=unsubscribe>
> > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> > >Date: Wed, 24 Jan 2001 17:14:17 -0800
> > ----------------------------------
> > >
> > >Hi All,
> > >
> > >Greg says that there are several extra lines at the top of things that
get sent
> > to the SF genex list (ie this message).  I don't see them (using
Netscape mail);
> > does anyone else?  could be they escape
> > >the header filter for Greg's mail reader?
> > >--
> > >Cheers,
> > >Harry
> > >
> > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
man...@ho...
> > >
> > >_______________________________________________
> > >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
>
> --
> Cheers,
> Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
man...@ho...
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

Re: [GeneX-dev] extra gibberish at top of list messages?

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

I am using Sun's DT mail.

Frankly I don't understand all this email filtering stuff. I have never really 
had a significant enough email problem that required me to even worry about 
filtering.

SourceForge email is the first case I've seen, where lots of extra lines appear 
in my header. That makes me think that something needs to be turned off at the 
"Source".

Greg

>From: Harry Mangalam <man...@ho...>
>X-Accept-Language: en
>MIME-Version: 1.0
>To: gen...@li...
>Subject: Re: [GeneX-dev] extra gibberish at top of list messages?
>Content-Transfer-Encoding: 7bit
>X-BeenThere: gen...@li...
>X-Mailman-Version: 2.0
>List-Help: <mailto:gen...@li...?subject=help>
>List-Post: <mailto:gen...@li...>
>List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, 
<mailto:gen...@li...?subject=subscribe>
>List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
>List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, 
<mailto:gen...@li...?subject=unsubscribe>
>List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
>Date: Thu, 25 Jan 2001 08:22:54 -0800
>
>What are youse guys using as mailers?
>
>Netscape Messenger (what I use) has a configurable header filter, so I don;t 
see anything odd.  Michael, living on the edge of safety and sanity, uses 
Outlook, ands also doesn;t see anything odd.
>
>hjm
>
>
>"Greg D. Colello" wrote:
>> 
>> This is what it looks like to me. Since I did a REPLY TO I assume your filter
>> will not recognize the lines anymore. The header you see in my REPLY copy 
should
>> have 17 lines. I have enclosed this area with two dashed lines.
>> 
>> By the way there is another odd behavior. When I do a REPLY TO ALL with my
>> mailer the group address (gen...@li...) appears twice.
>> 
>> Another strange thing I haven't analyzed is when Jason sends mail to this 
list,
>> I get two copies of his email. I don't believe this has happened with anyone
>> else.
>> 
>> Greg
>> 
>> ----------------------------------
>> >From: Harry Mangalam <man...@ho...>
>> >X-Accept-Language: en
>> >MIME-Version: 1.0
>> >To: genexdev at SF <gen...@li...>
>> >Content-Transfer-Encoding: 7bit
>> >Subject: [GeneX-dev] extra gibberish at top of list messages?
>> >X-BeenThere: gen...@li...
>> >X-Mailman-Version: 2.0
>> >List-Help: <mailto:gen...@li...?subject=help>
>> >List-Post: <mailto:gen...@li...>
>> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
>> <mailto:gen...@li...?subject=subscribe>
>> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
>> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
>> <mailto:gen...@li...?subject=unsubscribe>
>> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
>> >Date: Wed, 24 Jan 2001 17:14:17 -0800
>> ----------------------------------
>> >
>> >Hi All,
>> >
>> >Greg says that there are several extra lines at the top of things that get 
sent
>> to the SF genex list (ie this message).  I don't see them (using Netscape 
mail);
>> does anyone else?  could be they escape
>> >the header filter for Greg's mail reader?
>> >--
>> >Cheers,
>> >Harry
>> >
>> >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || 
man...@ho...
>> >
>> >_______________________________________________
>> >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
>
>-- 
>Cheers,
>Harry
>
>Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
>
>_______________________________________________
>Genex-dev mailing list
>Gen...@li...
>http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] extra gibberish at top of list messages?

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

I use an Emacs mail client, gnus, which also handles those headers
just fine.

I would say that the verdict is:
  Sun's mail tool is the cause

jas.

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

> What are youse guys using as mailers?
> 
> Netscape Messenger (what I use) has a configurable header filter, so I don;t see anything odd.  Michael, living on the edge of safety and sanity, uses Outlook, ands also doesn;t see anything odd.
> 
> hjm
> 
> 
> "Greg D. Colello" wrote:
> > 
> > This is what it looks like to me. Since I did a REPLY TO I assume your filter
> > will not recognize the lines anymore. The header you see in my REPLY copy should
> > have 17 lines. I have enclosed this area with two dashed lines.
> > 
> > By the way there is another odd behavior. When I do a REPLY TO ALL with my
> > mailer the group address (gen...@li...) appears twice.
> > 
> > Another strange thing I haven't analyzed is when Jason sends mail to this list,
> > I get two copies of his email. I don't believe this has happened with anyone
> > else.
> > 
> > Greg
> > 
> > ----------------------------------
> > >From: Harry Mangalam <man...@ho...>
> > >X-Accept-Language: en
> > >MIME-Version: 1.0
> > >To: genexdev at SF <gen...@li...>
> > >Content-Transfer-Encoding: 7bit
> > >Subject: [GeneX-dev] extra gibberish at top of list messages?
> > >X-BeenThere: gen...@li...
> > >X-Mailman-Version: 2.0
> > >List-Help: <mailto:gen...@li...?subject=help>
> > >List-Post: <mailto:gen...@li...>
> > >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > <mailto:gen...@li...?subject=subscribe>
> > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> > >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> > <mailto:gen...@li...?subject=unsubscribe>
> > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> > >Date: Wed, 24 Jan 2001 17:14:17 -0800
> > ----------------------------------
> > >
> > >Hi All,
> > >
> > >Greg says that there are several extra lines at the top of things that get sent
> > to the SF genex list (ie this message).  I don't see them (using Netscape mail);
> > does anyone else?  could be they escape
> > >the header filter for Greg's mail reader?
> > >--
> > >Cheers,
> > >Harry
> > >
> > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
> > >
> > >_______________________________________________
> > >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
> 
> -- 
> Cheers,
> Harry
> 
> Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Installation experience..

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

Hi Michael,

Can you tell Outlook to do text only mail?  Your mail come thru in a way that it doesn't get picked up when I try to reply (anyone else have that problem?)

Here are my comments on your (welcome) comments.  I have things just about cleared away so I can help Jason patch / test these today..

hjm


  # 
  # Hi Jason,
  #  
  # Here is some feedback regarding pre6...it is looking really good. There
  # is only one problem that really should be addressed in your script:
  # make sure that when an executable is supplied that it REALLY is an
  # executable file instead of a directory.
  # 
  # Other than that, many of the other things are fine tuning or
  # documentation in the INSTALL doc.
  # 
  # Great work! I know you'll be glad when this is over.
  #  
  # Regards,
  #  
  # Michael Pear
  #  
  # -----------------------------------
  # 
  # ****It is possible to enter a directory name as a substitute for an
  # executable in the section asking program names, and it is particularly
  # sticky once this is done. After installing dtd2html in my local
  # directory not in the path, I accidentally entered /var/genex/local/bin
  # without pointing all the way to the executable. After that, the only
  # way I could recover was to edit the Bio/Genex/Config.pm file directly.
  # Even when I ask to answer the installation questions again, it appears
  # that it is checking the location of the executables rather than asking,
  # so it keeps finding the directory. I think this is the most critical
  # issue left in the installation, for those of us prone to making
  # mistakes.

OK - Adding a check for -f and -x would cure this, no?

  # ***Perl modules are still one of the  most difficult to get right. I
  # suggest you recommend XML::Parser and XML::DOM to make sure that parser
  # works right before other tests. The problem with the XQL tests throws 
  # a wrinkle in because those problems are acceptable, but ones with the
  # XML:Parser for example aren't. Harry noted that Class::ObjectTemplate
  # isn't brought in automagically through dependency when installing
  # Class::ObjectTemplate::DB, so you need to make those separate.

And we should still automate this as much as possible.  I had volunteered
to check into rolling the automatic install ofperl modules into the
installation, bt I dropped the ball here.  We would have to careful about
which modules were completely auto-installable and which had to be manually
configured to ge the right params..

  # **Rcluster queue_master gets mentioned, but I didn't need to start it
  # before to get Rcluster to work....why not? ***Also, what happens on
  # system reboot? 

The original rcluster installation code automatically started a
queue-master regardless of how many were already running (so after several
passes of installation tests I was running 15 copies).  Instead of fixing
it at the time to detect this I  just commented out the code to allow me
to fix what I was after.  

Jason remedied this but it still needs to be added to a genex init script,
which DOES need to be installed as root in /etc/[rc.d]/init.d and
symlinked into the appro startup.  Because the different Linux distro's
put their scripts in different places, we could try to detect which distro
(I think Jason already added this code) and put it in the appro place (or
we could just write the script and have root install it where they want). 
The script will fail on Solaris unless we do some more testing, I think. 

  # **Installation itself completing  with no errors depends on dtd2html,
  # it appears, so you might as well check earlier and kick things out if
  # the it isn't installed.

Also, looking at the .subst-cache on genomics I also noted that several
apps were NOT detected (like sendmail below), but these errors 
were not caught at runtime or reported by the error reporting at the end.
  
  # **Question reusing cached values vs. setting new values is confusing.
  # Currently, the formatting always throws  me...I never quite know until
  # I read the question several times what enter will do. I suggest
  # changing this to a yes/no question with yes as default. "Enter/No"
  # isn't really a common way people look at answering questions.

Good point - there are a few of these inthe script - please tell us of
others that seem oddly phrased (says the chief odd-phrase maker...).

  # *Looks like all doc mods are made to INSTALL....README is out of date
  # and probably should be removed or changed to refer installer to INSTALL
  # file.

Yes - I think both Jason and I have been adding to INSTALL.

  # *Java dependency should be noted for Jpython. Jpythonc is part of
  # Jpython1.1. Direct installer to look for JPython1.1 rather than
  # jpythonc. It isn't clear what this is used for on the server, anyways.
  # Can it be left out? I thought this was more of a development issue for
  # the dendogram applet. (It will be nice to get rid of this in a future
  # release, python may be a great scripting language, but you have plenty
  # of languages to go around at the moment in GeneX!)

My fault (being Java-ignorant, I thought the class file had to be built for
each installation as APD has a jpythonc build line in his makefile).  
This should not be the case for the distro and in fact that line should be
removed from the rcluster build if we're distibuting the class file (which
we are, I think..)

  # *Xgobi directory requested...why? Xgobi/xgvis are requested later on
  # independent of this request. Also, it sort of throws me off in the flow
  # because my first instinct when it asks for xgobi again is to enter a
  # directory, not the executable. 

This is required to set the env variable XGOBID to point to the xgobi 
help files which are typically in a different place than the executables. 
If xgobi is installed in the genex directory, this could be more automated,
but I thought it would be so variable that I'd ask for it.

  # */usr/sbin/sendmail not detected, although it is a common location
  # often not in  non-root user's path.

Yup.  Hmmm.  It's typically on root's PATH, but not on users's....
we could try a `locate bin/sendmail | wc, check to see if there's more than
one and then ask which one it was if so...?  I'll play with this

  # *Looking for xcluster in path, but executable by default  from stanford
  # is cluster in xcluster directory.

?? I don't understand this. Could you rephrase?

  # *Missed picking up existing tmp file definition in rerun of install.
  # Most values are picked up and presented as defaults, but tmp file
  # definition is not for some reason. 

?!  Odd.  I'll check.


-- 
Cheers,
Harry

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

Re: [GeneX-dev] extra gibberish at top of list messages?

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

What are youse guys using as mailers?

Netscape Messenger (what I use) has a configurable header filter, so I don;t see anything odd.  Michael, living on the edge of safety and sanity, uses Outlook, ands also doesn;t see anything odd.

hjm


"Greg D. Colello" wrote:
> 
> This is what it looks like to me. Since I did a REPLY TO I assume your filter
> will not recognize the lines anymore. The header you see in my REPLY copy should
> have 17 lines. I have enclosed this area with two dashed lines.
> 
> By the way there is another odd behavior. When I do a REPLY TO ALL with my
> mailer the group address (gen...@li...) appears twice.
> 
> Another strange thing I haven't analyzed is when Jason sends mail to this list,
> I get two copies of his email. I don't believe this has happened with anyone
> else.
> 
> Greg
> 
> ----------------------------------
> >From: Harry Mangalam <man...@ho...>
> >X-Accept-Language: en
> >MIME-Version: 1.0
> >To: genexdev at SF <gen...@li...>
> >Content-Transfer-Encoding: 7bit
> >Subject: [GeneX-dev] extra gibberish at top of list messages?
> >X-BeenThere: gen...@li...
> >X-Mailman-Version: 2.0
> >List-Help: <mailto:gen...@li...?subject=help>
> >List-Post: <mailto:gen...@li...>
> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> <mailto:gen...@li...?subject=subscribe>
> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net>
> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>,
> <mailto:gen...@li...?subject=unsubscribe>
> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/>
> >Date: Wed, 24 Jan 2001 17:14:17 -0800
> ----------------------------------
> >
> >Hi All,
> >
> >Greg says that there are several extra lines at the top of things that get sent
> to the SF genex list (ie this message).  I don't see them (using Netscape mail);
> does anyone else?  could be they escape
> >the header filter for Greg's mail reader?
> >--
> >Cheers,
> >Harry
> >
> >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
> >
> >_______________________________________________
> >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

-- 
Cheers,
Harry

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