Merge branch 'main' of https://github.com/DARPA-ASKEM/TERArium into T…

…S/4840-project-download-upload-buttons

.github/workflows/publish-text-extraction-taskrunner.yml

@@ -0,0 +1,108 @@
+---
+# Automatically build and publish the text-extraction-taskrunner to the container registry.
+# This workflow is triggered on changes to the text-extraction-taskrunner directory.
+
+name: Build and Publish text-extraction-taskrunner
+
+# yamllint disable-line rule:truthy
+on:
+  push:
+    paths:
+      - 'packages/taskrunner/**'
+      - 'packages/text_extraction/**'
+    branches:
+      - 'main'
+    tags:
+      - '*'
+
+jobs:
+  image-tag:
+    name: Get tagged image name
+    uses: ./.github/workflows/image-tag.yml
+    with:
+      image-name: ghcr.io/darpa-askem/text-extraction-taskrunner
+
+  amd64:
+    runs-on: ubuntu-24.04
+    needs: image-tag
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Login to registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Checkout the repository
+        uses: actions/checkout@v4
+
+      - name: Validate GradleW JAR
+        uses: gradle/actions/wrapper-validation@v3
+
+      - name: Setup Java v17
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: 17
+          cache: gradle
+
+      - name: Create image and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./packages/text_extraction/Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: ${{ needs.image-tag.outputs.tagged-image-name }}--amd64
+
+  arm64-emulation:
+    runs-on: ubuntu-24.04
+    needs: image-tag
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Login to registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Checkout the repository
+        uses: actions/checkout@v4
+
+      - name: Validate GradleW JAR
+        uses: gradle/actions/wrapper-validation@v3
+
+      - name: Setup Java v17
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: 17
+          cache: gradle
+
+      - name: Create image and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./packages/text_extraction/Dockerfile
+          platforms: linux/arm64
+          push: true
+          tags: ${{ needs.image-tag.outputs.tagged-image-name }}--arm64
+
+  merge-images:
+    name: Merge AMD64 and ARM64 images under one manifest
+    needs:
+      - image-tag
+      - amd64
+      - arm64-emulation
+    uses: ./.github/workflows/merge-images.yml
+    with:
+      name: ${{ needs.image-tag.outputs.tagged-image-name }}

containers/scripts/docker-compose-taskrunner.yml

@@ -94,3 +94,26 @@ services:
       - ../../packages/equation_extraction:/equation_extraction_task
       - ../../packages/taskrunner:/taskrunner
     command: /equation_extraction_task/dev.sh
+
+  text_extraction-taskrunner:
+    build:
+      context: ../..
+      dockerfile: ./packages/text_extraction/Dockerfile
+      target: text_extraction_taskrunner_builder
+    container_name: text_extraction-taskrunner
+    networks:
+      - terarium
+    environment:
+      TERARIUM_MQ_ADDRESSES: "amqp://rabbitmq:5672"
+      TERARIUM_MQ_PASSWORD: "terarium123"
+      TERARIUM_MQ_USERNAME: "terarium"
+      TERARIUM_TASKRUNNER_REQUEST_TYPE: "text_extraction"
+    depends_on:
+      rabbitmq:
+        condition: service_healthy
+    extra_hosts:
+      - "${local_host_name}:host-gateway"
+    volumes:
+      - ../../packages/text_extraction:/text_extraction_task
+      - ../../packages/taskrunner:/taskrunner
+    command: /text_extraction_task/dev.sh

docker-bake.hcl

@@ -26,11 +26,11 @@ function "check_suffix" {
 
 # ---------------------------------
 group "prod" {
-  targets = ["hmi-client", "hmi-server", "gollm-taskrunner", "mira-taskrunner", "funman-taskrunner"]
+  targets = ["hmi-client", "hmi-server", "gollm-taskrunner", "mira-taskrunner", "funman-taskrunner", "text-extraction-taskrunner", "equation-extraction-taskrunner"]
 }
 
 group "default" {
-  targets = ["hmi-client-base", "hmi-server-base", "gollm-taskrunner-base", "mira-taskrunner-base", "funman-taskrunner-base"]
+  targets = ["hmi-client-base", "hmi-server-base", "gollm-taskrunner-base", "mira-taskrunner-base", "funman-taskrunner-base", "text-extraction-taskrunner-base", "equation-extraction-taskrunner-base"]
 }
 
 # ---------------------------------
@@ -87,3 +87,23 @@ target "funman-taskrunner-base" {
 target "funman-taskrunner" {
   inherits = ["_platforms", "funman-taskrunner-base"]
 }
+
+target "equation-extraction-taskrunner-base" {
+	context = "." # root of the repo
+	dockerfile = "./packages/equation_extraction/Dockerfile"
+	tags = tag("equation-extraction-taskrunner", "", "")
+}
+
+target "equation-extraction-taskrunner" {
+	inherits = ["_platforms", "equation-extraction-taskrunner-base"]
+}
+
+target "text-extraction-taskrunner-base" {
+	context = "." # root of the repo
+	dockerfile = "./packages/text_extraction/Dockerfile"
+	tags = tag("text-extraction-taskrunner", "", "")
+}
+
+target "text-extraction-taskrunner" {
+	inherits = ["_platforms", "text-extraction-taskrunner-base"]
+}

hmiServerDev.sh

@@ -8,6 +8,7 @@ SECRET_FILES=()
 SECRET_FILES+=("${SERVER_DIR}/src/main/resources/application-secrets.properties")
 SECRET_FILES+=("containers/secrets.env")
 VAULT_PASSWORD=""~/askem-vault-id.txt""
+export COMPOSE_PROJECT_NAME="terarium"
 
 function decrypt_secrets() {
   echo "Decrypting local secrets vault"

package.json

@@ -27,7 +27,7 @@
 	},
 	"devDependencies": {
 		"@vue/eslint-config-airbnb-with-typescript": "7.0.1",
-		"eslint": "8.57.0",
+		"eslint": "8.57.1",
 		"eslint-config-prettier": "8.10.0",
 		"eslint-plugin-vue": "9.27.0",
 		"husky": "8.0.3",

packages/client/graph-scaffolder/package.json

@@ -48,7 +48,7 @@
     "dagre": "0.8.5",
     "esbuild": "0.23.1",
     "esbuild-jest": "0.5.0",
-    "eslint": "8.57.0",
+    "eslint": "8.57.1",
     "eslint-config-esnext": "4.1.0",
     "eslint-plugin-import": "2.29.1",
     "globby": "13.2.2",

packages/client/hmi-client/package.json

@@ -45,7 +45,7 @@
 		"chroma-js": "2.4.2",
 		"d3": "7.8.5",
 		"dagre": "0.8.5",
-		"eslint-import-resolver-typescript": "3.6.1",
+		"eslint-import-resolver-typescript": "3.6.3",
 		"event-source-polyfill": "1.0.31",
 		"extended-eventsource": "1.4.9",
 		"feather-icons": "4.29.2",

packages/client/hmi-client/src/assets/css/reset.css

@@ -19,6 +19,12 @@ a, div, em, figure, footer, form, h1, h2, h3, h4, h5, h6, header, img, li, ol, p
 	vertical-align: baseline;
 }
 
+/* Prevent font inheritance for KaTeX elements */
+.katex * {
+	font-family: 'KaTeX_Main', 'Times New Roman', serif;
+	font-size: 1.1rem;
+}
+
 img {
 	display: block;
 	max-width: 100%;

packages/client/hmi-client/src/components/model/petrinet/model-configurations/tera-stratified-matrix-modal.vue

@@ -22,9 +22,7 @@
 			/>
 		</template>
 		<template #footer>
-			<!--FIXME: This design is odd, since these buttons do the same thing-->
 			<Button label="OK" @click="emit('close-modal')" />
-			<Button severity="secondary" class="p-button-outlined" label="Cancel" @click="emit('close-modal')" />
 		</template>
 	</tera-modal>
 </template>

packages/client/hmi-client/src/components/workflow/ops/calibrate-ciemss/tera-calibrate-ciemss-drilldown.vue

@@ -219,6 +219,7 @@
 						<br />
 						<template v-for="setting of selectedParameterSettings" :key="setting.id">
 							<vega-chart
+								v-if="preparedDistributionCharts[setting.selectedVariables[0]]"
 								expandable
 								:are-embed-actions-visible="true"
 								:visualization-spec="preparedDistributionCharts[setting.selectedVariables[0]].histogram"
@@ -734,16 +735,18 @@ const preparedCharts = computed(() => {
 });
 
 const preparedDistributionCharts = computed(() => {
-	if (!preparedChartInputs.value) return [];
+	if (!preparedChartInputs.value || _.isEmpty(pyciemssMap.value)) return {};
 	const { result } = preparedChartInputs.value;
+	// Note that we want to show the parameter distribution at the first timepoint only
+	const data = result.filter((d) => d.timepoint_id === 0);
 	const labelBefore = 'Before calibration';
 	const labelAfter = 'After calibration';
 	const charts = {};
 	selectedParameterSettings.value.forEach((setting) => {
 		const param = setting.selectedVariables[0];
 		const fieldName = pyciemssMap.value[param];
 		const beforeFieldName = `${fieldName}:pre`;
-		const histogram = createHistogramChart(result, {
+		const histogram = createHistogramChart(data, {
 			title: `${param}`,
 			width: chartSize.value.width,
 			height: chartSize.value.height,
@@ -758,10 +761,8 @@ const preparedDistributionCharts = computed(() => {
 		const toDisplayNumber = (num?: number) => (num ? displayNumber(num.toString()) : '');
 		const stat = {
 			header: [labelBefore, labelAfter],
-			mean: [mean(result, (d) => d[beforeFieldName]), mean(result, (d) => d[fieldName])].map(toDisplayNumber),
-			variance: [variance(result, (d) => d[beforeFieldName]), variance(result, (d) => d[fieldName])].map(
-				toDisplayNumber
-			)
+			mean: [mean(data, (d) => d[beforeFieldName]), mean(data, (d) => d[fieldName])].map(toDisplayNumber),
+			variance: [variance(data, (d) => d[beforeFieldName]), variance(data, (d) => d[fieldName])].map(toDisplayNumber)
 		};
 		charts[param] = { histogram, stat };
 	});