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From: <jas...@us...> - 2002-11-09 00:38:03
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Update of /cvsroot/genex/genex-server/Genex/GenexAdmin In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/GenexAdmin Modified Files: GenexAdmin.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:38:03
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Update of /cvsroot/genex/genex-server/Genex/ExternalDatabase In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ExternalDatabase Modified Files: ExternalDatabase.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/ExperimentSet In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ExperimentSet Modified Files: ExperimentSet.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/ContactType In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ContactType Modified Files: ContactType.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/Citation In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Citation Modified Files: Citation.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/Contact In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Contact Modified Files: Contact.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/ControlledVocab In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ControlledVocab Modified Files: ControlledVocab.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:09
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Update of /cvsroot/genex/genex-server/Genex/ExperimentFactors In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ExperimentFactors Modified Files: ExperimentFactors.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:08
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Update of /cvsroot/genex/genex-server/Genex/BlastHits In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/BlastHits Modified Files: BlastHits.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:08
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Update of /cvsroot/genex/genex-server/Genex/Audit In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Audit Modified Files: Audit.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:08
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Update of /cvsroot/genex/genex-server/Genex/Channel In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Channel Modified Files: Channel.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:08
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Update of /cvsroot/genex/genex-server/Genex/Chromosome In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Chromosome Modified Files: Chromosome.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:07
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Update of /cvsroot/genex/genex-server/Genex/AM_FactorValues In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/AM_FactorValues Modified Files: AM_FactorValues.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:07
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Update of /cvsroot/genex/genex-server/Genex/Array In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/Array Modified Files: Array.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:07
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Update of /cvsroot/genex/genex-server/Genex/ArrayDesign In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/ArrayDesign Modified Files: ArrayDesign.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:07
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Update of /cvsroot/genex/genex-server/Genex/AM_Spots In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/AM_Spots Modified Files: AM_Spots.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:36:07
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Update of /cvsroot/genex/genex-server/Genex/AM_SuspectSpots In directory usw-pr-cvs1:/tmp/cvs-serv21786/Genex/AM_SuspectSpots Modified Files: AM_SuspectSpots.pm Log Message: new |
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From: <jas...@us...> - 2002-11-09 00:34:08
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Update of /cvsroot/genex/genex-server/Genex/XMLUtils
In directory usw-pr-cvs1:/tmp/cvs-serv21585/Genex/XMLUtils
Modified Files:
XMLUtils.pm.in
Log Message:
* XMLUtils/XMLUtils.pm.in (Repository):
split out data_views (like Provider) from security views
Added rules for INSERT/UPDATE/DELETE on security views
Index: XMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/XMLUtils/XMLUtils.pm.in,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** XMLUtils.pm.in 7 Nov 2002 14:42:34 -0000 1.26
--- XMLUtils.pm.in 9 Nov 2002 00:34:05 -0000 1.27
***************
*** 305,309 ****
}
! =item ($sql,\@all_tables,\@audit_tables,\@all_views = xml2sql($dbh,@file_name_list);
Description: A method for converting an XML description of a relation
--- 305,309 ----
}
! =item ($sql,\@all_tables,\@data_views,\@audit_tables,\@sec_views = xml2sql($dbh,@file_name_list);
Description: A method for converting an XML description of a relation
***************
*** 313,318 ****
$sql = SQL string for creating the table
\@all_tables = array ref of table names to be created
\@audit_tables = array ref of table names with audit_fks
! \@all_views = array ref of view names to be created
Errors: Will call die() on error
--- 313,319 ----
$sql = SQL string for creating the table
\@all_tables = array ref of table names to be created
+ \@data_views = array ref of view names to be created
\@audit_tables = array ref of table names with audit_fks
! \@sec_views = array ref of security views to be created
Errors: Will call die() on error
***************
*** 323,332 ****
my ($dbh,@files) = @_;
assert_dbh($dbh);
! my $MASTER_SEQ = 'GENEX_ID_SEQ';
my @defer_fkeys;
my @defer_views;
! my @all_views;
my @all_tables;
my %audit_tables;
my $output;
--- 324,335 ----
my ($dbh,@files) = @_;
assert_dbh($dbh);
! my $MASTER_SEQ = '%%GENEX_MASTER_SEQ%%';
my @defer_fkeys;
my @defer_views;
! my @data_views;
! my @sec_views;
my @all_tables;
+ my @uniques;
my %audit_tables;
my $output;
***************
*** 401,404 ****
--- 404,408 ----
foreach my $doc (@inheritance_set) {
+ my $pkey;
my $table = $doc->getDocumentElement();
my $table_name = $table->getAttribute('name')
***************
*** 440,444 ****
# save the view name to return to the caller
! push(@all_views,$table_name);
} else {
@columns = $table->getElementsByTagName('column');
--- 444,448 ----
# save the view name to return to the caller
! push(@data_views,$table_name);
} else {
@columns = $table->getElementsByTagName('column');
***************
*** 451,454 ****
--- 455,461 ----
my $null = '';
$null = 'NOT NULL' if $attrs{not_null} eq 'true';
+ if ($attrs{type} eq 'serial') {
+ $attrs{type} = qq[int8 DEFAULT nextval('"$MASTER_SEQ"'::text)];
+ }
push(@column_sql,qq[\t"$attrs{name}"\t$attrs{type} $null]);
$has_ro_groupname = 1
***************
*** 466,470 ****
}
# do the primary key
! my ($pkey) = $table->getElementsByTagName('primary_key');
if (defined $pkey) {
my %attrs = $pkey->getAttributes();
--- 473,477 ----
}
# do the primary key
! ($pkey) = $table->getElementsByTagName('primary_key');
if (defined $pkey) {
my %attrs = $pkey->getAttributes();
***************
*** 509,513 ****
}
! my @uniques = $table->getElementsByTagName('unique');
foreach my $column (@uniques) {
my %attrs = $column->getAttributes();
--- 516,520 ----
}
! @uniques = $table->getElementsByTagName('unique');
foreach my $column (@uniques) {
my %attrs = $column->getAttributes();
***************
*** 538,547 ****
my $view = "$ {table_name}_view";
my @from = ($table_name);
my @args = (VIEW=>$view,
! COLUMNS=>[map {[$table_name,$_->getAttribute('name')]}
! @columns, @inherited_columns],
);
if ($has_ro_groupname) {
! push(@args,WHERE=>'ro_groupname=GroupLink.groupname AND GroupLink.username=user()');
push(@from,'GroupLink')
unless $table_name eq 'GroupLink';
--- 545,559 ----
my $view = "$ {table_name}_view";
my @from = ($table_name);
+ my @col_names = map {$_->getAttribute('name')}
+ @columns, @inherited_columns;
my @args = (VIEW=>$view,
! COLUMNS=>[map {[$table_name,$_]} @col_names],
);
+ my $ro_check = 'ro_groupname=GroupLink.groupname AND GroupLink.username=user()';
+ my $rw_check = $ro_check;
+ $rw_check =~ s/ro_groupname/rw_groupname/;
+
if ($has_ro_groupname) {
! push(@args,WHERE=>$ro_check);
push(@from,'GroupLink')
unless $table_name eq 'GroupLink';
***************
*** 551,554 ****
--- 563,625 ----
my $sql = $dbh->create_view_sql(@args);
+ # _view == 5, _ins/upd/del == 4
+ # rule names are limited to 32 characters
+ my $rule_name = $table_name;
+ if (length($rule_name) > 32 - 9) {
+ $rule_name = substr($rule_name,0,23);
+ }
+ $rule_name .= '_view';
+
+ my $ins_columns = join ",\n", map {qq[NEW."$_"]} @col_names;
+ my $columns = join ",\n", map {qq["$_"]} @col_names;
+ $sql .=<<INSERT;
+ CREATE RULE $ {rule_name}_ins AS ON INSERT TO $view
+ DO INSTEAD
+ INSERT INTO $table_name ($columns)
+ VALUES (
+ $ins_columns
+ );
+
+ INSERT
+
+ if (grep {$_ eq 'rw_groupname'} @col_names) {
+
+ my $upd_columns = join ",\n", map {qq["$_" = NEW."$_"]} @col_names;
+ my @wheres = ($rw_check);
+ my $WHERE;
+ if (defined $pkey) {
+ my $pkey_name = $pkey->getAttribute('column_id');
+ push(@wheres,qq["$pkey_name" = NEW."$pkey_name"]);
+ } elsif (scalar @uniques) {
+ # we just need one set of unique columns, so we take the first
+ my %attrs = $uniques[0]->getAttributes();
+
+ # split on whitespace, join on commas
+ my @unique_cols = split(' ',$attrs{column_ids});
+
+ push(@wheres,join(",\n", map {qq["$_" = NEW."$_"]} @unique_cols));
+ }
+ $WHERE = join(" AND ", @wheres);
+ $sql .=<<UPDATE;
+ CREATE RULE $ {rule_name}_upd AS ON UPDATE TO $view
+ DO INSTEAD
+ UPDATE $table_name SET
+ $upd_columns
+ WHERE $WHERE;
+
+ UPDATE
+
+ $WHERE =~ s/NEW\./OLD./g;
+ $sql .=<<DELETE;
+ CREATE RULE $ {rule_name}_del AS ON DELETE TO $view
+ DO INSTEAD
+ DELETE from $table_name
+ WHERE $WHERE;
+
+ DELETE
+ } else {
+ warn("skipping DELETE and UPDATE rules for $view");
+ }
+
# we defer creation of the view until after all tables are created
# this way we don't need to know when GroupLink is created
***************
*** 556,560 ****
# save the view name to return to the caller
! push(@all_views,$view);
--- 627,631 ----
# save the view name to return to the caller
! push(@sec_views,$view);
***************
*** 577,581 ****
# were created
$output .= join("\n",@defer_views,@defer_fkeys);
! return ($output,\@all_tables,[keys %audit_tables],\@all_views);
}
--- 648,652 ----
# were created
$output .= join("\n",@defer_views,@defer_fkeys);
! return ($output,\@all_tables,\@data_views,[keys %audit_tables],\@sec_views);
}
|
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From: <jas...@us...> - 2002-11-09 00:32:07
|
Update of /cvsroot/genex/genex-server/Genex/Connect In directory usw-pr-cvs1:/tmp/cvs-serv20821/Genex/Connect Modified Files: Connect.pm.in Log Message: removed bad =back Index: Connect.pm.in =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Connect/Connect.pm.in,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** Connect.pm.in 13 Oct 2002 07:35:30 -0000 1.8 --- Connect.pm.in 9 Nov 2002 00:32:04 -0000 1.9 *************** *** 342,347 **** Returns the username which the database handle is currently connected as. - =back - =cut --- 342,345 ---- *************** *** 360,365 **** Returns the true if the DB handle is in a transaction. - =back - =cut --- 358,361 ---- *************** *** 1778,1786 **** 1; __END__ - - =back - - - =head1 AUTHOR --- 1774,1777 ---- |
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From: <jas...@us...> - 2002-11-09 00:31:34
|
Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv20618/Genex
Modified Files:
Makefile.PL
Log Message:
* Makefile.PL (Repository):
removed cruft from when Genex.pm was installed outside system perl
library
Index: Makefile.PL
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Makefile.PL,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** Makefile.PL 30 Jan 2001 16:05:40 -0000 1.22
--- Makefile.PL 9 Nov 2002 00:31:32 -0000 1.23
***************
*** 29,34 ****
# since this is an update, we have to run configure.pl ourselves
! my $infile = './scripts/configure.pl.in';
! my $outfile = './scripts/configure.pl';
print STDERR "Running $outfile ...\n\n";
--- 29,34 ----
# since this is an update, we have to run configure.pl ourselves
! my $infile = './scripts/substitute.pl.in';
! my $outfile = './scripts/substitute.pl';
print STDERR "Running $outfile ...\n\n";
***************
*** 58,64 ****
$EXAMPLE_DIR = $Bio::Genex::Config->{'GENEX_EXAMPLE_DIR'};
- $GENEX_MAN1 = $Bio::Genex::Config->{'GENEX_MAN1'};
- $GENEX_MAN3 = $Bio::Genex::Config->{'GENEX_MAN3'};
- $GENEX_INSTALLSITE = $Bio::Genex::Config->{'GENEX_INSTALLSITE'};
###############################################################################
--- 58,61 ----
***************
*** 73,94 ****
my $PM = {'Genex.pm' => '$(INST_LIBDIR)/Genex.pm',
};
-
- print STDERR "EXAMPLE_DIR undefined!!!!\n"
- unless defined $EXAMPLE_DIR;
- print STDERR "MAN3_DIR undefined!!!!\n"
- unless defined $GENEX_MAN3;
- print STDERR "MAN1_DIR undefined!!!!\n"
- unless defined $GENEX_MAN1;
- print STDERR "INSTALLSITELIB undefined!!!!\n"
- unless defined $GENEX_INSTALLSITE;
-
- print STDOUT <<"EOM";
- Using the following installation parameters from Genex::Config:
-
- 'INSTALLSITELIB' => $GENEX_INSTALLSITE,
- 'INSTALLMAN1DIR' => $GENEX_MAN1,
- 'INSTALLMAN3DIR' => $GENEX_MAN3,
-
- EOM
WriteMakefile(
--- 70,73 ----
|
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From: <jas...@us...> - 2002-11-09 00:30:55
|
Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv20379/Genex
Modified Files:
Genex.pm.in
Log Message:
* Genex.pm.in (Repository):
new version (2.7.20021108)
Index: Genex.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Genex.pm.in,v
retrieving revision 1.48
retrieving revision 1.49
diff -C2 -d -r1.48 -r1.49
*** Genex.pm.in 7 Nov 2002 14:41:20 -0000 1.48
--- Genex.pm.in 9 Nov 2002 00:30:52 -0000 1.49
***************
*** 58,62 ****
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021106';
# Preloaded methods go here.
--- 58,62 ----
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021108';
# Preloaded methods go here.
|
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From: <jas...@us...> - 2002-11-09 00:29:58
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv19994
Modified Files:
Configure
Log Message:
* Configure (Repository):
Added GENEX_MASTER_SEQ
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Configure 7 Nov 2002 14:53:45 -0000 1.9
--- Configure 9 Nov 2002 00:29:55 -0000 1.10
***************
*** 113,116 ****
--- 113,117 ----
$GENEX_RO_USER $GENEX_RO_PASSWORD $GENEX_TEST_USER $GENEX_TEST_PASSWORD
$GENEX_PUBLIC_GROUP $GENEX_SUPERUSER_GROUP $GENEX_VOCAB_DIR
+ $GENEX_MASTER_SEQ
);
***************
*** 1030,1033 ****
--- 1031,1035 ----
}
+ $VARS{GENEX_MASTER_SEQ} = $GENEX_MASTER_SEQ = 'GENEX_ID_SEQ';
$VARS{VERSION_STRING} = $VERSION_STRING; # install-all version string
$VARS{LOCAL_ROOT} = $LOCAL_ROOT;
|
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From: <ki...@us...> - 2002-11-08 23:04:07
|
Update of /cvsroot/genex/genex-www/status/2003/sep In directory usw-pr-cvs1:/tmp/cvs-serv27695/sep Log Message: Directory /cvsroot/genex/genex-www/status/2003/sep added to the repository |
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From: <ki...@us...> - 2002-11-08 23:04:07
|
Update of /cvsroot/genex/genex-www/status/2003/oct In directory usw-pr-cvs1:/tmp/cvs-serv27695/oct Log Message: Directory /cvsroot/genex/genex-www/status/2003/oct added to the repository |
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From: <ki...@us...> - 2002-11-08 23:04:07
|
Update of /cvsroot/genex/genex-www/status/2003/nov In directory usw-pr-cvs1:/tmp/cvs-serv27695/nov Log Message: Directory /cvsroot/genex/genex-www/status/2003/nov added to the repository |
