$entry =~ s/\n//g;
# split the columns into separate variables
my ($obj_abbr_left,$int_type_left,$mode_of_action,$obj_abbr_right,$int_type_right,$interaction_type,$evidence,$evidence_code,$experiment,$comments) = split("\t", $entry);
- # skip if any of the variables are empty
- next if(!defined($obj_abbr_left) || $obj_abbr_left eq "");
- next if(!defined($obj_abbr_right) || $obj_abbr_right eq "");
- next if(!defined($int_type_left) || $int_type_left eq "");
- next if(!defined($int_type_right) || $int_type_right eq "");
- next if(!defined($mode_of_action) || $mode_of_action eq "");
- next if(!defined($interaction_type) || $interaction_type eq "");
- next if(!defined($evidence) || $evidence eq "");
- next if(!defined($evidence_code) || $evidence_code eq "");
- next if(!defined($experiment) || $experiment eq "");
+ #we need all the 3 values before we can insert data into the interaction table.
+ next if(isEmpty($obj_abbr_left));
+ next if(isEmpty($obj_abbr_right));
+ next if(isEmpty($interaction_type));
#get ids(primary keys) from other tables
$obj_id_left = getObjectIdFromAbbreviation($obj_abbr_left);
$obj_id_right = getObjectIdFromAbbreviation($obj_abbr_right);
$interaction_type_id = getInteractionTypeId($interaction_type);
- #we need a minimum of the above 3 values before we can insert data into the interaction table.
- next if(!defined($obj_id_left) || $obj_id_left eq "" || !defined($obj_id_right) || $obj_id_right eq "" || !defined($interaction_type_id) || $interaction_type_id eq "");
+ #if any of the above values are empty, it means they are empty. print that message and move to the next line
+ if(isEmpty($obj_id_left)){
+ print "$obj_abbr_left was not found in the db. Skipping this line\n";
+ next;
+ }
+ elsif(isEmpty($obj_id_right)){
+ print "$obj_abbr_right was not found in the db. Skipping this line\n";
+ next;
+ }
+ elsif(isEmpty($interaction_type_id)){
+ print "$interaction_type was not found in the db. Skipping this line\n";
+ next;
+ }
$int_type_id_left = getInteractorTypeId($int_type_left);
$int_type_id_right = getInteractorTypeId($int_type_right);
$mode_of_action_id = getModeOfActionId($mode_of_action);
$evidence_id = getEvidenceId($evidence);
$evidence_code_id = getEvidenceCodeId($evidence_code);
$experiment_id = getExperimentId($experiment);
- $curator_id = getCuratorId();
print $obj_id_left."\t".$obj_id_right."\t".$int_type_id_left."\t".$int_type_id_right."\t".$interaction_type_id.
"\t".$evidence_id."\t".$evidence_code_id."\t".$experiment_id.$curator_id."\n";
$entry =~ s/\n//g;
my ($accession, $is_gene,$is_metabolite,$symbol,$full_name,$synonym,$species_name,$ncbi_id) = split("\t", $entry);
-
- next if(!defined($accession) || $accession eq "");
- next if((!defined($is_gene) || $is_gene eq "") && (!defined($is_metabolite) || $is_metabolite eq ""));
- next if(!defined($symbol) || $symbol eq "");
- next if(!defined($full_name) || $full_name eq "");
- next if(!defined($synonym) || $synonym eq "");
- next if(!defined($species_name) || $species_name eq "");
- next if(!defined($ncbi_id) || $ncbi_id eq "");
-
- $object_type=1;
+ #skip the line if accession value is empty
+ next if(isEmpty($accession));
+ $object_type=1;
if($is_metabolite eq "yes"){
$object_type=2;
}
-
- #first, insert the species name into the species table.
- $query = "INSERT INTO Species(`species`,`NCBI_taxonomy_id`) VALUES ('$species_name','$ncbi_id') ON DUPLICATE KEY UPDATE species='$species_name'";
- executeDbQuery($query);
- #get the species_id
- $query = "SELECT species_id FROM Species WHERE species = '$species_name'";
- $species_id = executeDbQueryAndFetchRowArray($query);
+ $species_id = getSpeciesId($species_name,$ncbi_id);
+ #if the species is not present already, insert it
+ if(isEmpty($species_id)){
+ if(!isEmpty($ncbi_id)){
+ $query = "INSERT INTO Species(`species`,`NCBI_taxonomy_id`) VALUES ('$species_name','$ncbi_id')";
+ }
+ else{
+ $query = "INSERT INTO Species(`species`) VALUES ('$species_name')";
+ }
+ executeDbQuery($query);
+ $species_id = getSpeciesId($species_name,$ncbi_id);
+ }
- #insert synonym into the synonym table.
- $query = "INSERT INTO Synonym(`synonym`) VALUES('$synonym') ON DUPLICATE KEY UPDATE synonym='$synonym'";
- executeDbQuery($query);
-
- #get the synonym_id
- $query = "SELECT synonym_id FROM Synonym WHERE synonym = '$synonym'";
- $synonym_id = executeDbQueryAndFetchRowArray($query);
+ #gets synonym_id if exists already. else, inserts synonym and returns the id.
+ $synonym_id = getSynonymId($synonym);
- #insert gene information into the object table
- $query = "INSERT INTO Object(`object_accession`,`species_id`,`object_full_name`,`object_abbreviation`,`object_type_id`) VALUES('$accession','$species_id','$full_name','$symbol','$object_type') ON DUPLICATE KEY UPDATE object_accession='$accession'";
+ $query = "INSERT INTO Object(`object_accession`,`species_id`,`object_full_name`,`object_abbreviation`,`object_type_id`) VALUES('$accession','$species_id','$full_name','$symbol','$object_type') ON DUPLICATE KEY UPDATE object_accession='$accession' ";
+ if(!isEmpty($full_name)){
+ $query = $query." , object_full_name='$full_name'";
+ }
+ if(!isEmpty($full_name)){
+ $query = $query." , object_abbreviation='$symbol'";
+ }
+ if(!isEmpty($object_type)){
+ $query = $query." , object_type_id='$object_type'";
+ }
executeDbQuery($query);
-
- #get the object_id
- $query = "SELECT object_id FROM Object WHERE object_accession = '$accession'";
- $object_id = executeDbQueryAndFetchRowArray($query);
+ $object_id = getObjectIdFromAccession($accession);
#next, insert object_id and synonym_id into object_synonym table.
- $query = "INSERT INTO Object_synonym(`object_id`,`synonym_id`) VALUES ('$object_id','$synonym_id') ON DUPLICATE KEY UPDATE object_id='$object_id'";
+ $query = "INSERT INTO Object_synonym(`object_id`,`synonym_id`) VALUES ('$object_id','$synonym_id')";
executeDbQuery($query);
-
}
}
if($#ARGV != 1){
print "Invalid inputs\n";
showUsage();
+ die;
}
$optionId = $ARGV[0];
$fileName = $ARGV[1];
+$curatorId = "";
$labName = "";
$userName = "";
$dbh = setUpDBConnection();
}
case "2"
{
- getCuratorProperties();
+ $curatorId = getCuratorId(getCuratorProperties());
importSeedInteractionData();
}
else{
projects / old-jaiswallab-svn / .git / commitdiff