def ImportDataTable(calculationObject, datasetId, tableid, folder, importSettings):
Utils.CheckSafeIdentifier(tableid)
global tableOrder
with calculationObject.LogHeader('Importing datatable {0}'.format(tableid)):
print('Source: ' + folder)
DQXUtils.CheckValidIdentifier(tableid)
calculationObject.credentialInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(datasetId, 'tablecatalog'))
calculationObject.credentialInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(datasetId, 'propertycatalog'))
calculationObject.credentialInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(datasetId, 'relations'))
calculationObject.credentialInfo.VerifyCanDo(DQXDbTools.DbOperationWrite(datasetId, 'tablebasedsummaryvalues'))
tableSettings = SettingsLoader.SettingsLoader(os.path.join(os.path.join(folder, 'settings')))
tableSettings.RequireTokens(['NameSingle', 'NamePlural', 'PrimKey'])
tableSettings.AddTokenIfMissing('IsPositionOnGenome', False)
tableSettings.AddTokenIfMissing('IsRegionOnGenome', False)
tableSettings.AddTokenIfMissing('MaxTableSize', None)
tableSettings.AddTokenIfMissing('MaxCountQueryRecords', 200000)
tableSettings.AddTokenIfMissing('MaxCountQueryAggregated', 1000000)
tableSettings.AddTokenIfMissing('AllowSubSampling', False)
extraSettings = tableSettings.Clone()
extraSettings.DropTokens(['PrimKey', 'Properties'])
if tableSettings['MaxTableSize'] is not None:
print('WARNING: table size limited to '+str(tableSettings['MaxTableSize']))
# Drop existing tablecatalog record
sql = "DELETE FROM tablecatalog WHERE id='{0}'".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
# Add to tablecatalog
extraSettings.ConvertStringsToSafeSQL()
sql = "INSERT INTO tablecatalog VALUES ('{0}', '{1}', '{2}', {3}, '{4}', {5})".format(
tableid,
tableSettings['NamePlural'],
tableSettings['PrimKey'],
tableSettings['IsPositionOnGenome'],
extraSettings.ToJSON(),
tableOrder
)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
tableOrder += 1
properties = ImpUtils.LoadPropertyInfo(calculationObject, tableSettings, os.path.join(folder, 'data'))
sql = "DELETE FROM propertycatalog WHERE tableid='{0}'".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
sql = "DELETE FROM relations WHERE childtableid='{0}'".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
ranknr = 0
for property in properties:
propid = property['propid']
settings = property['Settings']
extraSettings = settings.Clone()
extraSettings.DropTokens(['Name', 'DataType', 'Order'])
sql = "INSERT INTO propertycatalog VALUES ('', 'fixed', '{0}', '{1}', '{2}', '{3}', {4}, '{5}')".format(
settings['DataType'],
propid,
tableid,
settings['Name'],
0,
extraSettings.ToJSON()
)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
if settings.HasToken('Relation'):
relationSettings = settings.GetSubSettings('Relation')
calculationObject.Log('Creating relation: '+relationSettings.ToJSON())
relationSettings.RequireTokens(['TableId'])
relationSettings.AddTokenIfMissing('ForwardName', 'belongs to')
relationSettings.AddTokenIfMissing('ReverseName', 'has')
sql = "INSERT INTO relations VALUES ('{0}', '{1}', '{2}', '{3}', '{4}', '{5}')".format(
tableid,
propid,
relationSettings['TableId'],
'',
relationSettings['ForwardName'],
relationSettings['ReverseName']
)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
ranknr += 1
propidList = []
propDict = {}
for property in properties:
propDict[property['propid']] = property
propidList.append(property['propid'])
if tableSettings['IsPositionOnGenome']:
if not tableSettings.HasToken('Chromosome'):
raise Exception('Missing settings tag Chromosome in genome position datatable.')
if not tableSettings.HasToken('Position'):
raise Exception('Missing settings tag Position in genome position datatable.')
if tableSettings['Chromosome'] not in propDict:
raise Exception('Genome position datatable {0} is missing property "{1}"'.format(tableid, tableSettings['Chromosome']))
if tableSettings['Position'] not in propDict:
raise Exception('Genome position datatable {0} is missing property "{1}"'.format(tableid, tableSettings['Position']))
if tableSettings['IsRegionOnGenome']:
if not tableSettings.HasToken('Chromosome'):
raise Exception('Missing setting "Chromosome" in genome region datatable {0}'.format(tableid))
if not tableSettings.HasToken('RegionStart'):
raise Exception('Missing setting "RegionStart" in genome region datatable {0}'.format(tableid))
if not tableSettings.HasToken('RegionStop'):
raise Exception('Missing setting "RegionStop" in genome region datatable {0}'.format(tableid))
if tableSettings['Chromosome'] not in propDict:
raise Exception('Genome region datatable {0} is missing property "{1}"'.format(tableid, tableSettings['Chromosome']))
if tableSettings['RegionStart'] not in propDict:
raise Exception('Genome region datatable {0} is missing property "{1}"'.format(tableid, tableSettings['RegionStart']))
if tableSettings['RegionStop'] not in propDict:
raise Exception('Genome region datatable {0} is missing property "{1}"'.format(tableid, tableSettings['RegionStop']))
propDict[tableSettings['Chromosome']]['Settings'].SetToken('Index', True)
propDict[tableSettings['RegionStart']]['Settings'].SetToken('Index', True)
propDict[tableSettings['RegionStop']]['Settings'].SetToken('Index', True)
if not importSettings['ConfigOnly']:
columns = [ {
'name': prop['propid'],
'DataType': prop['DataType'],
'Index': prop['Settings']['Index'],
'ReadData': prop['Settings']['ReadData']
}
for prop in properties if (prop['propid'] != 'AutoKey')]
LoadTable.LoadTable(
calculationObject,
os.path.join(folder, 'data'),
datasetId,
tableid,
columns,
tableSettings,
importSettings,
tableSettings['AllowSubSampling']
)
if tableSettings['IsPositionOnGenome']:
calculationObject.Log('Indexing chromosome')
scr = ImpUtils.SQLScript(calculationObject)
scr.AddCommand('create index {0}_chrompos ON {0}({1},{2})'.format(
tableid,
tableSettings['Chromosome'],
tableSettings['Position']
))
scr.Execute(datasetId)
print('Creating summary values')
sql = "DELETE FROM summaryvalues WHERE tableid='{0}'".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
for property in properties:
propid = property['propid']
settings = property['Settings']
if (settings.HasToken('SummaryValues')) and ImpUtils.IsValueDataTypeIdenfifier(property['DataType']):
with calculationObject.LogHeader('Creating numerical summary values for {0}.{1}'.format(tableid,propid)):
summSettings = settings.GetSubSettings('SummaryValues')
if settings.HasToken('minval'):
summSettings.AddTokenIfMissing('MinVal', settings['minval'])
if settings.HasToken('maxval'):
summSettings.AddTokenIfMissing('MaxVal', settings['maxval'])
sourceFileName = os.path.join(folder, 'data')
destFolder = os.path.join(config.BASEDIR, 'SummaryTracks', datasetId, propid)
if not os.path.exists(destFolder):
os.makedirs(destFolder)
dataFileName = os.path.join(destFolder, propid)
if not importSettings['ConfigOnly']:
ImpUtils.ExtractColumns(calculationObject, sourceFileName, dataFileName, [tableSettings['Chromosome'], tableSettings['Position'], propid], False, importSettings)
ImpUtils.CreateSummaryValues_Value(
calculationObject,
summSettings,
datasetId,
tableid,
'fixed',
'',
propid,
settings['Name'],
dataFileName,
importSettings
)
if (settings.HasToken('SummaryValues')) and (property['DataType'] == 'Text'):
with calculationObject.LogHeader('Creating categorical summary values for {0}.{1}'.format(tableid,propid)):
summSettings = settings.GetSubSettings('SummaryValues')
sourceFileName = os.path.join(folder, 'data')
destFolder = os.path.join(config.BASEDIR, 'SummaryTracks', datasetId, propid)
if not os.path.exists(destFolder):
os.makedirs(destFolder)
dataFileName = os.path.join(destFolder, propid)
if not importSettings['ConfigOnly']:
ImpUtils.ExtractColumns(calculationObject, sourceFileName, dataFileName, [tableSettings['Chromosome'], tableSettings['Position'], propid], False, importSettings)
categories = []
if settings.HasToken('categoryColors'):
stt = settings.GetSubSettings('categoryColors')
categories = [x for x in stt.Get()]
summSettings.AddTokenIfMissing('Categories', categories)
ImpUtils.CreateSummaryValues_Categorical(
calculationObject,
summSettings,
datasetId,
tableid,
'fixed',
'',
propid,
settings['Name'],
dataFileName,
importSettings
)
sql = "DELETE FROM tablebasedsummaryvalues WHERE tableid='{0}'".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
if tableSettings.HasToken('TableBasedSummaryValues'):
calculationObject.Log('Processing table-based summary values')
if not type(tableSettings['TableBasedSummaryValues']) is list:
raise Exception('TableBasedSummaryValues token should be a list')
for stt in tableSettings['TableBasedSummaryValues']:
summSettings = SettingsLoader.SettingsLoader()
summSettings.LoadDict(stt)
summSettings.RequireTokens(['Id', 'Name', 'MaxVal', 'BlockSizeMax'])
summSettings.AddTokenIfMissing('MinVal', 0)
summSettings.AddTokenIfMissing('BlockSizeMin', 1)
summSettings.DefineKnownTokens(['channelColor'])
summaryid = summSettings['Id']
with calculationObject.LogHeader('Table based summary value {0}, {1}'.format(tableid, summaryid)):
extraSummSettings = summSettings.Clone()
extraSummSettings.DropTokens(['Id', 'Name', 'MinVal', 'MaxVal', 'BlockSizeMin', 'BlockSizeMax'])
sql = "INSERT INTO tablebasedsummaryvalues VALUES ('{0}', '{1}', '{2}', '{3}', {4}, {5}, {6}, 0)".format(
tableid,
summaryid,
summSettings['Name'],
extraSummSettings.ToJSON(),
summSettings['MinVal'],
summSettings['MaxVal'],
summSettings['BlockSizeMin']
)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
if importSettings['ScopeStr'] == 'all':
itemtracknr = 0
for fileid in os.listdir(os.path.join(folder, summaryid)):
if not(os.path.isdir(os.path.join(folder, summaryid, fileid))):
itemtracknr += 1
calculationObject.Log('Processing {0}: {1}'.format(itemtracknr, fileid))
destFolder = os.path.join(config.BASEDIR, 'SummaryTracks', datasetId, 'TableTracks', tableid, summaryid, fileid)
calculationObject.Log('Destination: '+destFolder)
if not os.path.exists(destFolder):
os.makedirs(destFolder)
shutil.copyfile(os.path.join(folder, summaryid, fileid), os.path.join(destFolder, summaryid+'_'+fileid))
ImpUtils.ExecuteFilterbankSummary_Value(calculationObject, destFolder, summaryid+'_'+fileid, summSettings)
def ImportCustomData(calculationObject, datasetId, workspaceid, tableid,
sourceid, folder, importSettings):
with calculationObject.LogHeader('Importing custom data'):
print('Importing custom data into {0}, {1}, {2} FROM {3}'.format(
datasetId, workspaceid, tableid, folder))
credInfo = calculationObject.credentialInfo
if not ImpUtils.IsDatasetPresentInServer(
calculationObject.credentialInfo, datasetId):
raise Exception(
'Dataset {0} is not found. Please import the dataset first'.
format(datasetId))
db = DQXDbTools.OpenDatabase(credInfo, datasetId)
calculationObject.credentialInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(datasetId, 'propertycatalog'))
calculationObject.credentialInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(datasetId, 'workspaces'))
cur = db.cursor()
cur.execute(
'SELECT primkey, settings FROM tablecatalog WHERE id="{0}"'.format(
tableid))
row = cur.fetchone()
if row is None:
raise Exception(
'Unable to find table record for table {0} in dataset {1}'.
format(tableid, datasetId))
primkey = row[0]
tableSettingsStr = row[1]
db.close()
ImpUtils.ExecuteSQL(
calculationObject, datasetId,
'DELETE FROM customdatacatalog WHERE tableid="{tableid}" and sourceid="{sourceid}"'
.format(tableid=tableid, sourceid=sourceid))
tableSettings = SettingsLoader.SettingsLoader()
tableSettings.LoadDict(simplejson.loads(tableSettingsStr,
strict=False))
allowSubSampling = tableSettings['AllowSubSampling']
isPositionOnGenome = False
if tableSettings.HasToken(
'IsPositionOnGenome') and tableSettings['IsPositionOnGenome']:
isPositionOnGenome = True
chromField = tableSettings['Chromosome']
posField = tableSettings['Position']
settings = SettingsLoader.SettingsLoader(
os.path.join(os.path.join(folder, 'settings')))
ImpUtils.ExecuteSQL(
calculationObject, datasetId,
"INSERT INTO customdatacatalog VALUES ('{tableid}', '{sourceid}', '{settings}')"
.format(tableid=tableid,
sourceid=sourceid,
settings=settings.ToJSON()))
properties = ImpUtils.LoadPropertyInfo(calculationObject, settings,
os.path.join(folder, 'data'))
# remove primary key, just in case
properties = [prop for prop in properties if prop['propid'] != primkey]
sourcetable = Utils.GetTableWorkspaceProperties(workspaceid, tableid)
print('Source table: ' + sourcetable)
#Get list of existing properties
db = DQXDbTools.OpenDatabase(calculationObject.credentialInfo,
datasetId)
cur = db.cursor()
cur.execute(
'SELECT propid FROM propertycatalog WHERE (workspaceid="{0}") and (source="custom") and (tableid="{1}")'
.format(workspaceid, tableid))
existingProperties = [row[0] for row in cur.fetchall()]
print('Existing properties: ' + str(existingProperties))
db.close()
propidList = []
for property in properties:
DQXUtils.CheckValidIdentifier(property['propid'])
propidList.append(property['propid'])
db = DQXDbTools.OpenDatabase(calculationObject.credentialInfo,
datasetId)
cur = db.cursor()
if not importSettings['ConfigOnly']:
# Dropping columns that will be replaced
toRemoveExistingProperties = []
for existProperty in existingProperties:
if existProperty in propidList:
toRemoveExistingProperties.append(existProperty)
print('Removing outdated information:')
if len(toRemoveExistingProperties) > 0:
for prop in toRemoveExistingProperties:
print('Removing outdated information: {0} {1} {2}'.format(
workspaceid, prop, tableid))
sql = 'DELETE FROM propertycatalog WHERE (workspaceid="{0}") and (propid="{1}") and (tableid="{2}")'.format(
workspaceid, prop, tableid)
print(sql)
cur.execute(sql)
sql = "ALTER TABLE {0} ".format(sourcetable)
for prop in toRemoveExistingProperties:
if prop != toRemoveExistingProperties[0]:
sql += ", "
sql += "DROP COLUMN {0}".format(prop)
calculationObject.LogSQLCommand(sql)
cur.execute(sql)
ranknr = 0
for property in properties:
propid = property['propid']
settings = property['Settings']
extraSettings = settings.Clone()
extraSettings.DropTokens(
['Name', 'DataType', 'Order', 'SummaryValues'])
print('Create property catalog entry for {0} {1} {2}'.format(
workspaceid, tableid, propid))
sql = "DELETE FROM propertycatalog WHERE (workspaceid='{0}') and (propid='{1}') and (tableid='{2}')".format(
workspaceid, propid, tableid)
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
sql = "INSERT INTO propertycatalog VALUES ('{0}', 'custom', '{1}', '{2}', '{3}', '{4}', {5}, '{6}')".format(
workspaceid, settings['DataType'], propid, tableid,
settings['Name'], 0, extraSettings.ToJSON())
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
ranknr += 1
propDict = {}
for property in properties:
propDict[property['propid']] = property
if not importSettings['ConfigOnly']:
tmptable = Utils.GetTempID()
columns = [{
'name': prop['propid'],
'DataType': prop['DataType'],
'Index': prop['Settings']['Index'],
'ReadData': prop['Settings']['ReadData']
} for prop in properties]
columns.append({
'name': primkey,
'DataType': 'Text',
'Index': False,
'ReadData': True
})
# print('----------------------------------------------------------------')
# print(str(columns))
# print('----------------------------------------------------------------')
LoadTable.LoadTable(calculationObject,
os.path.join(folder, 'data'), datasetId,
tmptable, columns, {'PrimKey': primkey},
importSettings, False)
print('Creating new columns')
calculationObject.Log(
'WARNING: better mechanism to determine column types needed here'
) #TODO: implement
frst = True
sql = "ALTER TABLE {0} ".format(sourcetable)
for property in properties:
propid = property['propid']
if not frst:
sql += " ,"
sqldatatype = ImpUtils.GetSQLDataType(property['DataType'])
sql += "ADD COLUMN {0} {1}".format(propid, sqldatatype)
frst = False
calculationObject.LogSQLCommand(sql)
cur.execute(sql)
print('Joining information')
frst = True
credInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(datasetId, sourcetable))
sql = "update {0} left join {1} on {0}.{2}={1}.{2} set ".format(
sourcetable, tmptable, primkey)
for property in properties:
propid = property['propid']
if not frst:
sql += " ,"
sql += "{0}.{2}={1}.{2}".format(sourcetable, tmptable, propid)
frst = False
calculationObject.LogSQLCommand(sql)
cur.execute(sql)
print('Cleaning up')
cur.execute("DROP TABLE {0}".format(tmptable))
if not importSettings['ConfigOnly']:
print('Updating view')
Utils.UpdateTableInfoView(workspaceid, tableid, allowSubSampling,
cur)
db.commit()
db.close()
print('Creating summary values')
for property in properties:
propid = property['propid']
settings = property['Settings']
if settings.HasToken('SummaryValues'):
with calculationObject.LogHeader(
'Creating summary values for custom data {0}'.format(
tableid)):
summSettings = settings.GetSubSettings('SummaryValues')
if settings.HasToken('minval'):
summSettings.AddTokenIfMissing('MinVal',
settings['minval'])
summSettings.AddTokenIfMissing('MaxVal',
settings['maxval'])
destFolder = os.path.join(config.BASEDIR, 'SummaryTracks',
datasetId, propid)
if not os.path.exists(destFolder):
os.makedirs(destFolder)
dataFileName = os.path.join(destFolder, propid)
if not isPositionOnGenome:
raise Exception(
'Summary values defined for non-position table')
if not importSettings['ConfigOnly']:
calculationObject.Log('Extracting data to ' +
dataFileName)
script = ImpUtils.SQLScript(calculationObject)
script.AddCommand(
"SELECT {2} as chrom, {3} as pos, {0} FROM {1} ORDER BY {2},{3}"
.format(
propid,
Utils.GetTableWorkspaceView(
workspaceid, tableid), chromField,
posField))
script.Execute(datasetId, dataFileName)
calculationObject.LogFileTop(dataFileName, 10)
ImpUtils.CreateSummaryValues_Value(
calculationObject, summSettings, datasetId, tableid,
'custom', workspaceid, propid, settings['Name'],
dataFileName, importSettings)
