mutational signature feature

.prettierignore

@@ -27,3 +27,4 @@ yarn.lock
 .gitignore
 .kodiak.toml
 *.seg
+end-to-end-test/local/studies/**

end-to-end-test/local/specs/core/patientview.screenshot.spec.js

@@ -10,6 +10,9 @@ const patientViewUrl =
     CBIOPORTAL_URL + '/patient?studyId=teststudy_genepanels&caseId=patientA';
 const ascnPatientViewUrl =
     CBIOPORTAL_URL + '/patient?studyId=ascn_test_study&caseId=FAKE_P001';
+const genericAssayPatientViewUrl =
+    CBIOPORTAL_URL +
+    '/patient?studyId=lgg_ucsf_2014_test_generic_assay&sampleId=P01_Pri';
 
 describe('patient view page', function() {
     describe('mutation table for study with ASCN data', () => {
@@ -74,6 +77,60 @@ describe('patient view page', function() {
             doVafPlotScreenshotTest();
         });
     });
+
+    describe('patient view mutational signatures', () => {
+        beforeEach(() => {
+            goToUrlAndSetLocalStorage(genericAssayPatientViewUrl);
+            waitForPatientView();
+            browser.waitForVisible('a.tabAnchor_mutationalSignatures', 20000);
+            browser.click('a.tabAnchor_mutationalSignatures');
+            browser.waitForVisible(
+                'div[data-test="MutationalSignaturesContainer"]',
+                20000
+            );
+        });
+
+        it('show stacked bar chart for patient who has significant v2 significant signatures', () => {
+            browser.waitForVisible('div.patientSamples', 20000);
+            var res = browser.checkElement('div.patientSamples');
+            assertScreenShotMatch(res);
+        });
+
+        it('show tooltip for patient who has significant v2 significant signatures', () => {
+            browser.waitForVisible('div.progress', 20000);
+            browser.moveToObject('div.progress', 0, 0);
+            assertScreenShotMatch(browser.checkElement('div.patientViewPage'));
+        });
+
+        it('show mutational signatures table for patient who has significant v2 significant signatures', () => {
+            var res = browser.checkElement(
+                'div[data-test="MutationalSignaturesContainer"]'
+            );
+            assertScreenShotMatch(res);
+        });
+
+        it('show stacked bar chart for patient who has significant v3 significant signatures', () => {
+            selectMutationalSignaturesVersion3();
+            browser.waitForVisible('div.patientSamples', 20000);
+            var res = browser.checkElement('div.patientSamples');
+            assertScreenShotMatch(res);
+        });
+
+        it('show tooltip for patient who has significant v3 significant signatures', () => {
+            selectMutationalSignaturesVersion3();
+            browser.waitForVisible('div.progress', 20000);
+            browser.moveToObject('div.progress', 0, 0);
+            assertScreenShotMatch(browser.checkElement('div.patientViewPage'));
+        });
+
+        it('show mutational signatures table for patient who has significant v3 significant signatures', () => {
+            selectMutationalSignaturesVersion3();
+            var res = browser.checkElement(
+                'div[data-test="MutationalSignaturesContainer"]'
+            );
+            assertScreenShotMatch(res);
+        });
+    });
 });
 
 const switchGeneFilter = selectedOption => {
@@ -95,3 +152,13 @@ const doVafPlotScreenshotTest = () => {
     res = browser.checkElement('div[role=tooltip] [data-test=vaf-plot]'); // grabs the full plot
     assertScreenShotMatch(res);
 };
+
+const selectMutationalSignaturesVersion3 = () => {
+    browser.waitForVisible(
+        'div.mutationalSignaturesVersionSelector__indicators',
+        10000
+    );
+    browser.click('div.mutationalSignaturesVersionSelector__indicators');
+    browser.waitForVisible('div=Mutational Signature V3', 10000);
+    browser.click('div=Mutational Signature V3');
+};

end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/LICENSE

@@ -0,0 +1 @@
+The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license.

end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/case_lists/cases_all.txt

@@ -0,0 +1,6 @@
+cancer_study_identifier: lgg_ucsf_2014_test_generic_assay
+stable_id: lgg_ucsf_2014_test_generic_assay_all
+case_list_name: All samples
+case_list_description: All samples (61 samples)
+case_list_category: all_cases_in_study
+case_list_ids: P17_Pri_B	P17_Pri_C	P28_Rec	P17_Pri_A	P13_Rec	P07_Rec	P26_Pri_B	P26_Pri_A	P18_Pri_A	P18_Pri_C	P18_Pri_B	P18_Pri_D	P02_Pri	P16_Rec	P11_Rec	P01_Pri	P26_Rec1_B	P26_Rec1_A	P24_Rec2	P05_Pri	P08_Pri	P27_Pri_A	P24_Rec1	P12_Rec	P25_Pri	P29_Pri	P07_Pri	P06_Rec	P15_Pri	P27_Rec1_A	P11_Pri	P17_Rec1_A	P28_Pri	P04_Rec1	P04_Pri	P04_Rec3	P04_Rec2	P09_Rec	P10_Rec	P24_Pri	P25_Rec	P21_Rec	P27_Rec1_B	P29_Rec	P05_Rec	P02_Rec	P13_Pri	P18_Rec	P08_Rec	P16_Pri	P12_Pri	P09_Pri	P21_Pri	P01_Rec	P10_Pri	P27_Pri_B	P17_Rec1_C	P17_Rec1_B	P15_Rec	P06_Pri	P17_Rec1_D

end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/case_lists/cases_sequenced.txt

@@ -0,0 +1,6 @@
+cancer_study_identifier: lgg_ucsf_2014_test_generic_assay
+stable_id: lgg_ucsf_2014_test_generic_assay_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data (61 samples)
+case_list_category: all_cases_with_mutation_data
+case_list_ids: P17_Pri_B	P17_Pri_C	P17_Pri_A	P09_Pri	P21_Rec	P26_Pri_B	P26_Pri_A	P18_Pri_A	P18_Pri_C	P18_Pri_B	P18_Pri_D	P02_Pri	P16_Rec	P11_Rec	P17_Rec1_B	P01_Pri	P26_Rec1_B	P26_Rec1_A	P01_Rec	P05_Pri	P08_Pri	P27_Pri_A	P10_Pri	P05_Rec	P12_Rec	P25_Pri	P02_Rec	P07_Pri	P06_Rec	P15_Pri	P28_Pri	P04_Rec1	P04_Pri	P04_Rec3	P04_Rec2	P09_Rec	P07_Rec	P10_Rec	P21_Pri	P24_Pri	P15_Rec	P25_Rec	P11_Pri	P08_Rec	P29_Rec	P27_Rec1_B	P29_Pri	P13_Pri	P18_Rec	P12_Pri	P16_Pri	P13_Rec	P28_Rec	P24_Rec2	P24_Rec1	P27_Pri_B	P17_Rec1_C	P27_Rec1_A	P17_Rec1_A	P06_Pri	P17_Rec1_D

end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_clinical_patient.txt

@@ -0,0 +1,28 @@
+#Patient Identifier	Sex	Diagnosis Age	Overall Survival (Months)	Overall Survival Status
+#Identifier to uniquely specify a patient.	Sex	Age at which a condition or disease was first diagnosed.	Overall survival in months since initial diagonosis.	Overall patient survival status.
+#STRING	STRING	NUMBER	NUMBER	STRING
+#1	1	1	1	9
+PATIENT_ID	SEX	AGE	OS_MONTHS	OS_STATUS
+P01	Male	28	58	1:DECEASED
+P02	Female	26	5	
+P04	Male	22	61	1:DECEASED
+P05	Female	39	74	1:DECEASED
+P06	Male	22	87	1:DECEASED
+P07	Male	30	148	1:DECEASED
+P08	Male	44	103	1:DECEASED
+P09	Male	28	45	1:DECEASED
+P10	Female	41	44	1:DECEASED
+P11	Female	30	186	1:DECEASED
+P12	Male	35	82	0:LIVING
+P13	Male	24	106	1:DECEASED
+P15	Female	38	143	0:LIVING
+P16	Female	35	38	1:DECEASED
+P17	Male	27	59	0:LIVING
+P18	Male	49	106	0:LIVING
+P21	Male	27	35	1:DECEASED
+P24	Male	34	109	1:DECEASED
+P25	Male	39	42	0:LIVING
+P26	Female	36	47	0:LIVING
+P27	Male	56	54	0:LIVING
+P28	Male	30	137	0:LIVING
+P29	Male	52	109	1:DECEASED

end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_clinical_sample.txt

@@ -0,0 +1,66 @@
+#Patient Identifier	Sample Identifier	Sample Type	Oncotree Code	Neoplasm Histologic Grade	MGMT Status	IDH1 Mutation	1p/19q Status	Non-silent mutations in TP53, ATRX, CIC, FUBP1	Note	Cancer Type	Cancer Type Detailed	Somatic Status
+#Identifier to uniquely specify a patient.	A unique sample identifier.	The type of sample (i.e., normal, primary, met, recurrence).	Oncotree Code	Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.	MGMT Status	IDH1 mutation is present	1p/19q Status	Non-silent mutations in TP53, ATRX, CIC, FUBP1	Note.	Cancer Type	Cancer Type Detailed	Somatic Status
+#STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING	STRING
+#1	1	9	1	1	1	1	1	1	1	1	1	1
+PATIENT_ID	SAMPLE_ID	SAMPLE_TYPE	ONCOTREE_CODE	GRADE	MGMT_STATUS	IDH1_MUTATION	STATUS_1P_19Q	NON_SILENT_MUT_TP53_ATRX_CIC_FUBP1	NOTE	CANCER_TYPE	CANCER_TYPE_DETAILED	SOMATIC_STATUS
+P01	P01_Pri	Primary	ASTR	II	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P01	P01_Rec	Recurrent	GB	IV	Methylated	R132H	19q deletion	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P02	P02_Pri	Primary	OAST	II	Methylated	R132H	19q deletion	TP53	Patient lost follow up	Glioma	Oligoastrocytoma	Matched
+P02	P02_Rec	Recurrent	AASTR	III	Unmethylated	R132H	19q deletion	TP53	Patient lost follow up	Glioma	Anaplastic Astrocytoma	Matched
+P04	P04_Pri	Primary	ASTR	II	Unknown	R132C	Intact	TP53	NA	Glioma	Astrocytoma	Matched
+P04	P04_Rec1	Recurrent	AASTR	III	Unknown	R132C	Intact	TP53	NA	Glioma	Anaplastic Astrocytoma	Matched
+P04	P04_Rec2	Recurrent	AASTR	III	Unknown	R132C	Intact	TP53	NA	Glioma	Anaplastic Astrocytoma	Matched
+P04	P04_Rec3	Recurrent	AASTR	III	Unknown	R132C	Intact	TP53	NA	Glioma	Anaplastic Astrocytoma	Matched
+P05	P05_Pri	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P05	P05_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P06	P06_Pri	Primary	ASTR	II	Unmethylated	R132H	Intact	NA	NA	Glioma	Astrocytoma	Matched
+P06	P06_Rec	Recurrent	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P07	P07_Pri	Primary	ASTR	II	Unknown	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P07	P07_Rec	Recurrent	ASTR	II	Unknown	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P08	P08_Pri	Primary	OAST	II	Unknown	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P08	P08_Rec	Recurrent	GB	IV	Unknown	R132H	19q deletion	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P09	P09_Pri	Primary	ASTR	II	Methylated	R132H	Intact	TP53	NA	Glioma	Astrocytoma	Matched
+P09	P09_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	TP53	NA	Glioma	Glioblastoma	Matched
+P10	P10_Pri	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P10	P10_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P11	P11_Pri	Primary	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P11	P11_Rec	Recurrent	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P12	P12_Pri	Primary	ASTR	II	Unknown	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P12	P12_Rec	Recurrent	AASTR	III	Unknown	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P13	P13_Pri	Primary	OAST	II	Unmethylated	R132G	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P13	P13_Rec	Recurrent	OAST	II	Unmethylated	R132G	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P15	P15_Pri	Primary	OAST	II	Unknown	R132H	Co-deletion	NA	NA	Glioma	Oligoastrocytoma	Matched
+P15	P15_Rec	Recurrent	OAST	II	Unknown	R132H	Co-deletion	CIC	NA	Glioma	Oligoastrocytoma	Matched
+P16	P16_Pri	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P16	P16_Rec	Recurrent	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P17	P17_Pri_A	Primary	ODG	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligodendroglioma	Matched
+P17	P17_Pri_B	Primary	ODG	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligodendroglioma	Matched
+P17	P17_Pri_C	Primary	ODG	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligodendroglioma	Matched
+P17	P17_Rec1_A	Recurrent	GB	IV	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P17	P17_Rec1_B	Recurrent	GB	IV	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P17	P17_Rec1_C	Recurrent	GB	IV	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P17	P17_Rec1_D	Recurrent	GB	IV	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P18	P18_Pri_A	Primary	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P18	P18_Pri_B	Primary	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P18	P18_Pri_C	Primary	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P18	P18_Pri_D	Primary	OAST	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P18	P18_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P21	P21_Pri	Primary	OAST	II	Methylated	R132H	19q deletion	TP53, ATRX	NA	Glioma	Oligoastrocytoma	Matched
+P21	P21_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P24	P24_Pri	Primary	ASTR	II	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P24	P24_Rec1	Recurrent	ASTR	II	Unmethylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P24	P24_Rec2	Recurrent	GB	IV	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Glioblastoma	Matched
+P25	P25_Pri	Primary	ASTR	II	Methylated	R132H	Intact	ATRX	NA	Glioma	Astrocytoma	Matched
+P25	P25_Rec	Recurrent	GB	IV	Methylated	R132H	Intact	ATRX	NA	Glioma	Glioblastoma	Matched
+P26	P26_Pri_A	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P26	P26_Pri_B	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P26	P26_Rec1_A	Recurrent	AASTR	III	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P26	P26_Rec1_B	Recurrent	AASTR	III	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P27	P27_Pri_A	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P27	P27_Pri_B	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P27	P27_Rec1_A	Recurrent	AASTR	III	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P27	P27_Rec1_B	Recurrent	AASTR	III	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P28	P28_Pri	Primary	ASTR	II	Methylated	R132H	19q deletion	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P28	P28_Rec	Recurrent	AASTR	III	Methylated	R132H	19q deletion	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched
+P29	P29_Pri	Primary	ASTR	II	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Astrocytoma	Matched
+P29	P29_Rec	Recurrent	AASTR	III	Methylated	R132H	Intact	TP53, ATRX	NA	Glioma	Anaplastic Astrocytoma	Matched