--- /dev/null
+
+use DBI;
+use Config::IniFiles;
+
+
+$dbh = setUpDBConnection();
+$species_ncbi_hash={};
+loadSpeciesNcbiHash();
+#check of empty or undefined string
+sub isEmpty
+{
+ ($arg) = @_;
+ return (!defined($arg) || $arg eq "");
+}
+
+#executes a db query. doesn't return anything - for insert/update
+sub executeDbQuery{
+ ($query) = @_;
+ $stmnt = $dbh->prepare("$query");
+ #print $query;
+ $stmnt->execute() or die "Couldn't execute statement: " . $stmnt->errstr;
+}
+
+#executes a db query and returns the first row as an array.
+sub executeDbQueryAndFetchRowArray{
+ ($query) = @_;
+ $stmnt = $dbh->prepare("$query");
+ $stmnt->execute() or die "Couldn't execute statement: " . $stmnt->errstr;
+ return $stmnt->fetchrow_array();
+}
+
+#get object_id from Object table if object_abbreviation is given
+sub getObjectIdFromAbbreviation{
+ ($obj_abbr) = @_;
+ $query = "SELECT object_id FROM Object WHERE object_abbreviation = '$obj_abbr'";
+ return executeDbQueryAndFetchRowArray($query);
+}
+
+#get object_id from Object table if accession id is given
+sub getObjectIdFromAccession{
+ ($obj_acc) = @_;
+ $query = "SELECT object_id FROM Object WHERE object_accession = '$obj_acc'";
+ $obj_id = executeDbQueryAndFetchRowArray($query);
+ return $obj_id;
+}
+
+#get interactor type ID from Interactor_type table.
+#possible interactor types - DNA, RNA, gene, metabolite, protein, NA
+sub getInteractorTypeId{
+ ($int_type) = @_;
+ $query = "SELECT interactor_type_id FROM Interactor_type WHERE interactor_type = '$int_type'";
+ $int_type_id = executeDbQueryAndFetchRowArray($query);
+ return $int_type_id;
+}
+
+#get interaction type ID from Interaction_type table.
+#possible interactor types - protein-protein binding, down regulation, up regulation, co-expression
+sub getInteractionTypeId{
+ ($interaction_type) = @_;
+ $query = "SELECT interaction_type_id FROM Interaction_type WHERE interaction_type = '$interaction_type'";
+ $interaction_type_id = executeDbQueryAndFetchRowArray($query);
+ return $interaction_type_id;
+}
+
+#get synonym id from Synonym table. If not present already, insert it.
+sub getSynonymId{
+ ($synonym) = @_;
+ $query = "SELECT synonym_id FROM Synonym WHERE synonym = '$synonym'";
+ $synonym_id = executeDbQueryAndFetchRowArray($query);
+ if(isEmpty($synonym_id)){
+ $query = "INSERT INTO Synonym(`synonym`) VALUES('$synonym')";
+ executeDbQuery($query);
+ return getSynonymId($synonym);
+ }
+
+ return $synonym_id;
+}
+
+sub getModeOfActionId{
+ ($mode_of_action) = @_;
+ $query = "SELECT mode_of_action_id FROM Mode_of_action WHERE mode_of_action = '$mode_of_action'";
+ $mode_of_action_id = executeDbQueryAndFetchRowArray($query);
+ return $mode_of_action_id;
+}
+
+#get evidence id. If it doesn't exist already, insert into the table
+sub getEvidenceId{
+ ($evidence) = @_;
+ @evidenceArray = split(/:/,$evidence);
+ $query = "SELECT evidence_id FROM Evidence WHERE source_name = '$evidenceArray[0]' and source_id='$evidenceArray[1]'";
+ $evidence_id = executeDbQueryAndFetchRowArray($query);
+ if($evidence_id eq ""){
+ $query = "INSERT INTO Evidence(`source_name`,`source_id`) VALUES('$evidenceArray[0]','$evidenceArray[1]')";
+ executeDbQuery($query);
+ return getEvidenceId($evidence);
+ }
+ return $evidence_id;
+}
+
+sub getEvidenceCodeId{
+ ($evidence_code) = @_;
+ $query = "SELECT evidence_code_id FROM Evidence_code WHERE evidence_code = '$evidence_code'";
+ $evidence_code_id = executeDbQueryAndFetchRowArray($query);
+ return $evidence_code_id;
+}
+
+
+sub getExperimentId{
+ ($experiment) = @_;
+ $query = "SELECT experiment_id FROM Experiment WHERE experiment_name = '$experiment'";
+ $experiment_id = executeDbQueryAndFetchRowArray($query);
+ return $experiment_id;
+}
+
+#get interaction id from Interaction Table.
+sub getInteractionId{
+ ($accession_left_id,$interaction_type_id,$accession_right_id,$curatorId) = @_;
+ $query = "SELECT interaction_id from Interaction where `object_id_left` = '$accession_left_id' and `object_id_right` = '$accession_right_id' and `interaction_type_id` = '$interaction_type_id' and `curator_id` = '$curatorId'";
+ $interaction_id = executeDbQueryAndFetchRowArray($query);
+ if(!isEmpty($interaction_id)){
+ return $interaction_id;
+ }
+ #if the interaction type is neither up-regulation nor down-regulation, the interaction is not
+ #direction specific.try flipping the objects and see if the interaction exists.if yes, return that interaction_id
+ elsif($interaction_type_id ne 2 || $interaction_type_id ne 3){
+ $query = "SELECT interaction_id from Interaction where `object_id_left` = '$accession_right_id' and `object_id_right` = '$accession_left_id' and `interaction_type_id` = '$interaction_type_id' and `curator_id` = '$curatorId'";
+ $interaction_id = executeDbQueryAndFetchRowArray($query);
+ if(!isEmpty($interaction_id)){
+ return $interaction_id;
+ }
+ }
+ return "";
+}
+
+sub getCuratorId{
+ ($labName,$userName) = @_;
+ $query = "SELECT curator_id FROM Curator WHERE lab_name = '$labName' and user_name = '$userName'";
+ $curator_id = executeDbQueryAndFetchRowArray($query);
+ if(!isEmpty($curator_id)){
+ return $curator_id;
+ }
+ else{
+ $query = "INSERT INTO Curator(`lab_name`,`user_name`) VALUES('$labName','$userName')";
+ executeDbQuery($query);
+ return getCuratorId($labName,$userName);
+ }
+}
+
+
+sub setUpDBConnection
+{
+ #read config file for db config values
+ $ini = Config::IniFiles->new( -file => "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";
+ $labName = <STDIN>;
+ if($labName eq "\n"){
+ $labName = "Jaiswal lab";
+ }
+ print "Enter curator name or press 'enter'. Default is ''.\n";
+ $curatorName = <STDIN>;
+ if($curatorName eq "\n"){
+ $curatorName = "";
+ }
+ return ($labName,$curatorName);
+}
+
+
+sub getSpeciesProperties
+{
+ ($askForBoth) = @_;
+ print "\nEnter the name of the species\n";
+ $speciesName = <STDIN>;
+ $speciesName =~ s/\n//g;
+ if(isEmpty($speciesName) || $askForBoth == 1){
+ print "Enter the ncbi taxonomy id of the species\n";
+ $ncbi_id = <STDIN>;
+ $ncbi_id =~ s/\n//g;
+ }
+ #just to suppress warnings
+ if(isEmpty($speciesName)){
+ $speciesName = "";
+ }
+ #just to suppress warnings
+ if(isEmpty($ncbi_id)){
+ $ncbi_id = "";
+ }
+ return ("$speciesName","$ncbi_id");
+}
+
+sub getSpeciesId
+{
+ ($speciesName,$ncbi_id) = @_;
+ $query = "SELECT species_id from Species WHERE LOWER(`species`) = LOWER('$speciesName')";
+ $species_id = executeDbQueryAndFetchRowArray($query);
+ if(isEmpty($species_id) && !isEmpty($ncbi_id)){
+ $query = "SELECT species_id from Species WHERE `NCBI_taxonomy_id` = '$ncbi_id'";
+ $species_id = executeDbQueryAndFetchRowArray($query);
+ }
+ !isEmpty($species_id) || print "Your entry was not found. Choose from the list or check for spelling mistakes \n";
+
+ return $species_id;
+}
+sub addNewSpecies
+{
+ ($speciesName,$ncbi_id) = @_;
+ $speciesId = getSpeciesId(($speciesName,$ncbi_id));
+ if(!isEmpty($speciesId)){
+ print "$speciesName or $ncbi_id already exists\n";
+ return $speciesId;
+ }
+ else{
+ $query = "INSERT INTO Species(`species`,`NCBI_taxonomy_id`) VALUES('$speciesName','$ncbi_id')";
+ executeDbQuery($query);
+ print "New species successfully added\n";
+ return getSpeciesId($speciesName,$ncbi_id);
+ }
+}
+
+sub getHomologyIdAndScore
+{
+ ($obj_id_l,$obj_id_r,$score) = @_;
+ $query = "SELECT homology_id,score from Homology where `object_id_source` = '$obj_id_l' and `object_id_projection` = '$obj_id_r'";
+ ($homologyId,$score) = executeDbQueryAndFetchRowArray($query);
+ return ($homologyId,$score);
+}
+
+sub loadSpeciesNcbiHash
+{
+ $query = 'SELECT NCBI_taxonomy_id,species FROM Species';
+ $stmnt = $dbh->prepare("$query");
+ $stmnt->execute() or die "Couldn't execute statement: " . $stmnt->errstr;
+ while(($ncbi_id,$species) = $stmnt->fetchrow_array()){
+
+ # skip
+ next if(!defined($species) || !defined($species));
+ $species_ncbi_hash{"$ncbi_id"}="$species";
+ }
+}
+
+sub showAvailableSpecies
+{
+ print "Existing ncbi ids and species names:\n";
+ $out = "";
+ $i=0;
+ while (($key, $value) = each(%species_ncbi_hash)){
+ $out = $out."\t$key:$value\t";
+ #just some formatting - 3 species in a line
+ if($i == 1){
+ $i=0;
+ $out=$out."\n"
+ }
+ else{
+ $i=$i+1;
+ }
+ }
+ print $out."\n";
+}
+return 1;
projects / old-jaiswallab-svn / .git / commitdiff