completely removed PdbAnnotation API dependency (fix cBioPortal/cbiop…

…ortal#3159)

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

end-to-end-tests/specs/results.spec.js

@@ -132,6 +132,29 @@ describe('Results Page', function() {
 
     });
 
+    describe("Mutations Tab", () => {
+
+        describe('3D structure visualizer', () => {
+            before(() => {
+                var url = `${CBIOPORTAL_URL}/index.do?tab_index=tab_visualize&cancer_study_list=ov_tcga_pub&cancer_study_id=ov_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ov_tcga_pub_mutations&Z_SCORE_THRESHOLD=2.0&case_set_id=ov_tcga_pub_3way_complete&case_ids=&gene_list=BRCA1+BRCA2&gene_set_choice=user-defined-list&Action=Submit`;
+                browser.url(url);
+                browser.click("[href='#mutation_details']");
+                browser.waitForEnabled('[data-test=view3DStructure]', 10000);
+            });
+
+            it('populates PDB info properly', () => {
+                browser.click('[data-test=view3DStructure]');
+                browser.waitUntil(() => (browser.getText('[data-test=pdbChainInfoText]') !== "LOADING"), 10000);
+
+                var text = browser.getText('[data-test="pdbChainInfoText"]')[0].trim();
+                // text might be truncated depending on the actual browser, so using startsWith instead
+                assert.ok(text.startsWith('complex structure of brca1 brct with singly'));
+            });
+
+        });
+
+    });
+
 });
 
 

package.json

@@ -16,9 +16,6 @@
     "updateOncoKbAPI": "npm run fetchOncoKbAPI && npm run buildOncoKbAPI",
     "fetchOncoKbAPI": "curl http://oncokb.org/api/v1/v2/api-docs | json > src/shared/api/generated/OncoKbAPI-docs.json",
     "buildOncoKbAPI": "node scripts/generate-api.js src/shared/api/generated OncoKbAPI",
-    "updatePdbAnnotationAPI": "npm run fetchPdbAnnotationAPI && npm run buildPdbAnnotationAPI",
-    "fetchPdbAnnotationAPI": "curl https://cbioportal.mskcc.org/pdb-annotation/v2/api-docs?group=pdb_annotation | json > src/shared/api/generated/PdbAnnotationAPI-docs.json",
-    "buildPdbAnnotationAPI": "node scripts/generate-api.js src/shared/api/generated PdbAnnotationAPI",
     "updateG2SAPI": "npm run fetchG2SAPI && npm run buildG2SAPI",
     "fetchG2SAPI": "curl http://g2s.genomenexus.org/v2/api-docs?group=api > src/shared/api/generated/Genome2StructureAPI-docs.json",
     "buildG2SAPI": "node scripts/generate-api.js src/shared/api/generated Genome2StructureAPI",

src/pages/resultsView/mutation/MutationMapperStore.ts

@@ -10,7 +10,6 @@ import {IOncoKbData, IOncoKbDataWrapper} from "shared/model/OncoKB";
 import {IHotspotIndex} from "shared/model/CancerHotspots";
 import {IPdbChain, PdbAlignmentIndex} from "shared/model/Pdb";
 import {ICivicGene, ICivicVariant} from "shared/model/Civic";
-import PdbPositionMappingCache from "shared/cache/PdbPositionMappingCache";
 import ResidueMappingCache from "shared/cache/ResidueMappingCache";
 import {calcPdbIdNumericalValue, mergeIndexedPdbAlignments} from "shared/lib/PdbUtils";
 import {lazyMobXTableSort} from "shared/components/lazyMobXTable/LazyMobXTable";
@@ -244,11 +243,6 @@ export class MutationMapperStore {
         return new PdbChainDataStore(this.sortedMergedAlignmentData);
     }
 
-    @cached get pdbPositionMappingCache()
-    {
-        return new PdbPositionMappingCache();
-    }
-
     @cached get residueMappingCache()
     {
         return new ResidueMappingCache();