readSBML:compartment name and id is mapped, in Assignment rule a check made for integer in the expression,writeSBML:added autlayout which was required for writting cspace model while writting from command line, for cplxpool's x-y coordinates and motor/diff constant are added,fixXreac: check to see if object exist before _moose.connect, case where object is deleted but _xref_ annotation info field still hold the reference

hrani · hrani · commit eb88a23a04dd · 2019-10-24T17:09:38.000+05:30
diff --git a/python/moose/SBML/readSBML.py b/python/moose/SBML/readSBML.py
@@ -13,10 +13,12 @@
 **           copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
 Created : Thu May 13 10:19:00 2016(+0530)
 Version
-Last-Updated: Sat Jan 19 10:30:00 2019(+0530)
+Last-Updated: Mon Jun 16 10:30:00 2019(+0530)
           By:HarshaRani
 **********************************************************************/
 2019:
+Jun 06: - both compartment name and Id is mapped to the values in comptSbmlidMooseIdMap
+May 23: - check for interger for 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
@@ -149,7 +151,8 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
                     groupInfo  = {}
                     funcDef = {}
                     modelAnnotaInfo = {}
-                    comptSbmlidMooseIdMap = {}
+                    #comptSbmlidMooseIdMap = {}
+                    comptSbmlidMooseIdMap = dict()
                     globparameterIdValue = {}
 
                     mapParameter(model, globparameterIdValue)
@@ -277,7 +280,7 @@ def checkGroup(basePath,model,comptSbmlidMooseIdMap):
                     moosegrpinfo = moose.Annotator(moosegrp.path+'/info')
                     moosegrpinfo.color = groupAnnoInfo["bgColor"]
                 else:
-                    print ("Compartment not found")
+                    print ("Group's compartment not found in xml file")
             if p.getKind() == 2:
                 if p.getId() not in groupInfo:
                     memlists = []
@@ -934,6 +937,7 @@ def getMembers(node, ruleMemlist):
     found = True
     if node == None:
         pass
+
     elif node.getType() == libsbml.AST_POWER:
         pass
     
@@ -1009,6 +1013,12 @@ 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
@@ -1104,7 +1114,7 @@ def createRules(model, specInfoMap, globparameterIdValue):
                                     funcId.numVars = numVars + 1
 
                                 elif not(i in globparameterIdValue):
-                                    msg = msg + "check the variable name in mathML, this object neither pool or a constant \"" + i+"\" in assignmentRule " +rule.getVariable()
+                                    msg = msg + "check the variable name in mathML, this object neither pool or a constant \"" + str(i)+"\" in assignmentRule " +rule.getVariable()
 
                                 exp = rule.getFormula()
                                 exprOK = True
@@ -1437,9 +1447,11 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
                 mooseCmptId = moose.CubeMesh(basePath.path+'/'+name)
             
             mooseCmptId.volume = (msize * unitfactor)
-    
-            comptSbmlidMooseIdMap[sbmlCmptId] = {
-                "MooseId": mooseCmptId, "spatialDim": dimension, "size": msize}
+            #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:
diff --git a/python/moose/SBML/writeSBML.py b/python/moose/SBML/writeSBML.py
@@ -13,11 +13,14 @@
 **           copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
 Created : Friday May 27 12:19:00 2016(+0530)
 Version
-Last-Updated: Tue 29 Jan 15:15:10 2019(+0530)
+Last-Updated: Thr 18 July 15:15:10 2019(+0530)
           By: HarshaRani
 **********************************************************************/
 /****************************
 2019
+July 18: added a call for autolayout, this was required for cspace model while trying to write from cmd line
+         while writting file, the filepath is checked
+         now even for cplxpool's x and y co-ordinates,diff and motor constant are added
 Jan 29: getColor are taken from chemConnectUtil, group's width and height are written
 2018
 Dec 07: using fixXreac's restoreXreacs function to remove xfer
@@ -49,7 +52,7 @@
 import os
 import moose
 from moose.SBML.validation import validateModel
-from moose.chemUtil.chemConnectUtil import xyPosition,mooseIsInstance,findCompartment,getColor,setupItem
+from moose.chemUtil.chemConnectUtil import xyPosition,mooseIsInstance,findCompartment,getColor,setupItem,setupMeshObj
 from moose.chemUtil.graphUtils import *
 from moose.fixXreacs import restoreXreacs
 import numpy as np
@@ -61,6 +64,21 @@
 except Exception as e:
     pass
 
+def checkPath( dirName):
+    path = dirName
+    if (dirName == "~" or not dirName ):
+        if dirName:
+            dirName = os.path.expanduser(dirName)
+        else:
+            dirName = os.getcwd()
+    
+    if os.access(dirName, os.W_OK) is not True:
+        dirName = os.getcwd()
+        print(path +" not writable, writting to "+dirName+ " directory")
+        return dirName
+    else:
+        return dirName
+
 def mooseWriteSBML(modelpath, filename, sceneitems={}):
     global foundLibSBML_
     msg = " "
@@ -74,6 +92,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
 
     #sbmlDoc = SBMLDocument(3, 1)
     filepath, filenameExt = os.path.split(filename)
+    filepath = checkPath(filepath)
     if filenameExt.find('.') != -1:
         filename = filenameExt[:filenameExt.find('.')]
     else:
@@ -188,13 +207,14 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
                 
                 if moose.exists(key.path+'/info'):
                     ginfo = moose.element(key.path+'/info')
+                    textColor,color = getColor(ginfo)
                     if ginfo.height and ginfo.width:
                         grpAnno = grpAnno + "<moose:x>" + str(ginfo.x) + "</moose:x>\n"
                         grpAnno = grpAnno + "<moose:y>" + str(ginfo.y) + "</moose:y>\n"
                         grpAnno = grpAnno + "<moose:width>" + str(ginfo.width) + "</moose:width>\n"
                         grpAnno = grpAnno + "<moose:height>" + str(ginfo.height) + "</moose:height>\n"
                     if ginfo.color:
-                        grpAnno = grpAnno + "<moose:bgColor>" + ginfo.color + "</moose:bgColor>\n"
+                        grpAnno = grpAnno + "<moose:bgColor>" + color + "</moose:bgColor>\n"
                     if ginfo.notes:
                         grpAnno = grpAnno + "<moose:Notes>" + ginfo.notes + "</moose:Notes>\n"
                 grpAnno = grpAnno + "</moose:GroupAnnotation>"
@@ -207,11 +227,16 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
         consistencyMessages = ""
         SBMLok = validateModel(sbmlDoc)
         if (SBMLok):
-            writeTofile = filepath + "/" + filename + '.xml'
+            if filepath != [" ","\/","/"]:
+                writeTofile = filepath + "/" + filename + '.xml'
+            else:
+                writeTofile = filename+'.xml'
+
+            #writeTofile = filepath + "/" + filename + '.xml'
             writeSBMLToFile(sbmlDoc, writeTofile)
             return True, consistencyMessages, writeTofile
         
-        if (not SBMLok):
+        else:
             #cerr << "Errors encountered " << endl
             consistencyMessages = "Errors encountered"
             return -1, consistencyMessages
@@ -952,6 +977,14 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
                 if spename.find(
                         "cplx") != -1 and isinstance(moose.element(spe.parent), moose.EnzBase):
                     enz = spe.parent
+                    if not moose.exists(spe.path+'/info'):
+                        cplxinfo = moose.Annotator(spe.path+'/info')
+                        enzpath = moose.element(spe.parent.path+'/info')
+                        
+                        cplxinfo.x = moose.element(moose.element(spe.parent.path+'/info').x)
+                        
+                        cplxinfo.y = int((moose.element(spe.parent.path+'/info').y))+10
+                 
                     if (moose.element(enz.parent), moose.PoolBase):
                         # print " found a cplx name ",spe.parent,
                         # moose.element(spe.parent).parent
@@ -1038,6 +1071,13 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
                     speciAnno = speciAnno + "<moose:motorConstant>" + str(spe.motorConst)+ "</moose:motorConstant>\n" 
                     speciAnno = speciAnno + "</moose:ModelAnnotation>"
                     s1.setAnnotation(speciAnno)
+                else:
+                    #E.g cplx doesn't have info field but findsim layout expecting diffConstant and motorConstant.
+                    speciAnno = "<moose:ModelAnnotation>\n"
+                    speciAnno = speciAnno + "<moose:diffConstant>" + str(0.0) + "</moose:diffConstant>\n"
+                    speciAnno = speciAnno + "<moose:motorConstant>" + str(0.0)+ "</moose:motorConstant>\n" 
+                    speciAnno = speciAnno + "</moose:ModelAnnotation>"
+                    s1.setAnnotation(speciAnno)
     return True
 
 
@@ -1205,6 +1245,11 @@ def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
     else:
         srcdesConnection = {}
         setupItem(modelpath,srcdesConnection)
+        meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
+        if not positionInfoExist:
+            sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+        sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+
         #print srcdesConnection
         '''
         #meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
diff --git a/python/moose/chemUtil/chemConnectUtil.py b/python/moose/chemUtil/chemConnectUtil.py
@@ -17,7 +17,7 @@
 import matplotlib
 import os
 import random
-
+import re
 
 direct = os.path.dirname(__file__)
 colormap_file = open(os.path.join(direct, "rainbow2.pkl"), "r")  
@@ -69,7 +69,7 @@ def colorCheck(fc_bgcolor):
     if isinstance(fc_bgcolor,str):
         if fc_bgcolor.startswith("#"):
             fc_bgcolor = fc_bgcolor
-        elif fc_bgcolor.isdigit():
+        elif (fc_bgcolor.isdigit()):
             """ color is int  a map from int to r,g,b triplets from pickled color map file """
             tc = (int(fc_bgcolor))*2
             if tc < len(colorMap):
@@ -89,7 +89,7 @@ def colorCheck(fc_bgcolor):
             hexlist ="#"
             for n in fc_bgcolor:
                 if c < 3:
-                    hexlist = hexlist+str("%02x" % int(n))
+                    #hexlist = hexlist+str("%02x" % int(n))
                     c = c+1;
             fc_bgcolor = hexlist
         return(fc_bgcolor)
diff --git a/python/moose/fixXreacs.py b/python/moose/fixXreacs.py
@@ -188,7 +188,10 @@ def restoreXreacs( basepath ):
                 args = j.split( ' ' )
                 assert( len( args ) == 4 )
                 #_moose.showfield( args[0] )
-                _moose.connect( args[0], args[1], args[2], args[3] )
+                #check to see if object exist before moose.connect, cases where object is deleted but
+                #_xref_ annotation info field still holds the reference
+                if (_moose.exists(args[0]) and _moose.exists(args[2])):
+                    _moose.connect( args[0], args[1], args[2], args[3] )
                 #print( "Reconnecting {}".format( args ) )
                 #_moose.showfield( args[0] )
         restoreOldRates( oldRates, msgs )
diff --git a/python/moose/genesis/writeKkit.py b/python/moose/genesis/writeKkit.py
@@ -664,7 +664,8 @@ def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
             index = color
             return index
     elif isinstance(color, tuple):
-        color = [int(x) for x in color[0:3]]
+        #color = [int(x) for x in color[0:3]]
+        color = map(int,color)[0:3]
         index = nearestColorIndex(color, GENESIS_COLOR_SEQUENCE)
         return index
     elif isinstance(color, int):
@@ -691,8 +692,8 @@ def writeCompartment(modelpath,compts,f):
         if compt.name != "kinetics":
             x = xmin+6
             y = ymax+1
-            f.write("simundump group /kinetics/" + compt.name + " 0 " + "blue" + " " + "green"       + " x 0 0 \"\" defaultfile \\\n" )
-            f.write( "  defaultfile.g 0 0 0 " + str(int(x)) + " " + str(int(y)) + " 0\n")
+            #f.write("simundump group /kinetics/" + compt.name + " 0 " + "blue" + " " + "green"       + " x 0 0 \"\" defaultfile \\\n" )
+            #f.write( "  defaultfile.g 0 0 0 " + str(int(x)) + " " + str(int(y)) + " 0\n")
     i = 0
     l = len(compts)
     geometry = ""
