Fusion sv migration (#3358)

Frontend changes to use structure_variant able over mutations table for fusions ### Impacted pages #### Query page - Structural variant/Fusion profile is shown if the study has it - For multi-study selection: new molecular profile checkbox for structural variants #### Study view page - Rename fusion table to structural variant table #### Results page - Oncoprint tab - Rename fusion to structural variant - New track for fusion/structural variant profiled cases - Plots tab - Structural variants are shown as a new Data Type/selector - Comparison tab/alterations - no visual changes - Downloads tab #### Patient view page - All fusions in mutation table should be in new structural variants table Commits: * Migrate from fusions to sv in study-view * Add structural variant table in patient page * Migrate fusion to structural variant in oncoprint * Support structural variants in cancer summary and download tabs * Support structural variant profile in result page plots tab * Add structural variant enrichments analysis tab * Structural variant coloring in plots tab * update expression tab to use new code * plots tab refactoring * Fix sort order - structural variant goes on top of CNA, and show message indicating that * Update molecular profile filter parameter in query and results page * Fix error from merging master and failing e2e * Fix how unprofiled cna and unprofiled sv are handled in plots tab scatter plot annotation * Fix plots bug causing too-thick stroke width * Fix plots bug with cna and sv in legend when there is no cna or sv data * Fix issues in plots tab relating to structural variant migration * Fix bug in plots tab and fix e2e tests * SV: do not invoke api's if all samples are filtered out * Fix issues arising from mobx upgrade * Fix plots tab opacity issue * Use same color for stroke and fill in waterfall plot * Fix error selecting geneset profile and other e2e local tests * Alteration Enrichments: avoid sending duplicate sample during api query * SV table: show profiled samples count * Incude structural variants in VUS * Study page: fix SV table column width * Add tumor type to sv objects while invoking oncokb api * Update failing e2e tests * Regenerate api client files * Fix appearance of not-profiled-for-cna-and-sv * Fix bug in plots relating to not-profiled-for-cna-and-sv * Update failing e2e tests * Change color for not-profiled-for-cna-and-sv to match current production * Update localdb e2e tests * Fix condition for invoking alteration enrichment api * Set mutationType to fusion for structural variants * Fix group size in mini-oncoprint in alterations enrichment tab * Fix oncokb lookup issue for structural variants * Support old FUSION_GENES_TABLE from user settings * Update failing e2e test image * Update protein display name in mutation-mapper Co-authored-by: Adam Abeshouse <[email protected]> Co-authored-by: Adam Abeshouse <[email protected]> Former-commit-id: eefd23507ca721c863409dd8e8d43dedbec55ca6
cBioPortal · Apr 20, 2021 · ac0ea38 · ac0ea38
1 parent eb447ae
commit ac0ea38
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diff --git a/.prettierignore b/.prettierignore
@@ -29,4 +29,5 @@ yarn.lock
 *properties
 *.seg
 end-to-end-test/local/studies/**
-*.screenshottest
+*.screenshottest
+*.jks
diff --git a/end-to-end-test/local/specs/core/plotstab.spec.js b/end-to-end-test/local/specs/core/plotstab.spec.js
@@ -38,13 +38,13 @@ describe('plots tab', function() {
                 assert($('div.coloring-menu').isExisting());
                 assert(
                     $('div.coloring-menu').$$('input[type="checkbox"]')
-                        .length === 2
+                        .length === 3
                 );
             });
 
             it('shows mutation and copy number by default', () => {
                 loadPlotsTab(
-                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib`
+                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A6205%2C"dataType"%3A"TREATMENT_RESPONSE"%7D&plots_coloring_selection=%7B%7D&profileFilter=0`
                 );
                 selectTreatmentProfile();
                 const res = browser.checkElement('[id=plots-tab-plot-svg]');
@@ -53,7 +53,7 @@ describe('plots tab', function() {
 
             it('shows only mutation types when copy number is de-selected', () => {
                 loadPlotsTab(
-                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib`
+                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A6205%2C"dataType"%3A"TREATMENT_RESPONSE"%7D&plots_coloring_selection=%7B"colorByCopyNumber"%3A"false"%2C"colorBySv"%3A"false"%7D&profileFilter=0`
                 );
                 selectTreatmentProfile();
                 $('input[data-test="ViewCopyNumber"]').click();
@@ -63,7 +63,7 @@ describe('plots tab', function() {
 
             it('shows only CNA types when mutation checkbox is deselected', () => {
                 loadPlotsTab(
-                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib`
+                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A6205%2C"dataType"%3A"TREATMENT_RESPONSE"%7D&plots_coloring_selection=%7B"colorByMutationType"%3A"false"%2C"colorBySv"%3A"false"%7D&profileFilter=0`
                 );
                 selectTreatmentProfile();
                 $('input[data-test="ViewMutationType"]').click();
@@ -73,7 +73,7 @@ describe('plots tab', function() {
 
             it('removes sample stylings when selecting None in gene selection box', () => {
                 loadPlotsTab(
-                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib`
+                    `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic%2CPROFILED_IN_study_es_0_mrna_median_Zscores&data_priority=0&gene_list=RPS11&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=study_es_0_mrna_median_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&heatmap_track_groups=study_es_0_treatment_ic50%2CErlotinib&show_samples=false&tab_index=tab_visualize&treatment_list=Erlotinib&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"dataType"%3A"TREATMENT_RESPONSE"%7D&plots_coloring_selection=%7B"selectedOption"%3A"6205_undefined"%7D&profileFilter=0`
                 );
                 selectTreatmentProfile();
                 $('.gene-select').click();

diff --git a/end-to-end-test/local/specs/treatment.spec.js b/end-to-end-test/local/specs/treatment.spec.js
@@ -410,6 +410,7 @@ describe('treatment feature', function() {
                     })
                 );
 
+                $('[data-test=ViewLimitValues]').waitForExist();
                 assert($('[data-test=ViewLimitValues]').isVisible());
             });
 
@@ -436,6 +437,7 @@ describe('treatment feature', function() {
                     })
                 );
 
+                $('[data-test=ViewLimitValues]').waitForExist();
                 assert($('[data-test=ViewLimitValues]').isVisible());
             });
 

diff --git a/end-to-end-test/remote/specs/core/home.spec.js b/end-to-end-test/remote/specs/core/home.spec.js
@@ -290,7 +290,7 @@ describe('case set selection in front page query form', function() {
         clickQueryByGeneButton();
 
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
             10000
         );
 
@@ -356,11 +356,11 @@ describe('case set selection in front page query form', function() {
         clickQueryByGeneButton();
 
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
             10000
         );
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="cna-gistic-cna_rae-cna_consensus"]',
             10000
         );
         browser.waitForExist(selectedCaseSet_sel, 10000);
@@ -388,11 +388,11 @@ describe('case set selection in front page query form', function() {
         clickQueryByGeneButton();
 
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
             10000
         );
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]',
             10000
         );
         browser.waitForExist(selectedCaseSet_sel, 10000);
@@ -485,22 +485,22 @@ describe('genetic profile selection in front page query form', () => {
 
         // wait for data type priority selector to load
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
             10000
         );
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]',
             10000
         );
         assert(
             browser.isSelected(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]'
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]'
             ),
             "'Mutation' should be selected"
         );
         assert(
             browser.isSelected(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]'
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]'
             ),
             "'Copy number alterations' should be selected"
         );
@@ -551,22 +551,22 @@ describe('genetic profile selection in front page query form', () => {
 
         // wait for data type priority selector to load
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
             10000
         );
         browser.waitForExist(
-            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]',
+            '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]',
             10000
         );
         assert(
             browser.isSelected(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]'
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]'
             ),
             "'Mutation' should be selected"
         );
         assert(
             browser.isSelected(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]'
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]'
             ),
             "'Copy number alterations' should be selected"
         );
@@ -669,21 +669,17 @@ describe('auto-selecting needed profiles for oql in query form', () => {
         // wait for query to load
         waitForOncoprint(20000);
 
-        const query = browser.execute(function() {
-            return urlWrapper.query;
-        }).value;
+        const profileFilter = (
+            browser.execute(function() {
+                return urlWrapper.query;
+            }).value.profileFilter || ''
+        ).split(',');
         // mutation, cna, mrna profiles are there
+        assert.equal(profileFilter.includes('mutations'), true);
+        assert.equal(profileFilter.includes('gistic'), true);
         assert.equal(
-            query.genetic_profile_ids_PROFILE_MUTATION_EXTENDED,
-            'prad_tcga_pub_mutations'
-        );
-        assert.equal(
-            query.genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION,
-            'prad_tcga_pub_gistic'
-        );
-        assert.equal(
-            query.genetic_profile_ids_PROFILE_MRNA_EXPRESSION,
-            'prad_tcga_pub_rna_seq_v2_mrna_median_Zscores'
+            profileFilter.includes('rna_seq_v2_mrna_median_Zscores'),
+            true
         );
     });
 });
@@ -760,20 +756,17 @@ describe('results page quick oql edit', () => {
         waitForOncoprint(20000);
 
         // mutation, cna, mrna profiles are there
-        query = browser.execute(function() {
-            return urlWrapper.query;
-        }).value;
-        assert.equal(
-            query.genetic_profile_ids_PROFILE_MUTATION_EXTENDED,
-            'prad_tcga_pub_mutations'
-        );
-        assert.equal(
-            query.genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION,
-            'prad_tcga_pub_gistic'
-        );
+        let profileFilter = (
+            browser.execute(function() {
+                return urlWrapper.query;
+            }).value.profileFilter || ''
+        ).split(',');
+        // mutation, cna, mrna profiles are there
+        assert.equal(profileFilter.includes('mutations'), true);
+        assert.equal(profileFilter.includes('gistic'), true);
         assert.equal(
-            query.genetic_profile_ids_PROFILE_MRNA_EXPRESSION,
-            'prad_tcga_pub_rna_seq_v2_mrna_median_Zscores'
+            profileFilter.includes('rna_seq_v2_mrna_median_Zscores'),
+            true
         );
     });
 });
diff --git a/end-to-end-test/remote/specs/core/oncoprint.spec.js b/end-to-end-test/remote/specs/core/oncoprint.spec.js
@@ -556,11 +556,11 @@ describe('oncoprint', function() {
             clickQueryByGeneButton();
 
             browser.waitForExist(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="M"]',
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="mutations"]',
                 10000
             );
             browser.waitForExist(
-                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="C"]',
+                '[data-test="dataTypePrioritySelector"] input[type="checkbox"][data-test="gistic"]',
                 10000
             );
 

diff --git a/end-to-end-test/remote/specs/core/plots.screenshot.spec.js b/end-to-end-test/remote/specs/core/plots.screenshot.spec.js
@@ -457,6 +457,12 @@ describe('plots tab screenshot tests', function() {
         browser.click('.coloringLogScale');
         waitForAndCheckPlotsTab();
     });
+    it('plots tab with structural variant coloring', () => {
+        goToUrlAndSetLocalStorage(
+            `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=prad_mich&case_set_id=prad_mich_cna_seq&data_priority=0&gene_list=ERG&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=prad_mich_cna&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=prad_mich_mutations&genetic_profile_ids_PROFILE_STRUCTURAL_VARIANT=prad_mich_fusion&plots_coloring_selection=%7B"colorByCopyNumber"%3A"true"%2C"colorBySv"%3A"true"%7D&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A2078%2C"dataType"%3A"COPY_NUMBER_ALTERATION"%7D&profileFilter=0&tab_index=tab_visualize`
+        );
+        waitForAndCheckPlotsTab();
+    });
 });
 
 describe('plots tab multiple studies screenshot tests', function() {
-Original file line number
+Diff line change
@@ Expand Up / @@ -410,6 +410,7 @@ describe('treatment feature', function() { @@
                         })
                     );
+                    $('[data-test=ViewLimitValues]').waitForExist();
                     assert($('[data-test=ViewLimitValues]').isVisible());
                 });
@@ Expand All / @@ -436,6 +437,7 @@ describe('treatment feature', function() { @@
                         })
                     );
+                    $('[data-test=ViewLimitValues]').waitForExist();
                     assert($('[data-test=ViewLimitValues]').isVisible());
                 });
@@ Expand Down @@