Merge remote-tracking branch 'origin/kg2cleanup' #2411

.github/workflows/pytest.yml

@@ -67,7 +67,7 @@ jobs:
       run: sudo docker rmi $(sudo docker images -q)
 
     - name: Build docker image 
-      run: sudo docker build --no-cache=true --rm -t rtx:test DockerBuild/ -f DockerBuild/Merged-Dockerfile
+      run: sudo docker build --no-cache=true --rm -t rtx:test DockerBuild/ -f DockerBuild/CICD-Dockerfile
 
     - name: Run docker container
       run: sudo docker run -d -it --name rtx_test -v /mnt/data/orangeboard/databases:/mnt/data/orangeboard/databases -v /mnt/config/config_secrets.json:/mnt/data/orangeboard/production/RTX/code/config_secrets.json rtx:test

DockerBuild/Merged-Dockerfile → DockerBuild/CICD-Dockerfile

@@ -66,23 +66,3 @@ RUN update-rc.d RTX_Complete defaults
 
 # setup config.domain
 RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "Github actions ARAX test suite" > config.domain
-
-# Setup KG2
-
-# clone RTX repo into KG2
-RUN mkdir -p /mnt/data/orangeboard/kg2
-RUN chown -R rt.rt /mnt/data/orangeboard/kg2
-RUN su rt && cd /mnt/data/orangeboard/kg2 && git clone https://github.com/RTXteam/RTX.git
-RUN chown -R rt.rt /mnt/data/orangeboard/kg2/RTX
-COPY kg2-config.js /mnt/data/orangeboard/kg2/RTX/code/UI/interactive/config.js
-
-# setup KG2 services
-RUN export DEVAREA=kg2
-RUN cat /mnt/data/orangeboard/kg2/RTX/code/UI/OpenAPI/python-flask-server/KG2/RTX_OpenAPI_kg2 > /etc/init.d/RTX_OpenAPI_kg2
-RUN chmod 700 /etc/init.d/RTX_OpenAPI_kg2
-RUN update-rc.d RTX_OpenAPI_kg2 defaults
-RUN ln -s /mnt/data/orangeboard/kg2/RTX/code/UI/interactive /var/www/html/kg2
-
-# setup config.domain
-RUN su rt && cd /mnt/data/orangeboard/kg2/RTX/code/ && echo "Github actions ARAX test suite" > config.domain
-

DockerBuild/Dockerfile

@@ -70,4 +70,4 @@ RUN cd /mnt/data/orangeboard/production/RTX/code/autocomplete && sed -i 's/devED
 RUN update-rc.d RTX_Complete defaults
 
 # setup config.domain
-RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "arax.ci.transltr.io" > config.domain
+RUN su rt && cd /mnt/data/orangeboard/production/RTX/code/ && echo "arax.ci.transltr.io" > config.domain

code/ARAX/ARAXQuery/ARAX_decorator.py

@@ -57,7 +57,7 @@ def __init__(self):
         self.array_delimiter_char = "ǂ"
         self.kg2_infores_curie = "infores:rtx-kg2"  # Can't use expand_utilities.py here due to circular imports
 
-    def decorate_nodes(self, response: ARAXResponse) -> ARAXResponse:
+    def decorate_nodes(self, response: ARAXResponse, only_decorate_bare: bool = False) -> ARAXResponse:
         message = response.envelope.message
         response.debug(f"Decorating nodes with metadata from KG2c")
 
@@ -67,7 +67,10 @@ def decorate_nodes(self, response: ARAXResponse) -> ARAXResponse:
         # Extract the KG2c nodes from sqlite
         response.debug(f"Looking up corresponding KG2c nodes in sqlite")
         node_attributes_ordered = list(self.node_attributes)
-        node_keys = set(node_key.replace("'", "''") for node_key in message.knowledge_graph.nodes)  # Escape quotes
+        node_keys = set(node_key.replace("'", "''") for node_key, node in message.knowledge_graph.nodes.items()  # Escape quotes
+                        if not only_decorate_bare or not any(attribute for attribute in node.attributes
+                                                             if attribute.attribute_type_id == "biolink:description"))
+        response.debug(f"Identified {len(node_keys)} nodes to decorate (only_decorate_bare={only_decorate_bare})")
         node_keys_str = "','".join(node_keys)  # SQL wants ('node1', 'node2') format for string lists
         node_cols_str = ", ".join([f"N.{property_name}" for property_name in node_attributes_ordered])
         sql_query = f"SELECT N.id, {node_cols_str} " \