Merge pull request #36 from ScilifelabDataCentre/FREYA-894/Abdullah

Freya 894/abdullah | dc-dynamics refactoring
ScilifelabDataCentre · Oct 18, 2024 · b453ab7 · b453ab7
2 parents 599a496 + 512122a
commit b453ab7
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Showing 10 changed files with 17 additions and 107 deletions.
diff --git a/Dockerfile b/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
diff --git a/all.sh b/all.sh
diff --git a/runner_daily.sh → freya_runner_daily.sh b/runner_daily.sh → freya_runner_daily.sh
@@ -1,7 +1,5 @@
 export CODE_PATH=/code
 
-# Feed SciLifeLab figshare data to Slack
-python "$CODE_PATH"/slack_figshare.py
-
 # Update EBI index file
 PYTHONPATH="$CODE_PATH"/pathogens-portal-scripts/EBI_indexing python "$CODE_PATH"/pathogens-portal-scripts/EBI_indexing/update_index_json.py
+
diff --git a/runner_every10mins.sh → freya_runner_every10mins.sh b/runner_every10mins.sh → freya_runner_every10mins.sh
diff --git a/runner_weekly.sh → freya_runner_weekly.sh b/runner_weekly.sh → 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

diff --git a/gen_clouds.py b/gen_clouds.py
diff --git a/gen_recent_pub.py b/gen_recent_pub.py
diff --git a/requirements.txt b/requirements.txt
@@ -1,13 +1,4 @@
 # DC-DYNAMIC DEPENDENCIES
 beautifulsoup4==4.11.1
 requests==2.32.3
-lxml==4.9.1
-
-# VISUALISATIONS DEPENDENCIES
-matplotlib==3.9.1.post1
-numpy==2.0.1
-openpyxl==3.1.5
-pandas==2.2.2
-pillow==10.4.0
-plotly==5.23.0
-wordcloud==1.9.3
+lxml==4.9.1
diff --git a/slack_runner_daily.sh b/slack_runner_daily.sh
@@ -0,0 +1,4 @@
+export CODE_PATH=/code
+
+# Feed SciLifeLab figshare data to Slack
+python "$CODE_PATH"/slack_figshare.py
diff --git a/runner_hourly.sh → slack_runner_hourly.sh b/runner_hourly.sh → slack_runner_hourly.sh