def testJsonReadAndWriteSqg(self):
for include in self.jsonFiles:
logger.info("Going to use jsonRead to parse/write/parse SQG %s" % include)
#First read
file = os.path.join(getPysqgIncludeDir(), include + ".json")
sqg = readJsonSqgFile(file)
#Then write
writeJsonSqgFile(sqg, self.tempFile)
#Now parse again
readJsonSqgFile(self.tempFile)
"""Pretty prints the various sqg files in the include hierarchy
"""
import os
from pysqg.bioio import system
from pysqg.shared import getPysqgIncludeDir, getPysqgBaseDir
for file in os.listdir(getPysqgIncludeDir()):
if ".json" in file:
include = file[:-5]
absFile = os.path.join(getPysqgIncludeDir(), file)
outFile = os.path.join(getPysqgBaseDir(), "doc", "include", include + ".rst")
outFileHandle = open(outFile, "w")
outFileHandle.write("%s.sqg\n_________________________________\n\n>>>\n" % include)
outFileHandle.close()
system("cat %s | python -mjson.tool >> %s" % (absFile, outFile))
inheritanceGraph = Sqg(includes=["mixedGraph"])
arrayLists = InMemoryArrayList(type="arrayLists", inherits="node", variables=[ "name", "string", "arrayNames", "string", "arrayTypes", "string" ]) #Nodes representing array list types
sqgs = InMemoryArrayList(type="sqgs", inherits="node", variables=[ "name", "string" ]) #Nodes representing sqg definitions
inheritEdges = InMemoryArrayList(type="inherit", inherits="directedEdge") #Edges showing inheritance between array lists
graphEdges = InMemoryArrayList(type="graph", inherits="directedEdge") #Edges showing which show which sqg defined which array list
#Add them to the graph
inheritanceGraph.setArrayList(arrayLists)
inheritanceGraph.setArrayList(sqgs)
inheritanceGraph.setArrayList(inheritEdges)
inheritanceGraph.setArrayList(graphEdges)
#Build the nodes and connect the graphs to the array types
typeStringsToNodeNamesAndArrays = {}
i = 0
for file in os.listdir(getPysqgIncludeDir()):
if file[-5:] == ".json":
Sqg(includes=[file[:-5]]) #This ensures the graphs are in memory
graphNode = i
i = i+1
sqgs.addDict({ "nodeName":graphNode, "name":file[:-5] })
#Now iterate through the new array list types
fileHandle = open(os.path.join(getPysqgIncludeDir(), file), 'r')
jsonSqg = json.load(fileHandle)
fileHandle.close()
for arrayListType in jsonSqg.keys():
if arrayListType not in ("name", "include", "parents", "sharedVariables"): #This is very hacky, it would be nice to have a clean way to know which sqg defined which array list.
arrayList = InMemoryArrayList(type=arrayListType)
arrayNode = i
i = i+1
typeStringsToNodeNamesAndArrays[arrayListType] = (arrayNode, arrayList)
def testParseJsonFiles(self):
for include in self.jsonFiles:
logger.info("Going to parse %s" % include)
fileHandle = open(os.path.join(getPysqgIncludeDir(), include + ".json"), 'r')
json.load(fileHandle)
fileHandle.close()
def parseInclude(include):
includeFile = os.path.join(getPysqgIncludeDir(), include + ".json")
logger.debug("Going to parse the include file: %s", includeFile)
from pysqg.jsonSqg import readJsonSqgFile
return readJsonSqgFile(includeFile)
