Upgraded react-mutation-mapper version to 0.3.0 #2706

onursumer · 2019-09-17T18:44:43Z

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Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!
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onursumer · 2019-09-19T20:46:20Z

src/shared/components/mutationMapper/MutationMapperStore.ts

@@ -130,43 +130,6 @@ export default class MutationMapperStore extends DefaultMutationMapperStore
        return mutation.gene.entrezGeneId;
    }

-    @autobind
-    protected customFilterApplier(filter: DataFilter,


This logic has been moved as multiple separate methods into https://github.com/cBioPortal/react-mutation-mapper/blob/66648ae9b966f7a30069e397acfb0e6efc0a0c73/src/store/DefaultMutationMapperFilterApplier.ts#L24

onursumer · 2019-09-19T20:47:51Z

src/shared/components/mutationMapper/MutationMapper.tsx

@@ -188,18 +201,6 @@ export default class MutationMapper<P extends IMutationMapperProps> extends Defa
        ): null;
    }

-    protected get proteinImpactTypePanel(): JSX.Element | null


now we are using ProteinImpactTypeBadgeSelector component to enable multiple filtering

onursumer · 2019-09-19T20:49:49Z

src/pages/resultsView/mutation/MutationRateSummary.tsx

-                {this.somaticMutationFrequency()}
-                {this.germlineMutationFrequency()}
-            </div>
+            <MutationStatusSelector


This enables filtering by mutation status (somatic / germline)

package.json

alisman · 2019-10-04T20:31:14Z

@onursumer is this still draft? what's story?

onursumer · 2019-10-17T14:12:37Z

@alisman we can merge this as soon as Niki approves the latest UI changes. I still need to update the screenshot tests though.

alisman · 2019-11-18T20:57:28Z

src/shared/components/mutationMapper/MutationMapper.tsx

@@ -171,6 +186,10 @@ export default class MutationMapper<P extends IMutationMapperProps> extends Defa
                trackDataStatus={this.trackDataStatus}
                onTrackVisibilityChange={this.onTrackVisibilityChange}
                getLollipopColor={getColorForProteinImpactType}
+                filterResetPanel={
+                    !this.props.store.dataStore.showingAllData && this.filterResetPanel ?


could you just pass filterResetPanel whether it's defined or not? just kind confusing

The problem here is, for some reason, we initially defined filterResetPanel as JSX.Element | null instead of JSX.Element | undefined. When I just pass it, TS complains that null cannot be assigned to undefined.

For now just updated the check to this.filterResetPanel !== null, but we should probably revisit those function definitions (both here and in react-mutation-mapper)

alisman · 2019-11-18T21:00:26Z

src/shared/components/mutationMapper/MutationMapperDataStore.ts

+export const PROTEIN_IMPACT_TYPE_FILTER_ID = "_cBioPortalProteinImpactTypeFilter_";
+export const MUTATION_STATUS_FILTER_ID = "_cBioPortalMutationStatusFilter_";
+
+export function findMutationTypeFilter(dataFilters: DataFilter[])


function name sees strange because code finds a particular type of filter, right? shouldn't function name suggest that?

renamed to findProteinImpactTypeFilter

Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com> replaced ProteinImpactTypePanel with ProteinImpactTypeBadgeSelector Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com> enabled filtering for MutationRateSummary Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com> fixed mutation type filter counts Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>

Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>

onursumer force-pushed the react-mutation-mapper-0.3.0 branch 3 times, most recently from 2056fe5 to 76bb3ab Compare September 19, 2019 20:43

onursumer commented Sep 19, 2019

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onursumer marked this pull request as ready for review November 1, 2019 10:16

onursumer requested review from alisman, zhx828, adamabeshouse and inodb November 1, 2019 10:16

adamabeshouse approved these changes Nov 1, 2019

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onursumer force-pushed the react-mutation-mapper-0.3.0 branch from 56d8830 to ce6a5ac Compare November 5, 2019 18:42

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onursumer added 2 commits November 19, 2019 16:48

fixed broken tests and screenshots

21290e3

Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>

onursumer force-pushed the react-mutation-mapper-0.3.0 branch from b6dc4fd to 21290e3 Compare November 19, 2019 21:49

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alisman merged commit 4789052 into cBioPortal:master Nov 19, 2019

onursumer deleted the react-mutation-mapper-0.3.0 branch November 20, 2019 17:02

inodb added the feature label Nov 29, 2019

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Upgraded react-mutation-mapper version to 0.3.0 #2706

Upgraded react-mutation-mapper version to 0.3.0 #2706

onursumer commented Sep 17, 2019 •

edited

onursumer Sep 19, 2019

onursumer Sep 19, 2019

onursumer Sep 19, 2019

alisman commented Oct 4, 2019

onursumer commented Oct 17, 2019

alisman Nov 18, 2019

onursumer Nov 19, 2019

alisman Nov 18, 2019

onursumer Nov 19, 2019

Upgraded react-mutation-mapper version to 0.3.0 #2706

Upgraded react-mutation-mapper version to 0.3.0 #2706

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onursumer commented Sep 17, 2019 • edited

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onursumer commented Sep 17, 2019 •

edited