6876943628

Committed 08 Nov 2023 04:57PM UTC coverage: 23.472% (-0.04%) from 23.512%

Build # 6876943628

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #526 from ProteinsWebTeam/dev

Release 97.0

Run Details

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Branch coverage included in aggregate %.

0 of 20 new or added lines in 4 files covered. (0.0%)

4 existing lines in 2 files now uncovered.

2251 of 8064 relevant lines covered (27.91%)

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49.38

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

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

import descriptionToPath from 'utils/processDescription/descriptionToPath';

import config from 'config';

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

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';
              break;
            case 'taxonomy':
              _search.extra_fields = 'lineage,counters';
              break;
            case 'set':
              _search.extra_fields = 'counters,description';
              break;
            default:
              _search.extra_fields = 'counters';
              break;
          }
        }
        if (hash === 'table') {
          switch (description.main.key) {
            case 'taxonomy':
            case 'proteome':
              _search.extra_fields = 'counters';
              break;
            case 'set':
              _search.extra_fields = 'counters,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;
    let url = format({
      protocol,
      hostname,
      port,
      pathname: root + descriptionToPath(newDesc),
      query: {
        ..._search,
        extra_fields: 'counters',
        page_size: search.page_size || settingsPageSize,
      },
    });
    if (description.main.key === 'set' && description?.entry?.isFilter) {
      url = url.replace('counters', 'short_name');
    }
    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('/alignments', '/')
    .replace('/entry_alignments', '/')
    .replace('/logo', '/')
    .replace('/rosettafold', '/')
    .replace('/alphafold', '/')
    .replace('/domain_architecture', '/')
    .replace('/interactions', '/')
    .replace('/subfamilies', '/')
    .replace('/pathways', '/')
    .replace('/sequence', '/')
    .replace('/genome3d', '/')
    .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
8	const MULTIPLE_SLASHES = /([^:])\/{2,}/g;	30✔
9
10	export const cleanUpMultipleSlashes = (str = '') =>	30✔
11	str.replace(MULTIPLE_SLASHES, '$1/');	19✔
12
13	export const getUrlForMeta = createSelector(	30✔
14	(state) => state.settings.api,	1✔
15	({ protocol, hostname, port, root }) =>
16	cleanUpMultipleSlashes(	1✔
17	format({
18	protocol,
19	hostname,
20	port,
21	pathname: `${root}`,
22	}),
23	),
24	);
25
26	export const getUrlForRelease = (repoKey) =>	30✔
27	createSelector(	2✔
28	() => config.github[repoKey],	×
29	({ owner, repo }) =>
30	`https://api.github.com/repos/${owner}/${repo}/releases/latest`,	×
31	);
32	export const getReadTheDocsURL = (relativePath) =>	30✔
33	createSelector(	×
34	() => config.github.ReadTheDocs,	×
35	({ owner, repo, branch = 'master' }) =>	×
36	`https://raw.githubusercontent.com/${owner}/${repo}/${branch}/docs/${relativePath}`,	×
37	);
38
39	export const getUrl = createSelector(	30✔
40	// this one is just to memoize it
41	(key) => key,	1✔
42	(key) =>
43	createSelector(	1✔
44	(state) => state.settings[key],	15✔
45	(state) => state.settings.navigation.pageSize,	15✔
46	(state) => state.customLocation.description,	15✔
47	(state) => state.customLocation.search,	15✔
48	(state) => state.customLocation.hash,	15✔
49	// eslint-disable-next-line
50	(
51	{ protocol, hostname, port, root },
52	settingsPageSize,
53	description,
54	search,
55	hash,
56	) => {
57	const _search =
58	description.main.key && description[description.main.key].accession	15✔
59	? {}
60	: { ...(search \|\| {}) };	13✔
61	if (	15✔
62	!description[description.main.key].accession \|\|	23✔
63	Object.values(description).find(
64	({ isFilter, db }) => isFilter && db,	8✔
65	) \|\|
66	(description.entry && description.entry.memberDB)
67	)
68	_search.page_size = _search.page_size \|\| settingsPageSize;	12✔
69
70	if (hash === 'grid') {	15✔
71	switch (description.main.key) {	4!
72	case 'entry':
73	_search.extra_fields = 'description,literature,counters';	2✔
74	break;	2✔
75	case 'taxonomy':
76	_search.extra_fields = 'lineage,counters';	1✔
77	break;	1✔
78	case 'set':
79	_search.extra_fields = 'counters,description';	×
80	break;	×
81	default:
82	_search.extra_fields = 'counters';	1✔
83	break;	1✔
84	}
85	}
86	if (hash === 'table') {	15✔
87	switch (description.main.key) {	3!
88	case 'taxonomy':
89	case 'proteome':
90	_search.extra_fields = 'counters';	2✔
91	break;	2✔
92	case 'set':
93	_search.extra_fields = 'counters,description';	×
94	break;	×
95	default:
96	break;	1✔
97	}
98	}
99	if (hash === 'tree' && _search.search !== undefined) {	15!
100	delete _search.search;	×
101	}
102
103	// subpages will get the reverseURL, so its base dataLoader shold only get the accession payload
104	const _description =
105	description.main.key && description[description.main.key].accession	15✔
106	? {
107	main: description.main,
108	[description.main.key]: description[description.main.key],
109	}
110	: description;
111
112	const cursor = _search.cursor;	15✔
113	if (cursor) delete _search.cursor;	15!
114
115	const urlTmp = cleanUpMultipleSlashes(	15✔
116	format({
117	protocol,
118	hostname,
119	port,
120	pathname: root + descriptionToPath(_description),
121	query: _search,
122	}),
123	);
124	// Cursors can have symbols that shouldn't be escaped
125	if (cursor) {	15!
126	const sep = urlTmp.indexOf('?') === -1 ? '?' : '&';	×
127	return `${urlTmp}${sep}cursor=${cursor}`;	×
128	}
129	return urlTmp;	15✔
130	},
131	),
132	);
133
134	export const getReversedUrl = createSelector(	30✔
135	(state) => state.settings.api,	×
136	(state) => state.settings.navigation.pageSize,	×
137	(state) => state.customLocation.description,	×
138	(state) => state.customLocation.search,	×
139	(state) => state.customLocation.hash,	×
140	(
141	{ protocol, hostname, port, root },
142	settingsPageSize,
143	description,
144	search,
145	hash,
146	) => {
147	// copy of description, to modify it after
148	const newDesc = {};	×
149	const _search = { ...search };	×
150	if (hash === 'tree' && _search.search !== undefined) {	×
151	delete _search.search;	×
152	}
153	if (_search.model_page !== undefined) {	×
154	delete _search.model_page;	×
155	}
156
157	let newMain;
158	for (const [key, value] of Object.entries(description)) {	×
159	newDesc[key] = key === 'other' ? [...value] : { ...value };	×
160	if (value.isFilter && value.order === 1) {	×
161	newMain = key;	×
162	newDesc[key].isFilter = false;	×
163	}
164	}
165	newDesc[description.main.key].isFilter = true;	×
166	newDesc.main.key = newMain;	×
167	let url = format({	×
168	protocol,
169	hostname,
170	port,
171	pathname: root + descriptionToPath(newDesc),
172	query: {
173	..._search,
174	extra_fields: 'counters',
175	page_size: search.page_size \|\| settingsPageSize,	×
176	},
177	});
178	if (description.main.key === 'set' && description?.entry?.isFilter) {	×
NEW 179	url = url.replace('counters', 'short_name');	×
180	}
181	if (description.main.key === 'entry' && newMain === 'taxonomy') {	×
182	url = url.replace('/entry/', '/protein/entry/');	×
183	}
184	if (description.main.key === 'taxonomy' && newMain === 'proteome') {	×
185	url = url.replace('/taxonomy/', '/protein/taxonomy/');	×
186	}
187	return url;	×
188	},
189	);
190	export const includeTaxonFocusedOnURL = (url, focused) => {	30✔
191	const hasTaxIdRegex = /taxonomy\/uniprot\/\d+/gi;	×
192	if (focused && +focused !== 1 && !url.match(hasTaxIdRegex)) {	×
193	return url.replace(/taxonomy\/uniprot\//, `/taxonomy/uniprot/${focused}/`);	×
194	}
195	return url;	×
196	};
197
198	export const getUrlForApi = (...parameters) =>	30✔
199	getUrl('api')(...parameters)	16✔
200	.replace('/alignments', '/')
201	.replace('/entry_alignments', '/')
202	.replace('/logo', '/')
203	.replace('/rosettafold', '/')
204	.replace('/alphafold', '/')
205	.replace('/domain_architecture', '/')
206	.replace('/interactions', '/')
207	.replace('/subfamilies', '/')
208	.replace('/pathways', '/')
209	.replace('/sequence', '/')
210	.replace('/genome3d', '/')
211	.replace('/similar_proteins', '/')
212	.replace('/curation', '/');

ProteinsWebTeam / interpro7-client / 6876943628

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