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From: <jas...@us...> - 2002-10-20 19:59:30
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv10454
Modified Files:
INSTALL
Log Message:
* INSTALL (Repository):
added info about postgres authentication
added requirement for mod_perl
update info update using cpan
indicated which apps were optional and why
added info about install XML::Xerces
Index: INSTALL
===================================================================
RCS file: /cvsroot/genex/genex-server/INSTALL,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** INSTALL 11 Oct 2002 02:24:21 -0000 1.19
--- INSTALL 20 Oct 2002 19:59:27 -0000 1.20
***************
*** 64,86 ****
tree, and the root of your html document tree).
- - Utility software: All recent, full linux distros include (and
- GeneX depends on):
- * gnu tar,
- * gnu text & file utils
- * sendmail (or a sendmail replacement such as exim)
- * Perl >=5.005
- * apache web server, configured to support Server-Side-Includes (see the
- apache documentation about this:
- <URL http://httpd.apache.org/docs/mod/mod_include.html>,
- esp. the tutorial: <URL http://httpd.apache.org/docs/howto/ssi.html>
- this can often be done by adding the following lines to your [httpd.conf]
- or [srm.conf] file and then rebooting.
-
- # Allow Server-side Includes
- Options +Includes
- AddType text/html .shtml
- AddHandler server-parsed .shtml
- DirectoryIndex index.html index.htm index.shtml index.cgi
-
- Other Packages: Some distros will include these apps which are
also needed for full functionality. If you cannot find them on your
--- 64,67 ----
***************
*** 111,117 ****
postgresql-pl
libpgtcl
! * g77 GNU Fortran compiler (req. to compile R from source)
* R (>= 1.1.1) => http://cran.r-project.org
* ghostscript => http://www.cs.wisc.edu/~ghost
* xgobi/xgobi => http://www.research.att.com/areas/stat/xgobi
--- 92,125 ----
postgresql-pl
libpgtcl
+
+ NOTE: the -dev or -devel package is only needed if you are
+ building the DBD::Pg yourself or installing it using CPAN. If you
+ are installing a package, such as debian's libdbd-pg-perl, then
+ you will not need them.
! * gnu textutils
! * gnu fileutils
! * sendmail (or a sendmail replacement such as exim)
! * Perl >=5.6.1
! * apache web server (with mod_perl)
! configured to support Server-Side-Includes (see the apache
! documentation about this: <URL http://httpd.apache.org/docs/mod/mod_include.html>,
! esp. the tutorial: <URL http://httpd.apache.org/docs/howto/ssi.html>
! this can often be done by adding the following lines to your [httpd.conf]
! file and then rebooting.
!
! # Allow Server-side Includes
! Options +Includes
! AddType text/html .shtml
! AddHandler server-parsed .shtml
! DirectoryIndex index.html index.htm index.shtml index.cgi
!
! Optional:
* R (>= 1.1.1) => http://cran.r-project.org
+ R is needed by many of the analysis tools. You will be able to
+ install genex without it, but you will not be able to use many
+ of the analysis tools
+
+ * g77 GNU Fortran compiler (req. to compile R from source)
* ghostscript => http://www.cs.wisc.edu/~ghost
* xgobi/xgobi => http://www.research.att.com/areas/stat/xgobi
***************
*** 120,132 ****
* libexpat => http://sourceforge.net/projects/expat/
* perlSGML => http://genex.ncgr.org/genex/download/genex-server/perlSGML.2001Jan23.tar.gz
! (supplies the dtd2html utility to generate the docs for
! the DTDs)
! Optional:
* xcluster => http://genome-www.stanford.edu/~sherlock/cluster.html
* jpythonc => http://www.jpython.org
- * Java (>=1.2) => http://www-106.ibm.com/developerworks/java/jdk/
- (at least one utility (jar) from the Java Runtime Environment is
- required for some scripts and a Java VM is required to run the
- Curation Tool, if you plan on running it on the server machine)
!! These should be installed BEFORE ..repeat.. !!
--- 128,134 ----
* libexpat => http://sourceforge.net/projects/expat/
* perlSGML => http://genex.ncgr.org/genex/download/genex-server/perlSGML.2001Jan23.tar.gz
! supplies the dtd2html utility to generate HTML versions of the DTDs
* xcluster => http://genome-www.stanford.edu/~sherlock/cluster.html
* jpythonc => http://www.jpython.org
!! These should be installed BEFORE ..repeat.. !!
***************
*** 142,157 ****
Please see: http://www.postgresql.org/users-lounge/docs/#7.1
! Creating new users
! ---------------------------------
! Genex-2.0 requires that every user of the system has a DB
! login. Until there is a WWW/CGI script to do this you will have to
! create them by hand.
!
! As the postgres administrator (usually 'postgres')
! $ createuser somebody
! <fill in information> [CANNOT create databases, nor users]
2) Perl & Using the CPAN shell to install Modules
--- 144,168 ----
Please see: http://www.postgresql.org/users-lounge/docs/#7.1
! * Configuring Host Based Authentication for Postgres
! The default Postgres installation sets up all DB users to
! authenticate themselves based on their unix login name. Most users
! of the Genex DB will not have a Unix login on the server, so this
! must be modified. To do this you must edit the Postgres
! configuration file called pg_hba.conf (installed under
! /etc/postgresql in debian, and ??? under RedHat). You must ensure
! that the first two lines after all the comments look like:
! local template1 ident sameuser
! local all md5
!
! This will enable the unix user 'postgres' to login to the template1
! DB without a password, but will require all other users to
! authenticate themselves when logging in to template1. It will also
! require all users (including 'postgres') to provide a password when
! logging in to any other DB.
+ IF YOU FAIL TO SET THIS UP PROPERLY, THE INSTALLATION OF THE GENEX
+ DB WILL FAIL.
2) Perl & Using the CPAN shell to install Modules
***************
*** 171,215 ****
Class::ObjectTemplate::DB - used by everything
! You can install these in a single line by typing:
! perl -MCAPN -e 'install [module]'
! ie
! perl -MCAPN -e 'install Term::ReadKey'
!
! (allow the CPAN installer to resolve dependencies automatically, unless it
! looks like it's going to overwrite something major (like Perl itself).
!
! Alternatively, the above can be installed with the CPAN *shell* (setup and
! config described in full below). Once the shell is started, all you have to
! do is type:
!
! cpan> install Term::ReadKey
! cpan> install CGI
! .
! .
! etc (go thru the list above)
!
! (also allowing the CPAN installer to resolve dependencies).
!
! Known Problems using CPAN to install these modules
! --------------------------------------------------
!
! * DBD::Pg: Before running CPAN, you must set two environment
! variables (POSTGRES_INCLUDE and POSTGRES_LIB), or the build will
! fail. When running 'install DBD::Pg', make test will fail if
! root is not a registered user of the DB. So you should run
! 'force install DBD::Pg'.
! For the RedHat RPMs mentioned above, Ron Ophir mentioned that
! POSTGRES_LIB = /usr/lib
! but setting POSTGRES_INCLUDE wasn't required (YMMV)
!
! * XML::Xerces - FIXME
!
! * Ron Ophir notes that when he tried to use CPAN, it bugged him to install
! 'Bundle::libnet' in order to be able to install NET::FTP. This may cause
! a dependency problem which results in the upgrade of your entire Perl
! package. Be careful about following this advice.
!
! Using CPAN shell
! ----------------
To install any of the above, we STRONGLY recommend using the CPAN shell. To
--- 182,187 ----
Class::ObjectTemplate::DB - used by everything
! Using the CPAN shell to install Perl Modules
! --------------------------------------------
To install any of the above, we STRONGLY recommend using the CPAN shell. To
***************
*** 220,224 ****
$ su
<type-your-root-password>
! $ perl -MCPAN -e shell
--- 192,200 ----
$ su
<type-your-root-password>
! $ cpan
!
! (If you are using a version of Perl before 5.8.0, you may not have
! the 'cpan' program on your system, so you will need to run the
! following command instead: 'perl -MCPAN -e shell')
***************
*** 277,280 ****
--- 253,291 ----
build will fail at the 'perl Makefile.PL' phase.
+
+ Known Problems using CPAN to install these modules
+ --------------------------------------------------
+
+ * DBD::Pg: Before running CPAN, you must set two environment
+ variables (POSTGRES_INCLUDE and POSTGRES_LIB), or the build will
+ fail. When running 'install DBD::Pg', make test will fail if
+ root is not a registered user of the DB. So you should run
+ 'force install DBD::Pg'.
+ For the RedHat RPMs mentioned above, Ron Ophir mentioned that
+ POSTGRES_LIB = /usr/lib
+ but setting POSTGRES_INCLUDE wasn't required (YMMV)
+
+ * XML::Xerces: you cannot ask CPAN to install this module. Instead
+ do the following:
+
+ 1) download version 1.7 of the Xerces-C C++ library from Apache:
+
+ http://xml.apache.org/dist/xerces-c/stable/archives/Xerces-C_1_7_0/
+
+ use either the binary for your platform, or get the source
+ tarball and build it using the following instructions:
+
+ http://xml.apache.org/xerces-c/build-winunix.html#UNIX
+
+ 2) download version 1.7.0 of XML::Xerces from Apache:
+
+ http://xml.apache.org/dist/xerces-p/stable/
+
+ unpack it and follow the build instructions in the README file
+
+ * Ron Ophir notes that when he tried to use CPAN, it bugged him to install
+ 'Bundle::libnet' in order to be able to install NET::FTP. This may cause
+ a dependency problem which results in the upgrade of your entire Perl
+ package. Be careful about following this advice.
Installation script Assumptions
|
|
From: <jas...@us...> - 2002-10-20 19:58:08
|
Update of /cvsroot/genex/genex-server In directory usw-pr-cvs1:/tmp/cvs-serv9807 Modified Files: Configure Log Message: * Configure (Repository): updated the URL for SGMLutils set GENEX_VOCAB_DIR made changes to get_app() to indicate which apps were optional Index: Configure =================================================================== RCS file: /cvsroot/genex/genex-server/Configure,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** Configure 20 Oct 2002 14:54:54 -0000 1.6 --- Configure 20 Oct 2002 19:58:04 -0000 1.7 *************** *** 248,252 **** # jpythonc => 'http://www.jpython.org', # not needed for typical install xcluster => 'http://genome-www.stanford.edu/~sherlock/cluster.html', ! dtd2html => 'http://genex.ncgr.org/genex/download/genex-server/perlSGML.2001Jan23.tar.gz', # vncer => 'http://www.uk.research.att.com/vnc/', # debug line ); --- 248,252 ---- # jpythonc => 'http://www.jpython.org', # not needed for typical install xcluster => 'http://genome-www.stanford.edu/~sherlock/cluster.html', ! dtd2html => 'http://genex.sourceforge.net/download/supplementary/perlSGML.2001Jan23.tar.gz', # vncer => 'http://www.uk.research.att.com/vnc/', # debug line ); *************** *** 1033,1036 **** --- 1033,1037 ---- $VARS{XML_WRITER} = $XML_WRITER = "$GENEX_BIN_DIR/db2xml.pl"; $VARS{LOCAL_LIB} = $LOCAL_LIB = "$LOCAL_ROOT/lib"; + $VARS{GENEX_VOCAB_DIR} = $GENEX_VOCAB_DIR = "$LOCAL_ROOT/lib"; $VARS{GENEXML_DIR} = $GENEXML_DIR = "$LOCAL_LIB/dtd"; $VARS{DTD_HTML_DIR} = $DTD_HTML_DIR = "$GENEXML_DIR/genexml-html"; *************** *** 1617,1623 **** spacer(); print STDOUT <<"OTHERAPPS"; ! Testing for some other required apps. Some are pretty standard on Linux systems, others are not, but they all have to be installed and available. ! for the system to work OTHERAPPS --- 1618,1631 ---- spacer(); print STDOUT <<"OTHERAPPS"; ! Testing for some other useful apps. Some are pretty standard on Linux systems, others are not, but they all have to be installed and available. ! for the system to work. ! ! NOTE: None of these are required in order to install GeneX, but some ! may be required in order to run some of the analysis tools. If you do ! not yet have one of the tools, just hit <Enter> when I prompt you for ! a path, and I can continue without it. Then later, if you install the ! missing tool, you can re-configure your system by simply re-running ! 'make configure' and 'make install'. OTHERAPPS *************** *** 1629,1633 **** next if $key eq 'xcluster'; next if $key eq 'vncserver'; ! get_or_set("$key"); } --- 1637,1641 ---- next if $key eq 'xcluster'; next if $key eq 'vncserver'; ! get_or_set($key); } *************** *** 1800,1804 **** } else { # give them one more chance ! $path_to_app = get_app($app); } $APP_PATHS{$app} = $path_to_app; --- 1808,1812 ---- } else { # give them one more chance ! $path_to_app = get_app($app, my $optional=1); } $APP_PATHS{$app} = $path_to_app; *************** *** 1807,1819 **** sub get_app { ! my $app = shift; ! print STDOUT <<"EOT"; Could not find an installed [$app]. If you have one installed, but not visible on your PATH, please tell me where it is. Otherwise cancel (^C) this installation, get $APP_URLS{$app} compile & install it, then try this installation again. ! EOT ! print STDOUT "[Please enter the complete path] ? "; my $tmp = <STDIN>; $tmp =~ s/\s//g; --- 1815,1845 ---- sub get_app { ! my ($app,$optional) = @_; ! $optional = '' unless defined $optional; + my $msg; + if ($optional) { + $msg = <<EOM; + Could not find an installed [$app]. If you have one installed, but not + visible on your PATH, please tell me where it is. + + NOTE: This is tool is optional for the GeneX install, but some may be + required in order to run some of the analysis tools. If you do not yet + have this tool, just hit <Enter>, and I can continue without it. Then + later, if you install this, you can re-configure your system by simply + re-running 'make configure' and 'make install'. + + You can get this tool at $APP_URLS{$app}. + EOM + } else { + $msg = <<EOM; Could not find an installed [$app]. If you have one installed, but not visible on your PATH, please tell me where it is. Otherwise cancel (^C) this installation, get $APP_URLS{$app} compile & install it, then try this installation again. ! EOM ! } ! ! print STDOUT "$msg\n[Please enter the complete path] ? "; my $tmp = <STDIN>; $tmp =~ s/\s//g; |
|
From: <jas...@us...> - 2002-10-20 19:55:55
|
Update of /cvsroot/genex/genex-server/apache In directory usw-pr-cvs1:/tmp/cvs-serv8849/apache Modified Files: genex-2.conf.in Log Message: * apache/genex-2.conf.in (Repository): added loadmodule line for mod_perl Index: genex-2.conf.in =================================================================== RCS file: /cvsroot/genex/genex-server/apache/genex-2.conf.in,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** genex-2.conf.in 11 Oct 2002 02:33:01 -0000 1.1 --- genex-2.conf.in 20 Oct 2002 19:55:52 -0000 1.2 *************** *** 1,2 **** --- 1,4 ---- + LoadModule perl_module /usr/lib/apache/1.3/mod_perl.so + %%MASON_COMP_DATA_ROOT%% |
|
From: <jas...@us...> - 2002-10-20 19:55:27
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv8651/Genex/scripts
Modified Files:
create_genex_db.pl.in gendb.pl.in
Log Message:
* scripts/gendb.pl.in (Repository):
* scripts/create_genex_db.pl.in (Repository):
added --admin_db to kludge postgres authentication problem
Index: create_genex_db.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_db.pl.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** create_genex_db.pl.in 11 Oct 2002 21:43:18 -0000 1.3
--- create_genex_db.pl.in 20 Oct 2002 19:55:24 -0000 1.4
***************
*** 24,27 ****
--- 24,28 ----
'no_tables',
'help',
+ 'admin_db=s',
'dbname=s');
***************
*** 57,63 ****
my $dbname = 'template1';
my ($sth,$dbh);
$dbh = Bio::Genex::Connect->new(DBNAME=>$dbname,
- # TRANSACTION=>1,
USER=>$OPTIONS{username},
PASSWORD=>$OPTIONS{password});
--- 58,69 ----
my $dbname = 'template1';
+
+ # we need this kludge to get around Postgres7.2's lack of user-based
+ # authentication
+ $dbname = $OPTIONS{admin_db}
+ if exists $OPTIONS{admin_db};
+
my ($sth,$dbh);
$dbh = Bio::Genex::Connect->new(DBNAME=>$dbname,
USER=>$OPTIONS{username},
PASSWORD=>$OPTIONS{password});
Index: gendb.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/gendb.pl.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** gendb.pl.in 20 Oct 2002 14:51:32 -0000 1.6
--- gendb.pl.in 20 Oct 2002 19:55:24 -0000 1.7
***************
*** 32,36 ****
'no_protocol',
'no_accounts',
! 'dbname=s');
my $USAGE = <<"EOU";
--- 32,38 ----
'no_protocol',
'no_accounts',
! 'dbname=s',
! 'admin_db=s',
! );
my $USAGE = <<"EOU";
***************
*** 83,90 ****
@files);
print STDERR "Creating DB ...\n";
! printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
! system($cmd, @args, @params);
die $! if $?;
--- 85,98 ----
@files);
+ # we need this kludge to get around Postgres7.2's lack of user-based
+ # authentication
+ my @admin_args;
+ @admin_args = ('--admin_db'=>$OPTIONS{admin_db})
+ if exists $OPTIONS{admin_db};
+
print STDERR "Creating DB ...\n";
! printf STDERR "\t$cmd %s\n", join(' ', @args, @admin_args, @params);
! system($cmd, @args, @admin_args, @params);
die $! if $?;
|
|
From: <jas...@us...> - 2002-10-20 15:06:29
|
Update of /cvsroot/genex/genex-server/Genex/GenexAdmin
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/GenexAdmin
Modified Files:
GenexAdmin.pm
Log Message:
new
Index: GenexAdmin.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GenexAdmin/GenexAdmin.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** GenexAdmin.pm 15 Oct 2002 14:54:08 -0000 1.14
--- GenexAdmin.pm 20 Oct 2002 14:43:21 -0000 1.15
***************
*** 742,749 ****
list context: a list of Bio::Genex::GenexAdmin instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::GenexAdmin::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 742,745 ----
|
|
From: <jas...@us...> - 2002-10-20 15:06:29
|
Update of /cvsroot/genex/genex-server/Genex/GroupLink In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/GroupLink Modified Files: GroupLink.pm Log Message: new Index: GroupLink.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/GroupLink/GroupLink.pm,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 |
|
From: <jas...@us...> - 2002-10-20 15:06:28
|
Update of /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/FeatureExtractionSoftware
Modified Files:
FeatureExtractionSoftware.pm
Log Message:
new
Index: FeatureExtractionSoftware.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware/FeatureExtractionSoftware.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** FeatureExtractionSoftware.pm 15 Oct 2002 14:51:34 -0000 1.1
--- FeatureExtractionSoftware.pm 20 Oct 2002 14:43:21 -0000 1.2
***************
*** 43,46 ****
--- 43,49 ----
'fesw_pk',
'feature_identifier_string',
+ 'data_start_regex1',
+ 'data_start_regex2',
+ 'data_end_regex',
'qd_fk'
]
***************
*** 60,64 ****
--- 63,70 ----
$COLUMN2NAME = {
+ 'data_end_regex' => 'Data End Regular Expression',
+ 'data_start_regex2' => 'Data Start Regular Expression 2',
'feature_identifier_string' => 'Feature Identifier String',
+ 'data_start_regex1' => 'Data Start Regular Expression 1',
'fesw_pk' => 'Accession Number',
'qd_fk' => 'Quantitation Type Dimension'
***************
*** 66,71 ****
--- 72,80 ----
;
$NAME2COLUMN = {
+ 'Data End Regular Expression' => 'data_end_regex',
'Accession Number' => 'fesw_pk',
+ 'Data Start Regular Expression 1' => 'data_start_regex1',
'Feature Identifier String' => 'feature_identifier_string',
+ 'Data Start Regular Expression 2' => 'data_start_regex2',
'Quantitation Type Dimension' => 'qd_fk'
}
***************
*** 125,128 ****
--- 134,146 ----
$FeatureExtractionSoftware->feature_identifier_string($value);
+ my $data_start_regex1_val = $FeatureExtractionSoftware->data_start_regex1();
+ $FeatureExtractionSoftware->data_start_regex1($value);
+
+ my $data_start_regex2_val = $FeatureExtractionSoftware->data_start_regex2();
+ $FeatureExtractionSoftware->data_start_regex2($value);
+
+ my $data_end_regex_val = $FeatureExtractionSoftware->data_end_regex();
+ $FeatureExtractionSoftware->data_end_regex($value);
+
my $qd_fk_val = $FeatureExtractionSoftware->qd_fk();
$FeatureExtractionSoftware->qd_fk($value);
***************
*** 278,282 ****
# to initialize all the class attributes
# we get the no_lookup attributes from our superclass
! attributes (lookup=>['fesw_pk', 'feature_identifier_string', 'qd_fk', 'qd_obj']);
--- 296,300 ----
# to initialize all the class attributes
# we get the no_lookup attributes from our superclass
! attributes (lookup=>['fesw_pk', 'feature_identifier_string', 'data_start_regex1', 'data_start_regex2', 'data_end_regex', 'qd_fk', 'qd_obj']);
***************
*** 746,753 ****
list context: a list of Bio::Genex::FeatureExtractionSoftware instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::FeatureExtractionSoftware::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 764,767 ----
***************
*** 1097,1100 ****
--- 1111,1135 ----
Methods for the feature_identifier_string attribute.
+
+
+ =item $value = data_start_regex1();
+
+ =item data_start_regex1($value);
+
+ Methods for the data_start_regex1 attribute.
+
+
+ =item $value = data_start_regex2();
+
+ =item data_start_regex2($value);
+
+ Methods for the data_start_regex2 attribute.
+
+
+ =item $value = data_end_regex();
+
+ =item data_end_regex($value);
+
+ Methods for the data_end_regex attribute.
|
|
From: <jas...@us...> - 2002-10-20 15:06:28
|
Update of /cvsroot/genex/genex-server/Genex/Feature
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Feature
Modified Files:
Feature.pm
Log Message:
new
Index: Feature.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Feature/Feature.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Feature.pm 15 Oct 2002 14:54:08 -0000 1.9
--- Feature.pm 20 Oct 2002 14:43:21 -0000 1.10
***************
*** 849,856 ****
list context: a list of Bio::Genex::Feature instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Feature::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 849,852 ----
|
|
From: <jas...@us...> - 2002-10-20 15:06:28
|
Update of /cvsroot/genex/genex-server/Genex/ExternalDatabase
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ExternalDatabase
Modified Files:
ExternalDatabase.pm
Log Message:
new
Index: ExternalDatabase.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExternalDatabase/ExternalDatabase.pm,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** ExternalDatabase.pm 15 Oct 2002 14:54:08 -0000 1.27
--- ExternalDatabase.pm 20 Oct 2002 14:43:20 -0000 1.28
***************
*** 788,795 ****
list context: a list of Bio::Genex::ExternalDatabase instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ExternalDatabase::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 788,791 ----
|
|
From: <jas...@us...> - 2002-10-20 15:04:16
|
Update of /cvsroot/genex/genex-server/Genex In directory usw-pr-cvs1:/tmp/cvs-serv23060/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.113 retrieving revision 1.114 diff -C2 -d -r1.113 -r1.114 *** ChangeLog 15 Oct 2002 14:57:43 -0000 1.113 --- ChangeLog 20 Oct 2002 15:04:14 -0000 1.114 *************** *** 1,2 **** --- 1,15 ---- + 2002-10-20 Jason E. Stewart <ja...@op...> + + * scripts/mbad-insert.pl.in (Repository): + now get data regexes from DB + + * scripts/qtdim-insert.pl.in (Repository): + * scripts/gendb.pl.in (Repository): + added regexes to quantarray addition script + + * scripts/array-design-insert.pl.in (Repository): + added ro/rw_group options + outputs pkey to STDOUT + 2002-10-15 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2002-10-20 15:04:16
|
Update of /cvsroot/genex/genex-server In directory usw-pr-cvs1:/tmp/cvs-serv23060 Modified Files: ChangeLog TODO Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.99 retrieving revision 1.100 diff -C2 -d -r1.99 -r1.100 *** ChangeLog 15 Oct 2002 19:25:10 -0000 1.99 --- ChangeLog 20 Oct 2002 15:04:13 -0000 1.100 *************** *** 1,2 **** --- 1,25 ---- + 2002-10-20 Jason E. Stewart <ja...@op...> + + * Install (Repository): + added fix for db.pl not being able to run by postgres - was + multiple problems. First the install was in the wrong + directory, so one needed to do a chdir. Second the default + hba.conf for 7.2 dis-allows password authentication. + + * Configure (Repository): + added GENEX_UPLOAD_DIR + removed GENEX_SUBMISSION_HOME + renamed LOCAL_BIN -> GENEX_BIN_DIR + + * DB/xml/FeatureExtractionSoftware.xml (Repository): + added the data matching regexes needed for the data loader + + * DB/xml/ExperimentSet.xml (Repository): + renamed submission_date -> creation_date + + * G2G/mason/workspace.html.in (Repository): + fixed @local default + commented out session info - seemed to be messing up sub-components + 2002-10-15 Jason E. Stewart <ja...@op...> *************** *** 1471,1475 **** otherwise, a new '#!' is added to the beginning each time the script is run. ! Added a line to mkdir $LOCAL_BIN Genex.pm is now made from within the script GetOrSet() had it's logic re-ordered to deal with cached values. --- 1494,1498 ---- otherwise, a new '#!' is added to the beginning each time the script is run. ! Added a line to mkdir $GENEX_BIN_DIR Genex.pm is now made from within the script GetOrSet() had it's logic re-ordered to deal with cached values. Index: TODO =================================================================== RCS file: /cvsroot/genex/genex-server/TODO,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** TODO 27 May 2001 05:43:43 -0000 1.19 --- TODO 20 Oct 2002 15:04:13 -0000 1.20 *************** *** 1,4 **** --- 1,17 ---- TODO ======= + Thu Oct 17 13:41:31 MDT 2002 + * Where to meet + - AAAS Denver, Feb 2003 + - EOS, Nov 2002 + - VCU, Teleconference, Feb 2003 + * genex-user ml is revived + * Bugzilla to SF + * release of genex-1.x + * release of genex-2.x + - Procedure/Protocol/Step (feature addition) + - QC: test data sets (Affy - MAS4/5, QuantArray, GenePix) + - talk to Brandon about Caltech MAGE work + Sat May 26 23:38:47 MDT 2001 * update INSTALL to explain Xerces installation |
|
From: <jas...@us...> - 2002-10-20 15:03:57
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv22907
Modified Files:
Install
Log Message:
* Install (Repository):
added fix for db.pl not being able to run by postgres - was
multiple problems. First the install was in the wrong
directory, so one needed to do a chdir. Second the default
hba.conf for 7.2 dis-allows password authentication.
Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Install 20 Oct 2002 13:07:33 -0000 1.7
--- Install 20 Oct 2002 15:03:55 -0000 1.8
***************
*** 40,43 ****
--- 40,44 ----
use ExtUtils::MakeMaker qw(prompt);
use Cwd;
+ use DBI;
use strict;
use vars qw(
***************
*** 50,54 ****
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
$HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
! $LOCAL_BIN $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
$LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR
$MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
--- 51,55 ----
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
$HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
! $GENEX_BIN_DIR $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
$LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR
$MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
***************
*** 59,64 ****
$GENEX_QUERY_DIR $GENEX_CUR_TOOL_DIR $GENEX_RO_PASSWORD
$GENEX_SU_USER $GENEX_RO_USER $GENEX_DBMS
! $GENEX_SYSTEM_USER $GENEX_SYSTEM_GROUP $GENEX_SUBMISSION_HOME
! $GENEX_SUBMISSION_HOME_DEF $GENEXML_DIR $GENEXML_URL
$GENEX_URL_EXAMPLE $GENEX_URL_QUERY $GENEX_URL_CUR_TOOL
$PREFIX $PREFIX_DEF $SKIP_SUBSTITUTION %DefaultVars
--- 60,65 ----
$GENEX_QUERY_DIR $GENEX_CUR_TOOL_DIR $GENEX_RO_PASSWORD
$GENEX_SU_USER $GENEX_RO_USER $GENEX_DBMS
! $GENEX_SYSTEM_USER $GENEX_SYSTEM_GROUP $GENEX_UPLOAD_DIR
! $GENEXML_DIR $GENEXML_URL
$GENEX_URL_EXAMPLE $GENEX_URL_QUERY $GENEX_URL_CUR_TOOL
$PREFIX $PREFIX_DEF $SKIP_SUBSTITUTION %DefaultVars
***************
*** 166,170 ****
# $GENEX_EXP_CACHE_DIR
# $GENEX_CB_CACHE_DIR
- # $SUBMISSION_DIR
# $CGITMPDIR
# $CGITMPDIR/download
--- 167,170 ----
***************
*** 175,181 ****
--- 175,184 ----
$DIR = $VARS{GENEX_HTMLDIR}; # Brevity && Clarity!
genex_mkdir($DIR) unless -d $DIR;
+ $DIR = $VARS{GENEX_UPLOAD_DIR}; # Brevity && Clarity!
+ genex_mkdir($DIR, '777') unless -d $DIR;
# --------------- mason ----------------
# make the directory for the mason scripts
+
print STDERR "\n\nInstalling the mason scripts..\n\n";
$DIR = $VARS{GENEX_WORKSPACE_DIR}; # Brevity && Clarity!
***************
*** 188,195 ****
genex_system("chmod 777 $DIR");
if (0) {
# --------------- login ----------------
! # make the cgi-bin for login and move the scripts there
print STDERR "\n\nInstalling the login scripts..\n\n";
$DIR = "$CGIDIR/$LOGIN_DIR"; # Brevity && Clarity!
--- 191,206 ----
genex_system("chmod 777 $DIR");
+ # --------------- controlled vocabs ----------------
+ # make the directory for the controlled vocabularies
+
+ print STDERR "\n\nInstalling the controlled vocabularies..\n\n";
+ $DIR = $VARS{GENEX_VOCAB_DIR}; # Brevity && Clarity!
+ genex_mkdir($DIR) unless -d $DIR;
+ genex_system("cp -r $MOTHERDIR/DB/controlled_vocab/*.xml $DIR");
+
if (0) {
# --------------- login ----------------
! # make the cgi-bin for login and move the scripts there
print STDERR "\n\nInstalling the login scripts..\n\n";
$DIR = "$CGIDIR/$LOGIN_DIR"; # Brevity && Clarity!
***************
*** 206,212 ****
$DIR = "$VARS{CGIDIR}/$VARS{CYBERT_DIR}"; # Brevity && Clarity!
genex_mkdir($DIR) unless -d $DIR;
! genex_mkdir($LOCAL_BIN) unless -d $LOCAL_BIN;
genex_system("cd $MOTHERDIR/CyberT-dist; cp CyberT*pl $DIR;
! cp munge4R.pl cyberfilter.pl genex_reaper.pl $VARS{LOCAL_BIN}");
--- 217,223 ----
$DIR = "$VARS{CGIDIR}/$VARS{CYBERT_DIR}"; # Brevity && Clarity!
genex_mkdir($DIR) unless -d $DIR;
! genex_mkdir($GENEX_BIN_DIR) unless -d $GENEX_BIN_DIR;
genex_system("cd $MOTHERDIR/CyberT-dist; cp CyberT*pl $DIR;
! cp munge4R.pl cyberfilter.pl genex_reaper.pl $VARS{GENEX_BIN_DIR}");
***************
*** 266,269 ****
--- 277,281 ----
slow() if ($SLOW);
+
}
***************
*** 307,311 ****
$DIR = "$VARS{CGIDIR}/$VARS{MERGEM_DIR}"; # Brevity && Clarity!
genex_mkdir($DIR) unless -d $DIR;
! genex_system("cd $MOTHERDIR/mergem; cp *pl mergem $DIR; cp mergem $LOCAL_BIN");
slow() if ($SLOW);
--- 319,323 ----
$DIR = "$VARS{CGIDIR}/$VARS{MERGEM_DIR}"; # Brevity && Clarity!
genex_mkdir($DIR) unless -d $DIR;
! genex_system("cd $MOTHERDIR/mergem; cp *pl mergem $DIR; cp mergem $GENEX_BIN_DIR");
slow() if ($SLOW);
***************
*** 572,584 ****
all data in the DB.
EOT
! my $db_init = 'db.pl';
! my $command = "su -c '$^X $MOTHERDIR/$db_init' postgres";
! my $run_installer;
! unless (getpwuid($<) eq 'root') {
! $run_installer = 0;
! print STDOUT <<EOT;
Hmmm - you are not running this as root. I\'m going to execute the
--- 584,608 ----
all data in the DB.
+ NOTE:
+
+ If you have already run the DB installer, you need not re-run
+ it now (unfortunately I have no way of knowing this, so you
+ must tell me, sorry).
+
EOT
! my $continue = 1;
! my $tmp = prompt("> Continue installing DB?", 'Y');
! $tmp =~ s/\s//g;
! $continue = 0 unless uc($tmp) eq 'Y';
! if ($continue) {
! my $db_init = 'db.pl';
! my $command = "su -c '$^X $MOTHERDIR/$db_init' postgres";
!
! my $run_installer;
! unless (getpwuid($<) eq 'root') {
! $run_installer = 0;
! print STDOUT <<EOT;
Hmmm - you are not running this as root. I\'m going to execute the
***************
*** 592,602 ****
EOT
! print STDOUT "Should I run the installer? [N] ";
! $tmp = <STDIN>;
! $tmp =~ s/\s//g;
! $run_installer = 1 if $tmp =~ /^y$/i;
! }
! print STDOUT <<EOM;
If I encounter trouble, you can run the DB installer yourself using:
--- 616,626 ----
EOT
! print STDOUT "Should I run the installer? [N] ";
! $tmp = <STDIN>;
! $tmp =~ s/\s//g;
! $run_installer = 1 if $tmp =~ /^y$/i;
! }
! print STDOUT <<EOM;
If I encounter trouble, you can run the DB installer yourself using:
***************
*** 614,622 ****
EOE
! print STDOUT <<EOM;
Congratulations! You have successfully installed the DB into Postgres.
EOM
--- 638,653 ----
EOE
! print STDOUT <<EOM;
Congratulations! You have successfully installed the DB into Postgres.
EOM
+ } else {
+ print STDOUT <<EOM;
+
+ Ok... Skipping installation of DB as instructed.
+
+ EOM
+ }
***************
*** 717,721 ****
if (0) {
! genex_system("chmod -R a+rx $LOCAL_BIN");
# make sure that the web owner owns and can read everything
--- 748,752 ----
if (0) {
! genex_system("chmod -R a+rx $GENEX_BIN_DIR");
# make sure that the web owner owns and can read everything
|
|
From: <jas...@us...> - 2002-10-20 14:54:57
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv17691
Modified Files:
Configure
Log Message:
* Configure (Repository):
added GENEX_UPLOAD_DIR
removed GENEX_SUBMISSION_HOME
renamed LOCAL_BIN -> GENEX_BIN_DIR
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Configure 13 Oct 2002 07:24:53 -0000 1.5
--- Configure 20 Oct 2002 14:54:54 -0000 1.6
***************
*** 88,92 ****
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
$HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
! $LOCAL_BIN $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
$LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR
$MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
--- 88,92 ----
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
$HTTP_ERR_LOG $HTTP_ERR_LOG_DEF
! $GENEX_BIN_DIR $LOCAL_LIB $LOGIN_DIR $LOCAL_ROOT $LOCAL_ROOT_DEF $LOCAL_SHARE
$LOCAL_VAR $MAX_SYSTMP_SIZE $MAX_TMPFILE_AGE $MERGEM_DIR
$MPAGE $EPATH $R $RCLUST_DIR $R_VERSION $SENDMAIL $SLOW $START_PERL
***************
*** 97,102 ****
$GENEX_QUERY_DIR $GENEX_CUR_TOOL_DIR
$GENEX_SU_USER $GENEX_RO_USER $GENEX_DBMS
! $GENEX_SYSTEM_USER $GENEX_SYSTEM_GROUP $GENEX_SUBMISSION_HOME
! $GENEX_SUBMISSION_HOME_DEF $GENEXML_DIR $GENEXML_URL
$GENEX_URL_EXAMPLE $GENEX_URL_QUERY $GENEX_URL_CUR_TOOL
$PREFIX $PREFIX_DEF $SKIP_SUBSTITUTION %DEFAULT_VARS
--- 97,102 ----
$GENEX_QUERY_DIR $GENEX_CUR_TOOL_DIR
$GENEX_SU_USER $GENEX_RO_USER $GENEX_DBMS
! $GENEX_SYSTEM_USER $GENEX_SYSTEM_GROUP $GENEX_UPLOAD_DIR
! $GENEXML_DIR $GENEXML_URL
$GENEX_URL_EXAMPLE $GENEX_URL_QUERY $GENEX_URL_CUR_TOOL
$PREFIX $PREFIX_DEF $SKIP_SUBSTITUTION %DEFAULT_VARS
***************
*** 108,115 ****
$GENEX_SERVER_INSTALLATION_DATE $GENEX_SERVER_INSTALLED_BY
$ISO8601_DATE_FORMAT
! $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR $GENEX_WORKSPACE_DIR $APACHE_CONF_DIR_DEF
$GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
$GENEX_RO_USER $GENEX_RO_PASSWORD $GENEX_TEST_USER $GENEX_TEST_PASSWORD
! $GENEX_PUBLIC_GROUP $GENEX_SUPERUSER_GROUP
);
--- 108,116 ----
$GENEX_SERVER_INSTALLATION_DATE $GENEX_SERVER_INSTALLED_BY
$ISO8601_DATE_FORMAT
! $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR
! $GENEX_WORKSPACE_DIR $APACHE_CONF_DIR_DEF
$GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
$GENEX_RO_USER $GENEX_RO_PASSWORD $GENEX_TEST_USER $GENEX_TEST_PASSWORD
! $GENEX_PUBLIC_GROUP $GENEX_SUPERUSER_GROUP $GENEX_VOCAB_DIR
);
***************
*** 219,223 ****
$DB_NAME_DEF = 'genex' unless defined $DB_NAME;
$SYSTMP_DEF = '/tmp' unless defined $SYSTMP;
- $GENEX_SUBMISSION_HOME_DEF = '/tmp/submission' unless defined $GENEX_SUBMISSION_HOME_DEF;
my %GNU_APP_URLS =
--- 220,223 ----
***************
*** 1030,1035 ****
$VARS{VERSION_STRING} = $VERSION_STRING; # install-all version string
$VARS{LOCAL_ROOT} = $LOCAL_ROOT;
! $VARS{LOCAL_BIN} = $LOCAL_BIN = "$LOCAL_ROOT/bin";
! $VARS{XML_WRITER} = $XML_WRITER = "$LOCAL_BIN/db2xml.pl";
$VARS{LOCAL_LIB} = $LOCAL_LIB = "$LOCAL_ROOT/lib";
$VARS{GENEXML_DIR} = $GENEXML_DIR = "$LOCAL_LIB/dtd";
--- 1030,1035 ----
$VARS{VERSION_STRING} = $VERSION_STRING; # install-all version string
$VARS{LOCAL_ROOT} = $LOCAL_ROOT;
! $VARS{GENEX_BIN_DIR} = $GENEX_BIN_DIR = "$LOCAL_ROOT/bin";
! $VARS{XML_WRITER} = $XML_WRITER = "$GENEX_BIN_DIR/db2xml.pl";
$VARS{LOCAL_LIB} = $LOCAL_LIB = "$LOCAL_ROOT/lib";
$VARS{GENEXML_DIR} = $GENEXML_DIR = "$LOCAL_LIB/dtd";
***************
*** 1040,1051 ****
$VARS{GENEX_CB_CACHE_DIR} = $GENEX_CB_CACHE_DIR = "$GENEX_CACHE_DIR/db2xml/cb";
$VARS{GENEX_EXP_CACHE_DIR} = $GENEX_EXP_CACHE_DIR = "$GENEX_CACHE_DIR/db2xml/exp";
! $VARS{GENEX_SUBMISSION_HOME} = $GENEX_SUBMISSION_HOME = "$LOCAL_ROOT/submission";
print STDERR "\nOK... LOCAL_ROOT => $LOCAL_ROOT\n";
! print STDERR "\n\tSetting... LOCAL_BIN => $LOCAL_BIN ";
print STDERR "\n\tSetting... LOCAL_LIB => $LOCAL_LIB ";
print STDERR "\n\tSetting... LOCAL_VAR => $LOCAL_VAR ";
print STDERR "\n\tSetting... LOCAL_SHARE => $LOCAL_SHARE";
! print STDERR "\n\tSetting... GENEX_SUBMISSION_HOME => $GENEX_SUBMISSION_HOME";
print STDERR "\n\tSetting... GENEX_CACHE_DIR => $GENEX_CACHE_DIR";
print STDERR "\n\tSetting... GENEX_CB_CACHE_DIR => $GENEX_CB_CACHE_DIR";
--- 1040,1051 ----
$VARS{GENEX_CB_CACHE_DIR} = $GENEX_CB_CACHE_DIR = "$GENEX_CACHE_DIR/db2xml/cb";
$VARS{GENEX_EXP_CACHE_DIR} = $GENEX_EXP_CACHE_DIR = "$GENEX_CACHE_DIR/db2xml/exp";
! $VARS{GENEX_UPLOAD_DIR} = $GENEX_UPLOAD_DIR = "$LOCAL_ROOT/uploads";
print STDERR "\nOK... LOCAL_ROOT => $LOCAL_ROOT\n";
! print STDERR "\n\tSetting... GENEX_BIN_DIR => $GENEX_BIN_DIR ";
print STDERR "\n\tSetting... LOCAL_LIB => $LOCAL_LIB ";
print STDERR "\n\tSetting... LOCAL_VAR => $LOCAL_VAR ";
print STDERR "\n\tSetting... LOCAL_SHARE => $LOCAL_SHARE";
! print STDERR "\n\tSetting... GENEX_UPLOAD_DIR => $GENEX_UPLOAD_DIR";
print STDERR "\n\tSetting... GENEX_CACHE_DIR => $GENEX_CACHE_DIR";
print STDERR "\n\tSetting... GENEX_CB_CACHE_DIR => $GENEX_CB_CACHE_DIR";
|
|
From: <jas...@us...> - 2002-10-20 14:52:56
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv16782/Genex/scripts
Modified Files:
qtdim-insert.pl.in
Log Message:
* scripts/qtdim-insert.pl.in (Repository):
added regexes to quantarray addition script
Index: qtdim-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/qtdim-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** qtdim-insert.pl.in 15 Oct 2002 14:44:17 -0000 1.2
--- qtdim-insert.pl.in 20 Oct 2002 14:52:53 -0000 1.3
***************
*** 37,40 ****
--- 37,44 ----
: the string that defines how which columns to use
to create a feature identifier from the input
+ --data_start_regex1=regex : regular expression indicating where to
+ begin reading data
+ --data_start_regex2=regex : in case regex1 is not sufficient
+ --data_end_regex=regex : regex indicating when to stop reading
optional parameters:
***************
*** 50,53 ****
--- 54,60 ----
my $rc = GetOptions(\%OPTIONS,
'help',
+ 'data_start_regex1=s',
+ 'data_start_regex2=s',
+ 'data_end_regex=s',
'dbname=s',
'feature_identifier_string=s',
***************
*** 75,78 ****
--- 82,91 ----
die "Must specify --feature_identifier_string\n$USAGE"
unless exists $OPTIONS{feature_identifier_string};
+ die "Must specify --data_start_regex1\n$USAGE"
+ unless exists $OPTIONS{data_start_regex1};
+ die "Must specify --data_start_regex2\n$USAGE"
+ unless exists $OPTIONS{data_start_regex1};
+ die "Must specify --data_end_regex\n$USAGE"
+ unless exists $OPTIONS{data_end_regex};
my $reader = Bio::MAGE::XMLReader->new();
***************
*** 274,277 ****
--- 287,293 ----
qd_obj=>$qtdim_db,
feature_identifier_string=>$OPTIONS{feature_identifier_string},
+ data_start_regex1=>$OPTIONS{data_start_regex1},
+ data_start_regex2=>$OPTIONS{data_start_regex2},
+ data_end_regex=>$OPTIONS{data_end_regex},
);
|
|
From: <jas...@us...> - 2002-10-20 14:52:30
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv16537/Genex/scripts
Modified Files:
mbad-insert.pl.in
Log Message:
* scripts/mbad-insert.pl.in (Repository):
now get data regexes from DB
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** mbad-insert.pl.in 15 Oct 2002 14:43:39 -0000 1.1
--- mbad-insert.pl.in 20 Oct 2002 14:52:25 -0000 1.2
***************
*** 10,14 ****
use strict;
! use blib;
use Carp;
use Getopt::Long;
--- 10,14 ----
use strict;
! # use blib;
use Carp;
use Getopt::Long;
***************
*** 34,41 ****
--ad_pk=pk : the primary key of the ArrayDesign
--fe_sw_pk=pk : the primary key of the FeatureExtraction SW
- --end_regexp=string : regular expression to match end of data
- --data_start_regexp=string : regexp matching start of data section
- --reading_data_regexp=string : regexp matching data line before first
- data line
optional parameters:
--- 34,37 ----
***************
*** 61,67 ****
'debug',
'password=s',
- 'end_regexp=s',
- 'data_start_regexp=s',
- 'reading_data_regexp=s',
);
--- 57,60 ----
***************
*** 79,88 ****
die "Must specify --es_pk\n$USAGE"
unless exists $OPTIONS{es_pk};
- die "Must specify --end_regexp\n$USAGE"
- unless exists $OPTIONS{end_regexp};
- die "Must specify --data_start_regexp\n$USAGE"
- unless exists $OPTIONS{data_start_regexp};
- die "Must specify --reading_data_regexp\n$USAGE"
- unless exists $OPTIONS{reading_data_regexp};
# open up a writeable connection
--- 72,75 ----
***************
*** 209,215 ****
! my $data_start_regexp = qr/$OPTIONS{data_start_regexp}/o;
! my $reading_data_regexp = qr/$OPTIONS{reading_data_regexp}/o;
! my $end_regexp = qr/$OPTIONS{end_regexp}/o;
my $in_data;
--- 196,216 ----
! $dbh->error(@error_args,
! message=>"Couldn't find data_start_regex1 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
! )
! unless defined $fe_sw_db->data_start_regex1();
! my $data_start_regex1 = qr/$fe_sw_db->data_start_regex1/o;
!
! $dbh->error(@error_args,
! message=>"Couldn't find data_start_regex2 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
! )
! unless defined $fe_sw_db->data_start_regex2();
! my $data_start_regex2 = qr/$fe_sw_db->data_start_regex2/o;
!
! $dbh->error(@error_args,
! message=>"Couldn't find data_end_regex for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
! )
! unless defined $fe_sw_db->data_end_regex();
! my $end_regex = qr/$fe_sw_db->end_regex/o;
my $in_data;
***************
*** 245,250 ****
while (<IN>) {
# see if we've found the Data section already
! next unless $in_data or /$data_start_regexp/;
! if (/$data_start_regexp/) {
$in_data = 1;
next;
--- 246,251 ----
while (<IN>) {
# see if we've found the Data section already
! next unless $in_data or /$data_start_regex1/;
! if (/$data_start_regex1/) {
$in_data = 1;
next;
***************
*** 252,259 ****
# don't proceed unless we've past the Data section header line
! next unless $reading_data or /$reading_data_regexp/;
# check if this is the header line of the Data section
! if (/$reading_data_regexp/) {
$reading_data = 1;
next;
--- 253,260 ----
# don't proceed unless we've past the Data section header line
! next unless $reading_data or /$data_start_regex2/;
# check if this is the header line of the Data section
! if (/$data_start_regex2/) {
$reading_data = 1;
next;
***************
*** 261,265 ****
# when we reach the end of the Data section, we're done
! last if /$end_regexp/;
$count++;
--- 262,266 ----
# when we reach the end of the Data section, we're done
! last if /$end_regex/;
$count++;
|
|
From: <jas...@us...> - 2002-10-20 14:51:36
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv16073/Genex/scripts
Modified Files:
gendb.pl.in
Log Message:
* scripts/gendb.pl.in (Repository):
added regexes to quantarray addition script
Index: gendb.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/gendb.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** gendb.pl.in 15 Oct 2002 14:44:17 -0000 1.5
--- gendb.pl.in 20 Oct 2002 14:51:32 -0000 1.6
***************
*** 192,196 ****
'--name=QuantArray',
'--version=3.0',
! '--feat="1.2.3.4"'
);
print STDERR "Adding example QuantitationTypeDimension ...\n";
--- 192,199 ----
'--name=QuantArray',
'--version=3.0',
! '--feat="1.2.3.4"',
! '--data_start_regex1="^Begin\s+Data"',
! '--data_start_regex2="^Number"',
! '--data_end_regex="^End"',
);
print STDERR "Adding example QuantitationTypeDimension ...\n";
|
|
From: <jas...@us...> - 2002-10-20 14:50:52
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv15671/Genex/scripts
Modified Files:
create_genex_class.pl.in
Log Message:
removed bogus POD from get_all_objects()
Index: create_genex_class.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_class.pl.in,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** create_genex_class.pl.in 15 Oct 2002 14:44:16 -0000 1.16
--- create_genex_class.pl.in 20 Oct 2002 14:50:49 -0000 1.17
***************
*** 1870,1877 ****
list context: a list of $full_module_name instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<$ {full_module_name}::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 1870,1873 ----
|
|
From: <jas...@us...> - 2002-10-20 14:49:58
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv15280/Genex/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
added ro/rw_group options
outputs pkey to STDOUT
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** array-design-insert.pl.in 15 Oct 2002 14:44:16 -0000 1.2
--- array-design-insert.pl.in 20 Oct 2002 14:49:56 -0000 1.3
***************
*** 17,21 ****
%%GENEX_EXTRALIBS%%
! use blib;
use Bio::Genex qw(error);
use Bio::Genex::Connect;
--- 17,21 ----
%%GENEX_EXTRALIBS%%
! # use blib;
use Bio::Genex qw(error);
use Bio::Genex::Connect;
***************
*** 35,44 ****
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
! $OPTIONS{ro_group} = 'public';
! $OPTIONS{rw_group} = 'superuser';
my $rc = GetOptions(\%OPTIONS,
'dbname=s',
'username=s',
'password=s',
'no_reporter',
'help',
--- 35,46 ----
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
! $OPTIONS{ro_group} = '%%GENEX_PUBLIC_GROUP%%';
! $OPTIONS{rw_group} = '%%GENEX_SUPERUSER_GROUP%%';
my $rc = GetOptions(\%OPTIONS,
'dbname=s',
'username=s',
'password=s',
+ 'ro_group=s',
+ 'rw_group=s',
'no_reporter',
'help',
***************
*** 262,265 ****
--- 264,268 ----
# Now the Array Design
#
+ my $ad_pk;
my @mage_ads = ();
unless (exists $mage->packages->{ArrayDesign}) {
***************
*** 316,320 ****
$array_db->feature_obj(\@features);
! my $ad_pk = $array_db->insert_db(dbh=>$dbh);
$dbh->error(@error_args,
message=>"couldn't insert record for layout: $name")
--- 319,323 ----
$array_db->feature_obj(\@features);
! $ad_pk = $array_db->insert_db(dbh=>$dbh);
$dbh->error(@error_args,
message=>"couldn't insert record for layout: $name")
***************
*** 328,331 ****
--- 331,335 ----
} else {
$dbh->commit();
+ print STDOUT "$ad_pk\n";
}
$dbh->disconnect();
|
|
From: <jas...@us...> - 2002-10-20 14:48:24
|
Update of /cvsroot/genex/genex-server/Genex/QuantitationTypeDimension In directory usw-pr-cvs1:/tmp/cvs-serv14605/Genex/QuantitationTypeDimension Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/QuantitationTypeDimension/.cvsignore,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** .cvsignore 15 Oct 2002 19:22:27 -0000 1.1 --- .cvsignore 20 Oct 2002 14:48:21 -0000 1.2 *************** *** 1 **** --- 1,2 ---- Makefile + pm_to_blib |
|
From: <jas...@us...> - 2002-10-20 14:48:05
|
Update of /cvsroot/genex/genex-server/Genex/MeasuredBioAssay In directory usw-pr-cvs1:/tmp/cvs-serv14440/Genex/MeasuredBioAssay Added Files: .cvsignore Log Message: new --- NEW FILE: .cvsignore --- Makefile pm_to_blib |
|
From: <jas...@us...> - 2002-10-20 14:47:44
|
Update of /cvsroot/genex/genex-server/G2G/mason/comps In directory usw-pr-cvs1:/tmp/cvs-serv14274/G2G/mason/comps Added Files: .cvsignore Log Message: new --- NEW FILE: .cvsignore --- authenticate.mason |
|
From: <jas...@us...> - 2002-10-20 14:43:54
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentSet
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ExperimentSet
Modified Files:
ExperimentSet.pm
Log Message:
new
Index: ExperimentSet.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExperimentSet/ExperimentSet.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** ExperimentSet.pm 15 Oct 2002 14:54:08 -0000 1.33
--- ExperimentSet.pm 20 Oct 2002 14:43:20 -0000 1.34
***************
*** 20,29 ****
use Bio::Genex::GroupSec;
use Bio::Genex::Contact;
! use Bio::Genex::Citation;
! use Bio::Genex::Audit;
! use Bio::Genex::ExperimentFactors;
use Bio::Genex::PhysicalBioAssay;
use Bio::Genex::TreatmentLevel;
use Bio::Genex::HotSpots;
--- 20,30 ----
use Bio::Genex::GroupSec;
use Bio::Genex::Contact;
! use Bio::Genex::MeasuredBioAssay;
use Bio::Genex::PhysicalBioAssay;
use Bio::Genex::TreatmentLevel;
use Bio::Genex::HotSpots;
+ use Bio::Genex::Citation;
+ use Bio::Genex::Audit;
+ use Bio::Genex::ExperimentFactors;
***************
*** 60,64 ****
'quantity_series_type',
'release_date',
! 'submission_date',
'local_accession',
'archive_bundle_ref'
--- 61,65 ----
'quantity_series_type',
'release_date',
! 'creation_date',
'local_accession',
'archive_bundle_ref'
***************
*** 126,129 ****
--- 127,143 ----
'table_name' => 'HotSpots'
}, 'Bio::Genex::Fkey' ),
+ 'measuredbioassay_obj' => bless( {
+ 'fkey_name' => 'measuredbioassay_obj',
+ 'pkey_name' => 'es_fk',
+ 'can_self_reference' => undef,
+ 'fkey_type' => 'ONE_TO_MANY_OO',
+ 'table_name' => 'MeasuredBioAssay'
+ }, 'Bio::Genex::Fkey' ),
+ 'measuredbioassay_fk' => bless( {
+ 'fkey_name' => 'measuredbioassay_fk',
+ 'pkey_name' => 'es_fk',
+ 'fkey_type' => 'ONE_TO_MANY',
+ 'table_name' => 'MeasuredBioAssay'
+ }, 'Bio::Genex::Fkey' ),
'audit_obj' => bless( {
'fkey_name' => 'audit_obj',
***************
*** 174,181 ****
'biology_description' => 'Biology Description',
'es_pk' => 'Accession Number',
'quantity_series_type' => 'Quantity Series Type',
'ro_groupname' => 'Read-Only Group Name',
! 'archive_bundle_ref' => 'Archive Bundle Reference',
! 'submission_date' => 'Submission Date'
}
;
--- 188,195 ----
'biology_description' => 'Biology Description',
'es_pk' => 'Accession Number',
+ 'creation_date' => 'Creation Date',
'quantity_series_type' => 'Quantity Series Type',
'ro_groupname' => 'Read-Only Group Name',
! 'archive_bundle_ref' => 'Archive Bundle Reference'
}
;
***************
*** 189,196 ****
'Experiment Name' => 'name',
'Archive Bundle Reference' => 'archive_bundle_ref',
- 'Submission Date' => 'submission_date',
'Accession Number' => 'es_pk',
'Primary Citation' => 'cit_fk',
'Local Accession Number' => 'local_accession',
'Audit' => 'audit_fk',
'Release Date' => 'release_date',
--- 203,210 ----
'Experiment Name' => 'name',
'Archive Bundle Reference' => 'archive_bundle_ref',
'Accession Number' => 'es_pk',
'Primary Citation' => 'cit_fk',
'Local Accession Number' => 'local_accession',
+ 'Creation Date' => 'creation_date',
'Audit' => 'audit_fk',
'Release Date' => 'release_date',
***************
*** 207,211 ****
'ro_groupname_obj' => 'ro_groupname',
'hotspots_obj' => 'hotspots_fk',
! 'provider_con_obj' => 'provider_con_fk'
}
;
--- 221,226 ----
'ro_groupname_obj' => 'ro_groupname',
'hotspots_obj' => 'hotspots_fk',
! 'provider_con_obj' => 'provider_con_fk',
! 'measuredbioassay_obj' => 'measuredbioassay_fk'
}
;
***************
*** 288,293 ****
$ExperimentSet->release_date($value);
! my $submission_date_val = $ExperimentSet->submission_date();
! $ExperimentSet->submission_date($value);
my $local_accession_val = $ExperimentSet->local_accession();
--- 303,308 ----
$ExperimentSet->release_date($value);
! my $creation_date_val = $ExperimentSet->creation_date();
! $ExperimentSet->creation_date($value);
my $local_accession_val = $ExperimentSet->local_accession();
***************
*** 446,450 ****
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['es_pk', 'name', 'cit_fk', 'provider_con_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'biology_description', 'analysis_description', 'treatment_type', 'quantity_series_type', 'release_date', 'submission_date', 'local_accession', 'archive_bundle_ref', 'cit_obj', 'provider_con_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj', 'experimentfactors_obj', 'experimentfactors_fk', 'physicalbioassay_obj', 'physicalbioassay_fk', 'treatmentlevel_obj', 'treatmentlevel_fk', 'hotspots_obj', 'hotspots_fk']);
--- 461,465 ----
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['es_pk', 'name', 'cit_fk', 'provider_con_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'biology_description', 'analysis_description', 'treatment_type', 'quantity_series_type', 'release_date', 'creation_date', 'local_accession', 'archive_bundle_ref', 'cit_obj', 'provider_con_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj', 'measuredbioassay_obj', 'measuredbioassay_fk', 'experimentfactors_obj', 'experimentfactors_fk', 'physicalbioassay_obj', 'physicalbioassay_fk', 'treatmentlevel_obj', 'treatmentlevel_fk', 'hotspots_obj', 'hotspots_fk']);
***************
*** 931,938 ****
list context: a list of Bio::Genex::ExperimentSet instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ExperimentSet::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 946,949 ----
***************
*** 1184,1187 ****
--- 1195,1208 ----
+ =item @id_list = measuredbioassay_fk()
+
+ =item @obj_list = measuredbioassay_obj()
+
+ This is an attribute of type ONE_TO_MANY and refers to class
+ L<Bio::Genex::MeasuredBioAssay>. The raw accessor method, C<measuredbioassay_fk()> returns a list of
+ foreign key ids. The OO accessor method, C<measuredbioassay_obj()> returns a
+ list of objects of class Bio::Genex::MeasuredBioAssay.
+
+
=item @id_list = experimentfactors_fk()
***************
*** 1394,1402 ****
! =item $value = submission_date();
! =item submission_date($value);
! Methods for the submission_date attribute.
--- 1415,1423 ----
! =item $value = creation_date();
! =item creation_date($value);
! Methods for the creation_date attribute.
|
|
From: <jas...@us...> - 2002-10-20 14:43:54
|
Update of /cvsroot/genex/genex-server/Genex/ControlledVocab
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ControlledVocab
Modified Files:
ControlledVocab.pm
Log Message:
new
Index: ControlledVocab.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ControlledVocab/ControlledVocab.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** ControlledVocab.pm 15 Oct 2002 14:54:07 -0000 1.26
--- ControlledVocab.pm 20 Oct 2002 14:43:20 -0000 1.27
***************
*** 806,813 ****
list context: a list of Bio::Genex::ControlledVocab instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ControlledVocab::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 806,809 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:54
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentFactors
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ExperimentFactors
Modified Files:
ExperimentFactors.pm
Log Message:
new
Index: ExperimentFactors.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExperimentFactors/ExperimentFactors.pm,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** ExperimentFactors.pm 15 Oct 2002 14:54:08 -0000 1.27
--- ExperimentFactors.pm 20 Oct 2002 14:43:20 -0000 1.28
***************
*** 828,835 ****
list context: a list of Bio::Genex::ExperimentFactors instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ExperimentFactors::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 828,831 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:54
|
Update of /cvsroot/genex/genex-server/Genex/ContactType
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ContactType
Modified Files:
ContactType.pm
Log Message:
new
Index: ContactType.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ContactType/ContactType.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** ContactType.pm 15 Oct 2002 14:54:07 -0000 1.14
--- ContactType.pm 20 Oct 2002 14:43:20 -0000 1.15
***************
*** 733,740 ****
list context: a list of Bio::Genex::ContactType instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ContactType::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 733,736 ----
|
