From f95031063c982e4e73fd2de0eb9f128dc537dfc1 Mon Sep 17 00:00:00 2001
From: Yojana Gadiya <45199062+YojanaGadiya@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:35:51 +0200
Subject: [PATCH] add new image and update files

---
 .github/workflows/build_publish.yaml | 44 ++++++++++++++++++++++++++++
 AMR-KG_Database.py                   |  6 ++--
 Dockerfile                           | 12 ++++----
 3 files changed, 53 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/build_publish.yaml

diff --git a/.github/workflows/build_publish.yaml b/.github/workflows/build_publish.yaml
new file mode 100644
index 0000000..17f5915
--- /dev/null
+++ b/.github/workflows/build_publish.yaml
@@ -0,0 +1,44 @@
+name: Create and publish a Docker image to ghcr.io
+
+on:
+  push:
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value={{date 'YYYYMMDD-HHmmss' tz='Europe/Stockholm'}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
diff --git a/AMR-KG_Database.py b/AMR-KG_Database.py
index 887cf1e..9202969 100644
--- a/AMR-KG_Database.py
+++ b/AMR-KG_Database.py
@@ -13,8 +13,7 @@
 
 # Customize sidebar
 markdown = """
-**Info**: This is AMR-KG repository and the broad-spectrum prediction models trained on the datasets. 
-This work was done under the IMI project COMBINE.
+**Info**: This is AMR-KG repository and the broad-spectrum prediction models trained on the datasets.
 
 **Developers**:
 * [Yojana Gadiya](https://orcid.org/0000-0002-7683-0452)
@@ -22,7 +21,8 @@
 * [Philip Gribbon](https://orcid.org/0000-0001-7655-2459)
 
 **External links**:
-* [GitHub](https://github.com/IMI-COMBINE/broad_spectrum_prediction)
+* [Models](https://github.com/IMI-COMBINE/broad_spectrum_prediction)
+* [Devops](https://github.com/IMI-COMBINE/amr-kg-website)
 * [Website](https://www.itmp.fraunhofer.de/)
 """
 
diff --git a/Dockerfile b/Dockerfile
index f424800..27771be 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,12 +28,12 @@ COPY start-script.sh $HOME/kg/start-script.sh
 RUN mkdir $HOME/kg/models
 
 RUN apt-get install curl -y
-# RUN curl  https://zenodo.org/api/records/12514684/files/chem_phys_rf.pkl/content -o $HOME/kg/models/chem_phys_rf.pkl -L
-RUN curl  https://zenodo.org/api/records/12514684/files/ecfp4_rf.pkl/content -o $HOME/kg/models/ecfp4_rf.pkl
-RUN curl  https://zenodo.org/api/records/12514684/files/erg_rf.pkl/content -o $HOME/kg/models/erg_rf.pkl
-RUN curl  https://zenodo.org/api/records/12514684/files/maccs_rf.pkl/content -o $HOME/kg/models/maccs_rf.pkl
-RUN curl  https://zenodo.org/api/records/12514684/files/mhfp6_rf.pkl/content -o $HOME/kg/models/mhfp6_rf.pkl
-RUN curl  https://zenodo.org/api/records/12514684/files/rdkit_rf.pkl/content -o $HOME/kg/models/rdkit_rf.pkl
+# RUN curl  https://zenodo.org/api/records/13868088/files/chem_phys_rf.pkl/content -o $HOME/kg/models/chem_phys_rf.pkl -L
+RUN curl  https://zenodo.org/api/records/13868088/files/ecfp4_rf.pkl/content -o $HOME/kg/models/ecfp4_rf.pkl
+RUN curl  https://zenodo.org/api/records/13868088/files/erg_rf.pkl/content -o $HOME/kg/models/erg_rf.pkl
+RUN curl  https://zenodo.org/api/records/13868088/files/maccs_rf.pkl/content -o $HOME/kg/models/maccs_rf.pkl
+RUN curl  https://zenodo.org/api/records/13868088/files/mhfp6_rf.pkl/content -o $HOME/kg/models/mhfp6_rf.pkl
+RUN curl  https://zenodo.org/api/records/13868088/files/rdkit_rf.pkl/content -o $HOME/kg/models/rdkit_rf.pkl
 
 RUN pip install --no-cache-dir -r requirements.txt \
     && chmod +x start-script.sh \