cgds - npm Package Compare versions

Comparing version 0.1.1 to 0.1.2

lib/cgds.js

		@@ -19,14 +19,15 @@ "use strict";
		}
		// Browserify does not default to port 80 if the page
		// is served from a port other than 80.
		options.port = 80;
		http.get(options, function (res) {
		var body;
		body = new Buffer(0);
		// Browserify does not seem to work well with buffers ("no method copy"),
		// therefore fall back to strings.
		body = "";
		res.on("data", function (chunk) {
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		buffer = new Buffer(body.length + chunk.length);
		body.copy(buffer);
		chunk.copy(buffer, body.length);
		body = buffer;
		body += chunk;
		});
		res.on("end", function () {
		callback(null, body.toString("utf8"));
		callback(null, body);
		});
		@@ -33,0 +34,0 @@ });

package.json

		{
		"name": "cgds",
		"description": "A module for querying the Cancer Genomics Data Server (CGDS).",
		"version": "0.1.1",
		"version": "0.1.2",
		"author": {
		@@ -6,0 +6,0 @@ "name": "Alexander Grüneberg",

README.md

		CGDS-JS
		=======

		A Node.js module for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). Read more about this service at the [cBio Cancer Genomics Portal](http://www.cbioportal.org/public-portal/).
		A Node.js and browser module for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). Read more about this service at the [cBio Cancer Genomics Portal](http://www.cbioportal.org/public-portal/).

		Example
		-------

		var CGDS, cgds;
		CGDS = require("cgds");
		cgds = new CGDS("http://www.cbioportal.org/public-portal/webservice.do");
		cgds.getMutationData("brca_tcga_mutations", ["TP53", "GATA3"], "brca_tcga_all", function (err, res) {
		console.log(res);
		});

		Usage
		-----

		### Node.js

		1. Install it:
		@@ -23,2 +35,21 @@

		### Browser

		1. Include it:

		<script src="http://agrueneberg.github.io/CGDS-JS/cgds.min.js"></script>

		2. Require it:

		var CGDS = require("cgds");

		3. Instantiate a CGDS client (you will need a CORS proxy such as [Proxer](https://github.com/agrueneberg/Proxer) for this):

		var cgds = new CGDS({
		url: "http://www.cbioportal.org/public-portal/webservice.do",
		proxy: "http://example.com/corsproxy?url="
		});

		4. See below for a list of methods.

		Methods
		@@ -29,21 +60,51 @@ -------

		### `getTypesOfCancer(callback)`
		### getTypesOfCancer
		Retrieves a list of all the clinical types of cancer.

		### `getCancerStudies(callback)`
		###### Parameters
		1. `callback`

		### getCancerStudies
		Retrieves meta-data regarding cancer studies.

		### `getGeneticProfiles(cancer_study_id, callback)`
		###### Parameters
		1. `callback`

		### getGeneticProfiles
		Retrieves meta-data regarding all genetic profiles, e.g. mutation or copy number profiles, stored about a specific cancer study.

		### `getCaseLists(cancer_study_id, callback)`
		###### Parameters
		1. `cancer_study_id`
		2. `callback`

		### getCaseLists
		Retrieves meta-data regarding all case lists stored about a specific cancer study.

		### `getProfileData(case_set_id, genetic_profile_id, gene_list, callback)`
		###### Parameters
		1. `cancer_study_id`
		2. `callback`

		### getProfileData
		Retrieves genomic profile data for one or more genes.

		### `getMutationData(genetic_profile_id, case_set_id, gene_list, callback)`
		###### Parameters
		1. `case_set_id`
		2. `genetic_profile_id`
		3. `gene_list`
		4. `callback`

		### getMutationData
		Retrieves the full set of annotated extended mutation data.

		### `getClinicalData(case_set_id, callback)`
		###### Parameters
		1. `genetic_profile_id`
		2. `gene_list`
		3. `case_set_id` (optional)
		4. `callback`

		### getClinicalData
		Retrieves overall survival, disease free survival and age at diagnosis for specified cases.

		###### Parameters
		1. `case_set_id`
		2. `callback`

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