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Merge pull request #85 from superphy/rc6.3.0
Merge: add search functionality
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| import React, { Component } from 'react'; | ||
| // react-md | ||
| import { | ||
| TextField, | ||
| Button, | ||
| Collapse, | ||
| } from 'react-md'; | ||
| // redux | ||
| import { connect } from 'react-redux' | ||
| import { addJob } from '../actions' | ||
| // axios | ||
| import axios from 'axios' | ||
| import { API_ROOT } from '../middleware/api' | ||
| // router | ||
| import Loading from '../components/Loading' | ||
| import { RedirectToken } from '../components/RedirectToken' | ||
|
|
||
| class Search extends Component { | ||
| constructor(props) { | ||
| super(props); | ||
| this.state = { | ||
| st: 'gi|1370526529|gb|CP027599.1|', | ||
| collapsed: false, | ||
| submitted: false, | ||
| open: false, | ||
| jobId: "", | ||
| hasResult: false, | ||
| } | ||
| } | ||
| toggle = () => { | ||
| this.setState({ collapsed: !this.state.collapsed }); | ||
| }; | ||
| _updateSt = (value) => { | ||
| this.setState({ st: value }); | ||
| } | ||
| _handleSubmit = (e) => { | ||
| e.preventDefault() // disable default HTML form behavior | ||
| // Create form. | ||
| var data = new FormData() | ||
| data.append('st', this.state.st) | ||
| // POST | ||
| axios.post(API_ROOT + 'search', data) | ||
| .then(response => { | ||
| console.log("RESPONSE") | ||
| console.log(response) | ||
| let jobId = response.data | ||
| this.setState({ jobId }) | ||
| // Handle the return. | ||
| this.props.dispatch(addJob(jobId, | ||
| 'search', | ||
| new Date().toLocaleString(), | ||
| String('Search for ' + this.state.st + ' at: ' + new Date().toLocaleString()) | ||
| )) | ||
| this.setState({ hasResult: true }) | ||
| }) | ||
| }; | ||
| render(){ | ||
| const { st, hasResult, collapsed } = this.state; | ||
| const { token } = this.props; | ||
| return ( | ||
| <div> | ||
| <RedirectToken token={token} /> | ||
| {/* actual form */} | ||
| {(!hasResult)? | ||
| <form className="md-text-container md-grid"> | ||
| <div className="md-cell md-cell--12"> | ||
| {/* Help Text */} | ||
| <Button hidden raised primary swapTheming label='Help' onClick={this.toggle}> | ||
| help_outline | ||
| </Button> | ||
| <Collapse collapsed={collapsed}> | ||
| <div> | ||
| <br /> | ||
| <h6>Description:</h6> | ||
| <p> | ||
| We use the <a href='https://biopython.org/wiki/SeqIO'>SeqIO </a> | ||
| library to parse the identifiers from an isolate. | ||
| Specifically, we use the record.id which uses the combined | ||
| gi gb accession numbers. | ||
| </p> | ||
| <p> | ||
| For example, a <b>GenBank</b> record: | ||
| <br/> | ||
| <br/> | ||
| Escherichia coli strain 97-3250 chromosome, complete genome | ||
| <br/> | ||
| 5,942,969 bp circular DNA | ||
| <br/> | ||
| CP027599.1 GI:1370526529 | ||
| <br/> | ||
| <br/> | ||
| With fasta header: | ||
| <br/> | ||
| <br/> | ||
| >gi|1370526529|gb|CP027599.1| Escherichia coli strain 97-3250 chromosome, complete genome | ||
| <br/> | ||
| <br/> | ||
| Would have a record.id of <b>gi|1370526529|gb|CP027599.1|</b> | ||
| <br/> | ||
| <br/> | ||
| For <b>shotgun sequences</b>, search is indexed by sequence ids. | ||
| Seraching for any accession in a shotgun sequence will return results | ||
| for all sequences in the isolate (not just for the single sequence). | ||
| <br/> | ||
| For example, a sequence with header: | ||
| <br/> | ||
| <br/> | ||
| >MOKN01000001.1 Escherichia coli strain 443 BN4_443_1_(paired)_contig_1, whole genome shotgun sequence | ||
| <br/> | ||
| <br/> | ||
| Would have a record.id of <b>MOKN01000001.1</b> | ||
| </p> | ||
| </div> | ||
| </Collapse> | ||
| </div> | ||
| {/* End: Help Text */} | ||
| <div className="md-cell md-cell--12"> | ||
| <h5>Search By record.id</h5> | ||
| <TextField | ||
| id="st" | ||
| value={st} | ||
| onChange={this._updateSt} | ||
| helpText="gi|1370526529|gb|CP027599.1|" | ||
| /> | ||
| </div> | ||
| <div className="md-cell md-cell--12"> | ||
| <Button | ||
| raised | ||
| secondary | ||
| type="submit" | ||
| label="Submit" | ||
| onClick={this._handleSubmit} | ||
| /> | ||
| </div> | ||
| </form> : | ||
| <Loading jobId={this.state.jobId} /> | ||
| } | ||
| </div> | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| Search = connect()(Search) | ||
|
|
||
| export default Search |
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