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Allow URLs to be inputted as BED files #329

Merged
merged 16 commits into from
Aug 30, 2023
Merged

Allow URLs to be inputted as BED files #329

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485c780
allow selection dropdown to have creatable elements
ducku Aug 3, 2023
9df4962
add processing bed URLs
ducku Aug 9, 2023
c518ef5
restore progress
ducku Aug 13, 2023
37dd0fc
prepare_chunk now includes chunk file names in chunk directory
ducku Aug 14, 2023
74bb5d9
implement download file
ducku Aug 16, 2023
0718503
let server get chunk path from temp directory
ducku Aug 16, 2023
86739f2
allow tracks to autofill from downloaded chunks
ducku Aug 18, 2023
2ac003e
fetch get wrapper and safer url concatenation
ducku Aug 21, 2023
02575e2
chunks from bedURLs are downloaded as needed, instead of all at once …
ducku Aug 23, 2023
734185c
temporary directories containing downloaded chunk data are now hashed…
ducku Aug 25, 2023
8230ea9
use strict equality
ducku Aug 25, 2023
f3ff321
Merge remote-tracking branch 'origin/master' into HEAD
adamnovak Aug 30, 2023
f41941f
Centralize BED chunk path logic, and pass URLs/paths around instead o…
adamnovak Aug 30, 2023
69a836a
Restore error handling middleware by eliminating async API handlers
adamnovak Aug 30, 2023
b651a29
Switch to a secure hash function
adamnovak Aug 30, 2023
b2161ca
Bring back cactus.bed chunk data and fix handling BED regions without…
adamnovak Aug 30, 2023
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0 ...a/chunk-ref-1-20/chunk-1_0_ref_0_1921.gam → ...a/chunk-ref-1-20/chunk-1_0_ref_0_1926.gam
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57 changes: 31 additions & 26 deletions exampleData/chunk-ref-1-20/chunk.vg
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
VG¶
VGó

GT
d
Expand Down Expand Up @@ -41,32 +41,35 @@ d
d
`CAATTCTCCTGTCTCTGCCTCCTGAGTAGCTGGAATTACAGGCACATGCCATCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGGTTTC
d
`ACAATGTTGGCCAGGCTGCTCTGGAACTCCTGACCTCAGGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCA  
`ACAATGTTGGCCAGGCTGCTCTGGAACTCCTGACCTCAGGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCA

CCTGG  

    Ô
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Expand All @@ -90,7 +93,8 @@ d
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Expand All @@ -114,4 +118,5 @@ d
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0 ...-ref-1-20/chunk_0_ref_0_1921.annotate.txt → ...-ref-1-20/chunk_0_ref_0_1926.annotate.txt
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0 ...ata/chunk-ref-1-20/chunk_0_ref_0_1921.gam → ...ata/chunk-ref-1-20/chunk_0_ref_0_1926.gam
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6 changes: 6 additions & 0 deletions exampleData/chunk-ref-1-20/chunk_contents.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
chunk-1_0_ref_0_1926.gam
chunk.vg
chunk_0_ref_0_1926.annotate.txt
chunk_0_ref_0_1926.gam
regions.tsv
tracks.json
2 changes: 1 addition & 1 deletion exampleData/chunk-ref-1-20/regions.tsv
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@@ -1 +1 @@
ref 0 1922 chunk-ref-1-20/chunk_0_ref_0_1921.gam chunk-ref-1-20/chunk_0_ref_0_1921.annotate.txt
ref 0 1927 chunk-ref-1-20/chunk_0_ref_0_1926.gam chunk-ref-1-20/chunk_0_ref_0_1926.annotate.txt
8 changes: 7 additions & 1 deletion scripts/prepare_chunks.sh
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Expand Up @@ -54,4 +54,10 @@ JSON_STRING=$(jq -n \
--argjson gam_files "$GAM_FILES_JSON" \
'$ARGS.named' )

printf "%s\n" "$JSON_STRING" > $OUTDIR/tracks.json
printf "%s\n" "$JSON_STRING" > $OUTDIR/tracks.json


for file in `ls $OUTDIR/`
do
printf "$file\n" >> $OUTDIR/chunk_contents.txt
Comment on lines +60 to +63
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Do we have our own loop just to stop chunk_contents.txt from listing itself?

done
12 changes: 8 additions & 4 deletions src/components/SelectionDropdown.js
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@@ -1,6 +1,7 @@
import React, { Component } from "react";
import PropTypes from "prop-types";
import Select from "react-select";
//import Select from "react-select";
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Suggested change
//import Select from "react-select";

import CreatableSelect from 'react-select/creatable';

/**
* A searchable selection dropdown component.
Expand Down Expand Up @@ -63,13 +64,16 @@ export class SelectionDropdown extends Component {
};

return (
<Select
<CreatableSelect
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Has everywhere we use this been updated to cope with/disallow creating novel options?

getNewOptionData={(inputValue, optionLabel) => ({
label: optionLabel,
value: inputValue,
})}
id={this.props.id}
inputId={this.props.inputId}
className={this.props.className}
value={
dropdownOptions.find((option) => option.value === this.props.value) ||
{}
dropdownOptions.find((option) => option.value === this.props.value) || {label: this.props.value , value: this.props.value}
}
styles={styles}
isSearchable={true}
Expand Down
1 change: 1 addition & 0 deletions src/config.json
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Expand Up @@ -49,6 +49,7 @@
"vgPath": "",
"dataPath": "./exampleData",
"internalDataPath": "./exampleData/internal/",
"tempDirPath": "./temp",

"defaultHaplotypeColorPalette" : {
"mainPalette": "ygreys",
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