10790348688

Committed 10 Sep 2024 10:09AM UTC coverage: 25.212% (+4.3%) from 20.928%

Build # 10790348688

Build Type

Pull #657

github

Committed by

apolignano

Commit Message

Changed residue processing logic + changed viz rules for domain parent track

Pull Request Pull Request #657: Reorganize tracks

Run Details

520 of 2519 branches covered (20.64%)

Branch coverage included in aggregate %.

0 of 3 new or added lines in 1 file covered. (0.0%)

319 existing lines in 20 files now uncovered.

1118 of 3978 relevant lines covered (28.1%)

92.52 hits per line

Source File
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21.11

/src/components/BreadCrumbs/index.js

import React from 'react';
import T from 'prop-types';
import { customLocationSelector } from 'reducers/custom-location';

import { connect } from 'react-redux';
import { createSelector } from 'reselect';

import Link from 'components/generic/Link';

import { foundationPartial } from 'styles/foundation';
import fonts from 'EBI-Icon-fonts/fonts.css';
import styles from './style.css';
import config from 'config';

const f = foundationPartial(fonts, styles);

/*::
  type Endpoint ={
    detail: string,
    db: string,
    accession: string,
    isFilter: boolean,
    order: number,
  }
  type SearchLocation = {
    type: string,
    value: string,
    accession: string,
    isFilter: boolean,
    order: number,
  }
  type Location = {
    main: {
      key: string,
      isFilter: boolean,
      order: number,
    },
    search: SearchLocation,
    result: SearchLocation,
    [string]: Endpoint,
    other: Array<string>,
  }
*/

const locationType = T.shape({
  main: T.shape({ key: T.string }),
  entry: T.shape({
    detail: T.string,
    db: T.string,
    accession: T.string,
    isFilter: T.bool,
    order: T.number,
  }),
  other: T.arrayOf(T.string),
});
const BreadCrumb = (
  { to, children } /*: {
    children: any,
    to?: function | {description: Object}} */,
) => {
  const childrenToPass =
    typeof children === 'string' ? children.replace(/_/g, ' ') : children;
  return (
    <span>
      {' / '}
      {to ? (
        <Link to={to} className={f('breadcrumb-link')}>
          {childrenToPass}
        </Link>
      ) : (
        childrenToPass
      )}{' '}
    </span>
  );
};
BreadCrumb.propTypes = {
  to: T.oneOfType([T.func, T.object]),
  children: T.any,
};

const BreadCrumbsForOther = ({ other } /*: { other: Array<string>} */) => {
  if (!other.length) return null;
  return (
    <section className={f('main')}>
      {other.map((part, i) => (
        <BreadCrumb
          key={i}
          to={{
            description: { other: other.slice(0, i + 1) },
          }}
        >
          {part}
        </BreadCrumb>
      ))}
    </section>
  );
};
BreadCrumbsForOther.propTypes = {
  other: T.arrayOf(T.string),
};

const BreadCrumbsForSearchOrResult = (
  { location } /*: {location: Location} */,
) => {
  if (!['search', 'result'].includes(location?.main?.key)) return null;
  // $FlowFixMe[incompatible-type]
  const key /*: 'search' | 'result' */ = location.main.key;
  const { type, value, job, accession } = location[key];
  return (
    <>
      <section className={f('main')}>
        <BreadCrumb to={{ description: { main: location.main } }}>
          {location.main.key}
        </BreadCrumb>
        <BreadCrumb
          to={{
            description: { main: location.main, [location.main.key]: { type } },
          }}
        >
          {type}
        </BreadCrumb>
        {job && (
          <BreadCrumb
            to={{
              description: {
                main: location.main,
                [location.main.key]: { type, job },
              },
            }}
          >
            {job}
          </BreadCrumb>
        )}
        {accession && (
          <BreadCrumb
            to={{
              description: {
                main: location.main,
                [location.main.key]: { type, job, accession },
              },
            }}
          >
            {accession}
          </BreadCrumb>
        )}
        {value && <BreadCrumb>{value}</BreadCrumb>}
      </section>
      {accession && <BreadCrumbForSecondPart location={location} />}
    </>
  );
};
BreadCrumbsForSearchOrResult.propTypes = {
  location: locationType,
};

const BreadCrumbForFilters = ({ location, filters }) => {
  return filters.map((ep) => {
    const { db, accession } = location[ep];
    return (
      <section className={f('filter')} key={ep}>
        <BreadCrumb
          to={{
            description: { ...location, [ep]: { db, isFilter: true } },
          }}
        >
          {ep}{' '}
        </BreadCrumb>
        <BreadCrumb
          to={{
            description: { ...location, [ep]: { db, isFilter: true } },
          }}
        >
          {db}
        </BreadCrumb>
        {accession && (
          <BreadCrumb
            to={{
              description: {
                ...location,
                [ep]: { db, accession, isFilter: true },
              },
            }}
          >
            {accession}
          </BreadCrumb>
        )}
      </section>
    );
  });
};
BreadCrumbForFilters.propTypes = {
  location: locationType,
  filters: T.arrayOf(T.string),
};

const BreadCrumbForEntityDetail = (
  {
    location,
    detail,
    filters = [],
  } /*: {location: Location, detail?: string, filters: Array<string>} */,
) => {
  const detailToRender = !filters.length && !detail ? ' Overview' : detail;
  return (
    <section className={f('detail')}>
      {detailToRender && (
        <BreadCrumb
          to={
            detail && {
              description: {
                ...location,
                [location.main.key]: {
                  ...location[location.main.key],
                  detail,
                },
              },
            }
          }
        >
          {detailToRender}
        </BreadCrumb>
      )}
      <BreadCrumbForFilters location={location} filters={filters} />
    </section>
  );
};
BreadCrumbForEntityDetail.propTypes = {
  location: locationType,
  filters: T.arrayOf(T.string),
  detail: T.string,
};

const BreadCrumbForSecondPart = ({ location } /*: {location: Location} */) => {
  const { accession, detail } = location[location.main.key];
  const filters = Object.keys(location)
    // $FlowFixMe[prop-missing]
    .filter((ep) => location[ep]?.isFilter)
    .sort(
      (ep1, ep2) =>
        // $FlowFixMe[prop-missing]
        location[ep1]?.order - location[ep2].order,
    );
  return (
    <section className={f('secondary')}>
      {accession ? (
        <BreadCrumbForEntityDetail
          location={location}
          detail={detail}
          filters={filters}
        />
      ) : (
        <BreadCrumbForFilters location={location} filters={filters} />
      )}
    </section>
  );
};
BreadCrumbForSecondPart.propTypes = {
  location: locationType,
};

const BreadCrumbsForBrowse = ({ location } /*: {location: Location} */) => {
  const endpoint = location?.main?.key;
  if (!config.endpoints.includes(endpoint)) return null;
  const { db, accession } = location[location.main.key];
  return (
    <>
      <section className={f('main')}>
        <BreadCrumb
          to={{
            description: { main: { key: 'entry' }, entry: { db: 'interpro' } },
          }}
        >
          Browse
        </BreadCrumb>
        <BreadCrumb
          to={{
            description: { main: { key: endpoint }, [endpoint]: { db } },
          }}
        >
          By{' '}
          {db && db.toLowerCase() === 'pfam' && endpoint.toLowerCase() === 'set'
            ? 'clan'
            : endpoint}{' '}
        </BreadCrumb>
        <BreadCrumb
          to={{
            description: { main: { key: endpoint }, [endpoint]: { db } },
          }}
        >
          {db}
        </BreadCrumb>
        {accession && (
          <BreadCrumb
            to={{
              description: {
                main: { key: endpoint },
                [endpoint]: { db, accession },
              },
            }}
          >
            {accession}{' '}
          </BreadCrumb>
        )}
      </section>
      <BreadCrumbForSecondPart location={location} />
    </>
  );
};
BreadCrumbsForBrowse.propTypes = {
  location: locationType,
};

const BreadCrumbs = (
  { location, hash } /*: {location: Location, hash: string} */,
) => {
  // Dont show if it is at home
  if (!location?.main?.key && !location?.other?.length) return null;
  return (
    <nav className={f('breadcrumbs')}>
      <Link to={{ description: {} }} className={f('breadcrumb-link')}>
        <span
          className={f('small', 'icon', 'icon-common')}
          data-icon="&#xf015;"
          aria-label={'Home'}
        />
      </Link>

      <BreadCrumbsForOther other={location?.other} />
      <BreadCrumbsForSearchOrResult location={location} />
      <BreadCrumbsForBrowse location={location} />
      {location?.main?.key === 'result' && hash?.startsWith('/') && (
        <BreadCrumb>API Download Form</BreadCrumb>
      )}
    </nav>
  );
};
BreadCrumbs.propTypes = {
  location: locationType,
  hash: T.string,
};

const mapStateToProps = createSelector(
  customLocationSelector,
  (customLocation) => ({
    location: customLocation.description,
    hash: customLocation.hash,
  }),
);

export default connect(mapStateToProps)(BreadCrumbs);

1	import React from 'react';
2	import T from 'prop-types';
3	import { customLocationSelector } from 'reducers/custom-location';
4
5	import { connect } from 'react-redux';
6	import { createSelector } from 'reselect';
7
8	import Link from 'components/generic/Link';
9
10	import { foundationPartial } from 'styles/foundation';
11	import fonts from 'EBI-Icon-fonts/fonts.css';
12	import styles from './style.css';
13	import config from 'config';
14
15	const f = foundationPartial(fonts, styles);	1✔
16
17	/*::
18	type Endpoint ={
19	detail: string,
20	db: string,
21	accession: string,
22	isFilter: boolean,
23	order: number,
24	}
25	type SearchLocation = {
26	type: string,
27	value: string,
28	accession: string,
29	isFilter: boolean,
30	order: number,
31	}
32	type Location = {
33	main: {
34	key: string,
35	isFilter: boolean,
36	order: number,
37	},
38	search: SearchLocation,
39	result: SearchLocation,
40	[string]: Endpoint,
41	other: Array<string>,
42	}
43	*/
44
45	const locationType = T.shape({	1✔
46	main: T.shape({ key: T.string }),
47	entry: T.shape({
48	detail: T.string,
49	db: T.string,
50	accession: T.string,
51	isFilter: T.bool,
52	order: T.number,
53	}),
54	other: T.arrayOf(T.string),
55	});
56	const BreadCrumb = (	1✔
57	{ to, children } /*: {
58	children: any,
59	to?: function \| {description: Object}} */,
60	) => {
61	const childrenToPass =
UNCOV 62	typeof children === 'string' ? children.replace(/_/g, ' ') : children;	×
63	return (	×
64	<span>
65	{' / '}
66	{to ? (	×
67	<Link to={to} className={f('breadcrumb-link')}>
68	{childrenToPass}
69	</Link>
70	) : (
71	childrenToPass
72	)}{' '}
73	</span>
74	);
75	};
76	BreadCrumb.propTypes = {	1✔
77	to: T.oneOfType([T.func, T.object]),
78	children: T.any,
79	};
80
81	const BreadCrumbsForOther = ({ other } /: { other: Array<string>} /) => {	1✔
UNCOV 82	if (!other.length) return null;	×
83	return (	×
84	<section className={f('main')}>
85	{other.map((part, i) => (
UNCOV 86	<BreadCrumb	×
87	key={i}
88	to={{
89	description: { other: other.slice(0, i + 1) },
90	}}
91	>
92	{part}
93	</BreadCrumb>
94	))}
95	</section>
96	);
97	};
98	BreadCrumbsForOther.propTypes = {	1✔
99	other: T.arrayOf(T.string),
100	};
101
102	const BreadCrumbsForSearchOrResult = (	1✔
103	{ location } /: {location: Location} /,
104	) => {
UNCOV 105	if (!['search', 'result'].includes(location?.main?.key)) return null;	×
106	// $FlowFixMe[incompatible-type]
UNCOV 107	const key /: 'search' \| 'result' / = location.main.key;	×
108	const { type, value, job, accession } = location[key];	×
109	return (	×
110	<>
111	<section className={f('main')}>
112	<BreadCrumb to={{ description: { main: location.main } }}>
113	{location.main.key}
114	</BreadCrumb>
115	<BreadCrumb
116	to={{
117	description: { main: location.main, [location.main.key]: { type } },
118	}}
119	>
120	{type}
121	</BreadCrumb>
122	{job && (	×
123	<BreadCrumb
124	to={{
125	description: {
126	main: location.main,
127	[location.main.key]: { type, job },
128	},
129	}}
130	>
131	{job}
132	</BreadCrumb>
133	)}
134	{accession && (	×
135	<BreadCrumb
136	to={{
137	description: {
138	main: location.main,
139	[location.main.key]: { type, job, accession },
140	},
141	}}
142	>
143	{accession}
144	</BreadCrumb>
145	)}
146	{value && <BreadCrumb>{value}</BreadCrumb>}	×
147	</section>
148	{accession && <BreadCrumbForSecondPart location={location} />}	×
149	</>
150	);
151	};
152	BreadCrumbsForSearchOrResult.propTypes = {	1✔
153	location: locationType,
154	};
155
156	const BreadCrumbForFilters = ({ location, filters }) => {	1✔
UNCOV 157	return filters.map((ep) => {	×
158	const { db, accession } = location[ep];	×
159	return (	×
160	<section className={f('filter')} key={ep}>
161	<BreadCrumb
162	to={{
163	description: { ...location, [ep]: { db, isFilter: true } },
164	}}
165	>
166	{ep}{' '}
167	</BreadCrumb>
168	<BreadCrumb
169	to={{
170	description: { ...location, [ep]: { db, isFilter: true } },
171	}}
172	>
173	{db}
174	</BreadCrumb>
175	{accession && (	×
176	<BreadCrumb
177	to={{
178	description: {
179	...location,
180	[ep]: { db, accession, isFilter: true },
181	},
182	}}
183	>
184	{accession}
185	</BreadCrumb>
186	)}
187	</section>
188	);
189	});
190	};
191	BreadCrumbForFilters.propTypes = {	1✔
192	location: locationType,
193	filters: T.arrayOf(T.string),
194	};
195
196	const BreadCrumbForEntityDetail = (	1✔
197	{
198	location,
199	detail,
200	filters = [],	×
201	} /: {location: Location, detail?: string, filters: Array<string>} /,
202	) => {
UNCOV 203	const detailToRender = !filters.length && !detail ? ' Overview' : detail;	×
204	return (	×
205	<section className={f('detail')}>
206	{detailToRender && (	×
207	<BreadCrumb
208	to={
209	detail && {	×
210	description: {
211	...location,
212	[location.main.key]: {
213	...location[location.main.key],
214	detail,
215	},
216	},
217	}
218	}
219	>
220	{detailToRender}
221	</BreadCrumb>
222	)}
223	<BreadCrumbForFilters location={location} filters={filters} />
224	</section>
225	);
226	};
227	BreadCrumbForEntityDetail.propTypes = {	1✔
228	location: locationType,
229	filters: T.arrayOf(T.string),
230	detail: T.string,
231	};
232
233	const BreadCrumbForSecondPart = ({ location } /: {location: Location} /) => {	1✔
UNCOV 234	const { accession, detail } = location[location.main.key];	×
235	const filters = Object.keys(location)	×
236	// $FlowFixMe[prop-missing]
UNCOV 237	.filter((ep) => location[ep]?.isFilter)	×
238	.sort(
239	(ep1, ep2) =>
240	// $FlowFixMe[prop-missing]
UNCOV 241	location[ep1]?.order - location[ep2].order,	×
242	);
UNCOV 243	return (	×
244	<section className={f('secondary')}>
245	{accession ? (	×
246	<BreadCrumbForEntityDetail
247	location={location}
248	detail={detail}
249	filters={filters}
250	/>
251	) : (
252	<BreadCrumbForFilters location={location} filters={filters} />
253	)}
254	</section>
255	);
256	};
257	BreadCrumbForSecondPart.propTypes = {	1✔
258	location: locationType,
259	};
260
261	const BreadCrumbsForBrowse = ({ location } /: {location: Location} /) => {	1✔
UNCOV 262	const endpoint = location?.main?.key;	×
263	if (!config.endpoints.includes(endpoint)) return null;	×
264	const { db, accession } = location[location.main.key];	×
265	return (	×
266	<>
267	<section className={f('main')}>
268	<BreadCrumb
269	to={{
270	description: { main: { key: 'entry' }, entry: { db: 'interpro' } },
271	}}
272	>
273	Browse
274	</BreadCrumb>
275	<BreadCrumb
276	to={{
277	description: { main: { key: endpoint }, [endpoint]: { db } },
278	}}
279	>
280	By{' '}
281	{db && db.toLowerCase() === 'pfam' && endpoint.toLowerCase() === 'set'	×
282	? 'clan'
283	: endpoint}{' '}
284	</BreadCrumb>
285	<BreadCrumb
286	to={{
287	description: { main: { key: endpoint }, [endpoint]: { db } },
288	}}
289	>
290	{db}
291	</BreadCrumb>
292	{accession && (	×
293	<BreadCrumb
294	to={{
295	description: {
296	main: { key: endpoint },
297	[endpoint]: { db, accession },
298	},
299	}}
300	>
301	{accession}{' '}
302	</BreadCrumb>
303	)}
304	</section>
305	<BreadCrumbForSecondPart location={location} />
306	</>
307	);
308	};
309	BreadCrumbsForBrowse.propTypes = {	1✔
310	location: locationType,
311	};
312
313	const BreadCrumbs = (	1✔
314	{ location, hash } /: {location: Location, hash: string} /,
315	) => {
316	// Dont show if it is at home
UNCOV 317	if (!location?.main?.key && !location?.other?.length) return null;	×
318	return (	×
319	<nav className={f('breadcrumbs')}>
320	<Link to={{ description: {} }} className={f('breadcrumb-link')}>
321	<span
322	className={f('small', 'icon', 'icon-common')}
323	data-icon=""
324	aria-label={'Home'}
325	/>
326	</Link>
327
328	<BreadCrumbsForOther other={location?.other} />
329	<BreadCrumbsForSearchOrResult location={location} />
330	<BreadCrumbsForBrowse location={location} />
331	{location?.main?.key === 'result' && hash?.startsWith('/') && (	×
332	<BreadCrumb>API Download Form</BreadCrumb>
333	)}
334	</nav>
335	);
336	};
337	BreadCrumbs.propTypes = {	1✔
338	location: locationType,
339	hash: T.string,
340	};
341
342	const mapStateToProps = createSelector(	1✔
343	customLocationSelector,
UNCOV 344	(customLocation) => ({	×
345	location: customLocation.description,
346	hash: customLocation.hash,
347	}),
348	);
349
350	export default connect(mapStateToProps)(BreadCrumbs);

ProteinsWebTeam / interpro7-client / 10790348688

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