(function (angular) {
'use strict';
/**
* @memberof spApp
* @ngdoc service
* @name BiocacheService
* @description
* Methods to interact with ALA biocache-service
*/
angular.module('biocache-service', [])
.factory("BiocacheService", ["$http", "$q", function ($http, $q) {
var _httpDescription = function (method, httpconfig) {
if (httpconfig === undefined) {
httpconfig = {};
}
httpconfig.service = 'BiocacheService';
httpconfig.method = method;
return httpconfig;
};
var indexFields;
var thiz = {
/**
* Get the number of unique species (by facet names_and_lsid)
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(Integer)} Number of unique species
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Ouput:
* 10
*/
speciesCount: function (query, fqs, httpconfig) {
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when(0)
}
return $http.get(query.bs + "/occurrence/facets?facets=names_and_lsid&flimit=0&q=" + response.qid + fqList, _httpDescription('speciesCount', httpconfig)).then(function (response) {
if (response.data !== undefined && response.data.length > 0 && response.data[0].count !== undefined) {
return response.data[0].count;
} else {
return 0;
}
});
})
},
/**
* Get the number of unique endemic species (by facet names_and_lsid)
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(Integer)} Number of unique endemic species
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Ouput:
* 2
*/
speciesCountEndemic: function (query, fqs) {
var q;
if (fqs !== undefined) q = this.newLayerAddFq(query, fqs, '');
else q = query;
if (q == null) {
return $q.when(0)
} else {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when(0)
} else {
return $http.get(query.bs + "/explore/endemic/speciescount/" + response.qid.replace("qid:", "") + "?facets=names_and_lsid", _httpDescription('speciesCountEndemic')).then(function (response) {
return response.data.count;
});
}
})
}
},
/**
* Get species list CSV
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @param {Map} config (Optional) parameters for $http#get
* @returns {Promise(String)} Species list CSV
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
* - config
* Ouput:
* "names_and_lsid","Species Name","Scientific Name Authorship","Taxon Rank","Kingdom","Phylum","Class","Order","Family","Genus","Vernacular Name","Number of records","Conservation","Invasive"
* "Macropus giganteus|urn:lsid:biodiversity.org.au:afd.taxon:23f4784e-1116-482c-8e3e-b6b12733f588|Eastern Grey Kangaroo|Animalia|Macropodidae","Macropus giganteus","Shaw, 1790","species","ANIMALIA","CHORDATA","MAMMALIA","DIPROTODONTIA","MACROPODIDAE","Macropus","Eastern Grey Kangaroo","70654","South Australia : Conservation Status",""
* "Osphranter rufus|urn:lsid:biodiversity.org.au:afd.taxon:e6aff6af-ff36-4ad5-95f2-2dfdcca8caff|Red Kangaroo|Animalia|Macropodidae","Osphranter rufus","(Desmarest, 1822)","species","ANIMALIA","CHORDATA","MAMMALIA","DIPROTODONTIA","MACROPODIDAE","Osphranter","Red Kangaroo","47542","Northern Territory : Conservation Status",""
*/
speciesList: function (query, fqs, config) {
return this.speciesListUrl(query, fqs).then(function (url) {
if (url == null) {
return $q.when('')
}
return $http.get(url, _httpDescription('speciesList', config)).then(function (response) {
return response.data;
});
})
},
/**
* Build URL to GET species list CSV
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(String)} GET URL to species list CSV
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* "https://biocache-ws.ala.org.au/ws/occurrences/facets/download?facets=names_and_lsid&lookup=true&count=true&lists=true&q=Macropus&fq=geospatial_kosher:true"
*/
speciesListUrl: function (query, fqs) {
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return null
}
return query.bs + "/occurrences/facets/download?facets=names_and_lsid&lookup=true&count=true&lists=true&q=" + query.qid + fqList;
})
},
/**
* Get the endemic species list as CSV
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(String)} CSV of endemic species list
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* ```
* names_and_lsid Species Name Scientific Name Authorship Taxon Rank Kingdom Phylum Class Order Family Genus Vernacular Name Number of records
* Notamacropus agilis agilis|urn:lsid:biodiversity.org.au:afd.taxon:471127b3-a2c1-430e-931d-938cce4e58e8||Animalia|Macropodidae" Notamacropus agilis agilis (Gould, 1842) subspecies ANIMALIA CHORDATA MAMMALIA DIPROTODONTIA MACROPODIDAE Notamacropus 130
* Notamacropus agilis jardinii|urn:lsid:biodiversity.org.au:afd.taxon:bfe816bf-2b7e-47cb-87f8-ac386af751ab||Animalia|Macropodidae" Notamacropus agilis jardinii (De Vis, 1884) subspecies ANIMALIA CHORDATA MAMMALIA DIPROTODONTIA MACROPODIDAE Notamacropus 451
* ```
*/
speciesListEndemic: function (query, fqs, config) {
this.speciesListEndemicUrl(query, fqs).then(function (url) {
if (url == null) {
return $q.when('')
}
return $http.get(url, _httpDescription('speciesListEndemic', config)).then(function (response) {
return response.data;
});
})
},
/**
* Build URL to GET endemic species list CSV
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(String)} GET URL to endemic species list CSV
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* "http://biocache.ala.org.au/ws/explore/endemic/species/1234.csv?facets=names_and_lsid&lookup=true&count=true&lists=true"
*/
speciesListEndemicUrl: function (query, fqs) {
var q;
if (fqs !== undefined) q = this.newLayerAddFq(query, fqs, '');
else q = query;
if (q == null) {
return $q.when(false)
} else {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when(null)
} else {
return query.bs + "/explore/endemic/species/" + response.qid.replace("qid:", "") + ".csv?facets=names_and_lsid&lookup=true&count=true&lists=true";
}
})
}
},
/**
* List data providers
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(List)} List of data proviers
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* []
*/
dataProviderList: function (query, fqs) {
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when([])
}
return $http.get(query.bs + "/webportal/dataProviders?q=" + response.qid + fqList, _httpDescription('dataProviderList')).then(function (response) {
return response.data;
});
})
},
/**
* Get number of occurrences
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(Integer)} number of occurrences
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* 500
*/
count: function (query, fqs) {
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when(0)
}
var url = query.bs + "/occurrences/search?facet=false&pageSize=0&q=" + response.qid + fqList
return $http.get(url, _httpDescription('count')).then(function (response) {
if (response.data !== undefined && response.data.totalRecords !== undefined) {
return response.data.totalRecords ? response.data.totalRecords : 0
}
});
})
},
/**
* Get the default query title
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @returns {Promise(String)} formatted biocache-service query title
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* "<span>Macropus</span>"
*/
queryTitle: function (query) {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when("")
}
return $http.get(query.bs + "/webportal/params/details/" + response.qid.replace("qid:", ""), _httpDescription('queryTitle')).then(function (response) {
if (response.data !== undefined && response.data.displayString !== undefined) {
//remove html wrapping from title
var div = document.createElement('div');
div.innerHTML = response.data.displayString;
return div.innerText;
} else {
return ""
}
});
})
},
/**
* General search query URL
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @param {Integer} pageSize (Optional) page size (default=1)
* @param {Integer} offset (Optional) offset (default=0)
* @param {Boolean} facet (Optional) include server default facets (default=false)
* @returns {Promise(String)} search URL
*
* @example
* Input:
* - query
* {
* "q": ["Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - fqs
* ["geospatial_kosher:true"]
*
* Output:
* "http://biocache-ws.ala.org.au/ws/occurrences/search?q=Macropus&fq=geospatial_kosher:true&pageSize=1&offset=0&facet=false"
*/
constructSearchResultUrl: function (query, fqs, pageSize, offset, facet) {
facet = facet || false;
pageSize = pageSize === undefined ? 1 : pageSize;
offset = offset || 0;
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return null
}
return query.ws + "/occurrences/search?facet=" + facet + "&pageSize=" + pageSize + "&startIndex=" + offset + "&q=" + response.qid + fqList
})
},
/**
* Get search query output
* @memberof BiocacheService
* @param {Query} query Biocache query
* @param {List} fqs (Optional) additional fq terms
* @param {Integer} pageSize (Optional) page size (default=1)
* @param {Integer} offset (Optional) offset (default=0)
* @param {Boolean} facet (Optional) include server default facets (default=false)
* @returns {Promise(Map)} search results
*
* @example
* Input:
* - query
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
* - pageSize
* 0
*
* Output:
* {
* "pageSize": 0,
* "startIndex": 0,
* "totalRecords": 736,
* "sort": "score",
* "dir": "asc",
* "status": "OK",
* "occurrences": [],
* "facetResults": [],
* "query": "?q=taxon_name%3AMacropus",
* "urlParameters": "?q=taxon_name%3AMacropus",
* "queryTitle": "Scientific name:Macropus",
* "activeFacetMap": {}
* }
*/
searchForOccurrences: function (query, fqs, pageSize, offset, facet) {
facet = facet || false;
pageSize = pageSize === undefined ? 1 : pageSize;
offset = offset || 0;
var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs));
return this.registerQuery(query).then(function (response) {
if (response == null) {
return {}
}
return $http.get(query.bs + "/occurrences/search?facet=" + facet + "&pageSize=" + pageSize + "&startIndex=" + offset + "&q=" + response.qid + fqList + '&sort=id', _httpDescription('searchForOccurrences')).then(function (response) {
if (response.data !== undefined) {
return response.data;
}
})
})
},
/**
* Get facet list
* @memberof BiocacheService
* @param {String} facet Facet name
* @param {Query} query Biocache query
* @returns {Promise(List)} facets
*
* @example
* Input:
* - facet
* "taxon_name"
* - query
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
*
* Output:
* [{
"name": "Macropus giganteus",
"count": 70654,
"colour": 0,
"fq": "taxon_name:\"Macropus giganteus\"",
"red": 51,
"blue": 204,
"green": 102,
"displayname": "Macropus giganteus"
},
{
"name": "Osphranter rufus",
"count": 47542,
"colour": 0,
"fq": "taxon_name:\"Osphranter rufus\"",
"red": 220,
"blue": 18,
"green": 57
}]
*/
facet: function (facet, query, ranges) {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when([])
}
ranges = (ranges || []).join(",");
ranges = ranges.length > 0 ? "," + ranges : "";
return $http.get(query.bs + "/webportal/legend?cm=" + facet + ranges + "&q=" + response.qid + "&type=application/json", _httpDescription('facet',
{headers: {Accept: "application/json"}})).then(function (response) {
$.map(response.data, function (v, k) {
if (ranges.length > 0) {
// parse name for ranges: (optional '-') + facet + '.[' + min + ' TO ' + max + ']'
var match = ("" + v.name).match(/(-)*.*\[(.* TO .*)\]/);
if (match && match.length === 3) {
match[1] = match[1] || "";
// add "exclude" to label for facets with '-'
if (match[1] === '-' && match[2] === "* TO *") {
match[1] = "";
match[2] = $i18n(474, "Not supplied")
// 'min' is for numerical sorting
v.min = ''
} else {
// 'min' is for numerical sorting
v.min = parseFloat(match[2].split(' ')[0])
}
v.displayname = match[1] + match[2];
} else {
v.displayname = v.name
}
} else {
v.displayname = BiocacheI18n.get(facet + '.' + v.name, v.name ? v.name : "")
}
});
return response.data;
});
})
},
/**
* Get pageable facet list
* @memberof BiocacheService
* @param {String} facet Facet name
* @param {Query} query Biocache query
* @param {Integer} pageSize (Optional) page size (default=1)
* @param {Integer} offset (Optional) offset (default=0)
* @param {String} prefixFilter (Optional) keywords
* @param {String} sortBy (Optional) sorted by field (default=count)
* @param {List} config (Optional) parameters for $http#get
* @returns {Promise(List)} facets
*
* @example
* Input:
* - facet
* "taxon_name"
* - query
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
*
* Output:
* [{
"fieldName": "taxon_name",
"fieldResult":
[{
"label": "Macropus giganteus",
"count": 70654,
"fq": "taxon_name:\"Macropus giganteus\"",
"displaylabel": "Macropus giganteus"
},
{
"label": "Osphranter rufus",
"count": 47542,
"fq": "taxon_name:\"Osphranter rufus\"",
"displaylabel": "Osphranter rufus"
}]
}]
*/
facetGeneral: function (facet, query, pageSize, offset, prefixFilter, sortBy, config) {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when([])
}
var url = query.bs + "/occurrence/facets?facets=" + facet + "&flimit=" + pageSize + "&foffset=" + offset + "&fsort=" + (sortBy ? sortBy:"count") + "&q=" + response.qid;
if (prefixFilter !== undefined && prefixFilter.length > 0) url += "&fprefix=" + encodeURIComponent(prefixFilter);
return $http.get(url, _httpDescription('facetGeneral', config)).then(function (response) {
if (response.data && response.data[0] && response.data[0].fieldResult) {
$.map(response.data[0].fieldResult, function (v, k) {
v.displaylabel = BiocacheI18n.get(facet + '.' + v.label, v.label ? v.label : "")
});
return response.data;
} else {
return []
}
});
})
},
facetDownload: function (facet) {
return $SH.biocacheServiceUrl + '/occurrences/facets/download?facets=' + facet + '&count=true&lookup=true';
},
/**
* Encode and join a list of q and fq terms
*
* @memberof BiocacheService
* @param {List} list q and fqs
* @returns {String} query parameters as a string
*/
joinAndEncode: function (list) {
var q = '';
if (list instanceof Array) {
$.each(list, function (index, item) {
if (item !== undefined && item !== null) {
if (q.length > 0) q += '&fq=';
q += encodeURIComponent(item)
}
})
} else {
q = list
}
return q
},
/**
* Get query longitude and latitude bounding box
* @memberof BiocacheService
* @param {Query} query Biocache query
* @returns {Promise(List)} southWest corner and northEast corner as decimal latitude and longitude
*
* @example
* Input:
* - query
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
*
* Output:
* [[-180, -90], [180, 90]]
*/
bbox: function (query) {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when([[-180, -90], [180, 90]])
}
return $http.get(query.bs + "/webportal/bbox?q=" + response.qid + "&type=application/json", _httpDescription('bbox')).then(function (response) {
var bb = response.data.split(",");
return [[bb[1], bb[0]], [bb[3], bb[2]]];
});
})
},
/**
* Shorten a query
* @memberof BiocacheService
* @param {Query} query Biocache query
* @returns {Promise(Query)} qid
*
* @example
* Input:
* - query
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
*
* Output:
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au",
* "qid": 1234
* }
*/
registerQuery: function (query) {
if (query.qid) {
return $q.when(query)
} else {
if (!(query.q instanceof Array)) {
query.q = [query.q]
}
var q = jQuery.extend([], query.q);
var fq;
if (query.q instanceof Array) {
q = query.q[0];
if (query.q.length > 1) {
fq = query.q.slice();
fq.splice(0, 1)
}
}
return this.registerParam(query.bs, q, fq, query.wkt, query.qualityProfile, query.disableQualityFilter, query.disableAllQualityFilters)
}
},
/**
* Get qid for a query
* @memberof BiocacheService
* @param {String} url biocache-service URL
* @param {List} query q and fq terms
* @param {List} fq (optional) one fq term
* @param {String} wkt (optional) WKT search value
* @param {String} qualityProfile (optional) quality profile
* @param {Array} disableQualityFilter (optional) quality filters to disable
* @param {Boolean} disableAllQualityFilters (optional) whether to disable all quality filters
* @returns {Promise(Integer)} qid
*
* @example
* Input:
* - bs
* "https://biocache-ws.ala.org.au/ws"
* - q
* ["taxon_name:Macropus"]
*
* Output:
* 1234
*/
registerParam: function (bs, q, fq, wkt, qualityProfile, disableQualityFilter, disableAllQualityFilters) {
var data = {q: q, bs: bs};
if ($SH.qc !== undefined && $SH.qc !== null && $SH.qc.length > 0) data.qc = $SH.qc;
if (fq !== undefined && fq !== null) data.fq = fq;
if (wkt !== undefined && wkt !== null && wkt.length > 0) data.wkt = wkt;
if (disableAllQualityFilters !== undefined && disableAllQualityFilters !== null) data.disableAllQualityFilters = disableAllQualityFilters;
if (qualityProfile !== undefined && qualityProfile !== null) data.qualityProfile = qualityProfile;
if (disableQualityFilter !== undefined && disableQualityFilter !== null) data.disableQualityFilter = disableQualityFilter;
return $http.post($SH.baseUrl + "/portal/q", data, _httpDescription('registerParam')).then(function (response) {
if (thiz.validateQID(response.data.qid)) {
//Need to return 'qid:xxxxxx'
return {qid: "qid:" + response.data.qid}
} else {
bootbox.alert($i18n(478, "Failed to register query. Try again later."));
return null
}
}, function (response) {
bootbox.alert($i18n(478, "Failed to register query. Try again later."));
return null
});
},
/**
* Create a new #Query
* @memberof BiocacheService
* @param {List} query q and fq terms
* @param {name} name (optional) name for display
* @param {String} wkt (optional) WKT search value
* @returns {Query}
*
* @example
* Input:
* - q
* ["taxon_name:Macropus"]
*
* Output:
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au",
* "name": ""
* }
*/
newQuery: function (q, name, wkt) {
if (q === undefined) q = ["*:*"];
if (name === undefined) name = '';
return {
q: q,
wkt: wkt,
name: name,
bs: $SH.biocacheServiceUrl,
ws: $SH.biocacheUrl
}
},
/**
* Create a new #Layer suitable for adding to #MapService
* @memberof BiocacheService
* @param {List} query q and fq terms
* @param {Area} area (optional) area to limit the query
* @param {newName} name (optional) name for display
* @returns {Promise(Layer)}
*
* @example
* Input:
* - q
* ["taxon_name:Macropus"]
*
* Output:
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au",
* "name": ""
* }
*/
newLayer: function (query, area, newName) {
var fq = [];
if (query.q instanceof Array) {
fq = query.q
} else {
fq = [query.q]
}
if (query.fq !== undefined) {
fq = fq.concat(query.fq)
}
if (query.fqs !== undefined) {
fq = fq.concat(query.fqs)
}
var wkt = undefined;
if (area !== undefined && area instanceof Array && area.length > 0 && area[0] !== undefined) {
if (area[0].pid && (area[0].pid.length > 0) && area[0].pid.indexOf('~') < 0) {
wkt = area[0].pid
} else if (area[0].q !== undefined) {
if (area[0].q.length > 0) {
fq = fq.concat(area[0].q)
}
} else if (area[0].wkt && (area[0].wkt.length) > 0) {
wkt = area[0].wkt
}
}
if (query.wkt !== undefined) wkt = query.wkt;
return this.registerLayer(query.bs, query.ws, fq, wkt, query.qualityProfile, query.disableQualityFilter, query.disableAllQualityFilters, newName)
},
/**
* Create a new query #Layer
* @memberof BiocacheService
* @param {List} query q and fq terms
* @param {String} fq (optional) one fq term
* @param {newName} name (optional) name for display
* @returns {Promise(Layer)}
*
* @example
* Input:
* - q
* ["taxon_name:Macropus"]
*
* Output:
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au",
* "name": ""
* }
*/
newLayerAddFq: function (query, newFq, newName) {
var fqs;
if (query.q instanceof Array) fqs = $.merge([], query.q);
else fqs = [query.q];
if ((query.fq instanceof Array) && query.fq.length > 0) {
$.merge(fqs, query.fq)
}
if (newFq instanceof Array) {
$.merge(fqs, newFq)
} else if (newFq !== undefined) {
$.merge(fqs, [newFq])
}
return this.registerLayer(query.bs, query.ws, fqs, query.wkt, query.qualityProfile, query.disableQualityFilter, query.disableAllQualityFilters, newName).then(function (data) {
if (data == null) {
return null;
} else {
data.species_list = query.species_list
return data
}
})
},
/**
* Create a layer and register for qid
* @memberof BiocacheService
* @param {String} wsUrl biocache-service URL
* @param {String} hubUrl biocache-hub URL
* @param {List} fqs q and fq terms
* @param {String} wkt (optional) WKT
* @param {String} qualityProfile (optional) quality profile
* @param {Array} disableQualityFilter (optional) quality filters to disable
* @param {Boolean} disableAllQualityFilters (optional) whether to disable all quality filters
* @param {newName} name (optional) name for display
* @returns {Promise(Layer)}
*
* @example
* Input:
* - bs
* "https://biocache-ws.ala.org.au/ws"
* - ws
* "https://biocache.ala.org.au"
* - fq
* ["taxon_name:Macropus"]
*
* Output:
* {
* "q": ["taxon_name:Macropus"],
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au",
* "name": ""
* }
*/
registerLayer: function (bs, ws, fq, wkt, qualityProfile, disableQualityFilter, disableAllQualityFilters, name) {
fq = fq.slice();
for (var i = 0; i < fq.length; i++) {
if (fq[i] === '*:*') fq.splice(i, 1)
}
var q = "*:*";
if (fq.length > 0) {
q = fq[0];
fq.splice(0, 1)
}
if (fq.length > 0 || (wkt !== undefined && wkt !== null && wkt.length > 0) || qualityProfile || disableQualityFilter || disableAllQualityFilters != null) {
return this.registerParam(bs, q, fq, wkt, qualityProfile, disableQualityFilter, disableAllQualityFilters).then(function (data) {
if (data != null) {
return {
q: $.merge([q], fq),
wkt: wkt,
qid: "qid:" + data.qid,
bs: bs,
ws: ws,
name: name
}
} else {
return null
}
})
} else {
var qc = [];
if ($SH.qc !== undefined && $SH.qc != null && $SH.qc.length > 0) qc = [$SH.qc];
var qid = q;
if (qc.length > 0) qid = "(" + q + ") AND " + qc[0]
return $q.when({
q: $.merge(q, qc), //fq.length == 0 so it is safe to use qc here
wkt: wkt,
qid: qid,
bs: bs,
ws: ws,
name: name
})
}
},
getIndexFields: function () {
// use static index fields before biocache-service index fields
if (indexFields) {
return $q.when(indexFields)
} else {
return $http.get($SH.biocacheServiceUrl + "/index/fields", _httpDescription('getIndexFields')).then(function (response) {
indexFields = response.data;
for (var i = 0; i < indexFields.length; i++) {
indexFields[i].displayName = indexFields[i].dwcTerm || indexFields[i].description || indexFields[i].name
if (indexFields[i].classs === undefined) {
indexFields[i].classs = 'Other'
}
indexFields[i].class = indexFields[i].classs
indexFields[i].url = thiz.parseUrl(indexFields[i].info)
if (indexFields[i].url !== undefined) {
indexFields[i].info = indexFields[i].info.replace(indexFields[i].url, '')
} else {
indexFields[i].url = ''
}
if (indexFields[i].description === undefined) {
indexFields[i].description = ''
}
}
return indexFields
});
}
},
parseUrl: function (info) {
if (info !== undefined) {
var match = info.match("\\bhttps?://[^\\b]+")
if (match) {
return match[0]
}
}
return undefined
},
/**
* Get the minimum and maxium value for a facet in a given query.
* @param query
* @param facet
* @returns {Promise(Object)}
* Input:
* - facet
* {
* name: "year"
* ...
* }
* - query
* {
* "q": "frog",
* "bs": "https://biocache-ws.ala.org.au/ws",
* "ws": "https://biocache.ala.org.au"
* }
*
* Output:
* {
* "min":1896.0,
* "max":2019.0,
* "label":"year"
* }
*/
getFacetMinMax: function(query, facet) {
var defaultValue = {min: undefined, max: undefined, label: facet.name};
if (Util.isFacetOfRangeDataType(facet.dataType)) {
return this.registerQuery(query).then(function (response) {
if (response == null) {
return $q.when(defaultValue)
}
return $http.get(query.bs + "/chart?q=" + response.qid + "&statType=min,max&stats=" + facet.name).then(function (response) {
return response.data.data && response.data.data[0] && response.data.data[0].data && response.data.data[0].data[0] || defaultValue;
});
});
} else {
return $q.when(defaultValue);
}
},
facetsToFq: function (facet, ignoreEnabledFlag) {
var fqs = [];
if (facet && facet.length > 0) {
for (var i in facet) {
var term = this.facetToFq(facet[i], ignoreEnabledFlag)
if (term && term.fq) {
fqs.push(term.fq)
}
}
}
return fqs;
},
facetToFq: function (facet, ignoreEnabledFlag) {
if (facet.data === undefined || (!ignoreEnabledFlag && !facet.enabled)) {
return {sum: 0, fq: undefined}
}
var sel = '';
var invert = false;
var count = 0;
var sum = 0;
// sum only applies to the single facet
for (var i = 0; i < facet.data.length; i++) {
if (facet.data[i].selected) {
var fq = facet.data[i].fq;
if (fq.match(/^-/g) != null && (fq.match(/:\*$/g) != null || fq.match(/\[\* TO \*\]$/g) != null)) {
invert = true
}
count++;
sum += facet.data[i].count;
}
}
if (count == 0 /*|| count == facet.data.length*/) {
return {sum: 0, fq: undefined}
} else {
if (count === 1) invert = false;
for (i = 0; i < facet.data.length; i++) {
if (facet.data[i].selected) {
var fq = facet.data[i].fq;
if (invert) {
if (sel.length > 0) sel += " AND ";
if (fq.match(/^-/g) != null && (fq.match(/:\*$/g) != null || fq.match(/\[\* TO \*\]$/g) != null)) {
sel += fq.substring(1)
} else {
sel += '-' + fq
}
} else {
if (sel.length > 0) sel += " OR ";
sel += fq
}
}
}
if (invert) {
sel = '-(' + sel + ')'
}
return {sum: sum, fq: sel}
}
},
downloadAsync:function(species, area, doiApplicationData) {
var params = {
hubName: $SH.doiHubName || "CSDM",
file: species.name,
mintDoi: true,
reasonTypeId: $SH.doiReasonTypeId || 13,
fileType: 'csv',
qa: 'none',
sourceTypeId: $SH.doiSourceTypeId || 10002,
email: $SH.userEmail,
emailTemplate: $SH.doiEmailTemplate || 'csdm',
doiDisplayTemplate: $SH.doiDisplayTemplate || 'csdm'
};
// This should be a POST but the data binding in biocache-service isn't setup to bind from the POST body.
for (var key in doiApplicationData) {
if (doiApplicationData.hasOwnProperty(key)) {
params["doiMetadata["+key+"]"] = doiApplicationData[key];
}
}
return thiz.newLayer(species, area, species.name).then(function (query) {
if (query == null) {
return $q.when(null)
}
var downloadUrl = $SH.biocacheServiceUrl + '/occurrences/offline/download';
params.q = query.qid;
params.searchUrl = $SH.biocacheServiceUrl + '/occurrences/search?q=' + query.qid;
return $http.get(downloadUrl, _httpDescription("offlineDownload", {params: params}));
});
},
validateQID: function(qid){
return !isNaN(qid)
}
};
return thiz;
}])
}(angular));