public function uploadCsvList($hasHeader, $thesId) { set_time_limit(300); ini_set("max_input_time", 300); ini_set('auto_detect_line_endings', true); $successCnt = 0; $fh = fopen($_FILES['uploadfile']['tmp_name'], 'r') or die("Can't open file. File may be too large. Try uploading file in sections."); $headerArr = array(); if ($hasHeader) { $headerData = fgetcsv($fh); foreach ($headerData as $k => $v) { $vStr = strtolower($v); $vStr = str_replace(array(" ", ".", "_"), "", $vStr); $vStr = str_replace(array("scientificnamewithauthor", "scientificname", "taxa", "species", "taxon"), "sciname", $vStr); $headerArr[$vStr] = $k; } } else { $headerArr["sciname"] = 0; } if (array_key_exists("sciname", $headerArr)) { $cnt = 0; ob_flush(); flush(); $taxUtil = new TaxonomyUtilities(); while ($valueArr = fgetcsv($fh)) { $tid = 0; $rankId = 0; $sciName = ""; $family = ""; $sciNameStr = $this->cleanInStr($valueArr[$headerArr["sciname"]]); $noteStr = ''; if ($sciNameStr) { $sciNameArr = $taxUtil->parseSciName($sciNameStr); //Check name is in taxa table and grab tid if it is $sql = ""; if ($thesId && is_numeric($thesId)) { $sql = 'SELECT t2.tid, ts.family, t2.rankid ' . 'FROM (taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid) ' . 'INNER JOIN taxa t2 ON ts.tidaccepted = t2.tid ' . 'WHERE (ts.taxauthid = ' . $thesId . ') '; } else { $sql = 'SELECT t.tid, ts.family, t.rankid ' . 'FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid ' . 'WHERE ts.taxauthid = 1 '; } $cleanSciName = $this->encodeString($sciNameArr['sciname']); $sql .= 'AND (t.sciname IN("' . $sciNameStr . '"' . ($cleanSciName ? ',"' . $cleanSciName . '"' : '') . '))'; $rs = $this->conn->query($sql); if ($rs) { if ($row = $rs->fetch_object()) { $tid = $row->tid; $family = $row->family; $rankId = $row->rankid; } $rs->free(); } //Load taxon into checklist if ($tid) { if ($rankId >= 180) { $sqlInsert = ''; $sqlValues = ''; if (array_key_exists('family', $headerArr) && ($valueArr[$headerArr['family']] && strtolower($family) != strtolower($valueArr[$headerArr['family']]))) { $sqlInsert .= ',familyoverride'; $sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['family']]) . '"'; } if (array_key_exists('habitat', $headerArr) && $valueArr[$headerArr['habitat']]) { $sqlInsert .= ',habitat'; $sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['habitat']]) . '"'; } if (array_key_exists('abundance', $headerArr) && $valueArr[$headerArr['abundance']]) { $sqlInsert .= ',abundance'; $sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['abundance']]) . '"'; } if ($noteStr || array_key_exists('notes', $headerArr) && $valueArr[$headerArr['notes']]) { if (array_key_exists('notes', $headerArr) && $valueArr[$headerArr['notes']]) { if ($noteStr) { $noteStr .= '; '; } $noteStr .= $valueArr[$headerArr['notes']]; } $sqlInsert .= ',notes'; $sqlValues .= ',"' . $this->cleanInStr($noteStr) . '"'; } $sql = 'INSERT INTO fmchklsttaxalink (tid,clid' . $sqlInsert . ') VALUES (' . $tid . ', ' . $this->clid . $sqlValues . ')'; //echo $sql; if ($this->conn->query($sql)) { $successCnt++; } else { $this->errorArr[] = $sciNameStr . " (TID = {$tid}) failed to load<br />Error msg: " . $this->conn->error; //echo $sql."<br />"; } } else { $this->errorArr[] = $sciNameStr . " failed to load (taxon must be of genus, species, or infraspecific ranking)"; } } else { $this->problemTaxa[] = $cleanSciName; //$statusStr = $sciNameStr." failed to load (misspelled or not yet in taxonomic thesaurus)"; //$failCnt++; } $cnt++; if ($cnt % 500 == 0) { echo '<li style="margin-left:10px;">' . $cnt . ' taxa loaded</li>'; ob_flush(); flush(); } } } fclose($fh); if ($cnt && $this->clMeta['type'] == 'rarespp') { $occurMain = new OccurrenceMaintenance($this->conn); $occurMain->protectStateRareSpecies(); } } else { $this->errorStr = 'ERROR: unable to locate scientific name column'; } return $successCnt; }