graphdb-workbench-tests 2.8.0-TR6 → 2.8.0-TR8

package/fixtures/connectors/get-retrieval-connector.json

@@ -24,6 +24,6 @@
             "bulkUpdateBatchSize": 1000,
             "skipInitialIndexing": false
         },
-        "name": "gpt-connector"
+        "name": "retrieval-connector"
     }
 ]

package/fixtures/connectors/get-ttyg-chatgpt-connectors.json

@@ -0,0 +1,188 @@
+{
+    "starwars": [
+        {
+            "values": {
+                "retrievalBearerToken": "<replace-this-with-actual-value>",
+                "types": [
+                    "http://www.ontotext.com/example/wine#Wine"
+                ],
+                "retrievalUrl": "http://localhost:8000",
+                "fields": [
+                    {
+                        "propertyChain": [
+                            "localName()"
+                        ],
+                        "fieldName": "subject"
+                    },
+                    {
+                        "propertyChain": [
+                            "$self"
+                        ],
+                        "fieldName": "metadata",
+                        "objectFields": [
+                            {
+                                "propertyChain": [
+                                    "http://www.ontotext.com/example/wine#hasWinery"
+                                ],
+                                "fieldName": "author"
+                            }
+                        ]
+                    },
+                    {
+                        "valueFilter": "isExplicit($this)",
+                        "propertyChain": [
+                            "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
+                            "localName()"
+                        ],
+                        "fieldName": "type",
+                        "fieldTextPrefix": "is a"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#madeFromGrape",
+                            "http://www.w3.org/2000/01/rdf-schema#label"
+                        ],
+                        "fieldName": "grape",
+                        "fieldTextPrefix": "made from {}"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#hasSugar"
+                        ],
+                        "fieldName": "sugar"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#hasYear"
+                        ],
+                        "fieldName": "year"
+                    }
+                ]
+            },
+            "name": "ChatGPT_starwars_one"
+        },
+        {
+            "values": {
+                "retrievalBearerToken": "<replace-this-with-actual-value>",
+                "types": [
+                    "http://www.ontotext.com/example/wine#Wine"
+                ],
+                "retrievalUrl": "http://localhost:8000",
+                "fields": [
+                    {
+                        "propertyChain": [
+                            "localName()"
+                        ],
+                        "fieldName": "subject"
+                    },
+                    {
+                        "propertyChain": [
+                            "$self"
+                        ],
+                        "fieldName": "metadata",
+                        "objectFields": [
+                            {
+                                "propertyChain": [
+                                    "http://www.ontotext.com/example/wine#hasWinery"
+                                ],
+                                "fieldName": "author"
+                            }
+                        ]
+                    },
+                    {
+                        "valueFilter": "isExplicit($this)",
+                        "propertyChain": [
+                            "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
+                            "localName()"
+                        ],
+                        "fieldName": "type",
+                        "fieldTextPrefix": "is a"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#madeFromGrape",
+                            "http://www.w3.org/2000/01/rdf-schema#label"
+                        ],
+                        "fieldName": "grape",
+                        "fieldTextPrefix": "made from {}"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#hasSugar"
+                        ],
+                        "fieldName": "sugar"
+                    },
+                    {
+                        "propertyChain": [
+                            "http://www.ontotext.com/example/wine#hasYear"
+                        ],
+                        "fieldName": "year"
+                    }
+                ]
+            },
+            "name": "ChatGPT_starwars_two"
+        }
+    ],
+    "biomarkers": [ {
+        "values": {
+            "retrievalBearerToken": "<replace-this-with-actual-value>",
+            "types": [
+                "http://www.ontotext.com/example/wine#Wine"
+            ],
+            "retrievalUrl": "http://localhost:8000",
+            "fields": [
+                {
+                    "propertyChain": [
+                        "localName()"
+                    ],
+                    "fieldName": "subject"
+                },
+                {
+                    "propertyChain": [
+                        "$self"
+                    ],
+                    "fieldName": "metadata",
+                    "objectFields": [
+                        {
+                            "propertyChain": [
+                                "http://www.ontotext.com/example/wine#hasWinery"
+                            ],
+                            "fieldName": "author"
+                        }
+                    ]
+                },
+                {
+                    "valueFilter": "isExplicit($this)",
+                    "propertyChain": [
+                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
+                        "localName()"
+                    ],
+                    "fieldName": "type",
+                    "fieldTextPrefix": "is a"
+                },
+                {
+                    "propertyChain": [
+                        "http://www.ontotext.com/example/wine#madeFromGrape",
+                        "http://www.w3.org/2000/01/rdf-schema#label"
+                    ],
+                    "fieldName": "grape",
+                    "fieldTextPrefix": "made from {}"
+                },
+                {
+                    "propertyChain": [
+                        "http://www.ontotext.com/example/wine#hasSugar"
+                    ],
+                    "fieldName": "sugar"
+                },
+                {
+                    "propertyChain": [
+                        "http://www.ontotext.com/example/wine#hasYear"
+                    ],
+                    "fieldName": "year"
+                }
+            ]
+        },
+        "name": "ChatGPT_biomarkers_one"
+    }],
+    "ttyg-repo-1725518186812": []
+}

package/fixtures/locale-en.json

@@ -232,8 +232,13 @@
                 "body": "Do you really want to delete <b>{{chatName}}</b>? All chat history will be lost."
             }
         },
+        "messages": {
+            "text_copy_successful": "Successfully copied to the clipboard.",
+            "text_copy_failed": "Failed copying to the clipboard."
+        },
         "chat": {
             "loading_chats": "Loading chats...",
+            "deleting_chat": "Deleting chats...",
             "btn": {
                 "open_sidebar": {
                     "tooltip": "Open sidebar"
@@ -262,10 +267,17 @@
                 "rename_failure": "Failed to rename the conversation. Please try again.",
                 "delete_failure": "Failed to delete the conversation. Please try again.",
                 "export_failure": "Failed to export the conversation. Please try again."
+            },
+            "dialog": {
+                "chat_is_missing": {
+                    "title": "Error",
+                    "body": "Selected conversation cannot be found. Probably it was deleted."
+                }
             }
         },
         "chat_panel": {
             "hint": "Talk to your graph – simply ask a question!",
+            "deleted_agent": "<span class=\"text-warning\"><i class=\"fa-regular fa-triangle-exclamation fa-xs\"></i> deleted agent</span>",
             "btn": {
                 "ask": {
                     "label": "Ask"
@@ -275,19 +287,35 @@
                 },
                 "copy": {
                     "tooltip": "Copy"
+                },
+                "explain_response": {
+                    "tooltip": "Explain response"
+                },
+                "derive_answer": {
+                    "label": "How did you derive this answer?",
+                    "hint": "Hint: you can also ask the model, for example"
                 }
             },
-            "messages": {
-                "answer_copy_successful": "The answer was successfully copied to the clipboard.",
-                "answer_copy_failed": "Failed to copy the answer to the clipboard."
+            "labels": {
+                "query_method": "Query method",
+                "raw_query": "Raw query",
+                "sparql_query": "SPARQL query"
+
+            },
+            "query_name": {
+                "sparql_search":"SPARQL",
+                "fts_search": "Full-text search",
+                "similarity_search": "Similarity search",
+                "retrieval_search": "ChatGPT retrieval connector"
             },
             "dialog": {
-                "confirm_repository_change_before_open_similarity": {
-                    "body": "If you proceed with creating the similarity index, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
-                },
-                "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": {
+                    "body": "If you proceed with executing of SPARQL query, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
                 }
+            },
+            "messages": {
+                "explain_response_failure": "Failed to retrieve the explanation for the response.",
+                "agent_changed_info": "Agent changed to <b> {{agentName}} </b>"
             }
         },
         "agent": {
@@ -355,6 +383,11 @@
                             "message_1": "You must",
                             "message_2": "create a similarity index",
                             "message_3": "to use this method"
+                        },
+                        "btn": {
+                            "reload": {
+                                "tooltip": "Refresh the similarity indexes."
+                            }
                         }
                     },
                     "similarity_threshold": {
@@ -366,6 +399,11 @@
                             "message_1": "You must",
                             "message_2": "create ChatGPT retrieval connector",
                             "message_3": "to use this method"
+                        },
+                        "btn": {
+                            "reload": {
+                                "tooltip": "Refresh the ChatGPT retrieval connectors."
+                            }
                         }
                     },
                     "connector_id": {
@@ -403,6 +441,14 @@
                     "save": {
                         "label": "Save"
                     }
+                },
+                "dialog": {
+                    "confirm_repository_change_before_open_similarity": {
+                        "body": "If you proceed with creating the similarity index, GraphDB will open in a new tab and switch to the <b>{{repositoryId}}</b> repository."
+                    },
+                    "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."
+                    }
                 }
             },
             "delete_agent_modal": {

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

@@ -41,6 +41,34 @@
             "writable": true,
             "unsupported": false,
             "state": "INACTIVE"
+        },
+        {
+            "id": "Fedx_repository",
+            "title": "",
+            "uri": "http://localhost:8080/graphdb/repositories/Fedx_repository",
+            "externalUrl": "http://boyantonchev:9000/repositories/Fedx_repository",
+            "local": true,
+            "type": "fedx",
+            "sesameType": "graphdb:FedXRepository",
+            "location": "",
+            "readable": true,
+            "writable": true,
+            "unsupported": false,
+            "state": "INACTIVE"
+        },
+        {
+            "id": "Ontop_repository",
+            "title": "",
+            "uri": "http://localhost:8080/graphdb/repositories/Fedx_repository",
+            "externalUrl": "http://boyantonchev:9000/repositories/Fedx_repository",
+            "local": true,
+            "type": "ontop",
+            "sesameType": "graphdb:FedXRepository",
+            "location": "",
+            "readable": true,
+            "writable": true,
+            "unsupported": false,
+            "state": "INACTIVE"
         }
     ]
 }

package/fixtures/similarity/get-ttyg-similarity-connectors.json

@@ -0,0 +1,46 @@
+{
+    "starwars": [
+        {
+            "name": "similarity_index_starwars_one",
+            "options": "-termweight idf",
+            "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
+            "searchQuery": "PREFIX :<http://www.ontotext.com/graphdb/similarity/>\nPREFIX similarity-index:<http://www.ontotext.com/graphdb/similarity/instance/>\nPREFIX pubo: <http://ontology.ontotext.com/publishing#>\n\nSELECT ?documentID ?score {\n    ?search a ?index ;\n        ?searchType ?query;\n        :searchParameters ?parameters;\n        ?resultType ?result .\n    ?result :value ?documentID ;\n            :score ?score.\n}",
+            "analogicalQuery": "",
+            "stopList": null,
+            "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
+            "status": "BUILT",
+            "infer": true,
+            "sameAs": true,
+            "type": "text"
+        },
+        {
+            "name": "similarity_index_starwars_two",
+            "options": "-termweight idf",
+            "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
+            "searchQuery": "PREFIX :<http://www.ontotext.com/graphdb/similarity/>\nPREFIX similarity-index:<http://www.ontotext.com/graphdb/similarity/instance/>\nPREFIX pubo: <http://ontology.ontotext.com/publishing#>\n\nSELECT ?documentID ?score {\n    ?search a ?index ;\n        ?searchType ?query;\n        :searchParameters ?parameters;\n        ?resultType ?result .\n    ?result :value ?documentID ;\n            :score ?score.\n}",
+            "analogicalQuery": "",
+            "stopList": null,
+            "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
+            "status": "BUILT",
+            "infer": true,
+            "sameAs": true,
+            "type": "text"
+        }
+    ],
+    "biomarkers": [
+        {
+            "name": "similarity_index_biomarkers_one",
+            "options": "-termweight idf",
+            "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
+            "searchQuery": "PREFIX :<http://www.ontotext.com/graphdb/similarity/>\nPREFIX similarity-index:<http://www.ontotext.com/graphdb/similarity/instance/>\nPREFIX pubo: <http://ontology.ontotext.com/publishing#>\n\nSELECT ?documentID ?score {\n    ?search a ?index ;\n        ?searchType ?query;\n        :searchParameters ?parameters;\n        ?resultType ?result .\n    ?result :value ?documentID ;\n            :score ?score.\n}",
+            "analogicalQuery": "",
+            "stopList": null,
+            "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
+            "status": "BUILT",
+            "infer": true,
+            "sameAs": true,
+            "type": "text"
+        }
+    ],
+    "ttyg-repo-1725518186812": []
+}

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

@@ -0,0 +1,41 @@
+{
+    "id": "id",
+    "name": "Quadro",
+    "model": "gpt-4o",
+    "temperature": 0.7,
+    "topP": 1.0,
+    "seed": 0,
+    "repositoryId": "test-repository",
+    "instructions": {
+        "systemInstruction": "You are a helpful, knowledgeable, and friendly assistant. Your goal is to provide clear and accurate information while being polite, respectful, and professional.",
+        "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 .}}"
+        },
+        {
+            "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-new-agent.json

@@ -17,77 +17,5 @@
                 "sparqlQuery": "select ?s ?p ?o where {?s ?p ?o .}"
             }
         ]
-    },
-    {
-        "id": "asst_gAPcrHQQ9ZIxD5eXWH2BNFfo",
-        "name": "agent-1",
-        "model": "gpt-4o",
-        "temperature": 0.0,
-        "topP": 0.0,
-        "seed": null,
-        "repositoryId": "starwars",
-        "instructions": {
-            "systemInstruction": "",
-            "userInstruction": ""
-        },
-        "assistantExtractionMethods": [
-            {
-                "ftsMethod": "fts_search"
-            }
-        ]
-    },
-    {
-        "id": "asst_qMyCpCBmqxV9I2B8UoMfFzc5",
-        "name": "agent-2",
-        "model": "gpt-4o",
-        "temperature": 0.0,
-        "topP": 0.0,
-        "seed": null,
-        "repositoryId": null,
-        "instructions": {
-            "systemInstruction": "string\n\nstring",
-            "userInstruction": "string"
-        },
-        "assistantExtractionMethods": [
-            {
-                "ftsMethod": "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": [
-            {
-                "ftsMethod": "fts_search"
-            }
-        ]
-    },
-    {
-        "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": [
-            {
-                "ftsMethod": "fts_search"
-            }
-        ]
     }
 ]

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

@@ -0,0 +1,24 @@
+{
+    "id": "asst_G8EtHyT8kAGeDmCa3Nh6y74v",
+    "name": "Test agent",
+    "model": "gpt-4o",
+    "temperature": 0.7,
+    "topP": 1.0,
+    "repositoryId": "starwars",
+    "instructions": {
+        "systemInstruction": null,
+        "userInstruction": null
+    },
+    "assistantExtractionMethods": [
+        {
+            "method": "sparql_search",
+            "ontologyGraph": null,
+            "sparqlQuery": "CONSTRUCT {\n    ?s ?p ?o\n} WHERE {\n    GRAPH <http://example.com/sw-ont> {\n        ?s ?p ?o\n    }\n}"
+        }
+    ],
+    "additionalExtractionMethods": [
+        {
+            "method": "iri_discovery_search"
+        }
+    ]
+}