revisited special character section in read and write SBML files (#464)

* Special character specific to libsbml and moose

* Update pymoose.yml

clean and update

.github/workflows/pymoose.yml

@@ -20,6 +20,8 @@ jobs:
     - name: Install dependencies
       run: |
         export DEBIAN_FRONTEND=noninteractive
+        sudo -E apt clean
+        sudo -E apt update
         sudo -E apt install -y cmake libgsl-dev g++ gcc git 
         sudo -E apt install python3-tk python-tk
         sudo -E apt install -y libhdf5-dev doxygen

python/moose/SBML/readSBML.py

@@ -16,6 +16,10 @@
 Last-Updated: Tue Apr 5 17:10:00 2022(+0530)
           By:HarshaRani
 **********************************************************************/
+2023
+Aug3: SBMLread will not accept & and  < special character in the name
+      Moose will not accept '/' (bcos path kinetics/pool etc),#,&,[,],?,/,<
+      explicitly I was converting space to _space_ which is removed
 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
@@ -523,7 +527,7 @@ def getCmptAnnotation(obj):
 
 def getObjAnnotation(obj, modelAnnotationInfo):
     name = obj.getId()
-    name = name.replace(" ", "_space_")
+    #name = name.replace(" ", "_space_")
     # modelAnnotaInfo= {}
     annotateMap = {}
     if (obj.getAnnotation() is not None):
@@ -568,7 +572,7 @@ def getObjAnnotation(obj, modelAnnotationInfo):
 def getEnzAnnotation(obj, modelAnnotaInfo, rev,
                      globparameterIdValue, specInfoMap,funcDef):
     name = obj.getId()
-    name = name.replace(" ", "_space_")
+    #name = name.replace(" ", "_space_")
     # modelAnnotaInfo= {}
     annotateMap = {}
     if (obj.getAnnotation() is not None):
@@ -708,7 +712,7 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue,fun
             #     group = groups[0]
         if (reac.isSetName()):
             rName = reac.getName()
-            rName = rName.replace(" ", "_space_")
+            #rName = rName.replace(" ", "_space_")
         if not(rName):
             rName = rId
         rev = reac.getReversible()
@@ -1264,7 +1268,7 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
             #     group = groups[0]
             if spe.isSetName():
                 sName = spe.getName()
-                sName = sName.replace(" ", "_space_")
+                #sName = sName.replace(" ", "_space_")
 
             if spe.isSetCompartment():
                 comptId = spe.getCompartment()
@@ -1471,7 +1475,7 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
 
             if (compt.isSetName()):
                 name = compt.getName()
-                name = name.replace(" ", "_space")
+                #name = name.replace(" ", "_space")
 
             if (compt.isSetOutside()):
                 outside = compt.getOutside()
@@ -1613,9 +1617,12 @@ def idBeginWith(name):
 
 
 def convertSpecialChar(str1):
-    d = {"&": "_and", "<": "_lessthan_", ">": "_greaterthan_", "BEL": "&#176", "-": "_minus_", "'": "_prime_",
-         "+": "_plus_", "*": "_star_", "/": "_slash_", "(": "_bo_", ")": "_bc_",
-         "[": "_sbo_", "]": "_sbc_", " ": "_"
+    # d = {"&": "_and", "<": "_lessthan_", ">": "_greaterthan_", "BEL": "&#176", "-": "_minus_", "'": "_prime_",
+    #      "+": "_plus_", "*": "_star_", "/": "_slash_", "(": "_bo_", ")": "_bc_",
+    #      "[": "_sbo_", "]": "_sbc_", " ": "_"
+    #      }
+    d = {"BEL": "&#176" , "'": "_prime_", "/": "_slash_"   ,"[": "_sbo_", "]": "_sbc_",
+         "#"  :"_hash_" , "\"":"_quote_" , "?":"_question_" ,"\\":"_slash","&":"_and_","<":"_greater_"
          }
     for i, j in list(d.items()):
         str1 = str1.replace(i, j)

python/moose/SBML/writeSBML.py

@@ -17,6 +17,9 @@
           By: HarshaRani
 **********************************************************************/
 /****************************
+2023
+Aug 3 : revisited specialChar, like /,\,[,],#,?,prime,quotes, are not allowed in name both in moose and sbml
+        All special charater are not allowed to write in sbml id those are retained and added   
 2022
 Apr 5 : Added basepath in compartment Annotation
 2021
@@ -1074,22 +1077,28 @@ def findGroup_compt(melement):
     return melement
 
 def convertSpecialCharshot(str1):
+    #Checks  name str  for special char and convert as SBML ID doesnot allow special char
     d = { "BEL"     : "&#176", 
             "'"     : "_prime_",
             "\\"    : "_slash_",
             "/"     : "_slash_", 
             "["     : "_sbo_", 
             "]"     : "_sbc_",
-            ": "    : "_" , 
-            " "     : "_" }
+            "#"    : "_hash_" , 
+            "\""     : "_quote_" ,
+            "?":"_question_",
+            "&":"_and_",
+            "<":"_greater_"
+         }
     for i, j in d.items():
         str1 = str1.replace(i, j)
     return str1
 
 def convertSpecialChar(str1):
+    # Checks  Id str  for special char and convert as SBML ID doesnot allow special char 
     d = {"&": "_and", "<": "_lessthan_", ">": "_greaterthan_", "BEL": "&#176", "-": "_minus_", "'": "_prime_",
          "+": "_plus_", "*": "_star_", "/": "_slash_", "(": "_bo_", ")": "_bc_",
-         "[": "_sbo_", "]": "_sbc_", ".": "_dot_", " ": "_"
+         "[": "_sbo_", "]": "_sbc_", ".": "_dot_", " ": "_", "#" : "_hash_", "?": "_question_"
          }
     for i, j in d.items():
         str1 = str1.replace(i, j)
@@ -1106,7 +1115,6 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
             sName = convertSpecialChar(spe.name)
             comptVec = findCompartment(spe)
             speciannoexist = False
-
             if not comptVec.isA("ChemCompt"):
                 return -2
             else:

python/moose/chemMerge/merge.py

@@ -378,22 +378,22 @@ def deleteSolver(modelRoot):
             st_ksolve = st.ksolve
             moose.delete(st)
             if moose.exists((st_ksolve).path):
-                moose.delete(st_ksolve)
+                moose.delete(moose.element(st_ksolve))
 
 def poolMerge(comptS,comptD,poolNotcopiedyet):
     #Here from source file all the groups are check if exist, if doesn't exist then create those groups
     #Then for that group pools are copied
     SCmptGrp = moose.wildcardFind(comptS.path+'/#[TYPE=Neutral]')
-    SCmptGrp = SCmptGrp +(moose.element(comptS.path),)
+    SCmptGrp.append(moose.element(comptS.path))
 
     DCmptGrp = moose.wildcardFind(comptD.path+'/#[TYPE=Neutral]')
-    DCmptGrp = DCmptGrp +(moose.element(comptD.path),)
+    DCmptGrp.append(moose.element(comptD.path))
 
     objS = moose.element(comptS.path).parent.name
     objD = moose.element(comptD.path).parent.name
 
     for spath in SCmptGrp:
-        grp_cmpt = ((spath.path).replace(objS,objD)).replace('[0]','')
+        grp_cmpt = ((spath.path).replace(objS,objD,1)).replace('[0]','')
         if moose.exists(grp_cmpt):
             #If path exist, but its not the Neutral obj then creating a neutral obj with _grp
             #It has happened that pool, reac, enz name might exist with the same name, which when tried to create a group
@@ -408,10 +408,10 @@ def poolMerge(comptS,comptD,poolNotcopiedyet):
             #Neutral obj from src if doesn't exist in destination,then create src's Neutral obj in des
             src = spath
             srcpath = (spath.parent).path
-            des = srcpath.replace(objS,objD)
-            moose.Neutral(moose.element(des).path+'/'+spath.name)
-
-        dpath = moose.element(spath.path.replace(objS,objD))
+            des = srcpath.replace(objS,objD,1)
+            despath = moose.element(des).path
+            tt = moose.Neutral(moose.element(des).path+'/'+spath.name)
+        dpath = moose.element(spath.path.replace(objS,objD,1))
         spoollist = moose.wildcardFind(spath.path+'/#[ISA=PoolBase]')
         dpoollist = moose.wildcardFind(dpath.path+'/#[ISA=PoolBase]')
         #check made, for a given Neutral or group if pool doesn't exist then copied
@@ -578,12 +578,13 @@ def reacMerge(comptS,comptD,key,poolListina):
             # And assuming that pools are copied earlier EXPECT POOL CPLX
             # To be assured the it takes correct compartment name incase reaction sub's
             # belongs to different compt
-            key = findCompartment(rs).name
+            #key = findCompartment(rs).name
+            key = moose.element(rs.parent).name
             if rSsubname and rSprdname:
                 allexists =  checkexist(rSsubname,objS,objD)
                 allexistp =  checkexist(rSprdname,objS,objD)
                 if allexists and allexistp:
-                    rdpath = rs.parent.path.replace(objS,objD)
+                    rdpath = rs.parent.path.replace(objS,objD,1)
                     reac = moose.copy(rs,moose.element(rdpath))
                     connectObj(reac,rSsubname,"sub",comptD,war_msg)
                     connectObj(reac,rSprdname,"prd",comptD,war_msg)
@@ -703,7 +704,7 @@ def checkexist(spList,objB,objA):
     allexist = False
     for rsp in spList:
         found = False
-        rspPath = rsp.path.replace(objB,objA)
+        rspPath = rsp.path.replace(objB,objA,0)
         if moose.exists(rspPath):
             found = True
         allexistL.append(found)