Count atlas table viewers dynamically

[onursumer]

Fix #677

All counts are dynamically calculated by using the unfiltered files. cBioPortal counts are still hard-coded since we don't have that information as part of the data.

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Name	Status	Preview	Comments	Updated (UTC)
htan-portal-nextjs	✅ Ready (Inspect)	Visit Preview	💬 Add feedback	Dec 27, 2024 6:43pm

[inodb]

@onursumer somehow we're missing

• the BU CellxGene Viewer
• 2 CHOP BigQuery datasets
• ~100 HMS Autominerva views
• ~20 SARDANA Autominerva views
• 2 vanderbilt Autominerva views
• 2 MSK UCSC Xena viewers

any clue what happened to each of these?

[onursumer]

• There are these 3 files in the cellxgene mapping file which are completely missing in the Files tab. Not sure if any of them is a BU file though.

  htan-portal/data/cellxgene-mappings.json

  Lines 14 to 16 in 64e30e5

  	"Cohort_1_HTAN_NonEpithelial_AUCell_DR.h5ad": "https://cellxgene.cziscience.com/d/9899E3D8-ACE5-40BD-AC93-7AB7CE2AEC70.cxg/",
  	"nontcells_Seurat.h5ad": "https://cellxgene.cziscience.com/d/3DE2E3DB-9247-41B9-A3F5-35807CF85C3D.cxg/",
  	"tcells_Seurat.h5ad": "https://cellxgene.cziscience.com/d/BFAA0C46-7E34-4FA9-B08C-6DC6013B735A.cxg/",

• There is only one CHOP file (syn51301253) in the BigQuery mapping file:

  htan-portal/data/isbcgc-mappings.json

  Line 6 in fb8784a

  "syn51301253": "https://bq-search.isb-cgc.org/search?status=current&projectId=isb-cgc-bq&datasetId=HTAN&tableId=scRNAseq_CHOP_seurat_pool_logNorm_gini_FiveHD_10Xv3_downsample10000HSPC_current",

• There is only one MSK UCSC Xena file (HTA8_4_100001) in the mapping file:

  htan-portal/data/ucscxena-mappings.json

  Line 13 in 64e30e5

  "HTA8_4_100001":"https://beta.xenabrowser.net/singlecell/?hub=https://previewsinglecell.xenahubs.net:443&defaultTable=htan&study=msk_sclc_chan_2021"

• Missing Autominerva files are tricker to manually identify but it's most likely because those files are not in the mapping file https://github.com/ncihtan/htan-portal/blob/bd880195c6a4d43ed9ba5ddb1859c2a56ec8c618/data/htan-imaging-assets.json

[inodb]

@onursumer

There are these 3 files in the cellxgene mapping file which are completely missing in the Files tab. Not sure if any of them is a BU file though.

Yes one of these is the BU cellxgene instance (you can see the URL by clicking on the production cellxgene link in the explore page): https://cellxgene.cziscience.com/d/BFAA0C46-7E34-4FA9-B08C-6DC6013B735A.cxg/. Don't think this one was ever fully harmonized/curated btw. Can you maybe check with Subhi what's going on here? She's been helping us curate/harmonize these files

There is only one CHOP file (syn51301253) in the BigQuery mapping file

This might be something @PozhidayevaDarya might be able to provide?

There is only one MSK UCSC Xena file (HTA8_4_100001) in the mapping file:

I see, yeah i also only see Joe Chan's dataset on their website: https://beta.xenabrowser.net/singlecell/?hub=https://previewsinglecell.xenahubs.net:443&defaultTable=htan. So seeing just 1 in your PR might be correct ☑️, maybe it was a manual typo from before

Missing Autominerva files are tricker to manually identify but it's most likely because those files are not in the mapping file

Ok cool, less worried about those. Your new implementation is prolly correct and there might've been a manual error before