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'])
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, 'settings')
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.CredentialInformation(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = os.path.join(baseFolder, databaseName, 'refgenome', 'chromosomes')
try:
if not os.path.exists(settingsFile):
returndata['content'] = DQXbase64.b64encode_var2('chrom length\nChrom_01\t1.54\nChrom_02\t0.85\n')
else:
with open(settingsFile, 'r') as fp:
content = fp.read()
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
credInfo = DQXDbTools.CredentialInformation(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = os.path.join(baseFolder, databaseName, 'refgenome', 'settings')
try:
if not os.path.exists(settingsFile):
returndata['content'] = DQXbase64.b64encode_var2('AnnotMaxViewPortSize: 750000 # Maximum viewport (in bp) the genome browser can have in order to show the annotation track\nRefSequenceSumm: No # Include a summary track displaying the reference sequence\n')
else:
with open(settingsFile, 'r') as fp:
content = fp.read()
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
filename=returndata['name']
#!!!todo: add more integrity checks for the filename
if filename.find('..')>=0:
raise Exception('Invalid file name')
f=open(config.BASEDIR+'/'+filename+'.txt')
content=f.read()
f.close()
returndata['content']=DQXbase64.b64encode_var2(content)
return returndata
def response(returndata):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = os.path.join(baseFolder, databaseName, 'refgenome',
'chromosomes')
try:
if not os.path.exists(settingsFile):
returndata['content'] = DQXbase64.b64encode_var2(
'chrom length\nChrom_01\t1.54\nChrom_02\t0.85\n')
else:
with open(settingsFile, 'r') as fp:
content = fp.read()
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
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'])
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):
credInfo = DQXDbTools.ParseCredentialInfo(returndata)
databaseName = DQXDbTools.ToSafeIdentifier(returndata['database'])
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = os.path.join(baseFolder, databaseName, 'refgenome',
'settings')
try:
if not os.path.exists(settingsFile):
returndata['content'] = DQXbase64.b64encode_var2(
'AnnotMaxViewPortSize: 750000 # Maximum viewport (in bp) the genome browser can have in order to show the annotation track\nRefSequenceSumm: No # Include a summary track displaying the reference sequence\n'
)
else:
with open(settingsFile, 'r') as fp:
content = fp.read()
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
credInfo = DQXDbTools.CredentialInformation(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 == "2D_datatable":
settingsFile = os.path.join(baseFolder, databaseName, "2D_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):
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):
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'])
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
baseFolder = config.SOURCEDATADIR + '/datasets'
dataFile = None
if sourcetype == 'datatable':
dataFile = os.path.join(baseFolder, databaseName, 'datatables',
tableid, 'data')
if sourcetype == 'customdata':
dataFile = os.path.join(baseFolder, databaseName, 'workspaces',
workspaceid, 'customdata', tableid, sourceid,
'data')
if dataFile is None:
returndata['Error'] = 'Invalid file source type'
return returndata
try:
if not os.path.exists(dataFile):
returndata['content'] = ''
else:
with open(dataFile, 'r') as fp:
content = ''
linecount = 0
for line in fp:
content += line
if linecount > 100:
break
linecount += 1
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
credInfo = DQXDbTools.CredentialInformation(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'])
credInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
baseFolder = config.SOURCEDATADIR + '/datasets'
settingsFile = None
if sourcetype == 'dataset':
settingsFile = os.path.join(baseFolder, databaseName, 'settings')
if sourcetype == 'datatable':
settingsFile = os.path.join(baseFolder, databaseName, 'datatables', tableid, 'settings')
if sourcetype == '2D_datatable':
settingsFile = os.path.join(baseFolder, databaseName, '2D_datatables', tableid, 'settings')
if sourcetype == 'customdata':
settingsFile = os.path.join(baseFolder, databaseName, 'workspaces', workspaceid, 'customdata', tableid, sourceid, 'settings')
if sourcetype == 'workspace':
settingsFile = os.path.join(baseFolder, databaseName, 'workspaces', workspaceid, 'settings')
if settingsFile is None:
returndata['Error'] = 'Invalid file source type'
return returndata
try:
if not os.path.exists(settingsFile):
returndata['content'] = ''
else:
with open(settingsFile, 'r') as fp:
content = fp.read()
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
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'])
credInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(databaseName, 'workspaces'))
baseFolder = config.SOURCEDATADIR + '/datasets'
dataFile = None
if sourcetype == 'datatable':
dataFile = os.path.join(baseFolder, databaseName, 'datatables', tableid, 'data')
if sourcetype == 'customdata':
dataFile = os.path.join(baseFolder, databaseName, 'workspaces', workspaceid, 'customdata', tableid, sourceid, 'data')
if dataFile is None:
returndata['Error'] = 'Invalid file source type'
return returndata
try:
if not os.path.exists(dataFile):
returndata['content'] = ''
else:
with open(dataFile, 'r') as fp:
content = ''
linecount = 0
for line in fp:
content += line
if linecount > 100:
break
linecount += 1
returndata['content'] = DQXbase64.b64encode_var2(content)
except Exception as e:
returndata['Error'] = str(e)
return returndata
def response(returndata):
url = returndata['url']
cache = getCache()
cacheKey = json.dumps([url])
returndata['content'] = None
use_cache = returndata['cache'] and not os.getenv('STAGING', '')
if use_cache:
try:
returndata['content'] = cache[cacheKey]
except KeyError:
pass
if returndata['content'] is None:
file = urllib.request.urlopen(url)
data = file.read()
file.close()
data = xmltodict.parse(data)
returndata['content'] = DQXbase64.b64encode_var2(json.dumps(data))
if use_cache:
cache[cacheKey] = returndata['content']
return returndata
def response(returndata):
url = returndata['url']
cache = getCache()
cacheKey = json.dumps([url])
returndata['content'] = None
use_cache = returndata['cache'] and not os.getenv('STAGING', '')
if use_cache:
try:
returndata['content'] = cache[cacheKey]
except KeyError:
pass
if returndata['content'] is None:
file = urllib.request.urlopen(url)
data = file.read()
file.close()
data = xmltodict.parse(data)
returndata['content'] = DQXbase64.b64encode_var2(json.dumps(data))
if use_cache:
cache[cacheKey] = returndata['content']
return returndata
def Decode(self, str, noBase64=False):
if not noBase64:
str = DQXbase64.b64decode_var2(str)
self.query = simplejson.loads(str)
pass
def Decode(self, str, noBase64=False):
if not noBase64:
str = DQXbase64.b64decode_var2(str)
self.query = simplejson.loads(str)
pass
def Decode(self, encodedstr):
decodedstr = DQXbase64.b64decode_var2(encodedstr)
self.query = simplejson.loads(decodedstr)
pass
