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use JBrowse BlobFilehandleWrapper (fixes controlled access BAM) #102

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merged 2 commits into from
Sep 10, 2020
Merged

use JBrowse BlobFilehandleWrapper (fixes controlled access BAM) #102

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e8a8db7
use JBrowse BlobFilehandleWrapper
GFJHogue Sep 10, 2020
42cf09b
update tests
GFJHogue Sep 10, 2020
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14 changes: 7 additions & 7 deletions cypress/integration/ExploreGDC.js
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Original file line number Diff line number Diff line change
Expand Up @@ -121,9 +121,9 @@ describe('Explore GDC', function() {
})

checkAllResultsTab(
['Showing 1 to 20 of 3,111', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
['Showing 1 to 20 of 21,169', 'TP53', 'TTN'],
['Showing 1 to 20 of 120,896', 'chr2:g.208248388C>T', 'chr17:g.7673803G>A']
['Showing 1 to 20 of 3,127', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
['Showing 1 to 20 of 21,316', 'TTN', 'TP53'],
['Showing 1 to 20 of 132,784', 'chr7:g.140753336A>T', 'chr2:g.208248388C>T']
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Opened #103 to avoid stuff like this in the future

)

// Select is cancer gene census - 1
Expand All @@ -132,9 +132,9 @@ describe('Explore GDC', function() {
})

checkAllResultsTab(
['Showing 1 to 20 of 365', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
['Showing 1 to 20 of 575', 'TP53', 'PIK3CA'],
['Showing 1 to 20 of 5,952', 'chr7:g.140753336A>T', 'chr2:g.208248388C>T']
['Showing 1 to 20 of 457', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'],
['Showing 1 to 20 of 575', 'TP53', 'BRAF'],
['Showing 1 to 20 of 6,580', 'chr7:g.140753336A>T', 'chr2:g.208248388C>T']
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same as above comment

)

selectResultsTab(0)
Expand All @@ -155,4 +155,4 @@ describe('Explore GDC', function() {
cy.contains('GDC_SimpleSomaticMutations_TCGA-A5-A1OF')
cy.contains('GDC_CNVs_TCGA-A5-A1OF')
})
})
})
31 changes: 0 additions & 31 deletions gdc-viewer/js/Model/BlobFilehandleWrapper.js
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2 changes: 1 addition & 1 deletion gdc-viewer/js/Store/SeqFeature/BAM.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ const { BamFile } = cjsRequire('@gmod/bam')

const bamIndexedFilesCache = new LRU({ maxSize: 5 })

const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper')
const BlobFilehandleWrapper = cjsRequire('JBrowse/Model/BlobFilehandleWrapper')

class BamSlightlyLazyFeature {
_get_id() { this.record.id() }
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