Commit 74bf18b6 authored by Severine Duvaud's avatar Severine Duvaud
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Merge branch 'master' of gitlab.isb-sib.ch:ST/ga4gh-arraymap

parents 61451efa 8b0a01bb
Beacon queries and interface for the MongoDB based _arrayMap_ cancer genome repository.
Beacon queries and interface for the MongoDB based _[arrayMap](http://arraymap.org/ "arrayMap, visualizing cancer genome array data")_ cancer genome repository.
The structure of the project is the following:
Queries are contained inside the directory [mongo-queries](mongo-queries)
An alternative would be to transform the native _arrayMap_ data format into VCF, and to use [the Python Simple Beacon Server](https://github.com/maximilianh/ucscBeacon).
# mongo-queries:
Queries are contained inside the directory [mongo-queries](mongo-queries)
#### Download commands
The following command can be used to download a chunk of the _arrayMap_ dataset, e.g. to understand data structures.
```wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json```
```
wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json
```
The next command would replace the current local _arrayMap_ instance with the downloaded file.
```mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1```
```
mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1
```
# beacon-app
The directory contains the Beacon application itself.
The application is based on node and angular.
In order to run the application on your localhost, you need to have [npm](https://www.npmjs.com/ "Package manager for JavaScript") installed.
Then, run:
```
npm install
```
in order to get all the required Javascript packages (as listed in package.json), and then:
```
npm start
```
You should also have a __arrayMap__ MongoDB running on your __localhost__, on port __27017__ (see above).
This can be changed in the application container:
```
app.js
```
#### bin
Contains the www script which is used by
```
npm start
```
to start the server.
#### arraymap-beacon
Contains the implementation of the Beacon API. There is one sub-directory per API version.
#### test
Contains the functional tests (based on the [Chai](http://chaijs.com/ "Chai assertion library for node" ) assertion library).
#### public
Contains the scripts, CSS, images, HTML for the UI part.
#### routes
Contains the routing script.
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