Structural variants tab on results view (phase 1)

[fuzhaoyuan]

cBioPortal/cbioportal#10075

Describe changes proposed in this pull request:

Features:

• Add columns: Mutation Status, Cancer Type Detailed, Annotation
• Display number of duplicate samples

Refinements:

• Fulfill features: search Cancer Type Detailed, calculate exons
• Clean up: fusion bar / pie charts, unused columns
• Rename: Sample Id -> ID, Annotation -> SV Description
• Fix: sample link, gene tab switch

[tmazor]

I'm so excited about this! A few initial comments:

1. I think we wanted to call the tab 'Structural Variants' rather than 'Fusions'

2. Also change Fusions to Structural Variants here:
   

3. The Mutations tab includes text about duplicate events in patients with multiple samples
   
   We should have this text for Structural Variants tab too

4. Filtering doesn't work on the Cancer Type Detailed column, eg filtering for 'prostate' finds nothing here:

5. In this query: https://deploy-preview-4588--cbioportalfrontend.netlify.app/results/fusions?cancer_study_list=msk_impact_2017&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=msk_impact_2017_cnaseq&gene_list=EGFR&geneset_list=%20&tab_index=tab_visualize&Action=Submit
   there are a few issues which might be data or might be code, I'm not sure

5a) This is probably data, but Event Info should be 'EGFR-intragenic', not 'EGFR-interganic', eg P-0006768-T01-IM5

5b) Both the 'EGFR-Interganic' and 'Deletion of X exons' events should have Gene2=EGFR, eg P-0005539-T01-IM5

[alisman]

lets unit test this logic. put this in a helper function that accepts tableData. perhaps it should accept the flattened array. you can flatten the data outside the function

[alisman]

this should be unit tested

[alisman]

extract logic that produces this text into a pure function and unit test it