https://github.com/rdmpage/bionames

BioNames project
https://github.com/rdmpage/bionames

Last synced: 8 months ago
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BioNames project

• Host: GitHub
• URL: https://github.com/rdmpage/bionames
• Owner: rdmpage
• Created: 2013-05-14T12:16:23.000Z (about 13 years ago)
• Default Branch: master
• Last Pushed: 2024-06-23T15:43:57.000Z (almost 2 years ago)
• Last Synced: 2024-06-23T16:52:22.822Z (almost 2 years ago)
• Language: PHP
• Size: 2.57 MB
• Stars: 4
• Watchers: 4
• Forks: 0
• Open Issues: 21
• Metadata Files:
  • Readme: README.md

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README

          
bionames

========

BioNames project

#### ElasticSearch

If running CouchDB locally we need a fulltext search engine, such as Elastic Search.

Get ElasticSearch from [http://www.elasticsearch.org/download](http://www.elasticsearch.org/download)

Get CouchDB River plugin. Go to [https://github.com/elasticsearch/elasticsearch-river-couchdb/blob/master/README.md](https://github.com/elasticsearch/elasticsearch-river-couchdb/blob/master/README.md)

and follow instructions, i.e. in root of ElasticSearch folder run

    bin/plugin -install elasticsearch/elasticsearch-river-couchdb/1.2.0.

    

You should see something like this:

	> Installing elasticsearch/elasticsearch-river-couchdb/1.2.0...

	Trying http://download.elasticsearch.org/elasticsearch/elasticsearch-river-couchdb/elasticsearch-river-couchdb-1.2.0.zip...

	Downloading ...DONE

	Installed river-couchdb

Now, run ElasticSearch

	bin/elasticsearch -f

	

Then we need to filter the documents we want from CouchDB, in this case I want publications, so I create this view in CouchDB:

{

   "_id": "_design/app",

   "filters": {

       "publications": "function(doc, req) { var types = ['article','book','chapter','generic']; if(types.indexOf(doc.type) != -1) { return true; } else { return false; }}"

   }

}

This means we can get a list of publications that have changed:

http://localhost:5984/bionames/_changes?filter=app/publications

Now, we tell ElasticSearch to consume this

	curl -XPUT 'localhost:9200/_river/bionames/_meta' -d '{

		"type" : "couchdb",

		"couchdb" : {

			"host" : "localhost",

			"port" : 5984,

			"db" : "bionames",

			"filter" : "app/publications"

		},

		"index" : {

			"index" : "bionames",

			"type" : "bionames",

			"bulk_size" : "100",

			"bulk_timeout" : "10ms"

		}

	}'

Note, remove all line breaks before you use the above command.

### Querying

Now we are indexing the publications.

	http://localhost:9200/bionames/_search?q=replacement

	curl -XPOST 'localhost:9200/bionames/_search?pretty=true' -d ' { "query" : { "match" : { "title" : "New Zealand Bopyridae" } } }'

	

### Replication

	

Check that CouchDB can be accessed externally.

	netstat -an | grep 5984

You are looking for a line like this - see http://serverfault.com/questions/79453/why-cant-i-access-my-couchdb-instance-externally-on-ubuntu-9-04-server

	tcp4       0      0  *.5984                 *.*                    LISTEN     

#### Run replication

Local bionames database is source, remote instance (in this case cloudant) is target.

	curl http://localhost:5984/_replicate -H 'Content-Type: application/json' -d '{ "source": "bionames", "target": "https://:@rdmpage.cloudant.com/bionames", "continuous":true }'

You should get a response like this:

	{"ok":true,"_local_id":"7bf516ee63001a188a8186d7cf718194+continuous"}

	

Continuous replication can be expensive on Cloudant, so better to replicate manually:

		curl http://localhost:5984/_replicate -H 'Content-Type: application/json' -d '{ "source": "bionames", "target": "https://:@bionames.cloudant.com/bionames"}'

		curl http://localhost:5984/_replicate -H 'Content-Type: application/json' -d '{ "source": "archive", "target": "https://:@bionames.cloudant.com/archive"}'