def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
sourcetype = DQXDbTools.ToSafeIdentifier(returndata['sourcetype'])
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
workspaceid = DQXDbTools.ToSafeIdentifier(returndata['workspaceid'])
tableid = DQXDbTools.ToSafeIdentifier(returndata['tableid'])
sourceid = DQXDbTools.ToSafeIdentifier(returndata['sourceid'])
contentid = returndata['contentid']
filename = os.path.join(config.BASEDIR, 'temp', 'store_' + contentid)
with open(filename, 'r') as fp:
encodedstr = fp.read()
os.remove(filename)
content = DQXbase64.b64decode_var2(encodedstr)
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = None
if sourcetype == 'dataset':
settingsFile = os.path.join(baseFolder, databaseName, 'settings')
authorization.VerifyIsDataSetManager(credInfo, databaseName)
if sourcetype == 'datatable':
settingsFile = os.path.join(baseFolder, databaseName, 'datatables',
tableid, 'settings')
authorization.VerifyIsDataSetManager(credInfo, databaseName)
if sourcetype == 'workspace':
settingsFile = os.path.join(baseFolder, databaseName, 'workspaces',
workspaceid, 'settings')
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
if sourcetype == 'customdata':
settingsFile = os.path.join(baseFolder, databaseName, 'workspaces',
workspaceid, 'customdata', tableid,
sourceid, 'settings')
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
if settingsFile is None:
returndata['Error'] = 'Invalid file source type'
return returndata
try:
with open(settingsFile, 'w') as fp:
fp.write(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
workspaceid = DQXDbTools.ToSafeIdentifier(returndata['workspaceid'])
id = DQXDbTools.ToSafeIdentifier(returndata['id'])
method = returndata['tpe']
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
db = DQXDbTools.OpenDatabase(credInfo, databaseName)
credInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(None, 'storedviews'))
cur = db.cursor()
sqlstring = 'SELECT max(ordr) FROM introviews WHERE workspaceid="{0}"'.format(workspaceid)
cur.execute(sqlstring)
maxrank = 0
dbrank = cur.fetchone()[0]
if dbrank is not None:
maxrank = dbrank
sql = 'UPDATE introviews SET ordr={newrank} WHERE id="{id}"'.format(
id=id,
newrank=maxrank+1
)
cur.execute(sql)
db.commit()
db.close()
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
authorization.VerifyIsDataSetManager(credInfo, databaseName)
encodedstr = returndata['content']
content = DQXbase64.b64decode_var2(encodedstr)
baseFolder = config.SOURCEDATADIR + '/datasets'
genomeFolder = os.path.join(baseFolder, databaseName, 'refgenome')
settingsFile = os.path.join(genomeFolder, 'chromosomes')
try:
if not os.path.exists(genomeFolder):
os.makedirs(genomeFolder)
with open(settingsFile, 'w') as fp:
fp.write(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
workspaceid = DQXDbTools.ToSafeIdentifier(returndata['workspaceid'])
authorization.VerifyIsDataSetManager(credInfo, databaseName)
for char in ['.', ' ', ',', '/', '"', "'"]:
workspaceid = workspaceid.replace(char, '_')
returndata['workspaceid'] = workspaceid
baseFolder = config.SOURCEDATADIR + '/datasets'
try:
dataFolder = os.path.join(baseFolder, databaseName)
os.makedirs(os.path.join(dataFolder, 'workspaces', workspaceid))
with open(
os.path.join(dataFolder, 'workspaces', workspaceid,
'settings'), 'w') as fp:
fp.write('Name: ' + workspaceid + '\n')
except Exception as e:
returndata['Error'] = 'Failed to create workspace: ' + str(e)
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
authorization.VerifyIsDataSetManager(credInfo, databaseName)
for char in ['.', ' ', ',', '/', '"', "'"]:
databaseName = databaseName.replace(char, '_')
returndata['database'] = databaseName
baseFolder = config.SOURCEDATADIR + '/datasets'
try:
dataFolder = os.path.join(baseFolder, databaseName)
if os.path.exists(dataFolder):
returndata['Error'] = 'Dataset {0} already exists'.format(
databaseName)
return returndata
os.makedirs(dataFolder)
with open(os.path.join(dataFolder, 'settings'), 'w') as fp:
fp.write('Name: {0}\n'.format(databaseName))
os.makedirs(os.path.join(dataFolder, 'datatables'))
os.makedirs(os.path.join(dataFolder, 'workspaces', 'workspace1'))
with open(
os.path.join(dataFolder, 'workspaces', 'workspace1',
'settings'), 'w') as fp:
fp.write('Name: Workspace 1\n')
except Exception as e:
returndata['Error'] = 'Failed to create dataset: ' + str(e)
return returndata
def response(returndata):
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
id = DQXDbTools.ToSafeIdentifier(returndata['id'])
name ='No name'
if 'name' in returndata:
name = returndata['name']
section = ''
if 'section' in returndata:
section = returndata['section']
description = ''
if 'description' in returndata:
description = returndata['description']
#Obtain the settings from storeddata
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
db = DQXDbTools.OpenDatabase(credInfo, databaseName)
credInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(None, 'storedviews'))
cur = db.cursor()
sql = 'UPDATE introviews SET name="{name}", section="{section}", description="{description}" WHERE id="{id}"'.format(
name=name,
section=section,
description=description,
id=id
)
cur.execute(sql)
db.commit()
db.close()
return returndata
def response(returndata):
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
workspaceid = DQXDbTools.ToSafeIdentifier(returndata['workspaceid'])
name = 'No name'
if 'name' in returndata:
name = returndata['name']
section = ''
if 'section' in returndata:
section = returndata['section']
description = ''
if 'description' in returndata:
description = returndata['description']
url = returndata['url']
storeid = DQXDbTools.ToSafeIdentifier(returndata['storeid'])
viewstate = DQXDbTools.ToSafeIdentifier(returndata['viewstate'])
#Obtain the settings from storeddata
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
db = DQXDbTools.OpenDatabase(credInfo, databaseName)
credInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(None, 'storedviews'))
cur = db.cursor()
sqlstring = 'SELECT max(ordr) FROM introviews WHERE workspaceid="{0}"'.format(
workspaceid)
cur.execute(sqlstring)
rank = 0
dbrank = cur.fetchone()[0]
if dbrank is not None:
rank = dbrank + 1
sql = 'INSERT INTO introviews VALUES (0, "{workspace}", "{name}", "{section}", "{description}", {rank}, "{url}", "{id}", "{state}")'.format(
workspace=workspaceid,
name=name,
section=section,
description=description,
rank=rank,
url=url,
id=storeid,
state=viewstate)
cur.execute(sql)
db.commit()
db.close()
return returndata
def response(returndata):
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
id = DQXDbTools.ToSafeIdentifier(returndata['id'])
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
db = DQXDbTools.OpenDatabase(credInfo, databaseName)
cur = db.cursor()
sql = 'DELETE FROM introviews WHERE id={id}'.format(
id=id
)
cur.execute(sql)
db.commit()
db.close()
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
fileid = DQXDbTools.ToSafeIdentifier(returndata['fileid'])
authorization.VerifyIsDataSetManager(credInfo, databaseName)
baseFolder = config.SOURCEDATADIR + '/datasets'
filename = os.path.join(config.BASEDIR, 'Uploads',
DQXDbTools.ToSafeIdentifier(fileid))
destFolder = os.path.join(baseFolder, databaseName, 'refgenome')
try:
if not os.path.exists(destFolder):
os.makedirs(destFolder)
shutil.copyfile(filename, os.path.join(destFolder, 'annotation.gff'))
settingsFileName = os.path.join(destFolder, 'settings')
if not os.path.exists(settingsFileName):
with open(settingsFileName, 'w') as fp:
fp.write(
'AnnotMaxViewPortSize: 750000 # Maximum viewport (in bp) the genome browser can have in order to show the annotation track\n'
)
fp.write(
'RefSequenceSumm: No # Include a summary track displaying the reference sequence\n'
)
chromFileName = os.path.join(destFolder, 'chromosomes')
if not os.path.exists(chromFileName):
with open(chromFileName, 'w') as fp:
fp.write('chrom length\n')
fp.write('Chrom_01\t1.54\n')
fp.write('Chrom_02\t0.85\n')
except Exception as e:
returndata['Error'] = str(e)
os.remove(filename)
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
tableid = DQXDbTools.ToSafeIdentifier(returndata['tableid'])
fileid = DQXDbTools.ToSafeIdentifier(returndata['fileid'])
authorization.VerifyIsDataSetManager(credInfo, databaseName)
for char in ['.', ' ', ',', '/', '"', "'"]:
tableid = tableid.replace(char, '_')
if tableid in Utils.reservedTableNames:
tableid += '_'
baseFolder = config.SOURCEDATADIR + '/datasets'
filename = os.path.join(config.BASEDIR, 'Uploads',
DQXDbTools.ToSafeIdentifier(fileid))
destFolder = os.path.join(baseFolder, databaseName, 'datatables', tableid)
try:
if not os.path.exists(destFolder):
os.makedirs(destFolder)
shutil.copyfile(filename, os.path.join(destFolder, 'data'))
dataFileName = os.path.join(destFolder, 'settings')
if not os.path.exists(dataFileName):
with open(dataFileName, 'w') as fp:
fp.write(
'NameSingle: item\nNamePlural: items\nPrimKey: AutoKey\n\nAutoScanProperties: true\n'
)
except Exception as e:
returndata['Error'] = str(e)
os.remove(filename)
returndata['tableid'] = tableid
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
sourcetype = DQXDbTools.ToSafeIdentifier(returndata['sourcetype'])
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
workspaceid = DQXDbTools.ToSafeIdentifier(returndata['workspaceid'])
tableid = DQXDbTools.ToSafeIdentifier(returndata['tableid'])
sourceid = DQXDbTools.ToSafeIdentifier(returndata['sourceid'])
baseFolder = config.SOURCEDATADIR + '/datasets'
calculationObject = asyncresponder.CalculationThread(
'', None, {'isRunningLocal': 'True'}, '')
dataFolder = None
if sourcetype == 'dataset':
dataFolder = os.path.join(baseFolder, databaseName)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
ImpUtils.ExecuteSQL(calculationObject, config.DB,
'DROP DATABASE IF EXISTS {0}'.format(databaseName))
ImpUtils.ExecuteSQL(
calculationObject, config.DB,
'DELETE FROM datasetindex WHERE id="{0}"'.format(databaseName))
if sourcetype == 'datatable':
dataFolder = os.path.join(baseFolder, databaseName, 'datatables',
tableid)
authorization.VerifyIsDataSetManager(credInfo, databaseName)
ImpUtils.ExecuteSQL(calculationObject, databaseName,
'DROP TABLE IF EXISTS {0}'.format(tableid))
ImpUtils.ExecuteSQL(
calculationObject, databaseName,
'DELETE FROM tablecatalog WHERE id="{0}"'.format(tableid))
ImpUtils.ExecuteSQL(
calculationObject, databaseName,
'DELETE FROM propertycatalog WHERE tableid="{0}"'.format(tableid))
ImpUtils.ExecuteSQL(
calculationObject, databaseName,
'DELETE FROM summaryvalues WHERE tableid="{0}"'.format(tableid))
if sourcetype == 'workspace':
dataFolder = os.path.join(baseFolder, databaseName, 'workspaces',
workspaceid)
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
if sourcetype == 'customdata':
dataFolder = os.path.join(baseFolder, databaseName, 'workspaces',
workspaceid, 'customdata', tableid, sourceid)
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
if dataFolder is None:
returndata['Error'] = 'Invalid file source type'
return returndata
try:
shutil.rmtree(dataFolder)
except Exception as e:
returndata['Error'] = 'Failed to delete data: ' + str(e)
return returndata
