/*global define */
define(["jquery", "jqueryui", "underscore", "backbone"], function (
$,
$ui,
_,
Backbone
) {
"use strict";
/**
* @class LookupModel
* @classdesc A utility model that contains functions for looking up values
* from various services
* @classcategory Models
*/
var LookupModel = Backbone.Model.extend(
/** @lends LookupModel.prototype */ {
defaults: {
concepts: {},
},
initialize: function () {},
bioportalSearch: function (request, response, localValues, allValues) {
// make sure we have something to lookup
if (!MetacatUI.appModel.get("bioportalAPIKey")) {
response(localValues);
return;
}
var query =
MetacatUI.appModel.get("bioportalSearchUrl") +
"?q=" +
request.term +
"&apikey=" +
MetacatUI.appModel.get("bioportalAPIKey") +
"&ontologies=ECSO&pagesize=1000&suggest=true";
var availableTags = [];
$.get(query, function (data, textStatus, xhr) {
_.each(data.collection, function (obj) {
var choice = {};
choice.label = obj["prefLabel"];
var synonyms = obj["synonym"];
if (synonyms) {
choice.synonyms = [];
_.each(synonyms, function (synonym) {
choice.synonyms.push(synonym);
});
}
choice.filterLabel = obj["prefLabel"];
choice.value = obj["@id"];
if (obj["definition"]) {
choice.desc = obj["definition"][0];
}
// mark items that we know we have matches for
if (allValues) {
var matchingChoice = _.findWhere(allValues, {
value: choice.value,
});
if (matchingChoice) {
//choice.label = "*" + choice.label;
choice.match = true;
// remove it from the local value - why have two?
if (localValues) {
localValues = _.reject(localValues, function (obj) {
return obj.value == matchingChoice.value;
});
}
//availableTags.push(choice);
}
}
availableTags.push(choice);
});
// combine the lists if called that way
if (localValues) {
availableTags = localValues.concat(availableTags);
}
response(availableTags);
});
},
bioportalExpand: function (term) {
// make sure we have something to lookup
if (!MetacatUI.appModel.get("bioportalAPIKey")) {
response(null);
return;
}
var terms = [];
var countdown = 0;
var query =
MetacatUI.appModel.get("bioportalSearchUrl") +
"?q=" +
term +
"&apikey=" +
MetacatUI.appModel.get("bioportalAPIKey") +
"&ontologies=ECSO&pagesize=1000&suggest=true";
$.ajax({
url: query,
method: "GET",
async: false, // we want to wait for the response!
success: function (data, textStatus, xhr) {
_.each(data.collection, function (obj) {
// use the preferred label
var prefLabel = obj["prefLabel"];
terms.push(prefLabel);
// add the synonyms
var synonyms = obj["synonym"];
if (synonyms) {
_.each(synonyms, function (synonym) {
terms.push(synonym);
});
}
// process the descendants
var descendantsUrl = obj["links"]["descendants"];
//if (false) {
if (descendantsUrl && countdown > 0) {
countdown--;
$.ajax({
url:
descendantsUrl +
"?apikey=" +
MetacatUI.appModel.get("bioportalAPIKey"),
method: "GET",
async: false,
success: function (data, textStatus, xhr) {
_.each(data.collection, function (obj) {
var prefLabel = obj["prefLabel"];
var synonyms = obj["synonym"];
if (synonyms) {
_.each(synonyms, function (synonym) {
terms.push(synonym);
});
}
});
},
});
}
});
},
});
return terms;
},
bioportalGetConcepts: function (uri, callback) {
var concepts = this.get("concepts")[uri];
if (concepts) {
callback(concepts);
return;
} else {
concepts = [];
}
// make sure we have something to lookup
if (!MetacatUI.appModel.get("bioportalAPIKey")) {
return;
}
var query =
MetacatUI.appModel.get("bioportalSearchUrl") +
"?q=" +
encodeURIComponent(uri) +
"&apikey=" +
MetacatUI.appModel.get("bioportalAPIKey") +
"&ontologies=ECSO&pagesize=1000&suggest=true";
var availableTags = [];
var model = this;
$.get(query, function (data, textStatus, xhr) {
_.each(data.collection, function (obj) {
var concept = {};
concept.label = obj["prefLabel"];
concept.value = obj["@id"];
if (obj["definition"]) {
concept.desc = obj["definition"][0];
}
// add the synonyms
var synonyms = obj["synonym"];
if (synonyms) {
concept.synonyms = [];
_.each(synonyms, function (synonym) {
concept.synonyms.push(synonym);
});
}
concepts.push(concept);
});
model.get("concepts")[uri] = concepts;
callback(concepts);
});
},
bioportalGetConceptsBatch: function (uris, callback) {
// make sure we have something to lookup
if (!MetacatUI.appModel.get("bioportalBatchUrl")) {
return;
}
// prepare the request JSON
var batchData = {};
batchData["http://www.w3.org/2002/07/owl#Class"] = {};
batchData["http://www.w3.org/2002/07/owl#Class"]["display"] =
"prefLabel,synonym,definition";
batchData["http://www.w3.org/2002/07/owl#Class"]["collection"] = [];
_.each(uris, function (uri) {
var item = {};
item["class"] = uri;
item["ontology"] = "http://data.bioontology.org/ontologies/ECSO";
batchData["http://www.w3.org/2002/07/owl#Class"]["collection"].push(
item
);
});
var url = MetacatUI.appModel.get("bioportalBatchUrl");
var model = this;
$.ajax(url, {
method: "POST",
//url: url,
data: JSON.stringify(batchData),
contentType: "application/json",
headers: {
Authorization:
"apikey token=" + MetacatUI.appModel.get("bioportalAPIKey"),
},
error: function (e) {
console.log(e);
},
success: function (data, textStatus, xhr) {
_.each(data["http://www.w3.org/2002/07/owl#Class"], function (obj) {
var concept = {};
concept.label = obj["prefLabel"];
concept.value = obj["@id"];
if (obj["definition"]) {
concept.desc = obj["definition"][0];
}
// add the synonyms
var synonyms = obj["synonym"];
if (synonyms) {
concept.synonyms = [];
_.each(synonyms, function (synonym) {
concept.synonyms.push(synonym);
});
}
var conceptList = [];
conceptList.push(concept);
model.get("concepts")[concept.value] = conceptList;
});
callback.apply();
},
});
},
orcidGetConcepts: function (uri, callback) {
var people = this.get("concepts")[uri];
if (people) {
callback(people);
return;
} else {
people = [];
}
var query =
MetacatUI.appModel.get("orcidBaseUrl") +
uri.substring(uri.lastIndexOf("/"));
var model = this;
$.get(query, function (data, status, xhr) {
// get the orcid info
var profile = $(data).find("orcid-profile");
_.each(profile, function (obj) {
var choice = {};
choice.label =
$(obj).find("orcid-bio > personal-details > given-names").text() +
" " +
$(obj).find("orcid-bio > personal-details > family-name").text();
choice.value = $(obj).find("orcid-identifier > uri").text();
choice.desc = $(obj).find("orcid-bio > personal-details").text();
people.push(choice);
});
model.get("concepts")[uri] = people;
// callback with answers
callback(people);
});
},
/*
* Supplies search results for ORCiDs to autocomplete UI elements
*/
orcidSearch: function (request, response, more, ignore) {
var people = [];
if (!ignore) var ignore = [];
var query = MetacatUI.appModel.get("orcidSearchUrl") + request.term;
$.get(query, function (data, status, xhr) {
// get the orcid info
var profile = $(data).find("orcid-profile");
_.each(profile, function (obj) {
var choice = {};
choice.value = $(obj).find("orcid-identifier > uri").text();
if (_.contains(ignore, choice.value.toLowerCase())) return;
choice.label =
$(obj).find("orcid-bio > personal-details > given-names").text() +
" " +
$(obj).find("orcid-bio > personal-details > family-name").text();
choice.desc = $(obj).find("orcid-bio > personal-details").text();
people.push(choice);
});
// add more if called that way
if (more) {
people = more.concat(people);
}
// callback with answers
response(people);
});
},
/*
* Gets the bio of a person given an ORCID Updates the given user model
* with the bio info from ORCID
*/
orcidGetBio: function (options) {
if (!options || !options.userModel) return;
var orcid = options.userModel.get("username"),
onSuccess = options.success || function () {},
onError = options.error || function () {};
$.ajax({
url: MetacatUI.appModel.get("orcidSearchUrl") + orcid,
type: "GET",
//accepts: "application/orcid+json",
success: function (data, textStatus, xhr) {
// get the orcid info
var orcidNode = $(data).find("path:contains(" + orcid + ")"),
profile = orcidNode.length
? $(orcidNode).parents("orcid-profile")
: [];
if (!profile.length) return;
var fullName =
$(profile)
.find("orcid-bio > personal-details > given-names")
.text() +
" " +
$(profile)
.find("orcid-bio > personal-details > family-name")
.text();
options.userModel.set("fullName", fullName);
onSuccess(data, textStatus, xhr);
},
error: function (xhr, textStatus, error) {
onError(xhr, textStatus, error);
},
});
},
/**
* Using the NSF Award Search API, get a list of grants that match the
* given term, as long as the term is at least 3 characters long and
* doesn't consist of only digits. Used to populate the autocomplete list
* for the Funding fields in the metadata editor. For this method to work,
* there must be a grantsUrl set in the MetacatUI.appModel.
* @param {jQuery} request - The jQuery UI autocomplete request object
* @param {function} response - The jQuery UI autocomplete response function
* @see {@link https://www.research.gov/common/webapi/awardapisearch-v1.htm}
*/
getGrantAutocomplete: function (
request,
response,
beforeRequest,
afterRequest
) {
// Handle errors in this function or in the findGrants function
function handleError(error) {
if (typeof afterRequest == "function") afterRequest();
console.log("Error fetching awards from NSF: ", error);
response([]);
}
try {
let term = request.term;
// Only search after 3 characters or more, and not just digits
if (!term || term.length < 3 || /^\d+$/.test(term)) return;
// If the beforeRequest function was passed, call it now
if (typeof beforeRequest == "function") beforeRequest();
// Search for grants
this.findGrants(term)
.then((awards) => {
response(this.formatFundingForAutocomplete(awards));
})
.catch(handleError)
.finally(() => {
if (typeof afterRequest == "function") afterRequest();
});
} catch (error) {
handleError(error);
}
},
/**
* Search the NSF Award Search API for grants that match the given term.
* @param {string} term - The term to search for
* @param {number} [offset=1] - The offset to use in the search. Defaults
* to 1.
* @returns {Promise} A promise that resolves to an array of awards in the
* format {id: string, title: string}
* @since 2.28.0
*/
findGrants: function (term, offset = 1) {
let awards = [];
if (!term || term.length < 3) return awards;
const grantsUrl = MetacatUI.appModel.get("grantsUrl");
if (!grantsUrl) return awards;
term = $.ui.autocomplete.escapeRegex(term);
term = encodeURIComponent(term);
const filterBy = "keyword";
const url =
`${grantsUrl}?${filterBy}=${term}` +
`&printFields=title,id&offset=${offset}`;
return fetch(url)
.then((response) => {
return response.json();
})
.then((data) => {
if (!data || !data.response || !data.response.award) return awards;
return data.response.award;
})
.catch((error) => {
console.error("Error fetching data: ", error);
return awards;
});
},
/**
* Format awards from the NSF Award Search API for use in the jQuery UI
* autocomplete widget.
* @param {Array} awards - An array of awards in the format
* {id: string, title: string}
* @returns {Array} An array of awards in the format
* {value: string, label: string}
* @since 2.28.0
*/
formatFundingForAutocomplete: function (awards) {
if (!awards || !awards.length) return [];
return awards.map((award) => ({
value: award.id,
label: award.title,
}));
},
getAccountsAutocomplete: function (request, response) {
var searchTerm = $.ui.autocomplete.escapeRegex(request.term);
//Only search after 2 characters or more
if (searchTerm.length < 2) return;
var url =
MetacatUI.appModel.get("accountsUrl") + "?query=" + searchTerm;
// Send the AJAX request as a JSONP data type since it will be
// cross-origin
var requestSettings = {
url: url,
success: function (data, textStatus, xhr) {
if (!data) return [];
//If an XML doc was not returned from the server, then try to parse
//the response as XML
if (!XMLDocument.prototype.isPrototypeOf(data)) {
try {
data = $.parseXML(data);
} catch (e) {
//If the parsing XML failed, exit now
console.error(
"The accounts service did not return valid XML.",
e
);
return;
}
}
var list = [];
_.each(
$(data)
.children(/.+subjectInfo/)
.children(),
function (accountNode, i) {
var name = "";
var type = "";
if ($(accountNode).children("givenName").length) {
name =
$(accountNode).children("givenName").text() +
" " +
$(accountNode).children("familyName").text();
type = "person";
} else {
name = $(accountNode).children("groupName").text();
type = "group";
}
if (!name) {
name = $(accountNode).children("subject").text();
type = "unknown";
}
list.push({
value: $(accountNode).children("subject").text(),
label:
name +
" (" +
$(accountNode).children("subject").text() +
")",
type: type,
});
}
);
var term = $.ui.autocomplete.escapeRegex(request.term),
startsWithMatcher = new RegExp("^" + term, "i"),
startsWith = $.grep(list, function (value) {
return startsWithMatcher.test(
value.label || value.value || value
);
}),
containsMatcher = new RegExp(term, "i"),
contains = $.grep(list, function (value) {
return (
$.inArray(value, startsWith) < 0 &&
containsMatcher.test(value.label || value.value || value)
);
});
response(startsWith.concat(contains));
},
};
//Send the query
$.ajax(requestSettings);
},
/**
* Calls the monitor/status DataONE MN API and gets the size of the index
* queue.
* @param {function} [onSuccess]
* @param {function} [onError]
*/
getSizeOfIndexQueue: function (onSuccess, onError) {
try {
if (!MetacatUI.appModel.get("monitorStatusUrl")) {
if (typeof onSuccess == "function") {
onSuccess();
} else {
//Trigger a custom event for the size of the index queue.
this.trigger("sizeOfQueue", -1);
}
return false;
}
var model = this;
//Check if there is an indexing queue, because this model may still be
//indexing
var requestSettings = {
url: MetacatUI.appModel.get("monitorStatusUrl"),
type: "GET",
error: function () {
if (typeof onError == "function") {
onError();
}
},
success: function (data) {
var sizeOfQueue = parseInt(
$(data).find("status > index > sizeOfQueue").text()
);
if (sizeOfQueue > 0 || sizeOfQueue == 0) {
//Trigger a custom event for the size of the index queue.
model.trigger("sizeOfQueue", sizeOfQueue);
if (typeof onSuccess == "function") {
onSuccess(sizeOfQueue);
}
} else {
if (typeof onError == "function") {
onError();
}
}
},
};
$.ajax(
_.extend(
requestSettings,
MetacatUI.appUserModel.createAjaxSettings()
)
);
} catch (e) {
console.error(e);
if (typeof onError == "function") {
onError();
}
}
},
}
);
return LookupModel;
});