Merge pull request #87 from NFDI4Chem/development

Development

Author: vcnainala

.github/workflows/dev-build.yml

@@ -1,5 +1,5 @@
 
-# This worklflow will perform following actions when the code is pushed to development branch:
+# This worklflow will perform following actions when the code is pushed to the development branch:
 # - Build the latest docker image in development which needs test to pass first.
 # - Push the docker image to Docker Hub under namespace - nfdi4chem with tag:dev-latest.
 # 
@@ -16,7 +16,8 @@ on:
 env:
   DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_USERNAME  }}
   DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_PASSWORD  }}
-  REPOSITORY_NAME: nmrkit
+  NMRKIT_REPOSITORY_NAME: nmrkit
+  NMR_CLI_REPOSITORY_NAME: nmr-cli
   REPOSITORY_NAMESPACE: nfdi4chem
   RELEASE_TAG: dev-latest
 
@@ -27,7 +28,7 @@ jobs:
   push_to_registry:
     name: Push Docker image to Docker Hub
     runs-on: ubuntu-latest
-    needs: test_and_lint
+    #needs: test_and_lint
     steps:
       - name: Check out the repo
         uses: actions/checkout@v3
@@ -38,14 +39,26 @@ jobs:
           username: ${{ env.DOCKER_HUB_USERNAME  }}
           password: ${{ env.DOCKER_HUB_PASSWORD  }}
 
-      - name: Build and push Docker image
+      - name: Build and push nmrKit Docker image
         uses: docker/build-push-action@v4
         with:
           context: .
           file: ./Dockerfile
           push: true
           build-args: |
             RELEASE_VERSION=dev-latest
-          tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
+          tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
+          username: ${{ env.DOCKER_HUB_USERNAME  }}
+          password: ${{ env.DOCKER_HUB_PASSWORD  }}
+
+      - name: Build and push nmr-cli Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: ./app/scripts/nmr-cli/
+          file: ./app/scripts/nmr-cli/Dockerfile
+          push: true
+          build-args: |
+            RELEASE_VERSION=dev-latest
+          tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
           username: ${{ env.DOCKER_HUB_USERNAME  }}
           password: ${{ env.DOCKER_HUB_PASSWORD  }}

app/scripts/nmr-cli/.gitignore

@@ -0,0 +1,2 @@
+node_modules/
+build/

app/scripts/nmr-cli/Dockerfile

@@ -1,15 +1,16 @@
 # build the image ` docker build --tag nmr-cli  . ` 
 # run the container ` docker run -it nmr-cli bash `
 
-FROM mcr.microsoft.com/playwright:v1.40.0-jammy
+FROM mcr.microsoft.com/playwright:v1.56.1-noble
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
+
 WORKDIR /app
 
 #ENV BASE_NMRIUM_URL=https://nmrium.nmrxiv.org/
 ENV BASE_NMRIUM_URL=https://nmriumdev.nmrxiv.org/
-
+ENV NMR_PREDICTION_URL=https://nmrshiftdb.nmr.uni-koeln.de/NmrshiftdbServlet/nmrshiftdbaction/quickcheck
 
 COPY package.json ./
 COPY package-lock.json ./
@@ -18,8 +19,11 @@ RUN npm install
 
 COPY . ./
 
+RUN npm run build
+
 #install the nmr-cli as a global package 
-# for example, nmr-cli -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
+# for example, nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
+# nmr-cli predict -n "1H" --id 1 --type "nmr;1H;1d" --shifts "1" --solvent "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)" -m $"\n Ketcher  6122516162D 1   1.00000     0.00000     0\n\n 16 17  0  0  0  0  0  0  0  0999 V2000\n    1.1954   -4.6484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -4.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0622   -4.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -5.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1954   -5.6533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0644   -6.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7902   -4.1495    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6574   -4.6498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7964   -6.1512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6596   -5.6458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5228   -4.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5277   -6.1421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    6.3895   -4.6477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5216   -3.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    7.2548   -4.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1215   -4.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  3  1  2  0  0  0  0\n  1  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  4  1  0  0  0  0\n  4  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  4  9  1  0  0  0  0\n  9 10  2  0  0  0  0\n 10  8  1  0  0  0  0\n  8  7  2  0  0  0  0\n  7  2  1  0  0  0  0\n  8 11  1  0  0  0  0\n 10 12  1  0  0  0  0\n 11 13  1  0  0  0  0\n 11 14  2  0  0  0  0\n 13 15  1  0  0  0  0\n 15 16  1  0  0  0  0\nM  END"
 RUN npm install . -g