Monday, December 12, 2011

Exporting data from Australian Faunal Directory on CouchDB

Quick note to self about exporting data from my Australian Faunal Directory on CouchDB project. To export data from a CouchDB view you can use a list function (see Formatting with Show and List). Following the example on the Kanapes IDE blog, I created the following list function:

"_id": "_design/publication",
"_rev": "14-467dee8248e97d874f1141411f536848",
"language": "javascript",
"lists": {
"tsv": "function(head,req) {
var row;
'headers': {
'Content-Type': 'text/tsv'
while(row = getRow()) {
send(row.value + '\\t' + row.key + '\\n');
"views": {

I can use this function with the view below, which lists Australian Faunal Directory publications by UUID ("value"), indexed by DOI ("key").


I can get the tab-delimited dump from http://localhost:5984/afd/_design/publication/_list/tsv/doi. Note that instead of, say, /afd/_design/publication/_view/doi to get the view, we use /afd/_design/publication/_list/tsv/doi to get the tab-delimited dump.

I've created files listing DOIs and BioStor ids for publications in the Australian Faunal Directory. I'll play with lists a bit more, specially as I would like to extract the mapping from the Australian Faunal Directory on CouchDB project and add it to the iTaxon project.