Special Char changes

BhallaLab · Aug 4, 2023 · 6b21f95 · 6b21f95
1 parent 7b699e3
commit 6b21f95
Showing 1 changed file with 15 additions and 8 deletions.
diff --git a/python/moose/SBML/readSBML.py b/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)