def test_cleanPipeline_odkLastRun(self):
"""Test update of ODK_Conf.odkLastRun."""
os.makedirs("DHIS/blobs/", exist_ok = True)
dbFileName = "copy_Pipeline.db"
dbDirectory = "."
dbKey = "enilepiP"
useDHIS = True
pl = Pipeline(dbFileName, dbDirectory,
dbKey, useDHIS)
pl.closePipeline()
nowDate = datetime.datetime.now()
pipelineRunDate = nowDate.strftime("%Y-%m-%d_%H:%M:%S")
xferDB = TransferDB(dbFileName = dbFileName,
dbDirectory = dbDirectory,
dbKey = dbKey,
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
c.execute("SELECT odkLastRun FROM ODK_Conf;")
sqlQuery = c.fetchone()
results = [i for i in sqlQuery]
self.assertEqual(results[0], pipelineRunDate)
c.execute("UPDATE ODK_Conf SET odkLastRun = '1900-01-01_00:00:01';")
conn.commit()
conn.close()
def test_cleanPipeline_rmFiles(self):
"""Test file removal."""
if not os.path.isfile("ODKFiles/odkBCExportNew.csv"):
shutil.copy("ODKFiles/previous_bc_export.csv",
"ODKFiles/odkBCExportPrev.csv")
if not os.path.isfile("ODKFiles/odkBCExportPrev.csv"):
shutil.copy("ODKFiles/another_bc_export.csv",
"ODKFiles/odkBCExportNew.csv")
if not os.path.isfile("OpenVAFiles/openVA_input.csv"):
shutil.copy("OpenVAFiles/sample_openVA_input.csv",
"OpenVAFiles/openVA_input.csv")
if not os.path.isfile("OpenVAFiles/entityAttributeValue.csv"):
shutil.copy("OpenVAFiles/sampleEAV.csv",
"OpenVAFiles/entityAttributeValue.csv")
if not os.path.isfile("OpenVAFiles/recordStorage.csv"):
shutil.copy("OpenVAFiles/sample_recordStorage.csv",
"OpenVAFiles/recordStorage.csv")
if not os.path.isfile("OpenVAFiles/newStorage.csv"):
shutil.copy("OpenVAFiles/sample_newStorage.csv",
"OpenVAFiles/newStorage.csv")
os.makedirs("DHIS/blobs/", exist_ok = True)
shutil.copy("OpenVAFiles/sample_newStorage.csv",
"DHIS/blobs/001-002-003.db")
dbFileName = "copy_Pipeline.db"
dbDirectory = "."
dbKey = "enilepiP"
useDHIS = True
nowDate = datetime.datetime.now()
pipelineRunDate = nowDate.strftime("%Y-%m-%d_%H:%M:%S")
pl = Pipeline(dbFileName, dbDirectory, dbKey, useDHIS)
pl.closePipeline()
fileExist = False
if os.path.isfile("ODKFiles/odkBCExportNew.csv"):
fileExist = True
if os.path.isfile("ODKFiles/odkBCExportPrev.csv"):
fileExist = True
if os.path.isfile("ODKFiles/odkBCExportNew.csv"):
fileExist = True
if os.path.isfile("OpenVAFiles/openVA_input.csv"):
fileExist = True
if os.path.isfile("OpenVAFiles/entityAttributeValue.csv"):
fileExist = True
if os.path.isfile("OpenVAFiles/recordStorage.csv"):
fileExist = True
if os.path.isfile("OpenVAFiles/newStorage.csv"):
fileExist = True
if os.path.isfile("DHIS/blobs/001-002-003.db"):
fileExist = True
self.assertFalse(fileExist)
xferDB = TransferDB(dbFileName = dbFileName,
dbDirectory = dbDirectory,
dbKey = dbKey,
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
c.execute("UPDATE ODK_Conf SET odkLastRun = '1900-01-01_00:00:01';")
conn.commit()
conn.close()
def runPipeline(database_file_name,
database_directory,
database_key,
export_to_DHIS = True):
"""Runs through all steps of the OpenVA Pipeline
This function is a wrapper for the Pipeline class, which
runs through all steps of the OpenVA Pipeline -- (1) connect to
Transfer Database (to retrieve configuration settings); (2) connect to
ODK Aggregate to download a CSV file with VA records; (3) run openVA
(or SmartVA) to assign cause of death; and (4) store CoD results and
VA data in the Transfer Database as well as a DHIS2 VA Program (if
requested).
:param database_file_name: File name for the Transfer Database.
:param database_directory: Path of the Transfer Database.
:param datatbase_key: Encryption key for the Transfer Database
:param export_to_DHIS: Indicator for posting VA records to a DHIS2 server.
:type export_to_DHIS: (Boolean)
"""
pl = Pipeline(dbFileName = database_file_name,
dbDirectory = database_directory,
dbKey = database_key,
useDHIS = export_to_DHIS)
try:
settings = pl.config()
except PipelineConfigurationError as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
settingsPipeline = settings["pipeline"]
settingsODK = settings["odk"]
settingsOpenVA = settings["openVA"]
settingsDHIS = settings["dhis"]
try:
odkBC = pl.runODK(settingsODK,
settingsPipeline)
pl.logEvent("Briefcase Export Completed Successfully", "Event")
except ODKError as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
try:
rOut = pl.runOpenVA(settingsOpenVA,
settingsPipeline,
settingsODK.odkID,
pl.pipelineRunDate)
pl.logEvent("OpenVA Analysis Completed Successfully", "Event")
except (OpenVAError, SmartVAError) as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
if (rOut["zeroRecords"] == True):
pl.logEvent("No new VA records from ODK (now exiting)", "Event")
sys.exit(0)
if (export_to_DHIS):
try:
pipelineDHIS = pl.runDHIS(settingsDHIS,
settingsPipeline)
pl.logEvent("Posted Events to DHIS2 Successfully", "Event")
except DHISError as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
try:
pl.storeResultsDB()
pl.logEvent("Stored Records to Xfer Database Successfully", "Event")
except (PipelineError, DatabaseConnectionError,
PipelineConfigurationError) as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
try:
pl.closePipeline()
pl.logEvent("Successfully Completed Run of Pipeline", "Event")
except (DatabaseConnectionError, DatabaseConnectionError) as e:
pl.logEvent(str(e), "Error")
sys.exit(1)
