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.

That's it,
Pierre.

Freebase and Biohackathon 2010

This post is a quick overview of Freebase for the participants of biohackathon2010 who attended François Belleau's lecture this morning. It was suggested here that Freebase could be used to store and share some predicates for the semantic web. In the current post, I'm going to use CURL to programmatically add a new Namespace in freebase .

OK. First, let's send a MQL query to Freebase and get the schema for the type 'Namespace'. We ask for the name, the id and the expected_type of all the properties of /user/biohackathon/default_domain/namespace_1:

curl http://www.freebase.com/api/service/mqlread -d 'query={
"query1":
{
"query":
[{
"id":"/user/biohackathon/default_domain/namespace_1",
"/type/type/properties": [{
"name": null,
"id":null,
"expected_type": null
}]
}]
}
}'

The response is:

{
"code": "/api/status/ok",
"result": [
{
"/type/type/properties": [
{
"expected_type": "/type/uri",
"id": "/user/biohackathon/default_domain/namespace_1/uri",
"name": "URI"
},
{
"expected_type": "/type/uri",
"id": "/user/biohackathon/default_domain/namespace_1/url",
"name": "Documentation URL"
}
],
"id": "/user/biohackathon/default_domain/namespace_1"
}
],
"status": "200 OK",
"transaction_id": "cache;cache01.p01.sjc1:8101;2010-02-11T17:46:20Z;0024"
}

Ok, there are two properties for this 'Namespace': URI (a '/type/uri') and Documentation URL (a '/type/uri' too) Now we're going to insert a new Namespace. The namespace will be DOAP (Description of a Project). The URI for DOAP is http://usefulinc.com/ns/doap# and the Documentation URL is http://trac.usefulinc.com/doap.

Authenticate (only once)

curl -c cookies.txt -d "username=yourusername" -d "password=yourpassword" https://www.freebase.com/api/account/login
{
"code": "/api/status/ok",
"messages": [
{
"code": "/api/status/ok/account/login",
"message": "Login succeeded",
"username": "yourusername"
}
],
"status": "200 OK",
"transaction_id": "cache;xxxxx"
}

Insert the DOAP Namespace:

curl -b cookies.txt -H 'X-Requested-With: curl' https://www.freebase.com/api/service/mqlwrite -d 'query={"query":{
"create": "unless_exists",
"type":"/user/biohackathon/default_domain/namespace_1",
"id":null,
"name":"doap",
"/user/biohackathon/default_domain/namespace_1/uri":"http://usefulinc.com/ns/doap#",
"/user/biohackathon/default_domain/namespace_1/url":"http://trac.usefulinc.com/doap"
}}'

The anwser from freebase is:

{
"code": "/api/status/ok",
"result": {
"/user/biohackathon/default_domain/namespace_1/uri": "http://usefulinc.com/ns/doap#",
"/user/biohackathon/default_domain/namespace_1/url": "http://trac.usefulinc.com/doap",
"create": "created",
"id": "/guid/9202a8c04000641f8000000013e40eea",
"name": "doap",
"type": "/user/biohackathon/default_domain/namespace_1"
},
"status": "200 OK",
"transaction_id": "cache;cache02.p01.sjc1:8101;2010-02-11T18:47:45Z;0037"
}

You can now view this new Namespace at http://www.freebase.com/view/user/biohackathon/default_domain/views/namespace_1.


That's it !
Pierre

Tips: Sending Batch Invitations to Nature-Network.

A few minutes ago, I was looking for an quick method to send batch invitations to join Nature Network to my colleagues. I found a solution using the cURL utility.

1. Open firefox



2. log in to Nature Network



3. the site stores a cookie called '_session_id' on your browser. Open your Cookie Panel: Tools -> Options -> Privacy -> Cookies". Note the value of the cookie _session_id associated to the site network.nature.com



4. use cURL to send the form.
   

   
    curl -L -b '_session_id=THE_VALUE_OF_YOUR_COOKIE' -d 'referral[name]=Name' -d 'referral[email]=nobody.nowhere@mycompagny.com' -d 'referral[message]=this is an invitation to another social network'  -d 'commit=send'  'http://network.nature.com/referrals/create?locality='
   

   
   
   the option -L is used to follow any http redirection, -b set a cookie, -d set a key/value from the original html form. You can automatize this process using a simple loop over your addresses.
   

This solution worked fine at the time I wrote this post.

Pierre