globi-data
Version:
Find out who eats who in the world: what do rats (Rattus rattus) eat?, or what do hardhead catfish (Ariopsis felis) eat?. Data provided via Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) .
440 lines (392 loc) • 14.9 kB
JavaScript
var nodeXHR = require('xmlhttprequest');
var extend = require('extend');
var hash = require('object-hash');
var querystring = require('querystring');
var citation = require('./citation.js');
var request = require('request');
var globiData = {};
var urlPrefix = 'https://api.globalbioticinteractions.org';
globiData.addQueryParams = function (uri, search) {
function initParams(search) {
var alt = extend({}, search);
if (search.location) {
alt = extend(alt, search.location);
delete alt.location;
}
function replaceAndDelete(match, replace) {
if (search[match]) {
if (!alt[replace]) {
alt[replace] = search[match];
}
delete alt[match];
}
}
replaceAndDelete('sourceTaxa', 'sourceTaxon');
replaceAndDelete('targetTaxa', 'targetTaxon');
replaceAndDelete('fields', 'field');
if (search.includeObservations) {
alt.includeObservations = true;
}
if (search.exactNameMatchOnly) {
alt.exactNameMatchOnly = true;
}
if (search.excludeChildTaxa) {
alt.excludeChildTaxa = true;
}
return alt;
}
var qs = querystring.encode(initParams(search));
var altUri = uri;
if (qs.length > 0) {
altUri = uri + '&' + qs;
}
return altUri;
}
;
globiData.urlForFindCloseTaxonMatches = function (name) {
return urlPrefix + '/findCloseMatchesForTaxon/' + encodeURIComponent(name);
};
globiData.urlForTaxonInteractionQuery = function (search) {
var uri = urlPrefix;
var searchAlt = extend({}, search);
if (searchAlt.sourceTaxonScientificName) {
uri = uri + '/taxon/' + encodeURIComponent(searchAlt.sourceTaxonScientificName);
delete searchAlt.sourceTaxonScientificName;
if (searchAlt.interactionType) {
uri = uri + '/' + encodeURIComponent(searchAlt.interactionType);
delete searchAlt.interactionType;
}
if (searchAlt.targetTaxonScientificName) {
uri = uri + '/' + encodeURIComponent(searchAlt.targetTaxonScientificName);
delete searchAlt.targetTaxonScientificName;
}
} else {
uri = uri + '/interaction';
}
var ext = {'csv': '.csv', 'dot': '.dot'}
uri = uri + (ext[searchAlt.resultType] === undefined ? '' : ext[searchAlt.resultType]);
uri = uri + '?type=' + (searchAlt.resultType ? searchAlt.resultType : 'json.v2');
delete searchAlt.resultType;
return this.addQueryParams(uri, searchAlt);
};
globiData.urlForTaxonImageQuery = function (scientificName, opts) {
var suffix = '';
if (opts && opts.lang) {
suffix = '&lang=' + encodeURIComponent(opts.lang);
}
return urlPrefix + '/imagesForName?name=' + encodeURIComponent(scientificName) + suffix;
};
globiData.urlForTaxonImageByIdQuery = function (id) {
return urlPrefix + '/images/' + encodeURIComponent(id);
};
globiData.urlForTaxonImagesQuery = function (scientificNames) {
var nameQuery = '?';
if (scientificNames) {
for (var index in scientificNames) {
if (scientificNames.hasOwnProperty(index)) {
nameQuery += 'name=' + encodeURIComponent(scientificNames[index]) + '&';
}
}
}
return urlPrefix + '/imagesForNames' + nameQuery;
};
globiData.urlForStudyStats = function (search) {
var url = urlPrefix + '/reports/studies';
if (search.source) {
url = url + '?source=' + encodeURIComponent(search.source);
}
return url;
};
var createReq = function () {
var req;
if (typeof window === 'undefined') {
// perhaps running in node.js?
req = new nodeXHR.XMLHttpRequest();
} else if (window.XMLHttpRequest) { // Mozilla, Safari, ...
req = new XMLHttpRequest();
} else if ((typeof window !== 'undefined') && window.ActiveXObject) { // IE
try {
req = new ActiveXObject('Msxml2.XMLHTTP');
} catch (e) {
try {
req = new ActiveXObject('Microsoft.XMLHTTP');
} catch (e) {
}
}
}
return req;
};
globiData.findSources = function (callback) {
var req = createReq();
req.open('GET', urlPrefix + '/reports/sources', true);
req.onreadystatechange = function () {
if (req.readyState === 4 && req.status === 200) {
var result = JSON.parse(req.responseText);
callback(citation.extractCitations(result));
}
};
req.send(null);
};
globiData.findSourceNames = function (callback) {
function lookupSources(path, callback) {
request({ method: 'GET',
uri: urlPrefix + path,
withCredentials: false,
gzip: true
}, function (error, response, body) {
if (!error && response.statusCode == 200) {
var sources = JSON.parse(body);
var sourceNames = sources.map(function (source) {
if (source.study_source_id !== undefined) {
source.name = source.study_source_id.replace('globi:', '');
}
if (source.study_source_doi !== undefined) {
source.doi = source.study_source_doi;
}
return source;
});
callback(sourceNames);
}
});
}
lookupSources('/source/?type=json.v2', function(sourceNames) {
lookupSources('/dataset/?type=json.v2', function(sourcesAll) {
var sourceNamespacesWithReport = sourceNames.map(function(source) { return source.name; });
var sourcesNoReport = sourcesAll
.filter(function(source) { return sourceNamespacesWithReport.indexOf(source.name) === -1; })
callback(sourceNames.concat(sourcesNoReport));
});
});
};
globiData.findStudyStats = function (search, callback) {
var req = createReq();
var uri = globiData.urlForStudyStats(search);
req.open('GET', uri, true);
req.onreadystatechange = function () {
if (req.readyState === 4 && req.status === 200) {
var resp = JSON.parse(req.responseText);
var studyStats = [];
for (var i = 0; i < resp.data.length; i++) {
var row = resp.data[i];
var stats = { citation: row[0], source: row[3], totalInteractions: row[4], totalTaxa: row[5]};
var doi = row[2];
if (doi && doi.length > 0) {
stats.doi = doi;
}
var externalId = row[1];
if (externalId && externalId.length > 0 && externalId.match('^((http)|(https))://') !== null) {
stats.url = externalId;
}
studyStats[i] = stats;
}
callback(studyStats);
}
};
req.send(null);
};
globiData.findStats = function (search, callback) {
var req = createReq();
var uri = urlPrefix + '/reports/collections';
if (search.source) {
uri = uri + '?source=' + encodeURIComponent(search.source);
}
req.open('GET', uri, true);
req.onreadystatechange = function () {
if (req.readyState === 4 && req.status === 200) {
var resp = JSON.parse(req.responseText);
var stats = {numberOfStudies: resp.data[0][6],
totalInteractions: resp.data[0][4],
totalTaxa: resp.data[0][5],
numberOfDistinctSources: resp.data[0][7]};
callback(stats);
}
};
req.send(null);
};
globiData.sendRequest = function (req, callback) {
req.onreadystatechange = function () {
if (req.readyState === 4 && req.status === 200) {
if (callback.callback && callback.context) {
callback.callback.call(callback.context, JSON.parse(req.responseText));
} else {
callback(JSON.parse(req.responseText));
}
}
};
req.send(null);
};
globiData.findInteractionTypes = function (search, callback) {
if (arguments.length === 1) {
callback = search;
search = [];
}
search = search.map(function (item) {
return 'taxon=' + encodeURIComponent(item);
});
var urlQuery = search.length > 0 ? '?' + search.join('&') + '&type=json' : '';
var req = createReq();
req.open('GET', urlPrefix + '/interactionTypes' + urlQuery, true);
globiData.sendRequest(req, callback);
};
globiData.findSpeciesInteractions = function (search, callback) {
var searchAlt = extend({}, search);
var callbackAlt = callback;
if ('d3' === searchAlt.resultType) {
searchAlt.resultType = 'json';
callbackAlt = function(interactions) {
callback(callbackProxyForD3(interactions));
}
}
var uri = globiData.urlForTaxonInteractionQuery(searchAlt);
var req = createReq();
req.open('GET', uri, true);
globiData.sendRequest(req, callbackAlt);
};
globiData.findTaxon = function(scientificName, opts, callback) {
var uri = globiData.urlForTaxonImageQuery(scientificName, opts);
globiData.get(uri, callback);
}
globiData.findTaxonInfo = function (scientificName, callback) {
globiData.findTaxon(scientificName, { lang: "en" }, callback);
};
globiData.findTaxonLinks = function (scientificName, callback) {
var uri = urlPrefix + '/taxonLinks/' + encodeURIComponent(scientificName);
globiData.get(uri, callback);
}
globiData.findTaxaInfo = function (scientificNames, callback) {
var uri = globiData.urlForTaxonImagesQuery(scientificNames);
globiData.get(uri, callback);
};
globiData.get = function (uri, callback) {
var req = createReq();
req.open('GET', uri, true);
globiData.sendRequest(req, callback);
};
globiData.findCloseTaxonMatches = function (name, callback) {
var uri = globiData.urlForFindCloseTaxonMatches(name);
var req = createReq();
req.open('GET', uri, true);
req.onreadystatechange = function () {
if (req.readyState === 4 && req.status === 200) {
var response = JSON.parse(req.responseText);
var data = response.data;
var closeMatches = [];
data.forEach(function (element, index) {
var taxonHierarchy = [];
var commonNames = globiData.mapCommonNameList(element[1]);
var pathString = element[2];
pathString = pathString === null ? "" : pathString;
var path = pathString.split('|');
path.forEach(function (taxon, index) {
taxonHierarchy[index] = taxon.trim();
});
var scientificName = element[0].trim();
closeMatches[index] = { scientificName: scientificName, commonNames: commonNames, path: taxonHierarchy};
});
callback(closeMatches);
}
};
req.send(null);
};
/**
* Transforms a common name list string into a map
* f.x.:
* "foo @en | bar @de" => {en: "foo", de: "bar"}
*
* @param {string} pipedCommonNameList
* @param {boolean} [override]
* @returns {Object.<string, string>}
*/
globiData.mapCommonNameList = function (pipedCommonNameList, override) {
override = typeof override !== 'undefined' ? !!override : true;
pipedCommonNameList = typeof pipedCommonNameList !== 'string' ? '' : pipedCommonNameList;
var commonNameMap = { count: 0 };
var splittedByPipeList = pipedCommonNameList.split('|').map(function (item) {
return item.trim();
});
splittedByPipeList.forEach(function (item) {
if (typeof item !== 'undefined') {
var splittedByAtItemParts = item.split('@').map(function (item) {
return item.trim();
});
if (typeof splittedByAtItemParts[1] !== 'undefined') {
if (override || typeof commonNameMap[splittedByAtItemParts[1]] === 'undefined') {
if (typeof commonNameMap[splittedByAtItemParts[1]] === 'undefined') commonNameMap.count++;
commonNameMap[splittedByAtItemParts[1]] = splittedByAtItemParts[0];
}
}
}
});
return commonNameMap;
};
globiData.findThumbnailById = function (search, callback) {
search = search || {};
var uri = globiData.urlForTaxonImageByIdQuery(search);
var req = createReq();
req.open('GET', uri, true);
globiData.sendRequest(req, function (reponseData) {
var tumbnailUrl = reponseData.thumbnailURL;
callback(tumbnailUrl);
});
};
var callbackProxyForD3 = function (interactions) {
var columnNames = interactions.columns || [];
var sourceTaxonIds = columnNames.map(function (elem, i) {
if (elem.indexOf('source_') === -1) {
return -1;
} else {
return i;
}
}).filter(function (i) {
return i !== -1;
});
var targetTaxonIds = columnNames.map(function (elem, i) {
if (elem.indexOf('target_') === -1) {
return -1;
} else {
return i;
}
}).filter(function (i) {
return i !== -1;
});
var linkIds = columnNames.map(function (elem, i) {
if ((elem.indexOf('target_') === -1) && (elem.indexOf('source_') === -1)) {
return i;
} else {
return -1;
}
}).filter(function (i) {
return i !== -1;
});
var data = interactions.data || [];
var linksAndNodes = data.reduce(function (agg, row) {
var sourceTaxon = sourceTaxonIds.reduce(function (sourceObj, i) {
if (row[i] !== null) {
sourceObj[columnNames[i].substring('source_'.length)] = row[i];
}
return sourceObj;
}, {});
var targetTaxon = targetTaxonIds.reduce(function (targetObj, i) {
if (row[i] !== null) {
targetObj[columnNames[i].substring('target_'.length)] = row[i];
}
return targetObj;
}, {});
var link = linkIds.reduce(function (linkObj, i) {
linkObj[columnNames[i]] = row[i];
return linkObj;
}, { source: hash(sourceTaxon), target: hash(targetTaxon) });
agg.linksHash[hash(link)] = link;
agg.nodeHash[hash(sourceTaxon)] = sourceTaxon;
agg.nodeHash[hash(targetTaxon)] = targetTaxon;
return agg;
}, { linksHash: {}, nodeHash: {}});
var links = Object.keys(linksAndNodes.linksHash).map(function (i) {
return linksAndNodes.linksHash[i];
});
var nodes = Object.keys(linksAndNodes.nodeHash).map(function (i) {
return linksAndNodes.nodeHash[i];
});
return { links: links, nodes: nodes};
}
module.exports = globiData;