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Fix adapter inference with adapterHint only applying to a specific ex…
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…tension point
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@cmdcolin
cmdcolin committed Jan 28, 2022
1 parent 2dfdf88 commit 6d3a549
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Showing 10 changed files with 111 additions and 71 deletions.
5 changes: 1 addition & 4 deletions packages/core/util/tracks.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -164,10 +164,7 @@ export function guessAdapter(
model?: IAnyStateTreeNode,
) {
if (model) {
// @ts-ignore
const session = getSession(model)

const adapterGuesser = getEnv(session).pluginManager.evaluateExtensionPoint(
const adapterGuesser = getEnv(model).pluginManager.evaluateExtensionPoint(
'Core-guessAdapterForLocation',
(
_file: FileLocation,
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37 changes: 22 additions & 15 deletions plugins/alignments/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -60,12 +60,15 @@ export default class AlignmentsPlugin extends Plugin {
const regexGuess = /\.cram$/i
const adapterName = 'CramAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
cramLocation: file,
craiLocation: index || makeIndex(file, '.crai'),
}
const obj = {
type: adapterName,
cramLocation: file,
craiLocation: index || makeIndex(file, '.crai'),
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
Expand All @@ -84,15 +87,19 @@ export default class AlignmentsPlugin extends Plugin {
const adapterName = 'BamAdapter'
const fileName = getFileName(file)
const indexName = index && getFileName(index)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
bamLocation: file,
index: {
location: index || makeIndex(file, '.bai'),
indexType: makeIndexType(indexName, 'CSI', 'BAI'),
},
}

const obj = {
type: adapterName,
bamLocation: file,
index: {
location: index || makeIndex(file, '.bai'),
indexType: makeIndexType(indexName, 'CSI', 'BAI'),
},
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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14 changes: 9 additions & 5 deletions plugins/bed/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,15 @@ export default class BedPlugin extends Plugin {
const regexGuess = /\.(bb|bigbed)$/i
const adapterName = 'BigBedAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
bigBedLocation: file,
}
const obj = {
type: adapterName,
bigBedLocation: file,
}

if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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4 changes: 3 additions & 1 deletion plugins/data-management/src/AddTrackWidget/components/ConfirmTrack.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,9 @@ const TrackAdapterSelector = observer(({ model }: { model: AddTrackModel }) => {
helperText="Select an adapter type"
select
fullWidth
onChange={event => model.setAdapterHint(event.target.value)}
onChange={event => {
model.setAdapterHint(event.target.value)
}}
SelectProps={{
// @ts-ignore
SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
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13 changes: 8 additions & 5 deletions plugins/gff3/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -71,11 +71,14 @@ export default class extends Plugin {
const regexGuess = /\.gff3?$/i
const adapterName = 'Gff3Adapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
gffLocation: file,
}
const obj = {
type: adapterName,
gffLocation: file,
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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14 changes: 9 additions & 5 deletions plugins/gtf/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,15 @@ export default class GtfPlugin extends Plugin {
const regexGuess = /\.gtf(\.gz)?$/i
const adapterName = 'GtfAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
gtfLocation: file,
}

const obj = {
type: adapterName,
gtfLocation: file,
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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14 changes: 9 additions & 5 deletions plugins/hic/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -50,11 +50,15 @@ export default class HicPlugin extends Plugin {
const regexGuess = /\.hic/i
const adapterName = 'HicAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
hicLocation: file,
}
const obj = {
type: adapterName,
hicLocation: file,
}

if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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45 changes: 28 additions & 17 deletions plugins/sequence/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -71,11 +71,14 @@ export default class SequencePlugin extends Plugin {
const regexGuess = /\.2bit$/i
const adapterName = 'TwoBitAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
twoBitLocation: file,
}
const obj = {
type: adapterName,
twoBitLocation: file,
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
Expand Down Expand Up @@ -139,12 +142,16 @@ export default class SequencePlugin extends Plugin {
const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i
const adapterName = 'IndexedFastaAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
fastaLocation: file,
faiLocation: index || makeIndex(file, '.fai'),
}
const obj = {
type: adapterName,
fastaLocation: file,
faiLocation: index || makeIndex(file, '.fai'),
}

if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
Expand Down Expand Up @@ -191,12 +198,16 @@ export default class SequencePlugin extends Plugin {
const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i
const adapterName = 'BgzipFastaAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
faiLocation: makeIndex(file, '.fai'),
gziLocation: makeIndex(file, '.gzi'),
}
const obj = {
type: adapterName,
faiLocation: makeIndex(file, '.fai'),
gziLocation: makeIndex(file, '.gzi'),
}

if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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21 changes: 12 additions & 9 deletions plugins/variants/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -57,15 +57,18 @@ export default class VariantsPlugin extends Plugin {
const adapterName = 'VcfTabixAdapter'
const fileName = getFileName(file)
const indexName = index && getFileName(index)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
vcfGzLocation: file,
index: {
location: index || makeIndex(file, '.tbi'),
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
},
}
const obj = {
type: adapterName,
vcfGzLocation: file,
index: {
location: index || makeIndex(file, '.tbi'),
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
},
}
if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}
return adapterGuesser(file, index, adapterHint)
}
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15 changes: 10 additions & 5 deletions plugins/wiggle/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -103,12 +103,17 @@ export default class WigglePlugin extends Plugin {
const regexGuess = /\.(bw|bigwig)$/i
const adapterName = 'BigWigAdapter'
const fileName = getFileName(file)
if (regexGuess.test(fileName) || adapterHint === adapterName) {
return {
type: adapterName,
bigWigLocation: file,
}
const obj = {
type: adapterName,
bigWigLocation: file,
}

if (regexGuess.test(fileName) && !adapterHint) {
return obj
} else if (adapterHint === adapterName) {
return obj
}

return adapterGuesser(file, index, adapterHint)
}
},
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