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Update to DISK ontolog 1.3
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@hvarg
hvarg committed Apr 4, 2024
1 parent 518fe55 commit 8b88bb3
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2 changes: 1 addition & 1 deletion API
Submodule API updated 66 files
+5 −0 README.md
+5 −5 server/src/main/java/org/diskproject/server/adapters/AirFlowAdapter.java
+33 −178 server/src/main/java/org/diskproject/server/adapters/wings/WingsAdapter.java
+189 −0 server/src/main/java/org/diskproject/server/adapters/wings/WingsParser.java
+65 −115 server/src/main/java/org/diskproject/server/api/impl/DiskResource.java
+1,191 −0 server/src/main/java/org/diskproject/server/db/DiskDB.java
+459 −0 server/src/main/java/org/diskproject/server/db/QuestionDB.java
+2 −1 server/src/main/java/org/diskproject/server/filters/KeycloakAuthenticationFilter.java
+142 −0 server/src/main/java/org/diskproject/server/managers/DataAdapterManager.java
+65 −7 server/src/main/java/org/diskproject/server/managers/MethodAdapterManager.java
+13 −7 server/src/main/java/org/diskproject/server/managers/StorageManager.java
+113 −0 server/src/main/java/org/diskproject/server/managers/VocabularyManager.java
+328 −0 server/src/main/java/org/diskproject/server/quering/Match.java
+74 −0 server/src/main/java/org/diskproject/server/repository/DiskRDF.java
+354 −1,743 server/src/main/java/org/diskproject/server/repository/DiskRepository.java
+0 −154 server/src/main/java/org/diskproject/server/repository/KBRepository.java
+0 −1,244 server/src/main/java/org/diskproject/server/repository/WriteKBRepository.java
+14 −3 server/src/main/java/org/diskproject/server/threads/DataThread.java
+27 −24 server/src/main/java/org/diskproject/server/threads/ExecutionThread.java
+79 −65 server/src/main/java/org/diskproject/server/threads/MonitorThread.java
+37 −38 server/src/main/java/org/diskproject/server/threads/ThreadManager.java
+12 −0 server/src/main/java/org/diskproject/server/util/KBUtils.java
+21 −29 shared/src/main/java/org/diskproject/shared/api/DiskService.java
+17 −4 shared/src/main/java/org/diskproject/shared/classes/DISKResource.java
+9 −0 shared/src/main/java/org/diskproject/shared/classes/adapters/DataAdapter.java
+13 −4 shared/src/main/java/org/diskproject/shared/classes/adapters/MethodAdapter.java
+48 −0 shared/src/main/java/org/diskproject/shared/classes/common/Endpoint.java
+35 −0 shared/src/main/java/org/diskproject/shared/classes/common/Entity.java
+15 −0 shared/src/main/java/org/diskproject/shared/classes/common/Status.java
+0 −87 shared/src/main/java/org/diskproject/shared/classes/common/TreeItem.java
+1 −11 shared/src/main/java/org/diskproject/shared/classes/common/Triple.java
+0 −41 shared/src/main/java/org/diskproject/shared/classes/common/TripleDetails.java
+0 −6 shared/src/main/java/org/diskproject/shared/classes/common/Value.java
+48 −0 shared/src/main/java/org/diskproject/shared/classes/hypothesis/Goal.java
+62 −0 shared/src/main/java/org/diskproject/shared/classes/hypothesis/GoalResult.java
+0 −11 shared/src/main/java/org/diskproject/shared/classes/hypothesis/Hypothesis.java
+32 −0 shared/src/main/java/org/diskproject/shared/classes/loi/DataQueryResult.java
+66 −0 shared/src/main/java/org/diskproject/shared/classes/loi/DataQueryTemplate.java
+57 −0 shared/src/main/java/org/diskproject/shared/classes/loi/LOICommon.java
+30 −133 shared/src/main/java/org/diskproject/shared/classes/loi/LineOfInquiry.java
+0 −30 shared/src/main/java/org/diskproject/shared/classes/loi/MetaWorkflowDetails.java
+87 −110 shared/src/main/java/org/diskproject/shared/classes/loi/TriggeredLOI.java
+0 −182 shared/src/main/java/org/diskproject/shared/classes/loi/WorkflowBindings.java
+0 −57 shared/src/main/java/org/diskproject/shared/classes/method/Method.java
+0 −27 shared/src/main/java/org/diskproject/shared/classes/method/MethodBinding.java
+0 −7 shared/src/main/java/org/diskproject/shared/classes/method/MethodInput.java
+0 −7 shared/src/main/java/org/diskproject/shared/classes/method/MethodOutput.java
+0 −27 shared/src/main/java/org/diskproject/shared/classes/method/MethodParameter.java
+0 −45 shared/src/main/java/org/diskproject/shared/classes/method/MethodRun.java
+6 −0 shared/src/main/java/org/diskproject/shared/classes/question/Question.java
+10 −0 shared/src/main/java/org/diskproject/shared/classes/question/QuestionVariable.java
+3 −1 shared/src/main/java/org/diskproject/shared/classes/util/DataAdapterResponse.java
+21 −5 shared/src/main/java/org/diskproject/shared/classes/util/KBConstants.java
+6 −6 shared/src/main/java/org/diskproject/shared/classes/util/QuestionOptionsRequest.java
+48 −0 shared/src/main/java/org/diskproject/shared/classes/util/WorkflowTemplateResponse.java
+89 −0 shared/src/main/java/org/diskproject/shared/classes/workflow/Execution.java
+59 −0 shared/src/main/java/org/diskproject/shared/classes/workflow/ExecutionRecord.java
+152 −25 shared/src/main/java/org/diskproject/shared/classes/workflow/VariableBinding.java
+79 −0 shared/src/main/java/org/diskproject/shared/classes/workflow/WorkflowInstantiation.java
+2 −5 shared/src/main/java/org/diskproject/shared/classes/workflow/WorkflowRun.java
+122 −0 shared/src/main/java/org/diskproject/shared/classes/workflow/WorkflowSeed.java
+9 −9 shared/src/main/java/org/diskproject/shared/classes/workflow/WorkflowTemplate.java
+5 −0 shared/src/main/java/org/diskproject/shared/classes/workflow/comparable.java
+69 −51 shared/src/main/java/org/diskproject/shared/ontologies/DISK.java
+2 −0 shared/src/main/java/org/diskproject/shared/ontologies/SQO.java
+21 −0 shared/src/main/java/org/diskproject/shared/ontologies/WINGS.java
2 changes: 1 addition & 1 deletion WebUI
Submodule WebUI updated 82 files
+5 −5 docs/concepts.md
+6 −3 docs/developer-guide/architecture.md
+15 −19 docs/developer-guide/data-adapter.md
+27 −11 docs/developer-guide/method-adapter.md
+ − docs/figures/DISK-arq.png
+ − docs/figures/DISK-overview.png
+1 −1 docs/index.md
+9 −9 src/AppRouter.tsx
+155 −71 src/DISK/interfaces.tsx
+19 −14 src/DISK/util.tsx
+46 −0 src/components/DataQuery/DataQueryResultTable.tsx
+89 −0 src/components/DataQuery/DataQueryResultView.tsx
+213 −0 src/components/DataQuery/DataQueryTemplateForm.tsx
+15 −2 src/components/Fields.tsx
+0 −143 src/components/FileList.tsx
+0 −56 src/components/PrivateLink.tsx
+2 −83 src/components/ResultTable.tsx
+43 −41 src/components/RightMenu.tsx
+98 −0 src/components/SimpleTable.tsx
+1 −0 src/components/Styles.tsx
+132 −0 src/components/files/ExecutionOutputs.tsx
+135 −0 src/components/files/FileList.tsx
+42 −0 src/components/files/PrivateLink.tsx
+19 −0 src/components/files/download.tsx
+59 −0 src/components/files/outputs/index.tsx
+108 −0 src/components/files/outputs/table.tsx
+6 −6 src/components/goals/GoalsList.tsx
+34 −14 src/components/goals/GoalsPreview.tsx
+3 −3 src/components/lois/LOIList.tsx
+13 −5 src/components/lois/LOIPreview.tsx
+164 −0 src/components/methods/MethodInputSelector.tsx
+111 −0 src/components/methods/MethodOutputSelector.tsx
+165 −0 src/components/methods/MethodParameterSelector.tsx
+84 −49 src/components/methods/MethodVariableList.tsx
+0 −319 src/components/methods/MethodVariableSelector.tsx
+61 −0 src/components/methods/WorkflowInstantiationList.tsx
+206 −0 src/components/methods/WorkflowInstantiationPreview.tsx
+0 −269 src/components/methods/WorkflowPreview.tsx
+35 −25 src/components/methods/WorkflowSeedEditor.tsx
+31 −48 src/components/methods/WorkflowSeedList.tsx
+150 −0 src/components/methods/WorkflowSeedPreview.tsx
+20 −21 src/components/modal/BrainModal.tsx
+3 −3 src/components/modal/BrainVisualization.tsx
+17 −10 src/components/modal/NarrativeModal.tsx
+20 −19 src/components/modal/ShinyModal.tsx
+74 −0 src/components/modal/WorkflowInstantiationModal.tsx
+4 −4 src/components/questions/BoundingBoxMap.tsx
+3 −2 src/components/questions/FormalExpressionView.tsx
+22 −16 src/components/questions/QuestionHelpers.tsx
+3 −3 src/components/questions/QuestionLinker.tsx
+24 −20 src/components/questions/QuestionList.tsx
+7 −8 src/components/questions/QuestionPreview.tsx
+13 −9 src/components/questions/QuestionSelector.tsx
+5 −4 src/components/questions/QuestionTemplateFiller.tsx
+4 −5 src/components/questions/QuestionTemplateSelector.tsx
+3 −0 src/components/questions/QuestionTemplateView.tsx
+22 −9 src/components/questions/QuestionVariableSelector.tsx
+3 −3 src/components/questions/TimeIntervalVariable.tsx
+31 −25 src/components/tlois/ConfidencePlot.tsx
+38 −63 src/components/tlois/TLOIBundle.tsx
+0 −1 src/components/tlois/TLOIDeleteButton.tsx
+33 −35 src/components/tlois/TLOIEdit.tsx
+33 −16 src/components/tlois/TLOIPreview.tsx
+22 −95 src/components/tlois/TLOITable.tsx
+13 −9 src/constants/routes.tsx
+100 −53 src/pages/Goals/GoalEditor.tsx
+17 −15 src/pages/Goals/GoalView.tsx
+10 −10 src/pages/Goals/Goals.tsx
+106 −129 src/pages/LOI/LOIEditor.tsx
+56 −48 src/pages/LOI/LOIView.tsx
+2 −2 src/pages/LOI/LOIs.tsx
+42 −107 src/pages/TLOI/TLOIView.tsx
+58 −0 src/redux/apis/goals.tsx
+0 −57 src/redux/apis/hypotheses.tsx
+5 −4 src/redux/apis/lois.tsx
+4 −3 src/redux/apis/tlois.tsx
+5 −5 src/redux/brain.tsx
+1 −1 src/redux/hooks.ts
+8 −7 src/redux/hooks/tloi.tsx
+3 −5 src/redux/slices/forms.tsx
+3 −3 src/redux/store.ts
+24 −0 src/styles/index.css

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