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configuration.py
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configuration.py
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"""
The MIT License (MIT)
Copyright (c) 2016 Intel Corporation
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import json
class ConfigReader:
"""
Specialized config reader for a MAF importing.
"""
def __init__(self, config_file):
with open(config_file, "r") as fp:
jsonMap = json.load(fp)
self.DB_URI = getDictValue(jsonMap, "DB_URI")
self.TileDBAssembly = getDictValue(jsonMap, "TileDBAssembly")
self.TileDBSchema = getDictValue(jsonMap, "TileDBSchema")
getDictValue(self.TileDBSchema, "workspace")
getDictValue(self.TileDBSchema, "array")
getDictValue(self.TileDBSchema, "fields_list")
getDictValue(self.TileDBSchema, "ftypes_list")
# if the name ends with a / then remove it from the name.
# This is done only for consistency in workspace name
# since users could have / or not for the workspace.
self.TileDBSchema['workspace'] = self.TileDBSchema[
'workspace'].rstrip('/')
self.HeaderStartsWith = getDictValue(jsonMap, "HeaderStartsWith")
# Individual defaults to None
self.IndividualIdMap = jsonMap.get("IndividualId", None)
self.SourceSampleIdMap = getDictValue(jsonMap, "SourceSampleId")
self.TargetSampleIdMap = getDictValue(jsonMap, "TargetSampleId")
# Setup CallSetIdMap
self.CallSetIdMap = getDictValue(jsonMap, "CallSetId")
bDynamic = self.CallSetIdMap.get("Dynamic", False)
CallSetName = getDictValue(self.CallSetIdMap, "CallSetName")
self.CallSetIdMap = [bDynamic, CallSetName]
# Setup CallSetIdMap
self.VariantNameMap = getDictValue(jsonMap, "VariantSetMap")
bDynamic = self.VariantNameMap.get("Dynamic", False)
VariantName = getDictValue(self.VariantNameMap, "VariantSet")
bVariantLookup = self.VariantNameMap.get("VariantLookup", False)
VariantConfig = self.VariantNameMap.get("VariantConfig", None)
LookupIdx = self.VariantNameMap.get("LookupIdx", None)
if bVariantLookup:
fp = open(VariantConfig, 'r')
VariantConfig = json.load(fp)
fp.close()
self.VariantNameMap = [bDynamic, VariantName,
bVariantLookup, VariantConfig, LookupIdx]
# Setup PositionMap
self.PositionMap = getDictValue(jsonMap, "Position")
assembly = getDictValue(self.PositionMap, "assembly")
bDynamic = assembly.get("Dynamic", False)
assemblyName = getDictValue(assembly, "assemblyName")
self.PositionMap["assembly"] = [bDynamic, assemblyName]
# Verify other required fields in PositionMap are present so that we
# can avoid checks each time we access these fields
getDictValue(self.PositionMap, "chromosome")
getDictValue(self.PositionMap, "Location")
getDictValue(self.PositionMap, "End")
self.TileDBMap = getDictValue(jsonMap, "TileDBMapping")
# Verify other required fields in TileDBMap are present so that we
# can avoid checks each time we access these fields
getDictValue(self.TileDBMap, "ALT")
if 'GT' in self.TileDBMap.keys():
self.GTMap = getDictValue(jsonMap, 'GTMapping')
self.SeperatorMap = getDictValue(jsonMap, "Seperators")
# Verify other required fields in SeperatorMap are present so that we
# can avoid checks each time we access these fields
getDictValue(self.SeperatorMap, "line")
self.Constants = getDictValue(jsonMap, 'Constants')
getDictValue(self.Constants, 'PLOIDY')
def getDictValue(inDictionary, inString):
"""
Takes a dictionary object and looks for inString in the dictionary
If it is not available, an exception is raised.
Else, the object is returned
"""
returnObject = inDictionary.get(inString, None)
if(returnObject is None):
raise ValueError(inString + " is a required field")
return returnObject