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- <?php
- function tripal_pub_remote_search_PMID($search_array, $num_to_retrieve, $pager_id) {
-
-
-
- $num_criteria = $search_array['num_criteria'];
- $days = $search_array['days'];
- $search_str = '';
- for ($i = 0; $i <= $num_criteria; $i++) {
- $search_terms = $search_array['criteria'][$i]['search_terms'];
- $scope = $search_array['criteria'][$i]['scope'];
- $op = $search_array['criteria'][$i]['operation'];
-
- if ($op) {
- $search_str .= "$op";
- }
-
- $search_str .= '(';
- $search_str .= implode("+", preg_split('/\s+/', trim($search_terms)));
- if($scope == 'title') {
- $search_str .= '[Title]';
- }
- elseif($scope == 'author') {
- $search_str .= '[Author]';
- }
- elseif($scope == 'abstract') {
- $search_str .= '[Title/Abstract]';
- }
- elseif($scope == 'id') {
- $search_str .= '[Uid]';
- }
- $search_str .= ')';
- }
- $search_array['limit'] = $num_to_retrieve;
- $search_array['search_terms'] = $search_str;
-
- $pubs = tripal_pager_callback('tripal_pub_PMID_range',
- $num_to_retrieve, $pager_id, 'tripal_pub_PMID_count', $search_array);
-
- return $pubs;
- }
- function tripal_pub_PMID_count($search_array) {
- $terms = $search_array['search_terms'];
- $days = $search_array['days'];
- $limit = $search_array['limit'];
-
- $results = tripal_pub_PMID_search_init($terms, $limit, $days);
- $_SESSION['tripal_pub_PMID_query'][$terms]['Count'] = $results['Count'];
- $_SESSION['tripal_pub_PMID_query'][$terms]['WebEnv'] = $results['WebEnv'];
- $_SESSION['tripal_pub_PMID_query'][$terms]['QueryKey'] = $results['QueryKey'];
-
- return $results['Count'];
- }
- function tripal_pub_PMID_range($search_array, $start = 0, $limit = 10) {
- $terms = $search_array['search_terms'];
- $days = $search_array['days'];
- $limit = $search_array['limit'];
-
- $count = $_SESSION['tripal_pub_PMID_query'][$terms]['Count'];
-
-
- $query_key = $_SESSION['tripal_pub_PMID_query'][$terms]['QueryKey'];
- $web_env = $_SESSION['tripal_pub_PMID_query'][$terms]['WebEnv'];
-
-
-
- if (!$query_key) {
- $results = tripal_pub_PMID_search_init($terms, $limit, $days);
- $_SESSION['tripal_pub_PMID_query']['WebEnv'] = $results['WebEnv'];
- $_SESSION['tripal_pub_PMID_query']['QueryKey'] = $results['QueryKey'];
- $query_key = $results['QueryKey'];
- $web_env = $results['WebEnv'];
- }
-
- $pmids_txt = tripal_pub_PMID_fetch($query_key, $web_env, 'uilist', 'text', $start, $limit);
-
-
- $pmids = explode("\n", trim($pmids_txt));
- $pubs = array();
- foreach ($pmids as $pmid) {
-
- $pub_xml = tripal_pub_PMID_fetch($query_key, $web_env, 'null', 'xml', 0, 1, array('id' => $pmid));
- $pub = tripal_pub_PMID_parse_pubxml($pub_xml);
- $pubs[] = $pub;
- }
- return $pubs;
- }
- function tripal_pub_PMID_search_init($terms, $retmax, $days = 0){
-
-
-
-
- $query_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=Pubmed&retmax=$retmax&usehistory=y&term=$terms";
- if($days) {
- $query_url .= "&reldate=$days&datetype=edat";
- }
-
- $rfh = fopen($query_url, "r");
- if (!$rfh) {
- drupal_set_message('Could not perform Pubmed query. Cannot connect to Entrez.', 'error');
- return 0;
- }
-
-
- $query_xml = '';
- while (!feof($rfh)) {
- $query_xml .= fread($rfh, 255);
- }
- fclose($rfh);
-
- $xml = new XMLReader();
- $xml->xml($query_xml);
-
-
- $result = array();
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'WebEnv') {
-
-
- break;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
-
- switch ($element) {
- case 'Count':
- $xml->read();
- $result['Count'] = $xml->value;
- break;
- case 'WebEnv':
- $xml->read();
- $result['WebEnv'] = $xml->value;
- break;
- case 'QueryKey':
- $xml->read();
- $result['QueryKey'] = $xml->value;
- break;
- }
- }
- }
- return $result;
- }
- function tripal_pub_PMID_fetch($query_key, $web_env, $rettype = 'null',
- $retmod = 'null', $start = 0, $limit = 10, $args = array()){
-
-
- $fetch_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=$rettype&retmode=$retmod&retstart=$start&retmax=$limit&db=Pubmed&query_key=$query_key&WebEnv=$web_env";
-
- foreach ($args as $key => $value) {
- if(is_array($value)) {
- $fetch_url .= "&$key=";
- foreach ($value as $item) {
- $fetch_url .= "$item,";
- }
- $fetch_url = substr($fetch_url, 0, -1);
- }
- else {
- $fetch_url .= "&$key=$value";
- }
- }
-
- $rfh = fopen($fetch_url, "r");
- if (!$rfh) {
- drupal_set_message('Could not perform Pubmed query. Cannot connect to Entrez.', 'error');
- return '';
- }
- $results = '';
- if($rfh) {
- while (!feof($rfh)) {
- $results .= fread($rfh, 255);
- }
- fclose($rfh);
- }
-
- return $results;
- }
- function tripal_pub_PMID_parse_pubxml($pub_xml) {
- $pub = array();
-
- if (!$pub_xml) {
- return $pub;
- }
-
-
- $xml = new XMLReader();
- $xml->xml($pub_xml);
- while ($xml->read()) {
- $element = $xml->name;
- if ($xml->nodeType == XMLReader::ELEMENT) {
-
- switch ($element) {
- case 'PMID':
- $xml->read();
- $pub['Pub Accession'] = $xml->value;
- $pub['Publication Database'] = 'PMID';
- break;
- case 'Article':
- $pub_model = $xml->getAttribute('PubModel');
- $pub['Publication Model'] = $pub_model;
- tripal_pub_PMID_parse_article($xml, $pub);
- break;
- case 'MedlineJournalInfo':
- tripal_pub_PMID_parse_medline_journal_info($xml, $pub);
- break;
- case 'ChemicalList':
-
- break;
- case 'SupplMeshList':
-
- break;
- case 'CitationSubset':
-
- break;
- case 'CommentsCorrections':
-
- break;
- case 'GeneSymbolList':
-
- break;
- case 'MeshHeadingList':
-
- break;
- case 'NumberOfReferences':
-
- break;
- case 'PersonalNameSubjectList':
-
- break;
- case 'OtherID':
-
- break;
- case 'OtherAbstract':
-
- break;
- case 'KeywordList':
-
- break;
- case 'InvestigatorList':
-
- break;
- case 'GeneralNote':
-
- break;
- case 'DeleteCitation':
-
- break;
- default:
- break;
- }
- }
- }
- $pub['Citation'] = $pub['Author List'] .
- '. <a href="http://www.ncbi.nlm.nih.gov/pubmed/' . $pub['Pub Accession'] . '" target="_blank">' . $pub['Title'] . '</a> ' .
- $pub['Journal ISO Abbreviation']. '. ' . $pub['Publication Date'];
- if ($pub['Volume'] or $pub['Issue']) {
- $pub['Citation'] .= '; ';
- }
- if ($pub['Volume']) {
- $pub['Citation'] .= $pub['Volume'];
- }
- if ($pub['Issue']) {
- $pub['Citation'] .= '(' . $pub['Issue'] . ')';
- }
- if ($pub['Pages']) {
- $pub['Citation'] .= ':' . $pub['Pages'];
- }
- $pub['Citation'] .= '. PubMed PMID: ' . $pub['Pub Accession'];
-
-
- return $pub;
- }
- function tripal_pub_PMID_parse_medline_journal_info($xml, &$pub) {
- while ($xml->read()) {
-
- $element = $xml->name;
-
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'MedlineJournalInfo') {
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'Country':
-
- $xml->read();
- $pub['Journal Country'] = $xml->value;
- break;
- case 'MedlineTA':
-
- break;
- case 'NlmUniqueID':
-
- break;
- case 'ISSNLinking':
-
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_article($xml, &$pub) {
-
- while ($xml->read()) {
-
- $element = $xml->name;
-
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Article') {
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'Journal':
- tripal_pub_PMID_parse_journal($xml, $pub);
- break;
- case 'ArticleTitle':
- $xml->read();
- $pub['Title'] = $xml->value;
- break;
- case 'Abstract':
- tripal_pub_PMID_parse_abstract($xml, $pub);
- break;
- case 'Pagination':
- tripal_pub_PMID_parse_pagination($xml, $pub);
- break;
- case 'ELocationID':
- $type = $xml->getAttribute('EIdType');
- $valid = $xml->getAttribute('ValidYN');
- $xml->read();
- $elocation = $xml->value;
- if ($type == 'doi' and $valid == 'Y') {
- $pub['DOI'] = $elocation;
- }
- if ($type == 'pii' and $valid == 'Y') {
- $pub['PII'] = $elocation;
- }
- $pub['Elocation'] = $elocation;
- break;
- case 'Affiliation':
-
- $xml->read();
- $pub['Authors'][0]['Affiliation'] = $xml->value;
- break;
- case 'AuthorList':
- $complete = $xml->getAttribute('CompleteYN');
- tripal_pub_PMID_parse_authorlist($xml, $pub);
- break;
- case 'InvestigatorList':
-
-
- break;
- case 'Language':
- $xml->read();
- $lang_abbr = $xml->value;
-
- $pub['Language'][] = tripal_pub_remote_search_get_language($lang_abbr);
- $pub['Language Abbr'][] = $lang_abbr;
- break;
- case 'DataBankList':
-
- break;
- case 'GrantList':
-
- break;
- case 'PublicationTypeList':
- tripal_pub_PMID_parse_publication_type($xml, $pub);
- break;
- case 'VernacularTitle':
- $xml->read();
- $pub['Vernacular Title'][] = $xml->value;
- break;
- case 'ArticleDate':
-
-
-
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_publication_type($xml, &$pub) {
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'PublicationTypeList') {
-
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'PublicationType':
- $xml->read();
- $pub_cvterm = tripal_cv_get_cvterm_by_name($xml->value, NULL, 'tripal_pub');
- if (!$pub_cvterm) {
-
- $pub_cvterm = tripal_cv_get_cvterm_by_synonym($xml->value, NULL, 'tripal_pub');
- if (!$pub_cvterm) {
- watchdog('tpub_pubmed', 'Cannot find a valid vocabulary term for the publication type: "%term".',
- array('%term' => $xml->value), WATCHDOG_ERROR);
- }
- }
- else {
- $pub['Publication Type'][] = $pub_cvterm->name;
- }
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_abstract($xml, &$pub) {
- $abstract = '';
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Abstract') {
-
- $pub['Abstract'] = $abstract;
- return;
- }
-
-
-
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'AbstractText':
- $label = $xml->getAttribute('Label');
- $xml->read();
- if ($label) {
- $pub['Structured Abstract Part'][] = $xml->value;
- $abstract .= "<p><b>$label</b></br>" . $xml->value . '</p>';
- }
- else {
- $abstract .= '<p>' . $xml->value . '</p>';
- }
- break;
- case 'CopyrightInformation':
- $xml->read();
- $pub['Copyright'] = $xml->value;
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_pagination($xml, &$pub) {
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Pagination') {
-
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'MedlinePgn':
- $xml->read();
- if(trim($xml->value)) {
- $pub['Pages'] = $xml->value;
- }
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_journal($xml, &$pub) {
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Journal') {
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'ISSN':
- $issn_type = $xml->getAttribute('IssnType');
- $xml->read();
- $issn = $xml->value;
- $pub['ISSN'] = $issn;
- if ($issn_type == 'Electronic') {
- $pub['eISSN'] = $issn;
- }
- if ($issn_type == 'Print') {
- $pub['pISSN'] = $issn;
- }
- break;
- case 'JournalIssue':
-
- $cited_medium = $xml->getAttribute('CitedMedium');
- tripal_pub_PMID_parse_journal_issue($xml, $pub);
- break;
- case 'Title':
- $xml->read();
- $pub['Journal Name'] = $xml->value;
- break;
- case 'ISOAbbreviation':
- $xml->read();
- $pub['Journal ISO Abbreviation'] = $xml->value;
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_journal_issue($xml, &$pub) {
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'JournalIssue'){
-
- return;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'Volume':
- $xml->read();
- $pub['Volume'] = $xml->value;
- break;
- case 'Issue':
- $xml->read();
- $pub['Issue'] = $xml->value;
- break;
- case 'PubDate':
- $date = tripal_pub_PMID_parse_date($xml, 'PubDate');
- $year = $date['year'];
- $month = $date['month'];
- $day = $date['day'];
- $medline = $date['medline'];
-
- $pub['Year'] = $year;
- if ($month and $day and $year) {
- $pub['Publication Date'] = "$year $month $day";
- }
- elseif ($month and !$day and $year) {
- $pub['Publication Date'] = "$year $month";
- }
- elseif (!$month and !$day and $year) {
- $pub['Publication Date'] = $year;
- }
- elseif ($medline) {
- $pub['Publication Date'] = $medline;
- }
- else {
- $pub['Publication Date'] = "Date Unknown";
- }
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_date ($xml, $element_name) {
- $date = array();
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT and $element == $element_name){
-
- return $date;
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'Year':
- $xml->read();
- $date['year'] = $xml->value;
- break;
- case 'Month':
- $xml->read();
- $month =
- $date['month'] = $xml->value;
- break;
- case 'Day':
- $xml->read();
- $date['day'] = $xml->value;
- break;
- case 'MedlineDate':
-
- $xml->read();
- $date['medline'] = $xml->value;
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_PMID_parse_authorlist($xml, &$pub) {
- $num_authors = 0;
-
- while ($xml->read()) {
- $element = $xml->name;
-
- if ($xml->nodeType == XMLReader::END_ELEMENT){
-
- if($element == 'AuthorList') {
-
- $author_list = '';
- foreach ($pub['Authors'] as $author) {
- if ($author['valid'] == 'N') {
-
-
- continue;
- }
- if ($author['Collective']) {
- $author_list .= $author['Collective'] . ', ';
- }
- else {
- $author_list .= $author['Surname'] . ' ' . $author['First Initials'] . ', ';
- }
- }
- $author_list = substr($author_list, 0, -2);
- $pub['Author List'] = $author_list;
- return;
- }
-
-
- if($element == 'Author') {
- $num_authors++;
- }
- }
- if ($xml->nodeType == XMLReader::ELEMENT) {
- switch ($element) {
- case 'Author':
- $valid = $xml->getAttribute('ValidYN');
- $pub['Authors'][$num_authors]['valid'] = $valid;
- break;
- case 'LastName':
- $xml->read();
- $pub['Authors'][$num_authors]['Surname'] = $xml->value;
- break;
- case 'ForeName':
- $xml->read();
- $pub['Authors'][$num_authors]['Given Name'] = $xml->value;
- break;
- case 'Initials':
- $xml->read();
- $pub['Authors'][$num_authors]['First Initials'] = $xml->value;
- break;
- case 'Suffix':
- $xml->read();
- $pub['Authors'][$num_authors]['Suffix'] = $xml->value;
- break;
- case 'CollectiveName':
- $xml->read();
- $pub['Authors'][$num_authors]['Collective'] = $xml->value;
- break;
- case 'Identifier':
-
- break;
- default:
- break;
- }
- }
- }
- }
- function tripal_pub_remote_search_get_language($lang_abbr) {
- $languages = array(
- 'afr' => 'Afrikaans',
- 'alb' => 'Albanian',
- 'amh' => 'Amharic',
- 'ara' => 'Arabic',
- 'arm' => 'Armenian',
- 'aze' => 'Azerbaijani',
- 'ben' => 'Bengali',
- 'bos' => 'Bosnian',
- 'bul' => 'Bulgarian',
- 'cat' => 'Catalan',
- 'chi' => 'Chinese',
- 'cze' => 'Czech',
- 'dan' => 'Danish',
- 'dut' => 'Dutch',
- 'eng' => 'English',
- 'epo' => 'Esperanto',
- 'est' => 'Estonian',
- 'fin' => 'Finnish',
- 'fre' => 'French',
- 'geo' => 'Georgian',
- 'ger' => 'German',
- 'gla' => 'Scottish Gaelic',
- 'gre' => 'Greek, Modern',
- 'heb' => 'Hebrew',
- 'hin' => 'Hindi',
- 'hrv' => 'Croatian',
- 'hun' => 'Hungarian',
- 'ice' => 'Icelandic',
- 'ind' => 'Indonesian',
- 'ita' => 'Italian',
- 'jpn' => 'Japanese',
- 'kin' => 'Kinyarwanda',
- 'kor' => 'Korean',
- 'lat' => 'Latin',
- 'lav' => 'Latvian',
- 'lit' => 'Lithuanian',
- 'mac' => 'Macedonian',
- 'mal' => 'Malayalam',
- 'mao' => 'Maori',
- 'may' => 'Malay',
- 'mul' => 'Multiple languages',
- 'nor' => 'Norwegian',
- 'per' => 'Persian',
- 'pol' => 'Polish',
- 'por' => 'Portuguese',
- 'pus' => 'Pushto',
- 'rum' => 'Romanian, Rumanian, Moldovan',
- 'rus' => 'Russian',
- 'san' => 'Sanskrit',
- 'slo' => 'Slovak',
- 'slv' => 'Slovenian',
- 'spa' => 'Spanish',
- 'srp' => 'Serbian',
- 'swe' => 'Swedish',
- 'tha' => 'Thai',
- 'tur' => 'Turkish',
- 'ukr' => 'Ukrainian',
- 'und' => 'Undetermined',
- 'urd' => 'Urdu',
- 'vie' => 'Vietnamese',
- 'wel' => 'Welsh',
- );
- return $languages[$lang_abbr];
- }
|