17 |
82 |
86 |
87 |
88 |
95 |
96 |
97 |
98 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/index.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
18 |
48 |
49 | 19 | all files SearchBox/ 20 |
21 |
22 |
47 |
23 | 55.56%
24 | Statements
25 | 15/27
26 |
27 |
28 | 70%
29 | Branches
30 | 7/10
31 |
32 |
33 | 33.33%
34 | Functions
35 | 2/6
36 |
37 |
38 | 45.45%
39 | Lines
40 | 10/22
41 |
42 |
43 | 1 branch
44 | Ignored
45 |
46 |
50 |
51 |
52 |
80 |
81 | | File | 54 |55 | | Statements | 56 |57 | | Branches | 58 |59 | | Functions | 60 |61 | | Lines | 62 |63 | |
|---|---|---|---|---|---|---|---|---|---|
| SearchBox.vue | 67 |55.56% | 69 |15/27 | 70 |70% | 71 |7/10 | 72 |33.33% | 73 |2/6 | 74 |45.45% | 75 |10/22 | 76 |
17 |
95 |
99 |
100 |
101 |
108 |
109 |
110 |
111 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/SearchBox/OntologyData/tree.js.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
18 |
48 |
49 | 19 | / 20 |
21 |
22 |
47 |
23 | 83.33%
24 | Statements
25 | 60/72
26 |
27 |
28 | 82.14%
29 | Branches
30 | 23/28
31 |
32 |
33 | 66.67%
34 | Functions
35 | 8/12
36 |
37 |
38 | 80.65%
39 | Lines
40 | 50/62
41 |
42 |
43 | 2 branches
44 | Ignored
45 |
46 |
50 |
51 |
52 |
93 |
94 | | File | 54 |55 | | Statements | 56 |57 | | Branches | 58 |59 | | Functions | 60 |61 | | Lines | 62 |63 | |
|---|---|---|---|---|---|---|---|---|---|
| SearchBox/ | 67 |55.56% | 69 |15/27 | 70 |70% | 71 |7/10 | 72 |33.33% | 73 |2/6 | 74 |45.45% | 75 |10/22 | 76 ||
| SearchBox/OntologyData/ | 80 |100% | 82 |45/45 | 83 |88.89% | 84 |16/18 | 85 |100% | 86 |6/6 | 87 |100% | 88 |40/40 | 89 |
17 |
50 |
130 |
131 |
132 |
136 |
137 |
138 |
145 |
146 |
147 |
148 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/SearchBox/OntologyData/index.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
18 |
48 |
49 | 19 | all files / SearchBox/OntologyData/ tree.js 20 |
21 |
22 |
47 |
23 | 100%
24 | Statements
25 | 17/17
26 |
27 |
28 | 87.5%
29 | Branches
30 | 7/8
31 |
32 |
33 | 100%
34 | Functions
35 | 3/3
36 |
37 |
38 | 100%
39 | Lines
40 | 13/13
41 |
42 |
43 | 1 branch
44 | Ignored
45 |
46 | | 1 51 | 2 52 | 3 53 | 4 54 | 5 55 | 6 56 | 7 57 | 8 58 | 9 59 | 10 60 | 11 61 | 12 62 | 13 63 | 14 64 | 15 65 | 16 66 | 17 67 | 18 68 | 19 69 | 20 70 | 21 71 | 22 72 | 23 73 | 24 74 | 25 75 | 26 76 | 27 | 1× 77 | 78 | 79 | 80 | 1× 81 | 82 | 1× 83 | 84 | 1× 85 | 1× 86 | 3× 87 | 3× 88 | 3× 89 | 90 | 91 | 92 | 93 | 3× 94 | 3× 95 | 96 | 97 | 98 | 99 | 1× 100 | 1× 101 | 102 | | import {
103 | categoryRoots,
104 | categoryMap
105 | } from './categories';
106 | import ontologies from './ontologies';
107 |
108 | let ontologyMap = {};
109 |
110 | ontologies.forEach(function(element) {
111 | element.categories.forEach(function(category) {
112 | Eif (categoryMap[category]) {
113 | categoryMap[category].children = categoryMap[category].children || []
114 | let ontology = {
115 | id: element.acronym,
116 | label: element.acronym + ': ' + element.name,
117 | type: 'ontology'
118 | }
119 | categoryMap[category].children.push(ontology)
120 | ontologyMap[element.acronym] = ontology
121 | }
122 | })
123 | })
124 |
125 | export const options = categoryRoots;
126 | export const ontologyByAcronym = ontologyMap;
127 |
128 | |
17 |
108 |
112 |
113 |
114 |
121 |
122 |
123 |
124 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/sorter.js:
--------------------------------------------------------------------------------
1 | var addSorting = (function () {
2 | "use strict";
3 | var cols,
4 | currentSort = {
5 | index: 0,
6 | desc: false
7 | };
8 |
9 | // returns the summary table element
10 | function getTable() { return document.querySelector('.coverage-summary'); }
11 | // returns the thead element of the summary table
12 | function getTableHeader() { return getTable().querySelector('thead tr'); }
13 | // returns the tbody element of the summary table
14 | function getTableBody() { return getTable().querySelector('tbody'); }
15 | // returns the th element for nth column
16 | function getNthColumn(n) { return getTableHeader().querySelectorAll('th')[n]; }
17 |
18 | // loads all columns
19 | function loadColumns() {
20 | var colNodes = getTableHeader().querySelectorAll('th'),
21 | colNode,
22 | cols = [],
23 | col,
24 | i;
25 |
26 | for (i = 0; i < colNodes.length; i += 1) {
27 | colNode = colNodes[i];
28 | col = {
29 | key: colNode.getAttribute('data-col'),
30 | sortable: !colNode.getAttribute('data-nosort'),
31 | type: colNode.getAttribute('data-type') || 'string'
32 | };
33 | cols.push(col);
34 | if (col.sortable) {
35 | col.defaultDescSort = col.type === 'number';
36 | colNode.innerHTML = colNode.innerHTML + '';
37 | }
38 | }
39 | return cols;
40 | }
41 | // attaches a data attribute to every tr element with an object
42 | // of data values keyed by column name
43 | function loadRowData(tableRow) {
44 | var tableCols = tableRow.querySelectorAll('td'),
45 | colNode,
46 | col,
47 | data = {},
48 | i,
49 | val;
50 | for (i = 0; i < tableCols.length; i += 1) {
51 | colNode = tableCols[i];
52 | col = cols[i];
53 | val = colNode.getAttribute('data-value');
54 | if (col.type === 'number') {
55 | val = Number(val);
56 | }
57 | data[col.key] = val;
58 | }
59 | return data;
60 | }
61 | // loads all row data
62 | function loadData() {
63 | var rows = getTableBody().querySelectorAll('tr'),
64 | i;
65 |
66 | for (i = 0; i < rows.length; i += 1) {
67 | rows[i].data = loadRowData(rows[i]);
68 | }
69 | }
70 | // sorts the table using the data for the ith column
71 | function sortByIndex(index, desc) {
72 | var key = cols[index].key,
73 | sorter = function (a, b) {
74 | a = a.data[key];
75 | b = b.data[key];
76 | return a < b ? -1 : a > b ? 1 : 0;
77 | },
78 | finalSorter = sorter,
79 | tableBody = document.querySelector('.coverage-summary tbody'),
80 | rowNodes = tableBody.querySelectorAll('tr'),
81 | rows = [],
82 | i;
83 |
84 | if (desc) {
85 | finalSorter = function (a, b) {
86 | return -1 * sorter(a, b);
87 | };
88 | }
89 |
90 | for (i = 0; i < rowNodes.length; i += 1) {
91 | rows.push(rowNodes[i]);
92 | tableBody.removeChild(rowNodes[i]);
93 | }
94 |
95 | rows.sort(finalSorter);
96 |
97 | for (i = 0; i < rows.length; i += 1) {
98 | tableBody.appendChild(rows[i]);
99 | }
100 | }
101 | // removes sort indicators for current column being sorted
102 | function removeSortIndicators() {
103 | var col = getNthColumn(currentSort.index),
104 | cls = col.className;
105 |
106 | cls = cls.replace(/ sorted$/, '').replace(/ sorted-desc$/, '');
107 | col.className = cls;
108 | }
109 | // adds sort indicators for current column being sorted
110 | function addSortIndicators() {
111 | getNthColumn(currentSort.index).className += currentSort.desc ? ' sorted-desc' : ' sorted';
112 | }
113 | // adds event listeners for all sorter widgets
114 | function enableUI() {
115 | var i,
116 | el,
117 | ithSorter = function ithSorter(i) {
118 | var col = cols[i];
119 |
120 | return function () {
121 | var desc = col.defaultDescSort;
122 |
123 | if (currentSort.index === i) {
124 | desc = !currentSort.desc;
125 | }
126 | sortByIndex(i, desc);
127 | removeSortIndicators();
128 | currentSort.index = i;
129 | currentSort.desc = desc;
130 | addSortIndicators();
131 | };
132 | };
133 | for (i =0 ; i < cols.length; i += 1) {
134 | if (cols[i].sortable) {
135 | // add the click event handler on the th so users
136 | // dont have to click on those tiny arrows
137 | el = getNthColumn(i).querySelector('.sorter').parentElement;
138 | if (el.addEventListener) {
139 | el.addEventListener('click', ithSorter(i));
140 | } else {
141 | el.attachEvent('onclick', ithSorter(i));
142 | }
143 | }
144 | }
145 | }
146 | // adds sorting functionality to the UI
147 | return function () {
148 | if (!getTable()) {
149 | return;
150 | }
151 | cols = loadColumns();
152 | loadData(cols);
153 | addSortIndicators();
154 | enableUI();
155 | };
156 | })();
157 |
158 | window.addEventListener('load', addSorting);
159 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | # Ontoclick
2 |
3 | 
4 |
5 | #### Turn a free text description into a proper ontology term with just one click.
6 |
7 | ### Overview
8 |
9 | Ontoclick is a web browser extension for Chrome and Firefox browsers that lets the user highlight a piece of text and then tries to find a matching Ontology term for it.
10 |
11 | Ontoclick currently supports matching terms to the [Human Phenotype Ontology](https://hpo.jax.org/app/), [Gene Ontology](http://geneontology.org), [Mondo Disease Ontology](https://mondo.monarchinitiative.org), [Orphanet Rare Disease Ontology](http://www.orphadata.org/cgi-bin/index.php#ontologies) and [Human Disease Ontology](https://disease-ontology.org).
12 |
13 | Ontoclick uses the [NCBO BioPortal Search API](http://data.bioontology.org/documentation#nav_search) to find a matching ontology term, but searches can also be performed with the [NCBO BioPortal Annotator API](http://data.bioontology.org/documentation#nav_annotator), the [EBI Ontology Lookup Service Search API](https://www.ebi.ac.uk/ols/docs/api) or the [HPO Search API](https://hpo.jax.org/webjars/swagger-ui/3.20.9/index.html?url=/api/hpo/docs/) (the latter two only support searching the Human Phenotype Ontology).
14 |
15 | The search results can be copied to the clipboard or saved to a list that can be exported in .CSV format.
16 |
17 | ### Screeenshot
18 |
19 |
18 |
48 |
49 | 19 | all files SearchBox/OntologyData/ 20 |
21 |
22 |
47 |
23 | 100%
24 | Statements
25 | 45/45
26 |
27 |
28 | 88.89%
29 | Branches
30 | 16/18
31 |
32 |
33 | 100%
34 | Functions
35 | 6/6
36 |
37 |
38 | 100%
39 | Lines
40 | 40/40
41 |
42 |
43 | 1 branch
44 | Ignored
45 |
46 |
50 |
51 |
52 |
106 |
107 | | File | 54 |55 | | Statements | 56 |57 | | Branches | 58 |59 | | Functions | 60 |61 | | Lines | 62 |63 | |
|---|---|---|---|---|---|---|---|---|---|
| categories.js | 67 |100% | 69 |26/26 | 70 |90% | 71 |9/10 | 72 |100% | 73 |3/3 | 74 |100% | 75 |26/26 | 76 ||
| ontologies.js | 80 |100% | 82 |2/2 | 83 |100% | 84 |0/0 | 85 |100% | 86 |0/0 | 87 |100% | 88 |1/1 | 89 ||
| tree.js | 93 |100% | 95 |17/17 | 96 |87.5% | 97 |7/8 | 98 |100% | 99 |3/3 | 100 |100% | 101 |13/13 | 102 |
20 |
21 | ### Publication
22 |
23 | *Ontoclick: a web browser extension to facilitate biomedical knowledge curation*\
24 | [BioRxiv](https://www.biorxiv.org/content/10.1101/2021.03.04.433993v2) or [Bioinformatics (Oxford University Press)](https://doi.org/10.1093/bioinformatics/btab520)
25 |
26 | ### Acknowledgements
27 |
28 | Ontoclick was born at [Health Hack Sydney](https://speakerdeck.com/azankl/ontoclick-pitch-healthhack-2017) in November 2017. Many thanks to Team Ontoclick, in particular Graham Towse from [LivingryLabs](https://www.livingrylabs.net/) for developing the first prototype. Many thanks to Anthony Xu, Yifei (Frank) Luo, Aravind Venkateswaran, and Lianguizi (Alisa) Zhou, for further improving this prototype.
29 |
30 | ### Install for Chrome
31 |
32 | Ontoclick is available on the Chrome Store [here](https://chrome.google.com/webstore/detail/ontoclick/nepbilmonlfaigoeldkbimkeihligbgf).
33 |
34 | ### Install for Firefox
35 |
36 | Ontoclick is available as a Firefox Add-On [here](https://addons.mozilla.org/en-US/firefox/addon/ontoclick/)
37 |
38 | ### How to Use the Extension
39 |
40 | 1. Visit a web page in your browser
41 | 2. Highlight the text you want to search for, right-click to show the browser context menu and select Ontoclick from the context menu.
42 | 3. The Ontoclick popup opens and displays matching ontology terms from the Human Phenotype Ontology.
43 | 4. Click on the '+' icon in front of a term to see more information about the term (if available).
44 | 5. Hover over a term to see additional icons:
45 | - click the 'copy' icon next to the Ontology ID to copy the Ontology ID
46 | - click the 'copy' icon next to the Label to copy the Ontology Label
47 | - click the 'copy' icon in the 'Actions' column to copy the Ontology ID _and_ the Label
48 | - click the 'highlighter' icon in the 'Actions' column to copy the highlighted text _and_ the Ontology ID _and_ the Label.
49 | - click the 'disk' icon in the 'Actions' column to save the highlighted text, Ontology ID and Label to Ontoclick's history list. The number in the right upper corner of the Ontoclick window shows the number of items saved to the history list. Click the 'download' icon to download the history list as a .CSV file. Click the 'eraser' icon to erase the history list.
50 | 6. If no suitable terms are retrieved, click on the triangle next to 'NCBO Bioportal Search' to re-run the search with a different concept recogniser. The result window will update immediately with the new results. The different concept recognisers all have their strengths and weaknesses, try different ones to see what gives the best results.
51 | 7. Click on the triangle next to 'Human Phenotype Ontology' to select another (or additional) ontologies. This only works when 'NCBO Bioportal Search' or 'NCBO Bioportal Annotator' are selected.
52 | 8. The Ontoclick Popup can also be launched without selecting any text:
53 | - right-click anywhere in the browser window and select Ontoclick from the context menu that appears
54 | - click the Ontoclick icon in the browser toolbar
55 | - in both cases, you can now type your search term into the Ontoclick Search bar
56 | - Please note: the history list function is not available when launching the Ontoclick popup from the toolbar icon
57 |
58 | ### Install From Source
59 |
60 | **Build Prerequisites**
61 |
62 | * [Yarn](https://yarnpkg.com/en/docs/install)
63 |
64 | ``` bash
65 | # install dependencies
66 | yarn install
67 |
68 | # build for production with minification
69 | yarn run build
70 |
71 | # To install, follow these steps:
72 | Go to Chrome:
73 | 1. Visit chrome://extensions
74 | 2. Enable developer options
75 | 3. Click 'Load unpacked extension...'
76 | 4. Select the ontoclick/dist/ folder
77 | ```
78 |
79 |
80 | ### Development Setup
81 |
82 | ``` bash
83 | # install dependencies
84 | yarn install
85 |
86 | # get your BioPortal REST API key from https://bioportal.bioontology.org/account
87 | open https://bioportal.bioontology.org/account
88 |
89 | # add your API key for development builds
90 | cp api/example.api.json api/dev.api.json
91 | open api/dev.api.json
92 |
93 | # add your API key for production builds
94 | cp api/example.api.json api/prod.api.json
95 | open api/prod.api.json
96 |
97 | # serve with hot reload at localhost:8080
98 | yarn run dev
99 |
100 | # build for production with minification
101 | yarn run build
102 |
103 | # run unit tests
104 | yarn run unit
105 |
106 | # run e2e tests
107 | yarn run e2e
108 |
109 | # run all tests
110 | yarn test
111 | ```
112 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/base.css:
--------------------------------------------------------------------------------
1 | body, html {
2 | margin:0; padding: 0;
3 | height: 100%;
4 | }
5 | body {
6 | font-family: Helvetica Neue, Helvetica, Arial;
7 | font-size: 14px;
8 | color:#333;
9 | }
10 | .small { font-size: 12px; }
11 | *, *:after, *:before {
12 | -webkit-box-sizing:border-box;
13 | -moz-box-sizing:border-box;
14 | box-sizing:border-box;
15 | }
16 | h1 { font-size: 20px; margin: 0;}
17 | h2 { font-size: 14px; }
18 | pre {
19 | font: 12px/1.4 Consolas, "Liberation Mono", Menlo, Courier, monospace;
20 | margin: 0;
21 | padding: 0;
22 | -moz-tab-size: 2;
23 | -o-tab-size: 2;
24 | tab-size: 2;
25 | }
26 | a { color:#0074D9; text-decoration:none; }
27 | a:hover { text-decoration:underline; }
28 | .strong { font-weight: bold; }
29 | .space-top1 { padding: 10px 0 0 0; }
30 | .pad2y { padding: 20px 0; }
31 | .pad1y { padding: 10px 0; }
32 | .pad2x { padding: 0 20px; }
33 | .pad2 { padding: 20px; }
34 | .pad1 { padding: 10px; }
35 | .space-left2 { padding-left:55px; }
36 | .space-right2 { padding-right:20px; }
37 | .center { text-align:center; }
38 | .clearfix { display:block; }
39 | .clearfix:after {
40 | content:'';
41 | display:block;
42 | height:0;
43 | clear:both;
44 | visibility:hidden;
45 | }
46 | .fl { float: left; }
47 | @media only screen and (max-width:640px) {
48 | .col3 { width:100%; max-width:100%; }
49 | .hide-mobile { display:none!important; }
50 | }
51 |
52 | .quiet {
53 | color: #7f7f7f;
54 | color: rgba(0,0,0,0.5);
55 | }
56 | .quiet a { opacity: 0.7; }
57 |
58 | .fraction {
59 | font-family: Consolas, 'Liberation Mono', Menlo, Courier, monospace;
60 | font-size: 10px;
61 | color: #555;
62 | background: #E8E8E8;
63 | padding: 4px 5px;
64 | border-radius: 3px;
65 | vertical-align: middle;
66 | }
67 |
68 | div.path a:link, div.path a:visited { color: #333; }
69 | table.coverage {
70 | border-collapse: collapse;
71 | margin: 10px 0 0 0;
72 | padding: 0;
73 | }
74 |
75 | table.coverage td {
76 | margin: 0;
77 | padding: 0;
78 | vertical-align: top;
79 | }
80 | table.coverage td.line-count {
81 | text-align: right;
82 | padding: 0 5px 0 20px;
83 | }
84 | table.coverage td.line-coverage {
85 | text-align: right;
86 | padding-right: 10px;
87 | min-width:20px;
88 | }
89 |
90 | table.coverage td span.cline-any {
91 | display: inline-block;
92 | padding: 0 5px;
93 | width: 100%;
94 | }
95 | .missing-if-branch {
96 | display: inline-block;
97 | margin-right: 5px;
98 | border-radius: 3px;
99 | position: relative;
100 | padding: 0 4px;
101 | background: #333;
102 | color: yellow;
103 | }
104 |
105 | .skip-if-branch {
106 | display: none;
107 | margin-right: 10px;
108 | position: relative;
109 | padding: 0 4px;
110 | background: #ccc;
111 | color: white;
112 | }
113 | .missing-if-branch .typ, .skip-if-branch .typ {
114 | color: inherit !important;
115 | }
116 | .coverage-summary {
117 | border-collapse: collapse;
118 | width: 100%;
119 | }
120 | .coverage-summary tr { border-bottom: 1px solid #bbb; }
121 | .keyline-all { border: 1px solid #ddd; }
122 | .coverage-summary td, .coverage-summary th { padding: 10px; }
123 | .coverage-summary tbody { border: 1px solid #bbb; }
124 | .coverage-summary td { border-right: 1px solid #bbb; }
125 | .coverage-summary td:last-child { border-right: none; }
126 | .coverage-summary th {
127 | text-align: left;
128 | font-weight: normal;
129 | white-space: nowrap;
130 | }
131 | .coverage-summary th.file { border-right: none !important; }
132 | .coverage-summary th.pct { }
133 | .coverage-summary th.pic,
134 | .coverage-summary th.abs,
135 | .coverage-summary td.pct,
136 | .coverage-summary td.abs { text-align: right; }
137 | .coverage-summary td.file { white-space: nowrap; }
138 | .coverage-summary td.pic { min-width: 120px !important; }
139 | .coverage-summary tfoot td { }
140 |
141 | .coverage-summary .sorter {
142 | height: 10px;
143 | width: 7px;
144 | display: inline-block;
145 | margin-left: 0.5em;
146 | background: url(sort-arrow-sprite.png) no-repeat scroll 0 0 transparent;
147 | }
148 | .coverage-summary .sorted .sorter {
149 | background-position: 0 -20px;
150 | }
151 | .coverage-summary .sorted-desc .sorter {
152 | background-position: 0 -10px;
153 | }
154 | .status-line { height: 10px; }
155 | /* dark red */
156 | .red.solid, .status-line.low, .low .cover-fill { background:#C21F39 }
157 | .low .chart { border:1px solid #C21F39 }
158 | /* medium red */
159 | .cstat-no, .fstat-no, .cbranch-no, .cbranch-no { background:#F6C6CE }
160 | /* light red */
161 | .low, .cline-no { background:#FCE1E5 }
162 | /* light green */
163 | .high, .cline-yes { background:rgb(230,245,208) }
164 | /* medium green */
165 | .cstat-yes { background:rgb(161,215,106) }
166 | /* dark green */
167 | .status-line.high, .high .cover-fill { background:rgb(77,146,33) }
168 | .high .chart { border:1px solid rgb(77,146,33) }
169 | /* dark yellow (gold) */
170 | .medium .chart { border:1px solid #f9cd0b; }
171 | .status-line.medium, .medium .cover-fill { background: #f9cd0b; }
172 | /* light yellow */
173 | .medium { background: #fff4c2; }
174 | /* light gray */
175 | span.cline-neutral { background: #eaeaea; }
176 |
177 | .cbranch-no { background: yellow !important; color: #111; }
178 |
179 | .cstat-skip { background: #ddd; color: #111; }
180 | .fstat-skip { background: #ddd; color: #111 !important; }
181 | .cbranch-skip { background: #ddd !important; color: #111; }
182 |
183 |
184 | .cover-fill, .cover-empty {
185 | display:inline-block;
186 | height: 12px;
187 | }
188 | .chart {
189 | line-height: 0;
190 | }
191 | .cover-empty {
192 | background: white;
193 | }
194 | .cover-full {
195 | border-right: none !important;
196 | }
197 | pre.prettyprint {
198 | border: none !important;
199 | padding: 0 !important;
200 | margin: 0 !important;
201 | }
202 | .com { color: #999 !important; }
203 | .ignore-none { color: #999; font-weight: normal; }
204 |
205 | .wrapper {
206 | min-height: 100%;
207 | height: auto !important;
208 | height: 100%;
209 | margin: 0 auto -48px;
210 | }
211 | .footer, .push {
212 | height: 48px;
213 | }
214 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/SearchBox/SearchBox.vue.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
17 |
50 |
352 |
353 |
354 |
358 |
359 |
360 |
367 |
368 |
369 |
370 |
--------------------------------------------------------------------------------
/src/components/SearchBox/table/TableOptions.js:
--------------------------------------------------------------------------------
1 | import axios from 'axios';
2 |
3 | // NCBO Search = 0
4 | // NCBO Annotator = 1
5 | // data : response.data.collection
6 | // count : response.data.totalCount
7 | // https://data.bioontology.org/documentation
8 |
9 | // Pryzm Health = 2
10 | // https://track.health/api/
11 |
12 | // JAX = 3
13 | // data : response.data.terms
14 | // count : response.data.termsTotalCount
15 | // https://hpo.jax.org/api/hpo/docs/
16 |
17 | // OLS EBI = 4
18 | // data : response.data.
19 | // count: response.data.
20 | // https://www.ebi.ac.uk/ols/docs/api/search
21 |
22 | // Neural Concept Recogniser = 5
23 | // data: response.data.
24 | // count: response.data.
25 | // https://ncr.ccm.sickkids.ca/api_doc/
26 |
27 |
28 | const recogDict = {
29 | 'NCBO Bioportal Search': 0,
30 | 'NCBO Bioportal Annotator': 1,
31 | // 'Pryzm Health CR': 2,
32 | 'HPO Jax': 3,
33 | 'Ontology Lookup Search EBI': 4,
34 | // 'Neural Concept Recogniser': 5,
35 | };
36 | // Search HTML for concept recogniser dropdown list
37 | // Initial startup value will always be NCBO Search
38 | function getSelectedAPI() {
39 | let div = document.getElementsByName("conceptRecogniser")[0];
40 | let api;
41 | // let api = 'Ontology Lookup Search EBI';
42 | if (typeof div !== "undefined") {
43 | api = document.getElementsByClassName('vue-treeselect__single-value')[0].innerText;
44 | } else {
45 | api = 'NCBO Bioportal Search';
46 | }
47 | return recogDict[api];
48 | }
49 |
50 | // Search for ontologies selected from dropdown menu
51 | // Human Phenotype Ontology is the default value if no ontologies are selected
52 | function getOntologies() {
53 | let list = [];
54 | let div = document.getElementsByClassName('vue-treeselect__multi-value-label');
55 | for (var i = 0; i < div.length; i++) {
56 | let selected = div[i].innerText;
57 | // Extract ontology ID to be used for GET request
58 | let id = selected.match(/\(([^)]+)\)/)[1];
59 | if (!list.includes(id)) {
60 | list.push(id);
61 | }
62 | }
63 | return ((Array.isArray(list) && list.length) ? list.join(',') : 'HP');
64 | }
65 |
66 | // Renames the key for dictionary
67 | // Input: dictionary, keyToReplace, newKeyName
68 | const clone = (obj) => Object.assign({}, obj);
69 | const renameKey = (object, key, newKey) => {
70 | const clonedObj = clone(object);
71 | const targetKey = clonedObj[key];
72 | delete clonedObj[key];
73 | clonedObj[newKey] = targetKey;
74 | return clonedObj;
75 | };
76 |
77 | function keyLoop(data, init, fin) {
78 | var i;
79 | var arr = [];
80 | for (i = 0; i < data.length; i++) {
81 | let temp = renameKey(data[i], init, fin);
82 | arr.push(temp);
83 | }
84 | return arr;
85 | }
86 |
87 | export default {
88 | requestKeys: {
89 | query: 'q',
90 | limit: 'pagesize',
91 | page: 'page'
92 | },
93 | headings: {
94 | notation: 'Identifier',
95 | prefLabel: 'Label',
96 | spantext: 'Actions'
97 | },
98 | pagination: {
99 | dropdown: false
100 | },
101 | requestFunction: (data) => {
102 | let api = getSelectedAPI();
103 | let ontologies = getOntologies();
104 |
105 | const ncbo = [
106 | process.env.NCBO_SEARCH,
107 | process.env.NCBO_ANNOTATOR,
108 | {
109 | apikey: document.getElementById('apkey').innerHTML,
110 | q: data.q,
111 | pagesize: 5,
112 | page: data.page,
113 | include: 'prefLabel,synonym,definition,notation',
114 | ontologies: ontologies
115 | },
116 | {
117 | apikey: document.getElementById('apkey').innerHTML,
118 | text: data.q,
119 | pagesize: 5,
120 | page: data.page,
121 | include: 'prefLabel,synonym,definition,notation',
122 | ontologies: ontologies
123 | }
124 | ];
125 |
126 | const jax = [
127 | process.env.JAX,
128 | {
129 | q: data.q
130 | }
131 | ];
132 |
133 | const ebi = [
134 | process.env.EBI,
135 | {
136 | q: data.q,
137 | ontology: 'hp',
138 | groupField: 'iri',
139 | start: data.page,
140 | rows: 5,
141 | local: true
142 | }
143 | ];
144 |
145 | const neural = [
146 | process.env.NEURAL,
147 | {
148 | text: data.q
149 | }
150 | ];
151 |
152 | // const pryzm = [
153 | // process.env.PRYZM + process.env.PRYZM_KEY,
154 | // data.q
155 | // ]
156 |
157 | // Change the URL and parameters depending on the Concept Recogniser selected
158 | let apiURL, apiParam;
159 | switch(api) {
160 | case 0:
161 | apiURL = ncbo[0];
162 | apiParam = ncbo[2];
163 | break;
164 | case 1:
165 | apiURL = ncbo[1];
166 | apiParam = ncbo[3];
167 | break;
168 | case 3:
169 | apiURL = jax[0];
170 | apiParam = jax[1];
171 | break;
172 | case 4:
173 | apiURL = ebi[0];
174 | apiParam = ebi[1];
175 | break;
176 | // case 5:
177 | // apiURL = neural[0];
178 | // apiParam = neural[1];
179 | // break;
180 | default:
181 | apiURL = null;
182 | apiParam = null;
183 | };
184 |
185 | // Seperate from the other returns as Pryzm requires a POST request instead of GET request
186 | // if (api == 2) {
187 | // return axios.post(pryzm[0], {
188 | // payload: pryzm[1]
189 | // }).then((res) => {
190 | // for (var i = 0; i < res.data.data.length; i++) {
191 | // // Switch return object's keys to align with display rows in SearchBox.vue
192 | // res.data.data[i].notation = res.data.data[i].term.curie;
193 | // res.data.data[i].prefLabel = res.data.data[i].term.label;
194 | // res.data.data[i].definition = [];
195 | // res.data.data[i].definition.push(res.data.data[i].term.metadata.metadata.DEFINITION);
196 | // let arr = [];
197 | // for (var j = 0; j < res.data.data[i].term.synonyms.length; j++) {
198 | // arr.push(res.data.data[i].term.synonyms[j].synonym)
199 | // }
200 | // res.data.data[i].synonym = arr;
201 | // }
202 | // return res;
203 | // }).catch((err) => {
204 | // return null
205 | // })
206 | // }
207 |
208 | const ncbos_get = axios.get(ncbo[0], {params: ncbo[2]});
209 | const ncboa_get = axios.get(ncbo[1], {params: ncbo[3]});
210 | const jax_get = axios.get(jax[0], {params: jax[1]});
211 | const ebi_get = axios.get(ebi[0], {params: ebi[1]});
212 |
213 | return axios.all([ncbos_get, ncboa_get, jax_get, ebi_get]
214 | ).then(res => {
215 | const ncbos_res = res[0];
216 | const ncboa_res = res[1];
217 | const jax_res = res[2];
218 | const ebi_res = res[3];
219 |
220 | // Parse NCBO Search response
221 | // none needed
222 |
223 | // Parse NCBO Annotator response
224 | for (var i = 0; i < ncboa_res.data.length; i++) {
225 | // Switch return object's keys to align with display rows in SearchBox.vue
226 | ncboa_res.data[i].notation = ncboa_res.data[i].annotatedClass.notation;
227 | ncboa_res.data[i].prefLabel = ncboa_res.data[i].annotatedClass.prefLabel;
228 | ncboa_res.data[i].definition = ncboa_res.data[i].annotatedClass.definition;
229 | ncboa_res.data[i].synonym = ncboa_res.data[i].annotatedClass.synonym;
230 | ncboa_res.data[i].annotatedClass = null;
231 | }
232 |
233 | // Parse JAX response
234 | jax_res.data.terms = keyLoop(jax_res.data.terms, 'id', 'notation');
235 | jax_res.data.terms = keyLoop(jax_res.data.terms, 'name', 'prefLabel');
236 |
237 | // Parse EBI response
238 | ebi_res.data.response.docs = keyLoop(ebi_res.data.response.docs, 'obo_id', 'notation');
239 | ebi_res.data.response.docs = keyLoop(ebi_res.data.response.docs, 'label', 'prefLabel');
240 | ebi_res.data.response.docs = keyLoop(ebi_res.data.response.docs, 'description', 'definition');
241 |
242 | return [ncbos_res, ncboa_res, jax_res, ebi_res];
243 | }).catch((err) => {
244 | console.log(err);
245 | return null;
246 | });
247 |
248 | // return axios.get(apiURL, {
249 | // params: apiParam
250 | // }).then((res) => {
251 | // console.log("function api: " + api);
252 | // if (api == 0) {
253 | // console.log("request function 0");
254 | // return res;
255 | // } else if (api == 1) {
256 | // for (var i = 0; i < res.data.length; i++) {
257 | // // Switch return object's keys to align with display rows in SearchBox.vue
258 | // res.data[i].notation = res.data[i].annotatedClass.notation;
259 | // res.data[i].prefLabel = res.data[i].annotatedClass.prefLabel;
260 | // res.data[i].definition = res.data[i].annotatedClass.definition;
261 | // res.data[i].synonym = res.data[i].annotatedClass.synonym;
262 | // res.data[i].annotatedClass = null;
263 | // }
264 | // return res;
265 | // } else if (api == 3) {
266 | // res.data.terms = keyLoop(res.data.terms, 'id', 'notation');
267 | // res.data.terms = keyLoop(res.data.terms, 'name', 'prefLabel');
268 | // return res
269 | // } else if (api == 4) {
270 | // console.log("request function 4");
271 | // res.data.response.docs = keyLoop(res.data.response.docs, 'obo_id', 'notation');
272 | // res.data.response.docs = keyLoop(res.data.response.docs, 'label', 'prefLabel');
273 | // res.data.response.docs = keyLoop(res.data.response.docs, 'description', 'definition');
274 | // return res;
275 | // // } else if (api == 5) {
276 | // // res.data.matches = keyLoop(res.data.matches, 'hp_id', 'notation');
277 | // // var i;
278 | // // for (i = 0; i < res.data.matches.length; i++) {
279 | // // res.data.matches[i].prefLabel = res.data.matches[i].names[0];
280 | // // res.data.matches[i].names.shift();
281 | // // }
282 | // // res.data.matches = keyLoop(res.data.matches, 'names', 'synonym');
283 | // // return res;
284 | // } else {
285 | // return null;
286 | // }
287 | // }).catch((err) => {
288 | // return null;
289 | // });
290 | },
291 | responseAdapter: (response) => {
292 | let api = getSelectedAPI();
293 | if (response !== null) {
294 | if (api == 0) {
295 | response = response[0];
296 | return {
297 | data: response.data.collection,
298 | count: response.data.totalCount
299 | }
300 | } else if (api == 1) {
301 | response = response[1];
302 | return {
303 | data: response.data,
304 | count: response.data.length
305 | }
306 | // } else if (api == 2) {
307 | // return {
308 | // data: response.data.data,
309 | // count: response.data.data.length
310 | // }
311 | } else if (api == 3) {
312 | response = response[2];
313 | let count;
314 | let data;
315 | if (response.data.terms == undefined) {
316 | data = [];
317 | count = 0;
318 | } else if (response.data.terms.length >= 10) {
319 | data = response.data.terms;
320 | count = 1;
321 | } else if (response.data.terms.length == 0) {
322 | data = [];
323 | count = 0;
324 | } else {
325 | data = response.data.terms;
326 | count = response.data.terms.length;
327 | }
328 | return {
329 | data: data,
330 | // API only returns top 10 results, all results are returned on one single page
331 | // Let count be 1 to let user think there are no more result pages
332 | count: count
333 | }
334 | } else if (api == 4) {
335 | response = response[3];
336 | if (response.data.response == undefined) {
337 | return {
338 | data: [],
339 | count: 0
340 | }
341 | }
342 | if (response.data.response.numFound == 0) {
343 | return {
344 | data: [],
345 | count: 0
346 | }
347 | }
348 | return {
349 | data: response.data.response.docs,
350 | count: response.data.response.numFound
351 | }
352 | // } else if (api == 5) {
353 | // let count;
354 | // if (response.data.matches.length >= 10) {
355 | // count = 1;
356 | // } else {
357 | // count = response.data.matches.length;
358 | // }
359 | // return {
360 | // data: response.data.matches,
361 | // // API only returns top 10 results, all results are returned on one single page
362 | // // Let count be 1 to let user think there are no more result pages
363 | // count: count
364 | // }
365 | } else {
366 | return {
367 | data: [],
368 | count: 0
369 | }
370 | }
371 | } else {
372 | return {
373 | data: [],
374 | count: 0
375 | }
376 | }
377 | }
378 | }
379 |
380 |
--------------------------------------------------------------------------------
/src/components/SearchBox/OntologyData/mock.js:
--------------------------------------------------------------------------------
1 | export default {
2 | "page": 1,
3 | "pageCount": 5,
4 | "totalCount": 3269,
5 | "prevPage": null,
6 | "nextPage": 2,
7 | "links": {
8 | "nextPage": "http://data.bioontology.org/search?q=melanoma&include=prefLabel%2Cnotation&pagesize=10&display=prefLabel%2Cnotation&page=2",
9 | "prevPage": null
10 | },
11 | "collection": [{
12 | "prefLabel": "Melanoma",
13 | "notation": "LA14279-6",
14 | "@id": "http://purl.bioontology.org/ontology/LNC/LA14279-6",
15 | "@type": "http://www.w3.org/2002/07/owl#Class",
16 | "links": {
17 | "self": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6",
18 | "ontology": "http://data.bioontology.org/ontologies/LOINC",
19 | "children": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/children",
20 | "parents": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/parents",
21 | "descendants": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/descendants",
22 | "ancestors": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/ancestors",
23 | "instances": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/instances",
24 | "tree": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/tree",
25 | "notes": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/notes",
26 | "mappings": "http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6/mappings",
27 | "ui": "http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLA14279-6",
28 | "@context": {
29 | "self": "http://www.w3.org/2002/07/owl#Class",
30 | "ontology": "http://data.bioontology.org/metadata/Ontology",
31 | "children": "http://www.w3.org/2002/07/owl#Class",
32 | "parents": "http://www.w3.org/2002/07/owl#Class",
33 | "descendants": "http://www.w3.org/2002/07/owl#Class",
34 | "ancestors": "http://www.w3.org/2002/07/owl#Class",
35 | "instances": "http://data.bioontology.org/metadata/Instance",
36 | "tree": "http://www.w3.org/2002/07/owl#Class",
37 | "notes": "http://data.bioontology.org/metadata/Note",
38 | "mappings": "http://data.bioontology.org/metadata/Mapping",
39 | "ui": "http://www.w3.org/2002/07/owl#Class"
40 | }
41 | },
42 | "@context": {
43 | "@vocab": "http://data.bioontology.org/metadata/",
44 | "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel",
45 | "notation": "http://data.bioontology.org/metadata/skosnotation"
46 | }
47 | },
48 | {
49 | "prefLabel": "Melanoma",
50 | "notation": "D008545",
51 | "@id": "http://purl.bioontology.org/ontology/MESH/D008545",
52 | "@type": "http://www.w3.org/2002/07/owl#Class",
53 | "links": {
54 | "self": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545",
55 | "ontology": "http://data.bioontology.org/ontologies/MESH",
56 | "children": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/children",
57 | "parents": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/parents",
58 | "descendants": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/descendants",
59 | "ancestors": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/ancestors",
60 | "instances": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/instances",
61 | "tree": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/tree",
62 | "notes": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/notes",
63 | "mappings": "http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545/mappings",
64 | "ui": "http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD008545",
65 | "@context": {
66 | "self": "http://www.w3.org/2002/07/owl#Class",
67 | "ontology": "http://data.bioontology.org/metadata/Ontology",
68 | "children": "http://www.w3.org/2002/07/owl#Class",
69 | "parents": "http://www.w3.org/2002/07/owl#Class",
70 | "descendants": "http://www.w3.org/2002/07/owl#Class",
71 | "ancestors": "http://www.w3.org/2002/07/owl#Class",
72 | "instances": "http://data.bioontology.org/metadata/Instance",
73 | "tree": "http://www.w3.org/2002/07/owl#Class",
74 | "notes": "http://data.bioontology.org/metadata/Note",
75 | "mappings": "http://data.bioontology.org/metadata/Mapping",
76 | "ui": "http://www.w3.org/2002/07/owl#Class"
77 | }
78 | },
79 | "@context": {
80 | "@vocab": "http://data.bioontology.org/metadata/",
81 | "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel",
82 | "notation": "http://data.bioontology.org/metadata/skosnotation"
83 | }
84 | },
85 | {
86 | "prefLabel": "melanoma",
87 | "notation": "S77003",
88 | "@id": "http://purl.bioontology.org/ontology/ICPC2P/S77003",
89 | "@type": "http://www.w3.org/2002/07/owl#Class",
90 | "links": {
91 | "self": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003",
92 | "ontology": "http://data.bioontology.org/ontologies/ICPC2P",
93 | "children": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/children",
94 | "parents": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/parents",
95 | "descendants": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/descendants",
96 | "ancestors": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/ancestors",
97 | "instances": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/instances",
98 | "tree": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/tree",
99 | "notes": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/notes",
100 | "mappings": "http://data.bioontology.org/ontologies/ICPC2P/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003/mappings",
101 | "ui": "http://bioportal.bioontology.org/ontologies/ICPC2P?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICPC2P%2FS77003",
102 | "@context": {
103 | "self": "http://www.w3.org/2002/07/owl#Class",
104 | "ontology": "http://data.bioontology.org/metadata/Ontology",
105 | "children": "http://www.w3.org/2002/07/owl#Class",
106 | "parents": "http://www.w3.org/2002/07/owl#Class",
107 | "descendants": "http://www.w3.org/2002/07/owl#Class",
108 | "ancestors": "http://www.w3.org/2002/07/owl#Class",
109 | "instances": "http://data.bioontology.org/metadata/Instance",
110 | "tree": "http://www.w3.org/2002/07/owl#Class",
111 | "notes": "http://data.bioontology.org/metadata/Note",
112 | "mappings": "http://data.bioontology.org/metadata/Mapping",
113 | "ui": "http://www.w3.org/2002/07/owl#Class"
114 | }
115 | },
116 | "@context": {
117 | "@vocab": "http://data.bioontology.org/metadata/",
118 | "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel",
119 | "notation": "http://data.bioontology.org/metadata/skosnotation"
120 | }
121 | },
122 | {
123 | "prefLabel": "melanoma",
124 | "@id": "http://purl.obolibrary.org/obo/DOID_1909",
125 | "@type": "http://www.w3.org/2002/07/owl#Class",
126 | "links": {
127 | "self": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909",
128 | "ontology": "http://data.bioontology.org/ontologies/CLO",
129 | "children": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/children",
130 | "parents": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/parents",
131 | "descendants": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/descendants",
132 | "ancestors": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/ancestors",
133 | "instances": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/instances",
134 | "tree": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/tree",
135 | "notes": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/notes",
136 | "mappings": "http://data.bioontology.org/ontologies/CLO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909/mappings",
137 | "ui": "http://bioportal.bioontology.org/ontologies/CLO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909",
138 | "@context": {
139 | "self": "http://www.w3.org/2002/07/owl#Class",
140 | "ontology": "http://data.bioontology.org/metadata/Ontology",
141 | "children": "http://www.w3.org/2002/07/owl#Class",
142 | "parents": "http://www.w3.org/2002/07/owl#Class",
143 | "descendants": "http://www.w3.org/2002/07/owl#Class",
144 | "ancestors": "http://www.w3.org/2002/07/owl#Class",
145 | "instances": "http://data.bioontology.org/metadata/Instance",
146 | "tree": "http://www.w3.org/2002/07/owl#Class",
147 | "notes": "http://data.bioontology.org/metadata/Note",
148 | "mappings": "http://data.bioontology.org/metadata/Mapping",
149 | "ui": "http://www.w3.org/2002/07/owl#Class"
150 | }
151 | },
152 | "@context": {
153 | "@vocab": "http://data.bioontology.org/metadata/",
154 | "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel"
155 | }
156 | },
157 | {
158 | "prefLabel": "Melanoma",
159 | "@id": "http://phenomebrowser.net/ontologies/mesh/mesh.owl#C04.557.665.510",
160 | "@type": "http://www.w3.org/2002/07/owl#Class",
161 | "links": {
162 | "self": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510",
163 | "ontology": "http://data.bioontology.org/ontologies/RH-MESH",
164 | "children": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/children",
165 | "parents": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/parents",
166 | "descendants": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/descendants",
167 | "ancestors": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/ancestors",
168 | "instances": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/instances",
169 | "tree": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/tree",
170 | "notes": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/notes",
171 | "mappings": "http://data.bioontology.org/ontologies/RH-MESH/classes/http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510/mappings",
172 | "ui": "http://bioportal.bioontology.org/ontologies/RH-MESH?p=classes&conceptid=http%3A%2F%2Fphenomebrowser.net%2Fontologies%2Fmesh%2Fmesh.owl%23C04.557.665.510",
173 | "@context": {
174 | "self": "http://www.w3.org/2002/07/owl#Class",
175 | "ontology": "http://data.bioontology.org/metadata/Ontology",
176 | "children": "http://www.w3.org/2002/07/owl#Class",
177 | "parents": "http://www.w3.org/2002/07/owl#Class",
178 | "descendants": "http://www.w3.org/2002/07/owl#Class",
179 | "ancestors": "http://www.w3.org/2002/07/owl#Class",
180 | "instances": "http://data.bioontology.org/metadata/Instance",
181 | "tree": "http://www.w3.org/2002/07/owl#Class",
182 | "notes": "http://data.bioontology.org/metadata/Note",
183 | "mappings": "http://data.bioontology.org/metadata/Mapping",
184 | "ui": "http://www.w3.org/2002/07/owl#Class"
185 | }
186 | },
187 | "@context": {
188 | "@vocab": "http://data.bioontology.org/metadata/",
189 | "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel"
190 | }
191 | }
192 | ]
193 | }
194 |
--------------------------------------------------------------------------------
/test/unit/coverage/lcov-report/prettify.js:
--------------------------------------------------------------------------------
1 | window.PR_SHOULD_USE_CONTINUATION=true;(function(){var h=["break,continue,do,else,for,if,return,while"];var u=[h,"auto,case,char,const,default,double,enum,extern,float,goto,int,long,register,short,signed,sizeof,static,struct,switch,typedef,union,unsigned,void,volatile"];var p=[u,"catch,class,delete,false,import,new,operator,private,protected,public,this,throw,true,try,typeof"];var l=[p,"alignof,align_union,asm,axiom,bool,concept,concept_map,const_cast,constexpr,decltype,dynamic_cast,explicit,export,friend,inline,late_check,mutable,namespace,nullptr,reinterpret_cast,static_assert,static_cast,template,typeid,typename,using,virtual,where"];var x=[p,"abstract,boolean,byte,extends,final,finally,implements,import,instanceof,null,native,package,strictfp,super,synchronized,throws,transient"];var R=[x,"as,base,by,checked,decimal,delegate,descending,dynamic,event,fixed,foreach,from,group,implicit,in,interface,internal,into,is,lock,object,out,override,orderby,params,partial,readonly,ref,sbyte,sealed,stackalloc,string,select,uint,ulong,unchecked,unsafe,ushort,var"];var r="all,and,by,catch,class,else,extends,false,finally,for,if,in,is,isnt,loop,new,no,not,null,of,off,on,or,return,super,then,true,try,unless,until,when,while,yes";var w=[p,"debugger,eval,export,function,get,null,set,undefined,var,with,Infinity,NaN"];var s="caller,delete,die,do,dump,elsif,eval,exit,foreach,for,goto,if,import,last,local,my,next,no,our,print,package,redo,require,sub,undef,unless,until,use,wantarray,while,BEGIN,END";var I=[h,"and,as,assert,class,def,del,elif,except,exec,finally,from,global,import,in,is,lambda,nonlocal,not,or,pass,print,raise,try,with,yield,False,True,None"];var f=[h,"alias,and,begin,case,class,def,defined,elsif,end,ensure,false,in,module,next,nil,not,or,redo,rescue,retry,self,super,then,true,undef,unless,until,when,yield,BEGIN,END"];var H=[h,"case,done,elif,esac,eval,fi,function,in,local,set,then,until"];var A=[l,R,w,s+I,f,H];var e=/^(DIR|FILE|vector|(de|priority_)?queue|list|stack|(const_)?iterator|(multi)?(set|map)|bitset|u?(int|float)\d*)/;var C="str";var z="kwd";var j="com";var O="typ";var G="lit";var L="pun";var F="pln";var m="tag";var E="dec";var J="src";var P="atn";var n="atv";var N="nocode";var M="(?:^^\\.?|[+-]|\\!|\\!=|\\!==|\\#|\\%|\\%=|&|&&|&&=|&=|\\(|\\*|\\*=|\\+=|\\,|\\-=|\\->|\\/|\\/=|:|::|\\;|<|<<|<<=|<=|=|==|===|>|>=|>>|>>=|>>>|>>>=|\\?|\\@|\\[|\\^|\\^=|\\^\\^|\\^\\^=|\\{|\\||\\|=|\\|\\||\\|\\|=|\\~|break|case|continue|delete|do|else|finally|instanceof|return|throw|try|typeof)\\s*";function k(Z){var ad=0;var S=false;var ac=false;for(var V=0,U=Z.length;V
18 |
48 |
49 | 19 | all files / SearchBox/ SearchBox.vue 20 |
21 |
22 |
47 |
23 | 55.56%
24 | Statements
25 | 15/27
26 |
27 |
28 | 70%
29 | Branches
30 | 7/10
31 |
32 |
33 | 33.33%
34 | Functions
35 | 2/6
36 |
37 |
38 | 45.45%
39 | Lines
40 | 10/22
41 |
42 |
43 | 1 branch
44 | Ignored
45 |
46 | | 1 51 | 2 52 | 3 53 | 4 54 | 5 55 | 6 56 | 7 57 | 8 58 | 9 59 | 10 60 | 11 61 | 12 62 | 13 63 | 14 64 | 15 65 | 16 66 | 17 67 | 18 68 | 19 69 | 20 70 | 21 71 | 22 72 | 23 73 | 24 74 | 25 75 | 26 76 | 27 77 | 28 78 | 29 79 | 30 80 | 31 81 | 32 82 | 33 83 | 34 84 | 35 85 | 36 86 | 37 87 | 38 88 | 39 89 | 40 90 | 41 91 | 42 92 | 43 93 | 44 94 | 45 95 | 46 96 | 47 97 | 48 98 | 49 99 | 50 100 | 51 101 | 52 102 | 53 103 | 54 104 | 55 105 | 56 106 | 57 107 | 58 108 | 59 109 | 60 110 | 61 111 | 62 112 | 63 113 | 64 114 | 65 115 | 66 116 | 67 117 | 68 118 | 69 119 | 70 120 | 71 121 | 72 122 | 73 123 | 74 124 | 75 125 | 76 126 | 77 127 | 78 128 | 79 129 | 80 130 | 81 131 | 82 132 | 83 133 | 84 134 | 85 135 | 86 136 | 87 137 | 88 138 | 89 139 | 90 140 | 91 141 | 92 142 | 93 143 | 94 144 | 95 145 | 96 146 | 97 147 | 98 148 | 99 149 | 100 150 | 101 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 1× 181 | 1× 182 | 183 | 184 | 185 | 1× 186 | 187 | 1× 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 1× 205 | 1× 206 | 1× 207 | 1× 208 | 1× 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | | //
251 | //
252 | //
253 | //
254 | //
255 | //
256 | //
257 | //
258 | //
259 | //
260 | //
261 | //
262 | //
263 | //
264 | //
265 | //
266 | //
267 | //
268 | //
269 | //
270 | //
271 | //
272 | //
273 | //
274 | //
275 | //
276 | //
277 | //
278 | //
279 |
280 | import Treeselect from '@riophae/vue-treeselect'
281 | import {
282 | options,
283 | ontologyByAcronym
284 | } from './OntologyData/tree'
285 | import ontologies from './OntologyData/ontologies'
286 |
287 | function copyElementContent(srcElementId) {
288 | let srcElement = document.getElementById(srcElementId)
289 | var range = document.createRange();
290 | range.selectNodeContents(srcElement);
291 | let selection = document.getSelection();
292 | selection.removeAllRanges();
293 | selection.addRange(range);
294 | document.execCommand('Copy');
295 | selection.removeAllRanges();
296 | }
297 |
298 | export default {
299 | name: 'search-box',
300 | components: {
301 | Treeselect
302 | },
303 | data() {
304 | let query = document.location.search.match(/query=([^&]*)/)
305 | let ontology = document.location.search.match(/ontology=(.*)/)
306 | query = query ? unescape(query[1]) : undefined
307 | ontology = ontology ? unescape(ontology[1]) : undefined
308 | return {
309 | loading: true,
310 | url: 'https://data.bioontology.org/search',
311 | columns: ['notation', 'prefLabel' /*, 'Actions'*/ ],
312 | options: {
313 | initFilters: {
314 | 'GENERIC': query
315 | },
316 | sortable: [],
317 | perPage: 5,
318 | pagination: {
319 | chunk: 3
320 | },
321 | texts: {
322 | filterPlaceholder: 'Query'
323 | },
324 | skin: 'table table-hover'
325 | },
326 | query: query,
327 | ontologyValue: ontology ? [ontology] : [],
328 | ontologyOptions: options,
329 | results: [],
330 | request: null
331 | }
332 | },
333 | methods: {
334 | copyContent(srcElementId) {
335 | copyElementContent(srcElementId);
336 | window.parent.postMessage({
337 | type: 'copied'
338 | }, "*")
339 | },
340 | replaceWithContent(srcElementId) {
341 | copyElementContent(srcElementId);
342 | window.parent.postMessage({
343 | type: 'copied-paste'
344 | }, "*")
345 | },
346 | copyModel(model) {}
347 | }
348 | }
349 |
350 | |
3 |
17 |
42 |
43 |
44 |
45 |
394 |
395 |
507 |
--------------------------------------------------------------------------------
/src/components/SearchBox/OntologyData/categories.js:
--------------------------------------------------------------------------------
1 | function categoriesToTree(categories) {
2 | let ids = {};
3 | let roots = [];
4 | let branches = categories.map(function(category) {
5 | let branch = {};
6 | // need to track node type as we inject ontologies into the children array alongside categories
7 | branch.type = 'category';
8 | branch.id = category.acronym;
9 | branch.label = category.name;
10 | if (category.parentCategory) {
11 | branch.parent = category.parentCategory.match(/http:\/\/data\.bioontology\.org\/categories\/(.*)/);
12 | if (branch.parent) {
13 | branch.parent = branch.parent[1]; // set parent to acronym (trailing substring of category @id)
14 | }
15 | }
16 | ids[branch.id] = branch;
17 | if (branch.parent === undefined) {
18 | roots.push(branch);
19 | }
20 | return branch;
21 | });
22 | branches.forEach(function(branch) {
23 | if (branch.parent) {
24 | ids[branch.parent].children = ids[branch.parent].children || []
25 | ids[branch.parent].children.push(branch);
26 | }
27 | });
28 | return {
29 | roots: roots,
30 | ids: ids
31 | }
32 | }
33 |
34 | var categories = [{
35 | "id": "http://data.bioontology.org/categories/Imaging",
36 | "acronym": "Imaging",
37 | "name": "Imaging",
38 | "description": null,
39 | "created": "2013-09-18T19:09:59-07:00",
40 | "parentCategory": null,
41 | "@id": "http://data.bioontology.org/categories/Imaging",
42 | "@type": "http://data.bioontology.org/metadata/Category",
43 | "@context": {
44 | "@vocab": "http://data.bioontology.org/metadata/",
45 | "parentCategory": {
46 | "@id": "http://data.bioontology.org/metadata/Category",
47 | "@type": "@id"
48 | }
49 | }
50 | }, {
51 | "id": "http://data.bioontology.org/categories/Mouse_Anatomy",
52 | "acronym": "Mouse_Anatomy",
53 | "name": "Mouse Anatomy",
54 | "description": null,
55 | "created": "2013-09-18T19:09:55-07:00",
56 | "parentCategory": "http://data.bioontology.org/categories/Animal_Gross_Anatomy",
57 | "@id": "http://data.bioontology.org/categories/Mouse_Anatomy",
58 | "@type": "http://data.bioontology.org/metadata/Category",
59 | "@context": {
60 | "@vocab": "http://data.bioontology.org/metadata/",
61 | "parentCategory": {
62 | "@id": "http://data.bioontology.org/metadata/Category",
63 | "@type": "@id"
64 | }
65 | }
66 | }, {
67 | "id": "http://data.bioontology.org/categories/Ethology",
68 | "acronym": "Ethology",
69 | "name": "Ethology",
70 | "description": null,
71 | "created": "2013-09-18T19:09:58-07:00",
72 | "parentCategory": null,
73 | "@id": "http://data.bioontology.org/categories/Ethology",
74 | "@type": "http://data.bioontology.org/metadata/Category",
75 | "@context": {
76 | "@vocab": "http://data.bioontology.org/metadata/",
77 | "parentCategory": {
78 | "@id": "http://data.bioontology.org/metadata/Category",
79 | "@type": "@id"
80 | }
81 | }
82 | }, {
83 | "id": "http://data.bioontology.org/categories/Experimental_Conditions",
84 | "acronym": "Experimental_Conditions",
85 | "name": "Experimental Conditions",
86 | "description": null,
87 | "created": "2013-09-18T19:09:58-07:00",
88 | "parentCategory": null,
89 | "@id": "http://data.bioontology.org/categories/Experimental_Conditions",
90 | "@type": "http://data.bioontology.org/metadata/Category",
91 | "@context": {
92 | "@vocab": "http://data.bioontology.org/metadata/"
93 | }
94 | }, {
95 | "id": "http://data.bioontology.org/categories/Yeast",
96 | "acronym": "Yeast",
97 | "name": "Yeast",
98 | "description": null,
99 | "created": "2013-09-18T19:09:55-07:00",
100 | "parentCategory": null,
101 | "@id": "http://data.bioontology.org/categories/Yeast",
102 | "@type": "http://data.bioontology.org/metadata/Category",
103 | "@context": {
104 | "@vocab": "http://data.bioontology.org/metadata/",
105 | "parentCategory": {
106 | "@id": "http://data.bioontology.org/metadata/Category",
107 | "@type": "@id"
108 | }
109 | }
110 | }, {
111 | "id": "http://data.bioontology.org/categories/All_Organisms",
112 | "acronym": "All_Organisms",
113 | "name": "All Organisms",
114 | "description": null,
115 | "created": "2013-09-18T19:10:00-07:00",
116 | "parentCategory": null,
117 | "@id": "http://data.bioontology.org/categories/All_Organisms",
118 | "@type": "http://data.bioontology.org/metadata/Category",
119 | "@context": {
120 | "@vocab": "http://data.bioontology.org/metadata/",
121 | "parentCategory": {
122 | "@id": "http://data.bioontology.org/metadata/Category",
123 | "@type": "@id"
124 | }
125 | }
126 | }, {
127 | "id": "http://data.bioontology.org/categories/Immunology",
128 | "acronym": "Immunology",
129 | "name": "Immunology",
130 | "description": null,
131 | "created": "2013-09-18T19:09:59-07:00",
132 | "parentCategory": null,
133 | "@id": "http://data.bioontology.org/categories/Immunology",
134 | "@type": "http://data.bioontology.org/metadata/Category",
135 | "@context": {
136 | "@vocab": "http://data.bioontology.org/metadata/",
137 | "parentCategory": {
138 | "@id": "http://data.bioontology.org/metadata/Category",
139 | "@type": "@id"
140 | }
141 | }
142 | }, {
143 | "id": "http://data.bioontology.org/categories/Fish_Anatomy",
144 | "acronym": "Fish_Anatomy",
145 | "name": "Fish Anatomy",
146 | "description": null,
147 | "created": "2013-09-18T19:09:57-07:00",
148 | "parentCategory": "http://data.bioontology.org/categories/Animal_Gross_Anatomy",
149 | "@id": "http://data.bioontology.org/categories/Fish_Anatomy",
150 | "@type": "http://data.bioontology.org/metadata/Category",
151 | "@context": {
152 | "@vocab": "http://data.bioontology.org/metadata/",
153 | "parentCategory": {
154 | "@id": "http://data.bioontology.org/metadata/Category",
155 | "@type": "@id"
156 | }
157 | }
158 | }, {
159 | "id": "http://data.bioontology.org/categories/Cellular_anatomy_",
160 | "acronym": "Cellular_anatomy_",
161 | "name": "Cellular anatomy ",
162 | "description": null,
163 | "created": "2013-09-18T19:09:56-07:00",
164 | "parentCategory": null,
165 | "@id": "http://data.bioontology.org/categories/Cellular_anatomy_",
166 | "@type": "http://data.bioontology.org/metadata/Category",
167 | "@context": {
168 | "@vocab": "http://data.bioontology.org/metadata/",
169 | "parentCategory": {
170 | "@id": "http://data.bioontology.org/metadata/Category",
171 | "@type": "@id"
172 | }
173 | }
174 | }, {
175 | "id": "http://data.bioontology.org/categories/Taxonomic_Classification",
176 | "acronym": "Taxonomic_Classification",
177 | "name": "Taxonomic Classification",
178 | "description": null,
179 | "created": "2013-09-18T19:09:58-07:00",
180 | "parentCategory": null,
181 | "@id": "http://data.bioontology.org/categories/Taxonomic_Classification",
182 | "@type": "http://data.bioontology.org/metadata/Category",
183 | "@context": {
184 | "@vocab": "http://data.bioontology.org/metadata/",
185 | "parentCategory": {
186 | "@id": "http://data.bioontology.org/metadata/Category",
187 | "@type": "@id"
188 | }
189 | }
190 | }, {
191 | "id": "http://data.bioontology.org/categories/Molecule",
192 | "acronym": "Molecule",
193 | "name": "Molecule",
194 | "description": null,
195 | "created": "2013-09-18T19:09:56-07:00",
196 | "parentCategory": null,
197 | "@id": "http://data.bioontology.org/categories/Molecule",
198 | "@type": "http://data.bioontology.org/metadata/Category",
199 | "@context": {
200 | "@vocab": "http://data.bioontology.org/metadata/",
201 | "parentCategory": {
202 | "@id": "http://data.bioontology.org/metadata/Category",
203 | "@type": "@id"
204 | }
205 | }
206 | }, {
207 | "id": "http://data.bioontology.org/categories/Health",
208 | "acronym": "Health",
209 | "name": "Health",
210 | "description": null,
211 | "created": "2013-09-18T19:09:58-07:00",
212 | "parentCategory": null,
213 | "@id": "http://data.bioontology.org/categories/Health",
214 | "@type": "http://data.bioontology.org/metadata/Category",
215 | "@context": {
216 | "@vocab": "http://data.bioontology.org/metadata/",
217 | "parentCategory": {
218 | "@id": "http://data.bioontology.org/metadata/Category",
219 | "@type": "@id"
220 | }
221 | }
222 | }, {
223 | "id": "http://data.bioontology.org/categories/Gross_Anatomy",
224 | "acronym": "Gross_Anatomy",
225 | "name": "Gross Anatomy",
226 | "description": null,
227 | "created": "2013-09-18T19:09:57-07:00",
228 | "parentCategory": "http://data.bioontology.org/categories/Anatomy",
229 | "@id": "http://data.bioontology.org/categories/Gross_Anatomy",
230 | "@type": "http://data.bioontology.org/metadata/Category",
231 | "@context": {
232 | "@vocab": "http://data.bioontology.org/metadata/",
233 | "parentCategory": {
234 | "@id": "http://data.bioontology.org/metadata/Category",
235 | "@type": "@id"
236 | }
237 | }
238 | }, {
239 | "id": "http://data.bioontology.org/categories/Dysfunction",
240 | "acronym": "Dysfunction",
241 | "name": "Dysfunction",
242 | "description": null,
243 | "created": "2013-09-18T19:10:00-07:00",
244 | "parentCategory": null,
245 | "@id": "http://data.bioontology.org/categories/Dysfunction",
246 | "@type": "http://data.bioontology.org/metadata/Category",
247 | "@context": {
248 | "@vocab": "http://data.bioontology.org/metadata/",
249 | "parentCategory": {
250 | "@id": "http://data.bioontology.org/metadata/Category",
251 | "@type": "@id"
252 | }
253 | }
254 | }, {
255 | "id": "http://data.bioontology.org/categories/Biomedical_Resources",
256 | "acronym": "Biomedical_Resources",
257 | "name": "Biomedical Resources",
258 | "description": null,
259 | "created": "2013-09-18T19:09:58-07:00",
260 | "parentCategory": null,
261 | "@id": "http://data.bioontology.org/categories/Biomedical_Resources",
262 | "@type": "http://data.bioontology.org/metadata/Category",
263 | "@context": {
264 | "@vocab": "http://data.bioontology.org/metadata/",
265 | "parentCategory": {
266 | "@id": "http://data.bioontology.org/metadata/Category",
267 | "@type": "@id"
268 | }
269 | }
270 | }, {
271 | "id": "http://data.bioontology.org/categories/Genomic_and_Proteomic",
272 | "acronym": "Genomic_and_Proteomic",
273 | "name": "Genomic and Proteomic",
274 | "description": null,
275 | "created": "2013-09-18T19:09:58-07:00",
276 | "parentCategory": null,
277 | "@id": "http://data.bioontology.org/categories/Genomic_and_Proteomic",
278 | "@type": "http://data.bioontology.org/metadata/Category",
279 | "@context": {
280 | "@vocab": "http://data.bioontology.org/metadata/",
281 | "parentCategory": {
282 | "@id": "http://data.bioontology.org/metadata/Category",
283 | "@type": "@id"
284 | }
285 | }
286 | }, {
287 | "id": "http://data.bioontology.org/categories/Biological_Process",
288 | "acronym": "Biological_Process",
289 | "name": "Biological Process",
290 | "description": null,
291 | "created": "2013-09-18T19:09:54-07:00",
292 | "parentCategory": null,
293 | "@id": "http://data.bioontology.org/categories/Biological_Process",
294 | "@type": "http://data.bioontology.org/metadata/Category",
295 | "@context": {
296 | "@vocab": "http://data.bioontology.org/metadata/",
297 | "parentCategory": {
298 | "@id": "http://data.bioontology.org/metadata/Category",
299 | "@type": "@id"
300 | }
301 | }
302 | }, {
303 | "id": "http://data.bioontology.org/categories/Other",
304 | "acronym": "Other",
305 | "name": "Other",
306 | "description": null,
307 | "created": "2013-09-18T19:10:00-07:00",
308 | "parentCategory": null,
309 | "@id": "http://data.bioontology.org/categories/Other",
310 | "@type": "http://data.bioontology.org/metadata/Category",
311 | "@context": {
312 | "@vocab": "http://data.bioontology.org/metadata/",
313 | "parentCategory": {
314 | "@id": "http://data.bioontology.org/metadata/Category",
315 | "@type": "@id"
316 | }
317 | }
318 | }, {
319 | "id": "http://data.bioontology.org/categories/Subcellular",
320 | "acronym": "Subcellular",
321 | "name": "Subcellular",
322 | "description": null,
323 | "created": "2013-09-18T19:09:56-07:00",
324 | "parentCategory": null,
325 | "@id": "http://data.bioontology.org/categories/Subcellular",
326 | "@type": "http://data.bioontology.org/metadata/Category",
327 | "@context": {
328 | "@vocab": "http://data.bioontology.org/metadata/",
329 | "parentCategory": {
330 | "@id": "http://data.bioontology.org/metadata/Category",
331 | "@type": "@id"
332 | }
333 | }
334 | }, {
335 | "id": "http://data.bioontology.org/categories/Phenotype",
336 | "acronym": "Phenotype",
337 | "name": "Phenotype",
338 | "description": null,
339 | "created": "2013-09-18T19:09:58-07:00",
340 | "parentCategory": null,
341 | "@id": "http://data.bioontology.org/categories/Phenotype",
342 | "@type": "http://data.bioontology.org/metadata/Category",
343 | "@context": {
344 | "@vocab": "http://data.bioontology.org/metadata/",
345 | "parentCategory": {
346 | "@id": "http://data.bioontology.org/metadata/Category",
347 | "@type": "@id"
348 | }
349 | }
350 | }, {
351 | "id": "http://data.bioontology.org/categories/Human_Developmental_Anatomy",
352 | "acronym": "Human_Developmental_Anatomy",
353 | "name": "Human Developmental Anatomy",
354 | "description": null,
355 | "created": "2013-09-18T19:09:57-07:00",
356 | "parentCategory": "http://data.bioontology.org/categories/Animal_Gross_Anatomy",
357 | "@id": "http://data.bioontology.org/categories/Human_Developmental_Anatomy",
358 | "@type": "http://data.bioontology.org/metadata/Category",
359 | "@context": {
360 | "@vocab": "http://data.bioontology.org/metadata/",
361 | "parentCategory": {
362 | "@id": "http://data.bioontology.org/metadata/Category",
363 | "@type": "@id"
364 | }
365 | }
366 | }, {
367 | "id": "http://data.bioontology.org/categories/Plant_Anatomy",
368 | "acronym": "Plant_Anatomy",
369 | "name": "Plant Anatomy",
370 | "description": null,
371 | "created": "2013-09-18T19:09:57-07:00",
372 | "parentCategory": "http://data.bioontology.org/categories/Gross_Anatomy",
373 | "@id": "http://data.bioontology.org/categories/Plant_Anatomy",
374 | "@type": "http://data.bioontology.org/metadata/Category",
375 | "@context": {
376 | "@vocab": "http://data.bioontology.org/metadata/",
377 | "parentCategory": {
378 | "@id": "http://data.bioontology.org/metadata/Category",
379 | "@type": "@id"
380 | }
381 | }
382 | }, {
383 | "id": "http://data.bioontology.org/categories/Neurologic_Disease",
384 | "acronym": "Neurologic_Disease",
385 | "name": "Neurologic Disease",
386 | "description": null,
387 | "created": "2013-09-18T19:10:00-07:00",
388 | "parentCategory": null,
389 | "@id": "http://data.bioontology.org/categories/Neurologic_Disease",
390 | "@type": "http://data.bioontology.org/metadata/Category",
391 | "@context": {
392 | "@vocab": "http://data.bioontology.org/metadata/",
393 | "parentCategory": {
394 | "@id": "http://data.bioontology.org/metadata/Category",
395 | "@type": "@id"
396 | }
397 | }
398 | }, {
399 | "id": "http://data.bioontology.org/categories/Arabadopsis",
400 | "acronym": "Arabadopsis",
401 | "name": "Arabidopsis",
402 | "description": null,
403 | "created": "2013-09-18T19:09:55-07:00",
404 | "parentCategory": null,
405 | "@id": "http://data.bioontology.org/categories/Arabadopsis",
406 | "@type": "http://data.bioontology.org/metadata/Category",
407 | "@context": {
408 | "@vocab": "http://data.bioontology.org/metadata/",
409 | "parentCategory": {
410 | "@id": "http://data.bioontology.org/metadata/Category",
411 | "@type": "@id"
412 | }
413 | }
414 | }, {
415 | "id": "http://data.bioontology.org/categories/Neurological_Disorder",
416 | "acronym": "Neurological_Disorder",
417 | "name": "Neurological Disorder",
418 | "description": null,
419 | "created": "2013-09-18T19:10:00-07:00",
420 | "parentCategory": null,
421 | "@id": "http://data.bioontology.org/categories/Neurological_Disorder",
422 | "@type": "http://data.bioontology.org/metadata/Category",
423 | "@context": {
424 | "@vocab": "http://data.bioontology.org/metadata/",
425 | "parentCategory": {
426 | "@id": "http://data.bioontology.org/metadata/Category",
427 | "@type": "@id"
428 | }
429 | }
430 | }, {
431 | "id": "http://data.bioontology.org/categories/Anatomy",
432 | "acronym": "Anatomy",
433 | "name": "Anatomy",
434 | "description": null,
435 | "created": "2013-09-18T19:09:56-07:00",
436 | "parentCategory": null,
437 | "@id": "http://data.bioontology.org/categories/Anatomy",
438 | "@type": "http://data.bioontology.org/metadata/Category",
439 | "@context": {
440 | "@vocab": "http://data.bioontology.org/metadata/",
441 | "parentCategory": {
442 | "@id": "http://data.bioontology.org/metadata/Category",
443 | "@type": "@id"
444 | }
445 | }
446 | }, {
447 | "id": "http://data.bioontology.org/categories/Plant",
448 | "acronym": "Plant",
449 | "name": "Plant",
450 | "description": null,
451 | "created": "2013-09-18T19:09:55-07:00",
452 | "parentCategory": null,
453 | "@id": "http://data.bioontology.org/categories/Plant",
454 | "@type": "http://data.bioontology.org/metadata/Category",
455 | "@context": {
456 | "@vocab": "http://data.bioontology.org/metadata/",
457 | "parentCategory": {
458 | "@id": "http://data.bioontology.org/metadata/Category",
459 | "@type": "@id"
460 | }
461 | }
462 | }, {
463 | "id": "http://data.bioontology.org/categories/Human",
464 | "acronym": "Human",
465 | "name": "Human",
466 | "description": null,
467 | "created": "2013-09-18T19:09:55-07:00",
468 | "parentCategory": null,
469 | "@id": "http://data.bioontology.org/categories/Human",
470 | "@type": "http://data.bioontology.org/metadata/Category",
471 | "@context": {
472 | "@vocab": "http://data.bioontology.org/metadata/",
473 | "parentCategory": {
474 | "@id": "http://data.bioontology.org/metadata/Category",
475 | "@type": "@id"
476 | }
477 | }
478 | }, {
479 | "id": "http://data.bioontology.org/categories/Subcellular_anatomy",
480 | "acronym": "Subcellular_anatomy",
481 | "name": "Subcellular anatomy",
482 | "description": null,
483 | "created": "2013-09-18T19:09:56-07:00",
484 | "parentCategory": null,
485 | "@id": "http://data.bioontology.org/categories/Subcellular_anatomy",
486 | "@type": "http://data.bioontology.org/metadata/Category",
487 | "@context": {
488 | "@vocab": "http://data.bioontology.org/metadata/",
489 | "parentCategory": {
490 | "@id": "http://data.bioontology.org/metadata/Category",
491 | "@type": "@id"
492 | }
493 | }
494 | }, {
495 | "id": "http://data.bioontology.org/categories/Chemical",
496 | "acronym": "Chemical",
497 | "name": "Chemical",
498 | "description": null,
499 | "created": "2013-09-18T19:10:00-07:00",
500 | "parentCategory": null,
501 | "@id": "http://data.bioontology.org/categories/Chemical",
502 | "@type": "http://data.bioontology.org/metadata/Category",
503 | "@context": {
504 | "@vocab": "http://data.bioontology.org/metadata/",
505 | "parentCategory": {
506 | "@id": "http://data.bioontology.org/metadata/Category",
507 | "@type": "@id"
508 | }
509 | }
510 | }, {
511 | "id": "http://data.bioontology.org/categories/Microbial_Anatomy",
512 | "acronym": "Microbial_Anatomy",
513 | "name": "Microbial Anatomy",
514 | "description": null,
515 | "created": "2013-09-18T19:09:57-07:00",
516 | "parentCategory": "http://data.bioontology.org/categories/Gross_Anatomy",
517 | "@id": "http://data.bioontology.org/categories/Microbial_Anatomy",
518 | "@type": "http://data.bioontology.org/metadata/Category",
519 | "@context": {
520 | "@vocab": "http://data.bioontology.org/metadata/",
521 | "parentCategory": {
522 | "@id": "http://data.bioontology.org/metadata/Category",
523 | "@type": "@id"
524 | }
525 | }
526 | }, {
527 | "id": "http://data.bioontology.org/categories/Cell",
528 | "acronym": "Cell",
529 | "name": "Cell",
530 | "description": null,
531 | "created": "2013-09-18T19:09:56-07:00",
532 | "parentCategory": null,
533 | "@id": "http://data.bioontology.org/categories/Cell",
534 | "@type": "http://data.bioontology.org/metadata/Category",
535 | "@context": {
536 | "@vocab": "http://data.bioontology.org/metadata/",
537 | "parentCategory": {
538 | "@id": "http://data.bioontology.org/metadata/Category",
539 | "@type": "@id"
540 | }
541 | }
542 | }, {
543 | "id": "http://data.bioontology.org/categories/Development",
544 | "acronym": "Development",
545 | "name": "Development",
546 | "description": null,
547 | "created": "2013-09-18T19:09:59-07:00",
548 | "parentCategory": null,
549 | "@id": "http://data.bioontology.org/categories/Development",
550 | "@type": "http://data.bioontology.org/metadata/Category",
551 | "@context": {
552 | "@vocab": "http://data.bioontology.org/metadata/",
553 | "parentCategory": {
554 | "@id": "http://data.bioontology.org/metadata/Category",
555 | "@type": "@id"
556 | }
557 | }
558 | }, {
559 | "id": "http://data.bioontology.org/categories/Protein",
560 | "acronym": "Protein",
561 | "name": "Protein",
562 | "description": null,
563 | "created": "2013-09-18T19:09:59-07:00",
564 | "parentCategory": "http://data.bioontology.org/categories/Gene_Product",
565 | "@id": "http://data.bioontology.org/categories/Protein",
566 | "@type": "http://data.bioontology.org/metadata/Category",
567 | "@context": {
568 | "@vocab": "http://data.bioontology.org/metadata/",
569 | "parentCategory": {
570 | "@id": "http://data.bioontology.org/metadata/Category",
571 | "@type": "@id"
572 | }
573 | }
574 | }, {
575 | "id": "http://data.bioontology.org/categories/Animal_Gross_Anatomy",
576 | "acronym": "Animal_Gross_Anatomy",
577 | "name": "Animal Gross Anatomy",
578 | "description": null,
579 | "created": "2013-09-18T19:09:56-07:00",
580 | "parentCategory": "http://data.bioontology.org/categories/Gross_Anatomy",
581 | "@id": "http://data.bioontology.org/categories/Animal_Gross_Anatomy",
582 | "@type": "http://data.bioontology.org/metadata/Category",
583 | "@context": {
584 | "@vocab": "http://data.bioontology.org/metadata/",
585 | "parentCategory": {
586 | "@id": "http://data.bioontology.org/metadata/Category",
587 | "@type": "@id"
588 | }
589 | }
590 | }, {
591 | "id": "http://data.bioontology.org/categories/Gene_Product",
592 | "acronym": "Gene_Product",
593 | "name": "Gene Product",
594 | "description": null,
595 | "created": "2013-09-18T19:09:59-07:00",
596 | "parentCategory": "http://data.bioontology.org/categories/Genomic_and_Proteomic",
597 | "@id": "http://data.bioontology.org/categories/Gene_Product",
598 | "@type": "http://data.bioontology.org/metadata/Category",
599 | "@context": {
600 | "@vocab": "http://data.bioontology.org/metadata/",
601 | "parentCategory": {
602 | "@id": "http://data.bioontology.org/metadata/Category",
603 | "@type": "@id"
604 | }
605 | }
606 | }, {
607 | "id": "http://data.bioontology.org/categories/Vocabularies",
608 | "acronym": "Vocabularies",
609 | "name": "Vocabularies",
610 | "description": null,
611 | "created": "2013-09-18T19:09:57-07:00",
612 | "parentCategory": null,
613 | "@id": "http://data.bioontology.org/categories/Vocabularies",
614 | "@type": "http://data.bioontology.org/metadata/Category",
615 | "@context": {
616 | "@vocab": "http://data.bioontology.org/metadata/",
617 | "parentCategory": {
618 | "@id": "http://data.bioontology.org/metadata/Category",
619 | "@type": "@id"
620 | }
621 | }
622 | }, {
623 | "id": "http://data.bioontology.org/categories/Physicochemical",
624 | "acronym": "Physicochemical",
625 | "name": "Physicochemical",
626 | "description": null,
627 | "created": "2013-09-18T19:09:59-07:00",
628 | "parentCategory": null,
629 | "@id": "http://data.bioontology.org/categories/Physicochemical",
630 | "@type": "http://data.bioontology.org/metadata/Category",
631 | "@context": {
632 | "@vocab": "http://data.bioontology.org/metadata/",
633 | "acronym": "http://data.bioontology.org/metadata/omvacronym",
634 | "name": "http://data.bioontology.org/metadata/omvname"
635 | }
636 | }, {
637 | "id": "http://data.bioontology.org/categories/Upper_Level_Ontology",
638 | "acronym": "Upper_Level_Ontology",
639 | "name": "Upper Level Ontology",
640 | "description": null,
641 | "created": "2013-09-18T19:09:59-07:00",
642 | "parentCategory": null,
643 | "@id": "http://data.bioontology.org/categories/Upper_Level_Ontology",
644 | "@type": "http://data.bioontology.org/metadata/Category",
645 | "@context": {
646 | "@vocab": "http://data.bioontology.org/metadata/",
647 | "acronym": "http://data.bioontology.org/metadata/omvacronym",
648 | "name": "http://data.bioontology.org/metadata/omvname"
649 | }
650 | }, {
651 | "id": "http://data.bioontology.org/categories/Plant_Development",
652 | "acronym": "Plant_Development",
653 | "name": "Plant Development",
654 | "description": null,
655 | "created": "2013-09-18T19:09:55-07:00",
656 | "parentCategory": "http://data.bioontology.org/categories/Development",
657 | "@id": "http://data.bioontology.org/categories/Plant_Development",
658 | "@type": "http://data.bioontology.org/metadata/Category",
659 | "@context": {
660 | "@vocab": "http://data.bioontology.org/metadata/",
661 | "parentCategory": {
662 | "@id": "http://data.bioontology.org/metadata/Category",
663 | "@type": "@id"
664 | }
665 | }
666 | }, {
667 | "id": "http://data.bioontology.org/categories/Animal_Development",
668 | "acronym": "Animal_Development",
669 | "name": "Animal Development",
670 | "description": null,
671 | "created": "2013-09-18T19:09:54-07:00",
672 | "parentCategory": "http://data.bioontology.org/categories/Development",
673 | "@id": "http://data.bioontology.org/categories/Animal_Development",
674 | "@type": "http://data.bioontology.org/metadata/Category",
675 | "@context": {
676 | "@vocab": "http://data.bioontology.org/metadata/",
677 | "parentCategory": {
678 | "@id": "http://data.bioontology.org/metadata/Category",
679 | "@type": "@id"
680 | }
681 | }
682 | }]
683 |
684 | let tree = categoriesToTree(categories);
685 |
686 | export const categoryRoots = tree.roots;
687 | export const categoryMap = tree.ids;
688 |
--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
1 | GNU GENERAL PUBLIC LICENSE
2 | Version 3, 29 June 2007
3 |
4 | Copyright (C) 2007 Free Software Foundation, Inc.
4 |
16 |
5 | 
6 |
14 |
15 |
6 | ONTOCLICK
7 | 8 | 12 | 13 |
18 |
20 |
21 |
23 |
24 | Definition: {{props.row.definition[0]}}
25 | Synonyms: {{ typeof props.row.synonym === 'string' ? props.row.synonym : props.row.synonym.join(', ') }}
26 |
27 |
28 | {{props.row.notation}}
29 |
30 |
31 |
32 | {{props.row.prefLabel}}
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |