81 generate reports throwing errors

app/routes.py

@@ -144,7 +144,7 @@ def getReportsPDF(fundername):
     current_working_directory = os.getcwd()
     try:
         return send_file(
-            f'{current_working_directory}/reports/{fundername}/report.pdf',
+            f'{current_working_directory}/data/reports/{fundername}/report.pdf',
             attachment_filename=f'{fundername}.pdf',
             as_attachment=True
             )

deploy/data.Dockerfile

@@ -3,7 +3,9 @@
 
 FROM python:3.8-slim-buster
 
-RUN apt-get update
+RUN apt-get update -y
+RUN apt-get install latexmk -y
+RUN apt-get install -y texlive-latex-extra
 
 WORKDIR /app
 

docker-compose.yml

@@ -19,27 +19,29 @@ services:
 
   flask:
     container_name: gwas_flask
+    volumes:
+      - ./:/var/www
+      - ./data:/app/data
     build:
       context: ./
       dockerfile: deploy/flask.Dockerfile
     command: gunicorn --config gunicorn_config.py wsgi:app
-    volumes:
-      - ./:/var/www
-      - ./data:/app/data
     networks:
       my-network:
         aliases:
           - flask-app
+    depends_on:
+      - data
     restart: unless-stopped
 
   data:
     container_name: gwas_data
+    volumes:
+      - ./data:/app/data
     build:
       context: ./
       dockerfile: deploy/data.Dockerfile
     command: ["python3", "generate_data.py"]
-    volumes:
-      - ./data:/app/data
     networks:
       - my-network
     restart: on-failure

generate_data.py

@@ -1342,7 +1342,6 @@ def check_paths(data_path):
             os.mkdir(os.path.join(data_path, subdir))
     if os.path.exists(os.path.join(data_path, 'catalog', 'raw')) is False:
         os.mkdir(os.path.join(data_path, 'catalog', 'raw'))
-        os.mkdir(os.path.join(data_path, 'catalog', 'raw'))
     if os.path.exists(os.path.join(data_path, 'catalog', 'synthetic')) is False:
         os.mkdir(os.path.join(data_path, 'catalog', 'synthetic'))
 
@@ -1430,13 +1429,12 @@ def clean_funder_data(data_path):
     ebi_download = 'https://www.ebi.ac.uk/gwas/api/search/downloads/'
     final_year = determine_year(datetime.date.today())
     diversity_logger.info('final year is being set to: ' + str(final_year))
-    reports_path = os.path.join(os.getcwd(), 'reports')
+    reports_path = os.path.join(data_path, 'reports')
     try:
         if download_cat(data_path, ebi_download) is True:
             clean_gwas_cat(data_path)
             generate_funder_data(data_path)
             clean_funder_data(data_path)
-            generate_reports(data_path, reports_path, diversity_logger)
             make_bubbleplot_df(data_path)
             make_doughnut_df(data_path)
             tsinput = pd.read_csv(os.path.join(data_path, 'catalog', 'synthetic',
@@ -1451,6 +1449,7 @@ def clean_funder_data(data_path):
             zip_for_download(os.path.join(data_path, 'toplot'),
                              os.path.join(data_path, 'todownload'))
             json_converter(data_path)
+            generate_reports(data_path, reports_path, diversity_logger)
             diversity_logger.info('generate_data.py completed with new data!')
         else:
             diversity_logger.info('generate_data.py completed quickly: no new data!')

generate_reports.py

@@ -28,9 +28,8 @@ def get_agency_list(data_path):
 
 
 def watermark(path, data_path):
-    watermark_path = os.path.join('app',
-                                  'static',
-                                  'images',
+    watermark_path = os.path.join(os.getcwd(),
+                                  'data',
                                   'lcds_watermark.pdf')
     Doc = open(path+'.pdf', 'rb')
     pdfReader = PyPDF2.PdfReader(Doc)
@@ -150,4 +149,4 @@ def generate_reports(data_path, reports_path, diversity_logger):
         diversity_logger.info('Build of the reports: Complete')
     except Exception as e:
         print(traceback.format_exc())
-        diversity_logger.debug('Build of the reports: Failed with exception: ', e)
+        diversity_logger.debug('Build of the reports: Failed with exception: ', e)