diff --git a/README.md b/README.md index d311e3c..c93bde2 100644 --- a/README.md +++ b/README.md @@ -69,32 +69,18 @@ $ cbioportal-api-client getProfileData -s gbm_tcga_cnaseq -p gbm_tcga_mutations ## API Reference -## Modules - -
cbioPortal
Creates a new cBio Portal API client
-Promise
Converts tab delimited responses to JSON format
-Exports utility functions for summarizing gene alterations
-cbioPortal
Creates a new cBio Portal API client
-**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)
| Param | Type | Description |
| --- | --- | --- |
| config | Object
| Configuration options object. |
| config.includeRaw | Boolean
| Include the raw TSV response |
-**Example**
+**Example**
Basic usage:
```javascript
@@ -124,8 +110,8 @@ cbioPortal.getCancerStudies()
cbioPortal API Object Prototype. Used as the object prototype
when creating an API client object via the module factory method.
-**Kind**: inner constant of [cbioportal-api-client](#module_cbioportal-api-client)
-**See**: Use [CbioPortal()](#module_cbioportal-api-client) for object creation.
+**Kind**: inner constant of [cbioportal-api-client](#module_cbioportal-api-client)
+**See**: Use [CbioPortal()](#module_cbioportal-api-client) for object creation.
* [~cbioPortal](#module_cbioportal-api-client..cbioPortal) : Object
* [.getTypesOfCancer()](#module_cbioportal-api-client..cbioPortal+getTypesOfCancer) ⇒ Promise
@@ -141,9 +127,9 @@ when creating an API client object via the module factory method.
#### cbioPortal.getTypesOfCancer() ⇒ Promise
Retrieves a list of all the clinical types of cancer stored on the server.
-**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
-**Returns**: Promise
- See fullfills/rejects
-**Fulfills**: Array
response data converted from TSV to JSON
+**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**Returns**: Promise
- See fullfills/rejects
+**Fulfills**: Array
response data converted from TSV to JSON
-----
@@ -151,9 +137,9 @@ Retrieves a list of all the clinical types of cancer stored on the server.
#### cbioPortal.getCancerStudies() ⇒ Promise
Retrieves meta-data regarding cancer studies stored on the server.
-**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
-**Returns**: Promise
- See fullfills/rejects
-**Fulfills**: Array
response data converted from TSV to JSON
+**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**Returns**: Promise
- See fullfills/rejects
+**Fulfills**: Array
response data converted from TSV to JSON
-----
@@ -162,9 +148,9 @@ Retrieves meta-data regarding cancer studies stored on the server.
Retrieves meta-data regarding all genetic profiles, e.g.
mutation or copy number profiles, stored about a specific cancer study.
-**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
-**Returns**: Promise
- See fullfills/rejects
-**Fulfills**: Array
response data converted from TSV to JSON
+**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**Returns**: Promise
- See fullfills/rejects
+**Fulfills**: Array
response data converted from TSV to JSON
| Param | Type | Description |
| --- | --- | --- |
@@ -182,8 +168,8 @@ For example, a within a particular study, only some cases may have sequence data
Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.
-**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
-**Fulfill**: JSON formatted response
+**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**Fulfill**: JSON formatted response
| Param | Type | Description |
| --- | --- | --- |
@@ -197,8 +183,8 @@ Multiple case lists may be associated with each cancer study, and this method en
#### cbioPortal.getProfileData(query) ⇒ Promise
Retrieves genomic profile data for one or more genes.
-**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
-**Fulfill**: JSON formatted response
+**Kind**: instance method of [cbioPortal](#module_cbioportal-api-client..cbioPortal)
+**Fulfill**: JSON formatted response
| Param | Type | Description |
| --- | --- | --- |
@@ -210,71 +196,3 @@ Retrieves genomic profile data for one or more genes.
-----
-
-## cbioportal-api-client/utils/convertResponse ⇒ Promise
-Converts tab delimited responses to JSON format
-
-**Returns**: Promise
- Resolves with the response JSON
-
-| Param | Type | Description |
-| --- | --- | --- |
-| response | string
| TSV string |
-
-
------
-
-
-## cbioportal-api-client/utils/summarizeAlterations
-Exports utility functions for summarizing gene alterations
-
-
-* [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
- * [.summarizeMutations(mutations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeMutations) ⇒ Array
- * [.summarizeCopyNumberAlterations(copyNumberAlterations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations) ⇒ Array
- * [.summarizeAlterations(response)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations) ⇒ Promise
-
-
------
-
-
-### cbioportal-api-client/utils/summarizeAlterations.summarizeMutations(mutations) ⇒ Array
-Summarize mutations
-
-**Kind**: static method of [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
-**Returns**: Array
- Array of summaries
-
-| Param | Type | Description |
-| --- | --- | --- |
-| mutations | Array
| Array of mutation rows as parsed by this library |
-
-
------
-
-
-### cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations(copyNumberAlterations) ⇒ Array
-Summarize copy number alterations
-
-**Kind**: static method of [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
-**Returns**: Array
- Array of summaries
-
-| Param | Type | Description |
-| --- | --- | --- |
-| copyNumberAlterations | Array
| Array of copy number alteration rows as parsed by this library |
-
-
------
-
-
-### cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations(response) ⇒ Promise
-Converts tab delimited responses to JSON format
-
-**Kind**: static method of [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
-**Returns**: Promise
- Resolves with the response JSON
-
-| Param | Type | Description |
-| --- | --- | --- |
-| response | string
| TSV string |
-
-
------
-
diff --git a/lib/utils/index.js b/lib/utils/index.js
index 7e40883..55249ca 100644
--- a/lib/utils/index.js
+++ b/lib/utils/index.js
@@ -1,4 +1,4 @@
-import SummarizeAlterations from './summarizeAlterations';
+import * as SummarizeAlterations from './summarizeAlterations';
import ConvertResponse from './convertResponse';
export const summarizeAlterations = SummarizeAlterations;
diff --git a/lib/utils/summarizeAlterations.js b/lib/utils/summarizeAlterations.js
index ee2fd15..db8fc09 100644
--- a/lib/utils/summarizeAlterations.js
+++ b/lib/utils/summarizeAlterations.js
@@ -11,7 +11,14 @@ import _merge from 'lodash/merge';
/**
* Exports utility functions for summarizing gene alterations
*
- * @exports summarizeAlterations
+ * @example
+ * ```javascript
+ * import {
+ * summarizeMutations,
+ * summarize
+ * } from 'cbioportal-api-client/dist/utils/summarizeAlterations';
+ * ```
+ *
* @module cbioportal-api-client/utils/summarizeAlterations
*/
diff --git a/package.json b/package.json
index 0cc0f51..117d7ab 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
"coverage": "npm run clean:coverage && babel-node node_modules/.bin/isparta cover --report lcov --report text --report html test/index.js",
"coveralls": "cat ./coverage/lcov.info | coveralls",
"dev": "nodemon -w lib -w test --exec \"npm run -s lint && npm run -s test:dev\"",
- "docs": "jsdoc2md --src \"lib/**/*.js\" -t docs/README.md.hbs -d 2 --partial \"./docs/partials/**/*.hbs\" --separators -l JavaScript > README.md",
+ "docs": "jsdoc2md --src \"lib/index.js\" -t docs/README.md.hbs -d 2 --partial \"./docs/partials/**/*.hbs\" --separators -l JavaScript > README.md",
"lint": "eslint lib",
"precommit": "npm run docs",
"prepublish": "in-publish && npm run build || not-in-publish",