git actions and fix targets

.github/workflows/release.yaml

@@ -0,0 +1,45 @@
+name: 'Release a new version to Github Packages'
+
+on:
+    release:
+        types: [published]
+
+env:
+    REGISTRY: ghcr.io
+
+jobs:
+    push_to_registry:
+        name: Push Docker image to GitHub Packages tagged with "latest" and version number.
+        runs-on: ubuntu-latest
+        steps:
+            - name: Check out the repo
+              uses: actions/checkout@v2
+            - name: Get the version
+              id: get_version
+              run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
+            - name: Extract metadata (tags, labels) for Docker
+              id: meta_base_image
+              uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+              with:
+                images:
+                    ghcr.io/${{ github.repository }}
+            - name: Extract metadata (tags, labels) for Docker
+              id: meta_clustered_image
+              uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+              with:
+                images:
+                    ghcr.io/${{ github.repository }}-clustered
+            - name: Login to ghcr
+              uses: docker/login-action@v1
+              with:
+                  registry: ${{ env.REGISTRY }}
+                  username: ${{ github.actor }}
+                  password: ${{ secrets.GITHUB_TOKEN }}
+            - name: Build and push base image
+              uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+              with:
+                  context: ./
+                  push: true
+                  tags: ${{ steps.meta_base_image.outputs.tags }}
+                  labels: ${{ steps.meta_base_image.outputs.labels }}
+                  build-args: VERSION=${{ steps.get_version.outputs.VERSION }}

Dockerfile

@@ -0,0 +1,20 @@
+FROM renciorg/renci-python-image:v0.0.1
+
+ARG VERSION=main
+
+
+WORKDIR /home/benchmarks
+
+RUN git clone --branch ${VERSION} --single-branch https://github.com/TranslatorSRI/Benchmarks.git
+
+WORKDIR /home/benchmarks/Benchmarks
+
+ENV PYTHONPATH=/home/benchmarks/Benchmarks
+
+RUN pip install --upgrade pip
+
+RUN pip install .
+
+RUN chown nru:nru ./*
+
+USER nru

config/targets.json

@@ -1,45 +1,45 @@
 {
     "aragorn": {
         "fetch": {
-            "url": "https://aragorn.renci.org/1.2/query",
+            "url": "https://aragorn.renci.org/1.3/query",
             "workflow": [
                 {"id": "lookup"},
                 {"id": "overlay_connect_knodes"},
                 {"id": "score"}
             ]
         },
         "fetch_unscored": {
-            "url": "https://aragorn.renci.org/1.2/query",
+            "url": "https://aragorn.renci.org/1.3/query",
             "workflow": [
                 {"id": "lookup"},
                 {"id": "overlay_connect_knodes"}
             ]
         },
         "score": {
-            "url": "https://aragorn.renci.org/1.2/query",
+            "url": "https://aragorn.renci.org/1.3/query",
             "workflow": [
                 {"id": "score"}
             ]
         }
     },
     "arax": {
         "fetch": {
-            "url": "https://arax.ncats.io/api/arax/v1.2/query"
+            "url": "https://arax.transltr.io/api/arax/v1.3/query"
         }
     },
     "bte": {
         "fetch": {
-            "url": "https://api.bte.ncats.io/v1/query"
+            "url": "https://bte.transltr.io/v1/query"
         }
     },
     "explanatory": {
         "fetch": {
-            "url": "https://explanatory-agent.azurewebsites.net/v1.2/query"
+            "url": "https://explanatory-agent.transltr.io/v1.3/query"
         }
     },
     "improving": {
         "fetch": {
-            "url": "https://ia.healthdatascience.cloud/api/v1.2/query"
+            "url": "https://ia.transltr.io/api/v1.3/query"
         }
     }
 }