graphdb-workbench-tests 3.0.2 → 3.1.0-RC1

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

@@ -0,0 +1,87 @@
+import {RepositoriesStubs} from "../../../stubs/repositories/repositories-stubs";
+import {UserAndAccessSteps} from "../../../steps/setup/user-and-access-steps";
+import {LoginSteps} from "../../../steps/login-steps";
+import {ModalDialogSteps} from "../../../steps/modal-dialog-steps";
+import ImportSteps from "../../../steps/import/import-steps";
+import {MainMenuSteps} from "../../../steps/main-menu-steps";
+import {RepositorySelectorSteps} from "../../../steps/repository-selector-steps";
+import {ErrorSteps} from "../../../steps/error-steps";
+
+describe('User and Access', () => {
+
+    let repositoryId1;
+    let repositoryId2;
+    const graphqlUser = 'graphqlUser';
+
+    beforeEach(() => {
+        cy.viewport(1280, 1000);
+        RepositoriesStubs.spyGetRepositories();
+        repositoryId1 = 'user-access-repo1-' + Date.now();
+        repositoryId2 = 'user-access-repo2-' + Date.now();
+        cy.createRepository({id: repositoryId1});
+        cy.createRepository({id: repositoryId2});
+        cy.presetRepository(repositoryId1);
+        UserAndAccessSteps.visit();
+        // Users table should be visible
+        UserAndAccessSteps.getUsersTable().should('be.visible');
+    });
+
+    afterEach(() => {
+        cy.loginAsAdmin().then(() => {
+            cy.deleteRepository(repositoryId1, true);
+            cy.deleteRepository(repositoryId2, true);
+            cy.deleteUser(graphqlUser, true);
+            cy.switchOffFreeAccess(true);
+            cy.switchOffSecurity(true);
+        });
+
+    });
+
+    it('should restrict page when free access in on', () => {
+        // Given: There at least two repositories.
+        // When: I enable the security
+        UserAndAccessSteps.toggleSecurity();
+        LoginSteps.loginWithUser('admin', 'root');
+        // And: turn on Free Access
+        UserAndAccessSteps.getFreeAccessSwitchInput().should('not.be.checked');
+        UserAndAccessSteps.toggleFreeAccess();
+        // And: set graphql rights for the second repository when free access is ON
+        UserAndAccessSteps.clickFreeWriteAccessRepo(repositoryId2);
+        UserAndAccessSteps.clickFreeGraphqlAccessRepo(repositoryId2);
+        ModalDialogSteps.clickOKButton();
+
+        // When: I logout
+        LoginSteps.logout();
+        // And: repository with graphql rights is selected
+        RepositorySelectorSteps.selectRepository(repositoryId2);
+        // And: I click on the Import menu.
+        MainMenuSteps.clickOnMenuImport();
+
+        // Then: I should see the error message, because import view is available only for write access, repositoryId2 has only graphql rights.
+        ErrorSteps.verifyError('Some functionalities are not available because you do not have the required repository permissions.')
+    });
+
+    it('should restrict the repositories depending on whether free access is enabled and whether the user is logged in', () => {
+        // Given: There at least two repositories.
+        // When: I enable the security
+        UserAndAccessSteps.toggleSecurity();
+        LoginSteps.loginWithUser('admin', 'root');
+        // And: turn on Free Access
+        UserAndAccessSteps.toggleFreeAccess();
+        // And: set rights for the second repository when free access is ON
+        UserAndAccessSteps.clickFreeWriteAccessRepo(repositoryId2);
+        ModalDialogSteps.clickOKButton();
+
+        // When: I logout
+        LoginSteps.logout();
+        // Then: I should see only repositoryId2, as it is the only one configured for free access
+        RepositorySelectorSteps.getRepositorySelectorButton(repositoryId1).should('not.exist');
+        RepositorySelectorSteps.getRepositorySelectorButton(repositoryId2).should('exist');
+
+        // When: I log in again with a user who has access to all repositories
+        LoginSteps.loginWithUser('admin', 'root');
+        // Then: I should see both repositories in the repository selector, because the user has access to all repositories
+        RepositorySelectorSteps.getRepositorySelectorButton(repositoryId1).should('exist');
+        RepositorySelectorSteps.getRepositorySelectorButton(repositoryId2).should('exist');
+    });
+});

package/e2e-security/setup/users-and-access/users-and-access-initial-state.spec.js

@@ -0,0 +1,38 @@
+import {UserAndAccessSteps} from "../../../steps/setup/user-and-access-steps";
+import {MainMenuSteps} from "../../../steps/main-menu-steps";
+
+describe('Users and Access initial state', () => {
+    beforeEach(() => {
+        cy.intercept('GET', '**/rest/security/users').as('getUsers');
+    });
+
+    it('Should display the correct initial state when navigating via URL', () => {
+        // Given, I visit the Users and Access page via URL
+        UserAndAccessSteps.visit();
+        // Then,
+        validateInitialState();
+    });
+
+    it('Should display the correct initial state when navigating via the navigation menu', () => {
+        // Given, I visit the Users and Access page via the navigation menu
+        UserAndAccessSteps.visit();
+        MainMenuSteps.clickOnUsersAndAccess();
+        // Then,
+        validateInitialState();
+    });
+})
+
+function validateInitialState() {
+    cy.wait('@getUsers').then(({ response }) => {
+        const users = response.body;
+        expect(users).to.have.length(1);
+        expect(users[0].grantedAuthorities).to.have.length(1);
+    });
+
+    UserAndAccessSteps.getTableRow().should('have.length', 1);
+    UserAndAccessSteps.findUserInTable('admin')
+        .within(() => {
+            cy.get('.username').should('contain', 'admin');
+        });
+    UserAndAccessSteps.getToggleSecurityCheckbox().should('not.be.checked');
+}

package/fixtures/locale-en.json

@@ -285,7 +285,7 @@
         }
     },
     "ttyg": {
-        "helpInfo": "The <b>Talk to Your Graph</b> view lets you interact with your database through a conversational interface. You can ask natural language questions about the data and receive answers generated through the combined power of GraphDB and OpenAI. It supports multiple agent configurations and persistent chats for ongoing, contextual conversations.",
+        "helpInfo": "<b>Talk to Your Graph</b> lets you interact with your database through a conversational interface. Ask natural language questions about the data and receive answers generated through the combined power of GraphDB and LLMs. It supports multiple agent configurations and persistent chats for ongoing, contextual conversations.",
         "loading": "Loading...",
         "help": {
             "btn": {
@@ -397,6 +397,9 @@
                 "called": "Called {{('ttyg.chat_panel.query_name.' + name) | translate}}",
                 "no_query": "There is no query."
             },
+            "placeholder": {
+                "ask-input": "Ask anything"
+            },
             "query_name": {
                 "sparql_query":"SPARQL",
                 "fts_search": "Full-text search",
@@ -419,6 +422,13 @@
             "dialog": {
                 "confirm_repository_change": {
                     "body": "If you proceed with executing of SPARQL query, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
+                },
+                "token_usage_info": {
+                    "title": "Tokens usage",
+                    "prompt_tokens_info": "{{promptTokens}} prompt tokens",
+                    "prompt_tokens_info_description": "Tokens used to process instructions, chat history and user input.",
+                    "completion_tokens_info": "{{completionTokens}} completion tokens",
+                    "completion_tokens_info_description": "Tokens used to generate the response"
                 }
             },
             "messages": {
@@ -430,6 +440,7 @@
             "loading_agents": "Loading agents...",
             "deleting_agent": "Deleting agent...",
             "deleted_repository": "Deleted repository",
+            "incompatible_agent": "Incompatible with the current GraphDB version",
             "create_agent_modal": {
                 "title": {
                     "create": "Create Agent",
@@ -446,14 +457,26 @@
                         "placeholder": "Enter а user friendly name",
                         "tooltip": "A descriptive name that helps you identify this agent."
                     },
+                    "external_config": {
+                        "label": "External integration configuration",
+                        "tooltip": "Show URLs for the agent’s external access and integration"
+                    },
                     "repository": {
                         "label": "Repository ID",
                         "tooltip": "The ID of the repository that will be used to retrieve information from GraphDB. Ontop and FedX repositories are not supported."
                     },
                     "model": {
                         "label": "Model",
-                        "tooltip": "The model to use for this agent. More powerful models will provide better results.",
-                        "hint": "Check out the available OpenAI models <a href=\"https://platform.openai.com/docs/models\" target=\"_blank\">here</a>."
+                        "hint": "The default model is an admin-set property. Check with them for other available models.",
+                        "link_text": " Learn how to configure the model in the GraphDB documentation."
+                    },
+                    "context_size": {
+                        "label": "Context size",
+                        "tooltip": "Context window size - maximum number of tokens from prior messages included for contextual understanding. Ensure the model can handle the set context limit.",
+                        "field_addon": "tokens",
+                        "restore_default_btn": {
+                            "tooltip": "Reset to default"
+                        }
                     },
                     "temperature": {
                         "label": "Temperature",
@@ -609,7 +632,11 @@
                                 }
                             }
                         },
-                        "autocomplete_disabled_message": "You must <a href=\"{{autocompleteIndexPage}}\" target=\"_blank\">enable the Autocomplete index</a> on chosen repository to use this method",
+                        "autocomplete_disabled_message": {
+                            "message_1": "You must",
+                            "message_2": "enable the Autocomplete index",
+                            "message_3": "on chosen repository to use this method"
+                        },
                         "autocomplete_max_number_of_results_per_call": {
                             "label": "Max number of results (IRIs) per call",
                             "placeholder": "Automatic value",
@@ -642,6 +669,9 @@
                     },
                     "confirm_repository_change_before_open_connectors": {
                         "body": "If you proceed with creating the ChatGPT Retrieval connector, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
+                    },
+                    "confirm_repository_change_before_open_autocomplete_index": {
+                        "body": "If you proceed with enabling the autocomplete index, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
                     }
                 }
             },
@@ -679,6 +709,17 @@
                     }
                 }
             },
+            "external_integration_config_modal": {
+                "title": "Agent endpoints and external access",
+                "label": "Access {{agentName}} query methods via OpenAPI endpoints",
+                "agent_id_label": "Agent ID",
+                "query_methods": "Query methods via OpenAPI endpoints",
+                "dify_extension": "Dify extension",
+                "copy_tooltip": "Copy",
+                "agent_copied_tooltip": "Agent ID copied",
+                "openAPI_copied_tooltip": "OpenAPI endpoints link copied",
+                "dify_extension_copied_tooltip": "Dify extension link copied"
+            },
             "agent_select_menu": {
                 "no_selection_label": "Select an agent",
                 "deleted_agent": "[deleted agent]",
@@ -703,6 +744,7 @@
                     "tooltip": "Edit agent settings",
                     "tooltip_disabled": "You do not have permission to edit the agent"
                 },
+                "external_integration": "External integration",
                 "clone_agent": {
                     "label": "Clone",
                     "tooltip": "Clone Agent"
@@ -734,7 +776,7 @@
                 "no_agents": "No agents found for the selected filter.",
                 "help_1": "{{'ttyg.helpInfo'|translate|trustAsHtml}}",
                 "help_2": "{{'ttyg.help.how.content2'|translate|trustAsHtml}}",
-                "help_config": "To use <b>Talk to Your Graph</b>, GraphDB must first be configured to work with OpenAI. Please ensure that the necessary API keys and settings are in place before starting. For detailed setup instructions, refer to the <a href=\"{{talkToGraphDocumentationLink}}\" target=\"_blank\" rel=\"noopener\">documentation<i class=\"icon-external\"></i></a> or contact your administrator.",
+                "help_config": "To use <b>Talk to Your Graph</b>, GraphDB must first be configured to work with LLM API. Please ensure that the necessary LLM API type, url and key are in place before starting. For detailed setup instructions, refer to the <a href=\"{{talkToGraphDocumentationLink}}\" target=\"_blank\" rel=\"noopener\">documentation<i class=\"icon-external\"></i></a> or contact your administrator.",
                 "token_prop_warn1": "To enable this feature, set the config property",
                 "token_prop_warn2": "to your GPT token in",
                 "token_prop_warn3": "file.",
@@ -750,7 +792,7 @@
         "help.what.content": "{{'ttyg.helpInfo'|translate|trustAsHtml}}",
         "help.how.title": "How does it work?",
         "help.how.content": "The bot uses the ChatGPT Retrieval connector to fetch information it does not know about. As such, you must first create a suitable connector. See also the settings for fine-tuning the integration with the Retrieval connector.",
-        "help.how.content1": "<b>Talk to Your Graph</b> is powered by OpenAI's Assistants API. You begin by selecting or configuring an agent, which defines the context and rules for querying. Once set, you can start a conversation by asking questions in natural language. The assistant interprets your query, runs the appropriate query methods to retrieve data, and responds with an answer. Persistent chat ensures conversations stay contextually aware, enabling deeper, more coherent interactions over time. You can use multiple agents concurrently to cover various domains or data sources.",
+        "help.how.content1": "<b>Talk to Your Graph</b> is powered by LLM API configured by the database administrator. You begin by selecting or configuring an agent, which defines the context and rules for querying. Once set, you can start a conversation by asking questions in natural language. The assistant interprets your query, runs the appropriate query methods to retrieve data, and responds with an answer. Persistent chat ensures conversations stay contextually aware, enabling deeper, more coherent interactions over time. You can use multiple agents concurrently to cover various domains or data sources.",
         "help.how.content2": "An agent in <b>Talk to Your Graph</b> is an AI-driven assistant specifically configured to interact with your graph database. It uses advanced natural language processing to understand and respond to your questions by querying the database and delivering relevant information. Each agent is tailored to a specific context, making interactions seamless and efficient, whether you're retrieving data, exploring insights, or working on complex projects."
     },
     "graphql": {
@@ -1779,7 +1821,7 @@
     "view.roles.mapping.title": "Roles per Request Mapping",
     "view.register.license.title": "Register GraphDB License",
     "view.register.license.helpInfo": "The Register GraphDB license view is used to set a new GraphDB license. Upload the binary license or copy the license text in the designated text area.",
-    "view.existing.license.title": "Current GraphDB license",
+    "view.existing.license.title": "GraphDB license",
     "view.existing.license.helpInfo": "The Current GraphDB license view allows you to check the details of your current GraphDB license, as well as set a new license.",
     "view.similarity.indexes.title": "Similarity indexes",
     "view.similarity.indexes.helpInfo": "Similarity indexes help you look up semantically similar entities and text. Use this view to create, manage and view similarity indexes.",
@@ -2345,7 +2387,6 @@
     "delete.repo.warning.msg": "<p>Are you sure you want to delete the repository <strong>{{repositoryId}}</strong>?</p><p><span class=\"icon-2x icon-warning\" style=\"color: var(--primary-color-dark)\"></span>All data in the repository will be lost.</p>",
     "confirm.restart.repo": "Confirm restart",
     "confirm.restart.repo.warning.msg": "<p>Are you sure you want to restart the repository <strong>{{repositoryId}}</strong>?</p><p><span class=\"icon-2x icon-warning\" style=\"color: var(--primary-color-dark)\"></span>The repository will be shut down immediately and all running queries and updates will be cancelled.</p>",
-    "restart.repo.in.cluster.tooltip": "Restarting a repository is not supported in a cluster environment. To apply configuration changes, restart all cluster nodes.",
     "location.cannot.be.empty.error": "Location cannot be empty",
     "required.field": "This field is required",
     "invalid.field.value": "Invalid field value. The value should match the pattern '{{pattern}}'",
@@ -2514,6 +2555,7 @@
     "common.show_all": "Show all",
     "common.hide": "Hide",
     "common.learn_more_in_documentation": "Learn more in the GraphDB documentation",
+    "common.unsaved.changes": "You have unsaved changes. Are you sure that you want to exit?",
     "click.to": "Click to",
     "paginator.first.page.label": "First",
     "paginator.last.page.label": "Last",
@@ -2832,7 +2874,7 @@
     "sign.in": "Sign in",
     "sign.in.openid": "Sign in with OpenID",
     "gdb.license.info.header": "GraphDB License Information",
-    "supply.license.or.contact.us.warning": "Please supply a valid license. You can obtain a free license for GraphDB Free or an evaluation license for GraphDB Enterprise at <a href='https://www.ontotext.com/products/graphdb/'>Ontotext's website</a>.",
+    "supply.license.or.contact.us.warning": "Please supply a valid license. You can obtain a free license for GraphDB Free or an evaluation license for GraphDB Enterprise at <a rel=\"noopener\" target=\"_blank\" href='https://www.ontotext.com/products/graphdb/#try-graphdb'>Ontotext's website</a>.",
     "remove.license": "Remove license",
     "no.license.restrictions": "Without a valid license, GraphDB works in restricted mode and the only allowed operation is exporting repositories.",
     "no.license": "No license",
@@ -3171,7 +3213,7 @@
     "guide.step-action.edit-ttyg-agent": "Edit an agent",
     "guide.step-action.create-similarity-index": "Create Similarity index",
     "guide.step_plugin.execute-sparql-query.query-editor.content": "Enter the following SPARQL query: {{queryExplainMessageTranslated}}{{queryAsHtmlCodeElement}}",
-    "guide.step_plugin.execute-sparql-query.result-explain.content": "The table shows the results from executing the query.",
+    "guide.step_plugin.sparql-results-explain.content": "The table shows the results from executing the query.",
     "guide.step_plugin.execute-sparql-query.run-sparql-query.content": "Click on the <b>{{'query.editor.run.btn'|translate}}</b> button.",
     "guide.step_plugin.execute-sparql-query.copy-to-editor.button": "Copy to editor",
     "guide.step_plugin.import_rdf_file.content": "Click on the <b>{{'upload.rdf.files.label'|translate}}</b> button and choose a file with the name <b>{{resourceFile}}</b>.",
@@ -3191,7 +3233,7 @@
     "guide.step_plugin.visual-graph-link-focus.title": "Visual graph links",
     "guide.step_plugin.visual-graph-link-focus.content": "An arrow with a label represents one or more links between nodes. In this case, the arrow shows the relation <b>{{fromIriLabel}} &rarr; {{iriLabel}} &rarr; {{toIriLabel}}</b>.",
     "guide.step_plugin.download-guide-resource.title": "Download guide resources",
-    "guide.step_plugin.download-guide-resource.content": "This guide requires a file to be downloaded.<br>Please <a href=\"#\" ng-click=\"downloadGuidesFile('{{resourcePath}}', '{{resourceFile}}')\">download {{resourceFile}}</a>.",
+    "guide.step_plugin.download-guide-resource.content": "This guide requires a file to be downloaded.<br>Please <a href=\"#\" class=\"{{downloadButtonClass}}\">download {{resourceFile}}</a>.",
     "guide.step_plugin.download-guide-resource.download.message.failure": "Failed to download the '{{resourceFile}}' file!",
     "guide.step_plugin.choose-repository.content": "Click on the repository selection dropdown.",
     "guide.step_plugin.select-repository.content": "Click on the <b>{{getRepositoryId()}}</b> repository button.",
@@ -3213,17 +3255,18 @@
     "guide.step_plugin.visual-graph-properties-focus-property.content": "The values for generic properties like <b>{{focusProperty}}</b> are listed in dedicated sections.",
     "guide.step_plugin.visual-graph-expand.title": "Visual graph: expand node",
     "guide.step_plugin.visual-graph-expand.content": "Double click on <b>{{iriLabel}}</b> to expand the graph.",
-    "guide.step_plugin.class_hierarchy_intro.content": "The biggest circle shows all top-level classes. Every class may have subclasses shown as smaller circles within their parent class. The size of each circle indicates the proportion of RDF resources that belong to that class. Thus, bigger circles are classes that have more instances.",
-    "guide.step_plugin.class_hierarchy_zoom.content": "The class <b>{{iri}}</b> is a parent class that has subclasses. Zoom inside to have a better view by scrolling up with the mouse inside the circle.",
+    "guide.step_plugin.class-hierarchy-intro.content": "The biggest circle shows all top-level classes. Every class may have subclasses shown as smaller circles within their parent class. The size of each circle indicates the proportion of RDF resources that belong to that class. Thus, bigger circles are classes that have more instances.",
+    "guide.step_plugin.class-hierarchy-zoom-class.content": "The class <b>{{iri}}</b> is a parent class that has subclasses. Zoom inside to have a better view by scrolling up with the mouse inside the circle.",
     "guide.step_plugin.class-hierarchy-instances.title": "Class hierarchy instances",
-    "guide.step_plugin.class-hierarchy-instances.content": "Click on <b>{{iri}}</b> to show its instances.",
-    "guide.step_plugin.class-hierarchy-instances-side-panel.content": "The side panel shows the first 1,000 instances of the clicked class, <b>{{iri}}</b>.",
-    "guide.step_plugin.class-hierarchy-instances-focus.content": "<b>{{focusInstance}}</b> is an instance of the class <b>{{iri}}</b>.",
-    "guide.step_plugin.class-hierarchy-instances-count.content": "This link shows the number of instances for the selected class, <b>{{iri}}</b>. Click on the link to open the SPARQL editor with a preloaded query that selects all instances.",
-    "guide.step_plugin.class-hierarchy-instances-side-panel-close.content": "You can close the panel by clicking on the X icon.",
+    "guide.step_plugin.class-hierarchy-open-rdf-instances-side-panel.content": "Click on <b>{{iri}}</b> to show its instances.",
+    "guide.step_plugin.class-hierarchy-rdf-instances-side-panel-intro.content": "The side panel shows the first 1,000 instances of the clicked class, <b>{{iri}}</b>.",
+    "guide.step_plugin.class-hierarchy-explain-rdf-instance.content": "<b>{{focusInstance}}</b> is an instance of the class <b>{{iri}}</b>.",
+    "guide.step_plugin.class-hierarchy-rdf-instances-side-panel-open-all-instances-in-sparql.content": "This link shows the number of instances for the selected class, <b>{{iri}}</b>. Click on the link to open the SPARQL editor with a preloaded query that selects all instances.",
+    "guide.step_plugin.class-hierarchy-close-rdf-instances-side-panel.content": "You can close the panel by clicking on the X icon.",
     "guide.step_plugin.class-hierarchy-instances-query.content": "This SPARQL query selects all instances of the class <b>{{iri}}</b>. The query was entered automatically when you clicked on the view instances link.",
     "guide.step_plugin.class-hierarchy-instances-results.content": "The table shows the results. Note that in this particular case, the query was executed automatically.",
     "guide.step_plugin.class-hierarchy-instances-results.extraContent": "Do not worry &mdash; there will be a dedicated section on the SPARQL editor later in the guide.",
+    "guide.step_plugin.class-hierarchy-toggle-prefixes.content": "Click on <b>Show prefixes/Hide prefixes</b> to toggle the display of the prefixes.",
     "guide.step_plugin.table-graph-overview": "The table shows RDF statements where the subject is the selected IRI, <b>{{iriLabel}}</b>. The view can be configured to show statements where the IRI is the <i>subject</i>, <i>predicate</i>, <i>object</i>, <i>context</i> or in any position.",
     "guide.step_plugin.table-graph-link": "You can click on any IRI in the table to navigate to it. Click on <b>{{iriLabel}}</b>.",
     "guide.step_plugin.table-graph-role": "You can configure the view to show RDF statements where the current IRI is the <i>subject</i>, <i>predicate</i>, <i>object</i>, <i>context</i> or in any position. Click on the <b>{{role|translate}}</b> tab.",
@@ -3241,7 +3284,7 @@
     "guide.step_plugin.welcome-what.content": "{{translatedGuideDescription}}<p>Let's get started for real now!</p>",
     "guide.step_plugin.create-ttyg-agent.intro": "An agent is a helpful assistant that can answer your queries. You need to configure an agent in order to ask anything of Talk to Your Graph.",
     "guide.step_plugin.ttyg.missing-key.title": "Missing OpenAI key",
-    "guide.step_plugin.ttyg.missing-key.content": "To use <b>Talk to Your Graph</b>, GraphDB must first be configured to work with OpenAI. Please ensure that the necessary API keys and settings are in place before starting. For detailed setup instructions, refer to the documentation or contact your administrator.",
+    "guide.step_plugin.ttyg.missing-key.content": "To use <b>Talk to Your Graph</b>, GraphDB must first be configured to work with LLM API. Please ensure that the necessary LLM API type, url and key are in place before starting. For detailed setup instructions, refer to the documentation or contact your administrator.",
     "guide.step_plugin.create-ttyg-agent.create-agent": "Click on the create agent button to create a new agent.",
     "guide.step_plugin.create-ttyg-agent.save-agent-settings": "Click to save the agent settings.",
     "guide.step_plugin.sparql-search-method.content": "Enabling SPARQL search allows the agent to answers questions by performing a SPARQL query. This works well for datasets with good ontologies and performs well on closed-ended questions, including aggregations.",

package/fixtures/repositories/free-access.json

@@ -0,0 +1,13 @@
+{
+    "enabled": false,
+    "authorities": [
+        "READ_REPO_configurations@http://localhost:7202"
+    ],
+    "appSettings": {
+        "DEFAULT_INFERENCE": true,
+        "DEFAULT_VIS_GRAPH_SCHEMA": true,
+        "DEFAULT_SAMEAS": true,
+        "IGNORE_SHARED_QUERIES": false,
+        "EXECUTE_COUNT": true
+    }
+}

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

@@ -0,0 +1,44 @@
+{
+    "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-defaults.json

@@ -2,6 +2,8 @@
     "id": "id",
     "name": "Quadro",
     "model": "gpt-4o",
+    "api": "openai-completions",
+    "contextSize": 128000,
     "temperature": 0.7,
     "topP": 1.0,
     "seed": 0,

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

@@ -0,0 +1,79 @@
+[
+    {
+        "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/chats/ask-question.json

@@ -10,7 +10,12 @@
             "agentId": "requestBody.agentId",
             "message": "Reply to '${requestBody.question}' Second`",
             "timestamp": 53425243523,
-            "name": null
+            "name": null,
+            "usage": {
+                "completionTokens": 82,
+                "promptTokens": 10246,
+                "totalTokens": 10328
+            }
         },
         {
             "id": "msg_Bn07kVDCYT1qmgu1G7Zw0KNe_",
@@ -19,7 +24,12 @@
             "agentId": "requestBody.agentId",
             "message": "Reply to '${requestBody.question}",
             "timestamp": 23432424242,
-            "name": null
+            "name": null,
+            "usage": {
+                "completionTokens": 80,
+                "promptTokens": 10244,
+                "totalTokens": 10324
+            }
         }
     ]
 }

package/fixtures/ttyg/chats/get-chat.json

@@ -37,7 +37,12 @@
                 "role": "assistant",
                 "message": "Han Solo is a fictional character in the Star ",
                 "timestamp": "1725875332",
-                "name": null
+                "name": null,
+                "usage": {
+                    "completionTokens": 81,
+                    "promptTokens": 10245,
+                    "totalTokens": 10326
+                }
             }
         ],
         "timestamp": "1725875483"