Merge pull request #241 from sartography/dev

dev to testing

.travis.yml

@@ -31,14 +31,6 @@ script:
 after_success:
   - sonar-scanner
 
-deploy:
-  provider: script
-  script: bash deploy.sh sartography/cr-connect-workflow
-  skip_cleanup: true
-  on:
-    all_branches: true
-    condition: $TRAVIS_BRANCH =~ ^(dev|testing|demo|training|staging|master|rrt\/.*)$
-
 notifications:
   email:
     on_success: change

Dockerfile

@@ -1,15 +1,24 @@
-FROM sartography/cr-connect-python-base
+FROM python:3.8
+
+RUN pip install pipenv
+RUN useradd _gunicorn --no-create-home --user-group
+
+RUN apt-get update && \
+    apt-get install -y -q \
+        gcc libssl-dev \
+        curl postgresql-client git-core \
+        gunicorn3 postgresql-client
 
 WORKDIR /app
 COPY Pipfile Pipfile.lock /app/
+RUN cd /app && pipenv lock --keep-outdated --requirements > requirements.txt
+RUN pip install -r /app/requirements.txt
 
 RUN set -xe \
-  && pipenv install --dev \
   && apt-get remove -y gcc python3-dev libssl-dev \
   && apt-get autoremove -y \
   && apt-get clean -y \
-  && rm -rf /var/lib/apt/lists/* \
-  && useradd _gunicorn --no-create-home --user-group
+  && rm -rf /var/lib/apt/lists/*
 
 COPY . /app/
 WORKDIR /app

crc/scripts/email.py

@@ -26,7 +26,7 @@ Example:
 email ("My Subject", "dhf8r@virginia.edu", pi.email)
 """
 
-    def do_task_validate_only(self, task, *args, **kwargs):
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
         self.get_subject(args)
         self.get_email_recipients(task, args)
         self.get_content(task)

crc/services/workflow_service.py

@@ -172,6 +172,8 @@ class WorkflowService(object):
             # If we have a default_value or value_expression, try to set the default
             if field.has_property(Task.FIELD_PROP_VALUE_EXPRESSION) or (hasattr(field, 'default_value') and field.default_value):
                 form_data[field.id] = WorkflowService.get_default_value(field, task)
+                if not field.has_property(Task.FIELD_PROP_REPEAT):
+                    continue
 
             # If we are only populating required fields, and this isn't required. stop here.
             if required_only:

deploy.sh

@@ -1,45 +0,0 @@
-#!/bin/bash
-
-#########################################################################
-# Builds the Docker image for the current git branch on Travis CI and
-# publishes it to Docker Hub.
-#
-# Parameters:
-# $1: Docker Hub repository to publish to
-#
-# Required environment variables (place in Settings menu on Travis CI):
-# $DOCKER_USERNAME: Docker Hub username
-# $DOCKER_TOKEN: Docker Hub access token
-#########################################################################
-
-echo 'Building Docker image...'
-DOCKER_REPO="$1"
-
-function branch_to_tag () {
-  if [ "$1" == "master" ]; then echo "latest"; else echo "$1" ; fi
-}
-
-function branch_to_deploy_group() {
-  if [[ $1 =~ ^(rrt\/.*)$ ]]; then echo "rrt"; else echo "crconnect" ; fi
-}
-
-DOCKER_TAG=$(branch_to_tag "$TRAVIS_BRANCH")
-
-DEPLOY_GROUP=$(branch_to_deploy_group "$TRAVIS_BRANCH")
-
-if [ "$DEPLOY_GROUP" == "rrt" ]; then
-  IFS='/' read -ra ARR <<< "$TRAVIS_BRANCH"  # Split branch on '/' character
-  DOCKER_TAG=$(branch_to_tag "rrt_${ARR[1]}")
-fi
-
-echo "DOCKER_REPO = $DOCKER_REPO"
-echo "DOCKER_TAG = $DOCKER_TAG"
-
-echo "$DOCKER_TOKEN" | docker login -u "$DOCKER_USERNAME" --password-stdin || exit 1
-docker build -f Dockerfile -t "$DOCKER_REPO:$DOCKER_TAG" . || exit 1
-
-
-# Push Docker image to Docker Hub
-echo "Publishing to Docker Hub..."
-docker push "$DOCKER_REPO" || exit 1
-echo "Done."

tests/test_email_script.py

@@ -1,9 +1,19 @@
 from tests.base_test import BaseTest
 from crc import mail
+import json
 
 
 class TestEmailScript(BaseTest):
 
+    def test_email_script_validation(self):
+        # This validates scripts.email.do_task_validate_only
+        # It also tests that we don't overwrite the default email_address with random text during validation
+        # Otherwise json would have an error about parsing the email address
+        self.load_example_data()
+        spec_model = self.load_test_spec('email_script')
+        rv = self.app.get('/v1.0/workflow-specification/%s/validate' % spec_model.id, headers=self.logged_in_headers())
+        self.assertEqual([], rv.json)
+
     def test_email_script(self):
         with mail.record_messages() as outbox:
 
@@ -12,6 +22,7 @@ class TestEmailScript(BaseTest):
             first_task = self.get_workflow_api(workflow).next_task
 
             workflow = self.get_workflow_api(workflow)
+            self.assertEqual('dan@sartography.com', workflow.next_task.data['email_address'])
             self.complete_form(workflow, first_task, {'email_address': 'test@example.com'})
 
             self.assertEqual(1, len(outbox))