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NLM Style Checker API

The NLM Style Checker API allows programmatic access to the NLM Style Checker.

Base URL: https://www.ncbi.nlm.nih.gov/pmc/utils/style4/v1.0/.

Requests to the service use HTTP POST, with a set of parameters that specify the input data and response format. Responses may be delivered in JSON, XML, or HTML depending on the value set for the parameter -F format.

Parameters

Note: It is assumed most users will interact with the API via curl, so parameters and examples are expressed in that syntax.

  • -X POST - The service accepts only POST requests. (If using -d/--data or -f/--form, -X POST can be omitted, as -d/--data and -f/--form imply POST.)
  • -H "Content-Type: application/json" - use this if sending data in JSON format
  • -H "Content-Type: text/xml" - use this if sending data in XML format
  • -H "Accept: application/json" - to receive response JSON format
  • -H "Accept: text/xml" - to receive response in XML format

  • -d/--data - data to post. This can point to a JSON data file, or point directly to the XML file to be checked.

    Within the -d/--data parameter, the following properties are allowed

    • id: user-generated, will be returned in response for parsing purposes on part of the user
    • style: which stylechecker to use. Currently supported: pmc (default), pmc-nihms, pmc-books
    • doc_name: name of xml document to be checked. The name will be returned in the response, for parsing purposes on part of the user
    • digest_type: algorithm used to map document to a bit string. Currently only "md5" is supported
    • digest: alpha hash string that represents the mapping created by digest_type.
    • transcoding: gzip, base64 -- algorithm used to convert document into a string
    • data: the document-as-string generated by the transcoding algorithm

  • -F/--form - form upload. This uses the names of the form fields from the HTML version of the Style Checker.

  • -F nxml= (pasted text)
  • -F pxml= (XML file being checked)
  • -F style= (pmc [default], pmc-nihms, pmc-books)
  • -F format= (xml, json, html)
  • -F transcoding= (base64, plain)

Examples

Example 1: Upload a data file using -d/--data. The data file can be either JSON or XML. In it, provide the xml file to be checked, encoded as a base64 string.

JSON

curl -H "Content-Type: application/json" -d @data_file.json https://www.ncbi.nlm.nih.gov/pmc/utils/style4/v1.0/

where data_file.json looks like

{"id": "your-id",
 "style": "pmc",
 "doc_name": "test.xml",
 "transcoding": "gzip,base64",
 "data": "[content of test.xml encoded into base64 string]"}

XML

curl -H "Content-Type: text/xml" -d @data_file.xml https://www.ncbi.nlm.nih.gov/pmc/utils/style4/v1.0/

where data_file.xml looks like

<request>
 <id>your-id</id>
 <style>pmc</style>
 <doc_name>test.xml</doc_name>
 <transcoding>gzip,base64</transcoding>
 <data>[content of test.xml encoded into base64 string]</data>
</request>

Example 2: Upload an XML file using -F/--form. This mimics the HTML version of the Style Checker.

curl -i -F style=pmc -F pxml=@test.xml -F transcoding=plain -F format=xml https://www.ncbi.nlm.nih.gov/pmc/utils/style4/v1.0/

Use the "format" field to specify the format of the response. Allowed values are "json" and "xml".

Response

JSON – NO ERROR or WARNING

{
 "status": "ok",
 "responseDate": "2021-09-02 15:42:00",
 "request": "style=pmc-nihms;pxml=test.xml;transcoding=plain;format=json",
 "dtd_valid": true,
 "style_valid": true,
 "messages": [
 {
  "status": "OK",
  "caption": "DTD Validation",
  "ctx": {
   "transcoding": "plain",
   "data": "...",
}
},
{
  "status": "OK",
  "caption": "NIH Manuscript Style Check",
  "stat": {
   "errors": "0",
   "warnings": "0"
  },
  "ctx": {
   "transcoding": "plain",
   "data": "...",
  }
 }
]
}

JSON – INVALID

{
 "status": "ok",
 "responseDate": "2021-09-02 15:52:40",
 "request": "POSTDATA=%7B%20%20%20%20%22id%22%3A%20%22ABCDE-FGHIJ-12345-67890%22%
 2C%20%20%20%20%22style%22%3A%20%22pmc%22%2C%20%20%20%20%22doc_name%22%3A%20%22test.xml
 %22%2C%20%20%20%20%20%22url%22%3A%20%22https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Futils
 %2Fstyle4%2Ftest%2Ftest.xml%22%2C%20%20%20%20%22coding%22%3A%20%22plain%22%09%7D",
 "dtd_valid": true,
 "style_valid": false,
 "messages": [
 {
  "status": "OK",
  "caption": "DTD Validation",
  "ctx": {
   "transcoding": "plain",
   "data": "..."
}
},
{
  "status": "Errors",
  "caption": "PMC Style Check",
  "stat": {
   "errors": "2",
   "warnings": "0"
  },
  "html": {
   "transcoding": "plain",
   "data": "..."
},
"ctx": {
   "transcoding": "plain",
   "data": "..."
},
"rawerrors": [
    {
     "message": {
      "type": "error",
      "text": "fpage-elocation check: Either <fpage> or <elocation-id> must 
      be present in <article-meta>
      (Tagging Guidelines) see https:\/\/www.ncbi.nlm.nih.gov\/pmc\/pmcdoc\
      /tagging-guidelines\/article\/tags.html#el-fpage"
     }
    },
    {
     "message": {
      "type": "error",
      "text": "pub-date check: article-meta must contain a real publication date."
     }
}
]
}
]
}

XML – NO ERROR OR WARNING

<response status="ok">
 <request outtype="xml">
  <echo>style=pmc-nihms;pxml=test.xml;transcoding=plain;format=xml</echo>
 </request>
 <dtd_valid>true</dtd_valid>
 <style_valid>true</style_valid>
 <messages>
  <msg status="OK" caption="DTD Validation">
   <ctx><transcoding>plain</transcoding><data><![CDATA ... </data></ctx>
  </msg>
  <msg status="OK" caption="NIH Manuscript Style Check">
   <stat errors="0" warnings="0"/>
   <ctx><transcoding>plain</transcoding><data><![CDATA ... </data></ctx>
  </msg>
 </messages>
</response>

XML – INVALID

<response status="ok">
 <request outtype="xml">
  <echo>POSTDATA=%3Crequest%3E%20%20%3Cstyle%3Epmc%3C%2Fstyle%3E%20%20%3Cid%
  3EABCDE-FGHIJ-12345-67890%3C%2Fid%3E%20%20%3Cdoc_name%3Etest.xml%3C%2Fdoc_name
  %3E%20%20%3Curl%3Ehttps%3A%2F%2Fwww.ncbi.nlm.nih.gov
  %2Fpmc%2Futils%2Fstyle4%2Ftest%2Ftest.xml%3C%2Furl%3E%20%20%3Ccoding
  %3Eplain%3C%2Fcoding%3E%20%3C%2Frequest%3E</echo>
 </request>
 <dtd_valid>true</dtd_valid>
 <style_valid>false</style_valid>
 <messages>
  <msg status="OK" caption="DTD Validation">
   <ctx><transcoding>plain</transcoding><data><![CDATA ... </data></ctx>
  </msg>
  <msg status="Errors" caption="PMC Style Check">
   <stat errors="2" warnings="0"/>
   <html><transcoding>plain</transcoding><data><![CDATA ... </data></html>
   <ctx><transcoding>plain</transcoding><data><![CDATA ... </data></ctx>
   <rawerrors>
    <message type="error">fpage-elocation check: Either <fpage> or 
    <elocation-id> must be present in <article-meta> 
    (Tagging Guidelines) see https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/
    tagging-guidelines/article/tags.html#el-fpage</message>
    <message type="error">pub-date check: article-meta must contain a 
    real publication date.</message>
   </rawerrors>
  </msg>
 </messages>
</response>