merging in master

.github/workflows/main.yml

@@ -0,0 +1,41 @@
+name: Cypress tests
+on: [push]
+jobs:
+  cypress-run:
+    name: Cypress run
+    runs-on: ubuntu-16.04
+    strategy:
+      matrix:
+        # the actual items in the array do not matter,
+        # just the number - to force CI to sping 3 copies
+        # of the current job in parallel
+        machines: [1, 2, 3]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+
+      - name: Cypress run
+        uses: cypress-io/github-action@v2
+        with:
+          record: true
+          parallel: true
+          start: yarn start
+          wait-on: http://localhost:3344
+        env:
+          WITH_COVERAGE: true
+          # pass the Dashboard record key as an environment variable
+          CYPRESS_RECORD_KEY: 0dcf0c08-68ce-4547-aaaa-ac33af76e4a9
+          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Upload coverage to Codecov
+        if: always()
+        uses: codecov/codecov-action@v1
+        with:
+          directory: ./coverage/
+          name: codecov-umbrella
+          # fail_ci_if_error: true
+          path_to_write_report: ./coverage/codecov_report.gz
+      # - name: Upload coverage result
+      #   uses: actions/upload-artifact@v2
+      #   with:
+      #     name: cypress-coverage
+      #     path: coverage

.gitignore

@@ -10,4 +10,5 @@ npm-debug.log*
 /cypress/screenshots
 .linkEnv
 .idea
-.DS_Store
+.DS_Store
+.nyc_output

cypress/integration/alignment.spec.js

@@ -1,26 +1,126 @@
-describe("editor", function() {
-  beforeEach(() => {
+describe("editor", function () {
+  it("adding selection right click options should work", function () {
     cy.visit("#/Alignment");
+    cy.tgToggle("addSelectionRightClickOptions");
+    cy.selectAlignmentRange(10, 20);
+    cy.get(".veAlignmentSelectionLayer:first").rightclick({ force: true });
+    cy.contains(".bp3-menu-item", "I'm an additional option").click();
+    cy.contains(".bp3-toast", "You did it");
+  });
+  it("overriding right click options should work", function () {
+    cy.visit("#/Alignment");
+    cy.tgToggle("overrideSelectionRightClick");
+    cy.selectAlignmentRange(10, 20);
+    cy.get(".veAlignmentSelectionLayer:first").rightclick({ force: true });
+    cy.contains(".bp3-toast", "lezzz goooo!");
+  });
+  it("selection right click options should work and the additionalTopEl should be visible", function () {
+    cy.visit("#/Alignment");
+    cy.contains("Additional Top El");
+    cy.selectAlignmentRange(10, 20);
+    cy.get(".veAlignmentSelectionLayer:first").rightclick({ force: true });
+    cy.contains(".bp3-menu-item", "Copy Selection of F05225 as Fasta");
+    cy.contains(".bp3-menu-item", "Copy Selection of All Alignments ").click();
+    cy.contains(".bp3-toast", "Selection Copied");
   });
 
-  it("can drag the alignment", function() {
-    cy.get(".veRowViewSelectionLayer")
-      .first()
-      .should("not.be.visible");
-
-    cy.tgToggle("isFullyZoomedOut");
-    cy.contains("text", "355")
+  it("dragging in the alignment should only allow non-origin wrapping selections", function () {
+    cy.visit("#/Alignment");
+    cy.scrollAlignmentToPercent(0.0257);
+    cy.contains(`[data-alignment-track-index="1"] text`, 100).click();
+    cy.get("body").type("{shift}", { release: false });
+    cy.contains(`[data-alignment-track-index="1"] text`, 110).click();
+    cy.get(`[title="Selecting 10 bps from 101 to 110"]`);
+    cy.get(`[title="Caret Between Bases 100 and 101"]`)
       .first()
-      .then(el => {
-        cy.contains("text", "710")
+      .then((el) => {
+        cy.contains(`[data-alignment-track-index="1"] text`, 120)
           .first()
-          .then(el2 => {
-            cy.dragBetween(el, el2);
+          .then((el2) => {
+            cy.dragBetweenSimple(el, el2);
           });
       });
-    cy.get(".veRowViewSelectionLayer")
-      .first()
-      .should("be.visible");
+    cy.get(`[title="Selecting 11 bps from 111 to 121"]`);
+    cy.get(`[title="Caret Between Bases 121 and 122"]`).then((el) => {
+      cy.contains(`[data-alignment-track-index="1"] text`, 100)
+        .first()
+        .then((el2) => {
+          cy.dragBetweenSimple(el, el2);
+        });
+    });
+    cy.get(`[title="Selecting 10 bps from 101 to 110"]`);
+  });
+  it("shift clicking in the alignment should only allow non-origin wrapping selections (no selection present)", function () {
+    cy.visit("#/Alignment");
+    cy.contains(`[data-alignment-track-index="1"] text`, 10).click();
+    cy.get("body").type("{shift}", { release: false });
+    cy.scrollAlignmentToPercent(0.99);
+    cy.contains(`[data-alignment-track-index="1"] text`, 3510).click();
+    cy.get(`[title="Selecting 3500 bps from 11 to 3510"]`);
+  });
+  it("the alignment should show axis numbers correctly", function () {
+    cy.visit("#/Alignment?alignmentDataId=39");
+
+    cy.scrollAlignmentToPercent(0.3);
+    cy.contains(`[data-alignment-track-index="5"] .veAxis`, "290");
+    cy.contains(`[data-alignment-track-index="5"] .veAxis`, "300");
+    cy.contains(`[data-alignment-track-index="5"] .veAxis`, "310");
+  });
+  it("shift clicking in the alignment should only allow non-origin wrapping selections (with a selection already present)", function () {
+    cy.visit("#/Alignment");
+    // cy.tgToggle("isFullyZoomedOut");
+    cy.get(`[data-alignment-track-index="1"]`);
+    cy.selectAlignmentRange(56, 67);
+
+    cy.get("body").type("{shift}", { release: false });
+    cy.scrollAlignmentToPercent(0.99);
+    cy.contains(`[data-alignment-track-index="1"] text`, 3510).click();
+    cy.get(`[title="Selecting 3455 bps from 56 to 3510"]`);
+  });
+  it("scrolls the yellow scroll handle correctly", function () {
+    cy.visit("#/Alignment");
+    cy.contains("F05225").should("not.exist");
+    cy.get(`[data-lane-index="13"]`).click();
+    cy.contains("F05225").should("exist");
+  });
+  it("can turn on/off the axis with one click", function () {
+    cy.visit("#/Alignment");
+    cy.contains(".alignmentHolder .veRowViewAxis", 1);
+    cy.get("button .bp3-icon-eye-open").click();
+
+    cy.contains(".bp3-checkbox", "Axis").click();
+    cy.contains(".alignmentHolder .veRowViewAxis", 1).should("not.exist");
+  });
+
+  it("can drag the alignment", function () {
+    cy.visit("#/Alignment");
+    cy.get(".veAlignmentSelectionLayer").should("not.exist");
+    cy.tgToggle("isFullyZoomedOut");
+
+    cy.contains("text", "1000").then((el) => {
+      cy.contains("text", "2000")
+        .first()
+        .then((el2) => {
+          cy.dragBetweenSimple(el, el2);
+        });
+    });
+    cy.get(".veAlignmentSelectionLayer").first().should("be.visible");
+  });
+
+  it("can disable clicking and dragging within the alignment", function () {
+    cy.visit("#/Alignment");
+    cy.tgToggle("noClickDragHandlers");
+    cy.get(".veAlignmentSelectionLayer").should("not.exist");
+
+    cy.tgToggle("isFullyZoomedOut");
+    cy.contains("text", "1000").then((el) => {
+      cy.contains("text", "2000")
+        .first()
+        .then((el2) => {
+          cy.dragBetweenSimple(el, el2);
+        });
+    });
+    cy.get(".veAlignmentSelectionLayer").should("not.exist");
   });
 });