[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Wed Mar 19 16:55:35 UTC 2008
kawas
Wed Mar 19 12:55:35 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv28455/Perl/MOBY-Server/bin/scripts
Modified Files:
moby-s-install.pl
Log Message:
fixed bug where authority script wasnt being installed by script
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/03/06 16:44:55 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/03/19 16:55:35 1.3
@@ -90,7 +90,7 @@
check_module('WSRF::Lite');
check_module('Crypt::OpenSSL::X509');
check_module('IPC::Shareable');
- }
+ }
if ($errors_found) {
say "\nSorry, some needed modules were not found.";
@@ -131,20 +131,24 @@
}
sub prompt_for_directory_expand {
- my ($prompt, $prompted_dir) = @_;
- while (1) {
- my $dir = pprompt ("$prompt [$prompted_dir] ");
- $dir =~ s/^\s*//; $dir =~ s/\s*$//;
- $dir = $prompted_dir unless $dir;
- return $dir if -d $dir and -w $dir; # okay: writable directory
- $prompted_dir = $dir;
- next if -e $dir and say "'$dir' is not a writable directory. Try again please.";
- next unless pprompt ("Directory '$dir' does not exists. Create? ", -yn);
-
- # okay, we agreed to create it
- mkdir ($dir, 0755 )and return $dir;
- say "'$dir' not created: $!";
- }
+ my ( $prompt, $prompted_dir ) = @_;
+ while (1) {
+ my $dir = pprompt("$prompt [$prompted_dir] ");
+ $dir =~ s/^\s*//;
+ $dir =~ s/\s*$//;
+ $dir = $prompted_dir unless $dir;
+ return $dir if -d $dir and -w $dir; # okay: writable directory
+ $prompted_dir = $dir;
+ next
+ if -e $dir
+ and say "'$dir' is not a writable directory. Try again please.";
+ next
+ unless pprompt( "Directory '$dir' does not exists. Create? ", -yn );
+
+ # okay, we agreed to create it
+ mkdir( $dir, 0755 ) and return $dir;
+ say "'$dir' not created: $!";
+ }
}
sub prompt_user_input {
@@ -186,11 +190,14 @@
if ($@) {
say "ERROR: $file_desc was (probably) not created.\n$@";
} else {
- say "\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
+ say
+"\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
}
+
# try to make file executable
eval {
- my $mode = 0655; chmod $mode, "$file";
+ my $mode = 0655;
+ chmod $mode, "$file";
};
}
@@ -472,8 +479,7 @@
prompt_for_directory( "What is the path of the apache 'cgi-bin' directory?",
"$apache_base/cgi-bin" );
$perl_exec =
- prompt_user_input( "What is the path to your perl executable?",
- $perl_exec );
+ prompt_user_input( "What is the path to your perl executable?", $perl_exec );
$perl_exec = "$perl_exec -w";
say "\nusing $apache_base as base directory ...";
@@ -540,7 +546,7 @@
'MOBY', 'cgi/MOBY-Central.pl'
),
'MOBY-Central Dispatch file',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
);
file_from_template(
"$apache_cgi/OntologyServer.cgi",
@@ -548,8 +554,9 @@
'MOBY', 'cgi/OntologyServer.cgi'
),
'MOBY-Central Ontology Server file',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
);
+
#install the moby-admin module
file_from_template(
"$apache_cgi/MOBY-Admin.pl",
@@ -557,7 +564,7 @@
'MOBY', 'cgi/MOBY-Admin.pl'
),
'MOBY-Admin Dispatch file',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
);
# configure httpd.conf
@@ -662,12 +669,18 @@
do {
my $ready_to_go = 0;
- my $sql_error = 0;
+ my $sql_error = 0;
+
#check to see if we can call mysql ... if not, then die!
- print "mysql is installed ...\n" if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
- print "mysql is started ...\n" unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/ ;
+ print "mysql is installed ...\n"
+ if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
+ print "mysql is started ...\n"
+ unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/;
- unless ( `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/ and not (`mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/) ) {
+ unless ( `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/
+ and not( `mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/ )
+ )
+ {
say
"\nmysql doesn't seem to be accessible ... please ensure that it is on the path, started and try again.\n";
$sql_error = 1;
@@ -675,274 +688,278 @@
# proceed if mysql check was good
do {
- # have the values been set already?
- $ready_to_go = 1
- if $username
- and $url
- and $port
- and $m_object
- and $m_relationship
- and $m_service
- and $m_namespace
- and $m_central;
+
+ # have the values been set already?
+ $ready_to_go = 1
+ if $username
+ and $url
+ and $port
+ and $m_object
+ and $m_relationship
+ and $m_service
+ and $m_namespace
+ and $m_central;
#check to see if mobycentral.config has been created in the conf directory first -> if so, parse it
- if ( -e "$apache_conf/mobycentral.config"
- && !( -d "$apache_conf/mobycentral.config" )
- && !$ready_to_go )
- {
- my %db_sections = ();
- open IN, "$apache_conf/mobycentral.config"
- or die
+ if ( -e "$apache_conf/mobycentral.config"
+ && !( -d "$apache_conf/mobycentral.config" )
+ && !$ready_to_go )
+ {
+ my %db_sections = ();
+ open IN, "$apache_conf/mobycentral.config"
+ or die
"can't open MOBY Configuration file '$apache_conf/mobycentral.config' for unknown reasons: $!\n";
- my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
- foreach my $section (@sections) {
- my $dbConfig = MOBY::dbConfig->new( section => $section );
- next unless $dbConfig;
- my $dbname = $dbConfig->section_title;
- next unless $dbname;
- $db_sections{$dbname} = $dbConfig;
- }
+ my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+ foreach my $section (@sections) {
+ my $dbConfig = MOBY::dbConfig->new( section => $section );
+ next unless $dbConfig;
+ my $dbname = $dbConfig->section_title;
+ next unless $dbname;
+ $db_sections{$dbname} = $dbConfig;
+ }
- $username = $db_sections{mobycentral}->{username};
- $password = $db_sections{mobycentral}->{password} || "";
- $url = $db_sections{mobycentral}->{url};
- $port = $db_sections{mobycentral}->{port};
- $m_object = $db_sections{mobyobject}->{dbname};
- $m_relationship = $db_sections{mobyrelationship}->{dbname};
- $m_service = $db_sections{mobyservice}->{dbname};
- $m_namespace = $db_sections{mobynamespace}->{dbname};
- $m_central = $db_sections{mobycentral}->{dbname};
+ $username = $db_sections{mobycentral}->{username};
+ $password = $db_sections{mobycentral}->{password} || "";
+ $url = $db_sections{mobycentral}->{url};
+ $port = $db_sections{mobycentral}->{port};
+ $m_object = $db_sections{mobyobject}->{dbname};
+ $m_relationship = $db_sections{mobyrelationship}->{dbname};
+ $m_service = $db_sections{mobyservice}->{dbname};
+ $m_namespace = $db_sections{mobynamespace}->{dbname};
+ $m_central = $db_sections{mobycentral}->{dbname};
- $ready_to_go = 1;
- }
+ $ready_to_go = 1;
+ }
- # if the values havent been set, then prompt for them
- do {
+ # if the values havent been set, then prompt for them
+ do {
- say " Installing the file '$apache_conf/mobycentral.config' ...";
+ say " Installing the file '$apache_conf/mobycentral.config' ...";
- # fill out mobycentral.config
- (
- $username, $password, $url,
- $port, $m_object, $m_relationship,
- $m_service, $m_namespace, $m_central
- )
- = prompt_moby_config_info;
- fill_out_moby_conf(
- "$apache_conf/mobycentral.config",
- $username, $password, $url,
- $port, $m_object, $m_relationship,
- $m_service, $m_namespace, $m_central
- );
+ # fill out mobycentral.config
+ (
+ $username, $password, $url,
+ $port, $m_object, $m_relationship,
+ $m_service, $m_namespace, $m_central
+ )
+ = prompt_moby_config_info;
+ fill_out_moby_conf(
+ "$apache_conf/mobycentral.config",
+ $username, $password, $url,
+ $port, $m_object, $m_relationship,
+ $m_service, $m_namespace, $m_central
+ );
- } unless $ready_to_go;
+ } unless $ready_to_go;
- # now start creating the tables
- say " creating the tables to use for the registry ...";
- my %dbsections = (
- 'mobycentral' => $m_central,
- 'mobyobject' => $m_object,
- 'mobyservice' => $m_service,
- 'mobynamespace' => $m_namespace,
- 'mobyrelationship' => $m_relationship
- );
+ # now start creating the tables
+ say " creating the tables to use for the registry ...";
+ my %dbsections = (
+ 'mobycentral' => $m_central,
+ 'mobyobject' => $m_object,
+ 'mobyservice' => $m_service,
+ 'mobynamespace' => $m_namespace,
+ 'mobyrelationship' => $m_relationship
+ );
- my $clone = 0;
- my $central;
- do {
- $clone = 1;
- my %registries = (
- default => {
- url =>
-"http://moby.ucalgary.ca/moby/MOBY-Central.pl",
- uri => "http://moby.ucalgary.ca/MOBY/Central"
- },
- testing => {
- url =>
+ my $clone = 0;
+ my $central;
+ do {
+ $clone = 1;
+ my %registries = (
+ default => {
+ url => "http://moby.ucalgary.ca/moby/MOBY-Central.pl",
+ uri => "http://moby.ucalgary.ca/MOBY/Central"
+ },
+ testing => {
+ url =>
"http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl",
- uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
- },
- IRRI => {
+ uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
+ },
+ IRRI => {
url => "http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl",
uri => "http://cropwiki.irri.org/MOBY/Central"
- },
+ },
- # localhost => {
- # url=>"http://localhost/cgi-bin/MOBY-Central.pl",
- # uri=>"http://localhost/MOBY/Central"
- # },
- );
- my $registry = pprompt( "What registry to use? [b] ",
- -m => [ sort keys %registries ] );
+ # localhost => {
+ # url=>"http://localhost/cgi-bin/MOBY-Central.pl",
+ # uri=>"http://localhost/MOBY/Central"
+ # },
+ );
+ my $registry = pprompt( "What registry to use? [b] ",
+ -m => [ sort keys %registries ] );
- $central = MOBY::Client::Central->new(
+ $central = MOBY::Client::Central->new(
Registries => {
mobycentral => {
URL => $registries{$registry}{url},
URI => $registries{$registry}{uri}
}
}
- );
- }
- if pprompt( "Would you like to clone a mobycentral registry? [n] ",
- -ynd => 'n' ) eq 'y';
- my $error = 0;
- if ($clone) {
- say "Getting db dumps ...";
- my (
- $mobycentral, $mobyobject, $mobyservice,
- $mobynamespace, $mobyrelationship
- )
- = $central->MOBY::Client::Central::DUMP();
- my $drh = DBI->install_driver("mysql");
-
- my ( $fh, $filename ) = tempfile( UNLINK => 1 );
- say "Processing dump for service instances ...";
- print $fh $mobycentral;
- eval {
- $drh->func( 'dropdb', $dbsections{mobycentral},
- $url, $username, $password, 'admin' );
- };
- eval {
- $drh->func( 'createdb', $dbsections{mobycentral},
- $url, $username, $password, 'admin' );
- };
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{mobycentral}
- . "<$filename" ) == 0
- or ( say "Error populating service instance ontology ...\n$!"
- and $error++ );
-
- ( $fh, $filename ) = tempfile( UNLINK => 1 );
- say "Processing dump for the objects ontology ...";
- print $fh $mobyobject;
- eval {
- $drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
- $password, 'admin' );
- };
- eval {
- $drh->func( 'createdb', $dbsections{mobyobject}, $url, $username,
- $password, 'admin' );
- };
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{mobyobject}
- . "<$filename" ) == 0
- or ( say "Error populating objects ontology ...\n$!" and $error++ );
-
- ( $fh, $filename ) = tempfile( UNLINK => 1 );
- say "Processing dump for service types ...";
- print $fh $mobyservice;
- eval {
- $drh->func( 'dropdb', $dbsections{mobyservice},
- $url, $username, $password, 'admin' );
- };
- eval {
- $drh->func( 'createdb', $dbsections{mobyservice},
- $url, $username, $password, 'admin' );
- };
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{mobyservice}
- . "<$filename" ) == 0
- or ( say "Error populating service types ontology ...\n$!"
- and $error++ );
-
- ( $fh, $filename ) = tempfile( UNLINK => 1 );
- say "Processing dump for the namespace ontology ...";
- print $fh $mobynamespace;
- eval {
- $drh->func( 'dropdb', $dbsections{mobynamespace},
- $url, $username, $password, 'admin' );
- };
- eval {
- $drh->func( 'createdb', $dbsections{mobynamespace},
- $url, $username, $password, 'admin' );
- };
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{mobynamespace}
- . "<$filename" ) == 0
- or ( say "Error populating namespace ontology ...\n$!" and $error++ );
-
- ( $fh, $filename ) = tempfile( UNLINK => 1 );
- say "Processing dump for the relationships ontology ...";
- print $fh $mobyrelationship;
- eval {
- $drh->func( 'dropdb', $dbsections{mobyrelationship},
- $url, $username, $password, 'admin' );
- };
- eval {
- $drh->func( 'createdb', $dbsections{mobyrelationship},
- $url, $username, $password, 'admin' );
- };
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{mobyrelationship}
- . "<$filename" ) == 0
- or ( say "Error populating relationships ontology ...\n$!"
- and $error++ );
-
- } else {
-
- # no clone, so create minimalist databases
- my $drop_db = 0;
-
- #ask for permission on dropping data from db ...
- do {
- $drop_db = 1;
+ );
}
- if pprompt(
- "Shall I drop all pre-existing databases used by BioMOBY? [n] ",
- -ynd => 'n' ) eq 'y';
-
- #process each db
- foreach my $section ( keys %dbsections ) {
- my $sqlfilepath =
- File::ShareDir::dist_file( 'MOBY', "db/schema/$section.mysql" );
+ if pprompt( "Would you like to clone a mobycentral registry? [n] ",
+ -ynd => 'n' ) eq 'y';
+ my $error = 0;
+ if ($clone) {
+ say "Getting db dumps ...";
+ my (
+ $mobycentral, $mobyobject, $mobyservice,
+ $mobynamespace, $mobyrelationship
+ )
+ = $central->MOBY::Client::Central::DUMP();
my $drh = DBI->install_driver("mysql");
- # drop the db
+ my ( $fh, $filename ) = tempfile( UNLINK => 1 );
+ say "Processing dump for service instances ...";
+ print $fh $mobycentral;
eval {
- $drh->func( 'dropdb', $dbsections{$section}, $url, $username,
- $password, 'admin' );
- } if $drop_db;
-
- # create the db
+ $drh->func( 'dropdb', $dbsections{mobycentral},
+ $url, $username, $password, 'admin' );
+ };
eval {
- $drh->func( 'createdb', $dbsections{$section}, $url, $username,
+ $drh->func( 'createdb', $dbsections{mobycentral},
+ $url, $username, $password, 'admin' );
+ };
+ system( "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{mobycentral}
+ . "<$filename" ) == 0
+ or ( say "Error populating service instance ontology ...\n$!"
+ and $error++ );
+
+ ( $fh, $filename ) = tempfile( UNLINK => 1 );
+ say "Processing dump for the objects ontology ...";
+ print $fh $mobyobject;
+ eval {
+ $drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
$password, 'admin' );
};
+ eval {
+ $drh->func( 'createdb', $dbsections{mobyobject}, $url,
+ $username, $password, 'admin' );
+ };
+ system( "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{mobyobject}
+ . "<$filename" ) == 0
+ or
+ ( say "Error populating objects ontology ...\n$!" and $error++ );
+
+ ( $fh, $filename ) = tempfile( UNLINK => 1 );
+ say "Processing dump for service types ...";
+ print $fh $mobyservice;
+ eval {
+ $drh->func( 'dropdb', $dbsections{mobyservice},
+ $url, $username, $password, 'admin' );
+ };
+ eval {
+ $drh->func( 'createdb', $dbsections{mobyservice},
+ $url, $username, $password, 'admin' );
+ };
+ system( "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{mobyservice}
+ . "<$filename" ) == 0
+ or ( say "Error populating service types ontology ...\n$!"
+ and $error++ );
+
+ ( $fh, $filename ) = tempfile( UNLINK => 1 );
+ say "Processing dump for the namespace ontology ...";
+ print $fh $mobynamespace;
+ eval {
+ $drh->func( 'dropdb', $dbsections{mobynamespace},
+ $url, $username, $password, 'admin' );
+ };
+ eval {
+ $drh->func( 'createdb', $dbsections{mobynamespace},
+ $url, $username, $password, 'admin' );
+ };
+ system( "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{mobynamespace}
+ . "<$filename" ) == 0
+ or ( say "Error populating namespace ontology ...\n$!"
+ and $error++ );
+
+ ( $fh, $filename ) = tempfile( UNLINK => 1 );
+ say "Processing dump for the relationships ontology ...";
+ print $fh $mobyrelationship;
+ eval {
+ $drh->func( 'dropdb', $dbsections{mobyrelationship},
+ $url, $username, $password, 'admin' );
+ };
+ eval {
+ $drh->func( 'createdb', $dbsections{mobyrelationship},
+ $url, $username, $password, 'admin' );
+ };
+ system( "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{mobyrelationship}
+ . "<$filename" ) == 0
+ or ( say "Error populating relationships ontology ...\n$!"
+ and $error++ );
+
+ } else {
+
+ # no clone, so create minimalist databases
+ my $drop_db = 0;
- #create the tables in the db
+ #ask for permission on dropping data from db ...
do {
- say "\n\tProblem creating tables in the db: $section: $!";
+ $drop_db = 1;
}
- unless system(
+ if pprompt(
+ "Shall I drop all pre-existing databases used by BioMOBY? [n] ",
+ -ynd => 'n'
+ ) eq 'y';
+
+ #process each db
+ foreach my $section ( keys %dbsections ) {
+ my $sqlfilepath = File::ShareDir::dist_file( 'MOBY',
+ "db/schema/$section.mysql" );
+ my $drh = DBI->install_driver("mysql");
+
+ # drop the db
+ eval {
+ $drh->func( 'dropdb', $dbsections{$section}, $url,
+ $username, $password, 'admin' );
+ } if $drop_db;
+
+ # create the db
+ eval {
+ $drh->func( 'createdb', $dbsections{$section}, $url,
+ $username, $password, 'admin' );
+ };
+
+ #create the tables in the db
+ do {
+ say "\n\tProblem creating tables in the db: $section: $!";
+ }
+ unless system(
"mysql -h $url -P $port -u $username --password=$password "
. $dbsections{$section}
. "<$sqlfilepath" ) == 0;
- say "\tProcessing of $section completed ... ";
- }
- say "populating the tables with basic data ...";
- %dbsections = (
- 'mobyobject' => $m_object,
- 'mobyservice' => $m_service,
- 'mobyrelationship' => $m_relationship
- );
- foreach my $section ( keys %dbsections ) {
- my $sqlfilepath =
- File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
- system( "mysql -h $url -P $port -u $username --password=$password "
- . $dbsections{$section}
- . "<$sqlfilepath" ) == 0
- or say "\n\tProblem populating the db: $section: $!";
- say "\tPopulation processing for db $section completed ...";
+ say "\tProcessing of $section completed ... ";
+ }
+ say "populating the tables with basic data ...";
+ %dbsections = (
+ 'mobyobject' => $m_object,
+ 'mobyservice' => $m_service,
+ 'mobyrelationship' => $m_relationship
+ );
+ foreach my $section ( keys %dbsections ) {
+ my $sqlfilepath =
+ File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
+ system(
+ "mysql -h $url -P $port -u $username --password=$password "
+ . $dbsections{$section}
+ . "<$sqlfilepath" ) == 0
+ or say "\n\tProblem populating the db: $section: $!";
+ say "\tPopulation processing for db $section completed ...";
+ }
}
- }
- say "Set up of mySQL complete!" if $error == 0;
- say
+ say "Set up of mySQL complete!" if $error == 0;
+ say
"There were some problems encountered. Please correct the errors and re-run this script!"
- if $error > 0;
-} unless $sql_error;
+ if $error > 0;
+ } unless $sql_error;
} if pprompt( "Would you like to set up mySQL? [n] ", -ynd => 'n' ) eq 'y';
do {
@@ -957,15 +974,22 @@
if pprompt( "The RESOURCES script already exists, overwrite? [n] ",
-ynd => 'n' ) eq 'y';
} if -e "$apache_cgi/RESOURCES";
-
- my $rdf_cache_location = prompt_for_directory_expand( "Where would you like to store the RDF cache?", "$apache_base/moby_cache" );
-
- say 'Please make sure that you make that directory read/writable by your web server!\n';
-
+
+ my $rdf_cache_location =
+ prompt_for_directory_expand(
+ "Where would you like to store the RDF cache?",
+ "$apache_base/moby_cache" );
+
+ say
+"Please make sure that you make that directory read/writable by your web server!\n";
+
# copy the file
- file_from_template( "$apache_cgi/RESOURCES",
+ file_from_template(
+ "$apache_cgi/RESOURCES",
File::ShareDir::dist_file( 'MOBY', 'cgi/RESOURCES' ),
- 'RESOURCES script', {'#!/usr/bin/perl -w' => "#!$perl_exec",} )
+ 'RESOURCES script',
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ )
if $exists == 0;
# update mobycentral.config file to reflect the location of the script
@@ -985,7 +1009,7 @@
'mobycentral' => {
'resourceURL' => 0,
'allResources' => 0,
- 'rdf_cache' => 0
+ 'rdf_cache' => 0
},
'mobyobject' => { 'resourceURL' => 0 },
'mobyservice' => { 'resourceURL' => 0 },
@@ -1002,7 +1026,7 @@
'MOBY/SQL Configuration file',
# mysql settings
- {'rdf_cache' => "$rdf_cache_location"},
+ { 'rdf_cache' => "$rdf_cache_location" },
# db section mappings
{},
@@ -1039,16 +1063,16 @@
}
if pprompt( "The authority script already exists, overwrite? [n] ",
-ynd => 'n' ) eq 'y';
- file_from_template(
- "$apache_cgi/authority.pl",
- File::ShareDir::dist_file(
- 'MOBY', 'cgi/authority.pl'
- ),
- 'MOBY-Central LSID authority server file',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- ) if $exists == 0;
} if -e "$apache_cgi/authority.pl";
+ file_from_template(
+ "$apache_cgi/authority.pl",
+ File::ShareDir::dist_file( 'MOBY', 'cgi/authority.pl' ),
+ 'MOBY-Central LSID authority server file',
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ )
+ if $exists == 0;
+
# update mobycentral.config file to reflect the particulars of the script
do {
@@ -1167,97 +1191,99 @@
do {
- # prompt for a location for the service_tester_path
- my $service_tester_path = prompt_for_directory_expand( "Where would you like to place the service pinger script?", "$apache_base/moby_tester" );
- say 'Please make sure that you make that directory read/writable by your web server!\n';
- # make sure that the key service_tester_path exists for the config file
- my $search = search_config_file(
- "$apache_conf/mobycentral.config",
- {
- 'mobycentral' => {
- 'service_tester_path' => 0,
- }
- }
- );
- add_missing_keys_to_config_file( "$apache_conf/mobycentral.config", $search );
+ # prompt for a location for the service_tester_path
+ my $service_tester_path =
+ prompt_for_directory_expand(
+ "Where would you like to place the service pinger script?",
+ "$apache_base/moby_tester" );
+ say
+'Please make sure that you make that directory read/writable by your web server!\n';
- # copy the information
- config_file_from_template(
- "$apache_conf/mobycentral.config",
- "$apache_conf/mobycentral.config",
- 'MOBY/SQL Configuration file',
+ # make sure that the key service_tester_path exists for the config file
+ my $search = search_config_file( "$apache_conf/mobycentral.config",
+ { 'mobycentral' => { 'service_tester_path' => 0, } } );
+ add_missing_keys_to_config_file( "$apache_conf/mobycentral.config",
+ $search );
- # mysql settings
- {'service_tester_path' => "$service_tester_path"},
+ # copy the information
+ config_file_from_template(
+ "$apache_conf/mobycentral.config",
+ "$apache_conf/mobycentral.config",
+ 'MOBY/SQL Configuration file',
- # db section mappings
- {},
+ # mysql settings
+ { 'service_tester_path' => "$service_tester_path" },
- # resource urls
- {},
+ # db section mappings
+ {},
- # lsid info
- {}
- );
-
- file_from_template(
+ # resource urls
+ {},
+
+ # lsid info
+ {}
+ );
+
+ file_from_template(
"$service_tester_path/service_tester.pl",
File::ShareDir::dist_file(
- 'MOBY', 'cgi/service_tester.pl'
+ 'MOBY', 'cgi/service_tester.pl'
),
'MOBY-Central service tester script',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
- say 'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
-
- #copy the other scripts now
- file_from_template(
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
+ say
+'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
+
+ #copy the other scripts now
+ file_from_template(
"$apache_cgi/AgentRDFValidator",
File::ShareDir::dist_file(
- 'MOBY', 'cgi/AgentRDFValidator'
+ 'MOBY', 'cgi/AgentRDFValidator'
),
'The RDF agent validator page',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
- file_from_template(
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
+ file_from_template(
"$apache_cgi/GenerateRDF.cgi",
File::ShareDir::dist_file(
- 'MOBY', 'cgi/GenerateRDF.cgi'
+ 'MOBY', 'cgi/GenerateRDF.cgi'
),
'MOBY-Central service instance RDF generating form',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
- file_from_template(
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
+ file_from_template(
"$apache_cgi/Moby",
- File::ShareDir::dist_file(
- 'MOBY', 'cgi/Moby'
- ),
+ File::ShareDir::dist_file( 'MOBY', 'cgi/Moby' ),
'MOBY-Central test page for auxillary scripts',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
- file_from_template(
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
+ file_from_template(
"$apache_cgi/ServicePingerValidator",
File::ShareDir::dist_file(
- 'MOBY', 'cgi/ServicePingerValidator'
+ 'MOBY', 'cgi/ServicePingerValidator'
),
'MOBY-Central service invocation test form',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
- file_from_template(
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
+ file_from_template(
"$apache_cgi/ValidateService",
File::ShareDir::dist_file(
- 'MOBY', 'cgi/ValidateService'
+ 'MOBY', 'cgi/ValidateService'
),
'MOBY-Central service tester information page',
- {'#!/usr/bin/perl -w' => "#!$perl_exec",}
- );
+ { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+ );
}
- if pprompt( "Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
- -ynd => 'y' ) eq 'y';
+ if pprompt(
+"Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
+ -ynd => 'y'
+ ) eq 'y';
#
-say "Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
+say
+"Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
package SimplePrompt;
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