readsbml: compartment name & Id is mapped to the values in comptSbmlidMooseIdMap,writesbml: added annotation for cplxpool, autolayout for cspaccemodels (#374)

Author: hrani

python/moose/SBML/readSBML.py

@@ -18,7 +18,7 @@
 **********************************************************************/
 2019:
 Jun 06: - both compartment name and Id is mapped to the values in comptSbmlidMooseIdMap
-May 23: - check for interger for Assignment expr
+May 23: - checking for integer in Assignment expr
 Jan 19: - validator flag is set 'on' from True
          - groupname if missing in the sbml file then groupid is taken, 
          if both are missing then its not a valide sbml file
@@ -935,24 +935,17 @@ def unitsforRates(model):
 def getMembers(node, ruleMemlist):
     msg = ""
     found = True
+
     if node == None:
         pass
 
     elif node.getType() == libsbml.AST_POWER:
         pass
 
     elif node.getType() == libsbml.AST_FUNCTION:
-        #print " function"
-        #funcName = node.getName()
-        #funcValue = []
-        #functionfound = False
         for i in range(0,node.getNumChildren()):
-            #functionfound = True
-            #print " $$ ",node.getChild(i).getName()
-            #funcValue.append(node.getChild(i).getName())
             getMembers(node.getChild(i),ruleMemlist)
-        #funcKL[node.getName()] = funcValue
-
+    
     elif node.getType() == libsbml.AST_PLUS:
         #print " plus ", node.getNumChildren()
         if node.getNumChildren() == 0:
@@ -996,7 +989,6 @@ def getMembers(node, ruleMemlist):
         for i in range(1, node.getNumChildren()):
             # Multiplication
             getMembers(node.getChild(i), ruleMemlist)
-
     elif node.getType() == libsbml.AST_LAMBDA:
         #In lambda get Bvar values and getRighChild which will be kineticLaw
         if node.getNumChildren() == 0:
@@ -1013,15 +1005,15 @@ def getMembers(node, ruleMemlist):
         for i in range (0,node.getNumBvars()):
             ruleMemlist.append(node.getChild(i).getName())
         #funcD[funcName] = {"bvar" : bvar, "MathML":node.getRightChild()}
-
     elif node.getType() == libsbml.AST_INTEGER:
         #value is constant
         #ruleMemlist.append(node.getValue())
         pass
-    
+
     elif node.getType() == libsbml.AST_FUNCTION_POWER:
         msg = msg + "\n moose is yet to handle \""+node.getName() + "\" operator"
         found = False
+    
     elif node.getType() == libsbml.AST_FUNCTION_PIECEWISE:
         #print " piecewise ", libsbml.formulaToL3String(node)
         msg = msg + "\n moose is yet to handle \""+node.getName() + "\" operator"
@@ -1037,7 +1029,6 @@ def getMembers(node, ruleMemlist):
             getMembers(rchild, ruleMemlist)
         '''
     else:
-        #print(" this case need to be handled", node.getName())
         msg = msg + "\n moose is yet to handle \""+node.getName() + "\" operator"
         found = False
     # if len(ruleMemlist) > 2:
@@ -1122,7 +1113,6 @@ def createRules(model, specInfoMap, globparameterIdValue):
                             for mem in ruleMemlist:
                                 if (mem in specInfoMap):
                                     #exp1 = exp.replace(mem, str(speFunXterm[mem]))
-                                    #print " mem ",mem, "$ ", speFunXterm[mem], "$$ ",exp
                                     exp1 = re.sub(r'\b%s\b'% (mem), speFunXterm[mem], exp)
                                     exp = exp1
                                 elif(mem in globparameterIdValue):
@@ -1449,10 +1439,8 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
             mooseCmptId.volume = (msize * unitfactor)
             #both compartment name and Id is mapped to the values
             comptSbmlidMooseIdMap.update(dict.fromkeys([sbmlCmptId,name], {"MooseId": mooseCmptId, "spatialDim": dimension, "size": msize}))
-
             #comptSbmlidMooseIdMap[sbmlCmptId] = {
             #    "MooseId": mooseCmptId, "spatialDim": dimension, "size": msize}
-        
         for key,value in endo_surr.items():
             if value in comptSbmlidMooseIdMap:
                 endomesh = comptSbmlidMooseIdMap[key]["MooseId"]

python/moose/SBML/writeSBML.py

@@ -97,6 +97,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
         filename = filenameExt[:filenameExt.find('.')]
     else:
         filename = filenameExt
+    
     # validatemodel
     sbmlOk = False
     global spe_constTrue
@@ -231,7 +232,6 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
                 writeTofile = filepath + "/" + filename + '.xml'
             else:
                 writeTofile = filename+'.xml'
-
             #writeTofile = filepath + "/" + filename + '.xml'
             writeSBMLToFile(sbmlDoc, writeTofile)
             return True, consistencyMessages, writeTofile
@@ -1027,6 +1027,7 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
                     s1.setConstant(False)
                 s1.setUnits("substance")
                 s1.setHasOnlySubstanceUnits(False)
+
                 if moose.exists(spe.path + '/info'):
                     Anno = moose.Annotator(spe.path + '/info')
                     if Anno.notes != "":
@@ -1067,6 +1068,7 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
                     if Anno.textColor:
                         speciAnno = speciAnno + "<moose:textColor>" + \
                             Anno.textColor + "</moose:textColor>\n"
+                    
                     speciAnno = speciAnno + "<moose:diffConstant>" + str(spe.diffConst) + "</moose:diffConstant>\n"
                     speciAnno = speciAnno + "<moose:motorConstant>" + str(spe.motorConst)+ "</moose:motorConstant>\n" 
                     speciAnno = speciAnno + "</moose:ModelAnnotation>"
@@ -1247,6 +1249,7 @@ def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
         setupItem(modelpath,srcdesConnection)
         meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
         if not positionInfoExist:
+
             sceneitems = autoCoordinates(meshEntry,srcdesConnection)
         sceneitems = autoCoordinates(meshEntry,srcdesConnection)
 
@@ -1256,7 +1259,7 @@ def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
         #if not positionInfoExist:
             #cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
             sceneitems = autoCoordinates(meshEntry,srcdesConnection)
-        '''
+	'''        
 def writeUnits(cremodel_):
     unitVol = cremodel_.createUnitDefinition()
     unitVol.setId("volume")