Release 1.13.0 #1163
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Release 1.13.0 #1163
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Point to http://www.cbioportal.org/rc https://www.genomenexus.org We're using beta for testing release-1.12.0
e2e tests should not fail when no error.js present (use rm -rf)
Release to rc
Register callbacks to enable expansion options in the track menu of gene set heatmap tracks in the Oncoprint. When these are clicked, retrieve the list of correlated genes for the gene set and render these tracks as the expansions of the gene set tracks. Tweak the colour of the gene set tracks' labels in order to clearly distinguish them from gene tracks in the same group. This is a rewrite of the functionality originally reviewed in a pull request in early May 2017, using the functionality I later ported to the OncoprintJS library from that pull request.
The association of a gene set heatmap track with its expansions should not change when the heatmap moves to a differently numbered track group.
When re-rendering the gene set heatmap into a different track group to make room for other heatmaps, I did not update the expansions in the OncoprintJS state, causing erratic behaviour. Updating this state fixes the issue.
To clarify that one only functions as the input to the other, pass it as an argument rather than exposing it as a public property.
This prevents error messages and a crash in some browsers when a clustered gene set heatmap with expansion tracks has to move down for other heatmaps.
The .reset() method updated the iteration synchronously, while .next() only scheduled an update in a promise callback. Update the index in the order in which the methods are called by chaining all updates onto a single promise chain.
Expand correlated genes from gene set heatmaps
And remove references to window.oql_parser Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Expose OQL.genes to window
Show virtual study description gracefully
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org> Conflicts: end-to-end-tests/screenshots/reference/msk_impact_2017_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png end-to-end-tests/screenshots/reference/msk_impact_2017_with_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png package-lock.json package.json src/pages/resultsView/ResultsViewPageStore.ts src/pages/resultsView/ResultsViewPageStoreUtils.ts src/shared/components/oncoprint/geneticrules.ts
….13.0 Merge master to release 1.13.0
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Fix errors in release-1.13.0
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Fix release-1.13.0
Show samples count in case set when multi-studies or VS is selected
Internally germline is indicated as GERMLINE instead of Germline. Enable case insensitive matching.
Signed-off-by: Hongxin Zhang <hongxin@cbio.mskcc.org>
Fix oncoprint germline display for internal mskimpact
Increase the allowance for multi-studies view to 50 studies
Merge master to release 1.13.0
Conflicts: end-to-end-tests/screenshots/reference/download_tab_-_msk_impact_2017_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png end-to-end-tests/screenshots/reference/hcc_inserm_fr_2015_with_genes_including_tert_-_it_should_show_orange_promoter_mutations_in_tert_element_chrome_1600x1000.png end-to-end-tests/screenshots/reference/no_session_render_the_oncoprint_element_chrome_1600x1000.png end-to-end-tests/screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png end-to-end-tests/specs/home.spec.js
Signed-off-by: Hongxin Zhang <hongxin@cbio.mskcc.org>
Merge master to release 1.13.0
adamabeshouse
approved these changes
May 10, 2018
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