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Update CDS DRS mapping data #728

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merged 10 commits into from
Dec 12, 2024
Merged

Update CDS DRS mapping data #728

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8d980eb
update CDS DRS mapping data
onursumer Dec 5, 2024
ef6e177
Use drs_uri as source of truth for sequencing data
inodb Dec 6, 2024
bce9c22
fix imaging cds info
inodb Dec 6, 2024
30a0260
use v2 cds mapping table
inodb Dec 6, 2024
bbd1968
update processed syn url
inodb Dec 6, 2024
6f79b12
additional fixes CDS mapping
inodb Dec 11, 2024
3727b42
remove syn_data.json.gz from pr
inodb Dec 12, 2024
342a6e0
regenerate processed json
inodb Dec 12, 2024
d2960dc
replace with master syn_data
inodb Dec 12, 2024
34c606a
regenerate processed json (last time plz)
inodb Dec 12, 2024
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2 changes: 1 addition & 1 deletion data/processSynapseJSON.log
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ ncc: Using [email protected] (local user-provided)
40kB sourcemap-register.js
8675kB index.js
1425kB index.js.map
8715kB [26726ms] - ncc 0.28.6
8715kB [8766ms] - ncc 0.28.6
Missing ParentBiospecimenID: {
Component: 'ScRNA-seqLevel3',
Filename: 'single_cell_RNAseq_level_3_ped_glioma/HTAN_pHGG_161_New_Reg1_snRNA/barcodes.tsv.gz',
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7 changes: 2 additions & 5 deletions data/processSynapseJSON.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -400,13 +400,10 @@ function addDownloadSourcesInfo(
if (file.synapseId && dbgapImgSynapseSet.has(file.synapseId)) {
// Level 2 imaging data is open access
// ImagingLevel2, SRRSImagingLevel2 as specified in released.entities table (CDS_Release) column
if (
file.level === 'Level 2' &&
file.Component.startsWith('Imaging')
) {
if (file.viewers?.cds?.drs_uri) {
file.downloadSource = DownloadSourceCategory.cds;
} else {
file.downloadSource = DownloadSourceCategory.dbgap;
file.downloadSource = DownloadSourceCategory.comingSoon;
}
} else if (
file.Component === 'OtherAssay' &&
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2 changes: 1 addition & 1 deletion lib/helpers.ts
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Expand Up @@ -44,7 +44,7 @@ export async function fetchData(): Promise<LoadDataResult> {
const processedSynURL =
process.env.NODE_ENV === 'development'
? '/processed_syn_data.json'
: `${getCloudBaseUrl()}/processed_syn_data_20241205_1557.json`;
: `${getCloudBaseUrl()}/processed_syn_data_20241206_1308.json`;
return fetchSynData(processedSynURL);
}

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Binary file modified public/processed_syn_data.json.gz
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we don't need to update this file. original json should still be the same.

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hmm, actually, the file has changed. @inodb did you run the python script again to update the data?

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it's also possible that you had the previous version locally and never updated it to the latest

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good catch - fixed this now!

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