#319 Fix Build Process (#320)

* Update Travis to use Ubuntu Bionic with pre-installed docker-compose

* Docker should use Ubuntu 18.04 and install git for npm

* Remove unused variables

* Add missing migration

* Fix wrong string interpolation

* Label string as RegEx

.travis.yml

@@ -1,4 +1,5 @@
 sudo: required
+dist: bionic
 git:
   lfs_skip_smudge: true
 env:
@@ -11,17 +12,6 @@ python: 3.6
 before_install:
 - echo -e "machine github.com\n  login $GITHUB_TOKEN" >> ~/.netrc
 - git lfs pull
-- sudo sh -c 'echo "deb https://apt.dockerproject.org/repo ubuntu-trusty main" > /etc/apt/sources.list.d/docker.list'
-- sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
-- sudo apt-get update
-- sudo apt-key update
-- sudo apt-get --force-yes -qqy -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold"
-  install docker-engine=17.05.0~ce-0~ubuntu-trusty
-- sudo rm /usr/local/bin/docker-compose
-- curl -L https://github.com/docker/compose/releases/download/1.14.0/docker-compose-`uname
-  -s`-`uname -m` > docker-compose
-- chmod +x docker-compose
-- sudo mv docker-compose /usr/local/bin
 - docker-compose -v
 - docker -v
 install:

compose/base/Dockerfile-dev

@@ -1,6 +1,16 @@
-FROM ubuntu:rolling
-ENV PYTHONUNBUFFERED 1
-RUN apt-get update && apt-get install -y tcl tk python3.6 python3.6-tk wget python-opencv python3-distutils
+FROM ubuntu:18.04
+USER root
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update
+RUN apt-get install -y software-properties-common
+RUN add-apt-repository ppa:jonathonf/python-3.6
+RUN apt-get update
+
+RUN apt-get install -y build-essential python3.6 python3.6-dev python3-pip python3.6-venv
+RUN python3.6 -m pip install pip --upgrade
+
+RUN apt-get install -y tcl tk python3.6-tk wget python-opencv python3-distutils git
 RUN wget https://bootstrap.pypa.io/get-pip.py
 RUN python3.6 get-pip.py
 

compose/interface/Dockerfile-dev-vue

@@ -1,7 +1,7 @@
 FROM node:8-slim
 
 # Install Selenium dependencies
-RUN apt-get update && apt-get install -y bzip2
+RUN apt-get update && apt-get install -y bzip2 git
 
 # Install Node dependencies
 COPY ./interface/frontend /app

compose/interface/Dockerfile-e2e-test-vue

@@ -1,7 +1,7 @@
 FROM node:8-slim
 
 # Install Selenium dependencies
-RUN apt-get update && apt-get install -y bzip2
+RUN apt-get update && apt-get install -y bzip2 git
 
 # Install Node dependencies
 COPY ./interface/frontend /app

compose/interface/Dockerfile-unit-test-vue

@@ -1,7 +1,7 @@
 FROM node:8-slim
 
 # Install Selenium dependencies
-RUN apt-get update && apt-get install -y bzip2
+RUN apt-get update && apt-get install -y bzip2 git
 
 # Install Node dependencies
 COPY ./interface/frontend /app

interface/backend/api/views.py

@@ -99,7 +99,7 @@ def get(self, request):
         path = request.GET['dicom_location']
         try:
             return Response(ImageFile.load_dicom_data_from_disk(path, encode_image_data=True))
-        except IOError as err:
+        except IOError:
             raise NotFound(f"DICOM file not found on disk with path '{path}'")
 
 

interface/backend/images/factories.py

@@ -7,9 +7,9 @@ class ImageSeriesFactory(factory.django.DjangoModelFactory):
     class Meta:
         model = models.ImageSeries
 
-    patient_id = factory.Sequence(lambda n: "TEST-SERIES-{:4d}".format(n))
+    patient_id = factory.Sequence(lambda n: "TEST-SERIES-{:04d}".format(n))
 
-    series_instance_uid = factory.Sequence(lambda n: "1.3.6.1.4.1.14519.5.2.1.6279.6001.{:30d}".format(n))
+    series_instance_uid = factory.Sequence(lambda n: "1.3.6.1.4.1.14519.5.2.1.6279.6001.{:030d}".format(n))
 
     uri = factory.LazyAttribute(lambda f: 'file:///tmp/{}/'.format(f.series_instance_uid))
 

interface/backend/images/migrations/0006_auto_20191205_1249.py

@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.3 on 2019-12-05 12:49
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('images', '0005_remove_imagelocation_series'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='imagefile',
+            options={'ordering': ('slice_location',)},
+        ),
+    ]

interface/backend/images/tests.py

@@ -13,7 +13,7 @@
 class SmokeTest(TestCase):
     def test_create_image_series(self):
         image_series = ImageSeriesFactory()
-        self.assertRegex(image_series.series_instance_uid, '^[0-9\.]{64}')
+        self.assertRegex(image_series.series_instance_uid, r'^[0-9\.]{64}')
         self.assertIn(image_series.series_instance_uid, image_series.uri)
 
     def test_get_create_image_series(self):

prediction/src/preprocess/lung_segmentation.py

@@ -115,7 +115,7 @@ def load_patient(src_dir):
 
     try:
         slice_thickness = numpy.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])
-    except IndexError as e:
+    except IndexError:
         slice_thickness = numpy.abs(slices[0].SliceLocation - slices[1].SliceLocation)
 
     for s in slices: