9894545034

Committed 11 Jul 2024 03:47PM UTC coverage: 23.893% (+0.1%) from 23.767%

Build # 9894545034

Build Type

push

github

Committed by

gustavo-salazar

Commit Message

ipscan results refactory - first prototype

Run Details

537 of 2804 branches covered (19.15%)

Branch coverage included in aggregate %.

4 of 24 new or added lines in 5 files covered. (16.67%)

5 existing lines in 3 files now uncovered.

1189 of 4420 relevant lines covered (26.9%)

83.31 hits per line

Source File
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11.43

/src/components/IPScan/ImportResultSearch/LoadedFileDialog/index.js

import React from 'react';
import T from 'prop-types';

import { connect } from 'react-redux';
import { importJobFromData } from 'actions/creators';
import id from 'utils/cheap-unique-id';

import Modal from 'components/SimpleCommonComponents/Modal';
import IPScanVersionCheck from 'components/IPScan/IPScanVersionCheck';
import NucleotideCheck, {
  isNucleotideFile,
} from 'components/IPScan/NucleotideCheck';
// $FlowFixMe
import Button from 'components/SimpleCommonComponents/Button';

const isValid = (fileObj) => {
  return (
    typeof fileObj === 'object' &&
    'results' in fileObj &&
    'interproscan-version' in fileObj
  );
};
/*::
type ProteinResult = {
  xref: Array<{id: string}>,
  matches: Array<{signature:{entry: {}}}>,
  sequence: string,
  md5: string,
  group?: string,
  orf?: {},
}
type NucleotideResult = {
  id: string,
  sequence: string,
  md5: string,
  crossReferences: Array<{
    name: string,
    id: string,
  }>,
  openReadingFrames: Array<{
    id: number,
    start: number,
    end: number,
    strand: string,
    protein: ProteinResult,
  }>,
}
export type ProteinFile = {
  results: Array<ProteinResult>,
  'interproscan-version': string,
  applications: string[]|string,
}
export type NucleotideFile = {
  results: Array<NucleotideResult>,
  'interproscan-version': string,
  applications: string[]|string,
  }
type JobMetadata = {
  localID: string,
  localTitle: string,
  type: string,
  remoteID: string,
  hasResults: boolean,
  entries: Array<Object>,
  group?: string,
}
type Props = {
  show: Boolean,
  closeModal: function,
  fileContent: ProteinFile | NucleotideFile,
  fileName: string,
  importJobFromData: function,
}
*/

const saveJobInIDB = (
  results /*: Array<ProteinResult> */,
  remoteID /*: string */,
  localTitle /*: string|null */,
  ipScanVersion /*: string */,
  applications /*: ?string[]|string */,
  importJobFromData /*: function */,
) => {
  const localID = id(`internal-${Date.now()}`);
  const metadata /*: JobMetadata */ = {
    localID,
    localTitle,
    type: 'InterProScan',
    remoteID,
    hasResults: results.some((result) => result?.matches?.length > 0),
    entries: results.length, // countInterProFromMatches(result.matches),
  };
  const data = {
    localID,
    'interproscan-version': ipScanVersion,
    // input: result.sequence,
    results,
    applications,
  };
  // if (result.group) {
  //   metadata.group = result.group;
  // }
  importJobFromData({
    metadata,
    data,
  });
};

const LoadedFileDialog = (
  { show, closeModal, fileContent, fileName, importJobFromData } /*: Props */,
) => {
  const saveFileInIndexDB = () => {
    // TODO: nucleotides staff hasn't been migrated!
    if (isNucleotideFile(fileContent)) {
      for (let i = fileContent.results.length - 1; i >= 0; i--) {
        // prettier-ignore
        const result/*: NucleotideResult */ = (fileContent.results[i]/*: any */);
        const id = result.crossReferences?.[0]?.id;
        for (const orf of result.openReadingFrames) {
          const { protein, ...rest } = orf;
          protein.group = id;
          protein.orf = { ...rest, dnaSequence: result.sequence };
          if (protein.matches?.length) {
            saveJobInIDB(
              protein,
              `imported_file-${fileName}-${i + 1}-orf-${rest.id}`,
              `${id} - ORF:${rest.id}`,
              fileContent['interproscan-version'],
              fileContent.applications,
              importJobFromData,
            );
          }
        }
      }
    } else {
      // prettier-ignore
      // const result/*: ProteinResult */ = (fileContent.results[i]/*: any */);
      // result.group = fileName;
      saveJobInIDB(
        fileContent.results,
        `imported_file-${fileName}`,
        null, // result?.xref?.[0]?.id || `Seq ${i + 1} from ${fileName}`,
        fileContent['interproscan-version'],
        fileContent.applications,
        importJobFromData,
      );
    }

    closeModal();
  };
  return (
    <Modal show={show} closeModal={closeModal}>
      <h2 id="modalTitle">InterProScan File</h2>
      {fileContent && isValid(fileContent) ? (
        <>
          <p>
            Loading file: <code>{fileName}</code>
          </p>
          <p>
            You are about to load the analysis of{' '}
            <b>{fileContent.results.length} sequences</b> with InterProScan
            version {fileContent['interproscan-version']}
          </p>
          <IPScanVersionCheck
            ipScanVersion={fileContent['interproscan-version']}
          />
          <NucleotideCheck fileContent={fileContent} />
          <div style={{ textAlign: 'right' }}>
            <Button onClick={saveFileInIndexDB}>OK</Button>
          </div>
        </>
      ) : (
        <p>We couldn&apos;t load the file. Check its format and try again.</p>
      )}
    </Modal>
  );
};
LoadedFileDialog.propTypes = {
  show: T.bool,
  closeModal: T.func,
  fileContent: T.object,
  fileName: T.string,
  importJobFromData: T.func,
};

export default connect(undefined, { importJobFromData })(LoadedFileDialog);

1	import React from 'react';
2	import T from 'prop-types';
3
4	import { connect } from 'react-redux';
5	import { importJobFromData } from 'actions/creators';
6	import id from 'utils/cheap-unique-id';
7
8	import Modal from 'components/SimpleCommonComponents/Modal';
9	import IPScanVersionCheck from 'components/IPScan/IPScanVersionCheck';
10	import NucleotideCheck, {
11	isNucleotideFile,
12	} from 'components/IPScan/NucleotideCheck';
13	// $FlowFixMe
14	import Button from 'components/SimpleCommonComponents/Button';
15
16	const isValid = (fileObj) => {	1✔
17	return (	×
18	typeof fileObj === 'object' &&	×
19	'results' in fileObj &&
20	'interproscan-version' in fileObj
21	);
22	};
23	/*::
24	type ProteinResult = {
25	xref: Array<{id: string}>,
26	matches: Array<{signature:{entry: {}}}>,
27	sequence: string,
28	md5: string,
29	group?: string,
30	orf?: {},
31	}
32	type NucleotideResult = {
33	id: string,
34	sequence: string,
35	md5: string,
36	crossReferences: Array<{
37	name: string,
38	id: string,
39	}>,
40	openReadingFrames: Array<{
41	id: number,
42	start: number,
43	end: number,
44	strand: string,
45	protein: ProteinResult,
46	}>,
47	}
48	export type ProteinFile = {
49	results: Array<ProteinResult>,
50	'interproscan-version': string,
51	applications: string[]\|string,
52	}
53	export type NucleotideFile = {
54	results: Array<NucleotideResult>,
55	'interproscan-version': string,
56	applications: string[]\|string,
57	}
58	type JobMetadata = {
59	localID: string,
60	localTitle: string,
61	type: string,
62	remoteID: string,
63	hasResults: boolean,
64	entries: Array<Object>,
65	group?: string,
66	}
67	type Props = {
68	show: Boolean,
69	closeModal: function,
70	fileContent: ProteinFile \| NucleotideFile,
71	fileName: string,
72	importJobFromData: function,
73	}
74	*/
75
76	const saveJobInIDB = (	1✔
77	results /: Array<ProteinResult> /,
78	remoteID /: string /,
79	localTitle /: string\|null /,
80	ipScanVersion /: string /,
81	applications /: ?string[]\|string /,
82	importJobFromData /: function /,
83	) => {
84	const localID = id(`internal-${Date.now()}`);	×
85	const metadata /: JobMetadata / = {	×
86	localID,
87	localTitle,
88	type: 'InterProScan',
89	remoteID,
NEW 90	hasResults: results.some((result) => result?.matches?.length > 0),	×
91	entries: results.length, // countInterProFromMatches(result.matches),
92	};
93	const data = {	×
94	localID,
95	'interproscan-version': ipScanVersion,
96	// input: result.sequence,
97	results,
98	applications,
99	};
100	// if (result.group) {
101	// metadata.group = result.group;
102	// }
UNCOV 103	importJobFromData({	×
104	metadata,
105	data,
106	});
107	};
108
109	const LoadedFileDialog = (	1✔
110	{ show, closeModal, fileContent, fileName, importJobFromData } /: Props /,
111	) => {
112	const saveFileInIndexDB = () => {	×
113	// TODO: nucleotides staff hasn't been migrated!
NEW 114	if (isNucleotideFile(fileContent)) {	×
NEW 115	for (let i = fileContent.results.length - 1; i >= 0; i--) {	×
116	// prettier-ignore
117	const result/: NucleotideResult / = (fileContent.results[i]/: any /);	×
118	const id = result.crossReferences?.[0]?.id;	×
119	for (const orf of result.openReadingFrames) {	×
120	const { protein, ...rest } = orf;	×
121	protein.group = id;	×
122	protein.orf = { ...rest, dnaSequence: result.sequence };	×
123	if (protein.matches?.length) {	×
124	saveJobInIDB(	×
125	protein,
126	`imported_file-${fileName}-${i + 1}-orf-${rest.id}`,
127	`${id} - ORF:${rest.id}`,
128	fileContent['interproscan-version'],
129	fileContent.applications,
130	importJobFromData,
131	);
132	}
133	}
134	}
135	} else {
136	// prettier-ignore
137	// const result/: ProteinResult / = (fileContent.results[i]/: any /);
138	// result.group = fileName;
NEW 139	saveJobInIDB(	×
140	fileContent.results,
141	`imported_file-${fileName}`,
142	null, // result?.xref?.[0]?.id \|\| `Seq ${i + 1} from ${fileName}`,
143	fileContent['interproscan-version'],
144	fileContent.applications,
145	importJobFromData,
146	);
147	}
148
UNCOV 149	closeModal();	×
150	};
151	return (	×
152	<Modal show={show} closeModal={closeModal}>
153	<h2 id="modalTitle">InterProScan File</h2>
154	{fileContent && isValid(fileContent) ? (	×
155	<>
156	<p>
157	Loading file: <code>{fileName}</code>
158	</p>
159	<p>
160	You are about to load the analysis of{' '}
161	<b>{fileContent.results.length} sequences</b> with InterProScan
162	version {fileContent['interproscan-version']}
163	</p>
164	<IPScanVersionCheck
165	ipScanVersion={fileContent['interproscan-version']}
166	/>
167	<NucleotideCheck fileContent={fileContent} />
168	<div style={{ textAlign: 'right' }}>
169	<Button onClick={saveFileInIndexDB}>OK</Button>
170	</div>
171	</>
172	) : (
173	<p>We couldn't load the file. Check its format and try again.</p>
174	)}
175	</Modal>
176	);
177	};
178	LoadedFileDialog.propTypes = {	1✔
179	show: T.bool,
180	closeModal: T.func,
181	fileContent: T.object,
182	fileName: T.string,
183	importJobFromData: T.func,
184	};
185
186	export default connect(undefined, { importJobFromData })(LoadedFileDialog);

ProteinsWebTeam / interpro7-client / 9894545034

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