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Merge branch 'gbif-service' of github.com:NetsBlox/services into gbif…
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…-service
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@dragazo
dragazo committed Apr 9, 2024
2 parents c65a262 + f7b9d4e commit 8f416f7
Showing 1 changed file with 131 additions and 110 deletions.
241 changes: 131 additions & 110 deletions src/procedures/global-biodiversity/global-biodiversity.js
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Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,22 @@
"use strict";

const ApiConsumer = require("../utils/api-consumer");
const utils = require('../utils');
const types = require('../../input-types');
const _ = require('lodash');
const utils = require("../utils");
const types = require("../../input-types");
const _ = require("lodash");

types.defineType({
name: 'SpeciesNameType',
description: 'The type of species name to use in the :doc:`/services/GlobalBiodiversity/index` service.',
baseType: 'Enum',
baseParams: {
'common name': 'VERNACULAR',
'scientific name': 'SCIENTIFIC',
},
name: "SpeciesNameType",
description:
"The type of species name to use in the :doc:`/services/GlobalBiodiversity/index` service.",
baseType: "Enum",
baseParams: {
"common name": "VERNACULAR",
"scientific name": "SCIENTIFIC",
},
});

const BackBone = "d7dddbf4-2cf0-4f39-9b2a-bb099caae36c"
const BackBone = "d7dddbf4-2cf0-4f39-9b2a-bb099caae36c";

const GBIF = new ApiConsumer(
"GlobalBiodiversity",
Expand All @@ -30,170 +31,190 @@ const GBIF = new ApiConsumer(
);

function cleanSpecies(r) {
const res = {
id: r['key'],
};

if (r['canonicalName'] !== undefined) {
res['canonicalName'] = r['canonicalName'];
}
if (r['vernacularNames'] !== undefined) {
res['vernacularNames'] = _.uniq(r['vernacularNames'].filter((x) => !x.language || x.language === 'eng').map((x) => x.vernacularName.toLowerCase())).sort()
}
if (r['extinct'] !== undefined) {
res['extinct'] = r['extinct'];
}
if (r['threatStatuses'] !== undefined) {
res['threatStatuses'] = _.uniq(r['threatStatuses'].map((x) => x.toLowerCase().replace('_', ' '))).sort();
}
if (r['habitats'] !== undefined) {
res['habitats'] = _.uniq(r['habitats'].map((x) => x.toLowerCase())).sort();
}
if (r['descriptions'] !== undefined) {
res['descriptions'] = r['descriptions'].filter((x) => !x.language || x.language === 'eng').map((x) => x.description);
}
for (const k of ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']) {
if (r[k] !== undefined) {
res[k] = r[k];
}
const res = {
id: r["key"],
};

if (r["canonicalName"] !== undefined) {
res["canonicalName"] = r["canonicalName"];
}
if (r["vernacularNames"] !== undefined) {
res["vernacularNames"] = _.uniq(
r["vernacularNames"].filter((x) => !x.language || x.language === "eng")
.map((x) => x.vernacularName.toLowerCase()),
).sort();
}
if (r["extinct"] !== undefined) {
res["extinct"] = r["extinct"];
}
if (r["threatStatuses"] !== undefined) {
res["threatStatuses"] = _.uniq(
r["threatStatuses"].map((x) => x.toLowerCase().replace("_", " ")),
).sort();
}
if (r["habitats"] !== undefined) {
res["habitats"] = _.uniq(r["habitats"].map((x) => x.toLowerCase())).sort();
}
if (r["descriptions"] !== undefined) {
res["descriptions"] = r["descriptions"].filter((x) =>
!x.language || x.language === "eng"
).map((x) => x.description);
}
for (
const k of [
"kingdom",
"phylum",
"class",
"order",
"family",
"genus",
"species",
]
) {
if (r[k] !== undefined) {
res[k] = r[k];
}
}

return res;
return res;
}

/**
* Search the database for species of the given common or scientific name.
*
*
* Because there may be many matches, only up to 20 search results are returned per call to this RPC.
* You can check if there are more matches by increasing the ``page`` number of results to return.
* When there are no more results, an empty list is returned.
*
*
* @param {SpeciesNameType} nameType the type of name to search for
* @param {BoundedString<3>} name name of the species to search for
* @param {BoundedInteger<1>=} page page number of results to return (default ``1``)
* @returns {Array<Object>}
* @returns {Array<Object>}
*/
GBIF.searchSpecies = async function (nameType, name, page = 1) {
const limit = 20;
const offset = (page - 1) * limit;

// their api puts a hard cap at offset 100000 - just give empty results
if (offset > 100000) {
return [];
}

const res = await this._requestData({
path: 'species/search',
queryString: `datasetKey=${BackBone}&status=ACCEPTED&rank=SPECIES&qField=${nameType}&q=${encodeURIComponent(name)}&limit=${limit}&offset=${offset}`,
});

return res.results.map((r) => cleanSpecies(r));
const limit = 20;
const offset = (page - 1) * limit;

// their api puts a hard cap at offset 100000 - just give empty results
if (offset > 100000) {
return [];
}

const res = await this._requestData({
path: "species/search",
queryString:
`datasetKey=${BackBone}&status=ACCEPTED&rank=SPECIES&qField=${nameType}&q=${
encodeURIComponent(name)
}&limit=${limit}&offset=${offset}`,
});

return res.results.map((r) => cleanSpecies(r));
};

/**
* Get the taxonomical parent of a node/entry in the tree of life.
*
*
* @param {BoundedInteger<0>} id id of the taxonomy entry to get the parent of
* @returns {Object} taxonomical parent of the entry
*/
GBIF.getParent = async function (id) {
let res;
try {
res = await this._requestData({
path: `species/${id}/parents`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}
let res;
try {
res = await this._requestData({
path: `species/${id}/parents`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}

if (res.length === 0) {
throw Error(`taxonomy node ${id} has no parents`);
}
if (res.length === 0) {
throw Error(`taxonomy node ${id} has no parents`);
}

return cleanSpecies(res[res.length - 1]);
return cleanSpecies(res[res.length - 1]);
};

/**
* Get the taxonomical children of a node/entry in the tree of life.
*
*
* Because a node may have many children, only up to 20 children are returned per call to this RPC.
* You can check if there are more children by increasing the ``page`` number of children to return.
* When there are no more children, an empty list is returned.
*
*
* @param {BoundedInteger<0>} id id of the taxonomy entry to get the children of
* @param {BoundedInteger<1>=} page page number of results to return (default ``1``)
* @returns {Array<Object>} taxonomical children of the entry
*/
GBIF.getChildren = async function (id, page = 1) {
const limit = 20;
const offset = (page - 1) * limit;

// their api puts a hard cap at offset 100000 - just give empty results
if (offset > 100000) {
return [];
}

let res;
try {
res = await this._requestData({
path: `species/${id}/children`,
queryString: `limit=${limit}&offset=${offset}`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}
const limit = 20;
const offset = (page - 1) * limit;

// their api puts a hard cap at offset 100000 - just give empty results
if (offset > 100000) {
return [];
}

let res;
try {
res = await this._requestData({
path: `species/${id}/children`,
queryString: `limit=${limit}&offset=${offset}`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}

return res.results.map((r) => cleanSpecies(r));
return res.results.map((r) => cleanSpecies(r));
};

/**
* Get the URL of any media associated with a particular taxonomy node/entry in the tree of life.
* These URLs can then be passed to :func:`GlobalBiodiversity.getImage` or :func:`GlobalBiodiversity.getSound` to get the image/sound.
*
*
* Because there may be many associated media entries, only up to 20 URLs are returned per call to this RPC.
* You can check if there are more URLs by increasing the ``page`` number of results to return.
* When there are no more URLs, an empty list is returned.
*
*
* @param {Enum<image,sound>=} type the type of media to return
* @param {BoundedInteger<0>} id id of the taxonomy node to get media from
* @param {BoundedInteger<1>=} page page number of results to return (default ``1``)
* @returns {Array<String>} zero or more associated media URLs
*/
GBIF.getMediaURLs = async function (type, id, page = 1) {
type = { 'image': 'StillImage', 'sound': 'Sound' }[type];

const limit = 20;
const offset = (page - 1) * limit;

let res;
try {
res = await this._requestData({
path: `species/${id}/media`,
queryString: `limit=${limit}&offset=${offset}`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}
type = { "image": "StillImage", "sound": "Sound" }[type];

const limit = 20;
const offset = (page - 1) * limit;

let res;
try {
res = await this._requestData({
path: `species/${id}/media`,
queryString: `limit=${limit}&offset=${offset}`,
});
} catch (e) {
throw Error(`unknown taxonomy node: ${id}`);
}

return res.results.filter((r) => r.type === type).map((r) => r.identifier);
return res.results.filter((r) => r.type === type).map((r) => r.identifier);
};

/**
* Get an image from an image URL returned by :func:`GlobalBiodiversity.getImageURLs`.
*
*
* @param {String} url URL of the image to load
* @returns {Image} the downloaded image
*/
GBIF.getImage = async function (url) {
return this._sendImage({ baseUrl: url });
return this._sendImage({ baseUrl: url });
};

/**
* Get a sound from a sound URL returned by :func:`GlobalBiodiversity.getMediaURLs`.
*/
GBIF.getSound = async function (url) {
const data = await this._requestData({ baseUrl: url });
return utils.sendAudioBuffer(this.response, data);
}
const data = await this._requestData({ baseUrl: url });
return utils.sendAudioBuffer(this.response, data);
};

module.exports = GBIF;

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