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) {
-            var buffer;
-            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`

Fixed alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

29836

increased by3.65%

Lines of code

509

increased by0.2%

Number of lines in readme file

109

increased by127.08%

Number of medium supply chain risk alerts

1

decreased by-50%

No dependency changes