def setUpClass(cls):
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
if os.path.isfile('who_cod.R'):
os.remove('who_cod.R')
# if os.path.isfile('tariff_cod.py'):
# os.remove('tariff_cod.py')
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0,
0).strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName='Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=pipelineRunDate)
conn = xferDB.connectDB()
cls.cod_who = xferDB.configDHIS(conn, 'InSilicoVA')
cls.cod_tariff = xferDB.configDHIS(conn, 'SmartVA')
with open("who_cod.R", "w", newline="") as f:
f.write("data(causetextV5, package='InterVA5')\n")
f.write(
"write.csv(causetextV5, file='who_cod.csv', row.names=FALSE)\n"
)
rArgs = ["R", "CMD", "BATCH", "--vanilla", "who_cod.R"]
subprocess.run(args=rArgs,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True)
who = read_csv("who_cod.csv", index_col=0)
index_who_causes = [i for i in who.index if "b_" in i]
cls.who_causes = who.loc[index_who_causes, who.columns[0]].tolist()
def setUpClass(cls):
shutil.rmtree('DHIS/blobs/', ignore_errors = True)
shutil.copy('OpenVAFiles/sampleEAV.csv',
'OpenVAFiles/entityAttributeValue.csv')
shutil.copy('OpenVAFiles/sample_recordStorage.csv',
'OpenVAFiles/recordStorage.csv')
# Define valid parameters for SwissTPH DHIS2 Server.
dirOpenVA = 'OpenVAFiles'
dhisURL = 'https://va30se.swisstph-mis.ch'
# dhisURL = 'https://va25.swisstph-mis.ch'
dhisUser = '******'
dhisPassword = '******'
dhisOrgUnit = 'SCVeBskgiK6'
# parameters for connecting to DB (assuming DB is in tests folder)
dbFileName = 'Pipeline.db'
dbKey = 'enilepiP'
wrong_dbKey = 'wrongKey'
# dbDirectory = os.path.abspath(os.path.dirname(__file__))
dbDirectory = '.'
if not os.path.isfile('Pipeline.db'):
createTransferDB(dbFileName, dbDirectory, dbKey)
pipelineRunDate = datetime.datetime.now()
xferDB = TransferDB(dbFileName = dbFileName,
dbDirectory = dbDirectory,
dbKey = dbKey,
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
settingsDHIS = xferDB.configDHIS(conn, 'InSilicoVA')
cls.pipelineDHIS = dhis.DHIS(settingsDHIS, '.')
apiDHIS = cls.pipelineDHIS.connect()
cls.postLog = cls.pipelineDHIS.postVA(apiDHIS)
cls.pipelineDHIS.verifyPost(cls.postLog, apiDHIS)