dc-dynamics refactoring: remove scripts

Dockerfile

@@ -7,9 +7,14 @@ WORKDIR /code
 RUN git clone https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations.git && \
     git clone https://github.com/ScilifelabDataCentre/pathogens-portal-scripts.git
 
-COPY *.sh *.py requirements.txt /code/
-
+# Install Python dependencies from the current directory and both repositories
+COPY requirements.txt /code/
 RUN pip install -r requirements.txt && \
-    mkdir output
+    pip install -r pathogens-portal-visualisations/requirements.txt && \
+    pip install -r pathogens-portal-scripts/requirements.txt
+
+# Copy other necessary files to the /code directory
+COPY *.sh *.py /code/
 
-CMD ["/code/all.sh"]
+# Create an output directory if needed
+RUN mkdir /code/output

freya_runner_weekly.sh

@@ -1,11 +1,11 @@
 export CODE_PATH=/code
 
 # Wordclouds generator
-PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/Wordcloud python "$CODE_PATH"/gen_clouds.py
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/Wordcloud python "$CODE_PATH"/pathogens-portal-visualisations/Wordcloud/livewordcloud.py
 
 # Publication related updates
 PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/Count_publications python "$CODE_PATH"/pathogens-portal-visualisations/Count_publications/count_publications.py > "$CODE_PATH"/output/COVID_publication_count.json
-python "$CODE_PATH"/gen_recent_pub.py > "$CODE_PATH"/output/covid-portal-recent10.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/Count_publications python "$CODE_PATH"/pathogens-portal-visualisations/Count_publications/gen_recent_pub.py > "$CODE_PATH"/output/covid-portal-recent10.json
 
 
 # Upload generated files