解析curl结果为simpleXML并使用它们创建新的XML数据

时间：2016-12-05 21:54:19

标签： php curl pubmed

我将PubMed中的数据作为XML提取并使用curl处理那些我作为SimpleXML加载到另一个页面的结果。这允许我获取我需要的信息（酒吧ID列表）并将其用作另一个发布的变量。这个获取特定pub ID的摘要。这是我的第一个文件（$ name最终将是动态的）：

<?php 
header('Content-type: text/xml');
$name = 'white,theodore';

$ch = curl_init();
curl_setopt($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);

print $output;

curl_close($ch);

?>

导出包含（除其他外）Pub Ids列表的XML数据。

xml output 

<eSearchResult>
<Count>45</Count>
<RetMax>45</RetMax>
<RetStart>0</RetStart>
  <IdList>
  <Id>27431223</Id>
  <Id>26234644</Id>
  <Id>25824209</Id>
  <Id>25667269</Id>
  <Id>25646566</Id>
  <Id>25085959</Id>
  <Id>24453983</Id>
  <Id>23908482</Id>
  <Id>23845238</Id>
  <Id>23758576</Id>
  <Id>23606207</Id>
  <Id>23475705</Id>
  <Id>23253612</Id>
  <Id>22951933</Id>
  <Id>22479177</Id>
  <Id>22080454</Id>
  <Id>21977036</Id>
  <Id>21951709</Id>
  <Id>21247460</Id>
  <Id>21145410</Id>
  <Id>21078937</Id>
  <Id>20941354</Id>
  <Id>20737430</Id>
  <Id>20656915</Id>
  <Id>20430817</Id>
  <Id>20161440</Id>
  <Id>19880755</Id>
  <Id>18757808</Id>
  <Id>18675371</Id>
  <Id>18539886</Id>
  <Id>18436555</Id>
  <Id>18404551</Id>
  <Id>18343803</Id>
  <Id>18310042</Id>
  <Id>17951521</Id>
  <Id>17071565</Id>
  <Id>15980350</Id>
  <Id>15766602</Id>
  <Id>15590814</Id>
  <Id>15047513</Id>
  <Id>14653518</Id>
  <Id>12576598</Id>
  <Id>12517831</Id>
  <Id>12019079</Id>
  <Id>11932451</Id>
</IdList>
<TranslationSet>
<Translation>
  <From>white, theodore[author]</From>
  <To>White, Theodore[Full Author Name]</To>
</Translation>
</TranslationSet>
<TranslationStack>
<TermSet>
  <Term>White, Theodore[Full Author Name]</Term>
  <Field>Full Author Name</Field>
  <Count>45</Count>
  <Explode>N</Explode>
</TermSet>
<OP>GROUP</OP>
</TranslationStack>
<QueryTranslation>White, Theodore[Full Author Name] </QueryTranslation>
</eSearchResult>

然后我将其加载到另一个页面，以便我可以使用SimpleXML将Pub ID转换为变量。使用该变量，尝试另一个curl / pubmed请求，这个请求根据这些ID提取摘要：

<?php
$xml=simplexml_load_file('https://sbs2.umkc.edu/wp-content/themes/SBS_Theme/js/pubMedExport.php','SimpleXMLElement', LIBXML_NOCDATA) or die("Error: Cannot create object");
$idList = $xml->IdList;
foreach($idList->children() as $id) {
$idResult = $id . ",";
//echo $idResult;

$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id='.$id.'');
curl_setopt($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);

$result = curl_exec($ch);
echo $result . "</br></br>";

curl_close($ch);

}
?>

我可以将其作为单独的引文导出但我的问题是，我仍然需要抓住第二组数据，以便我可以格式化某些内容，如作者并排除不相关的数据。

full citations

这里是来自ONE结果的XML。

<?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>

我无法弄清楚如何抓取第二组数据中的项目。消息来源显示它仍然正确格式化但我不断得到＆＃34;试图获得非对象的属性＆＃34;错误。

我考虑将这些结果发送到另一个文件并使用SimpleXML来控制它，但是因为我正在解析第一个文件并在同一页面上添加另一个curl，所以它似乎并不喜欢它我添加标题

非常感谢任何帮助！

更新：感谢@EatPeanutButter指出我正确的方向。通过使用     $cxml=simplexml_load_string($result); 代替     $Cxml = new SimpleXMLElement($result); 我不仅能够获取我需要的数据，还能将卷曲组合到一个页面上，如下所示。

<?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);

$result = curl_exec($ch2);

curl_close($ch2);
// Parse those results and print only what is needed for Citation format
$cxml=simplexml_load_string($result);
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>";
}

?>

现在，当然，这已经创建了一个新问题，我将作为后续问题发布！

0 个答案:

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