Some leaks still present in xml parsing library.

Samo Penic

2016-02-29 bb40336eb8a2acc9f2e3d2e9059b7d90afe5c0c4

 src/restore.c

@@ -10,6 +10,10 @@
#include "vesicle.h"
#include "vertex.h"
#include "triangle.h"
#include "bond.h"
#include "energy.h"
#include "poly.h"
#include "initial_distribution.h"

ts_bool parseDump(char *dumpfname) {
   xmlDocPtr doc;
@@ -47,10 +51,12 @@
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
                     fprintf(stderr,"Found point data\n");
                     if(vesicle!=NULL)
                        parseXMLVertexPosition(vesicle, doc, cur);
                        parseXMLVertexPosition(vesicle, doc, cur2);
                  }
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
                  fprintf(stderr,"Found cell(Bonds) data\n");
                     if(vesicle!=NULL)
                        parseXMLBonds(vesicle, doc, cur2);
                  }
                  cur2=cur2->next;
               }   
@@ -63,9 +69,18 @@
   }
   
   xmlFreeDoc(doc);

   vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);

   init_normal_vectors(vesicle->tlist);
   mean_curvature_and_energy(vesicle);

/* TODO: cells, polymeres, filaments, core, tape */

   fprintf(stderr,"Restoration completed\n");
   exit(0);
//   write_vertex_xml_file(vesicle,999);
   vesicle_free(vesicle);
   exit(0);
   return TS_SUCCESS;
}

@@ -129,6 +144,9 @@
      if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
         parseTrisurfTria(vesicle, doc, child);
      }
      if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
         parseTrisurfTriaNeigh(vesicle, doc, child);
      }
       if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
         parseTrisurfTristar(vesicle, doc, child);
      }
@@ -177,14 +195,42 @@
   char *tria;
   char *vtx[3];
   
   ts_uint i;
   ts_uint i,j;
   triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   tria=(char *)triangles;
   for(i=0;i<3;i++)   vtx[i]=strtok(tria," ");
   vtx[0]=strtok(tria," ");
   for(i=1;i<3;i++)   vtx[i]=strtok(NULL," ");
   j=0;
   while(vtx[2]!=NULL){
      triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
      for(i=0;i<3;i++)   vtx[i]=strtok(NULL," ");
      j++;
   }   
   fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);	

   xmlFree(triangles);
   return TS_SUCCESS;
}


ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *triangles;
   char *tria;
   char *ntria[3];
   ts_uint i,j;
   triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   tria=(char *)triangles;
   ntria[0]=strtok(tria," ");
   for(i=1;i<3;i++)   ntria[i]=strtok(NULL," ");
   j=0;
   while(ntria[2]!=NULL){
      triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
      triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
      triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
      j++;
      for(i=0;i<3;i++)   ntria[i]=strtok(NULL," ");
   }	
   fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);	

   xmlFree(triangles);
   return TS_SUCCESS;
@@ -230,20 +276,54 @@
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
         points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         pts=(char *)points;
         for(i=0;i<3;i++)   token[i]=strtok(pts," ");
         token[0]=strtok(pts," ");
         token[1]=strtok(NULL," ");
         token[2]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
            vesicle->vlist->vtx[idx]->x=atof(token[0]);
            vesicle->vlist->vtx[idx]->y=atof(token[1]);
            vesicle->vlist->vtx[idx]->z=atof(token[2]);
            for(i=0;i<3;i++)   token[i]=strtok(NULL," ");	
            for(i=0;i<2;i++)   token[i]=strtok(NULL," ");	
            token[2]=strtok(NULL,"\n");
            idx++;
         }
         xmlFree(points);
      }
      child=child->next;
   }
   fprintf(stderr,"Vertices position j=%d\n",idx);	

   return TS_SUCCESS;
}
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *bonds, *conname;
   char *b;
   int idx;
   char *token[2];
   while (child != NULL) {
      conname=xmlGetProp(child, (xmlChar *)"Name");
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
         bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         b=(char *)bonds;
         token[0]=strtok(b," ");
         token[1]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
            bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
            token[0]=strtok(NULL," ");	
            token[1]=strtok(NULL,"\n");	
            idx++;
         }
         xmlFree(bonds);
      }
      xmlFree(conname);
      child=child->next;
   }
   fprintf(stderr,"Bond data j=%d\n",idx);	
   return TS_SUCCESS;
}