Switch to structure_variant table data for fusions

[jjgao]

Backend

• [ ] remove fusions from the mutation_event table and leave existing fetch mutations endpoints un-touched.
• [x] add a new web service endpoint to pull fusions out from the new structural-variants table, e.g . /structuralvariant-genes/fetch
• [x] a new web API to fetch structural variants
• [x] a new web API to fetch structural variant enrichments
• [ ] cleanup unnecessary code(temporary code added to support fusions) once data is fixed

Pipleline

• [ ] Import sv.txt
• [ ] Add documentation for importing structural variant data
• [ ] Are we still going to support fusions.txt?
• [ ] show_profile_in_analysis_tab is set to false for some of the fusion profile. should we write a migration script or update data files? - temporarily fixed by patching in code
• [ ] normalize profile names (e.g. for MSK-IMPACT they are just called Fusion. Which is not consistent with other profile names)

Frontend

• [x] Study view: add a new fusion gene table
• [x] Patient view: add a new structural variants table https://github.com/cBioPortal/cbioportal/issues/7545
• [ ] add a new structural variant track to the existing plot on the patient view (?)https://github.com/cBioPortal/cbioportal/issues/7546
• [x] add sv/fusion profile option in query interface of single-study query https://github.com/cBioPortal/cbioportal/issues/1874
• [x] add sv/fusion profile option in query interface of multi-study query https://github.com/cbioportal/cbioportal/issues/7882
• [x] OncoPrinttab: switch to sv api https://github.com/cBioPortal/cbioportal/issues/6965
• [x] Cancer Types Summary tab: switch to sv api (hopefully it's already using oncoprint data) https://github.com/cBioPortal/cbioportal/issues/7798
• [x] Download tab https://github.com/cBioPortal/cbioportal/issues/7798
  • [x] switch to sv api for the table (hopefully it's already using oncoprint data)
  • [x] add Fusions in the "Downloadable Data Files" section
• [x] Mutual Exclusivity tab: double check it works after switching
• [x] Plots tab(https://github.com/cBioPortal/cbioportal/issues/1879)
  • [x] add Fusion as a Data Type
  • [x] add Fusion as an option of "Style samples by"
• [ ] Mutations tab
  • [ ] Should we have SVs table? If so maybe we should have CNAs table as well? https://github.com/cBioPortal/cbioportal/issues/1877
  • [ ] More updates https://github.com/cBioPortal/cbioportal/issues/8092
• [x] Enrichments tab: add Structure Variants sub-tab (after Mutations) https://github.com/cBioPortal/cbioportal/issues/7832
• [x] Survival tab: double check the numbers are correct
• [x] Pathway (to be released): double check the numbers are correct

@khzhu @alisman @n1zea144

[khzhu]

use fetchStructuralVariantsUsingPOST to fetch only fusions then merge with mutations from fetchStructuralVariantsInMultipleMolecularProfilesUsingPOST in the frontend might be difficult since return sets from two apis have complete different attributes? add a new endpoint to fetch structure variants might be easier.

{
  "entrezGeneIds": [
   64759,9709
  ],
  "sampleMolecularIdentifiers": [
    {"molecularProfileId":"study_es_0_structural_variants","sampleId":"TCGA-A7-A13D-01"},{"molecularProfileId":"study_es_0_structural_variants","sampleId":"TCGA-BH-A0E6-01"}
  ]
}

[khzhu]

here is the development plan for using the new structural variants table:

Backend:

• [ ] remove fusions from the mutation_event table and leave existing fetch mutations endpoints un-touched.
• [ ] add a new web service endpoint to pull fusions out from the new structural-variants table e.g . /fusion-genes/fetch
• [ ] a new web API getSampleCountInMultipleMolecularProfilesForFusions to collect fusion genes counts for the summary view

Frontend

• [ ] add a new fusion gene table in the summary view
• [ ] add a new structural variants table in the patient view
• [ ] add a new structural variant track to the existing plot on the patient view

[jjgao]

thanks, @khzhu! I updated the to-do list in the description.

[jjgao]

It is a fairly big task. It would be a good idea to turn this into an epic and create separate issues for the tasks.

[khzhu]

thanks, @jjgao ! It is much clear now what I suppose to do. I will break down to a few sub tasks.

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.