graphdb-workbench-tests 3.4.0-TR2 → 3.4.0-TR4

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

@@ -1,44 +0,0 @@
-{
-    "id": "id",
-    "name": "Quadro",
-    "model": "gpt-4o",
-    "api": "openai-assistants",
-    "contextSize": 128000,
-    "temperature": 0.7,
-    "topP": 1.0,
-    "seed": 0,
-    "repositoryId": "test-repository",
-    "instructions": {
-        "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."
-    },
-    "assistantExtractionMethods": [
-        {
-            "method": "sparql_search",
-            "ontologyGraph": "http://example.com",
-            "sparqlQuery": "CONSTRUCT {?s ?p ?o} WHERE {GRAPH <http://example.org/ontology> {?s ?p ?o .}}",
-            "addMissingNamespaces": false
-        },
-        {
-            "method": "fts_search",
-            "maxNumberOfTriplesPerCall": 0
-        },
-        {
-            "method": "similarity_search",
-            "similarityIndex": "similarity-index",
-            "similarityIndexThreshold": 0.6,
-            "maxNumberOfTriplesPerCall": 0
-        },
-        {
-            "method": "retrieval_search",
-            "retrievalConnectorInstance": "retrieval-connector",
-            "queryTemplate": "{\"query\": \"string\"}",
-            "maxNumberOfTriplesPerCall": 0
-        }
-    ],
-    "additionalExtractionMethods": [
-        {
-            "method": "iri_discovery_search"
-        }
-    ]
-}

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

@@ -1,79 +0,0 @@
-[
-    {
-        "id": "asst_gAPcrHQQ9ZIxD5eXWH2BNFfo",
-        "name": "agent-1",
-        "model": "gpt-4o",
-        "temperature": 0.0,
-        "topP": 0.0,
-        "seed": null,
-        "repositoryId": "starwars",
-        "compatibility": "INCOMPATIBLE",
-        "instructions": {
-            "systemInstruction": "",
-            "userInstruction": ""
-        },
-        "assistantExtractionMethods": [
-            {
-                "method": "fts_search",
-                "maxNumberOfTriplesPerCall": 44
-            }
-        ]
-    },
-    {
-        "id": "asst_qMyCpCBmqxV9I2B8UoMfFzc5",
-        "name": "agent-2",
-        "model": "gpt-4o",
-        "temperature": 0.0,
-        "topP": 0.0,
-        "seed": null,
-        "repositoryId": "Not existing repo",
-        "compatibility": "COMPATIBLE",
-        "instructions": {
-            "systemInstruction": "string\n\nstring",
-            "userInstruction": "string"
-        },
-        "assistantExtractionMethods": [
-            {
-                "method": "fts_search"
-            }
-        ]
-    },
-    {
-        "id": "asst_Cr0RxobrY07WpOvvyQilEWMI",
-        "name": "Databricks-general-unbiased",
-        "model": "gpt-4o-2024-08-06",
-        "temperature": 1.0,
-        "topP": 1.0,
-        "seed": null,
-        "repositoryId": "starwars",
-        "instructions": {
-            "systemInstruction": "You are helpful assistant in discovering information regarding diagnostic biomarkers.",
-            "userInstruction": null
-        },
-        "assistantExtractionMethods": [
-            {
-                "method": "fts_search",
-                "maxNumberOfTriplesPerCall": 44
-            }
-        ]
-    },
-    {
-        "id": "asst_5GxNYTdaOh7Tl6lLl6Pya2aH",
-        "name": "Databricks-biomarkers",
-        "model": "gpt-3.5-turbo-0125",
-        "temperature": 1.0,
-        "topP": 1.0,
-        "seed": null,
-        "repositoryId": "biomarkers",
-        "instructions": {
-            "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
-        },
-        "assistantExtractionMethods": [
-            {
-                "method": "fts_search",
-                "maxNumberOfTriplesPerCall": 44
-            }
-        ]
-    }
-]

package/fixtures/ttyg/agent/get-similarity-indexes-for-another-repo.json

@@ -1,8 +0,0 @@
-{
-    "opensearch": [
-        {
-            "similarityIndex": "biomarkers-vector",
-            "connectorFields": ["docText1", "docText2"]
-        }
-    ]
-}

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

@@ -1,22 +0,0 @@
-{
-    "opensearch": [
-        {
-            "similarityIndex": "otkg-vector-new",
-            "connectorFields": ["docText1"]
-        }
-    ],
-    "elasticsearch": [
-        {
-            "similarityIndex": "otkg-vector",
-            "connectorFields": ["docText1", "docText2"]
-        }
-    ],
-    "similarity": [
-        {
-            "similarityIndex": "test"
-        },
-        {
-            "similarityIndex": "test_copy"
-        }
-    ]
-}

package/fixtures/ttyg/chats/ask-question-cancel.json

@@ -1,12 +0,0 @@
-{
-    "id": "thread_YHVy625Ir8TJkUuwy94l46Om",
-    "name": "New chat",
-    "messages": [],
-    "timestamp": 1756128759,
-    "continueRunId": null,
-    "usage": {
-        "completionTokens": 0,
-        "promptTokens": 0,
-        "totalTokens": 0
-    }
-}

package/fixtures/ttyg/chats/cancel-question-response.json

@@ -1 +0,0 @@
-{"runStatus":"cancelled","message":"Request cancelled by the user."}

package/fixtures/ttyg/chats/create/question-response-after-chat-creation.json

@@ -1,29 +0,0 @@
-{
-    "id": "thread_tpv1izmd9bIjxkhUiCd5x2Xz",
-    "name": "Hello! How can I assist you today?",
-    "messages": [
-        {
-            "id": "msg_drDW9OTkPkY0oGoXSdPD5qEx",
-            "conversationId": "thread_tpv1izmd9bIjxkhUiCd5x2Xz",
-            "agentId": "asst_0llP8yAJlFY2yCWrz8Ovfzjs",
-            "role": "assistant",
-            "message": "Hello! How can I assist you today?",
-            "timestamp": "creationDate",
-            "name": null,
-            "usage": {
-                "completionTokens": 11,
-                "promptTokens": 374,
-                "totalTokens": 385
-            },
-            "isTerminalState": false,
-            "terminalStatusCode": null
-        }
-    ],
-    "timestamp": "creationDate",
-    "continueRunId": null,
-    "usage": {
-        "completionTokens": 11,
-        "promptTokens": 374,
-        "totalTokens": 385
-    }
-}

package/fixtures/ttyg/chats/explain-response-3.json

@@ -1,12 +0,0 @@
-{
-    "conversationId": "thread_new_created_chat",
-    "answerId": "msg_drDW9OTkPkY0oGoXSdPD5qEx",
-    "queryMethods": [
-        {
-            "name": "sparql_query",
-            "rawQuery": "SELECT ?character ?name ?height WHERE {\n  ?character a voc:Character;\n             rdfs:label ?name;\n             voc:height ?height.\n  FILTER(?name = \"Luke Skywalker\" || ?name = \"Leia Organa\")\n}",
-            "query": "SELECT ?character ?name ?height WHERE {\n  ?character a voc:Character;\n             rdfs:label ?name;\n             voc:height ?height.\n  FILTER(?name = \"Luke Skywalker\" || ?name = \"Leia Organa\")\n}",
-            "queryType": "sparql"
-        }
-    ]
-}

package/steps/base-steps.js

@@ -1,29 +0,0 @@
-export class BaseSteps {
-  static visit(page) {
-    cy.visit(page);
-  }
-
-  static clickOutsideElement() {
-    cy.get('body').click(0,0);
-  }
-
-  static reloadPage(force = false) {
-    cy.reload(force);
-  }
-
-  static getByTestId(testId) {
-    return cy.getByTestId(testId);
-  }
-
-  static typeEscapeKey() {
-    cy.get('body').type('{esc}');
-  }
-
-  static getUrl() {
-    return cy.url();
-  }
-
-  static validateUrl(url) {
-    this.getUrl().should('include', url);
-  }
-}

package/steps/cookie-policy/cookie-consent-banner-steps.js

@@ -1,21 +0,0 @@
-export class CookieConsentBannerSteps {
-    static getCookieConsentBanner() {
-        return cy.get('.cookie-consent-banner');
-    }
-
-    static getCookieConsentButton() {
-        return this.getCookieConsentBanner().find('button');
-    }
-
-    static giveCookieConsent() {
-        return this.getCookieConsentButton().click();
-    }
-
-    static getCookiePolicyLink() {
-        return cy.get('.cookie-consent-content a');
-    }
-
-    static clickCookiePolicyLink() {
-        return this.getCookiePolicyLink().click();
-    }
-}

package/steps/cookie-policy/cookie-policy-modal.steps.js

@@ -1,56 +0,0 @@
-import {SharedModalDialogSteps} from '../shared-modal-dialog-steps';
-
-export class CookiePolicyModalSteps extends SharedModalDialogSteps {
-    static getDialogComponent(cssClass = '.cookie-policy-modal') {
-        return super.getDialogComponent(cssClass);
-    }
-
-    static getStatisticCookiesToggle() {
-        return this.getBody().find('.statistic-cookies-toggle .toggle-switch');
-    }
-
-    static getStatisticCookiesCheckbox() {
-        return this.getStatisticCookiesToggle().find('input');
-    }
-
-    static toggleStatisticCookies() {
-        this.getStatisticCookiesToggle().click();
-        // Wait here is intentional because there is a debounce before the checkbox state is updated
-        // eslint-disable-next-line cypress/no-unnecessary-waiting
-        cy.wait(500);
-    }
-
-    static getThirdPartyCookiesToggle() {
-        return this.getBody().find('.third-party-cookies-toggle .toggle-switch');
-    }
-
-    static getThirdPartyCookiesCheckbox() {
-        return this.getThirdPartyCookiesToggle().find('input');
-    }
-
-    static toggleThirdPartyCookies() {
-        this.getThirdPartyCookiesToggle().click();
-        // Wait here is intentional because there is a debounce before the checkbox state is updated
-        // eslint-disable-next-line cypress/no-unnecessary-waiting
-        cy.wait(500);
-    }
-
-    static closeDialog() {
-        this.getFooter().find('.close-btn').click();
-    }
-
-    /**
-     * Validates the cookie policy dialog by checking the visibility of the dialog and the state of the checkboxes for
-     * analytic and third party cookies.
-     * @param {boolean} expectedStatisticChecked
-     * @param {boolean} expectedThirdPartyChecked
-     */
-    static validateCookiePolicyDialog(expectedStatisticChecked, expectedThirdPartyChecked) {
-        // I should see the cookie policy
-        CookiePolicyModalSteps.getDialogComponent().should('be.visible');
-        CookiePolicyModalSteps.getBody().should('be.visible');
-        // And I expect to see that analytic and third party cookies are allowed
-        CookiePolicyModalSteps.getStatisticCookiesCheckbox().should(expectedStatisticChecked ? 'be.checked' : 'not.be.checked');
-        CookiePolicyModalSteps.getThirdPartyCookiesCheckbox().should(expectedThirdPartyChecked ? 'be.checked' : 'not.be.checked');
-    }
-}

package/steps/error-page-steps.js

@@ -1,9 +0,0 @@
-export class ErrorPageSteps {
-    static visit404() {
-        cy.visit('/404');
-    }
-
-    static get404Page() {
-        return cy.get('app-not-found-page');
-    }
-}

package/steps/explore/class-relationships-steps.js

@@ -1,64 +0,0 @@
-export class ClassRelationshipsSteps {
-    static visit() {
-        cy.visit('/relationships');
-    }
-
-    static getFilterField() {
-        return cy.get('.search-filter-field');
-    }
-
-    static filterByClass(name) {
-        this.getFilterField().type(name);
-    }
-
-    static getDirectionFilter() {
-        return cy.get('.direction-filter');
-    }
-
-    static verifySelectedDirectionFilter(name) {
-        this.getDirectionFilter().find('input[type=radio]:checked').should('have.value', name);
-    }
-
-    static getRelationsToolbar() {
-        return cy.get('.relations-toolbar');
-    }
-
-    static verifyRelationsToolbarContent() {
-        this.getRelationsToolbar().should('be.visible');
-        this.removeAllClassesButton().should('be.visible');
-        this.getReloadDiagramButton().should('be.visible');
-        this.getExportDiagramButton().should('be.visible');
-    }
-
-    static getDependenciesList() {
-        return cy.get('#wb-dependencies-classInClasses');
-    }
-
-    static verifyListLength(count) {
-        this.getDependenciesList().find('.item .row').should('have.length', count);
-    }
-
-    static getNoDataWarning() {
-        return cy.get('div.alert.alert-warning');
-    }
-
-    static getReloadDiagramButton() {
-        return cy.get('.reload-diagram-btn');
-    }
-
-    static getExportDiagramButton() {
-        return this.getRelationsToolbar().find('.export-diagram-btn');
-    }
-
-    static removeAllClassesButton() {
-        return this.getRelationsToolbar().find('.remove-all-classes-btn');
-    }
-
-    static getDependenciesDiagram() {
-        return cy.get('#dependencies-chord');
-    }
-
-    static getAvailableDependenciesLabel() {
-        return cy.get('.available-dependencies-label');
-    }
-}

package/steps/graphql/playground-editor-steps.js

@@ -1,46 +0,0 @@
-export class PlaygroundEditorSteps {
-
-    static getResponse() {
-        return cy.get('.graphiql-response');
-    }
-
-    static getResponseCodeMirror() {
-        return PlaygroundEditorSteps.getResponse().find('.CodeMirror');
-    }
-
-    static getGraphiqlEditors() {
-        return cy.get('.graphiql-editors');
-    }
-
-    static getGraphiqlEditorsCodeMirror() {
-        return PlaygroundEditorSteps.getGraphiqlEditors().find('.CodeMirror');
-    }
-
-    static getGraphiqlEditorTools() {
-        return cy.get('.graphiql-editor-tools');
-    }
-
-    static getGraphiqlEditorTool() {
-        return cy.get('.graphiql-editor-tool');
-    }
-
-    static getVariablesBtn() {
-        return PlaygroundEditorSteps.getGraphiqlEditorTools().find('button[data-name="variables"]');
-    }
-
-    static openVariables() {
-        PlaygroundEditorSteps.getVariablesBtn().click();
-    }
-
-    static getHeadersBtn() {
-        return PlaygroundEditorSteps.getGraphiqlEditorTools().find('button[data-name="headers"]');
-    }
-
-    static openHeaders() {
-        PlaygroundEditorSteps.getHeadersBtn().click();
-    }
-
-    static getActiveGraphiqlEditorToolCodeMirror() {
-        return PlaygroundEditorSteps.getGraphiqlEditorTool().find('.graphiql-editor:not(.hidden) .CodeMirror');
-    }
-}

package/steps/header-steps.js

@@ -1,22 +0,0 @@
-export class HeaderSteps {
-    static getHeader() {
-        return cy.get('onto-header');
-    }
-
-    static openHomePage() {
-        HeaderSteps.getHeader().find('.home-page').click();
-    }
-
-    static logout() {
-        this.getHeader().find('onto-user-menu').click();
-        cy.get('.onto-user-menu-dropdown')
-            .contains('Logout')
-            .first()
-            // Force the click because Cypress sometimes determines that the item has 0x0 dimensions
-            .click({force: true});
-    }
-
-    static login() {
-        this.getHeader().find('.onto-user-login').click();
-    }
-}

package/steps/monitoring/queries-and-updates-steps.js

@@ -1,20 +0,0 @@
-import {BaseSteps} from "../base-steps";
-
-export class QueriesAndUpdatesSteps extends BaseSteps {
-
-    static visit() {
-        super.visit('/monitor/queries');
-    }
-
-    static getQueryAndUpdatePage() {
-        return super.getByTestId('monitoring-queries-and-updates');
-    }
-
-    static getPauseButton() {
-        return this.getQueryAndUpdatePage().getByTestId('pause-button');
-    }
-
-    static getNoRunningQueriesOrUpdates() {
-        return this.getQueryAndUpdatePage().getByTestId('no-running-queries-or-updates-alert');
-    }
-}

package/steps/monitoring/system-monitoring-steps.js

@@ -1,40 +0,0 @@
-import {BaseSteps} from "../base-steps";
-
-export class SystemMonitoringSteps extends BaseSteps {
-    static visit() {
-        cy.visit('/monitor/system');
-    }
-
-    static getSystemMonitoringPage() {
-        return this.getByTestId('system-monitoring-page');
-    }
-
-    static getCPUUsageChart() {
-        return this.getSystemMonitoringPage().getByTestId('cpu-usage-chart');
-    }
-
-    static getFileDescriptorChart() {
-        return this.getSystemMonitoringPage().getByTestId('file-descriptor-chart');
-    }
-
-    static getHeapMemoryChart() {
-        return this.getSystemMonitoringPage().getByTestId('heap-memory-chart');
-    }
-
-    static getOffHeapMemoryChart() {
-        return this.getSystemMonitoringPage().getByTestId('off-heap-memory-chart');
-    }
-
-    static getDiskStorageChart() {
-        return this.getSystemMonitoringPage().getByTestId('disk-storage-chart');
-    }
-
-    static verifyInitialStateWithSelectedRepository() {
-        this.getSystemMonitoringPage().should('be.visible');
-        this.getCPUUsageChart().should('be.visible');
-        this.getFileDescriptorChart().should('be.visible');
-        this.getHeapMemoryChart().should('be.visible');
-        this.getOffHeapMemoryChart().should('be.visible');
-        this.getDiskStorageChart().should('be.visible');
-    }
-}

package/steps/not-found/not-found-steps.js

@@ -1,23 +0,0 @@
-import {BaseSteps} from "../base-steps.js";
-
-export class NotFoundSteps extends BaseSteps {
-    static visit(url) {
-        BaseSteps.visit(url);
-    }
-
-    static getNotFoundBanner() {
-        return cy.getByTestId('not-found-banner');
-    }
-
-    static getNotFoundContent() {
-        return this.getNotFoundBanner().invoke('text');
-    }
-
-    static getGoHomeButton() {
-        return this.getNotFoundBanner().find('a.btn.btn-primary');
-    }
-
-    static clickGoHomeButton() {
-        this.getGoHomeButton().click();
-    }
-}

package/steps/rdf-resource-search-steps.js

@@ -1,55 +0,0 @@
-import {BaseSteps} from "./base-steps";
-
-export class RdfResourceSearchSteps extends BaseSteps {
-
-    static getComponent() {
-        return this.getByTestId('onto-rdf-search-component');
-    }
-
-    static getShowViewResourceMessageButton() {
-        return this.getByTestId('onto-show-view-resource-message');
-    }
-
-    static clickOnShowViewResourceMessageButton() {
-        this.getShowViewResourceMessageButton().click();
-    }
-
-    static getOpenButton() {
-        return this.getByTestId('onto-open-rdf-search-button');
-    }
-
-    static clickOnRDFResourceSearch() {
-        this.getOpenButton().click();
-    }
-
-    static getRDFResourceSearchInput() {
-        return this.getComponent().getByTestId('rdfSearchContext');
-    }
-
-    static getCloseButton() {
-        return this.getComponent().getByTestId('onto-rdf-resource-search-close-btn');
-    }
-
-    static getAutocompleteResults() {
-        return this.getComponent().getByTestId('onto-autocomplete-results');
-    }
-
-    static getAutocompleteSuggestionByPartialText(partialText) {
-        return this.getAutocompleteResults().getByTestId('onto-autocomplete-suggestion').contains(partialText);
-    }
-
-    static clickOnAutocompleteSuggestionByPartialText(partialText) {
-        return this.getAutocompleteSuggestionByPartialText(partialText).click();
-    }
-
-    static openRdfSearchBox() {
-        RdfResourceSearchSteps.clickOnRDFResourceSearch();
-        RdfResourceSearchSteps.getRDFResourceSearchInput()
-            .should('be.visible')
-            .and('be.focused');
-    }
-
-    static closeRDFSearchBox() {
-        this.getCloseButton().click();
-    }
-}

package/steps/rest-api-documentation-steps.js

@@ -1,15 +0,0 @@
-import {BaseSteps} from "./base-steps";
-
-export class RestApiDocumentationSteps extends BaseSteps {
-    static visit() {
-        cy.visit('webapi');
-    }
-
-    static getRestApiContent() {
-        return this.getByTestId('rest-api-content');
-    }
-
-    static verifyInitialState() {
-        this.getRestApiContent().should('be.visible');
-    }
-}

package/steps/setup/connectors-steps.js

@@ -1,32 +0,0 @@
-import {BaseSteps} from "../base-steps";
-
-export class ConnectorsSteps extends BaseSteps {
-    static visit() {
-        super.visit('/connectors');
-    }
-
-    static getConnectorsPage() {
-        return this.getByTestId('connectors-page');
-    }
-
-    static getConnectorButton(buttonId) {
-        return this.getConnectorsPage().getByTestId(`connector-${buttonId}`);
-    }
-
-    static getReloadAllButton() {
-        return this.getConnectorsPage().getByTestId('reload-all-connectors');
-    }
-
-    static expandConnector(connectorName, instanceName) {
-        this.getByTestId(`connector-name-${connectorName}`).getByTestId(`${instanceName}-connector-toggle-button`).find('a').click();
-    }
-
-    static viewSPARQLQuery(connectorName, instanceName) {
-        const connectorContent = this.getByTestId(`connector-name-${connectorName}`).getByTestId(`${instanceName}-connector-content`);
-        connectorContent.getByTestId('open-view-sparql-query-dialog').click();
-    }
-
-    static closeSPARQLQueryDialog() {
-        this.getByTestId('close-view-query-dialog').click();
-    }
-}