graphdb-workbench-tests 2.7.6 → 2.8.0-RC1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (119) hide show
  1. package/cypress.config.js +3 -0
  2. package/fixtures/cluster/2-nodes-cluster-group-status-deleted.json +30 -0
  3. package/fixtures/cluster/2-nodes-cluster-group-status.json +30 -0
  4. package/fixtures/cluster/3-nodes-cluster-group-status-after-replace.json +44 -0
  5. package/fixtures/cluster/3-nodes-cluster-group-status-building-snapshot.json +4 -1
  6. package/fixtures/cluster/3-nodes-cluster-group-status-receiving-snapshot.json +4 -1
  7. package/fixtures/cluster/3-nodes-cluster-group-status-sending-snapshot.json +4 -1
  8. package/fixtures/cluster/3-nodes-cluster-group-status-waiting-for-snapshot.json +4 -1
  9. package/fixtures/cluster/3-nodes-cluster-group-status.json +12 -3
  10. package/fixtures/cluster/4-nodes-cluster-group-status.json +58 -0
  11. package/fixtures/cluster/cluster-config.json +1 -0
  12. package/fixtures/cluster/cluster-node-status.json +4 -1
  13. package/fixtures/connectors/get-connectors.json +8 -0
  14. package/fixtures/connectors/get-retrieval-connector-0.json +1 -0
  15. package/fixtures/connectors/get-retrieval-connector.json +29 -0
  16. package/fixtures/connectors/get-ttyg-chatgpt-connectors.json +188 -0
  17. package/fixtures/locale-en.json +630 -61
  18. package/fixtures/namespaces/get-repository-starwars-namespaces.json +252 -0
  19. package/fixtures/remote-location/get-0-remote-locations.json +1 -2
  20. package/fixtures/remote-location/get-1-remote-locations.json +2 -4
  21. package/fixtures/remote-location/get-2-remote-locations.json +3 -6
  22. package/fixtures/remote-location/get-3-remote-locations.json +4 -8
  23. package/fixtures/remote-location/get-4-remote-locations.json +54 -0
  24. package/fixtures/remote-location/remote-location-status-in-cluster.json +1 -2
  25. package/fixtures/remote-location/remote-location-status-not-in-cluster.json +1 -2
  26. package/fixtures/remote-location/remote-locations-filter.json +1 -2
  27. package/fixtures/repositories/get-locations.json +67 -0
  28. package/fixtures/repositories/get-repositories.json +106 -0
  29. package/fixtures/repositories/get-repository-config-starwars-disabled-fts.json +201 -0
  30. package/fixtures/repositories/get-repository-config-starwars-enabled-fts.json +201 -0
  31. package/fixtures/repositories/get-ttyg-repositories.json +74 -0
  32. package/fixtures/similarity/get-similarity-indexes-0.json +1 -0
  33. package/fixtures/similarity/get-similarity-indexes.json +15 -0
  34. package/fixtures/similarity/get-ttyg-similarity-connectors.json +46 -0
  35. package/fixtures/ttyg/agent/create-agent.json +20 -0
  36. package/fixtures/ttyg/agent/get-agent-defaults.json +42 -0
  37. package/fixtures/ttyg/agent/get-agent-list-0.json +1 -0
  38. package/fixtures/ttyg/agent/get-agent-list-after-deleted.json +56 -0
  39. package/fixtures/ttyg/agent/get-agent-list-new-agent.json +22 -0
  40. package/fixtures/ttyg/agent/get-agent-list.json +77 -0
  41. package/fixtures/ttyg/agent/get-agent.json +25 -0
  42. package/fixtures/ttyg/chats/ask-question.json +25 -0
  43. package/fixtures/ttyg/chats/create/create-chat-response.json +16 -0
  44. package/fixtures/ttyg/chats/create/get-chats-after-create.json +12 -0
  45. package/fixtures/ttyg/chats/create/get-chats-before-create.json +7 -0
  46. package/fixtures/ttyg/chats/deleted-chat.json +3 -0
  47. package/fixtures/ttyg/chats/explain-response-1.json +59 -0
  48. package/fixtures/ttyg/chats/explain-response-2.json +59 -0
  49. package/fixtures/ttyg/chats/export-chat.json +34 -0
  50. package/fixtures/ttyg/chats/get-chat-list-0.json +1 -0
  51. package/fixtures/ttyg/chats/get-chat-list-with-deleted-chat.json +17 -0
  52. package/fixtures/ttyg/chats/get-chat-list-with-renamed-chat.json +22 -0
  53. package/fixtures/ttyg/chats/get-chat-list.json +22 -0
  54. package/fixtures/ttyg/chats/get-chat.json +199 -0
  55. package/fixtures/ttyg/chats/renamed-chat.json +4 -0
  56. package/integration/cluster/cluster-management.spec.js +0 -170
  57. package/integration/cluster/edit-cluster-nodes-modal.spec.js +425 -0
  58. package/integration/explore/graphs.overview.spec.js +4 -0
  59. package/integration/home/cookie-policy.spec.js +65 -0
  60. package/integration/home/create-repository.spec.js +35 -0
  61. package/integration/home/documentation-link.spec.js +60 -0
  62. package/integration/home/google-analytics.spec.js +60 -0
  63. package/integration/home/language-selector.spec.js +19 -0
  64. package/integration/home/rdf-resource-search.spec.js +192 -0
  65. package/integration/home/view-resource-autocomplete.spec.js +52 -0
  66. package/integration/home/workbench.home.spec.js +1 -277
  67. package/integration/import/import-user-data-file-upload.spec.js +13 -0
  68. package/integration/import/import-user-data.spec.js +8 -2
  69. package/integration/import/import-view.spec.js +6 -1
  70. package/integration/repository/attach-remote-location.spec.js +203 -0
  71. package/integration/repository/ontop-repository.spec.js +87 -1
  72. package/integration/repository/repositories.spec.js +4 -19
  73. package/integration/setup/my-settings.spec.js +2 -0
  74. package/integration/ttyg/agent-list.spec.js +76 -0
  75. package/integration/ttyg/agent-select-menu.spec.js +141 -0
  76. package/integration/ttyg/chat-list.spec.js +286 -0
  77. package/integration/ttyg/chat-panel.spec.js +175 -0
  78. package/integration/ttyg/clone-agent.spec.js +75 -0
  79. package/integration/ttyg/create-agent.spec.js +560 -0
  80. package/integration/ttyg/create-chat.spec.js +69 -0
  81. package/integration/ttyg/delete-agent.spec.js +51 -0
  82. package/integration/ttyg/edit-agent.spec.js +54 -0
  83. package/integration/ttyg/ttyg-permission.spec.js +66 -0
  84. package/integration/ttyg/ttyg-view.spec.js +75 -0
  85. package/npm-shrinkwrap.json +215 -220
  86. package/package.json +5 -6
  87. package/steps/alert-dialog-steps.js +25 -0
  88. package/steps/cluster/cluster-page-steps.js +8 -0
  89. package/steps/cluster/custer-nodes-configuration-steps.js +107 -0
  90. package/steps/home-steps.js +48 -5
  91. package/steps/import/import-steps.js +11 -11
  92. package/steps/modal-dialog-steps.js +8 -0
  93. package/steps/ontop-repository-steps.js +26 -0
  94. package/steps/repositories/attach-repository-steps.js +118 -0
  95. package/steps/repository-steps.js +53 -5
  96. package/steps/setup/settings-steps.js +17 -0
  97. package/steps/ttyg/chat-panel-steps.js +62 -0
  98. package/steps/ttyg/ttyg-agent-settings-modal.steps.js +462 -0
  99. package/steps/ttyg/ttyg-view-steps.js +333 -0
  100. package/steps/window-steps.js +5 -0
  101. package/stubs/cluster/cluster-stubs.js +127 -7
  102. package/stubs/cluster/remote-location-stubs.js +46 -0
  103. package/stubs/connector-stubs.js +39 -0
  104. package/stubs/environment-stubs.js +27 -0
  105. package/stubs/license-stubs.js +101 -0
  106. package/stubs/repositories/repositories-stubs.js +133 -0
  107. package/stubs/repositories-stub.js +15 -0
  108. package/stubs/security-stubs.js +7 -0
  109. package/stubs/similarity-index-stubs.js +32 -0
  110. package/stubs/stubs.js +4 -0
  111. package/stubs/ttyg/ttyg-stubs.js +166 -0
  112. package/support/commands.js +2 -0
  113. package/support/index.js +17 -0
  114. package/support/security-command.js +25 -0
  115. package/support/settings-commands.js +4 -5
  116. package/support/user-commands.js +31 -0
  117. package/steps/cluster/add-remote-location-dialog-steps.js +0 -11
  118. package/steps/cluster/create-cluster-dialog-steps.js +0 -39
  119. package/steps/cluster/replace-nodes-dialog-steps.js +0 -39
@@ -0,0 +1,201 @@
1
+ {
2
+ "id":"starwars",
3
+ "title":"",
4
+ "type":"graphdb",
5
+ "sesameType":"graphdb:SailRepository",
6
+ "location":"",
7
+ "params":{
8
+ "queryTimeout":{
9
+ "name":"queryTimeout",
10
+ "label":"Query timeout (seconds)",
11
+ "value":"0"
12
+ },
13
+ "cacheSelectNodes":{
14
+ "name":"cacheSelectNodes",
15
+ "label":"Cache select nodes",
16
+ "value":"true"
17
+ },
18
+ "rdfsSubClassReasoning":{
19
+ "name":"rdfsSubClassReasoning",
20
+ "label":"RDFS subClass reasoning",
21
+ "value":"true"
22
+ },
23
+ "validationEnabled":{
24
+ "name":"validationEnabled",
25
+ "label":"Enable the SHACL validation",
26
+ "value":"true"
27
+ },
28
+ "ftsStringLiteralsIndex":{
29
+ "name":"ftsStringLiteralsIndex",
30
+ "label":"FTS index for xsd:string literals",
31
+ "value":"default"
32
+ },
33
+ "shapesGraph":{
34
+ "name":"shapesGraph",
35
+ "label":"Named graphs for SHACL shapes",
36
+ "value":"http://rdf4j.org/schema/rdf4j#SHACLShapeGraph"
37
+ },
38
+ "parallelValidation":{
39
+ "name":"parallelValidation",
40
+ "label":"Run parallel validation",
41
+ "value":"true"
42
+ },
43
+ "checkForInconsistencies":{
44
+ "name":"checkForInconsistencies",
45
+ "label":"Enable consistency checks",
46
+ "value":"false"
47
+ },
48
+ "performanceLogging":{
49
+ "name":"performanceLogging",
50
+ "label":"Log the execution time per shape",
51
+ "value":"false"
52
+ },
53
+ "disableSameAs":{
54
+ "name":"disableSameAs",
55
+ "label":"Disable owl:sameAs",
56
+ "value":"true"
57
+ },
58
+ "ftsIrisIndex":{
59
+ "name":"ftsIrisIndex",
60
+ "label":"FTS index for full-text indexing of IRIs",
61
+ "value":"none"
62
+ },
63
+ "entityIndexSize":{
64
+ "name":"entityIndexSize",
65
+ "label":"Entity index size",
66
+ "value":"10000000"
67
+ },
68
+ "dashDataShapes":{
69
+ "name":"dashDataShapes",
70
+ "label":"DASH data shapes extensions",
71
+ "value":"true"
72
+ },
73
+ "queryLimitResults":{
74
+ "name":"queryLimitResults",
75
+ "label":"Limit query results",
76
+ "value":"0"
77
+ },
78
+ "throwQueryEvaluationExceptionOnTimeout":{
79
+ "name":"throwQueryEvaluationExceptionOnTimeout",
80
+ "label":"Throw exception on query timeout",
81
+ "value":"false"
82
+ },
83
+ "member":{
84
+ "name":"member",
85
+ "label":"FedX repo members",
86
+ "value":[
87
+
88
+ ]
89
+ },
90
+ "storageFolder":{
91
+ "name":"storageFolder",
92
+ "label":"Storage folder",
93
+ "value":"storage"
94
+ },
95
+ "validationResultsLimitPerConstraint":{
96
+ "name":"validationResultsLimitPerConstraint",
97
+ "label":"Validation results limit per constraint",
98
+ "value":"1000"
99
+ },
100
+ "enablePredicateList":{
101
+ "name":"enablePredicateList",
102
+ "label":"Enable predicate list index",
103
+ "value":"true"
104
+ },
105
+ "transactionalValidationLimit":{
106
+ "name":"transactionalValidationLimit",
107
+ "label":"Transactional validation limit",
108
+ "value":"500000"
109
+ },
110
+ "ftsIndexes":{
111
+ "name":"ftsIndexes",
112
+ "label":"FTS indexes to build (comma delimited)",
113
+ "value":"default, iri"
114
+ },
115
+ "logValidationPlans":{
116
+ "name":"logValidationPlans",
117
+ "label":"Log the executed validation plans",
118
+ "value":"false"
119
+ },
120
+ "imports":{
121
+ "name":"imports",
122
+ "label":"Imported RDF files(';' delimited)",
123
+ "value":""
124
+ },
125
+ "isShacl":{
126
+ "name":"isShacl",
127
+ "label":"Enable SHACL validation",
128
+ "value":"false"
129
+ },
130
+ "inMemoryLiteralProperties":{
131
+ "name":"inMemoryLiteralProperties",
132
+ "label":"Cache literal language tags",
133
+ "value":"true"
134
+ },
135
+ "ruleset":{
136
+ "name":"ruleset",
137
+ "label":"Ruleset",
138
+ "value":"rdfsplus-optimized"
139
+ },
140
+ "readOnly":{
141
+ "name":"readOnly",
142
+ "label":"Read-only",
143
+ "value":"false"
144
+ },
145
+ "enableLiteralIndex":{
146
+ "name":"enableLiteralIndex",
147
+ "label":"Enable literal index",
148
+ "value":"true"
149
+ },
150
+ "enableFtsIndex":{
151
+ "name":"enableFtsIndex",
152
+ "label":"Enable full-text search (FTS) index",
153
+ "value":"false"
154
+ },
155
+ "defaultNS":{
156
+ "name":"defaultNS",
157
+ "label":"Default namespaces for imports(';' delimited)",
158
+ "value":""
159
+ },
160
+ "enableContextIndex":{
161
+ "name":"enableContextIndex",
162
+ "label":"Enable context index",
163
+ "value":"false"
164
+ },
165
+ "baseURL":{
166
+ "name":"baseURL",
167
+ "label":"Base URL",
168
+ "value":"http://example.org/owlim#"
169
+ },
170
+ "logValidationViolations":{
171
+ "name":"logValidationViolations",
172
+ "label":"Log validation violations",
173
+ "value":"false"
174
+ },
175
+ "globalLogValidationExecution":{
176
+ "name":"globalLogValidationExecution",
177
+ "label":"Log every execution step of the SHACL validation",
178
+ "value":"false"
179
+ },
180
+ "entityIdSize":{
181
+ "name":"entityIdSize",
182
+ "label":"Entity ID size",
183
+ "value":"32"
184
+ },
185
+ "repositoryType":{
186
+ "name":"repositoryType",
187
+ "label":"Repository type",
188
+ "value":"file-repository"
189
+ },
190
+ "eclipseRdf4jShaclExtensions":{
191
+ "name":"eclipseRdf4jShaclExtensions",
192
+ "label":"RDF4J SHACL extensions",
193
+ "value":"true"
194
+ },
195
+ "validationResultsLimitTotal":{
196
+ "name":"validationResultsLimitTotal",
197
+ "label":"Validation results limit total",
198
+ "value":"1000000"
199
+ }
200
+ }
201
+ }
@@ -0,0 +1,201 @@
1
+ {
2
+ "id":"starwars",
3
+ "title":"",
4
+ "type":"graphdb",
5
+ "sesameType":"graphdb:SailRepository",
6
+ "location":"",
7
+ "params":{
8
+ "queryTimeout":{
9
+ "name":"queryTimeout",
10
+ "label":"Query timeout (seconds)",
11
+ "value":"0"
12
+ },
13
+ "cacheSelectNodes":{
14
+ "name":"cacheSelectNodes",
15
+ "label":"Cache select nodes",
16
+ "value":"true"
17
+ },
18
+ "rdfsSubClassReasoning":{
19
+ "name":"rdfsSubClassReasoning",
20
+ "label":"RDFS subClass reasoning",
21
+ "value":"true"
22
+ },
23
+ "validationEnabled":{
24
+ "name":"validationEnabled",
25
+ "label":"Enable the SHACL validation",
26
+ "value":"true"
27
+ },
28
+ "ftsStringLiteralsIndex":{
29
+ "name":"ftsStringLiteralsIndex",
30
+ "label":"FTS index for xsd:string literals",
31
+ "value":"default"
32
+ },
33
+ "shapesGraph":{
34
+ "name":"shapesGraph",
35
+ "label":"Named graphs for SHACL shapes",
36
+ "value":"http://rdf4j.org/schema/rdf4j#SHACLShapeGraph"
37
+ },
38
+ "parallelValidation":{
39
+ "name":"parallelValidation",
40
+ "label":"Run parallel validation",
41
+ "value":"true"
42
+ },
43
+ "checkForInconsistencies":{
44
+ "name":"checkForInconsistencies",
45
+ "label":"Enable consistency checks",
46
+ "value":"false"
47
+ },
48
+ "performanceLogging":{
49
+ "name":"performanceLogging",
50
+ "label":"Log the execution time per shape",
51
+ "value":"false"
52
+ },
53
+ "disableSameAs":{
54
+ "name":"disableSameAs",
55
+ "label":"Disable owl:sameAs",
56
+ "value":"true"
57
+ },
58
+ "ftsIrisIndex":{
59
+ "name":"ftsIrisIndex",
60
+ "label":"FTS index for full-text indexing of IRIs",
61
+ "value":"none"
62
+ },
63
+ "entityIndexSize":{
64
+ "name":"entityIndexSize",
65
+ "label":"Entity index size",
66
+ "value":"10000000"
67
+ },
68
+ "dashDataShapes":{
69
+ "name":"dashDataShapes",
70
+ "label":"DASH data shapes extensions",
71
+ "value":"true"
72
+ },
73
+ "queryLimitResults":{
74
+ "name":"queryLimitResults",
75
+ "label":"Limit query results",
76
+ "value":"0"
77
+ },
78
+ "throwQueryEvaluationExceptionOnTimeout":{
79
+ "name":"throwQueryEvaluationExceptionOnTimeout",
80
+ "label":"Throw exception on query timeout",
81
+ "value":"false"
82
+ },
83
+ "member":{
84
+ "name":"member",
85
+ "label":"FedX repo members",
86
+ "value":[
87
+
88
+ ]
89
+ },
90
+ "storageFolder":{
91
+ "name":"storageFolder",
92
+ "label":"Storage folder",
93
+ "value":"storage"
94
+ },
95
+ "validationResultsLimitPerConstraint":{
96
+ "name":"validationResultsLimitPerConstraint",
97
+ "label":"Validation results limit per constraint",
98
+ "value":"1000"
99
+ },
100
+ "enablePredicateList":{
101
+ "name":"enablePredicateList",
102
+ "label":"Enable predicate list index",
103
+ "value":"true"
104
+ },
105
+ "transactionalValidationLimit":{
106
+ "name":"transactionalValidationLimit",
107
+ "label":"Transactional validation limit",
108
+ "value":"500000"
109
+ },
110
+ "ftsIndexes":{
111
+ "name":"ftsIndexes",
112
+ "label":"FTS indexes to build (comma delimited)",
113
+ "value":"default, iri"
114
+ },
115
+ "logValidationPlans":{
116
+ "name":"logValidationPlans",
117
+ "label":"Log the executed validation plans",
118
+ "value":"false"
119
+ },
120
+ "imports":{
121
+ "name":"imports",
122
+ "label":"Imported RDF files(';' delimited)",
123
+ "value":""
124
+ },
125
+ "isShacl":{
126
+ "name":"isShacl",
127
+ "label":"Enable SHACL validation",
128
+ "value":"false"
129
+ },
130
+ "inMemoryLiteralProperties":{
131
+ "name":"inMemoryLiteralProperties",
132
+ "label":"Cache literal language tags",
133
+ "value":"true"
134
+ },
135
+ "ruleset":{
136
+ "name":"ruleset",
137
+ "label":"Ruleset",
138
+ "value":"rdfsplus-optimized"
139
+ },
140
+ "readOnly":{
141
+ "name":"readOnly",
142
+ "label":"Read-only",
143
+ "value":"false"
144
+ },
145
+ "enableLiteralIndex":{
146
+ "name":"enableLiteralIndex",
147
+ "label":"Enable literal index",
148
+ "value":"true"
149
+ },
150
+ "enableFtsIndex":{
151
+ "name":"enableFtsIndex",
152
+ "label":"Enable full-text search (FTS) index",
153
+ "value":"true"
154
+ },
155
+ "defaultNS":{
156
+ "name":"defaultNS",
157
+ "label":"Default namespaces for imports(';' delimited)",
158
+ "value":""
159
+ },
160
+ "enableContextIndex":{
161
+ "name":"enableContextIndex",
162
+ "label":"Enable context index",
163
+ "value":"false"
164
+ },
165
+ "baseURL":{
166
+ "name":"baseURL",
167
+ "label":"Base URL",
168
+ "value":"http://example.org/owlim#"
169
+ },
170
+ "logValidationViolations":{
171
+ "name":"logValidationViolations",
172
+ "label":"Log validation violations",
173
+ "value":"false"
174
+ },
175
+ "globalLogValidationExecution":{
176
+ "name":"globalLogValidationExecution",
177
+ "label":"Log every execution step of the SHACL validation",
178
+ "value":"false"
179
+ },
180
+ "entityIdSize":{
181
+ "name":"entityIdSize",
182
+ "label":"Entity ID size",
183
+ "value":"32"
184
+ },
185
+ "repositoryType":{
186
+ "name":"repositoryType",
187
+ "label":"Repository type",
188
+ "value":"file-repository"
189
+ },
190
+ "eclipseRdf4jShaclExtensions":{
191
+ "name":"eclipseRdf4jShaclExtensions",
192
+ "label":"RDF4J SHACL extensions",
193
+ "value":"true"
194
+ },
195
+ "validationResultsLimitTotal":{
196
+ "name":"validationResultsLimitTotal",
197
+ "label":"Validation results limit total",
198
+ "value":"1000000"
199
+ }
200
+ }
201
+ }
@@ -0,0 +1,74 @@
1
+ {
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+ "": [
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+ {
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+ "id": "starwars",
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+ "title": "",
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+ "uri": "http://svelikov-desktop:9000/repositories/starwars",
7
+ "externalUrl": "http://svelikov-desktop:9000/repositories/starwars",
8
+ "local": true,
9
+ "type": "graphdb",
10
+ "sesameType": "graphdb:SailRepository",
11
+ "location": "",
12
+ "readable": true,
13
+ "writable": true,
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+ "unsupported": false,
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+ "state": "RUNNING"
16
+ },
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+ {
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+ "id": "ttyg-repo-1725518186812",
19
+ "title": "",
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+ "uri": "http://svelikov-desktop:9000/repositories/ttyg-repo-1725518186812",
21
+ "externalUrl": "http://svelikov-desktop:9000/repositories/ttyg-repo-1725518186812",
22
+ "local": true,
23
+ "type": "graphdb",
24
+ "sesameType": "graphdb:SailRepository",
25
+ "location": "",
26
+ "readable": true,
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+ "writable": true,
28
+ "unsupported": false,
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+ "state": "RUNNING"
30
+ },
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+ {
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+ "id": "biomarkers",
33
+ "title": "",
34
+ "uri": "http://svelikov-desktop:9000/repositories/biomarkers",
35
+ "externalUrl": "http://svelikov-desktop:9000/repositories/biomarkers",
36
+ "local": true,
37
+ "type": "graphdb",
38
+ "sesameType": "graphdb:SailRepository",
39
+ "location": "",
40
+ "readable": true,
41
+ "writable": true,
42
+ "unsupported": false,
43
+ "state": "INACTIVE"
44
+ },
45
+ {
46
+ "id": "Fedx_repository",
47
+ "title": "",
48
+ "uri": "http://localhost:8080/graphdb/repositories/Fedx_repository",
49
+ "externalUrl": "http://boyantonchev:9000/repositories/Fedx_repository",
50
+ "local": true,
51
+ "type": "fedx",
52
+ "sesameType": "graphdb:FedXRepository",
53
+ "location": "",
54
+ "readable": true,
55
+ "writable": true,
56
+ "unsupported": false,
57
+ "state": "INACTIVE"
58
+ },
59
+ {
60
+ "id": "Ontop_repository",
61
+ "title": "",
62
+ "uri": "http://localhost:8080/graphdb/repositories/Fedx_repository",
63
+ "externalUrl": "http://boyantonchev:9000/repositories/Fedx_repository",
64
+ "local": true,
65
+ "type": "ontop",
66
+ "sesameType": "graphdb:FedXRepository",
67
+ "location": "",
68
+ "readable": true,
69
+ "writable": true,
70
+ "unsupported": false,
71
+ "state": "INACTIVE"
72
+ }
73
+ ]
74
+ }
@@ -0,0 +1,15 @@
1
+ [
2
+ {
3
+ "name": "similarity-index",
4
+ "options": "-termweight idf",
5
+ "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
6
+ "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}",
7
+ "analogicalQuery": "",
8
+ "stopList": null,
9
+ "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
10
+ "status": "BUILT",
11
+ "infer": true,
12
+ "sameAs": true,
13
+ "type": "text"
14
+ }
15
+ ]
@@ -0,0 +1,46 @@
1
+ {
2
+ "starwars": [
3
+ {
4
+ "name": "similarity_index_starwars_one",
5
+ "options": "-termweight idf",
6
+ "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
7
+ "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}",
8
+ "analogicalQuery": "",
9
+ "stopList": null,
10
+ "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
11
+ "status": "BUILT",
12
+ "infer": true,
13
+ "sameAs": true,
14
+ "type": "text"
15
+ },
16
+ {
17
+ "name": "similarity_index_starwars_two",
18
+ "options": "-termweight idf",
19
+ "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
20
+ "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}",
21
+ "analogicalQuery": "",
22
+ "stopList": null,
23
+ "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
24
+ "status": "BUILT",
25
+ "infer": true,
26
+ "sameAs": true,
27
+ "type": "text"
28
+ }
29
+ ],
30
+ "biomarkers": [
31
+ {
32
+ "name": "similarity_index_biomarkers_one",
33
+ "options": "-termweight idf",
34
+ "selectQuery": "SELECT ?documentID ?documentText {\n\t?documentID ?p ?documentText .\n\tfilter(isLiteral(?documentText))\n}",
35
+ "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}",
36
+ "analogicalQuery": "",
37
+ "stopList": null,
38
+ "analyzer": "org.apache.lucene.analysis.en.EnglishAnalyzer",
39
+ "status": "BUILT",
40
+ "infer": true,
41
+ "sameAs": true,
42
+ "type": "text"
43
+ }
44
+ ],
45
+ "ttyg-repo-1725518186812": []
46
+ }
@@ -0,0 +1,20 @@
1
+ {
2
+ "id": "asst_a6jM68The7NqJax7U2PKLAe8",
3
+ "name": "Test Agent",
4
+ "model": "gpt-4o",
5
+ "temperature": 0.2,
6
+ "topP": 0.2,
7
+ "seed": 2,
8
+ "repositoryId": "starwars",
9
+ "instructions": {
10
+ "systemInstruction": "",
11
+ "userInstruction": ""
12
+ },
13
+ "assistantExtractionMethods": [
14
+ {
15
+ "method": "sparql_search",
16
+ "sparqlQuery": "select ?s ?p ?o where {?s ?p ?o .}",
17
+ "addMissingNamespaces": true
18
+ }
19
+ ]
20
+ }
@@ -0,0 +1,42 @@
1
+ {
2
+ "id": "id",
3
+ "name": "Quadro",
4
+ "model": "gpt-4o",
5
+ "temperature": 0.7,
6
+ "topP": 1.0,
7
+ "seed": 0,
8
+ "repositoryId": "test-repository",
9
+ "instructions": {
10
+ "systemInstruction": "",
11
+ "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."
12
+ },
13
+ "assistantExtractionMethods": [
14
+ {
15
+ "method": "sparql_search",
16
+ "ontologyGraph": "http://example.com",
17
+ "sparqlQuery": "CONSTRUCT {?s ?p ?o} WHERE {GRAPH <http://example.org/ontology> {?s ?p ?o .}}",
18
+ "addMissingNamespaces": false
19
+ },
20
+ {
21
+ "method": "fts_search",
22
+ "maxNumberOfTriplesPerCall": 0
23
+ },
24
+ {
25
+ "method": "similarity_search",
26
+ "similarityIndex": "similarity-index",
27
+ "similarityIndexThreshold": 0.6,
28
+ "maxNumberOfTriplesPerCall": 0
29
+ },
30
+ {
31
+ "method": "retrieval_search",
32
+ "retrievalConnectorInstance": "retrieval-connector",
33
+ "queryTemplate": "{\"query\": \"string\"}",
34
+ "maxNumberOfTriplesPerCall": 0
35
+ }
36
+ ],
37
+ "additionalExtractionMethods": [
38
+ {
39
+ "method": "iri_discovery_search"
40
+ }
41
+ ]
42
+ }
@@ -0,0 +1,56 @@
1
+ [
2
+ {
3
+ "id": "asst_qMyCpCBmqxV9I2B8UoMfFzc5",
4
+ "name": "agent-2",
5
+ "model": "gpt-4o",
6
+ "temperature": 0.0,
7
+ "topP": 0.0,
8
+ "seed": null,
9
+ "repositoryId": "Not existing repo",
10
+ "instructions": {
11
+ "systemInstruction": "string\n\nstring",
12
+ "userInstruction": "string"
13
+ },
14
+ "assistantExtractionMethods": [
15
+ {
16
+ "ftsMethod": "fts_search"
17
+ }
18
+ ]
19
+ },
20
+ {
21
+ "id": "asst_Cr0RxobrY07WpOvvyQilEWMI",
22
+ "name": "Databricks-general-unbiased",
23
+ "model": "gpt-4o-2024-08-06",
24
+ "temperature": 1.0,
25
+ "topP": 1.0,
26
+ "seed": null,
27
+ "repositoryId": "starwars",
28
+ "instructions": {
29
+ "systemInstruction": "You are helpful assistant in discovering information regarding diagnostic biomarkers.",
30
+ "userInstruction": null
31
+ },
32
+ "assistantExtractionMethods": [
33
+ {
34
+ "ftsMethod": "fts_search"
35
+ }
36
+ ]
37
+ },
38
+ {
39
+ "id": "asst_5GxNYTdaOh7Tl6lLl6Pya2aH",
40
+ "name": "Databricks-biomarkers",
41
+ "model": "gpt-3.5-turbo-0125",
42
+ "temperature": 1.0,
43
+ "topP": 1.0,
44
+ "seed": null,
45
+ "repositoryId": "biomarkers",
46
+ "instructions": {
47
+ "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",
48
+ "userInstruction": null
49
+ },
50
+ "assistantExtractionMethods": [
51
+ {
52
+ "ftsMethod": "fts_search"
53
+ }
54
+ ]
55
+ }
56
+ ]