Change some insertions through stored procedures and password hiding.

svn path=/; revision=475

diff --git a/image_annotation_db/ia_upload/DbiFloret.pm b/image_annotation_db/ia_upload/DbiFloret.pm
new file mode 100644 (file)
index 0000000..f27b3b7
--- /dev/null
+++ b/image_annotation_db/ia_upload/DbiFloret.pm
@@ -0,0 +1,45 @@
+
+package DbiFloret;
+
+use DBI;
+use Term::ReadKey;
+
+
+sub dbconnect {
+       my $self = @_;
+       
+       print "Username: ";
+       chomp(my $username = <STDIN>);
+       print "Password: ";
+       ReadMode('noecho');
+       chomp(my $password = <STDIN>);
+       ReadMode(0);
+       print "\nDatabase: ";
+       chomp(my $database = <STDIN>);
+       
+       my $dbh = DBI->connect("DBI:mysql:$database;host=floret.cgrb.oregonstate.edu", $username, $password,
+               { RaiseError=> 1, AutoCommit=>1 }
+               ) or die "Failed to connect to database: $DBI::errstr";
+               
+       
+       return $dbh;
+}
+
+sub dbconnect_auto {
+               my $self =@_;
+               
+               my $username = $_[0];
+               my $password = $_[1];
+               my $database = $_[2];
+               
+               my $dbh = DBI->connect("DBI:mysql:$database;host=floret.cgrb.oregonstate.edu", $username, $password,
+               { RaiseError=> 1, AutoCommit=>1 }
+               ) or die "Failed to connect to database: $DBI::errstr";
+               
+       
+       return $dbh;
+}
+       
+
+return 1;
+ 

diff --git a/image_annotation_db/ia_upload/annotation_data_importer.pl b/image_annotation_db/ia_upload/annotation_data_importer.pl
index 9dd9b212b41953957889870d5640e79d3f7e201d..80b972ff1c203c38f38819fb595e1eb25c466b0a 100644 (file)
--- a/image_annotation_db/ia_upload/annotation_data_importer.pl
+++ b/image_annotation_db/ia_upload/annotation_data_importer.pl
@@ -24,6 +24,7 @@
 use strict;
 use English;
 use DBI;
+use DbiFloret qw(dbconnect);
 use String::Util qw(:all);
 
 # configurations
@@ -32,9 +33,7 @@ use constant IMAGE_DATA_DIR => "image_data";
 
 sub establish_db_connection
 {
-  return DBI->connect('DBI:mysql:image_annotation;host=floret.cgrb.oregonstate.edu', 'lingutln', 'nikhil_iadb',
-         { RaiseError => 1 }
-        );
+  return DbiFloret::dbconnect();
 }
 
 
@@ -50,9 +49,11 @@ sub insert_collection_data_into_database
   my($contact_email)    = trim($collection_data_fields[3]);
   my($contributor_name) = trim($collection_data_fields[2]);
 
-  $dbh->do('INSERT INTO image_source (source_name, url, contact_email, contributor_name) VALUES(?, ?, ?, ?)', undef, $source_name, $url, $contact_email, $contributor_name);
-    my $image_source_id =  $dbh->{'mysql_insertid'};
-
+  my $image_source_id;
+  my $sth = $dbh->prepare("call import_image_source('$source_name', '$url', '$contact_email', '$contributor_name');");
+  $sth->execute();
+  $sth->bind_col(1, \$image_source_id);
+  $sth->fetch();
 
 
   #creating image_source_version
@@ -60,8 +61,12 @@ sub insert_collection_data_into_database
   my($contribution_date) = trim($collection_data_fields[4]);
   my($publication_id)    = trim($collection_data_fields[5]);
 
-  $dbh->do('INSERT INTO image_source_version (image_source_id, source_version, contribution_date, publication_id) VALUES(?, ?, ?, ?)', undef, $image_source_id, $source_version, $contribution_date, $publication_id);
-    my $image_source_version_id =  $dbh->{'mysql_insertid'};
+  my $image_source_version_id;
+  my $sth = $dbh->prepare("call import_image_source_version('$image_source_id', '$source_version', '$contribution_date', '$publication_id');");
+  $sth->execute();
+  $sth->bind_col(1, \$image_source_version_id);
+  $sth->fetch();
+
 
 }
 
@@ -79,27 +84,24 @@ sub insert_image_data_into_database
   my $curator_email                          = trim($image_data_fields[7]);
   my $curator_affiliation                     = trim($image_data_fields[8]);
   
-  $dbh->do('INSERT INTO curator (firstname, lastname, primary_email, affiliation) VALUES(?, ?, ?, ?)', undef, $curator_first_name, $curator_last_name, $curator_email, $curator_affiliation);
-  my $curator_id =  $dbh->{mysql_insert_id};
+  my $curator_id;
+  my $sth = $dbh->prepare("call import_curator('$curator_first_name', '$curator_last_name', '$curator_email', '$curator_affiliation');");
+  $sth->execute();
+  $sth->bind_col(1, \$curator_id);
+  $sth->fetch();
 
 
 
   # Creating taxon data and storing the respective id
   my $species               = trim($image_data_fields[4]);
-  my $species               = "temp";
   my ($genus, $species_name) = split(/\s/, $species, 2);
   my $species_id             = trim($image_data_fields[5]);
 
-  #$dbh->do('INSERT INTO taxon (species_id, species_name, genus) VALUES(?, ?, ?)', undef, $species_id, $species_name, $genus);
-  #$dbh->do("call import_taxon($species_id, $species_name, $genus);");
   my $taxon_id;
-  my $sth = $dbh->prepare("call import_taxon('temp_id', 'temp_name', 'temp_genus');");
+  my $sth = $dbh->prepare("call import_taxon('$species_id', '$species_name', '$genus');");
   $sth->execute();
   $sth->bind_col(1, \$taxon_id);
   $sth->fetch();
-  print "taxon_id is $taxon_id";
-
-  #my $taxon_id =  $dbh->{mysql_insert_id};
 
   # Forming image_path by concatinating import_location and filename
   my $image_path = trim($image_data_fields[1]) . trim($image_data_fields[0]);

diff --git a/image_annotation_db/ia_upload/stored_procedures.sql b/image_annotation_db/ia_upload/stored_procedures.sql
index 149e728499305f07a47a1e48b71b9417ff458dd5..513f10c9bf741c0fdf182495698eb523c14dd169 100644 (file)
--- a/image_annotation_db/ia_upload/stored_procedures.sql
+++ b/image_annotation_db/ia_upload/stored_procedures.sql
@@ -1,7 +1,42 @@
--- create stored procedure for importing taxon table
+-- create(drop and create if exists) stored procedure for importing data into image_source table
 
+DROP procedure if exists import_image_source;
+delimiter //
+create procedure import_image_source (source_name varchar(80), url varchar(255), contact_email varchar(80), contributor_name varchar(80))
+begin
+insert into image_source (source_name, url, contact_email, contributor_name) values (source_name, url, contact_email, contributor_name);
+select last_insert_id();
+end //
+
+
+-- create(drop and create if exists) stored procedure for importing data into image_source_version table
+
+DROP procedure if exists import_image_source_version;
+delimiter //
+create procedure import_image_source_version (image_source_id int(11), source_version varchar(45), contribution_date date, publication_id varchar(45))
+begin
+insert into image_source_version (image_source_id, source_version, contribution_date, publication_id) values (image_source_id, source_version, contribution_date, publication_id);
+select last_insert_id();
+end //
+
+-- create(drop and create if exists) stored procedure for importing data into curator table
+
+DROP procedure if exists import_curator;
+delimiter //
+create procedure import_curator (firstname varchar(80), lastname varchar(80), primary_email varchar(80), affiliation varchar(80))
+begin
+insert into curator (firstname, lastname, primary_email, affiliation) values (firstname, lastname, primary_email, affiliation);
+select last_insert_id();
+end //
+
+-- create(drop and create if exists) stored procedure for importing data into taxon table
+
+DROP procedure if exists import_taxon;
 delimiter //
 create procedure import_taxon (species_id varchar(45), species_name varchar(80), genus varchar(80))
+begin
 insert into taxon (species_id, species_name, genus) values (species_id, species_name, genus);
 select last_insert_id();
-end //
\ No newline at end of file
+end //
+
+