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‎src/LaunchProteinView/components/AlphaFoldDBSearch.tsx‎

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -35,6 +35,7 @@ import {
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3636
import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
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import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
38+
import ExternalLink from '../../components/ExternalLink'
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3940
const useStyles = makeStyles()({
4041
dialogContent: {
@@ -62,13 +63,10 @@ function EnterUniProtID() {
6263
return (
6364
<div>
6465
Please enter a valid UniProt ID. You can search for UniProt IDs at{' '}
65-
<a href="https://www.uniprot.org/" target="_blank" rel="noreferrer">
66-
UniProt.org
67-
</a>{' '}
68-
or{' '}
69-
<a href="https://alphafold.ebi.ac.uk/" target="_blank" rel="noreferrer">
66+
<ExternalLink href="https://www.uniprot.org/">UniProt</ExternalLink> or{' '}
67+
<ExternalLink href="https://alphafold.ebi.ac.uk/">
7068
AlphaFoldDB
71-
</a>
69+
</ExternalLink>
7270
</div>
7371
)
7472
}
@@ -182,20 +180,22 @@ const AlphaFoldDBSearch = observer(function ({
182180
</FormControl>
183181

184182
{lookupMode === 'manual' && (
185-
<TextField
186-
label="UniProt ID"
187-
variant="outlined"
188-
value={manualUniprotId}
189-
onChange={e => {
190-
setManualUniprotId(e.target.value)
191-
}}
192-
placeholder="Enter UniProt ID (e.g. P68871)"
193-
helperText="Enter a valid UniProt ID to load the corresponding protein structure"
194-
/>
183+
<div>
184+
<TextField
185+
label="UniProt ID"
186+
variant="outlined"
187+
placeholder="Enter UniProt ID (e.g. P68871)"
188+
helperText="Enter a valid UniProt ID to load the corresponding protein structure"
189+
value={manualUniprotId}
190+
onChange={e => {
191+
setManualUniprotId(e.target.value)
192+
}}
193+
/>
194+
</div>
195195
)}
196196
{loadingStatuses.length > 0
197197
? loadingStatuses.map(l => (
198-
<LoadingEllipses key={l} variant="h6" message={l} />
198+
<LoadingEllipses key={l} variant="subtitle2" message={l} />
199199
))
200200
: null}
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‎src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx‎

Lines changed: 13 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,22 @@
11
import React, { useState } from 'react'
22

33
import { Feature } from '@jbrowse/core/util'
4-
import { Button, Link, Typography } from '@mui/material'
4+
import { Button, Typography } from '@mui/material'
55

66
import MSATable from './MSATable'
77
import { getDisplayName } from './util'
88

9+
import ExternalLink from '../../components/ExternalLink'
10+
911
function NotFound({ uniprotId }: { uniprotId: string }) {
1012
return (
1113
<Typography>
1214
No structure found for this UniProtID in AlphaFoldDB{' '}
13-
<Link
14-
target="_blank"
15+
<ExternalLink
1516
href={`https://alphafold.ebi.ac.uk/search/text/${uniprotId}`}
1617
>
1718
(search for results)
18-
</Link>
19+
</ExternalLink>
1920
</Typography>
2021
)
2122
}
@@ -41,18 +42,14 @@ export default function AlphaFoldDBSearchStatus({
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4243
return uniprotId ? (
4344
<>
44-
<Typography>
45-
Found Uniprot ID:{' '}
46-
<a href={url2} target="_blank" rel="noreferrer">
47-
{uniprotId}
48-
</a>
49-
</Typography>
50-
<Typography>
51-
AlphaFoldDB link:{' '}
52-
<a href={url} target="_blank" rel="noreferrer">
53-
{url}
54-
</a>
55-
</Typography>
45+
<div>
46+
<Typography>
47+
UniProt link: <ExternalLink href={url2}>{uniprotId}</ExternalLink>
48+
</Typography>
49+
<Typography>
50+
AlphaFoldDB link: <ExternalLink href={url}>{url}</ExternalLink>
51+
</Typography>
52+
</div>
5653
{structureSequence ? (
5754
<div style={{ margin: 20 }}>
5855
<Button

‎src/LaunchProteinView/components/UserProvidedStructure.tsx‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@ import {
3636
} from './util'
3737

3838
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
39+
import ExternalLink from '../../components/ExternalLink'
3940

4041
const useStyles = makeStyles()(theme => ({
4142
dialogContent: {
@@ -54,9 +55,9 @@ function HelpText() {
5455
<div style={{ marginBottom: 20 }}>
5556
Manually supply a protein structure (PDB, mmCIF, etc) for a given
5657
transcript. You can open the file from the result of running, for example,{' '}
57-
<Link target="_blank" href="https://github.com/sokrypton/ColabFold">
58+
<ExternalLink href="https://github.com/sokrypton/ColabFold">
5859
ColabFold
59-
</Link>
60+
</ExternalLink>
6061
. This plugin will align the protein sequence calculated from the genome
6162
to the protein sequence embedded in the structure file which allows for
6263
slight differences in these two representations.

‎src/components/ExternalLink.tsx‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,14 @@
1+
import React from 'react'
2+
import { Link } from '@mui/material'
3+
import OpenInNewIcon from '@mui/icons-material/OpenInNew'
4+
5+
import type { LinkProps } from '@mui/material'
6+
7+
export default function ExternalLink(props: LinkProps) {
8+
const { children, ...rest } = props
9+
return (
10+
<Link {...rest} target="_blank" rel="noreferrer">
11+
{children} <OpenInNewIcon fontSize="small" />
12+
</Link>
13+
)
14+
}

‎yarn.lock‎

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@@ -658,22 +658,22 @@
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661-
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662-
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661+
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662+
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664664
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665665
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666666
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667-
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667+
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668668
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669669
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670670
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671671
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672672

673-
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674-
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675-
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676-
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673+
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674+
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675+
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677677
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678678
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679679
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@@ -937,16 +937,16 @@
937937
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938938

939939
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940-
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940+
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941+
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943943
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944944
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945945

946946
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947-
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948-
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950950
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951951
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952952

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976976
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978978
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979-
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980-
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979+
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982982
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983983
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18891889
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18901890

18911891
electron-to-chromium@^1.5.149:
1892-
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1893-
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1892+
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18951895

18961896
emoji-regex@^8.0.0:
18971897
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@@ -1916,26 +1916,26 @@ error-ex@^1.3.1:
19161916
is-arrayish "^0.2.1"
19171917

19181918
es-abstract@^1.17.5, es-abstract@^1.23.2, es-abstract@^1.23.3, es-abstract@^1.23.5, es-abstract@^1.23.6, es-abstract@^1.23.9:
1919-
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1920-
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1919+
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1920+
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19221922
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19231923
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19241924
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1927-
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1927+
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19291929
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19301930
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19311931
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19321932
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1933-
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1933+
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19341934
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19351935
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19361936
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1937-
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1938-
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1937+
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1938+
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19391939
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19401940
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19411941
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@@ -1951,13 +1951,13 @@ es-abstract@^1.17.5, es-abstract@^1.23.2, es-abstract@^1.23.3, es-abstract@^1.23
19511951
is-shared-array-buffer "^1.0.4"
19521952
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19531953
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1954-
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1954+
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19551955
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1956-
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1956+
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19571957
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19581958
object.assign "^4.1.7"
19591959
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1960-
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1960+
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19611961
safe-array-concat "^1.1.3"
19621962
safe-push-apply "^1.0.0"
19631963
safe-regex-test "^1.1.0"
@@ -1970,7 +1970,7 @@ es-abstract@^1.17.5, es-abstract@^1.23.2, es-abstract@^1.23.3, es-abstract@^1.23
19701970
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19711971
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19721972
unbox-primitive "^1.1.0"
1973-
which-typed-array "^1.1.18"
1973+
which-typed-array "^1.1.19"
19741974

19751975
es-array-method-boxes-properly@^1.0.0:
19761976
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@@ -3022,7 +3022,7 @@ is-weakmap@^2.0.2:
30223022
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3025-
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3025+
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30263026
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30603060
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30623062
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3063-
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30663066
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30673067
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36473647
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36533653
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36543654
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36553655
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@@ -3672,7 +3672,6 @@ molstar@^4.0.0:
36723672
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36733673
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36743674
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3675-
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36763675

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3753+
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@@ -4202,7 +4201,7 @@ regexp-tree@^0.1.27:
42024201
resolved "https://registry.yarnpkg.com/regexp-tree/-/regexp-tree-0.1.27.tgz#2198f0ef54518ffa743fe74d983b56ffd631b6cd"
42034202
integrity sha512-iETxpjK6YoRWJG5o6hXLwvjYAoW+FEZn9os0PD/b6AP6xQwsa/Y7lCVgIixBbUPMfhu+i2LtdeAqVTgGlQarfA==
42044203

4205-
regexp.prototype.flags@^1.5.3:
4204+
regexp.prototype.flags@^1.5.3, regexp.prototype.flags@^1.5.4:
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version "1.5.4"
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resolved "https://registry.yarnpkg.com/regexp.prototype.flags/-/regexp.prototype.flags-1.5.4.tgz#1ad6c62d44a259007e55b3970e00f746efbcaa19"
42084207
integrity sha512-dYqgNSZbDwkaJ2ceRd9ojCGjBq+mOm9LmtXnAnEGyHhN/5R7iDW2TRw3h+o/jCFxus3P2LfWIIiwowAjANm7IA==
@@ -4781,9 +4780,9 @@ supports-preserve-symlinks-flag@^1.0.0:
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integrity sha512-ot0WnXS9fgdkgIcePe6RHNk1WA8+muPa6cSjeR3V8K27q9BB1rTE3R1p7Hv0z1ZyAc8s6Vvv8DIyWf681MAt0w==
47824781

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swagger-ui-dist@^5.21.0:
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version "5.21.0"
4785-
resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.21.0.tgz#aed230fe6e294c9470217e67697d601e3bb8eb9d"
4786-
integrity sha512-E0K3AB6HvQd8yQNSMR7eE5bk+323AUxjtCz/4ZNKiahOlPhPJxqn3UPIGs00cyY/dhrTDJ61L7C/a8u6zhGrZg==
4783+
version "5.22.0"
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resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.22.0.tgz#8280cfa9659d90cf6f682c76f7e792b0da939946"
4785+
integrity sha512-8YlCSxiyb8uPFa7qoB1lRHYr1PBbT1NuV9RvQdFFPFPudRBTPf9coU5jl02KhzvrtmTEw4jXRgb0kg8pJvVuWQ==
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dependencies:
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"@scarf/scarf" "=1.4.0"
47894788

@@ -5214,7 +5213,7 @@ which-collection@^1.0.2:
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is-weakmap "^2.0.2"
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is-weakset "^2.0.3"
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5217-
which-typed-array@^1.1.16, which-typed-array@^1.1.18:
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which-typed-array@^1.1.16, which-typed-array@^1.1.19:
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version "1.1.19"
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resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.19.tgz#df03842e870b6b88e117524a4b364b6fc689f956"
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integrity sha512-rEvr90Bck4WZt9HHFC4DJMsjvu7x+r6bImz0/BrbWb7A2djJ8hnZMrWnHo9F8ssv0OMErasDhftrfROTyqSDrw==
@@ -5277,11 +5276,6 @@ wrappy@1:
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resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f"
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integrity sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==
52795278

5280-
xhr2@^0.2.1:
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version "0.2.1"
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resolved "https://registry.yarnpkg.com/xhr2/-/xhr2-0.2.1.tgz#4e73adc4f9cfec9cbd2157f73efdce3a5f108a93"
5283-
integrity sha512-sID0rrVCqkVNUn8t6xuv9+6FViXjUVXq8H5rWOH2rz9fDNQEd4g0EA2XlcEdJXRz5BMEn4O1pJFdT+z4YHhoWw==
5284-
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yaml@^1.10.0:
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version "1.10.2"
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resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b"

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