Cleanup sbml (#447)

* minimum gcc version is 5.X and hdf5 included in cmake as default

* CMake correction

* Added basepath if exist to compartment Annotation

* function input connection done after enzyme, func.expr fixed, corrected stoichiometry for edge case

* edgecase if extra path exist it is taken care while writting/reading into/from SBML

* correction in basepath to basePath in readSBML

Author: hrani

python/moose/SBML/readSBML.py

@@ -13,9 +13,22 @@
 **           copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
 Created : Thu May 13 10:19:00 2016(+0530)
 Version
-Last-Updated: Mon Sep 21 12:50:00 2020(+0530)
+Last-Updated: Tue Apr 5 17:10:00 2022(+0530)
           By:HarshaRani
 **********************************************************************/
+2022:
+Apr 05: - edge case NN_mapk15.g, extra Neutral path '/kinetics' exist which
+          was not created in xml file which was causing ex12.0* example break
+          This is fixed in writeSBML by adding basepath in compartment Annotation
+          And same is create in ReadSBML
+
+Mar 22: - function connection are done after Enzyme and Reaction are created
+          this is because cplx path is modified after Enzyme created, which
+          would be a problem as path changes
+        - edge case like pool is parent and product to enzyme, Stoichiometry
+          need to reduce (eg osc_different_vols)
+        - function expression fixed if multiple of same pool exist
+
 2020:
 Sep 21: - Complex pool which is created at species level is copied under enzyme,
           ensuring the value set at species is retained.
@@ -156,7 +169,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
 
                     mapParameter(model, globparameterIdValue)
                     msgCmpt = ""
-                    errorFlag,msgCmpt = createCompartment(
+                    errorFlag,msgCmpt,baseId = createCompartment(
                         baseId, model, comptSbmlidMooseIdMap)
 
                     groupInfo = checkGroup(baseId,model,comptSbmlidMooseIdMap)
@@ -165,15 +178,18 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
                         specInfoMap = {}
                         errorFlag,warning = createSpecies(
                             baseId, model, comptSbmlidMooseIdMap, specInfoMap, modelAnnotaInfo,groupInfo)
+
                         if errorFlag:
-                            msgRule = createRules(
-                                 model, specInfoMap, globparameterIdValue)
+                            errorFlag, msgReac = createReaction(
+                                model, specInfoMap, modelAnnotaInfo, globparameterIdValue,funcDef,groupInfo)
+                            if len(moose.wildcardFind(moose.element(loadpath).path+"/##[ISA=Reac],/##[ISA=EnzBase]")) == 0:
+                                errorFlag = False
+                                noRE = ("Atleast one reaction should be present to display in the widget ")
+
                             if errorFlag:
-                                errorFlag, msgReac = createReaction(
-                                    model, specInfoMap, modelAnnotaInfo, globparameterIdValue,funcDef,groupInfo)
-                                if len(moose.wildcardFind(moose.element(loadpath).path+"/##[ISA=Reac],/##[ISA=EnzBase]")) == 0:
-                                    errorFlag = False
-                                    noRE = ("Atleast one reaction should be present to display in the widget ")
+                                msgRule = createRules(
+                                 model, specInfoMap, globparameterIdValue)
+                            
                         getModelAnnotation(model, baseId)
                     if not errorFlag:
                         # Any time in the middle if SBML does not read then I
@@ -301,7 +317,8 @@ def setupEnzymaticReaction(enz, groupName, enzName, specInfoMap, modelAnnotaInfo
         complx1 = moose.copy(complx,enzyme_.path)
     else:
         complx1 = moose.element(enzyme_.path+'/'+complx.name)
-    specInfoMap[cplx]["Mpath"] = complx1
+    specInfoMap[cplx]["Mpath"] = moose.element(complx1)
+
     moose.connect(enzyme_, "cplx", complx1, "reac")
     moose.connect(enzyme_, "enz", enzParent, "reac")
     sublist = (modelAnnotaInfo[groupName]["substrate"])
@@ -321,7 +338,14 @@ def setupEnzymaticReaction(enz, groupName, enzName, specInfoMap, modelAnnotaInfo
     for tr in range(0,enz.getNumProducts()):
         sp = enz.getProduct(tr)
         spspieces = sp.getSpecies()
-        enz_prdlist[spspieces] = int(sp.getStoichiometry())
+        spspieces = sp.getSpecies()
+        # one of the edge (osc_different_vols) case where pool is a enzyme's parent and 
+        # product, which case the stoichiometry = 2 which is ideally correct for SBML simulator
+        # but for moose we need to reduce stoichiometry as we connect enzyme parent
+        if enzPool == spspieces and int(sp.getStoichiometry()) >1:
+            enz_prdlist[spspieces] = int(sp.getStoichiometry())-1
+        else:
+            enz_prdlist[spspieces] = int(sp.getStoichiometry())
 
     for si in range(0, len(sublist)):
         sl = sublist[si]
@@ -493,6 +517,8 @@ def getCmptAnnotation(obj):
                         annotateMap[nodeName] = nodeValue
                     if nodeName == "surround":
                         annotateMap[nodeName] = nodeValue
+                    if nodeName == "basePath":
+                        annotateMap[nodeName] = nodeValue
     return annotateMap
 
 def getObjAnnotation(obj, modelAnnotationInfo):
@@ -1144,7 +1170,8 @@ def createRules(model, specInfoMap, globparameterIdValue):
                                             comptvolume.append(poolsCompt.name)
                                     numVars = funcId.numVars
                                     x = funcId.path + '/x[' + str(numVars) + ']'
-                                    speFunXterm[i] = 'x' + str(numVars)
+                                    #speFunXterm[i] = 'x' + str(numVars)
+                                    speFunXterm['x'+str(numVars)] = i
                                     moose.connect(specMapList, 'nOut', x, 'input')
                                     funcId.numVars = numVars + 1
 
@@ -1157,7 +1184,10 @@ def createRules(model, specInfoMap, globparameterIdValue):
                             for mem in ruleMemlist:
                                 if (mem in specInfoMap):
                                     #exp1 = exp.replace(mem, str(speFunXterm[mem]))
-                                    exp1 = re.sub(r'\b%s\b'% (mem), speFunXterm[mem], exp)
+                                    #exp1 = re.sub(r'\b%s\b'% (mem), speFunXterm[mem], exp)
+                                    exp1 = re.sub(r'\b%s\b'% (mem), list(speFunXterm.keys())[list(speFunXterm.values()).index(mem)], exp,1)
+                                    speFunXterm.pop(list(speFunXterm.keys())[list(speFunXterm.values()).index(mem)])
+                                    
                                     exp = exp1
                                 elif(mem in globparameterIdValue):
                                     #exp1 = exp.replace(mem, str(globparameterIdValue[mem]))
@@ -1427,6 +1457,7 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
         return False, "Model has no compartment, atleast one compartment should exist to display in the widget"
     else:
         endo_surr = {}
+        toRewritebasepath = True
         for c in range(0, model.getNumCompartments()):
             compt = model.getCompartment(c)
             # print("Compartment " + str(c) + ": "+ UnitDefinition.printUnits(compt.getDerivedUnitDefinition()))
@@ -1461,6 +1492,18 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
                 name = sbmlCmptId
             cmptAnnotaInfo = {}
             cmptAnnotaInfo = getCmptAnnotation(compt)
+            if "basePath" in cmptAnnotaInfo.keys():
+                nl = list(filter(None, (cmptAnnotaInfo["basePath"]).split('/')))
+                pathAnno = ""
+                if len(nl) > 0:
+                    for i in range(0,len(nl)):
+                        pathAnno = pathAnno+'/'+nl[i]
+                        if not moose.exists(basePath.path+pathAnno):
+                            rewritebasepath = moose.Neutral(basePath.path+pathAnno)
+                if toRewritebasepath:
+                    basePath = rewritebasepath
+                    toRewritebasepath = False
+                
             if "Mesh" in cmptAnnotaInfo.keys():
                 if cmptAnnotaInfo["Mesh"] == "CubeMesh" or cmptAnnotaInfo["Mesh"] == "NeuroMesh":
                     mooseCmptId = moose.CubeMesh(basePath.path + '/' + name)
@@ -1492,7 +1535,7 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
             elif key in comptSbmlidMooseIdMap:
                 del(comptSbmlidMooseIdMap[key])
                 return False," EndoMesh's surrounding compartment missing or wrong deleting the compartment check the file"
-    return True,""
+    return True,"",basePath
 
 def setupConcChannel(reac, rName, specInfoMap, reactSBMLIdMooseId,
                           modelAnnotaInfo, model, globparameterIdValue):

python/moose/SBML/writeSBML.py

@@ -13,10 +13,12 @@
 **           copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
 Created : Friday May 27 12:19:00 2016(+0530)
 Version
-Last-Updated: Tue 08 Sep 02:22:10 2020(+0530)
+Last-Updated: Tue 05 Apr 11:22:10 2022(+0530)
           By: HarshaRani
 **********************************************************************/
 /****************************
+2022
+Apr 5 : Added basepath in compartment Annotation
 2021
 Apr 16: replace ReacBase to Reac and EnzBase to Enz as API can has changed
 2020
@@ -541,7 +543,6 @@ def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
                             enzAnno2 = enzAnno2 +"<moose:enzyme>" + \
                                 (str(idBeginWith(convertSpecialChar(
                                 nameList_[i])))) + "</moose:enzyme>\n"
-
                         enzPrd = enz.neighbors["prd"]
                         noofPrd = len(enzPrd)
                         if not enzPrd:
@@ -1242,6 +1243,12 @@ def writeCompt(modelpath, cremodel_):
                                 str(compt.dataIndex) +
                                 "_")))
         comptID_sbml[compt] = csetId
+        nl = list(filter(None, (compt.parent.path).split('/')))
+        pathAnno = ""
+        if len(nl) > 1:
+            for i in range(1,len(nl)):
+                pathAnno = pathAnno+'/'+nl[i]
+            
         if compt.isA("EndoMesh"):
             if comptID_sbml.get(compt.surround) == None:
                 createCompt = False
@@ -1253,7 +1260,10 @@ def writeCompt(modelpath, cremodel_):
                                     "<moose:surround>" + \
                                     str(comptID_sbml[compt.surround])+ "</moose:surround>\n" + \
                                     "<moose:isMembraneBound>" + \
-                                    str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" 
+                                    str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n"
+                if pathAnno != "":
+                    comptAnno = comptAnno + "<moose:basePath>" \
+                        + pathAnno + "</moose:basePath>"
                 if moose.exists(compt.path+'/info'):
                     if moose.element(compt.path+'/info').notes != "":
                         comptAnno = comptAnno + "<moose:Notes>" \
@@ -1269,6 +1279,10 @@ def writeCompt(modelpath, cremodel_):
                                 str(compt.diffLength)+ "</moose:diffLength>\n" + \
                                 "<moose:isMembraneBound>" + \
                                 str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n"
+            if pathAnno != "":
+                    comptAnno = comptAnno + "<moose:basePath>" \
+                        + pathAnno + "</moose:basePath>"
+
             if moose.exists(compt.path+'/info'):
                 if moose.element(compt.path+'/info').notes != "":
                     comptAnno = comptAnno + "<moose:Notes>" \
@@ -1279,6 +1293,10 @@ def writeCompt(modelpath, cremodel_):
                                 str(compt.className) + "</moose:Mesh>\n" + \
                                 "<moose:isMembraneBound>" + \
                                 str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" 
+            if pathAnno != "":
+                    comptAnno = comptAnno + "<moose:basePath>" \
+                        + pathAnno + "</moose:basePath>"
+
             if moose.exists(compt.path+'/info'):
                 if moose.element(compt.path+'/info').notes != "":
                     comptAnno = comptAnno + "<moose:Notes>" \