Commit cf545cfe authored by Keith Jolley's avatar Keith Jolley

Rationalise module use.

parent 0affbc6d
......@@ -31,76 +31,12 @@ use constant {
};
#######End Local configuration###############################################
use CGI;
use DBI;
use XML::Parser::PerlSAX;
use Log::Log4perl qw(get_logger); #Also need Log::Dispatch::File
use Error qw(:try);
use lib (LIB_DIR);
use BIGSdb::Application;
use BIGSdb::Curate;
use BIGSdb::Parser;
use BIGSdb::Dataconnector;
use BIGSdb::Datastore;
use BIGSdb::Utils;
use BIGSdb::Preferences;
use BIGSdb::Scheme;
use BIGSdb::Locus;
use BIGSdb::BIGSException;
use BIGSdb::Page;
use BIGSdb::IsolateInfoPage;
use BIGSdb::PubQueryPage;
use BIGSdb::SeqbinPage;
use BIGSdb::SeqbinToEMBL;
use BIGSdb::ExtractedSequencePage;
use BIGSdb::ErrorPage;
use BIGSdb::CuratePage;
use BIGSdb::CurateIndexPage;
use BIGSdb::CurateAddPage;
use BIGSdb::CurateDeletePage;
use BIGSdb::CurateDeleteAllPage;
use BIGSdb::CurateLinkToExperimentPage;
use BIGSdb::CurateUpdatePage;
use BIGSdb::CurateIsolateAddPage;
use BIGSdb::CurateIsolateDeletePage;
use BIGSdb::CurateBatchIsolateUpdatePage;
use BIGSdb::QueryPage;
use BIGSdb::BrowsePage;
use BIGSdb::ListQueryPage;
use BIGSdb::CurateIsolateUpdatePage;
use BIGSdb::CurateProfileAddPage;
use BIGSdb::CurateProfileUpdatePage;
use BIGSdb::CurateProfileBatchAddPage;
use BIGSdb::CuratePubmedQueryPage;
use BIGSdb::CurateBatchAddPage;
use BIGSdb::CurateBatchAddSeqbinPage;
use BIGSdb::CurateTableHeaderPage;
use BIGSdb::CurateCompositeQueryPage;
use BIGSdb::CurateCompositeUpdatePage;
use BIGSdb::CurateAlleleUpdatePage;
use BIGSdb::CurateTagScanPage;
use BIGSdb::CurateTagUpdatePage;
use BIGSdb::CurateDatabankScanPage;
use BIGSdb::CurateRenumber;
use BIGSdb::PluginManager;
use BIGSdb::ConfigCheckPage;
use BIGSdb::ConfigRepairPage;
use BIGSdb::LoginMD5;
use BIGSdb::ChangePasswordPage;
use BIGSdb::ProfileInfoPage;
use BIGSdb::AlleleInfoPage;
use BIGSdb::CurateIsolateACLPage;
use BIGSdb::ClientDB;
use BIGSdb::FieldHelpPage;
use BIGSdb::TableQueryPage;
use BIGSdb::DownloadSeqbinPage;
use BIGSdb::AlleleSequencePage;
use BIGSdb::OfflineJobManager;
use BIGSdb::OptionsPage;
use BIGSdb::CurateExportConfig;
my $r = shift; #Apache request object (used for mod_perl)
Log::Log4perl->init_once(CONFIG_DIR . '/logging.conf');
BIGSdb::Curate->new( CONFIG_DIR, LIB_DIR,DBASE_CONFIG_DIR, $r,1 );
BIGSdb::Curate->new( CONFIG_DIR, LIB_DIR,DBASE_CONFIG_DIR, $r, 1 );
......@@ -32,55 +32,10 @@ use constant {
};
#######End Local configuration################################
use CGI;
use DBI;
use Log::Log4perl qw(get_logger); #Also need Log::Dispatch::File
use Error qw(:try);
use lib (LIB_DIR);
use BIGSdb::Application;
use BIGSdb::Parser;
use BIGSdb::Utils;
use BIGSdb::Dataconnector;
use BIGSdb::Datastore;
use BIGSdb::Preferences;
use BIGSdb::Scheme;
use BIGSdb::Locus;
use BIGSdb::Page;
use BIGSdb::IndexPage;
use BIGSdb::ErrorPage;
use BIGSdb::BrowsePage;
use BIGSdb::IsolateInfoPage;
use BIGSdb::ProfileInfoPage;
use BIGSdb::VersionPage;
use BIGSdb::QueryPage;
use BIGSdb::TableQueryPage;
use BIGSdb::OptionsPage;
use BIGSdb::PubQueryPage;
use BIGSdb::ProfileQueryPage;
use BIGSdb::BatchProfileQueryPage;
use BIGSdb::DownloadAllelesPage;
use BIGSdb::DownloadProfilesPage;
use BIGSdb::DownloadSeqbinPage;
use BIGSdb::SeqbinPage;
use BIGSdb::ListQueryPage;
use BIGSdb::SequenceQueryPage;
use BIGSdb::CustomizePage;
use BIGSdb::RecordInfoPage;
use BIGSdb::BIGSException;
use BIGSdb::PluginManager;
use BIGSdb::Plugin;
use BIGSdb::SeqbinToEMBL;
use BIGSdb::AlleleSequencePage;
use BIGSdb::LoginMD5;
use BIGSdb::ChangePasswordPage;
use BIGSdb::AlleleInfoPage;
use BIGSdb::ClientDB;
use BIGSdb::FieldHelpPage;
use BIGSdb::ExtractedSequencePage;
use BIGSdb::AlleleQueryPage;
use BIGSdb::LocusInfoPage;
use BIGSdb::OfflineJobManager;
use BIGSdb::JobViewerPage;
my $r = shift; #Apache request object (used for mod_perl)
Log::Log4perl->init_once( CONFIG_DIR . '/logging.conf' );
......
#Written by Keith Jolley
#(c) 2010-2011, University of Oxford
#(c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -19,6 +19,43 @@
package BIGSdb::Application;
use strict;
use warnings;
use BIGSdb::AlleleInfoPage;
use BIGSdb::AlleleQueryPage;
use BIGSdb::AlleleSequencePage;
use BIGSdb::BatchProfileQueryPage;
use BIGSdb::BIGSException;
use BIGSdb::BrowsePage;
use BIGSdb::ChangePasswordPage;
use BIGSdb::CustomizePage;
use BIGSdb::Dataconnector;
use BIGSdb::Datastore;
use BIGSdb::DownloadAllelesPage;
use BIGSdb::DownloadProfilesPage;
use BIGSdb::DownloadSeqbinPage;
use BIGSdb::ErrorPage;
use BIGSdb::FieldHelpPage;
use BIGSdb::IndexPage;
use BIGSdb::IsolateInfoPage;
use BIGSdb::JobViewerPage;
use BIGSdb::ListQueryPage;
use BIGSdb::LocusInfoPage;
use BIGSdb::LoginMD5;
use BIGSdb::OptionsPage;
use BIGSdb::Parser;
use BIGSdb::PluginManager;
use BIGSdb::Preferences;
use BIGSdb::ProfileInfoPage;
use BIGSdb::ProfileQueryPage;
use BIGSdb::PubQueryPage;
use BIGSdb::QueryPage;
use BIGSdb::RecordInfoPage;
use BIGSdb::SeqbinPage;
use BIGSdb::SeqbinToEMBL;
use BIGSdb::SequenceQueryPage;
use BIGSdb::TableQueryPage;
use BIGSdb::VersionPage;
use CGI;
use DBI;
use Error qw(:try);
use Log::Log4perl qw(get_logger);
use Config::Tiny;
......
#Written by Keith Jolley
#Copyright (c) 2010-2011, University of Oxford
#Copyright (c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -20,6 +20,36 @@ package BIGSdb::Curate;
use strict;
use warnings;
use base qw(BIGSdb::Application);
use BIGSdb::ConfigCheckPage;
use BIGSdb::ConfigRepairPage;
use BIGSdb::CurateAddPage;
use BIGSdb::CurateAlleleUpdatePage;
use BIGSdb::CurateBatchAddPage;
use BIGSdb::CurateBatchAddSeqbinPage;
use BIGSdb::CurateBatchIsolateUpdatePage;
use BIGSdb::CurateCompositeQueryPage;
use BIGSdb::CurateCompositeUpdatePage;
use BIGSdb::CurateDatabankScanPage;
use BIGSdb::CurateDeleteAllPage;
use BIGSdb::CurateDeletePage;
use BIGSdb::CurateExportConfig;
use BIGSdb::CurateIndexPage;
use BIGSdb::CurateIsolateACLPage;
use BIGSdb::CurateIsolateAddPage;
use BIGSdb::CurateIsolateDeletePage;
use BIGSdb::CurateIsolateUpdatePage;
use BIGSdb::CurateLinkToExperimentPage;
use BIGSdb::CuratePage;
use BIGSdb::CurateProfileAddPage;
use BIGSdb::CurateProfileBatchAddPage;
use BIGSdb::CurateProfileUpdatePage;
use BIGSdb::CuratePubmedQueryPage;
use BIGSdb::CurateRenumber;
use BIGSdb::CurateTableHeaderPage;
use BIGSdb::CurateTagScanPage;
use BIGSdb::CurateTagUpdatePage;
use BIGSdb::CurateUpdatePage;
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -24,6 +24,7 @@ use List::MoreUtils qw(any);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Datastore');
use BIGSdb::Page qw(SEQ_METHODS DATABANKS SEQ_FLAGS);
use BIGSdb::ClientDB;
use BIGSdb::Locus;
use BIGSdb::Scheme;
......
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