Update mudations file url and fix docker compose

api/management/commands/acquiredata.py

@@ -35,5 +35,5 @@ def handle(self, *args, **options):
 
         mutation_path = os.path.join(options['path'], 'mutation-matrix.tsv.bz2')
         if not os.path.exists(mutation_path):
-            mutation_url = 'https://ndownloader.figshare.com/files/5864862'
+            mutation_url = 'https://ndownloader.figshare.com/files/7311953'
             urlretrieve(mutation_url, mutation_path)

api/management/commands/loaddata.py

@@ -20,6 +20,7 @@ def add_arguments(self, parser):
     def handle(self, *args, **options):
         # Diseases
         if Disease.objects.count() == 0:
+            print('Loading diseases table...')
             disease_path = os.path.join(options['path'], 'diseases.tsv')
             with open(disease_path) as disease_file:
                 disease_reader = csv.DictReader(disease_file, delimiter='\t')
@@ -34,6 +35,7 @@ def handle(self, *args, **options):
 
         # Samples
         if Sample.objects.count() == 0:
+            print('Loading samples table...')
             sample_path = os.path.join(options['path'], 'samples.tsv')
             with open(sample_path) as sample_file:
                 sample_reader = csv.DictReader(sample_file, delimiter='\t')
@@ -51,6 +53,7 @@ def handle(self, *args, **options):
 
         # Genes
         if Gene.objects.count() == 0:
+            print('Loading genes table...')
             gene_path = os.path.join(options['path'], 'genes.tsv')
             with open(gene_path) as gene_file:
                 gene_reader = csv.DictReader(gene_file, delimiter='\t')
@@ -70,6 +73,7 @@ def handle(self, *args, **options):
 
         # Mutations
         if Mutation.objects.count() == 0:
+            print('Loading mutations table...')
             mutation_path = os.path.join(options['path'], 'mutation-matrix.tsv.bz2')
             with bz2.open(mutation_path , 'rt') as mutation_file:
                 mutation_reader = csv.DictReader(mutation_file, delimiter='\t')

docker-compose.yml

@@ -4,7 +4,7 @@ services:
     image: postgres
   core:
     build: .
-    command: bash -c "python manage.py makemigrations genes && python manage.py makemigrations organisms && python manage.py migrate && python manage.py runserver 0.0.0.0:8000"
+    command: bash -c "python manage.py migrate && python manage.py runserver 0.0.0.0:8000"
     volumes:
       - .:/code
     ports: