Merge pull request #6 from mart-r/CU-869az43jq-distribut-cogstack-es

CU-869az43jq: MedCAT v2: Distribute cogstack-es and medcat-scripts

Author: vladd-bit

.github/workflows/submodule_sync.yml

@@ -7,6 +7,9 @@ ARG http_proxy
 ARG https_proxy
 ARG no_proxy
 
+# NOTE: set to ES8 or Elasticsearch 8 or OS for Opensearch
+ARG COGSTACK_BACKEND=ES9
+
 # set to "true" for the GPU build
 ARG GPU_BUILD=false
 
@@ -212,16 +215,20 @@ RUN uv pip install --upgrade --system pip setuptools wheel
 
 # install the rest of the packages including medcat
 COPY ./requirements.txt /srv/jupyterhub/
-# install requirements for working with cogstack scripts
-COPY notebooks/demo_working_with_cogstack/requirements.txt /srv/jupyterhub/working_with_cogstack_requirements.txt
 
 RUN if [ "$GPU_BUILD" = "true" ] && [ "$CPU_ARCHITECTURE" = "amd64" ]; then \
       uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt && \
-      uv pip install --system --no-cache-dir -r /srv/jupyterhub/working_with_cogstack_requirements.txt ; \
+      # NOTE: it'll create the medcat-scripts folder within
+      uv run python -m medcat download-scripts /srv/jupyterhub/ && \
+      uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt ; \
     else \
       uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ && \
-      uv pip install --system --no-cache-dir -r /srv/jupyterhub/working_with_cogstack_requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
-    fi
+      uv run python -m medcat download-scripts /srv/jupyterhub/ && \
+      uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
+    fi && \
+    # install cogstack-es (Cogstack class)
+    uv pip install "cogstack-es[$COGSTACK_BACKEND]" && \
+    mv /srv/jupyterhub/medcat-scripts/notebooks/* /home/jovyan/work/. # move notebooks
 
 #######################################################################################################
 

.gitmodules

@@ -1,4 +1,6 @@
 wheel==0.45.1
+medcat==2.2.0
+# TODO: cogstack-es
 virtualenv==20.31.2
 ipywidgets==8.1.7
 jupyter==1.1.1