8799828937

Committed 23 Apr 2024 11:46AM UTC coverage: 23.179% (-0.001%) from 23.18%

Build # 8799828937

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push

github

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web-flow

Commit Message

Merge pull request #604 from ProteinsWebTeam/show-short-name

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Branch coverage included in aggregate %.

2 of 5 new or added lines in 2 files covered. (40.0%)

1 existing line in 1 file now uncovered.

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45.16

/src/higherOrder/loadData/defaults/index.js

import { createSelector } from 'reselect';
import { format } from 'url';

import descriptionToPath from 'utils/processDescription/descriptionToPath';

import config from 'config';
import { getNeededCountersForSubpages } from './relatedCounters';

const MULTIPLE_SLASHES = /([^:])\/{2,}/g;

const DBS_WITH_SETS = ['pfam', 'cdd', 'pirsf'];

export const cleanUpMultipleSlashes = (str = '') =>
  str.replace(MULTIPLE_SLASHES, '$1/');

export const getUrlForMeta = createSelector(
  (state) => state.settings.api,
  ({ protocol, hostname, port, root }) =>
    cleanUpMultipleSlashes(
      format({
        protocol,
        hostname,
        port,
        pathname: `${root}`,
      }),
    ),
);

export const getUrlForRelease = (repoKey) =>
  createSelector(
    () => config.github[repoKey],
    ({ owner, repo }) =>
      `https://api.github.com/repos/${owner}/${repo}/releases/latest`,
  );
export const getReadTheDocsURL = (relativePath) =>
  createSelector(
    () => config.github.ReadTheDocs,
    ({ owner, repo, branch = 'master' }) =>
      `https://raw.githubusercontent.com/${owner}/${repo}/${branch}/docs/${relativePath}`,
  );

export const getUrl = createSelector(
  // this one is just to memoize it
  (key) => key,
  (key) =>
    createSelector(
      (state) => state.settings[key],
      (state) => state.settings.navigation.pageSize,
      (state) => state.customLocation.description,
      (state) => state.customLocation.search,
      (state) => state.customLocation.hash,
      // eslint-disable-next-line
      (
        { protocol, hostname, port, root },
        settingsPageSize,
        description,
        search,
        hash,
      ) => {
        const _search =
          description.main.key && description[description.main.key].accession
            ? {}
            : { ...(search || {}) };
        if (
          !description[description.main.key].accession ||
          Object.values(description).find(
            ({ isFilter, db }) => isFilter && db,
          ) ||
          (description.entry && description.entry.memberDB)
        )
          _search.page_size = _search.page_size || settingsPageSize;

        if (hash === 'grid') {
          switch (description.main.key) {
            case 'entry':
              _search.extra_fields =
                'description,literature,counters:protein-ida-taxonomy-structure';
              if (DBS_WITH_SETS.includes(description.entry.db))
                _search.extra_fields += '-set';
              break;
            case 'protein':
              _search.extra_fields = 'counters:entry-structure';
              break;
            case 'structure':
              _search.extra_fields = 'counters:entry-protein-taxonomy';
              break;
            case 'taxonomy':
              _search.extra_fields =
                'lineage,counters:entry-protein-structure-proteome';
              break;
            case 'proteome':
              _search.extra_fields = 'counters:entry-protein-structure';
              break;
            case 'set':
              _search.extra_fields = 'counters,description';
              break;
            default:
              _search.extra_fields = undefined;
              break;
          }
        }
        if (hash === 'table') {
          switch (description.main.key) {
            case 'entry':
              _search.extra_fields = 'short_name';
              break;
            case 'taxonomy':
            case 'proteome':
              _search.extra_fields = 'counters:entry-protein';
              break;
            case 'set':
              _search.extra_fields = 'counters:entry,description';
              break;
            default:
              break;
          }
        }
        if (hash === 'tree' && _search.search !== undefined) {
          delete _search.search;
        }

        // subpages will get the reverseURL, so its base dataLoader shold only get the accession payload
        const _description =
          description.main.key && description[description.main.key].accession
            ? {
                main: description.main,
                [description.main.key]: description[description.main.key],
              }
            : description;

        const cursor = _search.cursor;
        if (cursor) delete _search.cursor;

        const urlTmp = cleanUpMultipleSlashes(
          format({
            protocol,
            hostname,
            port,
            pathname: root + descriptionToPath(_description),
            query: _search,
          }),
        );
        // Cursors can have symbols that shouldn't be escaped
        if (cursor) {
          const sep = urlTmp.indexOf('?') === -1 ? '?' : '&';
          return `${urlTmp}${sep}cursor=${cursor}`;
        }
        return urlTmp;
      },
    ),
);

export const getReversedUrl = createSelector(
  (state) => state.settings.api,
  (state) => state.settings.navigation.pageSize,
  (state) => state.customLocation.description,
  (state) => state.customLocation.search,
  (state) => state.customLocation.hash,
  (
    { protocol, hostname, port, root },
    settingsPageSize,
    description,
    search,
    hash,
  ) => {
    // copy of description, to modify it after
    const newDesc = {};
    const _search = { ...search };
    if (hash === 'tree' && _search.search !== undefined) {
      delete _search.search;
    }
    if (_search.model_page !== undefined) {
      delete _search.model_page;
    }

    let newMain;
    for (const [key, value] of Object.entries(description)) {
      newDesc[key] = key === 'other' ? [...value] : { ...value };
      if (value.isFilter && value.order === 1) {
        newMain = key;
        newDesc[key].isFilter = false;
      }
    }
    newDesc[description.main.key].isFilter = true;
    newDesc.main.key = newMain;
    const newQuery = {
      ..._search,
      extra_fields: undefined,
      page_size: search.page_size || settingsPageSize,
    };
    if (newMain === 'entry') {
      newQuery.extra_fields = 'short_name';
    }
    const counters = getNeededCountersForSubpages(
      description.main.key,
      newMain,
    );
    if (counters) {
      if (newQuery.extra_fields) newQuery.extra_fields += `,${counters}`;
      else newQuery.extra_fields = counters;
    }

    let url = format({
      protocol,
      hostname,
      port,
      pathname: root + descriptionToPath(newDesc),
      query: newQuery,
    });
    if (description.main.key === 'entry' && newMain === 'taxonomy') {
      url = url.replace('/entry/', '/protein/entry/');
    }
    if (description.main.key === 'taxonomy' && newMain === 'proteome') {
      url = url.replace('/taxonomy/', '/protein/taxonomy/');
    }
    return url;
  },
);
export const includeTaxonFocusedOnURL = (url, focused) => {
  const hasTaxIdRegex = /taxonomy\/uniprot\/\d+/gi;
  if (focused && +focused !== 1 && !url.match(hasTaxIdRegex)) {
    return url.replace(/taxonomy\/uniprot\//, `/taxonomy/uniprot/${focused}/`);
  }
  return url;
};

export const getUrlForApi = (...parameters) =>
  getUrl('api')(...parameters)
    .replace('/entry_alignments', '/')
    .replace('/logo', '/')
    .replace('/alphafold', '/')
    .replace('/domain_architecture', '/')
    .replace('/interactions', '/')
    .replace('/subfamilies', '/')
    .replace('/pathways', '/')
    .replace('/sequence', '/')
    .replace('/similar_proteins', '/')
    .replace('/curation', '/');

1	import { createSelector } from 'reselect';
2	import { format } from 'url';
3
4	import descriptionToPath from 'utils/processDescription/descriptionToPath';
5
6	import config from 'config';
7	import { getNeededCountersForSubpages } from './relatedCounters';
8
9	const MULTIPLE_SLASHES = /([^:])\/{2,}/g;	30✔
10
11	const DBS_WITH_SETS = ['pfam', 'cdd', 'pirsf'];	30✔
12
13	export const cleanUpMultipleSlashes = (str = '') =>	30✔
14	str.replace(MULTIPLE_SLASHES, '$1/');	19✔
15
16	export const getUrlForMeta = createSelector(	30✔
17	(state) => state.settings.api,	2✔
18	({ protocol, hostname, port, root }) =>
19	cleanUpMultipleSlashes(	1✔
20	format({
21	protocol,
22	hostname,
23	port,
24	pathname: `${root}`,
25	}),
26	),
27	);
28
29	export const getUrlForRelease = (repoKey) =>	30✔
30	createSelector(	2✔
31	() => config.github[repoKey],	×
32	({ owner, repo }) =>
33	`https://api.github.com/repos/${owner}/${repo}/releases/latest`,	×
34	);
35	export const getReadTheDocsURL = (relativePath) =>	30✔
36	createSelector(	×
37	() => config.github.ReadTheDocs,	×
38	({ owner, repo, branch = 'master' }) =>	×
39	`https://raw.githubusercontent.com/${owner}/${repo}/${branch}/docs/${relativePath}`,	×
40	);
41
42	export const getUrl = createSelector(	30✔
43	// this one is just to memoize it
44	(key) => key,	2✔
45	(key) =>
46	createSelector(	1✔
47	(state) => state.settings[key],	16✔
48	(state) => state.settings.navigation.pageSize,	16✔
49	(state) => state.customLocation.description,	16✔
50	(state) => state.customLocation.search,	16✔
51	(state) => state.customLocation.hash,	16✔
52	// eslint-disable-next-line
53	(
54	{ protocol, hostname, port, root },
55	settingsPageSize,
56	description,
57	search,
58	hash,
59	) => {
60	const _search =
61	description.main.key && description[description.main.key].accession	15✔
62	? {}
63	: { ...(search \|\| {}) };	13✔
64	if (	15✔
65	!description[description.main.key].accession \|\|	23✔
66	Object.values(description).find(
67	({ isFilter, db }) => isFilter && db,	8✔
68	) \|\|
69	(description.entry && description.entry.memberDB)
70	)
71	_search.page_size = _search.page_size \|\| settingsPageSize;	12✔
72
73	if (hash === 'grid') {	15✔
74	switch (description.main.key) {	4!
75	case 'entry':
76	_search.extra_fields =	2✔
77	'description,literature,counters:protein-ida-taxonomy-structure';
78	if (DBS_WITH_SETS.includes(description.entry.db))	2!
79	_search.extra_fields += '-set';	×
80	break;	2✔
81	case 'protein':
82	_search.extra_fields = 'counters:entry-structure';	×
83	break;	×
84	case 'structure':
85	_search.extra_fields = 'counters:entry-protein-taxonomy';	×
86	break;	×
87	case 'taxonomy':
88	_search.extra_fields =	1✔
89	'lineage,counters:entry-protein-structure-proteome';
90	break;	1✔
91	case 'proteome':
92	_search.extra_fields = 'counters:entry-protein-structure';	1✔
93	break;	1✔
94	case 'set':
95	_search.extra_fields = 'counters,description';	×
96	break;	×
97	default:
98	_search.extra_fields = undefined;	×
99	break;	×
100	}
101	}
102	if (hash === 'table') {	15✔
103	switch (description.main.key) {	3!
104	case 'entry':
105	_search.extra_fields = 'short_name';	1✔
106	break;	1✔
107	case 'taxonomy':
108	case 'proteome':
109	_search.extra_fields = 'counters:entry-protein';	2✔
110	break;	2✔
111	case 'set':
112	_search.extra_fields = 'counters:entry,description';	×
113	break;	×
114	default:
UNCOV 115	break;	×
116	}
117	}
118	if (hash === 'tree' && _search.search !== undefined) {	15!
119	delete _search.search;	×
120	}
121
122	// subpages will get the reverseURL, so its base dataLoader shold only get the accession payload
123	const _description =
124	description.main.key && description[description.main.key].accession	15✔
125	? {
126	main: description.main,
127	[description.main.key]: description[description.main.key],
128	}
129	: description;
130
131	const cursor = _search.cursor;	15✔
132	if (cursor) delete _search.cursor;	15!
133
134	const urlTmp = cleanUpMultipleSlashes(	15✔
135	format({
136	protocol,
137	hostname,
138	port,
139	pathname: root + descriptionToPath(_description),
140	query: _search,
141	}),
142	);
143	// Cursors can have symbols that shouldn't be escaped
144	if (cursor) {	15!
145	const sep = urlTmp.indexOf('?') === -1 ? '?' : '&';	×
146	return `${urlTmp}${sep}cursor=${cursor}`;	×
147	}
148	return urlTmp;	15✔
149	},
150	),
151	);
152
153	export const getReversedUrl = createSelector(	30✔
154	(state) => state.settings.api,	×
155	(state) => state.settings.navigation.pageSize,	×
156	(state) => state.customLocation.description,	×
157	(state) => state.customLocation.search,	×
158	(state) => state.customLocation.hash,	×
159	(
160	{ protocol, hostname, port, root },
161	settingsPageSize,
162	description,
163	search,
164	hash,
165	) => {
166	// copy of description, to modify it after
167	const newDesc = {};	×
168	const _search = { ...search };	×
169	if (hash === 'tree' && _search.search !== undefined) {	×
170	delete _search.search;	×
171	}
172	if (_search.model_page !== undefined) {	×
173	delete _search.model_page;	×
174	}
175
176	let newMain;
177	for (const [key, value] of Object.entries(description)) {	×
178	newDesc[key] = key === 'other' ? [...value] : { ...value };	×
179	if (value.isFilter && value.order === 1) {	×
180	newMain = key;	×
181	newDesc[key].isFilter = false;	×
182	}
183	}
184	newDesc[description.main.key].isFilter = true;	×
185	newDesc.main.key = newMain;	×
186	const newQuery = {	×
187	..._search,
188	extra_fields: undefined,
189	page_size: search.page_size \|\| settingsPageSize,	×
190	};
NEW 191	if (newMain === 'entry') {	×
192	newQuery.extra_fields = 'short_name';	×
193	}
194	const counters = getNeededCountersForSubpages(	×
195	description.main.key,
196	newMain,
197	);
198	if (counters) {	×
199	if (newQuery.extra_fields) newQuery.extra_fields += `,${counters}`;	×
200	else newQuery.extra_fields = counters;	×
201	}
202
203	let url = format({	×
204	protocol,
205	hostname,
206	port,
207	pathname: root + descriptionToPath(newDesc),
208	query: newQuery,
209	});
210	if (description.main.key === 'entry' && newMain === 'taxonomy') {	×
211	url = url.replace('/entry/', '/protein/entry/');	×
212	}
213	if (description.main.key === 'taxonomy' && newMain === 'proteome') {	×
214	url = url.replace('/taxonomy/', '/protein/taxonomy/');	×
215	}
216	return url;	×
217	},
218	);
219	export const includeTaxonFocusedOnURL = (url, focused) => {	30✔
220	const hasTaxIdRegex = /taxonomy\/uniprot\/\d+/gi;	×
221	if (focused && +focused !== 1 && !url.match(hasTaxIdRegex)) {	×
222	return url.replace(/taxonomy\/uniprot\//, `/taxonomy/uniprot/${focused}/`);	×
223	}
224	return url;	×
225	};
226
227	export const getUrlForApi = (...parameters) =>	30✔
228	getUrl('api')(...parameters)	16✔
229	.replace('/entry_alignments', '/')
230	.replace('/logo', '/')
231	.replace('/alphafold', '/')
232	.replace('/domain_architecture', '/')
233	.replace('/interactions', '/')
234	.replace('/subfamilies', '/')
235	.replace('/pathways', '/')
236	.replace('/sequence', '/')
237	.replace('/similar_proteins', '/')
238	.replace('/curation', '/');

ProteinsWebTeam / interpro7-client / 8799828937

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