Fix #2, Small fixes & apply migrations in docker

docker-compose.yml

@@ -13,6 +13,7 @@ services:
     build: ./
     command: >
       bash -c "python wait_for_postgres.py &&
+               ./manage.py makemigrations &&
                ./manage.py migrate &&
                ./manage.py runserver 0.0.0.0:8000"
     volumes:

pkdb_app/data_management/create_master.py

@@ -1,3 +1,6 @@
+"""
+Creates json files in master folder
+"""
 import os
 import csv
 import sys
@@ -7,7 +10,7 @@
 import json
 
 BASEPATH = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '../'))
-Master = os.path.join(BASEPATH,"Master")
+Master = os.path.join(BASEPATH, "Master")
 if BASEPATH not in sys.path:
     sys.path.append(BASEPATH)
 
@@ -17,12 +20,12 @@
 PHARMACOKINETICSPATH = os.path.join(DATABASEPATH, "caffeine", "Pharmacokinetics.tsv")
 INTERVENTIONSPATH = os.path.join(DATABASEPATH, "caffeine", "Interventions.tsv")
 DOSINGPATH = os.path.join(DATABASEPATH, "caffeine", "Dosing.tsv")
-MASTERPATH =     os.path.join(DATABASEPATH, "Master")
+MASTERPATH = os.path.join(DATABASEPATH, "Master")
 STUDIESMASTERPATH = os.path.join(MASTERPATH, "Studies")
 
 
 def extract_studies(path):
-    reader = csv.DictReader(open(path),delimiter='\t')
+    reader = csv.DictReader(open(path), delimiter='\t')
     for line in reader:
         yield dict(line)
 
@@ -34,7 +37,7 @@ def pmid_to_int(d):
 
 def add_study_sid(d):
     sid = str(d["study"])
-    yield {**d ,'sid':sid}
+    yield {**d , 'sid': sid}
 
 
 def add_study_path(d):
@@ -73,14 +76,18 @@ def create_json(d):
     return {'json': json_dict, 'study_path' : d["study_path"]}
 
 
-#save
 def save_json(d):
     json_file = os.path.join(d["study_path"],"data.json")
     with open(json_file, 'w') as fp:
         json.dump(d['json'],fp, indent=4)
 
 
 def get_graph(**options):
+    """ Bonobo execution graph.
+
+    :param options:
+    :return:
+    """
     graph = bonobo.Graph()
     graph.add_chain(
         extract_studies(STUDIESPATH),
@@ -102,4 +109,4 @@ def get_services(**options):
 if __name__ == '__main__':
     parser = bonobo.get_argument_parser()
     with bonobo.parse_args(parser) as options:
-        bonobo.run(get_graph(**options), services=get_services(**options))
+        bonobo.run(get_graph(**options), services=get_services(**options))

pkdb_app/data_management/create_master_json.py

@@ -1,3 +1,9 @@
+"""
+TODO: check if still needed and remove
+
+"""
+
+
 import os
 import sys
 import bonobo

pkdb_app/data_management/fill_database.py

@@ -7,19 +7,23 @@
 client = coreapi.Client()
 document = client.get("http://0.0.0.0:8000/")
 
+
 def get_study_json_path():
     for root, dirs, files in os.walk(STUDIESMASTERPATH, topdown=False):
         if "data.json" in files:
-            yield os.path.join(root,'data.json')
+            yield os.path.join(root, 'data.json')
+
 
 def open_json(d):
     with open(d) as f:
         json_dict = json.loads(f.read())
     return json_dict
 
+
 def upload_study(json_study):
     client.action(document, ["studies", "create"], params=json_study)
 
+
 def get_graph(**options):
     graph = bonobo.Graph()
     #add studies
@@ -30,10 +34,12 @@ def get_graph(**options):
     )
     return graph
 
+
 def get_services(**options):
     return {}
 
+
 if __name__ == '__main__':
     parser = bonobo.get_argument_parser()
     with bonobo.parse_args(parser) as options:
-        bonobo.run(get_graph(**options), services=get_services(**options))
+        bonobo.run(get_graph(**options), services=get_services(**options))

pkdb_app/studies/migrations/0004_auto_20180629_1437.py

@@ -0,0 +1,32 @@
+# Generated by Django 2.0.6 on 2018-06-29 14:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('studies', '0003_auto_20180619_0834'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='study',
+            name='sid',
+        ),
+        migrations.AddField(
+            model_name='study',
+            name='abstract',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name='study',
+            name='authors',
+            field=models.ManyToManyField(blank=True, related_name='authors', to='studies.Author'),
+        ),
+        migrations.AlterField(
+            model_name='study',
+            name='title',
+            field=models.TextField(),
+        ),
+    ]

pkdb_app/studies/models.py

@@ -1,3 +1,6 @@
+"""
+Django model for Study.
+"""
 from django.db import models
 from .utils import CHAR_MAX_LENGTH
 from pkdb_app.behaviours import Sidable, Describable, Commentable
@@ -12,12 +15,19 @@ def __str__(self):
         return '%s %s' % (self.first_name, self.last_name)
 
 class Study(Commentable, Describable, models.Model):
+    """ Single clinical study.
+
+    Mainly reported as a single publication.
+    """
+
+
     title = models.TextField()
     pmid = models.CharField(max_length=CHAR_MAX_LENGTH)
     abstract = models.TextField(blank=True, null=True)
     file = models.FileField(upload_to="study", null=True, blank=True)
     authors = models.ManyToManyField(Author, blank=True, related_name='authors')
 
+
 class Intervention(Sidable, Commentable, Describable, models.Model):
     type = models.IntegerField(choices=INTERVENTION_CHOICES)
     study = models.ForeignKey(Study, null=True, blank=True, on_delete=True)