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treebase-guts
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From: <rv...@us...> - 2009-11-01 22:31:37
|
Revision: 229
http://treebase.svn.sourceforge.net/treebase/?rev=229&view=rev
Author: rvos
Date: 2009-11-01 22:31:20 +0000 (Sun, 01 Nov 2009)
Log Message:
-----------
reverting deletion of perl subtree. this folder structure contains scripts and supporting libraries for loading database dumps, checking for database consistency, running generic java classes and sql statements etc. this code is almost entirely due to mjdominus (who has left the project).
Added Paths:
-----------
trunk/treebase-core/src/main/perl/
trunk/treebase-core/src/main/perl/bin/
trunk/treebase-core/src/main/perl/bin/check
trunk/treebase-core/src/main/perl/bin/digester
trunk/treebase-core/src/main/perl/bin/dosql
trunk/treebase-core/src/main/perl/bin/findby
trunk/treebase-core/src/main/perl/bin/gc
trunk/treebase-core/src/main/perl/bin/publish
trunk/treebase-core/src/main/perl/bin/sel
trunk/treebase-core/src/main/perl/bin/show
trunk/treebase-core/src/main/perl/bin/sqldump
trunk/treebase-core/src/main/perl/bin/tbo
trunk/treebase-core/src/main/perl/bin/td
trunk/treebase-core/src/main/perl/bin/undump
trunk/treebase-core/src/main/perl/check/
trunk/treebase-core/src/main/perl/check/check
trunk/treebase-core/src/main/perl/check/digester
trunk/treebase-core/src/main/perl/check/gc
trunk/treebase-core/src/main/perl/dump/
trunk/treebase-core/src/main/perl/dump/dosql
trunk/treebase-core/src/main/perl/dump/findby
trunk/treebase-core/src/main/perl/dump/iq
trunk/treebase-core/src/main/perl/dump/loadspeed
trunk/treebase-core/src/main/perl/dump/sel
trunk/treebase-core/src/main/perl/dump/show
trunk/treebase-core/src/main/perl/dump/showanalyses
trunk/treebase-core/src/main/perl/dump/showmatrices
trunk/treebase-core/src/main/perl/dump/showmatrix
trunk/treebase-core/src/main/perl/dump/showtree
trunk/treebase-core/src/main/perl/dump/showtrees
trunk/treebase-core/src/main/perl/dump/sqldump
trunk/treebase-core/src/main/perl/dump/tbo
trunk/treebase-core/src/main/perl/dump/td
trunk/treebase-core/src/main/perl/jrun
trunk/treebase-core/src/main/perl/lib/
trunk/treebase-core/src/main/perl/lib/CIPRES/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBILogin.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/TreeBaseObjects.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/VeryBadORM.pm
trunk/treebase-core/src/main/perl/misc/
trunk/treebase-core/src/main/perl/misc/build_and_deploy_treebase.sh
trunk/treebase-core/src/main/perl/misc/fix-sequence
trunk/treebase-core/src/main/perl/misc/kill-jrun
trunk/treebase-core/src/main/perl/misc/publish
trunk/treebase-core/src/main/perl/misc/upload-manager
Removed Paths:
-------------
trunk/treebase-core/src/main/perl/bin/
trunk/treebase-core/src/main/perl/bin/check
trunk/treebase-core/src/main/perl/bin/digester
trunk/treebase-core/src/main/perl/bin/dosql
trunk/treebase-core/src/main/perl/bin/findby
trunk/treebase-core/src/main/perl/bin/gc
trunk/treebase-core/src/main/perl/bin/publish
trunk/treebase-core/src/main/perl/bin/sel
trunk/treebase-core/src/main/perl/bin/show
trunk/treebase-core/src/main/perl/bin/sqldump
trunk/treebase-core/src/main/perl/bin/tbo
trunk/treebase-core/src/main/perl/bin/td
trunk/treebase-core/src/main/perl/bin/undump
trunk/treebase-core/src/main/perl/check/
trunk/treebase-core/src/main/perl/check/check
trunk/treebase-core/src/main/perl/check/digester
trunk/treebase-core/src/main/perl/check/gc
trunk/treebase-core/src/main/perl/dump/
trunk/treebase-core/src/main/perl/dump/dosql
trunk/treebase-core/src/main/perl/dump/findby
trunk/treebase-core/src/main/perl/dump/iq
trunk/treebase-core/src/main/perl/dump/loadspeed
trunk/treebase-core/src/main/perl/dump/sel
trunk/treebase-core/src/main/perl/dump/show
trunk/treebase-core/src/main/perl/dump/showanalyses
trunk/treebase-core/src/main/perl/dump/showmatrices
trunk/treebase-core/src/main/perl/dump/showmatrix
trunk/treebase-core/src/main/perl/dump/showtree
trunk/treebase-core/src/main/perl/dump/showtrees
trunk/treebase-core/src/main/perl/dump/sqldump
trunk/treebase-core/src/main/perl/dump/tbo
trunk/treebase-core/src/main/perl/dump/td
trunk/treebase-core/src/main/perl/jrun
trunk/treebase-core/src/main/perl/lib/
trunk/treebase-core/src/main/perl/lib/CIPRES/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBILogin.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/TreeBaseObjects.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/VeryBadORM.pm
trunk/treebase-core/src/main/perl/misc/
trunk/treebase-core/src/main/perl/misc/build_and_deploy_treebase.sh
trunk/treebase-core/src/main/perl/misc/fix-sequence
trunk/treebase-core/src/main/perl/misc/kill-jrun
trunk/treebase-core/src/main/perl/misc/publish
trunk/treebase-core/src/main/perl/misc/upload-manager
Deleted: trunk/treebase-core/src/main/perl/bin/check
===================================================================
--- trunk/treebase-core/src/main/perl/bin/check 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/check
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/check (from rev 212, trunk/treebase-core/src/main/perl/bin/check)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/check (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/check
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/digester
===================================================================
--- trunk/treebase-core/src/main/perl/bin/digester 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/digester
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/digester (from rev 212, trunk/treebase-core/src/main/perl/bin/digester)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/digester (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/digester
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/dosql
===================================================================
--- trunk/treebase-core/src/main/perl/bin/dosql 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/dosql
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/dosql (from rev 212, trunk/treebase-core/src/main/perl/bin/dosql)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/dosql (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/dosql
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/findby
===================================================================
--- trunk/treebase-core/src/main/perl/bin/findby 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/findby
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/findby (from rev 212, trunk/treebase-core/src/main/perl/bin/findby)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/findby (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/findby
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/gc
===================================================================
--- trunk/treebase-core/src/main/perl/bin/gc 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/gc
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/gc (from rev 212, trunk/treebase-core/src/main/perl/bin/gc)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/gc (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/gc
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/publish
===================================================================
--- trunk/treebase-core/src/main/perl/bin/publish 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/publish 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../misc/publish
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/publish (from rev 212, trunk/treebase-core/src/main/perl/bin/publish)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/publish (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/publish 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../misc/publish
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/sel
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sel 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/sel
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/sel (from rev 212, trunk/treebase-core/src/main/perl/bin/sel)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sel (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/sel
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/show
===================================================================
--- trunk/treebase-core/src/main/perl/bin/show 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/show
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/show (from rev 212, trunk/treebase-core/src/main/perl/bin/show)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/show (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/show
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sqldump 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/sqldump 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/sqldump
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/sqldump (from rev 212, trunk/treebase-core/src/main/perl/bin/sqldump)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sqldump (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/sqldump 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/sqldump
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/tbo
===================================================================
--- trunk/treebase-core/src/main/perl/bin/tbo 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/tbo 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/tbo
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/tbo (from rev 212, trunk/treebase-core/src/main/perl/bin/tbo)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/tbo (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/tbo 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/tbo
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/td
===================================================================
--- trunk/treebase-core/src/main/perl/bin/td 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/td 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/td
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/td (from rev 212, trunk/treebase-core/src/main/perl/bin/td)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/td (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/td 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/td
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/undump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/undump 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/undump 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,92 +0,0 @@
-#!/usr/bin/perl
-# preprocess DB2 dump files for importation into pg via psql command
-#
-
-use Getopt::Std;
-my $commit_batch_size;
-my @pending; # records read but not written out
-getopts('xdn:', \%opt) or usage();
-$commit_batch_size ||= $opt{n};
-
-my $BEGIN = "BEGIN TRANSACTION;\n";
-$BEGIN .= "SET CONSTAINTS ALL DEFERRED;\n" if $opt{d};
-
-my $OK = 1;
-
-TABLE:
-for my $table (@ARGV) {
- if (-e $table) {
- my $FH;
- unless (open($FH, "<", $table) ) {
- warn "Couldn't open file '$table': $!; skipping\n";
- $OK = 0;
- next TABLE;
- }
- do_table($table, $FH);
- } elsif (-e "$table.gz") {
- my $fh = IO::Zlib->new;
- unless ($fh->open("$table.gz", "rb")) {
- warn "Couldn't open file '$table.gz': $!; skipping\n";
- $OK = 0;
- next TABLE;
- }
- do_table($table, $fh);
- } else {
- warn "Couldn't find dump file for table '$table'; skipping\n";
- $OK = 0;
- }
-}
-
-sub do_table {
- my ($table, $fh) = @_;
- my ($start, $length);
- local *_;
- local *.;
-
- while (<$fh>) {
- if ($. == 1) {
- /INSERT INTO \"/ or die "unparseable";
- $start = $+[0] - 1;
- substr($_, $start) =~ /(.*\)) VALUES \(/ or die "unparseable";
- $length = $+[1];
- die unless defined($start) && defined($length);
- }
-
-
- substr($_, $start, $length) =~ s/"(\w+?)"/"\L$1\E"/g;
-
- if (defined($commit_batch_size)) {
- push @pending, $_;
- if (@pending >= $commit_batch_size) {
- print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
- @pending = ();
- }
- } else {
- print;
- }
- if ($opt{x}) {
- warn "$.\n" if $. % 10_000 == 0;
- }
- }
-
-# possibly a final partial batch
- if (@pending) {
- print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
- @pending = ();
- }
-
- close $fh;
-}
-
-################################################################
-
-sub usage {
- print STDERR qq{Usage: $0 [-dx] [-n batchsize] TABLE...
- -d defer constraint checking to the end of each transaction
- -x print progress information to stderr
- -n batchsize commit records in batches of /batchsize/
-
- records for TABLE are read from file TABLE or from TABLE.gz
-};
- exit 1;
-}
Copied: trunk/treebase-core/src/main/perl/bin/undump (from rev 212, trunk/treebase-core/src/main/perl/bin/undump)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/undump (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/undump 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,92 @@
+#!/usr/bin/perl
+# preprocess DB2 dump files for importation into pg via psql command
+#
+
+use Getopt::Std;
+my $commit_batch_size;
+my @pending; # records read but not written out
+getopts('xdn:', \%opt) or usage();
+$commit_batch_size ||= $opt{n};
+
+my $BEGIN = "BEGIN TRANSACTION;\n";
+$BEGIN .= "SET CONSTAINTS ALL DEFERRED;\n" if $opt{d};
+
+my $OK = 1;
+
+TABLE:
+for my $table (@ARGV) {
+ if (-e $table) {
+ my $FH;
+ unless (open($FH, "<", $table) ) {
+ warn "Couldn't open file '$table': $!; skipping\n";
+ $OK = 0;
+ next TABLE;
+ }
+ do_table($table, $FH);
+ } elsif (-e "$table.gz") {
+ my $fh = IO::Zlib->new;
+ unless ($fh->open("$table.gz", "rb")) {
+ warn "Couldn't open file '$table.gz': $!; skipping\n";
+ $OK = 0;
+ next TABLE;
+ }
+ do_table($table, $fh);
+ } else {
+ warn "Couldn't find dump file for table '$table'; skipping\n";
+ $OK = 0;
+ }
+}
+
+sub do_table {
+ my ($table, $fh) = @_;
+ my ($start, $length);
+ local *_;
+ local *.;
+
+ while (<$fh>) {
+ if ($. == 1) {
+ /INSERT INTO \"/ or die "unparseable";
+ $start = $+[0] - 1;
+ substr($_, $start) =~ /(.*\)) VALUES \(/ or die "unparseable";
+ $length = $+[1];
+ die unless defined($start) && defined($length);
+ }
+
+
+ substr($_, $start, $length) =~ s/"(\w+?)"/"\L$1\E"/g;
+
+ if (defined($commit_batch_size)) {
+ push @pending, $_;
+ if (@pending >= $commit_batch_size) {
+ print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
+ @pending = ();
+ }
+ } else {
+ print;
+ }
+ if ($opt{x}) {
+ warn "$.\n" if $. % 10_000 == 0;
+ }
+ }
+
+# possibly a final partial batch
+ if (@pending) {
+ print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
+ @pending = ();
+ }
+
+ close $fh;
+}
+
+################################################################
+
+sub usage {
+ print STDERR qq{Usage: $0 [-dx] [-n batchsize] TABLE...
+ -d defer constraint checking to the end of each transaction
+ -x print progress information to stderr
+ -n batchsize commit records in batches of /batchsize/
+
+ records for TABLE are read from file TABLE or from TABLE.gz
+};
+ exit 1;
+}
Deleted: trunk/treebase-core/src/main/perl/check/check
===================================================================
--- trunk/treebase-core/src/main/perl/check/check 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,186 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use CIPRES::TreeBase::TreeBaseObjects;
-use Getopt::Std;
-our $indent = 0;
-
-my $TERMINAL;
-if (-t STDOUT) {
- $| = 1;
- $TERMINAL = 1;
-}
-
-my %opt;
-getopts('chasd:p:RC:X', \%opt) or usage();
-if ($opt{X}) { list_known_classes(); }
-if ($opt{h}) { usage(); }
-if ($opt{R}) {
- if ($opt{d}) { die "-R and -d are incompatible\n"; }
- $opt{d} = 0;
-}
-if ($opt{c}) {
- if ($opt{C}) { die "-c and -C are inconsistent\n"; }
- $opt{C} = ""; # set, but no classes
-}
-
-my %prune = map { $_ => 1 } split /,\s*/, $opt{p};
-my $all_consistency_checks = ! defined $opt{C};
-my %consistency_check = map { $_ => 1 } split /,\s*/, $opt{C};
-
-if ($opt{s}) {
- # prune out "small" classes
- $prune{$_} = 1 for qw(MatrixRow PhyloTreeNode TaxonLabel MatrixKind TreeType);
-}
-
-my $type = shift or usage();
-my $id = shift or usage();
-$id =~ s/^#//;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
-$dbh->{ShowErrorStatement} = 1;
-use Carp 'croak';
-sub full_str {
- my $self = shift;
- $self->reify;
- my @keys = sort(grep !/[^A-Z]/, keys %$self);
- my @components = map "$_ => $self->{$_}", @keys;
- return join ", ", @components;
-}
-
-sub attr_check {
- my ($obj, $attr_name, $attr, $warnings) = @_;
-# warn "checking to see that this object has $attr_name = $attr->{$attr_name}\n";
-
- # If $attr is just a scalar, fake up an attr hash with one attribute
- unless (ref $attr) {
- $attr = { $attr_name => $attr };
- }
-
- unless ($warnings || $attr->{warnings}) {
- croak "No warning target variable specified";
- }
-
- return 1 unless exists $attr->{$attr_name};
- if (not defined $obj->$attr_name) {
- # attribute is missing from the object
-
- # ... okay, if it is specifically required to be missing
- return 1 if ! defined $attr->{$attr_name};
-
- # otherwise, record an error
- push @$warnings,
- "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
- " should have $attr_name = $attr->{$attr_name}, ".
- " but it is missing.";
- return;
- }
-
- return 1 if $obj->$attr_name->id == $attr->{$attr_name};
- push @$warnings,
- "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
- " should have $attr_name = $attr->{$attr_name}, ".
- " but instead has " . $obj->$attr_name->id;
- return;
-}
-
-my $OK = 1;
-my @warnings;
-$type->new($id)->dump(action => \&prt, seen => {},
- prune => \%prune,
- show_all => $opt{a},
- warnings => \@warnings,
- attr_check => \&attr_check,
- defined($opt{d}) ? (maxdepth => $opt{d}) : (),
- );
-
-for my $w (@warnings) {
- print STDERR "*** $w\n";
-}
-if (! $OK) {
- warn "Inconsistencies detected\n";
- exit 1;
-} else {
- exit 0;
-}
-
-
-sub prt {
- my ($self, %attr) = @_;
- my $seen = $attr{seen}{$self->class}{$self->id}++;
- my $str = $attr{show_all} ? full_str($self) : $self->to_str;
- my $indent = " " x $attr{depth};
- my $consistent;
-
- my ($class, $id) = ($self->class, $self->id);
-
- if (! $seen) {
- my $z;
- if ($TERMINAL) {
- $z = "(Checking consistency of $class $id.)";
- print $z, "\r";
- }
-
- {
- my $do_check = $all_consistency_checks || $consistency_check{$class};
- $consistent = $do_check ? $self->consistent(%attr) : 1;
- }
-
- $OK &&= $consistent;
- if ($TERMINAL) {
- print " " x length($z), "\r";
- }
- }
-
- unless ($class->is_nested) {
- if (exists $attr{$class} &&
- $attr{$class} != $id) {
- push @{$attr{warnings}}, "** Expected $class $attr{$class}, found $id insead\n";
- }
- }
-
- my $mark = $seen ? "|-" : $consistent ? "| " : "|*";
- return 0 if $attr{prune}{$self->class};
- print "| " x $attr{depth}, "$mark$str\n";
-
- return !$seen;
-}
-
-sub list_known_classes {
- my $kch = CIPRES::TreeBase::VeryBadORM->known_class_hash();
- for my $k (sort values %$kch) {
- print "$k\n";
- }
- exit 0;
-}
-
-sub usage {
- print STDERR qq<Usage: $0 [-X] [-acsR] [-d n] [-pClass1,Class2,...] [-CClasses...] Class IDnumber
-
-Recursively print the contents of the specified object of the
-specified class. For example, "$0 Study 1234" prints out study #1234
-and all of its trees, matrices, analyses, etc., and their contents.
-
-Use "$0 -X" for a list of known classes.
-
-Options:
- -a: show *all* attributes of every object (default: pretty-print objects)
- -s: do not recurse into "small" objects (Currently: MatrixRow,
- PhyloTreeNode, TaxonLabel)
- -R: do not recurse at all, printing only the top object
- -c: Skip all consistency checking
-
- -d n: recurse only n levels deep
-
- -pClasses... : 'prune': do not display or recurse into objects of these
- classes.
- -CClasses... : Perform consistency checking of these classes only
->;
- exit 1;
-}
-
-
-1;
Copied: trunk/treebase-core/src/main/perl/check/check (from rev 212, trunk/treebase-core/src/main/perl/check/check)
===================================================================
--- trunk/treebase-core/src/main/perl/check/check (rev 0)
+++ trunk/treebase-core/src/main/perl/check/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,186 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use CIPRES::TreeBase::TreeBaseObjects;
+use Getopt::Std;
+our $indent = 0;
+
+my $TERMINAL;
+if (-t STDOUT) {
+ $| = 1;
+ $TERMINAL = 1;
+}
+
+my %opt;
+getopts('chasd:p:RC:X', \%opt) or usage();
+if ($opt{X}) { list_known_classes(); }
+if ($opt{h}) { usage(); }
+if ($opt{R}) {
+ if ($opt{d}) { die "-R and -d are incompatible\n"; }
+ $opt{d} = 0;
+}
+if ($opt{c}) {
+ if ($opt{C}) { die "-c and -C are inconsistent\n"; }
+ $opt{C} = ""; # set, but no classes
+}
+
+my %prune = map { $_ => 1 } split /,\s*/, $opt{p};
+my $all_consistency_checks = ! defined $opt{C};
+my %consistency_check = map { $_ => 1 } split /,\s*/, $opt{C};
+
+if ($opt{s}) {
+ # prune out "small" classes
+ $prune{$_} = 1 for qw(MatrixRow PhyloTreeNode TaxonLabel MatrixKind TreeType);
+}
+
+my $type = shift or usage();
+my $id = shift or usage();
+$id =~ s/^#//;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
+$dbh->{ShowErrorStatement} = 1;
+use Carp 'croak';
+sub full_str {
+ my $self = shift;
+ $self->reify;
+ my @keys = sort(grep !/[^A-Z]/, keys %$self);
+ my @components = map "$_ => $self->{$_}", @keys;
+ return join ", ", @components;
+}
+
+sub attr_check {
+ my ($obj, $attr_name, $attr, $warnings) = @_;
+# warn "checking to see that this object has $attr_name = $attr->{$attr_name}\n";
+
+ # If $attr is just a scalar, fake up an attr hash with one attribute
+ unless (ref $attr) {
+ $attr = { $attr_name => $attr };
+ }
+
+ unless ($warnings || $attr->{warnings}) {
+ croak "No warning target variable specified";
+ }
+
+ return 1 unless exists $attr->{$attr_name};
+ if (not defined $obj->$attr_name) {
+ # attribute is missing from the object
+
+ # ... okay, if it is specifically required to be missing
+ return 1 if ! defined $attr->{$attr_name};
+
+ # otherwise, record an error
+ push @$warnings,
+ "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
+ " should have $attr_name = $attr->{$attr_name}, ".
+ " but it is missing.";
+ return;
+ }
+
+ return 1 if $obj->$attr_name->id == $attr->{$attr_name};
+ push @$warnings,
+ "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
+ " should have $attr_name = $attr->{$attr_name}, ".
+ " but instead has " . $obj->$attr_name->id;
+ return;
+}
+
+my $OK = 1;
+my @warnings;
+$type->new($id)->dump(action => \&prt, seen => {},
+ prune => \%prune,
+ show_all => $opt{a},
+ warnings => \@warnings,
+ attr_check => \&attr_check,
+ defined($opt{d}) ? (maxdepth => $opt{d}) : (),
+ );
+
+for my $w (@warnings) {
+ print STDERR "*** $w\n";
+}
+if (! $OK) {
+ warn "Inconsistencies detected\n";
+ exit 1;
+} else {
+ exit 0;
+}
+
+
+sub prt {
+ my ($self, %attr) = @_;
+ my $seen = $attr{seen}{$self->class}{$self->id}++;
+ my $str = $attr{show_all} ? full_str($self) : $self->to_str;
+ my $indent = " " x $attr{depth};
+ my $consistent;
+
+ my ($class, $id) = ($self->class, $self->id);
+
+ if (! $seen) {
+ my $z;
+ if ($TERMINAL) {
+ $z = "(Checking consistency of $class $id.)";
+ print $z, "\r";
+ }
+
+ {
+ my $do_check = $all_consistency_checks || $consistency_check{$class};
+ $consistent = $do_check ? $self->consistent(%attr) : 1;
+ }
+
+ $OK &&= $consistent;
+ if ($TERMINAL) {
+ print " " x length($z), "\r";
+ }
+ }
+
+ unless ($class->is_nested) {
+ if (exists $attr{$class} &&
+ $attr{$class} != $id) {
+ push @{$attr{warnings}}, "** Expected $class $attr{$class}, found $id insead\n";
+ }
+ }
+
+ my $mark = $seen ? "|-" : $consistent ? "| " : "|*";
+ return 0 if $attr{prune}{$self->class};
+ print "| " x $attr{depth}, "$mark$str\n";
+
+ return !$seen;
+}
+
+sub list_known_classes {
+ my $kch = CIPRES::TreeBase::VeryBadORM->known_class_hash();
+ for my $k (sort values %$kch) {
+ print "$k\n";
+ }
+ exit 0;
+}
+
+sub usage {
+ print STDERR qq<Usage: $0 [-X] [-acsR] [-d n] [-pClass1,Class2,...] [-CClasses...] Class IDnumber
+
+Recursively print the contents of the specified object of the
+specified class. For example, "$0 Study 1234" prints out study #1234
+and all of its trees, matrices, analyses, etc., and their contents.
+
+Use "$0 -X" for a list of known classes.
+
+Options:
+ -a: show *all* attributes of every object (default: pretty-print objects)
+ -s: do not recurse into "small" objects (Currently: MatrixRow,
+ PhyloTreeNode, TaxonLabel)
+ -R: do not recurse at all, printing only the top object
+ -c: Skip all consistency checking
+
+ -d n: recurse only n levels deep
+
+ -pClasses... : 'prune': do not display or recurse into objects of these
+ classes.
+ -CClasses... : Perform consistency checking of these classes only
+>;
+ exit 1;
+}
+
+
+1;
Deleted: trunk/treebase-core/src/main/perl/check/digester
===================================================================
--- trunk/treebase-core/src/main/perl/check/digester 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,49 +0,0 @@
-#!/usr/bin/perl
-#
-# Digest reports that come out of the checker:
-# grep out all the lines that begin with '***'
-# pass them through this program
-# This program will sort each different kind of message into a separate file
-# To have the files placed in some other directory, use the -d option
-# 20090327 MJD
-#
-
-use Getopt::Std;
-my %opt = (d => ".");
-getopts('d:', \%opt) or die;
--d($opt{d}) || mkdir($opt{d}) || die "$opt{d}: $!";
-
-while (<>) {
- chomp;
- my $k = $_;
- $k =~ s/\d+/#/g;
- $k =~ s/#(\s*#)+/##/g;
- $k =~ s/^S#:\s+//;
- push @{$msg{$k}}, $_;
-}
-
-for my $k (keys %msg) {
- my $f = abbr($k);
- open my($fh), ">", "$opt{d}/$f" or die "$opt{d}/$f: $!";
- print $fh $_, "\n" for @{$msg{$k}};
- close $fh;
-}
-
-my $q;
-BEGIN { $q = 1 };
-my %seen;
-
-sub abbr {
- my $s = shift;
- $s =~ tr/A-Z /a-z_/;
- $s =~ tr/A-Za-z_//cd;
- $s =~ tr/_/_/s;
- $s =~ s/^_//;
-
- substr($s, 30) = "" if length($s) > 30;
- if ($seen{$s}) {
- $s .= $q++;
- }
- return $s;
-}
-
Copied: trunk/treebase-core/src/main/perl/check/digester (from rev 212, trunk/treebase-core/src/main/perl/check/digester)
===================================================================
--- trunk/treebase-core/src/main/perl/check/digester (rev 0)
+++ trunk/treebase-core/src/main/perl/check/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,49 @@
+#!/usr/bin/perl
+#
+# Digest reports that come out of the checker:
+# grep out all the lines that begin with '***'
+# pass them through this program
+# This program will sort each different kind of message into a separate file
+# To have the files placed in some other directory, use the -d option
+# 20090327 MJD
+#
+
+use Getopt::Std;
+my %opt = (d => ".");
+getopts('d:', \%opt) or die;
+-d($opt{d}) || mkdir($opt{d}) || die "$opt{d}: $!";
+
+while (<>) {
+ chomp;
+ my $k = $_;
+ $k =~ s/\d+/#/g;
+ $k =~ s/#(\s*#)+/##/g;
+ $k =~ s/^S#:\s+//;
+ push @{$msg{$k}}, $_;
+}
+
+for my $k (keys %msg) {
+ my $f = abbr($k);
+ open my($fh), ">", "$opt{d}/$f" or die "$opt{d}/$f: $!";
+ print $fh $_, "\n" for @{$msg{$k}};
+ close $fh;
+}
+
+my $q;
+BEGIN { $q = 1 };
+my %seen;
+
+sub abbr {
+ my $s = shift;
+ $s =~ tr/A-Z /a-z_/;
+ $s =~ tr/A-Za-z_//cd;
+ $s =~ tr/_/_/s;
+ $s =~ s/^_//;
+
+ substr($s, 30) = "" if length($s) > 30;
+ if ($seen{$s}) {
+ $s .= $q++;
+ }
+ return $s;
+}
+
Deleted: trunk/treebase-core/src/main/perl/check/gc
===================================================================
--- trunk/treebase-core/src/main/perl/check/gc 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,90 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use CIPRES::TreeBase::TreeBaseObjects;
-use Getopt::Std;
-use Carp 'croak';
-
-# $seen{$class}{$id} is 0 if the object was in the DB but unreferenced
-# 1 if the object was in the DB and referenced
-my %SEEN = ();
-my $count = 0;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
-
-my @CLASSES = qw(Analysis AnalysisStep AnalyzedData
- Matrix MatrixRow
- PhyloTree PhyloTreeNode
- Study
- TaxonLabel
- );
-
-
-for my $class (@CLASSES) {
- for my $id (get_all_ids($class)) {
- $SEEN{$class}{$id} = 0;
- }
- warn "Database contains ", scalar(keys %{$SEEN{$class}}), " $class items\n";
-}
-
-for my $study (map {Study->new($_)} keys %{$SEEN{Study}}) {
- next if $SEEN{Study}{$study->id}++;
- my $N = $study->analyzed_data;
- my $PREFIX = "S" . $study->id;
- print STDERR $PREFIX;
- my $C = 0;
-
- for my $analysis ($study->analyses) {
- next if $SEEN{Analysis}{$analysis->id}++;
- for my $astep ($analysis->analysissteps) {
- next if $SEEN{AnalysisStep}{$astep->id}++;
- for my $adata ($astep->analyzeddata) {
- next if $SEEN{AnalyzedData}{$adata->id}++;
- $C++;
- print STDERR " $C/$N\r$PREFIX";
- if (my $matrix = $adata->matrix) {
- next if $SEEN{Matrix}{$matrix->id}++;
- for my $row ($matrix->rows) {
- next if $SEEN{MatrixRow}{$row->id}++;
- $SEEN{TaxonLabel}{$row->taxonlabel->id} = 1 if $row->taxonlabel
- }
- } elsif (my $tree = $adata->phylotree) {
- for my $node ($tree->nodes) {
- next if $SEEN{PhyloTreeNode}{$node->id}++;
- $SEEN{TaxonLabel}{$node->taxonlabel->id} = 1 if $node->taxonlabel
- }
- }
- }
- }
- }
- print STDERR "\n";
-}
-
-for my $class (sort keys %SEEN) {
- my $classHash = $SEEN{$class};
- for my $id (sort {$a <=> $b} keys %$classHash) {
- if ($classHash->{$id} == 0) {
- print "* $class $id\n";
- }
- }
-}
-
-
-sub get_all_ids {
- my $class = shift;
- my $table = $class->table or croak "Unknown object class '$class'";
- my $id_attr = $class->id_attr or croak "Unknown object class '$class'";
- my $sql = "select $id_attr from $table";
- my $ids = $dbh->selectcol_arrayref($sql);
- return wantarray ? @$ids : $ids;
-}
-
-sub get_all {
- my $class = shift;
- my @ids = sort {$a<=>$b} get_all_ids($class);
- my @objs = map { $class->new($_) } @ids;
- return wantarray ? @objs : \@objs;
-}
Copied: trunk/treebase-core/src/main/perl/check/gc (from rev 212, trunk/treebase-core/src/main/perl/check/gc)
===================================================================
--- trunk/treebase-core/src/main/perl/check/gc (rev 0)
+++ trunk/treebase-core/src/main/perl/check/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,90 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use CIPRES::TreeBase::TreeBaseObjects;
+use Getopt::Std;
+use Carp 'croak';
+
+# $seen{$class}{$id} is 0 if the object was in the DB but unreferenced
+# 1 if the object was in the DB and referenced
+my %SEEN = ();
+my $count = 0;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
+
+my @CLASSES = qw(Analysis AnalysisStep AnalyzedData
+ Matrix MatrixRow
+ PhyloTree PhyloTreeNode
+ Study
+ TaxonLabel
+ );
+
+
+for my $class (@CLASSES) {
+ for my $id (get_all_ids($class)) {
+ $SEEN{$class}{$id} = 0;
+ }
+ warn "Database contains ", scalar(keys %{$SEEN{$class}}), " $class items\n";
+}
+
+for my $study (map {Study->new($_)} keys %{$SEEN{Study}}) {
+ next if $SEEN{Study}{$study->id}++;
+ my $N = $study->analyzed_data;
+ my $PREFIX = "S" . $study->id;
+ print STDERR $PREFIX;
+ my $C = 0;
+
+ for my $analysis ($study->analyses) {
+ next if $SEEN{Analysis}{$analysis->id}++;
+ for my $astep ($analysis->analysissteps) {
+ next if $SEEN{AnalysisStep}{$astep->id}++;
+ for my $adata ($astep->analyzeddata) {
+ next if $SEEN{AnalyzedData}{$adata->id}++;
+ $C++;
+ print STDERR " $C/$N\r$PREFIX";
+ if (my $matrix = $adata->matrix) {
+ next if $SEEN{Matrix}{$matrix->id}++;
+ for my $row ($matrix->rows) {
+ next if $SEEN{MatrixRow}{$row->id}++;
+ $SEEN{TaxonLabel}{$row->taxonlabel->id} = 1 if $row->taxonlabel
+ }
+ } elsif (my $tree = $adata->phylotree) {
+ for my $node ($tree->nodes) {
+ next if $SEEN{PhyloTreeNode}{$node->id}++;
+ $SEEN{TaxonLabel}{$node->taxonlabel->id} = 1 if $node->taxonlabel
+ }
+ }
+ }
+ }
+ }
+ print STDERR "\n";
+}
+
+for my $class (sort keys %SEEN) {
+ my $classHash = $SEEN{$class};
+ for my $id (sort {$a <=> $b} keys %$classHash) {
+ if ($classHash->{$id} == 0) {
+ print "* $class $id\n";
+ }
+ }
+}
+
+
+sub get_all_ids {
+ my $class = shift;
+ my $table = $class->table or croak "Unknown object class '$class'";
+ my $id_attr = $class->id_attr or croak "Unknown object class '$class'";
+ my $sql = "select $id_attr from $table";
+ my $ids = $dbh->selectcol_arrayref($sql);
+ return wantarray ? @$ids : $ids;
+}
+
+sub get_all {
+ my $class = shift;
+ my @ids = sort {$a<=>$b} get_all_ids($class);
+ my @objs = map { $class->new($_) } @ids;
+ return wantarray ? @objs : \@objs;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/dosql
===================================================================
--- trunk/treebase-core/src/main/perl/dump/dosql 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,25 +0,0 @@
-#!/usr/bin/perl
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-getopts('s') or die "Usage: $0 SQL statement on command line";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-
-if ($opt_s) {
- my @statements = split /;[ \t]*\r?\n/, join "", <ARGV>;
- for my $Q (@statements) {
- next unless $Q =~ /\S/;
- print "$Q\n";
- $dbh->do($Q)
- or die "Couldn't prepare statement:\n\t$Q\n\t" . $dbh->errstr;
- }
-} else {
- my $Q = join " ", @ARGV;
- $dbh->do($Q)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-}
-
-$dbh->disconnect;
Copied: trunk/treebase-core/src/main/perl/dump/dosql (from rev 212, trunk/treebase-core/src/main/perl/dump/dosql)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/dosql (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+getopts('s') or die "Usage: $0 SQL statement on command line";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+
+if ($opt_s) {
+ my @statements = split /;[ \t]*\r?\n/, join "", <ARGV>;
+ for my $Q (@statements) {
+ next unless $Q =~ /\S/;
+ print "$Q\n";
+ $dbh->do($Q)
+ or die "Couldn't prepare statement:\n\t$Q\n\t" . $dbh->errstr;
+ }
+} else {
+ my $Q = join " ", @ARGV;
+ $dbh->do($Q)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+}
+
+$dbh->disconnect;
Deleted: trunk/treebase-core/src/main/perl/dump/findby
===================================================================
--- trunk/treebase-core/src/main/perl/dump/findby 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,31 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = ();
-getopts('', \%opt) or usage();
-my ($class, $attr, $val) = @ARGV;
-defined($class) && defined($attr) && defined($val) or usage();
-
-my $query = "select $class\_id from $class where $attr = ?";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute($val)
- or die "Couldn't execute statement: " . $dbh->errstr;
-my $row;
-while (my ($id) = $sth->fetchrow_array) {
- print "$id\n";
-}
-
-$dbh->disconnect;
-
-sub usage {
- print "$0 [-n nullsymbol] table id#\n";
- exit 1;
-}
-
Copied: trunk/treebase-core/src/main/perl/dump/findby (from rev 212, trunk/treebase-core/src/main/perl/dump/findby)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/findby (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = ();
+getopts('', \%opt) or usage();
+my ($class, $attr, $val) = @ARGV;
+defined($class) && defined($attr) && defined($val) or usage();
+
+my $query = "select $class\_id from $class where $attr = ?";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute($val)
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my $row;
+while (my ($id) = $sth->fetchrow_array) {
+ print "$id\n";
+}
+
+$dbh->disconnect;
+
+sub usage {
+ print "$0 [-n nullsymbol] table id#\n";
+ exit 1;
+}
+
Deleted: trunk/treebase-core/src/main/perl/dump/iq
===================================================================
--- trunk/treebase-core/src/main/perl/dump/iq 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/iq 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,140 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-use Text::ParseWords;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-$dbh->{RaiseError} = undef;
-$dbh->{PrintError} = 'on';
-
-my %opt = (e => $ENV{IQEDITOR} || $ENV{VISUAL} || $ENV{EDITOR} || "vi",
- m => 20,
- n => "--",
- );
-getopts('e:m:n:', \%opt) or usage();
-
-my $query = "";
-my $sth;
-my $editor = $opt{e};
-my $maxrows = $opt{m};
-my @rows;
-
-while (1) {
-# print $query, "\n" if $query;
- print "> ";
- my $r = <>;
- trim($r);
- last if $r eq "";
-
- if ($r eq "e") {
- $query = edit($query);
- print "$query\n";
- $sth = maybe_run_query($query);
- } elsif (my ($pat, $rep, $g) = ($r =~ m{s/(.*)/(.*)/(g?)})) {
- if ($g) {
- $query =~ s/$pat/$rep/g;
- } else {
- $query =~ s/$pat/$rep/;
- }
- $sth = maybe_run_query($query);
- } elsif ($r =~ s/^x\s*//) {
- (my $q = $query) =~ tr/\n/ /;
- compile_query($query) unless defined $sth;
- run_query($sth, shellwords($r));
- } elsif ($r eq "p") {
- print_aoh(\@rows, $opt_n);
- } elsif ($r =~ s/^w\s*//) {
- if (open my($f), ">", $r) {
- my $ofh = select $f;
- print_aoh(\@rows, $opt_n);
- select $ofh;
- } else {
- warn "Couldn't open '$r' for writing: $!\n";
- }
- } else {
- $query = $r;
- $sth = maybe_run_query($query);
- }
-}
-
-exit;
-
-################################################################
-
-sub compile_query {
- my $query = shift;
- $query =~ tr/\n/ /;
- my $_sth;
- eval {
- $_sth = $dbh->prepare($query);
- };
- if ($_sth) {
- $sth = $_sth;
- } else {
- warn $dbh->errstr . "\n";
- }
- return defined($_sth);
-}
-
-sub maybe_run_query {
- eval {
- my $query = shift;
- compile_query($query) or return;
-
- return unless $sth->{NUM_OF_PARAMS} == 0;
-
-
- run_query($sth);
- return $sth;
- };
-}
-
-sub run_query {
- my $sth = shift;
- return unless defined $sth;
- my @params = @_;
- my @_rows;
-
- warn "Executing...\n";
- $sth->execute(@params) or return;
- while (my $row = $sth->fetchrow_hashref) {
- push @_rows, {%$row};
- }
-
-
- $sth->finish;
- if (@_rows == 0) {
- print "Empty result.\n";
- return;
- } elsif (@_rows <= $maxrows) {
- print_aoh(\@rows, $opt_n);
- } else {
- print "result: " . @_rows . " rows; use 'p' to display\n";
- }
- @rows = @_rows;
-}
-
-sub edit {
- my $tmp = "/tmp/iq.$$";
- my $data = shift;
- $data .= "\n" unless $data =~ /\n\z/;
- open my($f), ">", $tmp or die "Couldn't write temp file '$tmp': $!";
- print $f $data;
- close $f;
- if (system($editor, $tmp) == 0) {
- open my($f), "<", $tmp or die "Couldn't read modified temp file '$tmp': $!";
- $data = join "", <$f>;
- } else {
- warn "Editor failed; ignoring changes\n";
- }
- unlink $tmp;
- return $data;
-}
-
-sub trim {
- $_[0] =~ s/^\s+//;
- $_[0] =~ s/\s+$//;
-}
Copied: trunk/treebase-core/src/main/perl/dump/iq (from rev 212, trunk/treebase-core/src/main/perl/dump/iq)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/iq (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/iq 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,140 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+use Text::ParseWords;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+$dbh->{RaiseError} = undef;
+$dbh->{PrintError} = 'on';
+
+my %opt = (e => $ENV{IQEDITOR} || $ENV{VISUAL} || $ENV{EDITOR} || "vi",
+ m => 20,
+ n => "--",
+ );
+getopts('e:m:n:', \%opt) or usage();
+
+my $query = "";
+my $sth;
+my $editor = $opt{e};
+my $maxrows = $opt{m};
+my @rows;
+
+while (1) {
+# print $query, "\n" if $query;
+ print "> ";
+ my $r = <>;
+ trim($r);
+ last if $r eq "";
+
+ if ($r eq "e") {
+ $query = edit($query);
+ print "$query\n";
+ $sth = maybe_run_query($query);
+ } elsif (my ($pat, $rep, $g) = ($r =~ m{s/(.*)/(.*)/(g?)})) {
+ if ($g) {
+ $query =~ s/$pat/$rep/g;
+ } else {
+ $query =~ s/$pat/$rep/;
+ }
+ $sth = maybe_run_query($query);
+ } elsif ($r =~ s/^x\s*//) {
+ (my $q = $query) =~ tr/\n/ /;
+ compile_query($query) unless defined $sth;
+ run_query($sth, shellwords($r));
+ } elsif ($r eq "p") {
+ print_aoh(\@rows, $opt_n);
+ } elsif ($r =~ s/^w\s*//) {
+ if (open my($f), ">", $r) {
+ my $ofh = select $f;
+ print_aoh(\@rows, $opt_n);
+ select $ofh;
+ } else {
+ warn "Couldn't open '$r' for writing: $!\n";
+ }
+ } else {
+ $query = $r;
+ $sth = maybe_run_query($query);
+ }
+}
+
+exit;
+
+################################################################
+
+sub compile_query {
+ my $query = shift;
+ $query =~ tr/\n/ /;
+ my $_sth;
+ eval {
+ $_sth = $dbh->prepare($query);
+ };
+ if ($_sth) {
+ $sth = $_sth;
+ } else {
+ warn $dbh->errstr . "\n";
+ }
+ return defined($_sth);
+}
+
+sub maybe_run_query {
+ eval {
+ my $query = shift;
+ compile_query($query) or return;
+
+ return unless $sth->{NUM_OF_PARAMS} == 0;
+
+
+ run_query($sth);
+ return $sth;
+ };
+}
+
+sub run_query {
+ my $sth = shift;
+ return unless defined $sth;
+ my @params = @_;
+ my @_rows;
+
+ warn "Executing...\n";
+ $sth->execute(@params) or return;
+ while (my $row = $sth->fetchrow_hashref) {
+ push @_rows, {%$row};
+ }
+
+
+ $sth->finish;
+ if (@_rows == 0) {
+ print "Empty result.\n";
+ return;
+ } elsif (@_rows <= $maxrows) {
+ print_aoh(\@rows, $opt_n);
+ } else {
+ print "result: " . @_rows . " rows; use 'p' to display\n";
+ }
+ @rows = @_rows;
+}
+
+sub edit {
+ my $tmp = "/tmp/iq.$$";
+ my $data = shift;
+ $data .= "\n" unless $data =~ /\n\z/;
+ open my($f), ">", $tmp or die "Couldn't write temp file '$tmp': $!";
+ print $f $data;
+ close $f;
+ if (system($editor, $tmp) == 0) {
+ open my($f), "<", $tmp or die "Couldn't read modified temp file '$tmp': $!";
+ $data = join "", <$f>;
+ } else {
+ warn "Editor failed; ignoring changes\n";
+ }
+ unlink $tmp;
+ return $data;
+}
+
+sub trim {
+ $_[0] =~ s/^\s+//;
+ $_[0] =~ s/\s+$//;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/loadspeed
===================================================================
--- trunk/treebase-core/src/main/perl/dump/loadspeed 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/loadspeed 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,39 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (z => 30);
-getopts('sz:', \%opt) or usage();
-
-@ARGV || usage();
-my $table = shift;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare("select count(*) from $table")
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-my ($before) = $sth->fetchrow_array;
-$sth->finish;
-#1 while $sth->fetch;
-warn "$before rows\n" unless $opt{s};
-sleep $opt{z};
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-my ($after) = $sth->fetchrow_array;
-$sth->finish;
-warn "$after rows\n" unless $opt{s};
-my $rate = ($after-$before)*60/$opt{z};
-printf (($opt{s} ? "%.2f\n" : "%.2f records per minute\n"), $rate);
-
-$dbh->disconnect;
-exit;
-
-sub usage {
- print "$0 [-s] [-z time-delay] table-name\n";
- print " -s : short output format\n";
- exit 1;
-}
Copied: trunk/treebase-core/src/main/perl/dump/loadspeed (from rev 212, trunk/treebase-core/src/main/perl/dump/loadspeed)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/loadspeed (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/loadspeed 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,39 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (z => 30);
+getopts('sz:', \%opt) or usage();
+
+@ARGV || usage();
+my $table = shift;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare("select count(*) from $table")
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my ($before) = $sth->fetchrow_array;
+$sth->finish;
+#1 while $sth->fetch;
+warn "$before rows\n" unless $opt{s};
+sleep $opt{z};
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my ($after) = $sth->fetchrow_array;
+$sth->finish;
+warn "$after rows\n" unless $opt{s};
+my $rate = ($after-$before)*60/$opt{z};
+printf (($opt{s} ? "%.2f\n" : "%.2f records per minute\n"), $rate);
+
+$dbh->disconnect;
+exit;
+
+sub usage {
+ print "$0 [-s] [-z time-delay] table-name\n";
+ print " -s : short output format\n";
+ exit 1;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/sel
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sel 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,42 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (n => '--');
-getopts('n:', \%opt) or usage();
-
-@ARGV || usage();
-my $query = join " ", @ARGV;
-
-$query =~ s/^/SELECT / unless $query =~ /^select\s+/i;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-while (my $row = $sth->fetchrow_hashref) {
- push @rows, {%$row};
-}
-
-
-$dbh->disconnect;
-if (@rows) {
- if (@rows == 1 && keys %{$rows[0]} == 1) {
- # Special case for a single selected value
- my ($value) = values %{$rows[0]};
- print "$value\n";
- } else {
- print_aoh(\@rows, $opt_n);
- }
-} else {
- print "Empty result.\n";
-}
-
-sub usage {
- print "$0 [-n nullsymbol] '....'\n";
- exit 1;
-}
Copied: trunk/treebase-core/src/main/perl/dump/sel (from rev 212, trunk/treebase-core/src/main/perl/dump/sel)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sel (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,42 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (n => '--');
+getopts('n:', \%opt) or usage();
+
+@ARGV || usage();
+my $query = join " ", @ARGV;
+
+$query =~ s/^/SELECT / unless $query =~ /^select\s+/i;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+while (my $row = $sth->fetchrow_hashref) {
+ push @rows, {%$row};
+}
+
+
+$dbh->disconnect;
+if (@rows) {
+ if (@rows == 1 && keys %{$rows[0]} == 1) {
+ # Special case for a single selected value
+ my ($value) = values %{$rows[0]};
+ print "$value\n";
+ } else {
+ print_aoh(\@rows, $opt_n);
+ }
+} else {
+ print "Empty result.\n";
+}
+
+sub usage {
+ print "$0 [-n nullsymbol] '....'\n";
+ exit 1;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/show
===================================================================
--- trunk/treebase-core/src/main/perl/dump/show 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,51 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (n => $ENV{NULLSYMBOL} || '--');
-getopts('n:', \%opt) or usage();
-my ($class, $id) = @ARGV;
-defined($class) && defined($id) && $id =~ /^\d+$/ or usage();
-my $query = "select * from $class where $class\_id = ?";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute($id)
- or die "Couldn't execute statement: " . $dbh->errstr;
-my $row;
-while (my $r = $sth->fetchrow_hashref) {
- if (defined $row) {
- die "Multiple matching rows!!\n";
- }
- $row = $r;
-}
-
-$dbh->disconnect;
-if (! defined $row) { die "show: No such object\n"; }
-
-my $c1 = max(map length(), keys %$row);
-
-for my $k (sort keys %$row) {
- if (! defined $row->{$k}) { $row->{$k} = $opt{n} }
- print fill($c1, $k), " $row->{$k}\n";
-}
-
-sub usage {
- print "$0 [-n nullsymbol] table id#\n";
- exit 1;
-}
-
-sub max {
- my $m = shift;
- $m = $m > $_ ? $m : $_ for @_;
- return $m;
-}
-
-sub fill {
- my ($n, $s) = @_;
- return length($s) > $n ? $s : $s . " " x ($n - length($s));
-}
Copied: trunk/treebase-core/src/main/perl/dump/show (from rev 212, trunk/treebase-core/src/main/perl/dump/show)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/show (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,51 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (n => $ENV{NULLSYMBOL} || '--');
+getopts('n:', \%opt) or usage();
+my ($class, $id) = @ARGV;
+defined($class) && defined($id) && $id =~ /^\d+$/ or usage();
+my $query = "select * from $class where $class\_id = ?";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute($id)
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my $row;
+while (my $r = $sth->fetchrow_hashref) {
+ if (defined $row) {
+ die "Multiple matching rows!!\n";
+ }
+ $row = $r;
+}
+
+$dbh->disconnect;
+if (! defined $row) { die "show: No such object\n"; }
+
+my $c1 = max(map length(), keys %$row);
+
+for my $k (sort keys %$row) {
+ if (! defined $row->{$k}) { $row->{$k} = $opt{n} }
+ print fill($c1, $k), " $row->{$k}\n";
+}
+
+sub usage {
+ print "$0 [-n nullsymbol] table id#\n";
+ exit 1;
+}
+
+sub max {
+ my $m = shift;
+ $m = $m > $_ ? $m : $_ for @_;
+ return $m;
+}
+
+sub fill {
+ my ($n, $s) = @_;
+ return length($s) > $n ? $s : $s . " " x ($n - length($s));
+}
Deleted: trunk/treebase-core/src/main/perl/dump/showanalyses
===================================================================
--- trunk/treebase-core/src/main/perl/dump/showanalyses 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/showanalyses 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,76 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt;
-getopts('', \%opt) or usage();
-
-my $study_id = shift || usage();
-
-my $dbh = CIPRES::TreeBase::Util->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-
-for my $analysis_row (query("analysis", "study_id", $study_id)) {
- my $a_id = $analysis_row->{ANALYSIS_ID};
- print " Analysis $a_id:\n";
- for my $analysisstep_row (query("analysisstep", "analysis_id", $a_id)) {
- my $as_id = $analysisstep_row->{ANALYSISSTEP_ID};
- print " Step $as_id:\n";
- for my $analyzeddata_row (query("analyzeddata", "analysisstep_id", $as_id)) {
- my $ad_id = $analyzeddata_row->{ANALYZEDDATA_ID};
- my $type = $analyzeddata_row->{TYPE};
- my $Type = {M => "matrix", T => "phyloTree"}->{$type};
- my $input = $analyzeddata_row->{INPUT} ? "input" : "output";
- my $d_id = $analyzeddata_row->{"\U$Type\E_ID"};
- my $nameField = {M => "TITLE", T => "LABEL"}->{$type};
- print " Data $ad_id ($input):\n";
-# print " ", join " ", %$analyzeddata_row;
-
- for my $row (query($Type, $Type . "_id", $d_id)) {
- my $s_id = $row->{STUDY_ID};
- my $ERR = "";
- if (! defined $s_id) {
- $ERR = "(no study!) ";
- } elsif ($s_id != $study_id) {
- $ERR = "(study s_id) ";
- }
- if ($type eq "T" && not defined $row->{TREEBLOCK_ID}) {
- $ERR .= "(no treeblock!) "
- }
-
- my $spc = $ERR ? "**" : " ";
- print " $spc \u$Type $d_id: $ERR'$row->{$nameField}'\n";
- }
- }
- }
-}
-
-$dbh->disconnect;
-
-################################################################
-
-sub usage {
- print "$0 [-tb] tree-id\n";
- print "\t-t : check taxonlabels\n";
- print "\t-b : check treeblocks\n";
- exit 1;
-}
-
-################################################################
-
-sub query {
- my ($table, $qcolumn, $qvalue) = @_;
- unless (defined $qcolumn) {
- $qcolumn = $table . "_id";
- }
- my $sth = $dbh->prepare_cached("select * from $table where $qcolumn = ?");
- $sth->execute($qvalue);
- my @rows;
- while (my $row = $sth->fetchrow_hashref()) {
- push @rows, $row;
- }
- $sth->finish;
- return @rows;
-}
Copied: trunk/treebase-core/src/main/perl/dump/showanalyses (from rev 212, trunk/treebase-core/src/main/perl/dump/showanalyses)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/showanalyses (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/showanalyses 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,76 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt;
+getopts('', \%opt) or usage();
+
+my $study_id = shift || usage();
+
+my $dbh = CIPRES::TreeBase::Util->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+
+for my $analysis_row (query("analysis", "study_id", $study_id)) {
+ my $a_id = $analysis_row->{ANALYSIS_ID};
+ print " Analysis $a_id:\n";
+ for my $analysisstep_row (query(...
[truncated message content] |
|
From: <vga...@us...> - 2010-02-09 20:52:16
|
Revision: 487
http://treebase.svn.sourceforge.net/treebase/?rev=487&view=rev
Author: vgapeyev
Date: 2010-02-09 20:51:58 +0000 (Tue, 09 Feb 2010)
Log Message:
-----------
Split nexusService bean into 2: one for the webapp (init via JNDI) and another for the standalone tools (init from jdbc.properties)
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
trunk/treebase-core/src/main/resources/applicationContext-service.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2010-02-09 20:51:58 UTC (rev 487)
@@ -40,6 +40,9 @@
private MatrixDataTypeHome mMatrixDataTypeHome;
private ItemDefinitionHome mItemDefinitionHome;
+ private String mExplicitMesquiteFolder = null;
+ private String mJndiMesquiteFolder = null;
+
/**
* Constructor.
*/
@@ -104,24 +107,47 @@
return null; // do not need persistence service.
}
- /** Looks up where Mesquite is installed on the host system and informs MesquiteModule of the location.
+
+ /** Explicitly set Mesquite folder location that will be passed to mesquite.lib.MesquiteModule.
+ * Only for use in tests and stand-alone tools (the webapp looks up the location in afterPropertiesSet()).
+ *
+ * @param pMesquiteFolderDir
+ */
+ public void setMesquiteFolderDir(String pMesquiteFolderDir) {
+ mExplicitMesquiteFolder = pMesquiteFolderDir;
+ LOGGER.info("Mesquite folder location set explicitly to " + mExplicitMesquiteFolder);
+ //--
+ //System.setProperty(MESQUITE_FOLDER_DIR_KEY, pMesquiteFolderDir);
+ //MesquiteModule.mesquiteDirectory = new File(pMesquiteFolderDir);
+ //MesquiteModule.mesquiteDirectoryPath = pMesquiteFolderDir;
+ }
+
+
+ /** Looks up where Mesquite is installed on the host system and passes the location to mesquite.lib.MesquiteModule.
(This is an implementation of a standard Spring bean initialization method,
which is invoked after all properties are set.)
*/
public void afterPropertiesSet() throws Exception {
- String mesquiteFolderDir = null;
- InitialContext ic;
try {
- ic = new InitialContext();
- mesquiteFolderDir = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
+ InitialContext ic = new InitialContext();
+ mJndiMesquiteFolder = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
} catch (NamingException e) {
- LOGGER.fatal("Error looking up tb/MesquiteFolder via JNDI");
+ LOGGER.info("Failure looking up tb/MesquiteFolder via JNDI");
}
- mesquiteFolderDir = mesquiteFolderDir + "/foo"; //since the last path element is somehow dropped subsequently... VG 2010-02-07
- System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolderDir);
- MesquiteModule.mesquiteDirectory = new File(mesquiteFolderDir);
- MesquiteModule.mesquiteDirectoryPath = mesquiteFolderDir;
+ String mesquiteFolder;
+ if (mExplicitMesquiteFolder == null)
+ if (mJndiMesquiteFolder == null) { mesquiteFolder = null; LOGGER.fatal("Failed to determine Mesquite folder location"); }
+ else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.info("Setting mesquite folder location from JNDI: " + mJndiMesquiteFolder); }
+ else
+ if (mJndiMesquiteFolder == null) { mesquiteFolder = mExplicitMesquiteFolder; LOGGER.info("Using explicitly set Mesquite folder: " + mExplicitMesquiteFolder);}
+ else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.warn("Explicitly set Mesquite folder (" + mExplicitMesquiteFolder +
+ ") is overwritten by the one from JNDI: " + mJndiMesquiteFolder); }
+
+ mesquiteFolder = mesquiteFolder + "/foo"; //since the last path element is somehow dropped subsequently... VG 2010-02-07
+ System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolder);
+ MesquiteModule.mesquiteDirectory = new File(mesquiteFolder);
+ MesquiteModule.mesquiteDirectoryPath = mesquiteFolder;
}
Modified: trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml 2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml 2010-02-09 20:51:58 UTC (rev 487)
@@ -28,6 +28,12 @@
<property name="numHelperThreads" value="5" />
</bean>
+ <bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+ <property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
+ </bean>
</beans>
Modified: trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml 2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml 2010-02-09 20:51:58 UTC (rev 487)
@@ -13,4 +13,10 @@
<property name="jndiName" value="java:comp/env/jdbc/TreebaseDB"/>
</bean>
+ <bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+ <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
+ <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+ </bean>
+
</beans>
\ No newline at end of file
Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml 2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml 2010-02-09 20:51:58 UTC (rev 487)
@@ -137,13 +137,14 @@
<property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
<property name="taxonLabelHome" ref="taxonLabelHome"/>
</bean-->
-
+
+<!-- VG 2010-02-09 nexusService bean is now set in applicationContext-db-webappp.xml and in applicationContext-db-standalone.xml
<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
<property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
<property name="taxonLabelHome" ref="taxonLabelHome"/>
<property name="itemDefinitionHome" ref="itemDefinitionHome"/>
</bean>
-
+-->
<bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
<!-- property name="domainHome" ref="domainHome"/ -->
<property name="taxonLabelHome" ref="taxonLabelHome"/>
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|
|
From: <vga...@us...> - 2010-02-25 15:32:39
|
Revision: 518
http://treebase.svn.sourceforge.net/treebase/?rev=518&view=rev
Author: vgapeyev
Date: 2010-02-25 15:32:32 +0000 (Thu, 25 Feb 2010)
Log Message:
-----------
Fixed run-time errors caused by improper transaction handling.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java
trunk/treebase-core/src/main/resources/applicationContext-standalone.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java 2010-02-25 15:32:32 UTC (rev 518)
@@ -112,8 +112,8 @@
person.setFirstName(nameParts[1]);
person.setMiddleName("");
person.setEmailAddressString("");
- personHome.save(person);
- personHome.store(person);
+ //personHome.save(person); //-- VG 2010-02-24 These were messing up parent transactions by
+ //personHome.store(person); //-- VG saving too early.
}
warn(person.getLastName());
authors.add(person);
@@ -263,18 +263,136 @@
in = new BufferedReader(
new InputStreamReader(new FileInputStream(inFileName), "UTF8"));
- me.processCitationFile(in, testmode);
+ //me.processCitationFile(in, testmode); //VG-2010-02-25 now deprecated
+ me.processAllCitations(in, testmode);
}
catch ( Exception e ) {
e.printStackTrace();
}
}
+ /** Go through the open citation file and transactionally save each successfully processed citation.
+ * Processing stops on error, with prior transactions committed.
+ * Derived from the deprecated processCitationsFile by factoring out most of the while-loop code
+ * into its own method, so that Spring can make it transactional.
+ */
+ public void processAllCitations(BufferedReader in, boolean testMode) throws NumberFormatException, IOException {
+ String line;
+ while ( ( line = in.readLine()) != null ) {
+ String[] fields = line.split("\t");
+ processOneCitation(fields, testMode);
+ }
+ in.close();
+ }
+
+ /** Process one citation from the file and save the result transactionally.
+ * This method is declared PROPAGATION_REQUIRES_NEW in the bean descriptor.
+ */
+ public void processOneCitation(String[] fields, boolean testMode) throws NumberFormatException, IOException {
+ if ( fields[0].startsWith("*") ) {
+ warn("Line is commented out, skipping");
+ return;
+ }
+ String tb1StudyId = fields[18];
+ Study study = findStudy(tb1StudyId);
+ if ( study == null ) {
+ warn("No such study (TB1 accession): " + tb1StudyId);
+ return;
+ }
+ Citation citationStub = study.getCitation();
+ Citation citation = null;
+ if ( citationStub != null ) {
+ warn("Study "+tb1StudyId+" already associated with a citation "+citationStub.getId());
+// In general, citation stubs already exist for each study. However, these
+// stubs are all of type ArticleCitation, which means that, in the case of
+// BookCitations (for example) we'll get a class cast exception when we try
+// to cast the citation to a book in order to set the editors.
+ //getCitationService().deleteCitation(citationStub);
+ //citation = createCitation(fields[0]);
+ citation = citationStub;
+ }
+ else {
+ warn("No citation stub association with study (TB1 accession) " + tb1StudyId);
+ citation = createCitation(fields[0]);
+ }
+ if ( citation == null ) {
+ warn("No citation was instantiated, skipping this record (TB1 accession) "+tb1StudyId);
+ return;
+ }
+ for ( int i = 0; i < fields.length; i++ ) {
+ if ( ! TreebaseUtil.isEmpty(fields[i]) ) {
+ switch(i) {
+ case 0: citation.setCitationType(fields[i]); break;
+ case 1: setAuthors(citation,fields[i],personHome,false); break;
+ case 2: citation.setPublishYear(Integer.parseInt(fields[i])); break;
+ case 3: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setBookTitle(fields[i]);
+ citation.setTitle(fields[i]);
+ } else {
+ citation.setTitle(fields[i]);
+ } break;
+ case 4: setAuthors(citation,fields[i],personHome,true); break;
+ case 5: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setJournal(fields[i]);
+ warn("Setting journal name "+fields[i]);
+ } else {
+ warn("Setting book title "+fields[i]);
+ ((BookCitation)citation).setBookTitle(fields[i]);
+ } break;
+ case 6: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setCity(fields[i]);
+ } else {
+ warn("Record has an entry for city, yet it's not a book (TB1 accession) "+tb1StudyId);
+ } break;
+ case 7: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setPublisher(fields[i]);
+ } else {
+ warn("Record has an entry for publisher, yet it's not a book (TB1 accession) "+tb1StudyId);
+ } break;
+ case 8: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setVolume(fields[i]);
+ } else {
+ warn("Record has an entry for volume, yet it's not an article (TB1 accession) "+tb1StudyId);
+ } break;
+ case 10: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setIssue(fields[i]);
+ } else {
+ warn("Record has an entry for issue, yet it's not an article (TB1 accession)"+tb1StudyId);
+ } break;
+ case 11: citation.setPages(fields[i]); break;
+ case 15: if ( fields[i].equals("in press") ) {
+ citation.setCitationStatusDescription(CitationStatus.INPRESS);
+ }
+ case 16: citation.setKeywords(fields[i]); break;
+ case 17: citation.setAbstract(checkAbstractLength(fields[i])); break;
+ case 18: citation.setStudy(study); break;
+ case 19: citation.setURL(fields[i]); break;
+ case 20: citation.setDoi(fields[i]); break;
+ default: warn("Empty field expected, found: " + fields[i] + " for line: " + /*was: line */fields.toString()); break;
+ }
+ }
+ }
+ warn("Storing citation "+citation.getId());
+ warn(citation.getAuthorsCitationStyleWithoutHtml());
+ if ( ! testMode ) {
+ study.setCitation(citation);
+ getStudyService().update(study);
+ Long id = study.getCitation().getId();
+ warn("Stored citation at ID " + id);
+ }
+ else {
+ warn("Test run, not saving");
+ }
+ }
+
/**
- *
- *
- * @see org.cipres.treebase.util.CitationDataImporterInterface#processCitationFile(java.io.BufferedReader, boolean)
+ * Deprecated, use processAllCitations() instead.
+ * The programmatic transaction handling via the commit(); beginTransaction(); pair at the end of this method
+ * was leaving an open transaction, leading to an exception. Also, the "-test" command line switch had no effect.
+ * Instead, fine-grained transactions (for each citation) are now achieved by embracing Spring's declarative
+ * transactions: transactions are at boundaries of designated methods. VG-2010-02-25
*/
+ @Deprecated
public void processCitationFile(BufferedReader in, boolean testMode) throws NumberFormatException, IOException {
String line;
Long maxId = new Long(0);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java 2010-02-25 15:32:32 UTC (rev 518)
@@ -24,4 +24,7 @@
public void setCitationHome(CitationHome citationHome);
public void processCitationFile(BufferedReader in, boolean testMode) throws NumberFormatException, IOException;
+ public void processAllCitations(BufferedReader in, boolean testMode) throws NumberFormatException, IOException;
+ public void processOneCitation(String[] fields, boolean testMode) throws NumberFormatException, IOException;
+
}
Modified: trunk/treebase-core/src/main/resources/applicationContext-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-standalone.xml 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/resources/applicationContext-standalone.xml 2010-02-25 15:32:32 UTC (rev 518)
@@ -222,6 +222,8 @@
<property name="transactionAttributes">
<props>
<prop key="processCitationFile">PROPAGATION_REQUIRED</prop>
+ <prop key="processOneCitation">PROPAGATION_REQUIRES_NEW</prop>
+ <prop key="processAllCitations">PROPAGATION_SUPPORTS</prop>
</props>
</property>
</bean>
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|
|
From: <hs...@us...> - 2011-04-14 21:10:00
|
Revision: 784
http://treebase.svn.sourceforge.net/treebase/?rev=784&view=rev
Author: hshyket
Date: 2011-04-14 21:09:54 +0000 (Thu, 14 Apr 2011)
Log Message:
-----------
Setting limit for the number of trees allowed in a block. This is set in the treebase.properties file.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
trunk/treebase-core/src/main/resources/applicationContext-service.xml
trunk/treebase-core/src/main/resources/treebase.properties
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-04-14 21:09:54 UTC (rev 784)
@@ -7,7 +7,10 @@
import java.util.Collection;
import java.util.Date;
import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
import org.apache.log4j.Logger;
import org.cipres.treebase.dao.jdbc.MatrixJDBC;
import org.cipres.treebase.dao.jdbc.NexusDataSetJDBC;
@@ -65,6 +68,8 @@
private CitationService mCitationService;
private StudyService mStudyService;
private NexusService mNexusService;
+
+ private int mMaxTreeCount;
/**
* Constructor.
@@ -297,8 +302,25 @@
return sub;
}
+
+ /**
+ * Return the MaxTreeCount field.
+ *
+ * @return MatrixDataTypeHome mMatrixDataTypeHome
+ */
+ private int getMaxTreeCount() {
+ return mMaxTreeCount;
+ }
/**
+ * Set the MaxTreeCount field.
+ */
+ public void setMaxTreeCount(int maxTreeCount) {
+ mMaxTreeCount = maxTreeCount;
+ }
+
+
+ /**
*
* @see org.cipres.treebase.domain.study.SubmissionService#createSubmission(org.cipres.treebase.domain.admin.User,
* org.cipres.treebase.domain.study.Study)
@@ -680,8 +702,30 @@
// alltrees.addAll(block.getTreeList());
// }
// getPhyloTreeHome().storeAll(alltrees);
+
+
+ //If there are more than the number of trees in getMaxTreeCount trees in a TreeBlock we need to remove them
+ for (TreeBlock treeblock : data.getTreeBlocks()) {
+ if (treeblock.getTreeCount() > getMaxTreeCount()) {
+ Iterator tree = treeblock.getTreeListIterator();
+ int treecount = 1;
+
+ while(tree.hasNext()) {
+ if (treecount > getMaxTreeCount()) {
+ tree.remove();
+ }
+ tree.next();
+ treecount++;
+ }
+ }
+ }
+
getPhyloTreeHome().storeAll(data.getTreeBlocks());
sub.addPhyloTreeBlocks(data.getTreeBlocks());
+
+
+
+
getPhyloTreeHome().flush();
update(sub);
Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml 2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml 2011-04-14 21:09:54 UTC (rev 784)
@@ -243,6 +243,7 @@
<property name="taxonHome" ref="taxonHome"/>
<property name="taxonLabelHome" ref="taxonLabelHome"/>
<property name="userHome" ref="userHome"/>
+ <property name="maxTreeCount" value="${treeblock.trees.max_count}"/>
</bean>
</property>
</bean>
Modified: trunk/treebase-core/src/main/resources/treebase.properties
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.properties 2011-04-12 20:16:48 UTC (rev 783)
+++ trunk/treebase-core/src/main/resources/treebase.properties 2011-04-14 21:09:54 UTC (rev 784)
@@ -1,6 +1,9 @@
#options are: NexusServiceMesquite | NexusServiceNCL
nexus.parser.impl=NexusServiceMesquite
+#The number of trees allowed in a treeblock
+treeblock.trees.max_count=30
+
########################################################################
### Prior to 2010-04-29, these were in jdbc.properties,
### which now contains only properties not used by the web app
@@ -18,6 +21,8 @@
hibernate.format_sql=true
hibernate.generate_statistics=false
+
+
# options are: validate | update | create | create-drop
hibernate.hbm2ddl.auto=
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|
From: <hs...@us...> - 2011-12-09 15:00:30
|
Revision: 1001
http://treebase.svn.sourceforge.net/treebase/?rev=1001&view=rev
Author: hshyket
Date: 2011-12-09 15:00:21 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
Setting the study id for matrices on upload and setting the database creation script to have NOT NULL for the study id in the matrix table
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-08 22:15:08 UTC (rev 1000)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-09 15:00:21 UTC (rev 1001)
@@ -693,6 +693,9 @@
// Store matrice:
getMatrixHome().persistAll(data.getMatrices());
+ for (Matrix uploadMatrix : data.getMatrices()) {
+ uploadMatrix.setStudy(sub.getStudy());
+ }
sub.addMatrices(data.getMatrices());
getMatrixHome().flush();
Modified: trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
===================================================================
--- trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2011-12-08 22:15:08 UTC (rev 1000)
+++ trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2011-12-09 15:00:21 UTC (rev 1001)
@@ -526,7 +526,7 @@
casesensitive smallint,
matrixdatatype_id bigint,
matrixkind_id bigint,
- study_id bigint,
+ study_id bigint NOT NULL,
taxonlabelset_id bigint,
ancstateset_id bigint,
codonpositionset_id bigint,
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