Local Mozilla Ubiquity commands

apiloc_commands.js

CmdUtils.CreateCommand({
  names: ["genbank blast"],
  arguments: [{role: 'object', nountype: noun_arb_text, label: 'genbank id'},
      {role: 'goal', nountype: noun_arb_text, label: 'blast database'},
      {role: 'instrument', nountype: noun_arb_text, label: 'blast program'},
      {role: 'location', nountype: noun_arb_text, label: 'taxa'}],
  homepage: "http://gist.github.com/73638",
  help: 'genbank_blast <b>entrez_id</b> [with <b>blast_program</b>] [to <b>blast_database_name</b>]',
  author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
  contributors: ["Ben J. Woodcroft"],
  license: "GPL3",
  
  execute: function execute(args) {
    var urlStringStart = "http://apiloc.bio21.unimelb.edu.au/apiloc/blasts/blast_genbank?id="
    var urlStringEnd = ""
 
    genbankString = args.object.text;
    genbank_array = genbankString.split(",")
    
    modtext = args.instrument.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&program="+modtext;
    }
 
    modtext = args.goal.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&database="+modtext;
    }
 
    modtext = args.location.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&taxa="+modtext;
    }
 
 
    for(i=0; i<genbank_array.length; i = i+1){
      Utils.openUrlInBrowser(urlStringStart+genbank_array[i]+urlStringEnd);
    }
  }
})
 
 
CmdUtils.CreateCommand({
  names: ["apiloc"],
  icon: "http://www.mozilla.com/favicon.ico",
  description: "apiloc.",
  help: "How to use your command.",
  author: {name: "Your Name", email: "you@mozilla.com"},
  license: "GPL",
  homepage: "http://apiloc.bio21.unimelb.edu.au/",
  arguments: [{role: 'object', nountype: noun_arb_text}],
  preview: function preview(pblock, args) {
    pblock.innerHTML = "Your input is <b>" + args.object.html + "</b>.";
  },
  execute: function execute(args) {
    geneString = args.object.text;
    gene_array = geneString.split(" ")

    for(i=0; i<gene_array.length; i = i+1){
      var urlString = "http://apiloc.bio21.unimelb.edu.au/apiloc/apiloc/gene/"+gene_array[i];
      Utils.openUrlInBrowser(urlString);
    }
  }
});
 
CmdUtils.CreateCommand({
  names: ["sequence blast"],
  arguments: [{label: "sequence", nountype: noun_arb_text, role: 'object'},
      {role: 'goal', nountype: noun_arb_text, label: 'blast database'},
      {role: 'instrument', nountype: noun_arb_text, label: 'blast program'},
      {role: 'location', nountype: noun_arb_text, label: 'taxa'}],
  homepage: "apiloc.bio21.unimelb.edu.au",
  author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
  contributors: ["Ben J. Woodcroft"],
  license: "GPL3",
  description: "BLAST quicklier than PlasmoDB/ToxoDB.",
  preview: "BLAST quicklier than PlasmoDB/ToxoDB",
  
  execute: function(args) {
    var urlStringStart = "http://apiloc.bio21.unimelb.edu.au/apiloc/blasts/blast?sequence=";
    var urlStringEnd = "";
 
    genbankString = args.object.text;
    genbank_array = genbankString.split(",")
    
    modtext = args.instrument.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&program="+modtext;
    }
 
    modtext = args.goal.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&database="+modtext;
    }
 
    modtext = args.location.text
    if (modtext.length == undefined){;}
    else{
      urlStringEnd = urlStringEnd + "&taxa="+modtext;
    }
 
 
    for(i=0; i<genbank_array.length; i = i+1){
      Utils.openUrlInBrowser(urlStringStart+genbank_array[i]+urlStringEnd);
    }
  }
});
CmdUtils.CreateCommand({
  names: ["papiloc"],
  icon: "http://www.mozilla.com/favicon.ico",
  description: "apiloc.",
  help: "How to use your command.",
  author: {name: "Your Name", email: "you@mozilla.com"},
  license: "GPL",
  homepage: "http://reefedge.sols.uq.edu.au:3000/",
  arguments: [{role: 'object', nountype: noun_arb_text}],
  preview: function preview(pblock, args) {
    pblock.innerHTML = "Your input is <b>" + args.object.html + "</b>.";
  },
  execute: function execute(args) {
    var urlString = "http://reefedge.sols.uq.edu.au:3000/apiloc/publication/"+args.object.text;
    Utils.openUrlInBrowser(urlString);
  }
});