From 892e1bd302cc1fac7cf78c7758e4c53baec46490 Mon Sep 17 00:00:00 2001 From: athreyab Date: Mon, 23 Jan 2012 00:00:18 +0000 Subject: [PATCH] more changes svn path=/; revision=268 --- .../interactions/interactionPathsFromTsv.pl | 162 +++--------------- ...nInteraction.sql => interactionTables.sql} | 135 ++++++++++++--- 2 files changed, 130 insertions(+), 167 deletions(-) rename Personnel/athreyab/interactions/{insertTablesInInteraction.sql => interactionTables.sql} (62%) diff --git a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl index 4ee3af5..a70da8b 100644 --- a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl +++ b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl @@ -5,132 +5,11 @@ use DBI; use Config::IniFiles; use Switch; - +require "interactionPath.pl"; #use constant SITE_ADJECTIVE => ($ENV{'DevelopmentSite'} ? 'Development': 'Live'); use constant SITE_ADJECTIVE => 'Development'; - -sub executeDbQuery{ - ($query, $dbh) = @_; - $stmnt = $dbh->prepare("$query"); - $stmnt->execute() or die "Couldn't execute statement: " . $stmnt->errstr; -} - -sub executeDbQueryAndFetchRowArray{ - ($query, $dbh) = @_; - #print $query."\n"; - $stmnt = $dbh->prepare("$query"); - $stmnt->execute() or die "Couldn't execute statement: " . $stmnt->errstr; - return $stmnt->fetchrow_array(); -} - -sub getObjectId{ - ($obj_abbr, $dbh) = @_; - $query = "SELECT object_id FROM Object WHERE object_abbreviation = '$obj_abbr'"; - $obj_id = executeDbQueryAndFetchRowArray($query,$dbh); - $obj_id ne "" or die "$obj_abbr was not found in Object table"; - return $obj_id; -} - - -sub getInteractorTypeId{ - ($int_type, $dbh) = @_; - $query = "SELECT interactor_type_id FROM Interactor_type WHERE interactor_type = '$int_type'"; - $int_type_id = executeDbQueryAndFetchRowArray($query,$dbh); - $int_type_id ne "" or die "$int_type was not found in Interactor_type table"; - return $int_type_id; -} - - -sub getInteractionTypeId{ - ($interaction_type, $dbh) = @_; - $query = "SELECT interaction_type_id FROM Interaction_type WHERE interaction_type = '$interaction_type'"; - $interaction_type_id = executeDbQueryAndFetchRowArray($query,$dbh); - $interaction_type_id ne "" or die "$interaction_type was not found in Interaction_type table"; - return $interaction_type_id; -} - - -sub getModeOfActionId{ - ($mode_of_action, $dbh) = @_; - $query = "SELECT mode_of_action_id FROM Mode_of_action WHERE mode_of_action = '$mode_of_action'"; - $mode_of_action_id = executeDbQueryAndFetchRowArray($query,$dbh); - $mode_of_action_id ne "" or die "$mode_of_action was not found in ModeofAction table"; - return $mode_of_action_id; -} - -sub getEvidenceId{ - ($evidence, $dbh) = @_; - @evidenceArray = split(/:/,$evidence); - scalar(@evidenceArray) == 2 or die "Incorrect evidence information. Evidence source name or id missing"; - $query = "SELECT evidence_id FROM Evidence WHERE source_name = '$evidenceArray[0]' and source_id='$evidenceArray[1]'"; - $evidence_id = executeDbQueryAndFetchRowArray($query,$dbh); - if($evidence_id eq ""){ - $query = "INSERT INTO Evidence(`source_name`,`source_id`) VALUES('$evidenceArray[0]','$evidenceArray[1]')"; - executeDbQuery($query,$dbh); - return getEvidenceId($evidence,$dbh); - } - return $evidence_id; -} - -sub getEvidenceCodeId{ - ($evidence_code, $dbh) = @_; - $query = "SELECT evidence_code_id FROM Evidence_code WHERE evidence_code = '$evidence_code'"; - $evidence_code_id = executeDbQueryAndFetchRowArray($query,$dbh); - $evidence_code_id ne "" or die "$evidence_code was not found in Evidence table"; - return $evidence_code_id; -} - - -sub getExperimentId{ - ($experiment, $dbh) = @_; - $query = "SELECT experiment_id FROM Experiment WHERE experiment_name = '$experiment'"; - $experiment_id = executeDbQueryAndFetchRowArray($query,$dbh); - $experiment_id ne "" or die "$experiment was not found in Experiment table"; - return $experiment_id; -} - -sub getCuratorId{ - $query = "SELECT curator_id FROM Curator WHERE lab_name = '$labName' and user_name = '$userName'"; - $curator_id = executeDbQueryAndFetchRowArray($query,$dbh); - if($curator_id ne ""){ - return $curator_id; - } - else{ - $query = "INSERT INTO Curator(`lab_name`,`user_name`) VALUES('$labName','$userName')"; - executeDbQuery($query,$dbh); - return getCuratorId($labName,$userName); - } -} - - -sub setUpDBConnection -{ - #read config file for db config values - $ini = Config::IniFiles->new( -file => "/home/balaji/Documents/code/interactions/dbConfig.ini"); - $dbUser=$ini->val(SITE_ADJECTIVE, 'dbUser'); - $dbPw=$ini->val(SITE_ADJECTIVE, 'dbPw'); - $host=$ini->val(SITE_ADJECTIVE, 'host'); - $dbName=$ini->val(SITE_ADJECTIVE, 'dbName'); - $dbh = DBI->connect("DBI:mysql:$dbName;host=$host",$dbUser,$dbPw,{RaiseError=> 1}) or die("Failed to connect to database - $DBI::errstr"); - return $dbh; -} - -sub getCuratorProperties -{ - print "Enter curator lab name or press 'enter'. Default is Jaiswal Lab.\n"; - $labName = ; - if($labName eq "\n"){ - $labName = "Jaiswal lab"; - } - print "Enter curator name or press 'enter'. Default is ''.\n"; - $userName = ; - if($userName eq "\n"){ - $userName = ""; - } -} - sub showUsage(){ print "Usage: \n\tperl interactionPathsFromTsv