24 February 2016

Registering a tool in the @ELIXIREurope regisry using XML, XSLT, JSON and curl. My notebook.

The Elixir Registry / pmid:26538599 "A portal to bioinformatics resources world-wide. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools."
In this post, I will describe how I've used the bio.tools API to register some tools from jvarkit.

Authenticate with your credentials

using curl, the 'bio.tools' service returns a authentication token.

$ curl -s \
 -H "Content-type: application/json" \
 -X POST \
 -d '{"username":"my-login@univ-nantes.fr","password":"password1234"}' \
 https://bio.tools/api/auth/login |\
 python -m json.tool
{
    "token": "74dedea023dbad8ecda49ac57bb1074acd794f"
}

Creating a JSON describing the tool.

The tool I'm goind to use is VCFhead. A very simple tool printing the first variants of a VCF file. In jvarkit I don't write the code parsing the arguments, everything is described using a XML file that is going to be processed with a XSTL stylesheet to generate an abstract java code handling the options, etc....

xsltproc command2java VcfHead.xml > AbstractVcfHead.java

For VcfHead the XML descriptor is available here: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfHead.xml.

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<app xmlns="http://github.com/lindenb/jvarkit/" xmlns:h="http://www.w3.org/1999/xhtml" app="VcfHead" package="com.github.lindenb.jvarkit.tools.misc" >
  <description>Print the first variants of a VCF.</description>
  <input type="vcf"/>
  <output type="vcf"/>
  <options>
    <option name="count" type="int" opt="n" longopt="count" min-inclusive="0" default="10">
      <description>number of variants to be printed</description>
    </option>
  </options>
  <documentation>
    <h:h3>Example</h:h3>
   (...)
  </documentation>
</app>

Using a first XSLT stylesheet https://github.com/lindenb/jvarkit/blob/master/src/main/resources/xsl/jsonxelixir.xsl, 'VcfHead.xml' is firstly converted to the 'infamous' JSONx (JSON+XML) format .
xsltproc jsonxelixir VcfHead.xml > VcfHead.jsonx
The JSONx file:
<?xml version="1.0"?>
<jsonx:object xmlns:jsonx="http://www.ibm.com/xmlns/prod/2009/jsonx" xmlns:c="http://github.com/lindenb/jvarkit/" xmlns="http://www.w3.org/1999/xhtml" xmlns:x="http://www.ibm.com/xmlns/prod/2009/jsonx">
  <jsonx:string name="accessibility">Public</jsonx:string>
  <jsonx:string name="affiliation">univ-nantes.fr</jsonx:string>
  <jsonx:string name="cost">Free</jsonx:string>
  <jsonx:array name="platform">
    <jsonx:string>Linux</jsonx:string>
    <jsonx:string>Mac</jsonx:string>
  </jsonx:array>
  <jsonx:string name="version">1.0</jsonx:string>
  <jsonx:string name="homepage">https://github.com/lindenb/jvarkit/wiki/VcfHead</jsonx:string>
  <jsonx:array name="function">
    <jsonx:object>
      <jsonx:array name="input">
        <jsonx:object>
          <jsonx:object name="dataType">
            <jsonx:string name="term">File name</jsonx:string>
            <jsonx:string name="uri">http://edamontology.org/data_1050</jsonx:string>
          </jsonx:object>
          <jsonx:array name="dataFormat">
            <jsonx:object>
              <jsonx:string name="term">VCF</jsonx:string>
              <jsonx:string name="uri">http://edamontology.org/format_3016</jsonx:string>
            </jsonx:object>
          </jsonx:array>
        </jsonx:object>
      </jsonx:array>
      <jsonx:array name="output">
        <jsonx:object>
          <jsonx:object name="dataType">
            <jsonx:string name="term">File name</jsonx:string>
            <jsonx:string name="uri">http://edamontology.org/data_1050</jsonx:string>
          </jsonx:object>
          <jsonx:string name="dataDescription">any format</jsonx:string>
          <jsonx:array name="dataFormat">
            <jsonx:object>
              <jsonx:string name="term">VCF</jsonx:string>
              <jsonx:string name="uri">http://edamontology.org/format_3016</jsonx:string>
            </jsonx:object>
          </jsonx:array>
        </jsonx:object>
      </jsonx:array>
      <jsonx:array name="functionName">
        <jsonx:object>
          <jsonx:string name="term">Formatting</jsonx:string>
          <jsonx:string name="uri">http://edamontology.org/operation_0335</jsonx:string>
        </jsonx:object>
      </jsonx:array>
      <jsonx:string name="functionDescription">Print the first variants of a VCF.</jsonx:string>
    </jsonx:object>
  </jsonx:array>
  <jsonx:string name="description">Print the first variants of a VCF.</jsonx:string>
  <jsonx:object name="docs">
    <jsonx:string name="docsTermsOfUse">https://opensource.org/licenses/MIT</jsonx:string>
    <jsonx:string name="docsGithub">https://github.com/lindenb/jvarkit/wiki/VcfHead</jsonx:string>
    <jsonx:string name="docsHome">https://github.com/lindenb/jvarkit/wiki/VcfHead</jsonx:string>
    <jsonx:string name="docsCitationInstructions">https://github.com/lindenb/jvarkit/wiki/Citing</jsonx:string>
    <jsonx:string name="docsDownloadSource">https://github.com/lindenb/jvarkit/archive/master.zip</jsonx:string>
    <jsonx:string name="docsDownload">https://github.com/lindenb/jvarkit/archive/master.zip</jsonx:string>
  </jsonx:object>
  <jsonx:array name="collection">
    <jsonx:string>jvarkit</jsonx:string>
  </jsonx:array>
  <jsonx:object name="credits">
    <jsonx:array name="creditsInstitution">
      <jsonx:string>Institut du Thorax, Nantes, France</jsonx:string>
    </jsonx:array>
    <jsonx:array name="creditsDeveloper">
      <jsonx:string>Pierre Lindenbaum</jsonx:string>
    </jsonx:array>
  </jsonx:object>
  <jsonx:array name="interface">
    <jsonx:object>
      <jsonx:string name="interfaceType">Command line</jsonx:string>
    </jsonx:object>
  </jsonx:array>
  <jsonx:string name="name">VcfHead</jsonx:string>
  <jsonx:array name="topic">
    <jsonx:object>
      <jsonx:string name="term">Omics</jsonx:string>
      <jsonx:string name="uri">http://edamontology.org/topic_3391</jsonx:string>
    </jsonx:object>
  </jsonx:array>
  <jsonx:string name="license">MIT License</jsonx:string>
  <jsonx:array name="language">
    <jsonx:string>Java</jsonx:string>
  </jsonx:array>
  <jsonx:array name="resourceType">
    <jsonx:string>Tool</jsonx:string>
  </jsonx:array>
  <jsonx:string name="maturity">Stable</jsonx:string>
  <jsonx:array name="contact">
    <jsonx:object>
      <jsonx:string name="contactURL">https://github.com/lindenb</jsonx:string>
      <jsonx:string name="contactName">Pierre Lindenbaum</jsonx:string>
      <jsonx:array name="contactRole">
        <jsonx:string>Developer</jsonx:string>
        <jsonx:string>Maintainer</jsonx:string>
        <jsonx:string>Helpdesk</jsonx:string>
      </jsonx:array>
    </jsonx:object>
  </jsonx:array>
  <jsonx:object name="publications">
    <jsonx:string name="publicationsPrimaryID">doi:10.6084/m9.figshare.1425030.v1</jsonx:string>
  </jsonx:object>
</jsonx:object>

Using another XSLT stylesheet jsonx2json.xsl, the JSONx is converted to a JSON file.
xsltproc jsonx2json.xsl VcfHead.jsonx > VcfHead.json
the JSON file:
{
    "accessibility": "Public", 
    "affiliation": "univ-nantes.fr", 
    "collection": [
        "jvarkit"
    ], 
    "contact": [
        {
            "contactName": "Pierre Lindenbaum", 
            "contactRole": [
                "Developer", 
                "Maintainer", 
                "Helpdesk"
            ], 
            "contactURL": "https://github.com/lindenb"
        }
    ], 
    "cost": "Free", 
    "credits": {
        "creditsDeveloper": [
            "Pierre Lindenbaum"
        ], 
        "creditsInstitution": [
            "Institut du Thorax, Nantes, France"
        ]
    }, 
    "description": "Print the first variants of a VCF.", 
    "docs": {
        "docsCitationInstructions": "https://github.com/lindenb/jvarkit/wiki/Citing", 
        "docsDownload": "https://github.com/lindenb/jvarkit/archive/master.zip", 
        "docsDownloadSource": "https://github.com/lindenb/jvarkit/archive/master.zip", 
        "docsGithub": "https://github.com/lindenb/jvarkit/wiki/VcfHead", 
        "docsHome": "https://github.com/lindenb/jvarkit/wiki/VcfHead", 
        "docsTermsOfUse": "https://opensource.org/licenses/MIT"
    }, 
    "function": [
        {
            "functionDescription": "Print the first variants of a VCF.", 
            "functionName": [
                {
                    "term": "Formatting", 
                    "uri": "http://edamontology.org/operation_0335"
                }
            ], 
            "input": [
                {
                    "dataFormat": [
                        {
                            "term": "VCF", 
                            "uri": "http://edamontology.org/format_3016"
                        }
                    ], 
                    "dataType": {
                        "term": "File name", 
                        "uri": "http://edamontology.org/data_1050"
                    }
                }
            ], 
            "output": [
                {
                    "dataDescription": "any format", 
                    "dataFormat": [
                        {
                            "term": "VCF", 
                            "uri": "http://edamontology.org/format_3016"
                        }
                    ], 
                    "dataType": {
                        "term": "File name", 
                        "uri": "http://edamontology.org/data_1050"
                    }
                }
            ]
        }
    ], 
    "homepage": "https://github.com/lindenb/jvarkit/wiki/VcfHead", 
    "interface": [
        {
            "interfaceType": "Command line"
        }
    ], 
    "language": [
        "Java"
    ], 
    "license": "MIT License", 
    "maturity": "Stable", 
    "name": "VcfHead", 
    "platform": [
        "Linux", 
        "Mac"
    ], 
    "publications": {
        "publicationsPrimaryID": "doi:10.6084/m9.figshare.1425030.v1"
    }, 
    "resourceType": [
        "Tool"
    ], 
    "topic": [
        {
            "term": "Omics", 
            "uri": "http://edamontology.org/topic_3391"
        }
    ], 
    "version": "1.0"
}

Registering the tool

Now we have the Token and the json descriptor we can add VcfHead to Elixir using curl:
curl  -H "Content-type: application/json" \
 -H "Authorization: Token 74dedea023dbad8ecda49ac57bb1074acd794f" \
 -X POST \
 -d  @path/to/VcfHead.json \
 "https://bio.tools/api/tool" |\
 python -m json.tool
output:
{
    "accessibility": "Public", 
    "additionDate": "2016-02-24T11:37:17.458Z", 
    "affiliation": "univ-nantes.fr", 
    "collection": [
        "jvarkit"
    ], 
    "contact": [
        {
            "contactName": "Pierre Lindenbaum", 
            "contactRole": [
                "Developer", 
                "Maintainer", 
                "Helpdesk"
            ], 
            "contactURL": "https://github.com/lindenb"
(...)

VCfhead is now visible from the Elixir Registry at https://bio.tools/tool/univ-nantes.fr/VcfHead/1.0.
http://i.imgur.com/PjEMjX6.jpg

That's it,
Pierre.

Publié par Pierre Lindenbaum at 12:53 PM 0 commentaires

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