Pull Dev changes into Master branch for upcoming update to prod site

.gitignore

@@ -8,6 +8,8 @@
 # dependencies
 /node_modules
 /node_modules_dev
+/node_modules_classic
+/node_modules_ang
 /dev_node_modules
 /Hantavirus_Testing
 
@@ -62,4 +64,10 @@ slr/*
 slr_linux.tgz
 .agignore
 
-.scignore
+.scignore
+
+cypress/screenshots/*
+cypress/downloads/*
+
+# Maven
+target/

cypress.config.ts

@@ -0,0 +1,12 @@
+import { defineConfig } from "cypress";
+
+export default defineConfig({
+  e2e: {
+    baseUrl: 'http://localhost:4200', // Set your app's base URL
+    viewportWidth: 1280,
+    viewportHeight: 720,
+    setupNodeEvents(on, config) {
+      // implement node event listeners here
+    },
+  },
+});

cypress/e2e/alignment-plugin.cy.ts

@@ -0,0 +1,32 @@
+describe('Alignment View', () => {
+    const selectors = {
+      container: '.msa-viewer-container',
+      settingsBtn: 'a[title="Open Settings"]',
+      settingsPane: '#alignment-settings-pane',
+    };
+
+    beforeEach(() => {
+      cy.visit('/');
+      cy.wait(6000);
+
+      cy.contains('button', 'Continue with Sample Dataset', { timeout: 10000 }).click({ force: true });
+      cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+      cy.contains('button', 'View').click();
+      cy.contains('button[mat-menu-item]', 'Alignment View').click();
+
+      cy.get(selectors.container, { timeout: 15000 }).should('be.visible');
+    });
+
+    it('renders the alignment viewer with sample data', () => {
+      cy.get(selectors.container).find('#msa-viewer').should('exist');
+    });
+
+    it('opens and closes the alignment settings', () => {
+      cy.get(selectors.settingsBtn).click();
+      cy.get(selectors.settingsPane, { timeout: 10000 }).should('be.visible');
+
+      cy.get(selectors.settingsPane).find('.p-dialog-header-icon').click({ force: true });
+      cy.get(selectors.settingsPane).should('not.be.visible');
+    });
+  });

cypress/e2e/bubble-plugin.cy.ts

@@ -0,0 +1,32 @@
+describe('Bubble View', () => {
+    const selectors = {
+      container: '#cyBubble',
+      settingsBtn: 'a[title="Open Settings"]',
+      settingsPane: '.p-dialog-header:contains("Bubble Settings")',
+    };
+
+    beforeEach(() => {
+      cy.visit('/');
+      cy.wait(6000);
+
+      cy.contains('button', 'Continue with Sample Dataset', { timeout: 10000 }).click({ force: true });
+      cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+      cy.contains('button', 'View').click();
+      cy.contains('button[mat-menu-item]', 'Bubble').click();
+
+      cy.get(selectors.container, { timeout: 15000 }).should('be.visible');
+    });
+
+    it('renders bubble view canvas', () => {
+      cy.get(selectors.container).should('exist');
+    });
+
+    it('opens and closes the bubble settings dialog', () => {
+      cy.get(selectors.settingsBtn).click();
+      cy.contains('div.p-dialog', 'Bubble Settings', { timeout: 10000 }).should('be.visible');
+
+      cy.contains('div.p-dialog', 'Bubble Settings').find('.p-dialog-header-icon').click({ force: true });
+      cy.contains('div.p-dialog', 'Bubble Settings').should('not.be.visible');
+    });
+  });

cypress/e2e/files-plugin.cy.ts

@@ -0,0 +1,191 @@
+// cypress/e2e/files-plugin.cy.ts
+/// <reference types="cypress" />
+
+describe('File Handling and Processing', () => {
+  const nodeFile = 'AngularTesting_nodelist_withseqs_TN93_BS.csv';
+  const linkFile = 'AngularTesting_Epi_linklist_BS.csv';
+
+  beforeEach(() => {
+    cy.visit('/');
+    // The initial wait is to allow the default session to load,
+    // which we will clear by uploading our own file.
+    cy.wait(2000); 
+  });
+
+  it('uploads multiple files and then sets the datatype and the fields', () => {
+    // mostly an example of this function
+    cy.loadFiles([
+      {name: 'AngularTesting_DistanceMatrix_TN93_BS.xlsx', datatype: 'matrix'},
+      {name: 'AngularTesting_seqs_TN93_BS.fasta', datatype: 'fasta'},
+      {name: 'AngularTesting_nodes_Map.csv', datatype: 'node', field1: 'seq', field2: '_id'}
+    ])
+  })
+
+  it('uploads a single node list, auto-configures it, and enables launch', () => {
+    // Upload the file from the overlay
+    cy.attach_file('#fileDropRef', nodeFile);
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    // Assert the file row is visible
+    cy.contains('#file-table .file-table-row', nodeFile).should('be.visible');
+    cy.get('#launch').should('not.be.disabled');
+
+    // Assert file type is auto-detected as "Node"
+    cy.contains('.file-table-row', nodeFile).find('input[data-type="node"]').should('be.checked');
+
+    // Use attribute selector to handle special characters in the ID
+    cy.get(`[id="file-${nodeFile}-field-1"]`).should('have.value', '_id');
+    cy.get(`[id="file-${nodeFile}-field-2"]`).should('have.value', 'seq');
+  });
+
+  it('updates column mapping labels when file type is changed manually', () => {
+    cy.attach_file('#fileDropRef', nodeFile);
+
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    // Initial state: Node - We re-query the row for each assertion for robustness.
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label').contains('ID').should('be.visible');
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label').contains('Sequence').should('be.visible');
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label:contains("Distance")').parent().should('not.be.visible');
+
+    // Change to Link type
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('input[data-type="link"]').click({ force: true });
+
+    // Assert labels changed
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label').contains('Source').should('be.visible');
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label').contains('Target').should('be.visible');
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label').contains('Distance').should('be.visible');
+    cy.contains('#file-table .file-table-row', nodeFile)
+      .find('label:contains("Sequence")').should('not.exist');
+  });
+
+  it('allows a file to be removed', () => {
+    cy.attach_file('#fileDropRef', nodeFile);
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    // Ensure the file row exists
+    cy.contains('#file-table .file-table-row', nodeFile).should('be.visible');
+
+    // Click the remove button
+    cy.contains('.file-table-row', nodeFile).find('.flaticon-delete-1').click();
+
+    // Assert the file row is gone and the prompt is back
+    cy.contains('#file-table .file-table-row', nodeFile).should('not.exist');
+    cy.get('#file-prompt').should('be.visible');
+  });
+
+  it('opens and closes the sequence controls modal', () => {
+    cy.attach_file('#fileDropRef', nodeFile);
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    // The p-dialog component exists in the DOM but isn't visible
+    cy.get('#sequence-controls-modal').should('not.be.visible');
+
+    // Click button to open sequence controls
+    cy.contains('button', 'Sequence Controls').click();
+
+    // Assert that content inside the modal is now visible
+    cy.get('#sequence-controls-modal').contains('Alignment').should('be.visible');
+
+    // Click the "Confirm" button to close it
+    cy.get('#sequence-controls-modal').contains('button', 'Confirm').click();
+    cy.get('#sequence-controls-modal').should('not.be.visible');
+  });
+
+  it('opens and closes the file settings modal', () => {
+    cy.attach_file('#fileDropRef', nodeFile);
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    // Modal should not be visible initially
+    cy.get('#file-settings-pane').should('not.be.visible');
+
+    // Click the settings icon to open the modal
+    cy.get('a[title="Settings"]').click();
+    cy.get('#file-settings-pane').contains('Distance Metric').should('be.visible');
+
+    // **FIX**: Target the clickable button, not the inner icon span
+    cy.get('#file-settings-pane').find('button.p-dialog-close-button').click();
+
+    cy.get('#file-settings-pane').should('not.be.visible');
+  });
+
+
+  it('launches a network from separate node and link lists', () => {
+    cy.attach_file('#fileDropRef', nodeFile);
+    cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+
+    cy.attach_file('#data-files1', linkFile); // Use the "Add File(s)" button
+
+    cy.get('#launch').click();
+    cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', '2D Network');
+
+    cy.window().its('commonService.session.data.nodes').should('have.length', 14);
+    cy.window().its('commonService.session.data.links').should('have.length.greaterThan', 0);
+
+    // Verify data from both files was merged
+    cy.window().then((win) => {
+      const node = win.commonService.session.data.nodes.find(n => n._id === 'KF773425');
+      expect(node.subtype).to.equal('C');
+
+      const link = win.commonService.session.data.links.find(l => 
+        (l.source === 'KF773571' && l.target === 'KF773578')
+      );
+      expect(link.Contact).to.equal('Bar');
+    });
+  });
+});
+
+describe('Files Plugin - Settings', () => {
+ const nodeFile = 'AngularTesting_nodelist_withseqs_TN93_small (2).csv';
+
+ beforeEach(() => {
+   cy.visit('/');
+   cy.wait(2000); 
+   cy.attach_file('#fileDropRef', nodeFile);
+   cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
+   cy.get('#tool-btn-container a[title="Settings"]').click();
+ });
+
+ it('should change the Distance Metric and update the session', () => {
+   cy.window().its('commonService.session.style.widgets.default-distance-metric').should('equal', 'snps');
+   cy.get('#default-distance-metric').select('tn93');
+   cy.window().its('commonService.session.style.widgets.default-distance-metric').should('equal', 'tn93');
+ });
+
+ it('should change the Ambiguity Resolution Strategy and update the session', () => {
+   cy.window().its('commonService.session.style.widgets.ambiguity-resolution-strategy').should('equal', 'AVERAGE');
+   cy.get('#default-distance-metric').select('tn93');
+   cy.get('#ambiguity-resolution-strategy').select('RESOLVE');
+   cy.window().its('commonService.session.style.widgets.ambiguity-resolution-strategy').should('equal', 'RESOLVE');
+ });
+
+//  it('should show and update the Ambiguity Threshold when strategy is RESOLVE', () => {
+//   const newThreshold = '0.025';
+//   cy.get('#ambiguity-threshold-row').should('not.be.visible');
+//   cy.get('#ambiguity-resolution-strategy').select('RESOLVE');
+//   cy.get('#ambiguity-threshold-row').should('be.visible');
+//   cy.get('#ambiguity-threshold').clear().type(newThreshold);
+//   cy.window().its('commonService.session.style.widgets.ambiguity-threshold').should('equal', parseFloat(newThreshold));
+//  });
+
+ it('should change the Link Threshold and update the session', () => {
+   const newThreshold = '4';
+   // snps initally
+   cy.window().its('commonService.session.style.widgets.link-threshold').should('equal', 164);
+  cy.get('#default-distance-threshold').clear().type(newThreshold);
+  cy.window().its('commonService.session.style.widgets.link-threshold').should('equal', parseFloat(newThreshold));
+ });
+
+  it('should change the View to Launch and update the session', () => {
+   cy.window().its('commonService.session.style.widgets.default-view').should('equal', '2d_network');
+   cy.get('#default-view').select('Table');
+   cy.window().its('commonService.session.style.widgets.default-view').should('equal', 'Table');
+ });
+});

cypress/e2e/journeys/datasets/profile.ts

@@ -0,0 +1,39 @@
+// cypress/e2e/journeys/datasets/profile.ts
+// Central registry for dataset profiles used by journey tests.
+// Re-export types so flows can keep importing from this file.
+
+export * from './types';
+
+import type { DatasetProfile } from './types';
+
+import { NN_PROFILES } from './profiles/nn';
+import { STYLE_PROFILES } from './profiles/style';
+import { GROUPING_PROFILES } from './profiles/grouping';
+
+export const DATASET_PROFILES: DatasetProfile[] = [
+  ...NN_PROFILES,
+  ...STYLE_PROFILES,
+  ...GROUPING_PROFILES,
+];
+
+export const DATASET_PROFILE_MAP: Record<string, DatasetProfile> = DATASET_PROFILES
+  .reduce((acc, p) => {
+    acc[p.id] = p;
+    return acc;
+  }, {} as Record<string, DatasetProfile>);
+
+export function getProfile(id: string): DatasetProfile {
+  const p = DATASET_PROFILE_MAP[id];
+  if (!p) {
+    throw new Error(`Unknown dataset profile id: ${id}`);
+  }
+  return p;
+}
+
+export function getProfilesByTag(tag: string): DatasetProfile[] {
+  return DATASET_PROFILES.filter(p => p.tags.includes(tag));
+}
+
+export function getProfilesByTags(tags: string[]): DatasetProfile[] {
+  return DATASET_PROFILES.filter(p => tags.every(t => p.tags.includes(t)));
+}