- ";
$lg .= "
- "; $lg .= "".$refs["title"]." "; } else { $lg = "
- "; $lg .= "".$refs["translated_title"]." "; $lg .= "
- "; $lg .= " "; $lg .= $refs["title"]." "; } $lg .= "
- "; $lg .= " "; $lg .= " "; $lg .= "
- "; $lg .= " "; $lg .= " ".$refs["journal_title"]." "; $lg .= "
- "; $lg .= " "; $lg .= "".$refs["year"]." ".$refs["month"]." "; $lg .= "
- "; $lg .= " "; $lg .= "".$refs["iso"]." "; // Keywords $lg .= "
- "; $lg .= " "; if (!empty($refs["mesh"])) { $lg .= "".implode(', ',$refs["mesh"])." "; } else if (!empty($refs["keywords"])) { $lg .= "".implode(', ',$refs["keywords"]).""; } else { $lg .= "Aucun mots clés"; } $lg .= " "; // User added HASHTAGS if (!empty($refs["hashtags"])) { $lg .= "
- "; $lg .= " "; $lg .= " "; } // Links $lg .= "
- "; $lg .= "Liens "; $lg .= "
- "; $lg .= " "; $lg .= " Traduction automatique en Français sur Google Translate "; $lg .= "
- "; $lg .= " "; $lg .= " DOI: ".$refs["doi"]." "; $lg .= "
- "; $lg .= " "; $lg .= " PMID: ".$refs["pmid"]." "; if (!empty($refs["similarurl"])) { $lg .= "
- "; $lg .= " "; $lg .= " Articles similaires "; } if (!empty($refs["citedbyurl"])) { $lg .= "
- "; $lg .= " "; $lg .= " Cité par "; } if (!empty($refs["referencesurl"])) { $lg .= "
- "; $lg .= " "; $lg .= " Références "; } if (!empty($refs["pmcid"])) { $lg .= "
- "; $lg .= " "; $lg .= " Texte complet gratuit "; } // Twitter $lg .= "
- "; $lg .= "Twitter "; $lg .= "
- "; $lg .= " "; $lg .= " Twitter cet article (lien vers l'article) "; $lg .= "
- "; $lg .= " "; $lg .= " Twitter cet article (lien vers cette page) "; $lg .= "
";
$lg .= "
";
$outputString = str_replace("%listgroup%", $lg, hsc($outputString));
}
// Remove double points separated with a span tag
$outputString = str_replace("..", '.', $outputString);
return $outputString;
}
/**
* Create output
* We have different database to extract data
* "pmid" = pubmed
* "pmcid" = pmc
*/
function render($mode, Doku_Renderer $renderer, $data) {
if ($mode != 'xhtml')
return false;
// Get the command and its arg(s)
list($state, $query) = $data;
list($base, $req) = $query;
list($cmd, $id) = explode(':', $req, 2);
$cmd = strtolower($cmd);
// If command is empty (in this case, command is the numeric pmids)
// Catch default command in plugin's preferences
$regex = '/^[0-9,]+$/';
// if (preg_match($regex, $cmd) === 1) {
if (empty($id)) {
$id = $cmd;
$cmd = $this->documentFormat;
}
// Manage the article reference commands in :
// short, long, long_abstract, vancouver,
// or user
$this->outputTpl["user"] = $this->getConf('user_defined_output');
// Allow user to define a document format
if ($cmd === "doc_format") {
$this->documentFormat = $id;
$this->useDocumentFormat = true;
return true;
} else if ($this->useDocumentFormat && (!in_array($cmd, $this->commands))) {
$cmd = $this->documentFormat;
}
//echo $cmd.PHP_EOL;
if (array_key_exists($cmd, $this->outputTpl)) {
// Check and open multiple PMIDs
$multipleIds = strpos($id, ",");
if ($multipleIds) {
$renderer->doc .= "- ";
$lg .= "
- ";
}
$id = explode(",", $id);
// With multiple PMIDs, the first one can be a word
if ($id[0] === "sort") {
// Remove [0]
array_shift($id);
// Sort ids
sort($id);
$id = array_reverse($id);
}
// Remove duplicates
$id = array_unique($id, SORT_REGULAR);
// Add each PMID to the renderer
foreach ($id as $curId) {
$renderer->doc .= $this->getIdOutput($cmd, $base, $curId, $multipleIds);
}
// Close multiple PMIDs
if ($multipleIds) {
$renderer->doc .= "
".htmlspecialchars($raw, ENT_QUOTES).""; } // Foreach PMIDs return true; case 'clear_raw_medline': $this->pubmedCache->clearCache(); $renderer->doc .= 'Cleared.'; return true; case 'remove_dir': $this->pubmedCache->removeDir(); $renderer->doc .= 'Directory cleared.'; return true; case 'search': $link = $this->pubmed2020->getPubmedSearchURL($id); $renderer->doc .=''; $renderer->doc .= ''.$link[0].''; $renderer->doc .=''; return true; case 'recreate_cross_refs': $this->pubmedCache->recreateCrossRefFile(); return true; case 'full_pdf_list': // Get all PMID from cache $mediaList = array_keys($this->pubmedCache->getAllMediaPaths()); // Get all PMID using the local PDF filename $pdfPmids = $this->pubmedCache->GetAllAvailableLocalPdfByPMIDs(); // Remove all local PDF PMIDs already in the media list $pdfPmids = array_diff($pdfPmids, $mediaList); // Remove all pdfPmid if present in the mediaList $pdfDois = $this->pubmedCache->GetAllAvailableLocalPdfByDOIs(); // Get PMIDs from DOIs $pmids = $this->pubmedCache->PmidFromDoi($pdfDois); // $i = 0; foreach($pdfDois as $doi) { // if (++$i == 5) // break; $raw = $this->pubmed2020->getDataFromCtxp($base, "", $doi); if (!empty($raw)) { $this->pubmedCache->saveRawMedlineContent($base, $raw); } } // Create a complete list of PMIDs to show //$fullPmids = array_merge($pdfPmids, $pmids, $mediaList); $fullPmids = array_merge($pdfPmids, $pmids); // Check multiple PMIDs (PMIDs can be passed in a coma separated list) $renderer->doc .= "
- ";
foreach($fullPmids as $currentPmid) {
$renderer->doc .= $this->getIdOutput("long_abstract", $base, $currentPmid, true);
} // Foreach PMIDs
foreach($pdfDois as $doi) {
$renderer->doc .=
"
';
$renderer->doc .= sprintf($this->getLang('plugin_cmd_not_found'),$cmd);
$renderer->doc .= '
';
$renderer->doc .= '';
$renderer->doc .= $this->getLang('pubmed_available_cmd');
$renderer->doc .= '
';
return true;
}
}
}
/**
* Get Medline raw data from cache or get it from NCBI
*/
function getMedlineContent($base, $id) {
global $conf;
$cached = $this->pubmedCache->getMedlineContent($base, $id);
if ($cached !== false) {
return $cached;
}
// Get content from PubMed website
$raw = $this->pubmed2020->getDataFromCtxp($base, $id);
// Save to cache
$this->pubmedCache->saveRawMedlineContent($base, $raw);
return $raw;
}
/**
* Check PMID format
*/
function checkIdFormat($base, $id) {
// Check PMID/PMCID format (numeric, 7 or 8 length)
if (!is_numeric($id) || (strlen($id) < 6 || strlen($id) > 8)) {
return false;
}
return true;
} // Ok pubmed2020
/**
* Get pubmed string output according to the given unique
* ID code passed and the command.
* $multipleIds : boolean, use it if the output in inside a multiple ids request
*/
function getIdOutput($cmd, $base, $id, $multipleIds) {
if (!$this->checkIdFormat($base, $id)) {
return sprintf($this->getLang('pubmed_wrong_format'));
}
// Get article content (from cache or web)
$raw = $this->getMedlineContent($base, $id);
if (empty($raw)) {
return sprintf($this->getLang('pubmed_not_found'), $id);
return false;
}
// Get the abstract of the article
$refs = $this->pubmed2020->readMedlineContent($raw, $this);
// Catch updated user output template
$outputTpl['user'] = $this->getConf('user_defined_output');
// Construct reference to article (author.title.rev.year..) according to command
$output = "";
if ($multipleIds)
$output .= ""; // Test CTXP URLs $retrieved = $this->pubmed2020->getDataFromCtxp("pmid", "15924077", "doi"); // Test MedLine Format Reader $myfile = fopen(DOKU_PLUGIN.'pubmed/tests/PM15924077.nbib', "r") or die("Unable to open file!"); $s = fread($myfile, filesize(DOKU_PLUGIN.'pubmed/tests/PM15924077.nbib')); fclose($myfile); // Check retrieved files if ($retrieved === $s) echo "File Content: Ok".PHP_EOL; else echo "File Content: NOT Ok".PHP_EOL; $this->pubmed2020->readMedlineContent($s, "PMID", $this); } } ?>