SP-1061, SWE-36: Some refactoring and extension of framework. Assertion part...

SP-1061, SWE-36: Some refactoring and extension of framework. Assertion part of test_ev.py extended.

SVN: 30246

integration-tests/source/systemtest/testcase.py

@@ -13,6 +13,7 @@ DATAMOVER_PROJECT = 'datamover'
 
 PLAYGROUND = 'targets/playground'
 TEMPLATES = 'templates'
+TEST_DATA = 'testData'
 PSQL_EXE = 'psql'
 
 class TestCase(object):
@@ -256,6 +257,33 @@ class _Controller(object):
         self.installPath = installPath
         print "Controller created for instance '%s'. Installation path: %s" % (instanceName, installPath)
 
+
+    def assertEmptyFolder(self, pathRelativeToInstallPath):
+        """
+        Asserts that the specified path (relative to the installation path) is an empty folder.
+        """
+        relativePath = "%s/%s" % (self.installPath, pathRelativeToInstallPath)
+        files = self._getFiles(relativePath)
+        if len(files) == 0:
+            print "Empty folder as expected: %s" % relativePath
+        else:
+            self.testCase.fail("%s isn't empty. It contains the following files:\n  %s" % (relativePath, files))
+            
+    def assertFiles(self, folderPathRelativeToInstallPath, expectedFiles):
+        """
+        Asserts that the specified path (relative to the installation path) contains the specified files.
+        """
+        relativePath = "%s/%s" % (self.installPath, folderPathRelativeToInstallPath)
+        files = self._getFiles(relativePath)
+        self.testCase.assertEquals("Files in %s" % relativePath, expectedFiles, sorted(files))
+        
+    def _getFiles(self, relativePath):
+        if not os.path.isdir(relativePath):
+            self.testCase.fail("Doesn't exist or isn't a folder: %s" % relativePath)
+        files = os.listdir(relativePath)
+        return files
+
+            
 class ScriptBasedServerController(_Controller):
     def __init__(self, testCase, testName, installPath, instanceName, startCommand, stopCommand):
         super(ScriptBasedServerController, self).__init__(testCase, testName, installPath, instanceName)
@@ -325,7 +353,7 @@ class DatamoverController(_Controller):
         
     def drop(self, testDataSetName):
         """ Drops the specified test data set into incoming folder. """
-        util.copyFromTo("testData", "%s/data/incoming" % self.installPath, testDataSetName)
+        util.copyFromTo(TEST_DATA, "%s/data/incoming" % self.installPath, testDataSetName)
 
             
 class ScreeningTestClient(object):
@@ -347,6 +375,26 @@ class ScreeningTestClient(object):
                 log.write("%s\n" % line)
         return output
     
+class DataSet(object):
+        def __init__(self, resultSetRow):
+            self.id = resultSetRow[0]
+            self.dataStore = resultSetRow[1]
+            self.experimentCode = resultSetRow[2]
+            self.code = resultSetRow[3]
+            self.type = resultSetRow[4]
+            self.location = resultSetRow[5]
+            self.producer = resultSetRow[6]
+            self.productionTimeStamp = resultSetRow[7]
+            self.parents = []
+            self.children = []
+        
+        def __str__(self):
+            parents = [d.id for d in self.parents]  
+            children = [d.id for d in self.children]
+            return "%s,%s,%s,%s,%s,%s,%s,%s,%s,%s" % (self.id, self.dataStore, self.code, self.type, 
+                                                      self.location, parents, children, self.experimentCode, 
+                                                      self.producer, self.productionTimeStamp) 
+    
 class OpenbisController(_Controller):
     """
     Class to control AS and DSS of an installed openBIS instance.
@@ -390,6 +438,9 @@ class OpenbisController(_Controller):
         """ Sets the code of the Data Store Server. """
         self.dssProperties['data-store-server-code'] = code
         
+    def getDataStoreServerCode(self):
+        return self.dssProperties['data-store-server-code']
+        
     def setDataStoreServerPort(self, port):
         """ Sets the port of the Data Store Server. """
         self.dssProperties['port'] = port
@@ -408,33 +459,56 @@ class OpenbisController(_Controller):
         else:
             self.testCase.fail("Path doesn't exist: %s" % relativePath)
             
-    def assertEmptyFolder(self, pathRelativeToInstallPath):
+    def assertDataSetContent(self, pathToOriginal, dataSet):
+        path = "%s/data/store/1/%s/original" % (self.installPath, dataSet.location)
+        path = "%s/%s" % (path, os.listdir(path)[0])
+        numberOfDifferences = util.getNumberOfDifferences(pathToOriginal, path)
+        if numberOfDifferences > 0:
+            self.testCase.fail("%s differences found." % numberOfDifferences)
+            
+    def assertNumberOfDataSets(self, expectedNumberOfDataSets, dataSets):
         """
-        Asserts that the specified path (relative to the installation path) is an empty folder.
+        Asserts that the specified number of data sets from the specified list of DataSet instances 
+        are in the data store. 
         """
-        relativePath = "%s/%s" % (self.installPath, pathRelativeToInstallPath)
-        if not os.path.isdir(relativePath):
-            self.testCase.fail("Doesn't exist or isn't a folder: %s" % relativePath)
-        files = os.listdir(relativePath)
-        if len(files) == 0:
-            print "Empty folder as expected: %s" % relativePath
-        else:
-            self.testCase.fail("%s isn't empty. It contains the following files:\n  %s" % (relativePath, files))
-            
-    def assertNumberOfDataSets(self, expectedNumberOfDataSets):
-        """
-        Asserts that the specified number of data sets are in the store and in the database.
-        Some meta data of all data sets are returned.
-        """
-        metaData = self.queryDatabase("openbis", "select e.code,data.code,t.code,location from data"
-                                               + " join external_data as ed on ed.data_id = data.id" 
-                                               + " join data_set_types as t on data.dsty_id = t.id"
-                                               + " join experiments as e on data.expe_id = e.id")
-        util.printResultSet(metaData)
-        self.testCase.assertEquals('number of data sets', expectedNumberOfDataSets, len(metaData));
-        for row in metaData:
-            self.assertFileExist("data/store/1/%s/original" % row[3])
-        return metaData
+        count = 0
+        for dataSet in dataSets:
+            if dataSet.dataStore != self.getDataStoreServerCode():
+                continue
+            count += 1
+            self.assertFileExist("data/store/1/%s/original" % dataSet.location)
+        self.testCase.assertEquals("Number of data sets in data store %s" % self.getDataStoreServerCode(), 
+                                   expectedNumberOfDataSets, count)
+    
+    def getDataSets(self):
+        """
+        Returns all data sets as a list (ordered by data set ids) of instances of class DataSet.
+        """
+        resultSet = self.queryDatabase('openbis', 
+                                       "select data.id,ds.code,e.code,data.code,t.code,location,"
+                                       + "    data.data_producer_code,data.production_timestamp from data"
+                                       + " join external_data as ed on ed.data_id = data.id" 
+                                       + " join data_set_types as t on data.dsty_id = t.id"
+                                       + " join experiments as e on data.expe_id = e.id"
+                                       + " join data_stores as ds on data.dast_id = ds.id order by data.id")
+        dataSets = []
+        dataSetsById = {}
+        for row in resultSet:
+            dataSet = DataSet(row)
+            dataSets.append(dataSet)
+            dataSetsById[dataSet.id] = dataSet
+        relationships = self.queryDatabase('openbis', 
+                                           "select data_id_parent, data_id_child from data_set_relationships"
+                                           + " order by data_id_parent, data_id_child")
+        for parent_id, child_id in relationships:
+            parent = dataSetsById[parent_id]
+            child = dataSetsById[child_id]
+            parent.children.append(child)
+            child.parents.append(parent)
+        print "All data sets:\nid,dataStore,code,type,location,experiment,parents,children\n"
+        for dataSet in dataSets:
+            print dataSet
+        return dataSets 
         
     def createTestDatabase(self, databaseType):
         """

integration-tests/source/systemtest/util.py

+import filecmp
 import os
 import os.path
 import re
@@ -137,6 +138,18 @@ def printResultSet(resultSet):
     """
     for row in resultSet:
         print row
+
+def getNumberOfDifferences(fileOrFolder1, fileOrFolder2):
+    """
+    Gets and reports differences in file system structures between both arguments.
+    """
+    result = filecmp.dircmp(fileOrFolder1, fileOrFolder2, ignore=['.svn'])
+    result.report()
+    return len(result.left_only) + len(result.right_only) + len(result.diff_files)
+
+def getContent(path):
+    with open(path, "r") as f:
+        return [ l.rstrip() for l in f.readlines()]
     
 class LogMonitor():
     """

integration-tests/test_3v.py

@@ -4,6 +4,7 @@ import shutil
 import settings
 import systemtest.testcase
 import systemtest.util as util
+from systemtest.testcase import TEST_DATA
 
 class TestCase(systemtest.testcase.TestCase):
 
@@ -51,26 +52,67 @@ class TestCase(systemtest.testcase.TestCase):
         openbis2.waitUntilDataSetRegistrationFinished()
         
         
-    def executeInDevMode(self):
-        openbis1 = self.createOpenbisController(instanceName='openbis1', dropDatabases=False)
-        openbis2 = self.createOpenbisController(instanceName='openbis2', dropDatabases=False)
-        datamover1 = self.createDatamoverController("datamover1")
-        datamover1.setPrefixForIncoming('microX_200801011213_')
-        datamover1.setTreatIncomingAsRemote(True)
-        datamover1.setOutgoingTarget('../openbis1/data/incoming-raw')
-        datamover1.setExtraCopyDir('data/extra_local_copy')
-        datamover2 = self.createDatamoverController("datamover2")
-        datamover2.setOutgoingTarget('../openbis1/data/incoming-analysis')
-        dummyImageAnalyser = self.createScriptBasedServerController('dummy-img-analyser')
-        """
-        openbis1.allUp()
-        openbis2.dssUp()
-        datamover1.start()
-        datamover2.start()
-        dummyImageAnalyser.start()
-        """
-        openbis1.assertNumberOfDataSets(6)
-        openbis2.assertNumberOfDataSets(1)
+        datamover1.assertEmptyFolder('data/incoming')
+        datamover1.assertEmptyFolder('data/extra_local_copy')
+        datamover2.assertEmptyFolder('data/incoming')
+        openbis1.assertFiles('data/incoming-raw', 
+                             ['.MARKER_is_finished_microX_200801011213_3VCP1', '.faulty_paths', 
+                              'microX_200801011213_3VCP1'])
+        openbis1.assertEmptyFolder('data/incoming-analysis')
+        openbis2.assertEmptyFolder('data/incoming')
+        dataCompletedLog = util.getContent("%s/data-completed-info.txt" % datamover1.installPath)
+        self.assertEquals("data completion log", 
+                          ['Data complete: /data/incoming/3VCP1', 'Data complete: /data/incoming/3VCP1', 
+                           'Data complete: /data/incoming/3VCP3', 'Data complete: /data/incoming/UnknownPlate'], 
+                          [l.replace(datamover1.installPath, '') for l in dataCompletedLog])
+        
+        dataSets = openbis1.getDataSets()
+        openbis1.assertNumberOfDataSets(5, dataSets)
+        openbis2.assertNumberOfDataSets(1, dataSets)
+        self.assertEquals("Experiments", ['EXP1'] * 6, [d.experimentCode for d in dataSets])
+        self.assertEquals("Producers", ['microX'] * 2, [d.producer for d in dataSets if d.code.startswith('MIC')])
+        self.assertEquals("Production timestamp", ['2008-01-01 12:13:00+01'] * 2, 
+                          [d.productionTimeStamp for d in dataSets if d.code.startswith('MIC')])
+        dataSet1 = self.getDataSetByCode(dataSets, 'MICROX-3VCP1')
+        openbis1.assertDataSetContent("%s/%s" % (TEST_DATA, '3VCP1'), dataSet1)
+        dataSet2 = self.getDataSetByCode(dataSets, 'MICROX-3VCP3')
+        openbis1.assertDataSetContent("%s/%s" % (TEST_DATA, '3VCP3'), dataSet2)
+        child = dataSet1.children[0]
+        self.assertEquals("data set type", 'HCS_IMAGE', child.type)
+        self.assertEquals("child of %s" % dataSet2.code, child, dataSet2.children[0])
+        count = 0
+        for dataSet in dataSets:
+            if dataSet.type != 'HCS_IMAGE_ANALYSIS_DATA':
+                continue
+            count += 1
+            path = "%s/data/store/1/%s/original" % (openbis1.installPath, dataSet.location)
+            code = os.listdir(path)[0].split('_')[-1]
+            openbis1.assertDataSetContent("%s/%s" % (TEST_DATA, code), dataSet)
+        self.assertEquals("number of analysis data sets", 3, count)
+        self.assertUnidentified(openbis1, 'HCS_IMAGE')
+        self.assertUnidentified(openbis1, 'HCS_IMAGE_ANALYSIS_DATA')
+        content = util.getContent("%s/data/store/1/%s/original/nemo.exp1_MICROX-3VCP1.MICROX-3VCP3.txt" 
+                                  % (openbis2.installPath, dataSets[-1].location))
+        self.assertEquals("parent data set content", ['hello world'], content)
+        self.assertDropBoxDrop(openbis2, 'drop-box1')
+        self.assertDropBoxDrop(openbis2, 'drop-box2')
+        
+    def assertDropBoxDrop(self, openbisController, dropbox):
+        path = "%s/data/%s" % (openbisController.installPath, dropbox)
+        content = util.getContent("%s/%s" % (path, os.listdir(path)[0]))
+        self.assertEquals("Content of %s" % dropbox, ['hello world'], content)
+        
+    def assertUnidentified(self, openbisController, type):
+        path = "%s/data/store/1/unidentified/DataSetType_%s" % (openbisController.installPath, type)
+        n = util.getNumberOfDifferences("%s/UnknownPlate" % TEST_DATA, "%s/%s" % (path, os.listdir(path)[0]))
+        if n > 0:
+            self.fail("unidentified data set of type %s not as expected" % type)
+        
 
+    def getDataSetByCode(self, dataSets, code):
+        for dataSet in dataSets:
+            if dataSet.code == code:
+                return dataSet
+        self.fail("No data set with code %s found." % code)
         
 TestCase(settings, __file__).runTest()
\ No newline at end of file

integration-tests/test_screening.py

@@ -16,7 +16,7 @@ class TestCase(systemtest.testcase.TestCase):
         openbisController.assertEmptyFolder('data/incoming-analysis');
         openbisController.assertEmptyFolder('data/incoming-images-merged-channels');
         openbisController.assertEmptyFolder('data/incoming-images-split-channels');
-        openbisController.assertNumberOfDataSets(3)
+        openbisController.assertNumberOfDataSets(3, openbisController.getDataSets())
         self.assertSpotSizes(openbisController, [['24', '16'], ['24', '16']])
         self.assertFeatureVectorLabel(openbisController, 'HITRATE', 'Hit Rate')
         self.assertFeatureVectorLabel(openbisController, 'CELLNUMBER', 'cellNumber')