解析 PubMed 查询的 curl 结果并将其格式化为引文

Question

这是 this 问题的后续问题。

同样的想法：我从 PubMed 中提取数据作为 XML 并使用 curl 来处理这些结果。这允许我获取我需要的信息（pub ID 列表）并将其用作另一个 PubMed 抓取的变量。 $name 最终将是动态的。

<?php 
$name = 'white,theodore';
// Return xml data from PubMed based on author search name
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term='.$name.'[author]&retmode=xml&retmax=50');
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch, CURLOPT_SSL_VERIFYPEER, false);
curl_setopt($ch, CURLOPT_VERBOSE, 0);
curl_setopt($ch, CURLOPT_FOLLOWLOCATION, true);
curl_setopt($ch, CURLOPT_AUTOREFERER, true);
curl_setopt($ch, CURLOPT_MAXREDIRS, 10);
curl_setopt($ch, CURLOPT_CUSTOMREQUEST, 'POST');
curl_setopt($ch, CURLOPT_FRESH_CONNECT, 1);

$output = curl_exec($ch);

curl_close($ch);

// Parse the results and concatenate into a string of Publication IDs
$xml=simplexml_load_string($output);
$idList = $xml->IdList;
$ids = "";
foreach($idList->children() as $id) {
    $ids .= $id . ",";
}

// Plug that string of IDs into another PubMed search, this one returning XML data for Publication Summaries
$path = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id='.$ids;

$ch2 = curl_init();
curl_setopt($ch2, CURLOPT_URL, $path);
curl_setopt($ch2, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch2, CURLOPT_SSL_VERIFYPEER, false);
curl_setopt($ch2, CURLOPT_VERBOSE, 0);
curl_setopt($ch2, CURLOPT_FOLLOWLOCATION, true);
curl_setopt($ch2, CURLOPT_AUTOREFERER, true);
curl_setopt($ch2, CURLOPT_MAXREDIRS, 10);
curl_setopt($ch2, CURLOPT_CUSTOMREQUEST, 'POST');
curl_setopt($ch2, CURLOPT_FRESH_CONNECT, 1);

$data = curl_exec($ch2);

curl_close($ch2);
// Parse those results and print only what is needed for Citation format
$cxml=simplexml_load_string($data);
foreach($cxml->children() as $docsum) {
  foreach($docsum->children() as $item) {
    foreach($item->children() as $details) {
        if ((string) $details['Name'] === 'Author') {echo $details . "., ";}
    }
    if ((string) $item['Name'] === 'FullJournalName') { echo $item . ". "; }
    if ((string) $item['Name'] === 'Title') { echo "<strong>" . $item . "</strong> "; }
    if ((string) $item['Name'] === 'Volume') { echo "Vol." . $item . ", "; }
    if ((string) $item['Name'] === 'Issue') { echo "Issue" . $item . ". "; }
    if ((string) $item['Name'] === 'PubDate') { echo $item . ". "; }
    foreach($item->children() as $details) {
            if ((string) $details['Name'] === 'PubType') {echo $details . ", ";}
        }
  }
  echo "</br></br>";
}

?>

return以下 XML 数据（这是一个结果）。

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
<eSummaryResult>
  <DocSum>
    <Id>27431223</Id>
    <Item Name="PubDate" Type="Date">2016 Oct</Item>
    <Item Name="EPubDate" Type="Date">2016 Sep 23</Item>
    <Item Name="Source" Type="String">Antimicrob Agents Chemother</Item>
    <Item Name="AuthorList" Type="List">
      <Item Name="Author" Type="String">Bhattacharya S</Item>
      <Item Name="Author" Type="String">Sobel JD</Item>
      <Item Name="Author" Type="String">White TC</Item>
    </Item>
    <Item Name="LastAuthor" Type="String">White TC</Item>
    <Item Name="Title" Type="String">A Combination Fluorescence Assay Demonstrates Increased Efflux Pump Activity as a Resistance Mechanism in Azole-Resistant Vaginal Candida albicans Isolates.</Item>
    <Item Name="Volume" Type="String">60</Item>
    <Item Name="Issue" Type="String">10</Item>
    <Item Name="Pages" Type="String">5858-66</Item>
    <Item Name="LangList" Type="List">
    <Item Name="Lang" Type="String">English</Item>
    </Item>
    <Item Name="NlmUniqueID" Type="String">0315061</Item>
    <Item Name="ISSN" Type="String">0066-4804</Item>
    <Item Name="ESSN" Type="String">1098-6596</Item>
    <Item Name="PubTypeList" Type="List">
      <Item Name="PubType" Type="String">Journal Article</Item>
    </Item>
    <Item Name="RecordStatus" Type="String">Unknown status</Item>
    <Item Name="PubStatus" Type="String">epublish</Item>
    <Item Name="ArticleIds" Type="List">
      <Item Name="pubmed" Type="String">27431223</Item>
      <Item Name="pii" Type="String">AAC.01252-16</Item>
      <Item Name="doi" Type="String">10.1128/AAC.01252-16</Item>
      <Item Name="pmc" Type="String">PMC5038269</Item>
      <Item Name="rid" Type="String">27431223</Item>
      <Item Name="eid" Type="String">27431223</Item>
      <Item Name="pmcid" Type="String">pmc-id: PMC5038269;embargo-date: 2017/04/01;</Item>
    </Item>
    <Item Name="DOI" Type="String">10.1128/AAC.01252-16</Item>
    <Item Name="History" Type="List">
      <Item Name="received" Type="Date">2016/06/10 00:00</Item>
      <Item Name="accepted" Type="Date">2016/07/12 00:00</Item>
      <Item Name="pmc-release" Type="Date">2017/04/01 00:00</Item>
      <Item Name="entrez" Type="Date">2016/07/20 06:00</Item>
      <Item Name="pubmed" Type="Date">2016/07/20 06:00</Item>
      <Item Name="medline" Type="Date">2016/07/20 06:00</Item>
    </Item>
    <Item Name="References" Type="List"></Item>
    <Item Name="HasAbstract" Type="Integer">1</Item>
    <Item Name="PmcRefCount" Type="Integer">0</Item>
    <Item Name="FullJournalName" Type="String">Antimicrobial agents and chemotherapy</Item>
    <Item Name="ELocationID" Type="String">doi: 10.1128/AAC.01252-16</Item>
    <Item Name="SO" Type="String">2016 Oct;60(10):5858-66</Item>
</DocSum>

</eSummaryResult>
</br></br>

这与此相呼应：

2016 Oct. Bhattacharya S., Sobel JD., White TC., A Combination Fluorescence Assay Demonstrates Increased Efflux Pump Activity as a Resistance Mechanism in Azole-Resistant Vaginal Candida albicans Isolates. Vol.60, Issue10. Journal Article, Antimicrobial agents and chemotherapy.

Zavrel M., White TC., Medically important fungi respond to azole drugs: an update. Vol.10, Issue8. Journal Article, Review, Future microbiology.

Esquivel BD., Smith AR., Zavrel M., White TC., Azole drug import into the pathogenic fungus Aspergillus fumigatus. Vol.59, Issue6. Journal Article, Antimicrobial agents and chemotherapy.

2015 Apr. Achterman RR., Moyes DL., Thavaraj S., Smith AR., Blair KM., White TC., Naglik JR., Dermatophytes activate skin keratinocytes via mitogen-activated protein kinase signaling and induce immune responses. Vol.83, Issue4. Journal Article, Infection and immunity.

2015 Feb 3. Ford CB., Funt JM., Abbey D., Issi L., Guiducci C., Martinez DA., Delorey T., Li BY., White TC., Cuomo C., Rao RP., Berman J., Thompson DA., Regev A., The evolution of drug resistance in clinical isolates of Candida albicans. Vol.4, Issue. Journal Article, eLife.

2014 Aug 1. White TC., Findley K., Dawson TL Jr., Scheynius A., Boekhout T., Cuomo CA., Xu J., Saunders CW., Fungi on the skin: dermatophytes and Malassezia. Vol.4, Issue8. Journal Article, Review, Cold Spring Harbor perspectives in medicine.

2014 Jan. Maguire SL., Wang C., Holland LM., Brunel F., Neuvéglise C., Nicaud JM., Zavrel M., White TC., Wolfe KH., Butler G., Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. Vol.10, Issue1. Journal Article, PLoS genetics.

2013 Nov 15. Campoli P., Perlin DS., Kristof AS., White TC., Filler SG., Sheppard DC., Pharmacokinetics of posaconazole within epithelial cells and fungi: insights into potential mechanisms of action during treatment and prophylaxis. Vol.208, Issue10. Journal Article, The Journal of infectious diseases.

2013 Jul 8. Achterman RR., White TC., Dermatophytes. Vol.23, Issue13. Journal Article, Current biology : CB.

ETC.

这一切都很好，只用我需要的数据产生引用，但我无法重新排序结果，所以作者排在第一位，PubDate 排在最后，等等。我尝试了很多选项，但我不够熟悉与他们中的任何一个，似乎无法破解它。

我试过附加 XSLT 样式 sheet，但我认为这不起作用，因为我实际上并没有输出 XML 文件。也许吧？

我尝试使用以下 XPath 而不是底部的 SimpleXML 块来 return 引用，但始终得到空白结果。因为所有数据都被标记为 <Item>，我尝试使用 Name 属性失败。

$content = simplexml_load_string($data);
$results = $content->xpath('Item[@Name]');
foreach($results as $result) {
  $title = $result->xpath('[@Name="Title"]');
  // Make sure there's an author attribute
  if($title) {
    // because we have a list of elements even if there's one result
    $items = $title[0]->attributes();
    $title = $items['value'];
  }
echo $results;
}

我也试过 DOMXPath 和 GetElementsByTagName 都无济于事。

基本上，我被卡住了。我已经尝试了很多变体并得到了很多错误，我觉得我在原地飞来飞去。有更多 Xpath 或 XSLT 经验的人有想法吗？

Answer 1

考虑以下纯 XSLT 解决方案（不需要 foreach 循环）处理节点重新排序甚至最终输出，因为 XSLT 可以将 XML 内容转换为文本（即 PHP 字符串）当然还有 HTML.

保持整个 CURL 调用不变，但替换嵌套的 foreach 循环。下面的 XSLT 脚本作为字符串嵌入，需要在 .ini 文件中启用 PHP 的 php_xsl 扩展才能访问 PHP 的内置 XSLT 1.0 处理器（即 libxslt）：

// ... same CURL call ...

// Parse those results and print only what is needed for Citation format
$cxml=simplexml_load_string($data);

$xslstr = '<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output indent="yes" method="text"/>
<xsl:strip-space elements="*"/>

<xsl:template match="DocSum">
    <xsl:if test="Item[@Name=\'AuthorList\' and .!=\'\']">
        <xsl:for-each select="Item[@Name=\'AuthorList\' and .!=\'\']/*">
            <xsl:value-of select="." />
            <xsl:if test="position() != last()">
                <xsl:text>, </xsl:text>
            </xsl:if>           
        </xsl:for-each><xsl:text>. </xsl:text>
    </xsl:if>

    <xsl:if test="Item[@Name=\'FullJournalName\' and .!=\'\']">
        <xsl:value-of select="concat(\'&lt;strong&gt;\', Item[@Name=\'FullJournalName\'], 
                                     \'&lt;/strong&gt;\')" />
        <xsl:text>. </xsl:text>
    </xsl:if>
    <xsl:if test="Item[@Name=\'Title\' and .!=\'\']">                        
        <xsl:value-of select="Item[@Name=\'Title\']" /><xsl:text>, </xsl:text>
    </xsl:if>
    <xsl:if test="Item[@Name=\'Volume\' and .!=\'\']">
        <xsl:value-of select="Item[@Name=\'Volume\']" /><xsl:text>. </xsl:text>
    </xsl:if>
    <xsl:if test="Item[@Name=\'Issue\' and .!=\'\']">
        <xsl:value-of select="Item[@Name=\'Issue\']" /><xsl:text>. </xsl:text>
    </xsl:if>
    <xsl:if test="Item[@Name=\'PubDate\' and .!=\'\']">
        <xsl:value-of select="Item[@Name=\'PubDate\']" /><xsl:text>. </xsl:text>
    </xsl:if>

    <xsl:if test="Item[@Name=\'PubTypeList\' and .!=\'\']">
        <xsl:for-each select="Item[@Name=\'PubTypeList\']/*">
            <xsl:value-of select="." />
            <xsl:if test="position() != last()">
                <xsl:text>, </xsl:text>
            </xsl:if>           
        </xsl:for-each><xsl:text>. </xsl:text>
    </xsl:if>

    <xsl:text>&lt;br&gt;&lt;br&gt;</xsl:text>
</xsl:template>     
</xsl:stylesheet>';

$xsl=simplexml_load_string($xslstr);

// XSLT TRANSFORMATION
$proc = new XSLTProcessor;
$proc->importStyleSheet($xsl); 
$newXML = $proc->transformToXML($cxml);

echo $newXML;

输出

解析 PubMed 查询的 curl 结果并将其格式化为引文

Parsing curl results from a PubMed query and formatting them into a citation

php

xslt

xpath

curl

pubmed