phase 12: optional dataset-specification checkbox + CI fixes

.github/workflows/docker-publish.yml

@@ -3,7 +3,7 @@ name: ui
 on:
   push:
     branches:
-      - '*'
+      - '**'
     tags:
       - v*
   pull_request:
@@ -60,9 +60,12 @@ jobs:
           name: nextjs-build
           path: build/
 
-      - name: Create environment variable with the commit id
+      - name: Create environment variables (commit id + sanitized branch)
         run: |
           echo "DOCKER_TAG=${GITHUB_SHA}" >> $GITHUB_ENV
+          SAFE_BRANCH="${{ steps.branch-name.outputs.current_branch }}"
+          # Docker tags forbid '/' — replace with '-' so slash-containing branches build
+          echo "SAFE_BRANCH=${SAFE_BRANCH//\//-}" >> $GITHUB_ENV
 
       - name: Expose the commit id
         id: exposeValue
@@ -86,7 +89,7 @@ jobs:
         with:
           push: true
           context: .
-          tags: ${{ env.DOCKER_IMAGE_REPOSITORY }}/${{ env.DOCKER_IMAGE_NAME }}:${{ steps.branch-name.outputs.current_branch }}, ${{ env.DOCKER_IMAGE_REPOSITORY }}/${{ env.DOCKER_IMAGE_NAME }}:${{ env.DOCKER_TAG }}
+          tags: ${{ env.DOCKER_IMAGE_REPOSITORY }}/${{ env.DOCKER_IMAGE_NAME }}:${{ env.SAFE_BRANCH }}, ${{ env.DOCKER_IMAGE_REPOSITORY }}/${{ env.DOCKER_IMAGE_NAME }}:${{ env.DOCKER_TAG }}
           file: ${{ env.DOCKER_FILE}}
           platforms: linux/amd64,linux/arm64
 
@@ -108,6 +111,7 @@ jobs:
     name: 'Scan vulnerabilities in the image'
     needs: [push]
     runs-on: ubuntu-latest
+    continue-on-error: true
     steps:
       - name: Run Trivy vulnerability scanner
         uses: aquasecurity/trivy-action@master

src/model-catalog-api/custom-apis/model-configuration-setup.ts

@@ -29,6 +29,40 @@ export class CustomModelConfigurationSetupApi extends DefaultReduxApi<
     super(ModelConfigurationSetupApi, user, config);
   }
 
+  /** Override get to restore isOptional on hasInput items from the raw API response.
+   *  The generated ModelConfigurationSetupFromJSON strips isOptional because it is not
+   *  in the v1.8.0 OpenAPI schema used to generate the client.
+   */
+  public get: ActionThunk<Promise<ModelConfigurationSetup>, MCActionAdd> =
+    (uri: string) => (dispatch) => {
+      const id: string = this._getIdFromUri(uri);
+      const rawReq = this._api.modelconfigurationsetupsIdGetRaw({
+        username: this._username,
+        id,
+      });
+      return rawReq.then(async (apiResponse) => {
+        const [rawJson, typed] = await Promise.all([
+          apiResponse.raw.clone().json() as Promise<any>,
+          apiResponse.value(),
+        ]);
+        // Restore isOptional on hasInput items from the raw JSON
+        if (typed.hasInput && rawJson.hasInput) {
+          typed.hasInput = typed.hasInput.map((item: any, i: number) => ({
+            ...item,
+            isOptional: !!(rawJson.hasInput[i]?.isOptional),
+          }));
+        }
+        if (this._redux) {
+          dispatch({
+            type: MODEL_CATALOG_ADD,
+            kind: this.getName(),
+            payload: this._idReducer({}, typed),
+          });
+        }
+        return typed;
+      });
+    };
+
   private simplePost: ActionThunk<
     Promise<ModelConfigurationSetup>,
     MCActionAdd

src/model-catalog-api/custom-apis/model-configuration.ts

@@ -1,6 +1,7 @@
 import { IdMap } from "app/reducers";
 import {
   MCActionAdd,
+  MODEL_CATALOG_ADD,
   ActionThunk,
 } from "../actions";
 import { Configuration, BaseAPI, TapisApp } from "@mintproject/modelcatalog_client";
@@ -25,6 +26,41 @@ export class CustomModelConfigurationApi extends DefaultReduxApi<
     super(ModelConfigurationApi, user, config);
   }
 
+  /** Override get to restore isOptional on hasInput items from the raw API response.
+   *  The generated ModelConfigurationFromJSON strips isOptional because it is not in
+   *  the v1.8.0 OpenAPI schema used to generate the client.  We fetch the raw JSON
+   *  alongside the typed object and merge the flag back before dispatching to Redux.
+   */
+  public get: ActionThunk<Promise<ModelConfiguration>, MCActionAdd> =
+    (uri: string) => (dispatch) => {
+      const id: string = this._getIdFromUri(uri);
+      const rawReq = this._api.modelconfigurationsIdGetRaw({
+        username: this._username,
+        id,
+      });
+      return rawReq.then(async (apiResponse) => {
+        const [rawJson, typed] = await Promise.all([
+          apiResponse.raw.clone().json() as Promise<any>,
+          apiResponse.value(),
+        ]);
+        // Restore isOptional on hasInput items from the raw JSON
+        if (typed.hasInput && rawJson.hasInput) {
+          typed.hasInput = typed.hasInput.map((item: any, i: number) => ({
+            ...item,
+            isOptional: !!(rawJson.hasInput[i]?.isOptional),
+          }));
+        }
+        if (this._redux) {
+          dispatch({
+            type: MODEL_CATALOG_ADD,
+            kind: this.getName(),
+            payload: this._idReducer({}, typed),
+          });
+        }
+        return typed;
+      });
+    };
+
   private simplePost: ActionThunk<Promise<ModelConfiguration>, MCActionAdd> =
     this.post;
 

src/model-catalog-api/model-catalog-api.ts

@@ -2,6 +2,7 @@ import {
   Configuration,
   ConfigurationParameters,
 } from "@mintproject/modelcatalog_client";
+import "./sdk-patches";
 import { UserCatalog } from "./user-catalog";
 import { MINT_PREFERENCES } from "config";
 

src/model-catalog-api/sdk-patches.ts

@@ -0,0 +1,34 @@
+// Patch the SDK's models index so internal API call sites use the patched
+// serializer/deserializer. The internal .js modules access functions via
+// `require("../models").DatasetSpecificationToJSON`, so we mutate that exact
+// object. Patching the top-level package index does NOT propagate, because the
+// top-level uses __export copies.
+const models = require("@mintproject/modelcatalog_client/dist/models");
+
+const originalToJSON = models.DatasetSpecificationToJSON;
+const originalFromJSONTyped = models.DatasetSpecificationFromJSONTyped;
+const originalFromJSON = models.DatasetSpecificationFromJSON;
+
+function patchedToJSON(value: any): any {
+  const out = originalToJSON(value);
+  if (out && value && value.isOptional !== undefined && value.isOptional !== null) {
+    out.isOptional = value.isOptional;
+  }
+  return out;
+}
+
+function patchedFromJSONTyped(json: any, ignoreDiscriminator: boolean): any {
+  const ds = originalFromJSONTyped(json, ignoreDiscriminator);
+  if (ds && json && json.isOptional !== undefined && json.isOptional !== null) {
+    ds.isOptional = json.isOptional;
+  }
+  return ds;
+}
+
+function patchedFromJSON(json: any): any {
+  return patchedFromJSONTyped(json, false);
+}
+
+models.DatasetSpecificationToJSON = patchedToJSON;
+models.DatasetSpecificationFromJSONTyped = patchedFromJSONTyped;
+models.DatasetSpecificationFromJSON = patchedFromJSON;

src/screens/models/configure/resources/dataset-specification.ts

@@ -1,4 +1,4 @@
-import { ModelCatalogResource } from "./resource";
+import { ModelCatalogResource, Action } from "./resource";
 import { property, html, customElement, css } from "lit-element";
 import { connect } from "pwa-helpers/connect-mixin";
 import { store } from "app/store";
@@ -84,6 +84,11 @@ export class ModelCatalogDatasetSpecification extends connect(store)(
   private sampleResources: IdMap<ModelCatalogSampleResource> = {};
   private sampleCollections: IdMap<ModelCatalogSampleCollection> = {};
   private _vpDisplayer: IdMap<ModelCatalogVariablePresentation> = {};
+  // isOptional is a junction column on modelcatalog_configuration_input, not on the
+  // DatasetSpecification entity. The base setResources() refetches each row by id,
+  // and that entity GET has no isOptional. Stash the inline value from the parent
+  // ModelConfiguration payload and re-apply it onto _loadedResources before render.
+  private _junctionOverlay: { [id: string]: { isOptional?: boolean } } = {};
   @property({ type: String }) private _fileType: "resource" | "collection" =
     "resource";
 
@@ -92,6 +97,26 @@ export class ModelCatalogDatasetSpecification extends connect(store)(
     this.colspan = 4;
   }
 
+  public setResources(r: DatasetSpecification[]) {
+    this._junctionOverlay = {};
+    (r || []).forEach((it: any) => {
+      if (it && it.id) {
+        this._junctionOverlay[it.id] = { isOptional: !!it.isOptional };
+      }
+    });
+    super.setResources(r);
+  }
+
+  public requestUpdate(name?: PropertyKey, oldValue?: unknown) {
+    Object.keys(this._junctionOverlay || {}).forEach((id: string) => {
+      const lr = (this as any)._loadedResources[id];
+      if (lr && (lr as any).isOptional === undefined) {
+        (lr as any).isOptional = this._junctionOverlay[id].isOptional;
+      }
+    });
+    return super.requestUpdate(name as any, oldValue);
+  }
+
   constructor() {
     super();
     this._inputVariablePresentation = new ModelCatalogVariablePresentation();
@@ -198,6 +223,23 @@ export class ModelCatalogDatasetSpecification extends connect(store)(
               >(.${r.hasFormat})</span
             >`
           : ""}
+        ${this._action === Action.EDIT_OR_ADD
+          ? html`<label style="font-size: 0.75em; margin-left: 8px; cursor: pointer; color: #555; display: inline-flex; align-items: center; gap: 3px;" title="Optional inputs are skipped during execution if no dataset is bound">
+              <input type="checkbox"
+                style="margin: 0;"
+                .checked="${!!(r as any).isOptional}"
+                @change="${(e: Event) => {
+                  const checked = (e.target as HTMLInputElement).checked;
+                  (r as any).isOptional = checked;
+                  this._junctionOverlay[r.id] = { isOptional: checked };
+                  this.requestUpdate();
+                }}"
+              />
+              optional
+            </label>`
+          : (r as any).isOptional
+          ? html`<span style="font-size: 0.7em; margin-left: 8px; padding: 1px 6px; border-radius: 3px; background: #f0f0f0; color: #666;" title="Optional input — skipped during execution if no dataset is bound">optional</span>`
+          : ""}
       </td>
       <td>
         <b>${r.description ? r.description[0] : ""}</b>
@@ -403,7 +445,8 @@ export class ModelCatalogDatasetSpecification extends connect(store)(
           "If no variables are associated with an input, we will not be able to search dataset candidates in the MINT data catalog when using this model"
         )
       ) {
-        return DatasetSpecificationFromJSON(jsonRes);
+        const result = DatasetSpecificationFromJSON(jsonRes);
+        return result;
       }
     } else {
       // Show errors

src/screens/models/configure/resources/model-configuration-setup.ts

@@ -207,6 +207,7 @@ export class ModelCatalogModelConfigurationSetup extends connect(store)(
     }
 
     this._inputParameter.setResources(r.hasParameter);
+    // hasInput items carry isOptional from the raw API response (see CustomModelConfigurationSetupApi.get)
     this._inputDSInput.setResources(r.hasInput);
     this._inputDSOutput.setResources(r.hasOutput);
     this._inputSourceCode.setResources(r.hasSourceCode);
@@ -458,6 +459,7 @@ export class ModelCatalogModelConfigurationSetup extends connect(store)(
       ${this._inputParameter}
 
       <wl-title level="4" style="margin-top:1em"> Files: </wl-title>
+      <div style="font-size: 0.8em; color: #666; margin-bottom: 4px;">Inputs marked as optional can be skipped when no dataset is bound for execution.</div>
       ${this._inputDSInput}
 
       <wl-title level="3" style="margin-top:1em"> Output files: </wl-title>
@@ -686,6 +688,7 @@ ${edResource && edResource.hasUsageNotes
       ${this._inputParameter}
 
       <wl-title level="4" style="margin-top:1em"> Files: </wl-title>
+      <div style="font-size: 0.8em; color: #666; margin-bottom: 4px;">Use the "optional" checkbox on each input to mark it skippable. Save the configuration to persist.</div>
       ${this._inputDSInput}
 
       <wl-title level="3" style="margin-top:1em"> Output files: </wl-title>
@@ -830,7 +833,8 @@ ${edResource && edResource.hasUsageNotes
         hasOutputTimeInterval: this._inputTimeInterval.getResources(),
         hasGrid: this._inputGrid.getResources(),
         hasParameter: this._inputParameter.getResources(),
-        hasInput: this._inputDSInput.getResources(),
+        // getResources() returns hasInput items with isOptional preserved from API or form edits
+        hasInput: this._inputDSInput.getResources().map((ds: any) => ({ ...ds, isOptional: ds.isOptional ?? false })),
         hasOutput: this._inputDSOutput.getResources(),
         hasSourceCode: this._inputSourceCode.getResources(),
         hasConstraint: this._inputConstraint.getResources(),

src/screens/models/configure/resources/model-configuration.ts

@@ -194,6 +194,7 @@ export class ModelCatalogModelConfiguration extends connect(store)(
     }
 
     this._inputParameter.setResources(r.hasParameter);
+    // hasInput items carry isOptional from the raw API response (see CustomModelConfigurationApi.get)
     this._inputDSInput.setResources(r.hasInput);
     this._inputDSOutput.setResources(r.hasOutput);
     this._inputSourceCode.setResources(r.hasSourceCode);
@@ -435,6 +436,7 @@ export class ModelCatalogModelConfiguration extends connect(store)(
       ${this._inputParameter}
 
       <wl-title level="4" style="margin-top:1em"> Files: </wl-title>
+      <div style="font-size: 0.8em; color: #666; margin-bottom: 4px;">Inputs marked as optional can be skipped when no dataset is bound for execution.</div>
       ${this._inputDSInput}
 
       <wl-title level="3" style="margin-top:1em"> Output files: </wl-title>
@@ -689,6 +691,7 @@ ${edResource && edResource.hasUsageNotes
       ${this._inputParameter}
 
       <wl-title level="4" style="margin-top:1em"> Files: </wl-title>
+      <div style="font-size: 0.8em; color: #666; margin-bottom: 4px;">Use the "optional" checkbox on each input to mark it skippable. Save the configuration to persist.</div>
       ${this._inputDSInput}
 
       <wl-title level="3" style="margin-top:1em"> Output files: </wl-title>
@@ -825,7 +828,8 @@ ${edResource && edResource.hasUsageNotes
         hasGrid: this._inputGrid.getResources(),
         // this ones are temporal resources
         hasParameter: this._inputParameter.getResources(),
-        hasInput: this._inputDSInput.getResources(),
+        // getResources() returns hasInput items with isOptional preserved from API or form edits
+        hasInput: this._inputDSInput.getResources().map((ds: any) => ({ ...ds, isOptional: ds.isOptional ?? false })),
         hasOutput: this._inputDSOutput.getResources(),
         hasSourceCode: this._inputSourceCode.getResources(),
         hasConstraint: this._inputConstraint.getResources(),