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Remove unnecessary OncoKB query parameter in oncoprinter #4238

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merged 2 commits into from
May 2, 2022

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dippindots
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@dippindots dippindots added the bug label Apr 28, 2022
@dippindots dippindots self-assigned this Apr 28, 2022
@dippindots
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There is one e2e test fail related to this change, there are three more samples that can find putative driver information.
I verified in cbioportal network event and also verified through oncokb API, that these three samples do have driver information, so I will update the screenshot.

    {
        "query": {
            "id": "7157_P191del",
            "referenceGenome": "GRCh37",
            "hugoSymbol": "TP53",
            "entrezGeneId": 7157,
            "alteration": "P191del",
            "alterationType": null,
            "svType": null,
            "tumorType": null,
            "consequence": null,
            "proteinStart": 191,
            "proteinEnd": 191,
            "hgvs": null
        },
        "geneExist": true,
        "variantExist": true,
        "alleleExist": false,
        "oncogenic": "Likely Oncogenic",
        "mutationEffect": {
            "knownEffect": "Unknown",
            "description": "",
            "citations": {
                "pmids": [],
                "abstracts": []
            }
        },
        "highestSensitiveLevel": null,
        "highestResistanceLevel": null,
        "highestDiagnosticImplicationLevel": null,
        "highestPrognosticImplicationLevel": null,
        "otherSignificantSensitiveLevels": [],
        "otherSignificantResistanceLevels": [],
        "hotspot": true,
        "geneSummary": "",
        "variantSummary": "",
        "tumorTypeSummary": "",
        "prognosticSummary": "",
        "diagnosticSummary": "",
        "diagnosticImplications": [],
        "prognosticImplications": [],
        "treatments": [],
        "dataVersion": "v3.12",
        "lastUpdate": "03/29/2022",
        "vus": false
    },
    {
        "query": {
            "id": "7157_T256del",
            "referenceGenome": "GRCh37",
            "hugoSymbol": "TP53",
            "entrezGeneId": 7157,
            "alteration": "T256del",
            "alterationType": null,
            "svType": null,
            "tumorType": null,
            "consequence": null,
            "proteinStart": 256,
            "proteinEnd": 256,
            "hgvs": null
        },
        "geneExist": true,
        "variantExist": true,
        "alleleExist": false,
        "oncogenic": "Likely Oncogenic",
        "mutationEffect": {
            "knownEffect": "Unknown",
            "description": "",
            "citations": {
                "pmids": [],
                "abstracts": []
            }
        },
        "highestSensitiveLevel": null,
        "highestResistanceLevel": null,
        "highestDiagnosticImplicationLevel": null,
        "highestPrognosticImplicationLevel": null,
        "otherSignificantSensitiveLevels": [],
        "otherSignificantResistanceLevels": [],
        "hotspot": false,
        "geneSummary": "",
        "variantSummary": "",
        "tumorTypeSummary": "",
        "prognosticSummary": "",
        "diagnosticSummary": "",
        "diagnosticImplications": [],
        "prognosticImplications": [],
        "treatments": [],
        "dataVersion": "v3.12",
        "lastUpdate": "03/29/2022",
        "vus": false
    },
    {
        "query": {
            "id": "7157_MCN237del",
            "referenceGenome": "GRCh37",
            "hugoSymbol": "TP53",
            "entrezGeneId": 7157,
            "alteration": "MCN237del",
            "alterationType": null,
            "svType": null,
            "tumorType": null,
            "consequence": null,
            "proteinStart": 237,
            "proteinEnd": 237,
            "hgvs": null
        },
        "geneExist": true,
        "variantExist": true,
        "alleleExist": false,
        "oncogenic": "Likely Oncogenic",
        "mutationEffect": {
            "knownEffect": "Unknown",
            "description": "",
            "citations": {
                "pmids": [],
                "abstracts": []
            }
        },
        "highestSensitiveLevel": null,
        "highestResistanceLevel": null,
        "highestDiagnosticImplicationLevel": null,
        "highestPrognosticImplicationLevel": null,
        "otherSignificantSensitiveLevels": [],
        "otherSignificantResistanceLevels": [],
        "hotspot": false,
        "geneSummary": "",
        "variantSummary": "",
        "tumorTypeSummary": "",
        "prognosticSummary": "",
        "diagnosticSummary": "",
        "diagnosticImplications": [],
        "prognosticImplications": [],
        "treatments": [],
        "dataVersion": "v3.12",
        "lastUpdate": "03/29/2022",
        "vus": false
    },

@dippindots
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This is the follow up issue for the oncoprinter feature: cBioPortal/cbioportal#9500

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LGTM

@alisman alisman merged commit 11fd1a0 into cBioPortal:master May 2, 2022
@dippindots dippindots deleted the fix-9484 branch May 4, 2022 16:25
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(OncoPrinter) OncoKB driver annotation inframe event error
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