COMP: Move data directory to Testing/Data, create Testing/Integration directory

Applications/CMakeLists.txt

@@ -39,7 +39,7 @@ if( NOT CMAKE_PROJECT_NAME STREQUAL "SuperElastix" )
   #TODO SuperElastix Application should not link against elastix libraries
   # If OpenMP is supported by this machine, elastix will be compiled with
   # OpenMP flags, and we need to add them here as well
-  find_package( OpenMP )
+  find_package( OpenMP QUIET )
   if (OPENMP_FOUND)
     set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}" )
     set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )

CMakeLists.txt

@@ -104,6 +104,21 @@ selxmodule_enable( ModuleController )
 # ---------------------------------------------------------------------
 # Testing
 
+set( SUPERELASTIX_INPUT_DATA_DIR ${CMAKE_CURRENT_BINARY_DIR}/Testing/Data/Input )
+set( SUPERELASTIX_OUTPUT_DATA_DIR ${CMAKE_CURRENT_BINARY_DIR}/Testing/Data/Output )
+set( SUPERELASTIX_BASELINE_DATA_DIR ${CMAKE_CURRENT_BINARY_DIR}/Testing/Data/Baseline )
+set( SUPERELASTIX_CONFIGURATION_DATA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Testing/Data/Configuration )
+
+if( NOT EXISTS ${SUPERELASTIX_OUTPUT_DATA_DIR} )
+  file( MAKE_DIRECTORY ${SUPERELASTIX_OUTPUT_DATA_DIR} )
+endif()
+
+if( NOT EXISTS ${SUPERELASTIX_OUTPUT_DATA_DIR} )
+  message( FATAL_ERROR 
+    "Could not create directory for output data. Make sure CMake has write permissions."
+  )
+endif()
+
 option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ON )
 if( ${SUPERELASTIX_BUILD_TESTING} )
   mark_as_advanced( SUPERELASTIX_BUILD_LONG_TESTS )

Modules/Components/Elastix/ModuleElastix.cmake

@@ -21,7 +21,7 @@ set( MODULE ModuleElastix )
 
 # If OpenMP is supported by this machine, elastix will be compiled with
 # OpenMP flags, and we need to add them here as well
-find_package( OpenMP )
+find_package( OpenMP QUIET )
 if (OPENMP_FOUND)
   set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}" )
   set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )

Testing/Benchmark/CMakeLists.txt

-#=========================================================================
-#
-#  Copyright Leiden University Medical Center, Erasmus University Medical 
-#  Center and contributors
-#
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#        http://www.apache.org/licenses/LICENSE-2.0.txt
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-#
-#=========================================================================
-

Testing/CMakeLists.txt

@@ -54,28 +54,28 @@ ExternalData_Add_Target( SuperElastixData )
 find_package( GTest REQUIRED )
 include_directories( ${GTEST_INCLUDE_DIRS} )
 
-set( TEST_LIBRARIES
-  ${GTEST_BOTH_LIBRARIES}
+set( TEST_LIBRARIES ${GTEST_BOTH_LIBRARIES} )
+
+# ---------------------------------------------------------------------
+# Build data manager
+
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/selxDataDirectories.h.in
+  ${CMAKE_CURRENT_BINARY_DIR}/selxDataDirectories.h
+  ESCAPE_QUOTES
 )
 
+include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ) # selxDataManager.h
+include_directories( ${CMAKE_CURRENT_BINARY_DIR} ) # selxDataDirectories.h
+add_library( DataManager selxDataManager.cxx )
+
+list( APPEND TEST_LIBRARIES DataManager )
+
 # ---------------------------------------------------------------------
 # Build test suite
 
 set( CTEST_CONFIGURATION_TYPE Debug )
 
-# Unit tests
 add_subdirectory( Unit )
+add_subdirectory( Integration )
 
-# Make data directories available parent cmake for installation of SuperElastix
-set( SUPERELASTIX_UNITTEST_INPUT_DATA_DIR ${SUPERELASTIX_UNITTEST_INPUT_DATA_DIR} PARENT_SCOPE )
-set( SUPERELASTIX_UNITTEST_BASELINE_DATA_DIR ${SUPERELASTIX_UNITTEST_BASELINE_DATA_DIR} PARENT_SCOPE )
-set( SUPERELASTIX_UNITTEST_CONFIGURATION_DATA_DIR ${SUPERELASTIX_UNITTEST_CONFIGURATION_DATA_DIR} PARENT_SCOPE )
-
-# ---------------------------------------------------------------------
-# Configure dashboard
-mark_as_advanced( SUPERELASTIX_BUILD_DASHBOARD )
-option( SUPERELASTIX_BUILD_DASHBOARD "Enable SuperElastix dashboard." OFF )
-
-if( ${SUPERELASTIX_BUILD_DASHBOARD} )
-  add_subdirectory( Dashboard )
-endif()

Testing/Dashboard/CMakeLists.txt

-#=========================================================================
-#
-#  Copyright Leiden University Medical Center, Erasmus University Medical 
-#  Center and contributors
-#
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#        http://www.apache.org/licenses/LICENSE-2.0.txt
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-#
-#=========================================================================
-
-# ---------------------------------------------------------------------
-# Dashboard configuration
-
-mark_as_advanced( SUPERELASTIX_DASHBOARD_SOURCE_DIR )
-set( SUPERELASTIX_DASHBOARD_SOURCE_DIR "${CMAKE_SOURCE_DIR}/Testing/Dashboard" )
-
-mark_as_advanced( SUPERELASTIX_DASHBOARD_BINARY_DIR )
-set( SUPERELASTIX_DASHBOARD_BINARY_DIR "${CMAKE_BINARY_DIR}/Testing/Dashboard" )
-
-mark_as_advanced( SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE )
-set( SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE "selxLogstash.crt" )
-
-mark_as_advanced( SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY )
-set( SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY "selxLogstash.key" )
-
-mark_as_advanced( SUPERELASTIX_DASHBOARD_VOLUME )
-if( NOT EXISTS "${SUPERELASTIX_DASHBOARD_VOLUME}" )
-  set( ELASTIX_DASHBOARD_VOLUME "${SUPERELASTIX_DASHBOARD_BINARY_DIR}/Data" )
-  file( MAKE_DIRECTORY "${SUPERELASTIX_DASHBOARD_VOLUME}" )
-endif()
-
-# Test/Benchmark results will be forwarded to this IP. You will probably
-# have change this in order to match docker settings on your own machine. 
-mark_as_advanced( SUPERELASTIX_DASHBOARD_IP )
-set( SUPERELASTIX_DASHBOARD_IP "192.168.59.103" )
-
-configure_file(
-  ${SUPERELASTIX_DASHBOARD_SOURCE_DIR}/selxDashboard.yml.in
-  ${SUPERELASTIX_DASHBOARD_BINARY_DIR}/selxDashboard.yml
-)
-
-configure_file(
-  ${SUPERELASTIX_DASHBOARD_SOURCE_DIR}/selxLogstashForwarder.yml.in
-  ${SUPERELASTIX_DASHBOARD_BINARY_DIR}/selxLogstashForwarder.yml
-)
-
-configure_file(
-  ${SUPERELASTIX_DASHBOARD_SOURCE_DIR}/selxLogstash.conf.in
-  ${SUPERELASTIX_DASHBOARD_BINARY_DIR}/Logstash/selxLogstash.conf
-)
-
-configure_file(
-  ${SUPERELASTIX_DASHBOARD_SOURCE_DIR}/selxLogstashForwarder.json.in
-  ${SUPERELASTIX_DASHBOARD_BINARY_DIR}/selxLogstashForwarder.json
-)
-
-# ---------------------------------------------------------------------
-# SSL certificates
-# Use the following OpenSSL command to generate a test certificate and key if needed
-# openssl req -subj '/CN=*/' -x509 -batch -nodes -days 9999 -newkey rsa:2048 -keyout selxLogstash.key -out selxLogstash.crt

Testing/Dashboard/selxDashboard.yml.in

-SuperElastix:
-    image: willdurand/elk
-    ports:
-        - "80:80"
-        - "5043:5043"
-    volumes_from:
-        - data
-
-data:
-    image: busybox
-    volumes:
-        - @SUPERELASTIX_DASHBOARD_SOURCE_DIR@:/etc/ssl
-        - @SUPERELASTIX_DASHBOARD_VOLUME@:/data                   
-        - @SUPERELASTIX_DASHBOARD_BINARY_DIR@/Logstash:/etc/logstash

Testing/Dashboard/selxLogstash.conf.in

-input {
-  lumberjack {
-    port => 5043
-    ssl_certificate => "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@"
-    ssl_key => "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY@"
-  }
-}
-
-filter {
-  xml {
-    source => message
-    target => result
-  }
-}
-
-output {
-  elasticsearch {
-  	protocol => http
-  }
-}
\ No newline at end of file

Testing/Dashboard/selxLogstash.crt

------BEGIN CERTIFICATE-----
-MIIDCDCCAfCgAwIBAgIJANZVoY3O+DQaMA0GCSqGSIb3DQEBBQUAMAwxCjAIBgNV
-BAMUASowHhcNMTUxMDEzMjEyNzEwWhcNNDMwMjI3MjEyNzEwWjAMMQowCAYDVQQD
-FAEqMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAvtF4l3oqDRL/4m7C
-kCnzE6colB1Ii7KHoRuFyyL7PrZiyrKelRVDr6yDB0lIJevOxuuSJlA+BNccyI0h
-08/c3SRDkKb83MwQnABpDPS4/EhLGOJdTKutSo0FzCrn+uT470EYfCFvLLKMSnIO
-ECf5st3EN+VJoSu80B9sZ4TEfdO4Gedy0vlL3iNGGDn1TqconTDjB5HKHteEjZ1Z
-XzqBJUXITjzfD1VpYbSsj/wcFvurmaOMliqvsl1uFN7wXPjd1L8fAqcsAU5yBwLJ
-88NFqJrlgqTXnuHeMCqhiVwOOFUeBbvEk/Faw3P3BKgppl7P01WXzUky0CVyegG7
-qagK7QIDAQABo20wazAdBgNVHQ4EFgQUtsodBU4f6bCvbrYc+ix21auh7mowPAYD
-VR0jBDUwM4AUtsodBU4f6bCvbrYc+ix21auh7mqhEKQOMAwxCjAIBgNVBAMUASqC
-CQDWVaGNzvg0GjAMBgNVHRMEBTADAQH/MA0GCSqGSIb3DQEBBQUAA4IBAQAOPEH1
-Otzm6Eu8FNQoppXKBuVW0kqRi6/CM7JxJ0f21YajEu1+vb0BdlNAoCpmcmxCY9Hf
-cbmzeKyu/6wIXOOdqmTu/CGvEThtLNmrgjkj9sTe4i0C0H5fkOlkD6aSCHSVUwCv
-9nOmPMsu9snEhU+UMXIDqFJzCpN3TSXu/J+V4xV5TYGj0SfbIZXLsw4QcB+iwind
-oC1OorwxPsXVYnlMQeZAi7qaScOlq/82A3erXLKW7dRHIyXbgScs4VZ6kjg+YTH2
-YZW7y3xgUowj7xeWaoH9YciDfqV2SbxK4RoP2NeesuW0On0YebVQ5Z3qLeYb5fkV
-CiA5NpyBDPdElzWW
------END CERTIFICATE-----

Testing/Dashboard/selxLogstash.key

------BEGIN RSA PRIVATE KEY-----
-MIIEowIBAAKCAQEAvtF4l3oqDRL/4m7CkCnzE6colB1Ii7KHoRuFyyL7PrZiyrKe
-lRVDr6yDB0lIJevOxuuSJlA+BNccyI0h08/c3SRDkKb83MwQnABpDPS4/EhLGOJd
-TKutSo0FzCrn+uT470EYfCFvLLKMSnIOECf5st3EN+VJoSu80B9sZ4TEfdO4Gedy
-0vlL3iNGGDn1TqconTDjB5HKHteEjZ1ZXzqBJUXITjzfD1VpYbSsj/wcFvurmaOM
-liqvsl1uFN7wXPjd1L8fAqcsAU5yBwLJ88NFqJrlgqTXnuHeMCqhiVwOOFUeBbvE
-k/Faw3P3BKgppl7P01WXzUky0CVyegG7qagK7QIDAQABAoIBAAm9RUtt99F9A8R5
-5MJY8cgyAvc0W2yN6zBE6FpK6cn0oyw3W7K+SBsiUfnAOsd8tqwef/ImrFOw6w4t
-bemStXIwFKbAby2R2NMtji8UGpD9259khmCQbqLcecxG8Fo076O+jdJgHn2Ii3KN
-Sbx3Xd5MRWSY9l4cjmGNCQprk1/cpOjTF+OgNzYVISP6wx3bOafQ4O4Ui9sxjmPv
-G3Fend2YU3r1YGqREHb0Y6hjVoTAKt1RkZwYexQWkquLFO0neRC61k9UkPW+o2T5
-LlyMl9MbwbyA0gh52fh+Qi2oeVsGAmIwT1JTNVzrG8qEzuM45CvLQGLr5YjSTS9H
-bCi4Ul0CgYEA78zdf9UQiqIOlvLM+RDO25V7PrdwxqZtFASqnFplGjS2sKKQX/K8
-jAEkBrFSyX7ctPBjhDNRwq3M0j7AhIhL84KC2KAmdyn0PT9hc1216A/GPLluXjFe
-Ryq4/l5C07pyyx9BaHP1Xx5vlQkCYOVDCTu6tKk+TesEgTHIXoedkAMCgYEAy7WB
-SOHj8h2r5QQ33VoPIqDPORg5WwsFEPw+efCzevmTOCzLYwdcZudtA3xRZPSE7wwY
-s2J1MO9QzKeuzSldsBCUDeQoXblOVUJX/qveCka+Zn1AE4pztq3fo6JJIvVSpFC6
-YNJDfOXNwtMdwWeoy1x9aJl/auykMdSwzARi3k8CgYA9oO4QK2b76hhLzQzGuf4f
-yvQIs0Zll2ITMfvTARxYttF45d6q+gxhAu4KVkpLhLIeQmWhFTtfCCHKqtv5c7np
-VFJicA5Ss9KUZxSZfK0CfgNZmeJ2jMOJEL7IiNst5Q4Zi+fYe2zFTGIq8EzPMDyh
-Q9uBELn1doAK4At51+qzlwKBgETOMbTkV5HX48+e9R+W47XWiyfFvtm5hySNjqyx
-WG4ZDljTCH+SZOt9D501yGhJDv2PIGi2wM6ehrQZjzlM15A4iUmH3vqJNKQnnIEw
-m/bsnjMP6yyufxcc84TZs8pTAm7ttYYufw0Ysb80f8Brut+1hcZm0lrTQ0JxjKXc
-dWiRAoGBANIerU9KV0GYgvY0wvBitwP/0j4jLfHfVPCp6Y515MB5hXCf6RF3vAg4
-WWOu55cOqBGzouJoCJGcYR5Re/7b2AKqsfjnfFF6gl87T7xSGFEHjNK0q/UcPQQ/
-FxCfc2iwx90m56ZahbFnMh1y1i/NVqD0y3xUyJN0kt6zIT3j+BR1
------END RSA PRIVATE KEY-----

Testing/Dashboard/selxLogstashForwarder.json.in

-{
-  "network": {
-    "servers": [ "SuperElastix:5043" ],
-    "timeout": 15,
-    "ssl certificate": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@",
-    "ssl key": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY@",
-    "ssl ca": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@"
-  },
-  "files": [
-    {
-      "paths": [
-        "/var/unit/*.xml"
-       ],
-      "fields": { 
-        "type": "unittest",
-        "lib": "SuperElastix" 
-      }
-    },
-    {
-      "paths": [
-        "/var/benchmark/*.xml"
-       ],
-      "fields": { 
-        "type": "benchmark",
-        "lib": "SuperElastix" 
-      }
-    }
-   ]
-}

Testing/Dashboard/selxLogstashForwarder.yml.in

-forwarder:
-    image: willdurand/logstash-forwarder
-    extra_hosts:
-        - "SuperElastix:@SUPERELASTIX_DASHBOARD_IP@"
-    volumes_from:
-        - data
-
-data:
-    image: busybox
-    volumes:
-        - @SUPERELASTIX_DASHBOARD_BINARY_DIR@/selxLogstashForwarder.json:/etc/logstash-forwarder/config.json
-        - @SUPERELASTIX_DASHBOARD_SOURCE_DIR@:/etc/ssl
-        - @CMAKE_BINARY_DIR@/Testing/Unit:/var/unit
-        - @CMAKE_BINARY_DIR@/Testing/Benchmark:/var/benchmark