def ImportRefGenomeSummaryData(calculationObject, datasetId, folder,
importSettings):
if not os.path.exists(os.path.join(folder, 'summaryvalues')):
return
calculationObject.credentialInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(datasetId, 'summaryvalues'))
summaryids = []
for dir in os.listdir(os.path.join(folder, 'summaryvalues')):
if os.path.isdir(os.path.join(folder, 'summaryvalues', dir)):
summaryids.append(dir)
for summaryid in summaryids:
with calculationObject.LogHeader(
'Importing reference genome summary data ' + summaryid):
DQXUtils.CheckValidIdentifier(summaryid)
destFolder = os.path.join(config.BASEDIR, 'SummaryTracks',
datasetId, summaryid)
if not os.path.exists(destFolder):
os.makedirs(destFolder)
dataFileName = os.path.join(destFolder, summaryid)
shutil.copyfile(
os.path.join(folder, 'summaryvalues', summaryid, 'values'),
dataFileName)
settings = SettingsLoader.SettingsLoader(
os.path.join(folder, 'summaryvalues', summaryid, 'settings'))
settings.RequireTokens(
['Name', 'MaxVal', 'MaxVal', 'BlockSizeMax'])
settings.AddTokenIfMissing('MinVal', 0)
settings.AddTokenIfMissing('BlockSizeMin', 1)
settings.AddTokenIfMissing('ChannelColor', 'rgb(0,0,0)')
settings.AddTokenIfMissing('Order', 99999)
settings.DefineKnownTokens(['channelColor'])
settings.AddTokenIfMissing('ScopeStr', importSettings['ScopeStr'])
print('SETTINGS: ' + settings.ToJSON())
if importSettings['ScopeStr'] == 'all':
print('Executing filter bank')
ImpUtils.ExecuteFilterbankSummary_Value(
calculationObject, destFolder, summaryid, settings)
else:
calculationObject.Log(
'WARNING: Skipping filterbanking genome summary data')
extraSettings = settings.Clone()
extraSettings.DropTokens([
'Name', 'Order', 'MinVal', 'MaxVal', 'BlockSizeMin',
'BlockSizeMax'
])
sql = "INSERT INTO summaryvalues VALUES ('', 'fixed', '{0}', '-', '{1}', {2}, '{3}', {4}, {5}, {6})".format(
summaryid, settings['Name'], settings['Order'],
extraSettings.ToJSON(), settings['MinVal'], settings['MaxVal'],
settings['BlockSizeMin'])
ImpUtils.ExecuteSQL(calculationObject, datasetId, sql)
def ImportDataTable(calculation_object, dataset_id, tableid, folder, import_settings):
global tableOrder, property_order
with calculation_object.LogHeader('Importing 2D datatable {0}'.format(tableid)):
print('Source: ' + folder)
DQXUtils.CheckValidIdentifier(tableid)
table_settings = SettingsLoader.SettingsLoader(os.path.join(os.path.join(folder, 'settings')))
table_settings.RequireTokens(['NameSingle', 'NamePlural', 'FirstArrayDimension'])
table_settings.AddTokenIfMissing('ShowInGenomeBrowser', False)
table_settings.AddTokenIfMissing('ColumnDataTable', '')
table_settings.AddTokenIfMissing('RowDataTable', '')
extra_settings = table_settings.Clone()
extra_settings.DropTokens(['ColumnDataTable',
'ColumnIndexField',
'RowDataTable',
'RowIndexField',
'Properties'])
remote_hdf5 = h5py.File(os.path.join(folder, 'data.hdf5'), 'r')
#Check that the referenced tables exist and have the primary key specified.
if table_settings['ColumnDataTable']:
sql = "SELECT id FROM tablecatalog WHERE id = '{0}'".format(table_settings['ColumnDataTable'])
id = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
try:
id = id[0][0]
except IndexError:
raise Exception("Index Table " + table_settings['ColumnDataTable'] + " doesn't exist")
sql = "SELECT {0} FROM {1} LIMIT 1".format(table_settings['ColumnIndexField'],
table_settings['ColumnDataTable'])
try:
field = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
except:
raise Exception(table_settings['ColumnIndexField'] + " column index field doesn't exist in table " + table_settings['ColumnDataTable'])
if table_settings['RowDataTable']:
sql = "SELECT id FROM tablecatalog WHERE id = '{0}'".format(table_settings['RowDataTable'])
id = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
try:
id = id[0][0]
except IndexError:
raise Exception("Index Table " + table_settings['RowDataTable'] + " doesn't exist")
sql = "SELECT {0} FROM {1} LIMIT 1".format(table_settings['RowIndexField'],
table_settings['RowDataTable'])
try:
field = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
except:
raise Exception(table_settings['RowIndexField'] + " row index field doesn't exist in table " + table_settings['RowDataTable'])
if table_settings['ShowInGenomeBrowser']:
sql = "SELECT IsPositionOnGenome FROM tablecatalog WHERE id='{0}' ".format(table_settings['ColumnDataTable'])
is_position = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)[0][0]
if not is_position:
raise Exception(table_settings['ColumnDataTable'] + ' is not a genomic position based table (IsPositionOnGenome in config), but you have asked to use this table as a column index on a genome browseable 2D array.')
if table_settings['FirstArrayDimension'] not in ['column', 'row']:
raise Exception("FirstArrayDimension must be column or row")
# Add to tablecatalog
extra_settings.ConvertStringsToSafeSQL()
sql = "INSERT INTO 2D_tablecatalog VALUES ('{0}', '{1}', '{2}', '{3}', '{4}', '{5}', {6})".format(
tableid,
table_settings['NamePlural'],
table_settings['ColumnDataTable'],
table_settings['RowDataTable'],
table_settings['FirstArrayDimension'],
extra_settings.ToJSON(),
tableOrder
)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
tableOrder += 1
for property in table_settings['Properties']:
extra_settings = copy.deepcopy(property)
dtype = arraybuffer._strict_dtype_string(remote_hdf5[property['Id']].dtype)
del extra_settings['Id']
del extra_settings['Name']
sql = "INSERT INTO 2D_propertycatalog VALUES ('{0}', '{1}', '{2}', '{3}', '{4}', {5}, '{6}', '{7}')".format(
property['Id'],
tableid,
table_settings['ColumnDataTable'],
table_settings['RowDataTable'],
property['Name'],
property_order,
dtype,
simplejson.dumps(extra_settings)
)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
property_order += 1
if not import_settings['ConfigOnly']:
#Insert an index column into the index tables
if table_settings['ColumnDataTable']:
if table_settings.HasToken('ColumnIndexArray'):
#We have an array that matches to a column in the 1D SQL, we add an index to the 1D SQL
#Firstly create a temporay table with the index array
try:
column_index = remote_hdf5[table_settings['ColumnIndexArray']]
except KeyError:
raise Exception("HDF5 doesn't contain {0} at the root".format(table_settings['ColumnIndexArray']))
for property in table_settings['Properties']:
if len(column_index) != remote_hdf5[property['Id']].shape[0 if table_settings['FirstArrayDimension'] == 'column' else 1]:
raise Exception("Property {0} has a different column length to the column index".format(property))
sql = ImpUtils.Numpy_to_SQL().create_table('TempColIndex', table_settings['ColumnIndexField'], column_index)
ImpUtils.ExecuteSQLGenerator(calculation_object, dataset_id, sql)
#We have a datatable - add an index to it then copy that index across to the data table
sql = """ALTER TABLE `TempColIndex` ADD `index` INT DEFAULT NULL;
SELECT @i:=-1;UPDATE `TempColIndex` SET `index` = @i:=@i+1;
ALTER TABLE `{0}` ADD `{2}_column_index` INT DEFAULT NULL;
UPDATE `{0}` INNER JOIN `TempColIndex` ON `{0}`.`{1}` = `TempColIndex`.`{1}` SET `{0}`.`{2}_column_index` = `TempColIndex`.`index`;
DROP TABLE `TempColIndex`""".format(
table_settings['ColumnDataTable'],
table_settings['ColumnIndexField'],
tableid)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
#Now check we have no NULLS
sql = "SELECT `{1}_column_index` from `{0}` where `{1}_column_index` IS NULL".format(
table_settings['ColumnDataTable'],
tableid)
nulls = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
if len(nulls) > 0:
raise Exception("Not all rows in {0} have a corresponding column in 2D datatable {1}".format(table_settings['ColumnDataTable'], tableid))
else:
#We don't have an array of keys into a column so we are being told the data in HDF5 is in the same order as sorted "ColumnIndexField" so we index by that column in order
sql = """ALTER TABLE `{0}` ADD `{2}_column_index` INT DEFAULT NULL;
SELECT @i:=-1;UPDATE `{0}` SET `{2}_column_index` = @i:=@i+1 ORDER BY `{1}`;
""".format(
table_settings['ColumnDataTable'],
table_settings['ColumnIndexField'],
tableid)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
if table_settings['RowDataTable']:
if table_settings.HasToken('RowIndexArray'):
#We have an array that matches to a column in the 1D SQL, we add an index to the 1D SQL
#Firstly create a temporay table with the index array
try:
row_index = remote_hdf5[table_settings['RowIndexArray']]
except KeyError:
raise Exception("HDF5 doesn't contain {0} at the root".format(table_settings['RowIndexArray']))
for property in table_settings['Properties']:
if len(row_index) != remote_hdf5[property['Id']].shape[0 if table_settings['FirstArrayDimension'] == 'row' else 1]:
raise Exception("Property {0} has a different row length to the row index".format(property))
sql = ImpUtils.Numpy_to_SQL().create_table('TempRowIndex', table_settings['RowIndexField'], row_index)
ImpUtils.ExecuteSQLGenerator(calculation_object, dataset_id, sql)
#We have a datatable - add an index to it then copy that index across to the data table
sql = """ALTER TABLE `TempRowIndex` ADD `index` INT DEFAULT NULL;
SELECT @i:=-1;UPDATE `TempRowIndex` SET `index` = @i:=@i+1;
ALTER TABLE `{0}` ADD `{2}_row_index` INT DEFAULT NULL;
UPDATE `{0}` INNER JOIN `TempRowIndex` ON `{0}`.`{1}` = `TempRowIndex`.`{1}` SET `{0}`.`{2}_row_index` = `TempRowIndex`.`index`;
DROP TABLE `TempRowIndex`""".format(
table_settings['RowDataTable'],
table_settings['RowIndexField'],
tableid)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
#Now check we have no NULLS
sql = "SELECT `{1}_row_index` from `{0}` where `{1}_row_index` IS NULL".format(
table_settings['RowDataTable'],
tableid)
nulls = ImpUtils.ExecuteSQLQuery(calculation_object, dataset_id, sql)
if len(nulls) > 0:
raise Exception("Not all rows in {0} have a corresponding row in 2D datatable {1}".format(table_settings['RowDataTable'], tableid))
else:
#We don't have an array of keys into a column so we are being told the data in HDF5 is in the same order as sorted "RowIndexField" so we index by that column in order
sql = """ALTER TABLE `{0}` ADD `{2}_row_index` INT DEFAULT NULL;
SELECT @i:=-1;UPDATE `{0}` SET `{2}_row_index` = @i:=@i+1 ORDER BY `{1}`;
""".format(
table_settings['RowDataTable'],
table_settings['RowIndexField'],
tableid)
ImpUtils.ExecuteSQL(calculation_object, dataset_id, sql)
#We have the indexes - now we need a local copy of the HDF5 data for each property
ImpUtils.mkdir(os.path.join(config.BASEDIR, '2D_data'))
local_hdf5 = h5py.File(os.path.join(config.BASEDIR, '2D_data', dataset_id+'_'+tableid+'.hdf5'), 'w', libver='latest')
print "Copying HDF5 datasets"
for property in table_settings['Properties']:
print "..", property
local_hdf5.copy(remote_hdf5[property['Id']], property['Id'])
print "done"
print "all copies complete"
local_hdf5.close()
remote_hdf5.close()
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)
def ImportDataSet(calculationObject, baseFolder, datasetId, importSettings):
Utils.CheckSafeIdentifier(datasetId)
with calculationObject.LogHeader(
'Importing dataset {0}'.format(datasetId)):
calculationObject.Log('Import settings: ' + str(importSettings))
DQXUtils.CheckValidIdentifier(datasetId)
datasetFolder = os.path.join(baseFolder, datasetId)
indexDb = config.DB
calculationObject.credentialInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(indexDb, 'datasetindex'))
calculationObject.credentialInfo.VerifyCanDo(
DQXDbTools.DbOperationWrite(datasetId))
# Remove current reference in the index first: if import fails, nothing will show up
ImpUtils.ExecuteSQL(
calculationObject, indexDb,
'DELETE FROM datasetindex WHERE id="{0}"'.format(datasetId))
globalSettings = SettingsLoader.SettingsLoader(
os.path.join(datasetFolder, 'settings'))
globalSettings.RequireTokens(['Name'])
globalSettings.AddTokenIfMissing('Description', '')
print('Global settings: ' + str(globalSettings.Get()))
if not importSettings['ConfigOnly']:
# Dropping existing database
calculationObject.SetInfo('Dropping database')
print('Dropping database')
try:
ImpUtils.ExecuteSQL(
calculationObject, indexDb,
'DROP DATABASE IF EXISTS {0}'.format(datasetId))
except:
pass
ImpUtils.ExecuteSQL(calculationObject, indexDb,
'CREATE DATABASE {0}'.format(datasetId))
# Creating new database
scriptPath = os.path.dirname(os.path.realpath(__file__))
calculationObject.SetInfo('Creating database')
print('Creating new database')
ImpUtils.ExecuteSQLScript(calculationObject,
scriptPath + '/createdataset.sql',
datasetId)
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM propertycatalog')
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM summaryvalues')
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM tablecatalog')
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM settings')
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM customdatacatalog')
datatables = []
if globalSettings.HasToken('DataTables'):
if not type(globalSettings['DataTables']) is list:
raise Exception('DataTables token should be a list')
datatables = globalSettings['DataTables']
for dir in os.listdir(os.path.join(datasetFolder, 'datatables')):
if os.path.isdir(os.path.join(datasetFolder, 'datatables', dir)):
if dir not in datatables:
datatables.append(dir)
print('Data tables: ' + str(datatables))
for datatable in datatables:
ImportDataTable.ImportDataTable(
calculationObject, datasetId, datatable,
os.path.join(datasetFolder, 'datatables', datatable),
importSettings)
try:
datatables_2D = globalSettings['2D_DataTables']
except KeyError:
datatables_2D = []
if type(datatables_2D) is not list:
raise TypeError('2D_DataTables token should be a list')
for datatable in datatables_2D:
Import2DDataTable.ImportDataTable(
calculationObject, datasetId, datatable,
os.path.join(datasetFolder, '2D_datatables', datatable),
importSettings)
if os.path.exists(os.path.join(datasetFolder, 'refgenome')):
ImportRefGenome.ImportRefGenome(
calculationObject, datasetId,
os.path.join(datasetFolder, 'refgenome'), importSettings)
globalSettings.AddTokenIfMissing('hasGenomeBrowser', True)
ImportWorkspaces.ImportWorkspaces(calculationObject, datasetFolder,
datasetId, importSettings)
# Global settings
print('Defining global settings')
ImpUtils.ImportGlobalSettings(calculationObject, datasetId,
globalSettings)
# Finalise: register dataset
print('Registering dataset')
importtime = 0
if not importSettings['ConfigOnly']:
importtime = time.time()
ImpUtils.ExecuteSQL(
calculationObject, indexDb,
'INSERT INTO datasetindex VALUES ("{0}", "{1}", "{2}")'.format(
datasetId, globalSettings['Name'], str(math.ceil(importtime))))
def LoadTable(calculationObject, sourceFileName, databaseid, tableid, columns, loadSettings, importSettings, allowSubSampling):
def DecoId(id):
return '`' + id + '`'
def EncodeCell(icontent, col):
content = icontent
if col['IsString']:
if len(icontent) == 0:
content = "''"
else:
try:
content = content.encode('ascii', 'ignore')
except UnicodeDecodeError:
print('Unable to encode '+content)
content='*failed encoding*'
content = content.replace("\x92", "'")
content = content.replace("\xC2", "'")
content = content.replace("\x91", "'")
#filter(lambda x: x in string.printable, val)
content = content.replace("'", "\\'")
content = content.replace('\r\n', '\\n')
content = content.replace('\n\r', '\\n')
content = '\'' + content + '\''
if col['IsValue']:
if (content == 'NA') or (content == '') or (content == 'None') or (content == 'NULL') or (content == 'null') or (content == 'inf') or (content == '-'):
content = 'NULL'
if col['IsDate']:
if len(content)>=5:
try:
dt = dateutil.parser.parse(content)
tmdiff =(dt - datetime.datetime(1970, 1, 1)).days
tmdiff += 2440587.5 +0.5 # note: extra 0.5 because we set datestamp at noon
content = str(tmdiff)
except:
print('ERROR: date parsing string '+content)
content = 'NULL'
else:
content = 'NULL'
if col['IsBoolean']:
vl = content
content = 'NULL'
if (vl.lower() == 'true') or (vl.lower() == 'yes') or (vl.lower() == 'y') or (vl == '1'):
content = '1'
if (vl.lower() == 'false') or (vl.lower() == 'no') or (vl.lower() == 'n') or (vl == '0'):
content = '0'
return content
calculationObject.Log('Loading table {0} from {1}'.format(tableid, sourceFileName))
colDict = {col['name']: col for col in columns}
colNameList = [col['name'] for col in columns]
primkey = loadSettings['PrimKey']
autoPrimKey = (primkey == 'AutoKey')
print('Column info: ' + str(columns))
print('Primary key: ' + primkey)
for col in columns:
col['IsString'] = (col['DataType'] == 'Text')
col['IsValue'] = ImpUtils.IsValueDataTypeIdenfifier(col['DataType'])
col['IsDate'] = ImpUtils.IsDateDataTypeIdenfifier(col['DataType'])
col['IsBoolean'] = (col['DataType'] == 'Boolean')
col['MaxLen'] = 0
destFileName = ImpUtils.GetTempFileName()
maxLineCount = -1
if importSettings['ScopeStr'] == '1k':
maxLineCount = 1000
if importSettings['ScopeStr'] == '10k':
maxLineCount = 10000
if importSettings['ScopeStr'] == '100k':
maxLineCount = 100000
if importSettings['ScopeStr'] == '1M':
maxLineCount = 1000000
if importSettings['ScopeStr'] == '10M':
maxLineCount = 10000000
with open(sourceFileName, 'r') as ifp:
if ifp is None:
raise Exception('Unable to read file '+sourceFileName)
with open(destFileName, 'w') as ofp:
if ofp is None:
raise Exception('Unable to write to temporary file ' + destFileName)
fileColNames = ifp.readline().rstrip('\n\r').split('\t')
calculationObject.Log('File columns: ' + str(fileColNames))
fileColIndex = {fileColNames[i]: i for i in range(len(fileColNames))}
if not(autoPrimKey) and (primkey not in fileColIndex):
raise Exception('File is missing primary key '+primkey)
for col in columns:
# if 'ReadData' not in col:
# print('==========' + str(col))
colname = col['name']
if (col['ReadData']) and (colname not in fileColIndex):
raise Exception('File is missing column '+colname)
blockSize = 499
blockStarted = False
lineCount = 0
for line in ifp:
line = line.rstrip('\r\n')
if len(line) > 0:
sourceCells = line.split('\t')
writeCells = []
for col in columns:
content = 'NULL'
if col['name'] in fileColIndex:
content = sourceCells[fileColIndex[col['name']]]
content = EncodeCell(content, col)
writeCells.append(content)
if col['IsString']:
col['MaxLen'] = max(col['MaxLen'], len(content))
if not(blockStarted):
ofp.write('INSERT INTO {0} ({1}) VALUES '.format(DecoId(tableid), ', '.join([DecoId(col) for col in colNameList])))
blockStarted = True
blockNr = 0
if blockNr > 0:
ofp.write(',')
ofp.write('(')
ofp.write(','.join(writeCells))
ofp.write(')')
blockNr += 1
if blockNr >= blockSize:
ofp.write(';\n')
blockStarted = False
lineCount += 1
if lineCount % 250000 == 0:
calculationObject.Log('Line '+str(lineCount))
if (maxLineCount>0) and (lineCount >= maxLineCount):
calculationObject.Log('WARNING:Terminating import at {0} lines'.format(lineCount))
break
calculationObject.Log('Column sizes: '+str({col['name']: col['MaxLen'] for col in columns}))
calculationObject.Log('Creating schema')
scr = ImpUtils.SQLScript(calculationObject)
scr.AddCommand('drop table if exists {0};'.format(DecoId(tableid)))
sql = 'CREATE TABLE {0} (\n'.format(DecoId(tableid))
colTokens = []
if autoPrimKey:
colTokens.append("{0} int AUTO_INCREMENT PRIMARY KEY".format(primkey))
if allowSubSampling:
colTokens.append("_randomval_ double")
for col in columns:
st = DecoId(col['name'])
typestr = ''
if col['DataType'] == 'Text':
typestr = 'varchar({0})'.format(max(1, col['MaxLen']))
if len(typestr) == 0:
typestr = ImpUtils.GetSQLDataType(col['DataType'])
if len(typestr) == 0:
raise Exception('Invalid property data type ' + col['DataType'])
st += ' '+typestr
colTokens.append(st)
sql += ', '.join(colTokens)
sql +=')'
scr.AddCommand(sql)
calculationObject.Log('Creation statement: '+sql)
if not(autoPrimKey):
scr.AddCommand('create unique index {0}_{1} ON {0}({1})'.format(tableid, primkey))
for col in columns:
if ('Index' in col) and (col['Index']) and (col['name'] != primkey):
scr.AddCommand('create index {0}_{1} ON {0}({1})'.format(tableid, col['name']))
scr.Execute(databaseid)
calculationObject.Log('Importing data')
ImpUtils.ExecuteSQLScript(calculationObject, destFileName, databaseid)
if allowSubSampling:
with calculationObject.LogHeader('Create subsampling table'):
calculationObject.Log('Creating random data column')
sql = "UPDATE {0} SET _randomval_=RAND()".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "CREATE INDEX {0}_randomindex ON {0}(_randomval_)".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "DROP TABLE IF EXISTS {0}_SORTRAND".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "CREATE TABLE {0}_SORTRAND LIKE {0}".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
if autoPrimKey:
calculationObject.Log('Restructuring AutoKey')
sql = "alter table {0}_SORTRAND drop column AutoKey".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "alter table {0}_SORTRAND add column AutoKey int FIRST".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "create index idx_autokey on {0}_SORTRAND(AutoKey)".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "alter table {0}_SORTRAND add column RandPrimKey int AUTO_INCREMENT PRIMARY KEY".format(tableid)
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
sql = "insert into {0}_SORTRAND select *,0 from {0} order by _randomval_".format(tableid)
sql += ' LIMIT 5000000' # NOTE: there is little point in importing more than that!
ImpUtils.ExecuteSQL(calculationObject, databaseid, sql)
os.remove(destFileName)
def ImportRefGenome(calculationObject, datasetId, folder, importSettings):
with calculationObject.LogHeader('Importing reference genome data'):
ImportRefGenomeSummaryData(calculationObject, datasetId, folder,
importSettings)
settings = SettingsLoader.SettingsLoader(
os.path.join(folder, 'settings'))
settings.DefineKnownTokens(['AnnotMaxViewportSize', 'RefSequenceSumm'])
print('Settings: ' + str(settings.Get()))
ImpUtils.ImportGlobalSettings(calculationObject, datasetId, settings)
# Import reference genome
if importSettings['ScopeStr'] == 'all':
refsequencefile = os.path.join(folder, 'refsequence.fa')
if os.path.exists(refsequencefile):
with calculationObject.LogHeader(
'Converting reference genome'):
destfolder = config.BASEDIR + '/SummaryTracks/' + datasetId + '/Sequence'
if not os.path.exists(destfolder):
os.makedirs(destfolder)
tempfastafile = destfolder + '/refsequence.fa'
shutil.copyfile(refsequencefile, tempfastafile)
ImpUtils.RunConvertor(calculationObject,
'Fasta2FilterBankData', destfolder,
['refsequence.fa'])
else:
calculationObject.Log(
'WARNING: missing reference sequence file')
else:
calculationObject.Log(
'WARNING: Skipping converting reference genome')
# Import chromosomes
with calculationObject.LogHeader('Loading chromosomes'):
tb = VTTable.VTTable()
tb.allColumnsText = True
try:
tb.LoadFile(os.path.join(folder, 'chromosomes'))
except Exception as e:
raise Exception('Error while reading chromosomes file: ' +
str(e))
tb.RequireColumnSet(['chrom', 'length'])
tb.RenameCol('chrom', 'id')
tb.RenameCol('length', 'len')
tb.ConvertColToValue('len')
with calculationObject.LogDataDump():
tb.PrintRows(0, 99)
sqlfile = ImpUtils.GetTempFileName()
tb.SaveSQLDump(sqlfile, 'chromosomes')
ImpUtils.ExecuteSQL(calculationObject, datasetId,
'DELETE FROM chromosomes')
ImpUtils.ExecuteSQLScript(calculationObject, sqlfile, datasetId)
os.remove(sqlfile)
if importSettings['ScopeStr'] == 'all':
# Import annotation
with calculationObject.LogHeader('Converting annotation'):
tempgfffile = ImpUtils.GetTempFileName()
temppath = os.path.dirname(tempgfffile)
shutil.copyfile(os.path.join(folder, 'annotation.gff'),
tempgfffile)
ImpUtils.RunConvertor(calculationObject, 'ParseGFF', temppath,
[os.path.basename(tempgfffile)])
print('Importing annotation')
ImpUtils.ExecuteSQLScript(
calculationObject,
os.path.join(temppath, 'annotation_dump.sql'), datasetId)
os.remove(tempgfffile)
os.remove(os.path.join(temppath, 'annotation.txt'))
os.remove(os.path.join(temppath, 'annotation_dump.sql'))
os.remove(os.path.join(temppath, 'annotation_create.sql'))
else:
calculationObject.Log('WARNING: Skipping converting annotation')
