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Merge pull request #1844 from cvisionai/dev/1829-additional-worms-opt…
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…ions

Closes #1829
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@marktaipan-cvisionai
marktaipan-cvisionai authored Oct 6, 2024
2 parents 0c496b6 + f35c7b6 commit f420f1a
Showing 1 changed file with 221 additions and 100 deletions.
321 changes: 221 additions & 100 deletions ui/src/js/components/text-autocomplete.js
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Original file line number Diff line number Diff line change
Expand Up @@ -37,33 +37,111 @@ export class WormsAutoComplete {
});
}

/// Filters out matches based on configuration options.
/// View worms_fetch for more information about configuration options.
createFilteredMatches(scientific_matches, only_accepted, ignore_extinct) {
var filtered_matches = [];
for (const match of scientific_matches) {
if (only_accepted && match["status"] != "accepted") {
continue;
}
if (ignore_extinct && match["isExtinct"] == 1) {
continue;
}
filtered_matches.push(match);
}
return filtered_matches;
}

/// Implementation to process results from WoRMs marine database.
/// This routine calls the autocomplete callback with a list of formatted
/// suggestions per the API requirements (https://github.com/kraaden/autocomplete)
///
/// Configuration options:
/// marine_only = 0/1 (default 0)
/// ignore_extinct = 0/1 (default 0, 1 ignores extinct species)
/// only_accepted = 0/1 (default 0, 1 only returns accepted species)
/// max_name_results = 50 (default 50, maximum number of name results to fetch
///
/// Note: These options may not be in the configuration. Will default.
/// Also may be ignored if the configuration value is incorrect.
worms_fetch(config, text, callback) {
text = text.trim();
if (text == "") {
callback([]);
return false;
}

var marine_only_param_str = "marine_only=false";
if (config?.marine_only == 1) {
marine_only_param_str = "marine_only=true";
}

var ignore_extinct = false;
if (config?.ignore_extinct == 1) {
ignore_extinct = true;
}

var only_accepted = false;
if (config?.only_accepted == 1) {
only_accepted = true;
}

// Note: The maximum number of results returned is 50 for the name and vernacular endpoints.
// Thus we will need to paginate if we want more than 50 results. Determine the number
// of fetches we need here.
const max_worms_results_per_fetch = 50;
var max_name_results = max_worms_results_per_fetch;
if (config?.max_name_results) {
max_name_results = config.max_name_results;
}
var num_fetches = Math.ceil(max_name_results / max_worms_results_per_fetch);

const worms_service_url = "https://www.marinespecies.org/rest";
if (this._useCommon == false) {
let name_url = worms_service_url;
name_url += "/AphiaRecordsByName/";
name_url += text;
name_url += "?like=true&marine_only=false";
let name_request = new Request(name_url);
fetch(name_request).then((resp) => {
if (resp.status == 204) {
name_url += "?like=true";
name_url += "&";
name_url += marine_only_param_str;

var requests = [];
for (let i = 0; i < num_fetches; i++) {
let offset = 1 + i * max_worms_results_per_fetch;
let current_url = name_url + "&offset=" + offset;
let name_request = new Request(current_url);
requests.push(fetch(name_request));
}

Promise.all(requests).then((nameResponses) => {
// Check responses for 200. 200 indicates a result was returned
// 204 indicates no results were returned.
var jsonResults = [];
for (let response of nameResponses) {
if (response.status == 200) {
jsonResults.push(response.json());
}
}

// If no results were returned, call the callback with an empty list
if (jsonResults.length == 0) {
document.body.style.cursor = null;
this._input_element.style.cursor = null;
callback([]);
return false;
}
resp.json().then((scientific_matches) => {
this.finalize_worms_result(text, callback, scientific_matches, []);

// Process all the results
Promise.all(jsonResults).then((nameMatches) => {
var filtered_matches = this.createFilteredMatches(
nameMatches.flat(),
only_accepted,
ignore_extinct
);
this.finalize_worms_result(text, callback, filtered_matches, []);
return true;
});
return true;
});
} else {
let vernacular_url = worms_service_url;
Expand All @@ -72,116 +150,154 @@ export class WormsAutoComplete {
vernacular_url += "?like=true";
let vernacular_request = new Request(vernacular_url);

let vernacular_detail_url = worms_service_url;
vernacular_detail_url += "/AphiaVernacularsByAphiaID/";
let vernacular_promise = fetch(vernacular_request);

let name_url = worms_service_url;
name_url += "/AphiaRecordsByName/";
name_url += text;
name_url += "?like=true&marine_only=false";
let name_request = new Request(name_url);

let vernacular_detail_url = worms_service_url;
vernacular_detail_url += "/AphiaVernacularsByAphiaID/";
name_url += "?like=true";
name_url += "&";
name_url += marine_only_param_str;

var nameRequests = [];
for (let i = 0; i < num_fetches; i++) {
let offset = 1 + i * max_worms_results_per_fetch;
let current_url = name_url + "&offset=" + offset;
let name_request = new Request(current_url);
nameRequests.push(fetch(name_request));
}

let vernacular_promise = fetch(vernacular_request);
let name_promise = fetch(name_request);

// Handle all the respones and subrequests in parallel
Promise.all([vernacular_promise, name_promise]).then(
(topLevel_responses) => {
// Response 0 is vernaculars, response 1 is scientific name matches
if (
topLevel_responses[0].status == 204 &&
topLevel_responses[1].status == 204
) {
document.body.style.cursor = null;
this._input_element.style.cursor = null;
callback([]);
return false;
Promise.all(nameRequests).then((nameResponses) => {
// Check responses for 200. 200 indicates a result was returned
// 204 indicates no results were returned.
var nameJsonResults = [];
for (let response of nameResponses) {
if (response.status == 200) {
nameJsonResults.push(response.json());
}
}

vernacular_promise.then((initialVernacularResponse) => {
if (initialVernacularResponse.status == 204) {
// No vernaculars found, check the scientific names
if (nameJsonResults.length == 0) {
// Got no results from both endpoints.
document.body.style.cursor = null;
this._input_element.style.cursor = null;
callback([]);
return false;
}

// response 0 is empty, so we just have scientific matches
if (topLevel_responses[0].status == 204) {
topLevel_responses[1].json().then((scientific_matches) => {
this.finalize_worms_result(
text,
callback,
scientific_matches,
[]
// Got no vernaculars, but we have at least one scientific name match
Promise.all(nameJsonResults).then((nameMatches) => {
var filtered_matches = this.createFilteredMatches(
nameMatches.flat(),
only_accepted,
ignore_extinct
);
this.finalize_worms_result(text, callback, filtered_matches, []);
return true;
});
return true;
}
topLevel_responses[0].json().then((vernacular_response) => {
let vernacular_requests = [];
let vernacular_matches = [];

let common_matches = 0;
// Process the JSON of the vernacular response to build a match list
for (const aphiaRecord of vernacular_response) {
if (aphiaRecord["taxonRankID"] >= this._minLevel) {
vernacular_matches.push(aphiaRecord);
vernacular_requests.push(
fetch(
new Request(vernacular_detail_url + aphiaRecord["AphiaID"])
)
);
common_matches += 1;
}

// Limit common matches to 5 for performance
// reasons.
if (common_matches >= 5) {
break;
}
}
} else {
// We at least have vernaculars. Send out corresponding fetches.
initialVernacularResponse.json().then((initialVernacularResult) => {
let secondVernacularRequests = [];
let vernacular_matches = [];

let common_matches = 0;
// Process the JSON of the vernacular response to build a match list
for (const aphiaRecord of initialVernacularResult) {
if (only_accepted && aphiaRecord?.["status"] != "accepted") {
continue;
}
if (ignore_extinct && aphiaRecord?.["isExtinct"] == 1) {
continue;
}

Promise.all(vernacular_requests).then((vernacular_responses) => {
let json_promises = [];
let count = 0;
for (const response of vernacular_responses) {
if (response.status == 200) {
json_promises.push(response.json());
} else {
// If we get a 204 back for vernaculars we need to specify there are
// no vernaculars
json_promises.push(
new Promise((resolve) => {
resolve(null);
})
if (aphiaRecord["taxonRankID"] >= this._minLevel) {
vernacular_matches.push(aphiaRecord);
secondVernacularRequests.push(
fetch(
new Request(
vernacular_detail_url + aphiaRecord["AphiaID"]
)
)
);
common_matches += 1;
}
}

Promise.all(json_promises).then((each_result) => {
for (const response of each_result) {
// Augment each aphia record with the list of vernaculars
vernacular_matches[count]["vernaculars"] = response;
count += 1;
// Limit common matches to 5 for performance
// reasons.
if (common_matches >= 5) {
break;
}
}

if (topLevel_responses[1].status == 204) {
this.finalize_worms_result(
text,
callback,
[],
vernacular_matches
);
} else {
// Finally have all the vernaculars loaded up, we can get the scientific match
// and call the finalize function
topLevel_responses[1].json().then((scientific_matches) => {
this.finalize_worms_result(
text,
callback,
scientific_matches,
vernacular_matches
);
Promise.all(secondVernacularRequests).then(
(secondVernacularResponses) => {
let json_promises = [];
let count = 0;
for (const response of secondVernacularResponses) {
if (response.status == 200) {
json_promises.push(response.json());
} else {
// If we get a 204 back for vernaculars we need to specify there are
// no vernaculars
json_promises.push(
new Promise((resolve) => {
resolve(null);
})
);
}
}

Promise.all(json_promises).then((each_result) => {
for (const response of each_result) {
// Augment each aphia record with the list of vernaculars
if (only_accepted && response?.["status"] != "accepted") {
continue;
}
if (ignore_extinct && response?.["isExtinct"] == 1) {
continue;
}

vernacular_matches[count]["vernaculars"] = response;
count += 1;
}

if (nameJsonResults.length == 0) {
// We have no scientific name matches, process only vernacular matches
this.finalize_worms_result(
text,
callback,
[],
vernacular_matches
);
} else {
// We have scientific name matches, process both scientific and vernacular matches
Promise.all(nameJsonResults).then((nameMatches) => {
var filtered_matches = this.createFilteredMatches(
nameMatches.flat(),
only_accepted,
ignore_extinct
);
this.finalize_worms_result(
text,
callback,
filtered_matches,
vernacular_matches
);
});
}
});
}
});
);
});
});
}
);
}
});
});
}
return true;
}
Expand Down Expand Up @@ -284,6 +400,11 @@ export class WormsAutoComplete {
suggestions.push(obj);
}
callback(suggestions);

if (suggestions.length == 0) {
document.body.style.cursor = null;
this._input_element.style.cursor = null;
}
}
}

Expand Down

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