def setUp(self):
shutil.rmtree('ODKFiles/ODK Briefcase Storage/', ignore_errors=True)
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/previous_bc_export.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/another_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
self.old_mtimePrev = os.path.getmtime('ODKFiles/odkBCExportPrev.csv')
self.old_mtimeNew = os.path.getmtime('ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('ODK-Briefcase-v1.18.0.jar'):
downloadBriefcase()
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
self.dbFileName = 'Pipeline.db'
self.dbDirectory = '.'
self.dbKey = 'enilepiP'
self.useDHIS = True
self.pl = Pipeline(self.dbFileName, self.dbDirectory, self.dbKey,
self.useDHIS)
settings = self.pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
self.odkBC = self.pl.runODK(settingsODK, settingsPipeline)
self.new_mtimePrev = os.path.getmtime('ODKFiles/odkBCExportPrev.csv')
self.new_mtimeNew = os.path.getmtime('ODKFiles/odkBCExportNew.csv')
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):
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
pl = Pipeline('Pipeline.db', '.', 'enilepiP', True)
settings = pl.config()
cls.settingsPipeline = settings['pipeline']
cls.settingsODK = settings['odk']
cls.settingsOpenVA = settings['openVA']
cls.settingsDHIS = settings['dhis']
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-1.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-2.csv',
'ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('smartva'):
downloadSmartVA()
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'copy_Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('SmartVA', 'SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1')
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsSmartVA = xferDB.configOpenVA(conn,
'SmartVA',
settingsPipeline.workingDirectory)
conn.rollback()
conn.close()
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', cls.staticRunDate),
ignore_errors = True
)
cliSmartVA = OpenVA(vaArgs = settingsSmartVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
zeroRecords = cliSmartVA.copyVA()
cls.completed = cliSmartVA.getCOD()
cls.svaOut = os.path.join(
'OpenVAFiles',
cls.staticRunDate,
'1-individual-cause-of-death/individual-cause-of-death.csv'
)
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/previous_bc_export.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/another_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
if os.path.isfile('Check_InSilicoVA_Pipeline.db'):
os.remove('Check_InSilicoVA_Pipeline.db')
createTransferDB('Check_InSilicoVA_Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'Check_InSilicoVA_Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InSilicoVA', 'InSilicoVA-2016|1.0.0|InterVA|5|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
sql = 'UPDATE InSilicoVA_Conf SET data_type = ?'
par = ('WHO2016',)
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsInSilicoVA = xferDB.configOpenVA(conn,
'InSilicoVA',
settingsPipeline.workingDirectory)
# conn.rollback()
conn.close()
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
cls.rScript = os.path.join('OpenVAFiles', cls.staticRunDate,
'Rscript_' + cls.staticRunDate + '.R')
cls.rOutFile = os.path.join('OpenVAFiles', cls.staticRunDate,
'Rscript_' + cls.staticRunDate + '.Rout')
rOpenVA = OpenVA(vaArgs = settingsInSilicoVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
zeroRecords = rOpenVA.copyVA()
rOpenVA.rScript()
cls.completed = rOpenVA.getCOD()
def setUpClass(cls):
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
if os.path.isfile('OpenVAFiles/newStorage.csv'):
os.remove('OpenVAFiles/newStorage.csv')
shutil.copy('OpenVAFiles/sample_newStorage.csv',
'OpenVAFiles/newStorage.csv')
nowDate = datetime.datetime.now()
pipelineRunDate = nowDate.strftime('%Y-%m-%d_%H:%M:%S')
xferDB = TransferDB(dbFileName='Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
c.execute('DELETE FROM VA_Storage;')
conn.commit()
conn.close()
pl = Pipeline('Pipeline.db', '.', 'enilepiP', True)
settings = pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
pl.storeResultsDB()
xferDB = TransferDB(dbFileName='Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'SELECT id FROM VA_Storage'
c.execute(sql)
vaIDs = c.fetchall()
conn.close()
vaIDsList = [j for i in vaIDs for j in i]
cls.s1 = set(vaIDsList)
dfNewStorage = read_csv('OpenVAFiles/newStorage.csv')
dfNewStorageID = dfNewStorage['odkMetaInstanceID']
cls.s2 = set(dfNewStorageID)
def setUpClass(cls):
shutil.rmtree('ODKFiles/ODK Briefcase Storage/', ignore_errors=True)
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
if not os.path.isfile('ODK-Briefcase-v1.18.0.jar'):
downloadBriefcase()
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
pl = Pipeline('Pipeline.db', '.', 'enilepiP', True)
settings = pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
cls.odkBC = pl.runODK(settingsODK, settingsPipeline)
def setUpClass(cls):
if os.path.isfile('InterVA_Pipeline.db'):
os.remove('InterVA_Pipeline.db')
createTransferDB('InterVA_Pipeline.db', '.', 'enilepiP')
nowDate = datetime.datetime.now()
pipelineRunDate = nowDate.strftime('%Y-%m-%d_%H:%M:%S')
xferDB = TransferDB(dbFileName='InterVA_Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InterVA',
'InterVA5|5|InterVA|5|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
conn.commit()
conn.close()
cls.pl = Pipeline('copy_Pipeline.db', '.', 'enilepiP', True)
settings = cls.pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/previous_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
shutil.copy('ODKFiles/another_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
if os.path.isfile('OpenVAFiles/recordStorage.csv'):
os.remove('OpenVAFiles/recordStorage.csv')
if os.path.isfile('OpenVAFiles/entityAttributeValue.csv'):
os.remove('OpenVAFiles/entityAttributeValue.csv')
cls.rOut = cls.pl.runOpenVA(settingsOpenVA, settingsPipeline,
settingsODK.odkID, cls.pl.pipelineRunDate)
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/zeroRecords_bc_export.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/zeroRecords_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
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()
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsInterVA = xferDB.configOpenVA(conn,
'InterVA',
settingsPipeline.workingDirectory)
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', cls.staticRunDate),
ignore_errors = True
)
rOpenVA = OpenVA(vaArgs = settingsInterVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
cls.zeroRecords = rOpenVA.copyVA()
def setUpClass(cls):
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_prev_who_v151.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_new_who_v151.csv',
'ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
pl = Pipeline('Pipeline.db', '.', 'enilepiP', True)
settings = pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
cls.rOut = pl.runOpenVA(settingsOpenVA, settingsPipeline,
settingsODK.odkID, pl.pipelineRunDate)
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)
def setUpClass(cls):
shutil.rmtree('DHIS/blobs/', ignore_errors=True)
if os.path.isfile('OpenVAFiles/entityAttributeValue.csv'):
os.remove('OpenVAFiles/entityAttributeValue.csv')
if os.path.isfile('OpenVAFiles/recordStorage.csv'):
os.remove('OpenVAFiles/recordStorage.csv')
shutil.copy('OpenVAFiles/sampleEAV.csv',
'OpenVAFiles/entityAttributeValue.csv')
shutil.copy('OpenVAFiles/sample_recordStorage.csv',
'OpenVAFiles/recordStorage.csv')
shutil.copy('OpenVAFiles/sample_newStorage.csv',
'OpenVAFiles/newStorage.csv')
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
pl = Pipeline('Pipeline.db', '.', 'enilepiP', True)
plRunDate = pl.pipelineRunDate
settings = pl.config()
settingsPipeline = settings['pipeline']
settingsODK = settings['odk']
settingsOpenVA = settings['openVA']
settingsDHIS = settings['dhis']
cls.pipelineDHIS = pl.runDHIS(settingsDHIS, settingsPipeline)
def setUpClass(cls):
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
