Merge branch 'main' into cme-feature/attribute-manipulation-package-l…

…ock-fix

Resolve merge conflicts

.dockerignore

@@ -1,4 +1,4 @@
-**/*.
+**/.*
 documentation
 **/node_modules
 schemas
@@ -7,5 +7,4 @@ LICENSE
 README.md
 !.npmrc
 services/backend/database
-**/dist
-**/*.md
+**/dist

.github/workflows/docker-ws.yml

@@ -1,10 +1,11 @@
-name: Create and publish a Docker image
+name: Docker image
 
 on:
   push:
     branches:
       - main
-      - stable
+    tags:
+      - "v*"
 
 env:
   REGISTRY: ghcr.io
@@ -32,6 +33,8 @@ jobs:
           tags: |
             type=raw,value=latest,enable={{is_default_branch}}
             type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
       - name: Get commit metadata
         id: commit_meta
         run: |
@@ -44,12 +47,12 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          file: ./docker-ws/Dockerfile
+          file: ./Dockerfile
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             GIT_COMMIT=${{ github.sha }}
             GIT_REF=${{ github.ref }}
             GIT_COMMIT_DATE=${{ env.COMMIT_DATE }}
-            GIT_COMMIT_NUMBER=${{ env.COMMIT_NUMBER }}
+            GIT_COMMIT_NUMBER=${{ env.COMMIT_NUMBER }}

docker-ws/Dockerfile → Dockerfile

@@ -41,10 +41,10 @@ RUN --mount=type=cache,target=/root/.npm npm i -g prisma && \
   chmod -R a+rwx /usr/local/lib/node_modules/prisma
 
 # Configure nginx
-COPY --chmod=777 ./docker-ws/nginx.conf /etc/nginx/nginx.conf-template
+COPY --chmod=777 ./docker/ws/nginx.conf /etc/nginx/nginx.conf-template
 RUN chmod -R a+rwx /etc/nginx/
 
-COPY --chmod=777 ./docker-ws/docker-entrypoint.sh ./docker-ws/docker-healthcheck.sh .
+COPY --chmod=777 ./docker/ws/docker-entrypoint.sh ./docker/ws/docker-healthcheck.sh .
 
 RUN chmod a+rwx /usr/share/nginx/html && mkdir /usr/src/app/database && chmod a+rwx /usr/src/app/database
 
@@ -62,6 +62,7 @@ RUN mkdir -p /usr/src/app/database && \
 # Copy frontend
 COPY --from=builder /usr/src/app/.dist /usr/share/nginx/html-template
 
+VOLUME /usr/src/app/database
 EXPOSE 80
 HEALTHCHECK CMD ./docker-healthcheck.sh
 ENTRYPOINT ["./docker-entrypoint.sh"]

README.md

@@ -8,7 +8,38 @@ Check our website [dataspecer.com](https://dataspecer.com/) for more information
 
 You can easily run the whole application in a Docker container.
 
-Instructions are in [docker-ws directory](./docker-ws/README.md).
+If you just want to try it out for a while and don't care where the data is stored, use following command and then go open [http://localhost:3000/](http://localhost:3000/).
+
+```bash
+docker run -it --rm -eBASE_URL=http://localhost:3000/ -p3000:80 ghcr.io/dataspecer/ws
+```
+
+---
+
+- The container exposes port 80.
+- Mount `/usr/src/app/database` directory to your local directory that will be filled with `database.db` file and `stores` directory. If the directory is empty, files would be created. **You need to mkdir the mounted directory with the correct user otherwise Docker will create it as root**.
+- If you want to run the Dataspecer under specific user, use `USER` env variable with desired UID.
+- You MUST specify full base URL using `BASE_URL` env. Some functionalities need to know the domain name and the relative subdirectory is also important. If you are using reverse proxy, it is expected that the base path *is preserved*. (For example, `https://example.com/dataspecer-instance-1/schema` should point to `http://localhost:3001/dataspecer-instance-1/schema`)
+
+Use the following docker run command:
+```bash
+docker run -it --name dataspecer -eBASE_URL=http://localhost/ -eUSER=1000 -v ./database:/usr/src/app/database -p80:80 ghcr.io/dataspecer/ws
+```
+
+Or use following docker-compose file
+```yaml
+services:
+  dataspecer:
+    image: ghcr.io/dataspecer/ws
+    environment:
+      BASE_URL: http://localhost
+      USER: 1000
+    ports:
+      - 80:80 # Change the first number to your desired port
+    volumes:
+      - ./database:/usr/src/app/database
+      #- ./main.config.js:/usr/src/main.config.js # Backend configuration
+```
 
 ## Documentation
 
@@ -38,4 +69,7 @@ Then
 - Run `npm install` to install all external packages (including TypeScript for typechecking and Turborepo for building) and link all dependencies between local packages.
 - Run `npm run build` to build everything. This will execute `turbo build` under the hood. This will build packages, which are necessary for the development of other packages and applications; and it also build applications themselves, which is not necessary for development (see the next step). (If you want to build only packages necessary for a specific package or application, use `npx turbo run build --filter=<package-name>`. Obtain the name of the package from `package.json` file.)
 
-To develop a concrete package or application, there is *usually* an `npm run dev` script that will run live server, which updates everything. See individual packages for more details.
+To develop a concrete package or application, there is *usually* an `npm run dev` script that will run live server, which updates everything. See individual packages for more details.
+
+### Inside Docker
+

applications/conceptual-model-editor/src/action/add-class-profile-to-visual-model.ts

@@ -8,29 +8,44 @@ import { withAggregatedEntity } from "./utilities";
 import { addRelatedEntitiesAction } from "./add-related-entities-to-visual-model";
 import { ClassesContextType } from "../context/classes-context";
 import { findPositionForNewNodesUsingLayouting } from "./layout-visual-model";
+import { findSourceModelOfEntity } from "../service/model-service";
+import { createLogger } from "../application";
 import { getVisualNodeContentBasedOnExistingEntities } from "./add-semantic-attribute-to-visual-model";
 
+const LOG = createLogger(import.meta.url);
+
 export async function addSemanticClassProfileToVisualModelAction(
   notifications: UseNotificationServiceWriterType,
   graph: ModelGraphContextType,
   classes: ClassesContextType,
   visualModel: WritableVisualModel,
   diagram: UseDiagramType,
   entityIdentifier: string,
-  modelIdentifier: string,
+  // We ignore following property, as we may get invalid model.
+  // Sometimes, it is a model of the profiled entity not the profile.
+  _modelIdentifier: string,
   position: { x: number, y: number } | null,
 ) {
   const entities = graph.aggregatorView.getEntities();
   if(position === null) {
-    position = (await findPositionForNewNodesUsingLayouting(notifications, diagram, graph, visualModel, classes, [entityIdentifier]))[entityIdentifier];
+    const positions = await findPositionForNewNodesUsingLayouting(
+      notifications, diagram, graph, visualModel, classes, [entityIdentifier]);
+    position = positions[entityIdentifier];
+  }
+
+  const model = findSourceModelOfEntity(entityIdentifier, graph.models);
+  if (model === null) {
+    LOG.error("Operation ignored, we fail to find model for given entity.", {entity: entityIdentifier});
+    notifications.error("Can not find model for given entity");
+    return;
   }
 
   withAggregatedEntity(notifications, entities,
-    entityIdentifier, modelIdentifier,
+    entityIdentifier, model.getId(),
     isSemanticModelClassUsage, (entity) => {
       addSemanticClassProfileToVisualModelCommand(
         classes, visualModel, entity,
-        modelIdentifier, position);
+        model.getId(), position);
       addRelatedEntitiesAction(
         notifications, graph, visualModel, Object.values(entities),
         graph.models, entity);

applications/conceptual-model-editor/src/action/add-profile-to-visual-model.ts

@@ -12,8 +12,8 @@ export function addSemanticProfileToVisualModelAction(
   profile: SemanticModelEntity,
   modelIdentifier: string,
 ) {
-  const visualSource = visualModel.getVisualEntityForRepresented(profiled.id);
-  const visualTarget = visualModel.getVisualEntityForRepresented(profile.id);
+  const visualSource = visualModel.getVisualEntityForRepresented(profile.id);
+  const visualTarget = visualModel.getVisualEntityForRepresented(profiled.id);
   if (visualSource === null || visualTarget === null) {
     console.warn("Ignored request to add profile as ends are missing in visual model.",
       {visualModel, profiled, profile});

applications/conceptual-model-editor/src/action/add-related-entities-to-visual-model.ts

@@ -60,12 +60,17 @@ export function addRelatedEntitiesAction(
     }
     if (isSemanticModelClassUsage(candidate)) {
       if (shouldAddProfile(visualModel, identifier, candidate)) {
+        // "candidate" is profile of "identifier"
         addSemanticProfileToVisualModelAction(
           visualModel, entity, candidate, model.getId());
+      } else if (addingProfile && shouldAddProfile(visualModel, candidate.id, entity)) {
+        // "identifier" is profile of "candidate"
+        addSemanticProfileToVisualModelAction(
+          visualModel, candidate, entity, model.getId());
       }
     }
     if (addingProfile && isSemanticModelClass(candidate)) {
-      // We are adding profile and the entity is a class.
+      // We are adding profile, candidate is a class, it could profiled class.
       if (entity.usageOf === candidate.id) {
         addSemanticProfileToVisualModelAction(
           visualModel, candidate, entity, model.getId());
@@ -124,17 +129,17 @@ function shouldAddRelationshipUsage(
 
 function shouldAddProfile(
   visualModel: VisualModel,
-  identifier: string,
-  candidate: SemanticModelClassUsage,
+  profiled: string,
+  profile: SemanticModelClassUsage,
 ): boolean {
-  if (candidate.id === identifier) {
+  if (profile.id === profiled) {
     // We do not support self profiles.
     return false;
   }
   // The candidate may be specialization of what we are adding.
-  if (candidate.usageOf === identifier) {
+  if (profile.usageOf === profiled) {
     // We return true if the other is in the visual model.
-    return visualModel.getVisualEntityForRepresented(candidate.id) !== null;
+    return visualModel.getVisualEntityForRepresented(profile.id) !== null;
   }
   return false;
 }

applications/conceptual-model-editor/src/action/open-create-association-dialog.tsx

@@ -36,7 +36,7 @@ export function openCreateAssociationDialogAction(
   }
 
   const state = createCreateAssociationDialogState(
-    classes, graph, visualModel, options.language);
+    classes, graph, visualModel, options.language, model.getId());
 
   const onConfirm = (state: EditAssociationDialogState) => {
     createSemanticAssociation(notifications, visualModel, graph, state, true);

applications/conceptual-model-editor/src/action/open-create-attribute-dialog.tsx

@@ -97,6 +97,6 @@ function openCreateAttributeDialog(
   onConfirm: (state: EditAttributeDialogState) => void,
 ) {
   const state = createNewAttributeDialogState(
-    classes, graph, visualModel, options.language);
+    classes, graph, visualModel, options.language, model.getId());
   dialogs.openDialog(createNewAttributeDialog(state, onConfirm));
 }

applications/conceptual-model-editor/src/action/open-create-class-dialog-with-edge.ts

@@ -108,7 +108,7 @@ function createAssociationToCreatedClass(
   createdClassData: CreatedSemanticEntityData,
   editClassDialogState: EditClassDialogState
 ) {
-  const defaultEditAssociationState = createCreateAssociationDialogState(classes, graph, visualModel, options.language);
+  const defaultEditAssociationState = createCreateAssociationDialogState(classes, graph, visualModel, options.language, null);
 
   const node = visualModel.getVisualEntity(nodeIdentifier);
   if(node === null) {

applications/conceptual-model-editor/src/action/open-create-class-dialog.tsx

@@ -118,6 +118,6 @@ function openCreateClassDialog(
   onConfirm: (state: EditClassDialogState) => void,
 ) {
   const state = createNewClassDialogState(
-    classes, graph, visualModel, options.language);
+    classes, graph, visualModel, options.language, model.getId());
   dialogs.openDialog(createNewClassDialog(state, onConfirm));
 }

applications/conceptual-model-editor/src/action/open-edit-association-profile-dialog.tsx

@@ -28,7 +28,7 @@ export function openEditAssociationProfileDialogAction(
   entity: SemanticModelRelationshipUsage,
 ) {
   const state = createEditAssociationProfileDialogState(
-    classes, graph, visualModel, options.language, model, entity);
+    classes, graph, visualModel, options.language, model, entity.id);
 
   const onConfirm = (nextState: EditAssociationProfileDialogState) => {
     updateSemanticAssociationProfile(notifications, graph.models, entity, state, nextState);

applications/conceptual-model-editor/src/action/open-edit-attribute-profile-dialog.tsx

@@ -28,7 +28,7 @@ export function openEditAttributeProfileDialogAction(
   entity: SemanticModelRelationshipUsage,
 ) {
   const state = createEditAttributeProfileDialogState(
-    classes, graph, visualModel, options.language, model, entity);
+    classes, graph, visualModel, options.language, model, entity.id);
 
   const onConfirm = (nextState: EditAttributeProfileDialogState) => {
     updateSemanticAttributeProfile(notifications, graph.models, entity, state, nextState);

applications/conceptual-model-editor/src/action/open-edit-class-profile-dialog.tsx

@@ -24,7 +24,7 @@ export function openEditClassProfileDialogAction(
   entity: SemanticModelClassUsage,
 ) {
   const state = createEditClassProfileDialogState(
-    classes, graph, visualModel, options.language, model, entity);
+    classes, graph, visualModel, options.language, model, entity.id);
 
   const onConfirm = (nextState: EditClassProfileDialogState) => {
     updateSemanticClassProfile(notifications, entity, graph.models, state, nextState);

applications/conceptual-model-editor/src/dialog/association-profile/create-edit-association-profile-dialog-state.ts

@@ -1,13 +1,13 @@
 
 import { VisualModel } from "@dataspecer/core-v2/visual-model";
 import { InMemorySemanticModel } from "@dataspecer/core-v2/semantic-model/in-memory";
-import { SemanticModelRelationshipUsage, isSemanticModelClassUsage, isSemanticModelRelationshipUsage } from "@dataspecer/core-v2/semantic-model/usage/concepts";
+import { isSemanticModelClassUsage, isSemanticModelRelationshipUsage } from "@dataspecer/core-v2/semantic-model/usage/concepts";
 
 import { ClassesContextType } from "../../context/classes-context";
 import { ModelGraphContextType } from "../../context/model-context";
 import { EditAssociationProfileDialogState } from "./edit-association-profile-dialog-controller";
 import { getDomainAndRange } from "../../util/relationship-utils";
-import { InvalidAggregation, MissingRelationshipEnds } from "../../application/error";
+import { InvalidAggregation, MissingEntity, MissingRelationshipEnds } from "../../application/error";
 import { createEntityProfileStateForEdit } from "../utilities/entity-profile-utilities";
 import { createRelationshipProfileStateForEdit } from "../utilities/relationship-profile-utilities";
 import { entityModelsMapToCmeVocabulary } from "../../dataspecer/semantic-model/semantic-model-adapter";
@@ -21,11 +21,16 @@ export function createEditAssociationProfileDialogState(
   visualModel: VisualModel | null,
   language: string,
   model: InMemorySemanticModel,
-  entity: SemanticModelRelationshipUsage,
+  entityIdentifier: string,
 ): EditAssociationProfileDialogState {
   const entities = graphContext.aggregatorView.getEntities();
-  const aggregated = entities[entity.id]?.aggregatedEntity;
-  if (!isSemanticModelRelationshipUsage(aggregated)) {
+  const aggregate = entities[entityIdentifier];
+  const entity = aggregate.rawEntity;
+  const aggregated = aggregate.aggregatedEntity;
+  if (entity === null) {
+    throw new MissingEntity(entityIdentifier);
+  }
+  if (!isSemanticModelRelationshipUsage(entity) || !isSemanticModelRelationshipUsage(aggregated)) {
     throw new InvalidAggregation(entity, null);
   }
 

applications/conceptual-model-editor/src/dialog/association-profile/create-new-association-profile-dialog-state.ts

@@ -94,9 +94,11 @@ function createForAssociation(
 
   const owlThing = representOwlThing();
 
+  const availableDomains = [owlThing, ...classProfiles];
+  const availableRanges = [owlThing, ...classProfiles];
   const relationshipProfileState = createRelationshipProfileStateForNew(
-    domain.concept, owlThing, domain.cardinality, classProfiles,
-    range.concept, owlThing, range.cardinality, classProfiles);
+    domain.concept, owlThing, domain.cardinality, availableDomains,
+    range.concept, owlThing, range.cardinality, availableRanges);
 
   return {
     ...entityProfileState,
@@ -134,9 +136,11 @@ function createForAssociationProfile(
 
   const owlThing = representOwlThing();
 
+  const availableDomains = [owlThing, ...classProfiles];
+  const availableRanges = [owlThing, ...classProfiles];
   const relationshipProfileState = createRelationshipProfileStateForNew(
-    domain.concept, owlThing, domain.cardinality, classProfiles,
-    range.concept, owlThing, range.cardinality, classProfiles);
+    domain.concept, owlThing, domain.cardinality, availableDomains,
+    range.concept, owlThing, range.cardinality, availableRanges);
 
   return {
     ...entityProfileState,

applications/conceptual-model-editor/src/dialog/association/create-new-association-dialog-state.ts

@@ -16,6 +16,7 @@ export function createCreateAssociationDialogState(
   graphContext: ModelGraphContextType,
   visualModel: VisualModel | null,
   language: string,
+  defaultModelIdentifier: string | null,
 ): EditAssociationDialogState {
 
   const models = [...graphContext.models.values()];
@@ -24,7 +25,8 @@ export function createCreateAssociationDialogState(
 
   // EntityState
 
-  const entityState = createEntityStateForNew(language, vocabularies, configuration().nameToIri);
+  const entityState = createEntityStateForNew(
+    language, defaultModelIdentifier, vocabularies, configuration().nameToIri);
 
   // SpecializationState
 

applications/conceptual-model-editor/src/dialog/attribute-profile/create-add-attribute-profile-dialog-state.ts

@@ -102,8 +102,9 @@ function createForAttribute(
   const undefinedDataType = representUndefinedDataType();
   const dataTypes = [undefinedDataType, ...representDataTypes()];
 
+  const availableDomains = [owlThing, ...classProfiles];
   const relationshipProfileState = createRelationshipProfileStateForNew(
-    domain.concept, owlThing, domain.cardinality, classProfiles,
+    domain.concept, owlThing, domain.cardinality, availableDomains,
     range.concept, undefinedDataType, range.cardinality, dataTypes);
 
   return {
@@ -152,8 +153,9 @@ function createForAttributeProfile(
   const undefinedDataType = representUndefinedDataType();
   const dataTypes = [undefinedDataType, ...representDataTypes()];
 
+  const availableDomains = [owlThing, ...classProfiles];
   const relationshipProfileState = createRelationshipProfileStateForNew(
-    domain.concept, owlThing, domain.cardinality, classProfiles,
+    domain.concept, owlThing, domain.cardinality, availableDomains,
     range.concept, undefinedDataType, range.cardinality, dataTypes);
 
   return {