1: <?php
  2: 
  3: namespace cli_import;
  4: 
  5: require_once ROOT . 'classes/AbstractImporter.php';
  6: 
  7: class Importer_Expressions extends AbstractImporter {
  8: 
  9:     /**
 10:      * This function will import Quantification data from a tab-separated file.
 11:      * First line will be skiped as header.
 12:      * @inheritDoc
 13:      */
 14:     static function import($options) {
 15: 
 16:         $filename = $options['file'];
 17:         $quantification_id = $options['quantification_id'];
 18:         $analysis_id = $options['analysis_id'];
 19: 
 20:         $lines_total = trim(`wc -l $filename | cut -d' ' -f1`) - 1; //-1 for header line
 21:         self::setLineCount($lines_total);
 22: 
 23:         global $db;
 24: 
 25:         $lines_imported = 0;
 26:         $inserts_executed = 0;
 27: 
 28:         try {
 29: 
 30:             $db->beginTransaction();
 31: 
 32:             #shared parameters
 33:             $param_feature_id = null;
 34:             $param_value = null;
 35:             $param_biomaterial_id = null;
 36: 
 37:             // statement for insertion of expressionresult
 38:             $statement_insert_quant = $db->prepare('INSERT INTO expressionresult (feature_id, quantification_id, biomaterial_id, analysis_id, value) '
 39:                     . 'VALUES (:feature_id, :quantification_id, :biomaterial_id, :analysis_id, :value)');
 40:             $statement_insert_quant->bindParam('feature_id', $param_feature_id, PDO::PARAM_STR);
 41:             $statement_insert_quant->bindParam('value', $param_value, PDO::PARAM_STR);
 42:             $statement_insert_quant->bindParam('biomaterial_id', $param_biomaterial_id, PDO::PARAM_INT);
 43:             $statement_insert_quant->bindValue('quantification_id', $quantification_id, PDO::PARAM_INT);
 44:             $statement_insert_quant->bindValue('analysis_id', $analysis_id, PDO::PARAM_INT);
 45: 
 46:             //statement to get biomaterial ids
 47:             $statement_get_biomaterial_id = $db->prepare('SELECT biomaterial_id FROM biomaterial WHERE name=? LIMIT 1');
 48: 
 49:             //statement for feature ids
 50:             $statement_get_feature_id = $db->prepare('SELECT feature_id FROM feature WHERE uniquename=?  AND organism_id=? LIMIT 1');
 51: 
 52:             $file = fopen($filename, 'r');
 53:             if (feof($file))
 54:                 return;
 55:             //process header line, get biomaterial_ids for names
 56:             $biomaterial_names = fgetcsv($file, 0, "\t");
 57:             $biomaterial_ids = array();
 58:             for ($i = 1; $i < count($biomaterial_names); $i++) {
 59:                 $statement_get_biomaterial_id->execute(array($biomaterial_names[$i]));
 60:                 $biomaterial_ids[$i] = $statement_get_biomaterial_id->fetchColumn();
 61:                 if (!$biomaterial_ids[$i]) {
 62:                     throw new ErrorException('Biomaterial with this name not defined');
 63:                 }
 64:             }
 65: 
 66:             //process count lines
 67:             while (($line = fgetcsv($file, 0, "\t")) !== false) {
 68:                 if (count($line) == 0)
 69:                     continue;
 70:                 //get feature id once per line
 71:                 $feature_uniquename = IMPORT_PREFIX . "_" . $line[0];
 72:                 $statement_get_feature_id->execute(array($feature_uniquename, DB_ORGANISM_ID));
 73:                 $param_feature_id = $statement_get_feature_id->fetchColumn();
 74: 
 75:                 //for all columns >1, insert counts based on feature_id and biomaterial_id
 76:                 for ($i = 1; $i < count($line); $i++) {
 77:                     $param_value = $line[$i];
 78:                     $param_biomaterial_id = $biomaterial_ids[$i];
 79:                     $statement_insert_quant->execute();
 80:                     $inserts_executed++;
 81:                 }
 82: 
 83:                 self::updateProgress(++$lines_imported);
 84:             }
 85: 
 86:             self::preCommitMsg();
 87:             if (!$db->commit()) {
 88:                 $err = $db->errorInfo();
 89:                 throw new ErrorException($err[2], ERRCODE_TRANSACTION_NOT_COMPLETED, 1);
 90:             }
 91:         } catch (\Exception $error) {
 92:             $db->rollback();
 93:             throw $error;
 94:         }
 95:         return array(LINES_IMPORTED => $lines_imported, 'inserts executed' => $inserts_executed);
 96:     }
 97: 
 98:     /**
 99:      * @inheritDoc
100:      */
101:     public static function CLI_getCommand(\Console_CommandLine $parser) {
102:         $command = parent::CLI_getCommand($parser);
103:         $command->addOption('quantification_id', array(
104:             'short_name' => '-q',
105:             'long_name' => '--quantification_id',
106:             'description' => 'quantification id'
107:         ));
108: 
109:         $command->addOption('analysis_id', array(
110:             'short_name' => '-a',
111:             'long_name' => '--analysis_id',
112:             'description' => 'analysis_id.'
113:         ));
114:         return $command;
115:     }
116: 
117:     /**
118:      * @inheritDoc
119:      */
120:     public static function CLI_checkRequiredOpts(\Console_CommandLine_Result $command) {
121:         parent::CLI_checkRequiredOpts($command);
122:         $options = $command->options;
123:         AbstractImporter::dieOnMissingArg($options, 'quantification_id');
124:         AbstractImporter::dieOnMissingArg($options, 'analysis_id');
125:     }
126: 
127:     /**
128:      * @inheritDoc
129:      */
130:     public static function CLI_commandDescription() {
131:         return "Importer for expression result \"count matrix\" files";
132:     }
133: 
134:     /**
135:      * @inheritDoc
136:      */
137:     public static function CLI_commandName() {
138:         return 'expressions';
139:     }
140: 
141:     /**
142:      * @inheritDoc
143:      */
144:     public static function CLI_longHelp() {
145:         return <<<EOF
146:    
147: Imports output files from Anna-Lena Keller's "aggregator_CountMat.pl" script.
148: 
149: File format looks like:
150: ID      flower_L1       flower_L2       flower_L3       coronatin_L1    coronatin_L2    coronatin_L3
151: comp234711_c0_seq9      21.93   11.26   8.83    2.40    0.00    2.25
152: 
153: The labels in the header have to match the condition sample names in the database
154: \033[0;31mThis import requires a successful Sequence ID Import!\033[0m
155: EOF;
156:     }
157: 
158: }
159: 
160: ?>
161: