Merge pull request #29 from ScilifelabDataCentre/rename

WIP: Source repo renamed

Dockerfile

@@ -4,7 +4,7 @@ RUN apt-get update && apt-get upgrade -y && apt-get install -y git curl
 
 WORKDIR /code
 
-RUN git clone https://github.com/ScilifelabDataCentre/covid-portal-visualisations.git
+RUN git clone https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations.git
 
 COPY *.sh *.py requirements.txt /code/
 

runner_every10mins.sh

@@ -1,17 +1,18 @@
 export CODE_PATH=/code
 
 # Covid quatification SLU
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/combined_slu_regular.py > "$CODE_PATH"/output/wastewater_combined_slu_regular.json
-# Covid quatification KTH (not currently updating)
-#PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/combined_stockholm_regular.py > "$CODE_PATH"/output/wastewater_combined_stockholm.json
-#PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/quant_malmo_kthplot.py > "$CODE_PATH"/output/wastewater_kthmalmo.json
+
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/combined_slu_regular.py > "$CODE_PATH"/output/wastewater_combined_slu_regular.json
+# Covid quatification KTH
+#PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/combined_stockholm_regular.py > "$CODE_PATH"/output/wastewater_combined_stockholm.json
+#PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/quant_malmo_kthplot.py > "$CODE_PATH"/output/wastewater_kthmalmo.json
 # Covid quatification GU
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/gothenburg_covid.py > "$CODE_PATH"/output/wastewater_gothenburg.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/gothenburg_covid.py > "$CODE_PATH"/output/wastewater_gothenburg.json
 # Enteric virus GU
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/enteric_viruses_gu.py > "$CODE_PATH"/output/enteric_graph_gu.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/enteric_viruses_gu.py > "$CODE_PATH"/output/enteric_graph_gu.json
 # Influenza virus SLU
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/combined_slu_influenza_a.py > "$CODE_PATH"/output/wastewater_slu_infA.json
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/wastewater python "$CODE_PATH"/covid-portal-visualisations/wastewater/combined_slu_influenza_b.py > "$CODE_PATH"/output/wastewater_slu_infB.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/combined_slu_influenza_a.py > "$CODE_PATH"/output/wastewater_slu_infA.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE_PATH"/pathogens-portal-visualisations/wastewater/combined_slu_influenza_b.py > "$CODE_PATH"/output/wastewater_slu_infB.json
 
 
 # Upload generated files

runner_weekly.sh

@@ -1,6 +1,6 @@
 export CODE_PATH=/code
 
-PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/Wordcloud python "$CODE_PATH"/gen_clouds.py
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/Wordcloud python "$CODE_PATH"/gen_clouds.py
 
 # Publication related updates
 PYTHONPATH="$CODE_PATH"/covid-portal-visualisations/Count_publications python "$CODE_PATH"/covid-portal-visualisations/Count_publications/count_publications.py > "$CODE_PATH"/output/COVID_publication_count.json