From 61e18c823075ec6d9cc5ab8f6f7f0bd2a44bb3ee Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 14 May 2018 15:34:16 -0400
Subject: [PATCH] Tests for workflow testing script.

---
 .travis.yml                    | 38 +++++++++++------
 Makefile                       |  3 ++
 scripts/run_workflow_tests.sh  | 78 ++++++++++++++++++++++++++++++++++
 scripts/test_workflow_tests.sh | 21 +++++++++
 tox.ini                        |  7 ++-
 5 files changed, 132 insertions(+), 15 deletions(-)
 create mode 100644 scripts/run_workflow_tests.sh
 create mode 100644 scripts/test_workflow_tests.sh

diff --git a/.travis.yml b/.travis.yml
index d10dae8bd..9329c8ffa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,18 +1,26 @@
 language: python
-sudo: false
+sudo: true
 python: 2.7
 env:
-  - TOX_ENV=py27-lint
-  - TOX_ENV=py34-lint
-  - TOX_ENV=py27-lint-readme
-  - TOX_ENV=py27-lint-docs
-  - TOX_ENV=py34-quick
-  - TOX_ENV=py27
-  - TOX_ENV=py34
-  - TOX_ENV=py34-gx-1801
-  - TOX_ENV=py34-gx-dev
-  - TOX_ENV=py34-gx-1709
-  - TOX_ENV=py27-lint-docstrings
+  global:
+    - PLANEMO_SKIP_REDUNDANT_TESTS=1
+    - PLANEMO_ENABLE_POSTGRES_TESTS=1
+    - PLANEMO_SKIP_GALAXY_CWL_TESTS=1
+    - PLANEMO_TEST_WORKFLOW_RUN_PROFILE=travisworkflowtests
+  matrix:
+    - TOX_ENV=py27-lint
+    - TOX_ENV=py34-lint
+    - TOX_ENV=py27-lint-readme
+    - TOX_ENV=py27-lint-docs
+    - TOX_ENV=py34-quick
+    - TOX_ENV=py27
+    - TOX_ENV=py34
+    - TOX_ENV=py34-gx-1801
+    - TOX_ENV=py34-gx-dev
+    - TOX_ENV=py34-gx-1709
+    - TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=docker_test
+    - TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=serve_and_test
+    - TOX_ENV=py27-lint-docstrings
 
 install:
   # Setup git to allow git operations.
@@ -23,11 +31,13 @@ install:
 matrix:
   allow_failures:
     - env: TOX_ENV=py27-lint-docstrings
+    - TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=docker_test
 
-script: PLANEMO_SKIP_REDUNDANT_TESTS=1 PLANEMO_ENABLE_POSTGRES_TESTS=1 PLANEMO_SKIP_GALAXY_CWL_TESTS=1 PLANEMO_TEST_WORKFLOW_RUN_PROFILE=travisworkflowtests tox -e $TOX_ENV
+script: tox -e $TOX_ENV
 
 after_success:
   - coveralls
 
 services:
-  - postgresql
\ No newline at end of file
+  - postgresql
+  - docker
diff --git a/Makefile b/Makefile
index 8b53c5910..2282eb8bb 100644
--- a/Makefile
+++ b/Makefile
@@ -75,6 +75,9 @@ test: ## run tests with the default Python (faster than tox)
 quick-test: ## run quickest tests with the default Python
 	$(IN_VENV) PLANEMO_SKIP_SLOW_TESTS=1 PLANEMO_SKIP_GALAXY_TESTS=1 nosetests $(NOSE_TESTS)
 
+gxwf-test-test:  ## run test of workflow testing script
+	bash $(BUILD_SCRIPTS_DIR)/test_workflow_tests.sh
+
 tox: ## run tests with tox in the specified ENV, defaults to py27
 	$(IN_VENV) tox -e $(ENV) -- $(ARGS)
 
diff --git a/scripts/run_workflow_tests.sh b/scripts/run_workflow_tests.sh
new file mode 100644
index 000000000..a59716545
--- /dev/null
+++ b/scripts/run_workflow_tests.sh
@@ -0,0 +1,78 @@
+#!/bin/bash
+
+: ${PLANEMO_TARGET:="planemo==0.50.1"}
+: ${PLANEMO_OPTIONS:="--verbose"}
+: ${PLANEMO_PROFILE_NAME:="wxflowtest"}
+: ${PLANEMO_SERVE_PORT:="9019"}
+: ${PLANEMO_TEST_STYLE:="serve_and_test"}  # profile_serve_and_test, serve_and_test, docker_serve_and_test, test, docker_test
+: ${PLANEMO_SERVE_DATABASE_TYPE:="postgres"}  # used if not using Docker with PLANEMO_TEST_STYLE
+: ${PLANEMO_DOCKER_GALAXY_IMAGE:="quay.io/bgruening/galaxy:18.01"}  # used if used Docker with PLANEMO_TEST_STYLE
+
+GALAXY_URL="http://localhost:$PLANEMO_SERVE_PORT"
+
+# Ensure Planemo is installed.
+if [ ! -d .venv ]; then
+    virtualenv .venv
+    . .venv/bin/activate
+    pip install -U pip
+    # Intentionally expand wildcards in PLANEMO_TARGET.
+    shopt -s extglob
+    pip install ${PLANEMO_TARGET}
+fi
+. .venv/bin/activate
+
+# Run test.
+# This example shows off a bunch of different ways one could test with Planemo,
+# but for actual workflow testing projects - probably best just to take one of the last
+# two very easy invocations to simplify things.
+if [ "$PLANEMO_TEST_STYLE" = "profile_serve_and_test" ]; then
+    planemo $PLANEMO_OPTIONS profile_create \
+        --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
+        "$PLANEMO_PROFILE_NAME"
+    planemo $PLANEMO_OPTIONS serve \
+        --daemon \
+        --profile "$PLANEMO_PROFILE_NAME" \
+        --port "$PLANEMO_SERVE_PORT" \
+        "$1"
+    planemo $PLANEMO_OPTIONS test \
+        --galaxy_url "$GALAXY_URL" \
+        --engine external_galaxy \
+        "$1"
+elif [ "$PLANEMO_TEST_STYLE" = "serve_and_test" ]; then
+    planemo $PLANEMO_OPTIONS serve \
+        --daemon \
+        --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
+        --port "$PLANEMO_SERVE_PORT" \
+        "$1"
+    planemo $PLANEMO_OPTIONS test \
+        --galaxy_url "$GALAXY_URL" \
+        --engine external_galaxy \
+        "$1"
+elif [ "$PLANEMO_TEST_STYLE" = "docker_serve_and_test" ]; then
+    docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}"
+    planemo $PLANEMO_OPTIONS serve \
+        --daemon \
+        --engine docker_galaxy \
+        --docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \
+        --docker_extra_volume . \
+        --port "$PLANEMO_SERVE_PORT" \
+        "$1"
+    planemo $PLANEMO_OPTIONS test \
+        --galaxy_url "$GALAXY_URL" \
+        --engine external_galaxy \
+        "$1"
+elif [ "$PLANEMO_TEST_STYLE" = "test" ]; then
+    planemo $PLANEMO_OPTIONS test \
+        --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
+        "$1"
+elif [ "$PLANEMO_TEST_STYLE" = "docker_test" ]; then
+    docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}"
+    planemo $PLANEMO_OPTIONS test \
+        --engine docker_galaxy \
+        --docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \
+        --docker_extra_volume . \
+        "$1" > /dev/null
+else
+    echo "Unknown test style ${PLANEMO_TEST_STYLE}"
+    exit 1
+fi
diff --git a/scripts/test_workflow_tests.sh b/scripts/test_workflow_tests.sh
new file mode 100644
index 000000000..631e0ac91
--- /dev/null
+++ b/scripts/test_workflow_tests.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Ensure working directory is planemo project.
+SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+PROJECT_DIRECTORY="${SCRIPTS_DIRECTORY}/.."
+
+TEMP_DIRECTORY=`mktemp -d 2>/dev/null || mktemp -d -t 'planemowftest'`
+cp "$SCRIPTS_DIRECTORY/run_workflow_tests.sh" "$TEMP_DIRECTORY"
+cp "$PROJECT_DIRECTORY/tests/data/"wf4* "$TEMP_DIRECTORY"
+cp "$PROJECT_DIRECTORY/tests/data/1.bed" "$TEMP_DIRECTORY"
+
+cd $PROJECT_DIRECTORY
+
+# Build Planemo wheel.
+make dist
+
+# Test against wheel.
+export PLANEMO_TARGET="$PROJECT_DIRECTORY/dist/planemo*whl"
+
+cd $TEMP_DIRECTORY
+bash run_workflow_tests.sh "wf4-distro-tools.gxwf.yml"
diff --git a/tox.ini b/tox.ini
index ca2c5ab2b..b86808b19 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,6 @@
 # TODO: implement doc linting
 [tox]
-envlist = py{27,34}-lint, py{27,34,35}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}, py{27,34,35}-gx-{master,dev,1801,1709,1705}
+envlist = py{27,34}-lint, py{27,34,35}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}, py{27,34,35}-gx-{master,dev,1801,1709,1705}, py27-gxwf-test-test
 source_dir = planemo
 test_dir = tests
 
@@ -64,3 +64,8 @@ whitelist_externals = make
 deps =
     -rrequirements.txt
     -rdev-requirements.txt
+
+[testenv:py27-gxwf-test-test]
+commands = make gxwf-test-test
+skip_install = True
+whitelist_externals = make