align.cgi: Use core/json.h to create output

algo/cgi/align.cpp

@@ -6,9 +6,47 @@
 #include "../core/dynprog.h"
 #include "../core/fasta.h"
 #include "../core/lazy_msa.h"
+#include "../core/json.h"
 
 using namespace std;
 
+bool check_cgi_parameters(JsonList &result) {
+  char * requestMethod = getenv("REQUEST_METHOD");
+  if(!requestMethod) {
+    result.add("Error", "requestMethod");
+    return false;
+  } else if(strcmp(requestMethod, "POST") != 0) {
+    result.add("Error", "requestMethod =/= post");
+    return false;
+  }
+  char * contentType = getenv("CONTENT_TYPE");
+  if(!contentType) {
+    result.add("Error", "content_type");
+    return false;
+  }
+  result.add("requestMethod",requestMethod);
+  result.add("contentType", contentType);
+  return true;
+}
+
+bool create_fasta_file(JsonList &result, int fd) {
+  char temp[1024];
+  FILE *f;
+  f = fdopen(fd,"w");
+  if(f == NULL){
+    result.add("Error", "opening tempfile");
+    return false;
+  }else{
+    while(cin) {
+      cin.getline(temp, 1024);
+      fputs(temp, f);
+      fputs("\n", f);
+    }
+  }
+      
+  fclose(f);
+  return true;
+}
 
 int main(int argc, char* argv[])
 {
@@ -18,56 +56,25 @@ int main(int argc, char* argv[])
   ostream * p; 
   p=&ost;
   char filename[] = "VidjilAlignXXXXXX";
-  int fd = mkstemp(filename);
-
-  if (fd == -1) {
-    perror("Creation of temporary file");
-    exit(1);
-  }
+  JsonList result;
+  bool error = false;
 
   bool cgi_mode;
   
     if (argc <= 1){
       cgi_mode=true;
-      
-      cout <<"Content-type: text/html"<<endl<<endl;
-      cout<< "{"<<endl;
-      
-      char * requestMethod = getenv("REQUEST_METHOD");
-      cout<<"\"requestMethod\" : \""<<requestMethod<<"\""<<endl;
-      if(!requestMethod) {
-	cout<<",\"Error\": \"requestMethod\"}"<<endl;
-	return 0;
-      }
-      if(strcmp(requestMethod, "POST") != 0) {
-	cout<<",\"Error\": \"requestMethod =/= post\"}"<<endl;
-	return 0;
-      }
-      char * contentType = getenv("CONTENT_TYPE");
-      if(!contentType) {
-	cout<<",\"Error\": \"content_type\"}"<<endl;
-	return 0;
-      }
-	cout<<",\"contentType\": \""<<contentType<<"\""<<endl;
-
-      char temp[1024];
-      FILE *f;
-      f = fdopen(fd,"w");
-      if(f == NULL){
-	cout<<",\"Error\": \"save\""<<filename<<"}"<<endl;
 
-	return 0;
-      }else{
-	while(cin) {
-	  cin.getline(temp, 1024);
-	  fputs(temp, f);
-	  fputs("\n", f);
-	}
+      error = ! check_cgi_parameters(result);
+      if (! error) {
+        int fd = mkstemp(filename);
+        if (fd == -1) {
+          result.add("Error", "Temporary file");
+          error = true;
+        } else {
+          error = ! create_fasta_file(result, fd);
+          fdata = filename;
+        }
       }
-      
-      fclose(f);
-      fdata = filename;
-      
     }else{
       cgi_mode=false;
       fdata = argv[1];
@@ -87,28 +94,33 @@ int main(int argc, char* argv[])
       lm.add(seq1);
     }
     
-    string *result;
-    result =new string[lm.sizeUsed+2];
-    lm.align(result);
+    string *align_str;
+    align_str =new string[lm.sizeUsed+2];
+    lm.align(align_str);
     
-    if (cgi_mode){
-      cout<<",\"seq\" : [\""<<result[0]<<"\""<<endl;
-      for (int i=1; i<lm.sizeUsed+2; i++){
-	cout<<",\""<<result[i]<<"\""<<endl;
-      }
-      cout<<"]}";
+
+    if (cgi_mode) {
+      if (! error) {
+        JsonArray alignment;
       
+        for (int i=0; i<lm.sizeUsed+2; i++){
+          alignment.add(align_str[i]);
+        }
+        result.add("seq", alignment);
+      }
+
       remove(filename);
-      
+      cout <<"Content-type: text/html"<<endl<<endl;
+      cout << result.toString();
     }else{
       int length=60;
-      int n=result[0].size();
+      int n=align_str[0].size();
       int j=0;
       
       while (n > 0){
 	for (int i=0; i<lm.sizeUsed+2; i++){
 	  
-	  cout<<" >  "<<result[i].substr(j*length,length)<<"  <  "<<fa.label(i)<<endl;
+	  cout<<" >  "<<align_str[i].substr(j*length,length)<<"  <  "<<fa.label(i)<<endl;
 	}
 	cout<<endl;
 	n=n-length;