graphdb-workbench-tests 3.1.0-TR2 → 3.1.0-TR4

package/.nycrc

@@ -0,0 +1,10 @@
+{
+    "temp-directory": "../.nyc_output",
+    "include": [
+      "packages/legacy-workbench/src/**/*.js"
+    ],
+    "exclude": [
+      "packages/root-config/**",
+      "packages/shared-components/**"
+    ]
+}

package/cypress-legacy.config.js

@@ -1,5 +1,7 @@
 const {defineConfig} = require('cypress');
 
+const isCoverage = process.env.COVERAGE === 'true';
+
 module.exports = defineConfig({
     projectId: 'v35btb',
     fixturesFolder: 'fixtures',
@@ -8,6 +10,8 @@ module.exports = defineConfig({
     video: true,
     defaultCommandTimeout: 25000,
     numTestsKeptInMemory: 10,
+    viewportWidth: 1280,
+    viewportHeight: 720,
     e2e: {
         retries: {
             runMode: 2,
@@ -16,7 +20,11 @@ module.exports = defineConfig({
         // We've imported your old cypress plugins here.
         // You may want to clean this up later by importing these.
         setupNodeEvents(on, config) {
-            return require('./plugins')(on, config);
+            require('./plugins')(on, config);
+            if (isCoverage) {
+                require('@bahmutov/cypress-code-coverage/plugin')(on, config)
+            }
+            return config;
         },
         baseUrl: 'http://localhost:9000',
         specPattern: 'e2e-legacy/**/*.{js,jsx,ts,tsx}',

package/e2e-legacy/graphql/import-graphql-endpoint-definitions.spec.js

@@ -85,10 +85,7 @@ describe('Graphql: import endpoint definitions', () => {
         ]);
     });
 
-    /**
-     * TODO Fixme broken due migration (Error unknown)
-     */
-    it.skip('should be able to import broken endpoint definition', () => {
+    it('should be able to import broken endpoint definition', () => {
         visitAndOpenImportModal();
         // When I select the file to upload
         ImportEndpointDefinitionModalSteps.selectFile(brokenSwapiDefinitionPath);

package/e2e-legacy/home/cookie-policy.spec.js

@@ -7,10 +7,7 @@ import {LicenseStubs} from "../../stubs/license-stubs";
 Cypress.env('set_default_user_data', false);
 
 
-/**
- * TODO: Fix me. Broken due to migration (Cookie policy is not implemented in the new footer)
- */
-describe.skip('Cookie policy', () => {
+describe('Cookie policy', () => {
     beforeEach(() => {
         cy.setDefaultUserData(false);
         cy.viewport(1280, 1000);
@@ -19,71 +16,70 @@ describe.skip('Cookie policy', () => {
 
     afterEach(() => cy.setDefaultUserData());
 
-    it('Should show consent popup to user', () => {
-        HomeSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
-        HomeSteps.getCookieConsentPopup().should('exist').and('be.visible');
-        // When I click on the link
-        HomeSteps.clickCookiePolicyLink();
-        // Then I see the cookie policy
-        HomeSteps.getCookiePolicyModal().should('exist').and('be.visible');
-    });
+    context('should show', () => {
+        it('Should show consent popup to user', () => {
+            HomeSteps.visitInProdMode();
+            HomeSteps.getCookieConsentPopup().should('exist').and('be.visible');
+            // When I click on the link
+            HomeSteps.clickCookiePolicyLink();
+            // Then I see the cookie policy
+            HomeSteps.getCookiePolicyModal().should('exist').and('be.visible');
+        });
 
-    it('Should show cookie policy to user in user settings', () => {
-        SettingsSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
-        SettingsSteps.getCookiePolicyButton().should('exist').and('be.visible');
+        it('Should show cookie policy to user in user settings', () => {
+            SettingsSteps.visitInProdMode();
+            SettingsSteps.getCookiePolicyButton().should('exist').and('be.visible');
 
-        // When I click on the link
-        SettingsSteps.clickCookiePolicyLink();
-        // Then I see the cookie policy
-        SettingsSteps.getCookiePolicyModal().should('exist').and('be.visible');
-    });
+            // When I click on the link
+            SettingsSteps.clickCookiePolicyLink();
+            // Then I see the cookie policy
+            SettingsSteps.getCookiePolicyModal().should('exist').and('be.visible');
+        });
 
-    it('Should NOT show consent popup to user when tracking is not applicable', () => {
-        HomeSteps.visit();
-        HomeSteps.getCookieConsentPopup().should('not.exist');
-    });
+        it('Should save consent in user settings', () => {
+            HomeSteps.visitInProdMode();
+            SecurityStubs.stubUpdateUserData('admin');
 
-    it('Should NOT show cookie policy to user when tracking is not applicable', () => {
-        SettingsSteps.visit();
-        SettingsSteps.getCookiePolicyButton().should('not.exist');
-    });
+            // When I click Agree button
+            HomeSteps.clickAgreeButton();
 
-    it('Should save consent in user settings', () => {
-        HomeSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
-        SecurityStubs.stubUpdateUserData('admin');
+            // I expect to save cookie consent in user settings
+            cy.wait('@updateUser').then((xhr) => {
+                expect(xhr.request.body.appSettings).to.include({
+                    DEFAULT_INFERENCE: true,
+                    DEFAULT_VIS_GRAPH_SCHEMA: true,
+                    DEFAULT_SAMEAS: true,
+                    IGNORE_SHARED_QUERIES: false,
+                    EXECUTE_COUNT: true
+                });
 
-        // When I click Agree button
-        HomeSteps.clickAgreeButton();
+                // Assert COOKIE_CONSENT properties, excluding updatedAt
+                expect(xhr.request.body.appSettings.COOKIE_CONSENT).to.include({
+                    policyAccepted: true
+                });
 
-        // I expect to save cookie consent in user settings
-        cy.wait('@updateUser').then((xhr) => {
-            expect(xhr.request.body.appSettings).to.include({
-                DEFAULT_INFERENCE: true,
-                DEFAULT_VIS_GRAPH_SCHEMA: true,
-                DEFAULT_SAMEAS: true,
-                IGNORE_SHARED_QUERIES: false,
-                EXECUTE_COUNT: true
-            });
+                // Assert that updatedAt is present, is a number, and is a reasonable timestamp
+                const updatedAt = xhr.request.body.appSettings.COOKIE_CONSENT.updatedAt;
+                expect(updatedAt).to.exist;
+                expect(updatedAt).to.be.a('number');
 
-            // Assert COOKIE_CONSENT properties, excluding updatedAt
-            expect(xhr.request.body.appSettings.COOKIE_CONSENT).to.include({
-                policyAccepted: true,
-                statistic: true,
-                thirdParty: true
+                // Check that updatedAt is within 1 hour of the current time
+                const oneHourInMilliseconds = 60 * 60 * 1000;
+                const now = Date.now();
+                expect(updatedAt).to.be.within(now - oneHourInMilliseconds, now + oneHourInMilliseconds);
             });
+        });
+    })
 
-            // Assert that updatedAt is present, is a number, and is a reasonable timestamp
-            const updatedAt = xhr.request.body.appSettings.COOKIE_CONSENT.updatedAt;
-            expect(updatedAt).to.exist;
-            expect(updatedAt).to.be.a('number');
+    context('should not show', () => {
+        it('Should NOT show consent popup to user when tracking is not applicable', () => {
+            HomeSteps.visitInDevMode();
+            HomeSteps.getCookieConsentPopup().should('not.exist');
+        });
 
-            // Check that updatedAt is within 1 hour of the current time
-            const oneHourInMilliseconds = 60 * 60 * 1000;
-            const now = Date.now();
-            expect(updatedAt).to.be.within(now - oneHourInMilliseconds, now + oneHourInMilliseconds);
+        it('Should NOT show cookie policy to user when tracking is not applicable', () => {
+            SettingsSteps.visitInDevMode();
+            SettingsSteps.getCookiePolicyButton().should('not.exist');
         });
     });
 });

package/e2e-legacy/home/documentation-link.spec.js

@@ -11,10 +11,9 @@ describe('Documentation links resolver', () => {
     });
 
     it('Should link to master version when in dev mode', () => {
-        HomeSteps.visit();
+        HomeSteps.visitInDevMode();
         waitForProductInfo();
         BrowserStubs.stubWindowOpen();
-        EnvironmentStubs.stubWbDevMode();
         MainMenuSteps.clickOnMenuHelp();
         // Assert that links point to the master version
         assertDocumentationLinks('master');
@@ -23,10 +22,9 @@ describe('Documentation links resolver', () => {
 
     it('Should link to master version when in prod mode and unofficial version', () => {
         EnvironmentStubs.stubProductInfo('10.8-TR1-test');
-        HomeSteps.visit();
+        HomeSteps.visitInProdMode();
         waitForProductInfo();
         BrowserStubs.stubWindowOpen();
-        EnvironmentStubs.stubWbProdMode();
         MainMenuSteps.clickOnMenuHelp();
         // Assert that links point to the master version
         assertDocumentationLinks('master');
@@ -34,10 +32,9 @@ describe('Documentation links resolver', () => {
 
     it('Should link to GDB version when in prod mode and official version', () => {
         EnvironmentStubs.stubProductInfo('10.8');
-        HomeSteps.visit();
+        HomeSteps.visitInProdMode();
         waitForProductInfo();
         BrowserStubs.stubWindowOpen();
-        EnvironmentStubs.stubWbProdMode();
         MainMenuSteps.clickOnMenuHelp();
         // Assert that links point to the specific GDB version
         assertDocumentationLinks('10.8');

package/e2e-legacy/home/google-analytics.spec.js

@@ -11,8 +11,7 @@ describe('Google analytics', () => {
     // Note: Google API calls are stubbed for all specs in support/index.js
     it('Should set GA tracking code in header and a cookie when free license and prodMode', () => {
         LicenseStubs.stubFreeLicense();
-        HomeSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
+        HomeSteps.visitInProdMode();
 
         cy.document()
             .get('head script')
@@ -28,8 +27,7 @@ describe('Google analytics', () => {
 
     it('Should set GA tracking code in header and cookie when evaluation enterprise license and prodMode', () => {
         LicenseStubs.stubEvaluationLicense();
-        HomeSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
+        HomeSteps.visitInProdMode();
 
         cy.document()
             .get('head script')
@@ -45,8 +43,7 @@ describe('Google analytics', () => {
 
     it('Should NOT set GA tracking code in header and cookie when enterprise license in prodMode', () => {
         LicenseStubs.stubEnterpriseLicense();
-        HomeSteps.visit();
-        EnvironmentStubs.stubWbProdMode();
+        HomeSteps.visitInProdMode();
 
         cy.document()
             .get('head script')

package/e2e-legacy/home/rdf-resource-search.spec.js

@@ -14,7 +14,6 @@ describe('RDF resource search', () => {
         cy.createRepository({id: repositoryId});
         cy.initializeRepository(repositoryId);
         cy.enableAutocomplete(repositoryId);
-        BrowserStubs.stubCryptoUUID();
     });
 
     afterEach(() => {

package/e2e-legacy/setup/users-and-access/user-and-access.spec.js

@@ -5,11 +5,9 @@ import {ModalDialogSteps} from "../../../steps/modal-dialog-steps";
 import {ToasterSteps} from "../../../steps/toaster-steps";
 import HomeSteps from "../../../steps/home-steps";
 import {LoginSteps} from "../../../steps/login-steps";
+import {MainMenuSteps} from "../../../steps/main-menu-steps";
 
 
-/**
- * TODO: Fix me. Broken due to migration (Error: unknown)
- */
 describe('User and Access', () => {
 
     const PASSWORD = "password";
@@ -179,6 +177,7 @@ describe('User and Access', () => {
                 cy.deleteRepository(repositoryId2, true);
                 cy.deleteRepository(repositoryId3, true);
                 cy.deleteUser(graphqlUser, true);
+                cy.switchOffFreeAccess(true);
                 cy.switchOffSecurity(true);
             });
 
@@ -454,9 +453,9 @@ describe('User and Access', () => {
     function navigateMenuPath(pathArray, expectedUrl, expectedTitle) {
         pathArray.forEach((label, index) => {
             if (index === 0) {
-                UserAndAccessSteps.clickMenuItem(label);
+                MainMenuSteps.clickOnMenu(label);
             } else {
-                UserAndAccessSteps.clickSubmenuItem(label);
+                MainMenuSteps.clickOnSubMenu(label);
                 const title = expectedTitle ? expectedTitle : label;
                 cy.get('h1').should('contain', title);
             }

package/e2e-legacy/sparql-editor/saved-query/share-query.spec.js

@@ -46,7 +46,7 @@ describe('Share saved queries', () => {
     });
 
     // FIX: Skipped because the functionality is not working. There is a bug in the application https://graphwise.atlassian.net/browse/GDB-12633
-    it.skip('Should be able to open a share link in a new editor tab', () => {
+    it('Should be able to open a share link in a new editor tab', () => {
         // Given I have created a query
         YasguiSteps.getTabs().should('have.length', 1);
         const savedQueryName = SavedQuery.generateQueryName();

package/e2e-legacy/ttyg/ttyg-permission.spec.js

@@ -1,10 +1,12 @@
 import {RepositoriesStubs} from "../../stubs/repositories/repositories-stubs";
 import {RepositoriesStub} from "../../stubs/repositories-stub";
-import {UserAndAccessSteps} from "../../steps/setup/user-and-access-steps";
 import {TTYGStubs} from "../../stubs/ttyg/ttyg-stubs";
 import {TTYGViewSteps} from "../../steps/ttyg/ttyg-view-steps";
 import {LoginSteps} from "../../steps/login-steps";
+import {SecurityStubs} from "../../stubs/security-stubs";
+import {RepositorySelectorSteps} from "../../steps/repository-selector-steps";
 
+const REPOSITORY_ID = 'starwars';
 const USER_WITH_ROLE_USER = 'ttyg_user';
 const USER_WITH_ROLE_REPO_MANAGER = 'ttyg_repo_manager';
 const USER_ADMINISTRATOR = 'admin';
@@ -14,12 +16,8 @@ const DISABLED = false;
 
 describe('TTYG permissions', () => {
 
-
     before(() => {
-        RepositoriesStubs.stubRepositories(0, '/repositories/get-ttyg-repositories.json');
-        RepositoriesStub.stubBaseEndpoints('starwars');
         cy.loginAsAdmin();
-        cy.presetRepository('starwars');
         cy.createUser({username: USER_WITH_ROLE_USER, password: PASSWORD});
         cy.createUser({
             username: USER_WITH_ROLE_REPO_MANAGER,
@@ -29,6 +27,12 @@ describe('TTYG permissions', () => {
         cy.switchOnSecurity();
     });
 
+    beforeEach(() => {
+        SecurityStubs.spyOnAuthenticatedUser();
+        RepositoriesStubs.stubRepositories(0, '/repositories/get-ttyg-repositories.json');
+        RepositoriesStub.stubBaseEndpoints(REPOSITORY_ID);
+    })
+
     after(() => {
         cy.loginAsAdmin();
         cy.deleteUser(USER_WITH_ROLE_USER, true);
@@ -36,14 +40,17 @@ describe('TTYG permissions', () => {
         cy.switchOffSecurity(true);
     });
 
-    it('should disable all buttons that can modify the agent', () => {
-
+    it('should disable all buttons that can modify the agent when user is with ROLE_USER', () => {
         // When I log in with a user who has the ROLE_USER role, I expect all buttons modifying the agent to be disabled.
         verifyCanCreateAgentForFirstTime(USER_WITH_ROLE_USER, PASSWORD, DISABLED);
+    });
 
+    it('should enable all buttons that can modify the agent when user is with role ROLE_REPO_MANAGER', () => {
         // When I log in with a user who has the ROLE_REPO_MANAGER role, I expect all buttons modifying the agent to be enabled.
         verifyCanCreateAgentForFirstTime(USER_WITH_ROLE_REPO_MANAGER, PASSWORD, ENABLED);
+    });
 
+    it('should enable all buttons that can modify the agent when user is admin', () => {
         // When I log in with a user who is administrator, I expect all buttons modifying the agent to be enabled.
         verifyCanCreateAgentForFirstTime(USER_ADMINISTRATOR, PASSWORD, ENABLED);
     });
@@ -52,7 +59,12 @@ describe('TTYG permissions', () => {
         const shouldBe = enable ? 'be.enabled' : 'be.disabled';
         TTYGStubs.stubAgentListGet('/ttyg/agent/get-agent-list-0.json');
         TTYGViewSteps.visit();
+        cy.url().should('include', '/login');
+        cy.wait('@get-authenticated-user');
+        cy.wait('@get-authenticated-user');
+        cy.wait('@get-authenticated-user');
         LoginSteps.loginWithUser(user, password);
+        RepositorySelectorSteps.selectRepository(REPOSITORY_ID);
         TTYGViewSteps.getCreateFirstAgentButton().should(shouldBe);
         TTYGStubs.stubChatsListGet();
         TTYGStubs.stubAgentListGet();
@@ -61,6 +73,5 @@ describe('TTYG permissions', () => {
         TTYGViewSteps.getCreateAgentButton().should(shouldBe);
         TTYGViewSteps.getEditCurrentAgentButton().should(shouldBe);
         TTYGViewSteps.getToggleAgentsSidebarButton().should(shouldBe);
-        LoginSteps.logout();
     }
 });

package/fixtures/ttyg/agent/get-agent-defaults.json

@@ -6,7 +6,7 @@
     "topP": 1.0,
     "seed": 0,
     "repositoryId": "test-repository",
-    "instructions": {
+    "assistantsInstructions": {
         "systemInstruction": "",
         "userInstruction": "If you need to write a SPARQL query, use only the classes and properties provided in the schema and don't invent or guess any. Always try to return human-readable names or labels and not only the IRIs. If SPARQL fails to provide the necessary information you can try another tool too."
     },

package/fixtures/ttyg/agent/get-agent-list-after-deleted.json

@@ -7,7 +7,7 @@
         "topP": 0.0,
         "seed": null,
         "repositoryId": "Not existing repo",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "string\n\nstring",
             "userInstruction": "string"
         },
@@ -25,7 +25,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You are helpful assistant in discovering information regarding diagnostic biomarkers.",
             "userInstruction": null
         },
@@ -43,7 +43,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "biomarkers",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You're a helpful assistant in discovering new diagnostic biomarkers for given diseases. I'll submit a set of publication abstracts discussing given disease and your task is to find in the abstracts any potential new biomarkers which are not yet listed in the appropriate databases. Each abstract is preceded by identifier - its PubMed id called for short PMID. \n\nReturn the set of biomarkers listed one per row, each marker followed by the | and PMID of the respective abstract if was mentioned in.\n\nExample: \nInput: 36418457\t[Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases', 'amyotrophic lateral sclerosis', and 'endocytosis' KEGG terms. Further, some of other modules related to ALS were enriched in 'autophagy' and 'amyotrophic lateral sclerosis'. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.]\n\nYour response: BCLAF1|36418457\nGNA13|36418457\nARL6IP5|36418457\nARGLU1|36418457\nYPEL5|36418457",
             "userInstruction": null
         },

package/fixtures/ttyg/agent/get-agent-list-autocomplete-query.json

@@ -6,7 +6,7 @@
         "temperature": 0.7,
         "topP": 1.0,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": null,
             "userInstruction": null
         },

package/fixtures/ttyg/agent/get-agent-list-new-agent.json

@@ -7,7 +7,7 @@
         "topP": 0.2,
         "seed": 2,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "",
             "userInstruction": ""
         },

package/fixtures/ttyg/agent/get-agent-list-with-incompatible-agents.json

@@ -8,7 +8,7 @@
         "seed": null,
         "repositoryId": "starwars",
         "compatibility": "INCOMPATIBLE",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "",
             "userInstruction": ""
         },
@@ -28,7 +28,7 @@
         "seed": null,
         "repositoryId": "Not existing repo",
         "compatibility": "COMPATIBLE",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "string\n\nstring",
             "userInstruction": "string"
         },
@@ -46,7 +46,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You are helpful assistant in discovering information regarding diagnostic biomarkers.",
             "userInstruction": null
         },
@@ -65,7 +65,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "biomarkers",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You're a helpful assistant in discovering new diagnostic biomarkers for given diseases. I'll submit a set of publication abstracts discussing given disease and your task is to find in the abstracts any potential new biomarkers which are not yet listed in the appropriate databases. Each abstract is preceded by identifier - its PubMed id called for short PMID. \n\nReturn the set of biomarkers listed one per row, each marker followed by the | and PMID of the respective abstract if was mentioned in.\n\nExample: \nInput: 36418457\t[Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases', 'amyotrophic lateral sclerosis', and 'endocytosis' KEGG terms. Further, some of other modules related to ALS were enriched in 'autophagy' and 'amyotrophic lateral sclerosis'. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.]\n\nYour response: BCLAF1|36418457\nGNA13|36418457\nARL6IP5|36418457\nARGLU1|36418457\nYPEL5|36418457",
             "userInstruction": null
         },

package/fixtures/ttyg/agent/get-agent-list.json

@@ -7,7 +7,7 @@
         "topP": 0.0,
         "seed": null,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "",
             "userInstruction": ""
         },
@@ -26,7 +26,7 @@
         "topP": 0.0,
         "seed": null,
         "repositoryId": "Not existing repo",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "string\n\nstring",
             "userInstruction": "string"
         },
@@ -44,7 +44,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "starwars",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You are helpful assistant in discovering information regarding diagnostic biomarkers.",
             "userInstruction": null
         },
@@ -63,7 +63,7 @@
         "topP": 1.0,
         "seed": null,
         "repositoryId": "biomarkers",
-        "instructions": {
+        "assistantsInstructions": {
             "systemInstruction": "You're a helpful assistant in discovering new diagnostic biomarkers for given diseases. I'll submit a set of publication abstracts discussing given disease and your task is to find in the abstracts any potential new biomarkers which are not yet listed in the appropriate databases. Each abstract is preceded by identifier - its PubMed id called for short PMID. \n\nReturn the set of biomarkers listed one per row, each marker followed by the | and PMID of the respective abstract if was mentioned in.\n\nExample: \nInput: 36418457\t[Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases', 'amyotrophic lateral sclerosis', and 'endocytosis' KEGG terms. Further, some of other modules related to ALS were enriched in 'autophagy' and 'amyotrophic lateral sclerosis'. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.]\n\nYour response: BCLAF1|36418457\nGNA13|36418457\nARL6IP5|36418457\nARGLU1|36418457\nYPEL5|36418457",
             "userInstruction": null
         },

package/fixtures/ttyg/agent/get-agent.json

@@ -5,7 +5,7 @@
     "temperature": 0.7,
     "topP": 1.0,
     "repositoryId": "starwars",
-    "instructions": {
+    "assistantsInstructions": {
         "systemInstruction": null,
         "userInstruction": null
     },