Revised version of RDF generation: it follows Dylan Stark's vocabulary

(as suggested on http://www.cct.lsu.edu/~dstark/cctk/0.1/) as much as possible
and produces valid RDF/XML documents which can be queried with SPARQL.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusUtils/Formaline/trunk@92 83718e91-0e4f-0410-abf4-91180603181f

1 files changed, 330 insertions, 78 deletions

diff --git a/src/rdf.cc b/src/rdf.cc
index 3335adc..82cda95 100644
--- a/src/rdf.cc
+++ b/src/rdf.cc
@@ -18,6 +18,8 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
+#include "cctk_Version.h"
+#include "util_String.h"
 #include "util_Network.h"
 
 #include "rdf.hh"
@@ -30,48 +32,292 @@ namespace Formaline
 {
 
   using namespace std;
-  
-  
+
 
   static bool
   is_clean_for_shell (char const * str);
-  
+
+#if 0
   static list<string>
   parse (char const * const key, string& node);
+#endif
+
 
-  
-  
   rdf::
   rdf (char const * const id,
        enum state const st)
     : storage (st)
   {
+    //
+    // This code was copied over from function Formaline_AnnounceInitial()
+    // in announce.cc and modified here to create a valid RDF/XML (rather then
+    // an unstructured plain XML document).
+    //
+    DECLARE_CCTK_PARAMETERS;
+
+    if (verbose) CCTK_INFO ("Announcing initial RDF metadata information");
+
+    //
+    // RDF/XML document header with some namespace definitions
+    //
     msgbuf
 << "<?xml version=\"1.0\" encoding=\"utf-8\"?>" << endl
 << "<!DOCTYPE owl [" << endl
-// << "  <!ENTITY dc 'http://purl.org/dc/elements/1.1/'>" << endl
-// << "  <!ENTITY doap 'http://usefulinc.com/ns/doap#'>" << endl
-// << "  <!ENTITY foaf 'http://xmlns.com/foaf/0.1/'>" << endl
-<< "  <!ENTITY rdf 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>" << endl
-<< "  <!ENTITY xsd 'http://www.w3.org/2001/XMLSchema#'>" << endl
-// << "  <!ENTITY rdfs 'http://www.w3.org/2000/01/rdf-schema#'>" << endl
-<< "" << endl
-// << "  <!ENTITY cctk 'http://www.cct.lsu.edu/~dstark/cctk/0.1/'>" << endl
-<< "  <!ENTITY form 'http://www.aei.mpg.de/form#'>" << endl
+// << "\t<!ENTITY dc   'http://purl.org/dc/elements/1.1/'>" << endl
+// << "\t<!ENTITY doap 'http://usefulinc.com/ns/doap#'>" << endl
+// << "\t<!ENTITY foaf 'http://xmlns.com/foaf/0.1/'>" << endl
+<< "\t<!ENTITY rdf  'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>" << endl
+<< "\t<!ENTITY xsd  'http://www.w3.org/2001/XMLSchema#'>" << endl
+// << "\t<!ENTITY rdfs 'http://www.w3.org/2000/01/rdf-schema#'>" << endl
+<< "\t<!ENTITY cctk 'http://www.cct.lsu.edu/~dstark/cctk/0.1/'>" << endl
+// << "\t<!ENTITY form 'http://www.aei.mpg.de/form#'>" << endl
 << "]>" << endl
-<< "<rdf:RDF" << endl
-// << "    xmlns:dc=\"&dc;\"" << endl
-// << "    xmlns:doap=\"&doap;\"" << endl
-// << "    xmlns:foaf=\"&foaf;\"" << endl
-<< "    xmlns:rdf=\"&rdf;\"" << endl
-<< "    xmlns:xsd=\"&xsd;\"" << endl
-// << "    xmlns:rdfs=\"&rdfs;\"" << endl
-// << "    xmlns:cctk=\"&cctk;\"" << endl
-<< "    xmlns:form=\"&form;\"" << endl
-<< ">" << endl
-<< endl
-<< "<form:Simulation>" << endl
-<< "  <form:jobid>" << clean (string (id)) << "</form:jobid>" << endl;
+<< "<rdf:RDF xmlns:rdf=\"&rdf;\""
+<< endl << "\txmlns:xsd=\"&xsd;\""
+// << endl << "\txmlns:dc=\"&dc;\""
+// << endl << "\txmlns:doap=\"&doap;\""
+// << endl << "\txmlns:foaf=\"&foaf;\""
+// << endl << "\txmlns:rdfs=\"&rdfs;\""
+<< endl << "\txmlns:cctk=\"&cctk;\""
+// << endl << "\txmlns:form=\"&form;\""
+<< endl << ">" << endl << endl;
+
+    //
+    // general metadata with inlined attribute values
+    //
+    const string jobID = clean (string (id));
+    char hostbuf[512] = "";
+    Util_GetHostName (hostbuf, sizeof (hostbuf));
+    const string host = clean (hostbuf);
+    const cGH* const cctkGH = NULL;
+    const int nprocs = CCTK_nProcs (cctkGH);
+#if 0
+    const string user = clean (CCTK_RunUser());
+#else
+    const string user = clean (getenv ("USER"));
+#endif
+    char** argv;
+    CCTK_CommandLine (&argv);
+    const string executable = clean (argv[0]);
+    char parfilebuf[512] = "";
+    CCTK_ParameterFilename (sizeof (parfilebuf), parfilebuf);
+    const string parfile = clean (parfilebuf);
+    const string version = clean (CCTK_FullVersion ());
+    ostringstream compiled_at_buf;
+    compiled_at_buf << CCTK_CompileDate () << " " << CCTK_CompileTime ();
+    const string compiled_at (clean (compiled_at_buf.str()));
+    char rundatebuf[32] = "";
+    char runtimebuf[32] = "";
+    Util_CurrentDate (sizeof (rundatebuf), rundatebuf);
+    Util_CurrentTime (sizeof (runtimebuf), runtimebuf);
+    ostringstream started_at_buf;
+    started_at_buf << rundatebuf << " " << runtimebuf;
+    const string started_at (clean (started_at_buf.str()));
+    char cwdbuf[512];
+    getcwd (cwdbuf, sizeof (cwdbuf));
+    const string cwd (clean (cwdbuf));
+
+
+    msgbuf
+<< "<cctk:Simulation rdf:about=\"#" << jobID << "\">" << endl
+<< "\t<cctk:simulationID>"  << jobID       << "</cctk:simulationID>" << endl
+<< "\t<cctk:host>"          << host        << "</cctk:host>" << endl
+<< "\t<cctk:nProcs>"        << nprocs      << "</cctk:nProcs>" << endl
+<< "\t<cctk:user>"          << user        << "</cctk:user>" << endl
+<< "\t<cctk:executable>"    << executable  << "</cctk:executable>" << endl
+<< "\t<cctk:parameterFile>" << parfile     << "</cctk:parameterFile>" << endl
+<< "\t<cctk:hasVersion>"    << version     << "</cctk:hasVersion>" << endl
+<< "\t<cctk:compiledAt>"    << compiled_at << "</cctk:compiledAt>" << endl
+<< "\t<cctk:startedAt>"     << started_at  << "</cctk:startedAt>" << endl
+<< "\t<cctk:cwd>"           << cwd         << "</cctk:cwd>" << endl
+<< "</cctk:Simulation>" << endl << endl;
+
+
+    //
+    // metadata as references to other nodes
+    //
+    msgbuf << "<cctk:Simulation rdf:about=\"#" << jobID << "\">" << endl
+           << "\t<cctk:hasThornList rdf:resource=\"#ThornList\"/>" << endl
+           << "\t<cctk:hasParameterFile rdf:resource=\"#ParameterFile\"/>" << endl
+           << "</cctk:Simulation>" << endl << endl;
+
+    // store thorn list
+    msgbuf << "<cctk:ThornList rdf:about=\"#ThornList\">" << endl;
+    const int numthorns = CCTK_NumCompiledThorns ();
+    for (int thorn = 0; thorn < numthorns; ++ thorn) {
+      const char* const thornname = CCTK_CompiledThorn (thorn);
+
+      msgbuf << "\t<cctk:containsThorn rdf:resource=\"#Thorns/"
+             << thornname << "\"/>" << endl;
+    }
+    msgbuf << "</cctk:ThornList>" << endl << endl;
+
+    // store parameter file contents
+    msgbuf << "<cctk:ParameterFile rdf:about=\"#ParameterFile\">" << endl
+           << "\t<rdf:value>";
+    ifstream file (parfile.c_str());
+    char c;
+    ostringstream filebuf;
+    while (filebuf and file.get (c)) filebuf.put (c);
+    file.close();
+    msgbuf << clean (filebuf.str());
+    filebuf.clear();
+    msgbuf << "</rdf:value>" << endl
+           << "</cctk:ParameterFile>" << endl << endl;
+
+    // store all parameters which have been set in the parfile
+    msgbuf
+<< "<!-- ============================================================ -->" << endl
+<< "<!-- thorn graphs with their parameters                           -->" << endl
+<< "<!-- ============================================================ -->" << endl;
+    ostringstream parambuf;
+    parambuf
+<< "<!-- ============================================================ -->" << endl
+<< "<!-- list of parameters and their values                          -->" << endl
+<< "<!-- ============================================================ -->" << endl;
+
+    for (int thorn = 0; thorn < numthorns; ++ thorn) {
+      const char* const thornname = CCTK_CompiledThorn (thorn);
+
+      msgbuf << "<cctk:Thorn rdf:about=\"#Thorns/"
+             << thornname << "\">" << endl;
+      msgbuf << "\t<cctk:hasName>" << thornname << "</cctk:hasName>" << endl;
+
+      // skip parameters that belong to inactive thorns
+      const bool is_active = CCTK_IsThornActive (thornname);
+      msgbuf << "\t<cctk:isActive>" << (is_active ? "true" : "false")
+             << "</cctk:isActive>" << endl;
+
+      // loop over all parameters of this thorn (if it is active)
+      if (is_active) {
+        for (int first = 1; ; first = 0) {
+          char* fullname = NULL;
+          const cParamData* pdata = NULL;
+
+          // get the first/next parameter
+          const int ierr = CCTK_ParameterWalk (first, thornname,&fullname,&pdata);
+          assert (ierr >= 0);
+          if (ierr > 0) break;
+
+          msgbuf << "\t<cctk:hasParameter rdf:resource=\"#Parameters/"
+                 << pdata->thorn << "/" << pdata->name << "\"/>" << endl;
+
+          // get its value
+          const void* const pvalue
+            = CCTK_ParameterGet (pdata->name, pdata->thorn, NULL);
+          assert (pvalue);
+
+          switch (pdata->type) {
+            case PARAMETER_BOOLEAN:
+            {
+//            CCTK_INT default_value;
+//            const int ierr = CCTK_SetBoolean (&default_value, pdata->defval);
+//            assert (! ierr);
+              const CCTK_INT value = * static_cast<const CCTK_INT*> (pvalue);
+//            if (pdata->n_set > 0 or value != default_value) {
+                parambuf << "<cctk:BooleanParameter rdf:about=\"#Parameters/"
+                         << pdata->thorn << "/" << pdata->name << "\">" << endl
+                         << "\t<cctk:hasName>" << fullname
+                         << "</cctk:hasName>" << endl
+                         << "\t<cctk:hasValue>" << (value ? "true" : "false")
+                         << "</cctk:hasValue>" << endl
+                         << "</cctk:BooleanParameter>" << endl;
+              }
+//          }
+            break;
+
+            case PARAMETER_INT:
+            {
+//            const CCTK_INT default_value = strtol (pdata->defval, 0, 0);
+              const CCTK_INT value = *static_cast<const CCTK_INT*> (pvalue);
+//            if (pdata->n_set > 0 or value != default_value) {
+                parambuf << "<cctk:IntegerParameter rdf:about=\"#Parameters/"
+                         << pdata->thorn << "/" << pdata->name << "\">" << endl
+                         << "\t<cctk:hasName>" << fullname
+                         << "</cctk:hasName>" << endl
+                         << "\t<cctk:hasValue>" << value
+                         << "</cctk:hasValue>" << endl
+                         << "</cctk:IntegerParameter>" << endl;
+//            }
+            }
+            break;
+
+            case PARAMETER_REAL:
+            {
+//            char* const default_string = strdup (pdata->defval);
+//            assert (default_string);
+              // Convert "d" and "D" to "e" and "E", because this is what
+              // strtod() expects
+//            for (char* p = default_string; *p; ++p) {
+//              switch (*p) {
+//                case 'd': *p = 'e'; break;
+//                case 'D': *p = 'E'; break;
+//              }
+//            }
+//            CCTK_REAL const default_value = strtod (default_string, 0);
+//            free (default_string);
+              CCTK_REAL const value = *static_cast<CCTK_REAL const *> (pvalue);
+//              if (pdata->n_set > 0 or value != default_value) {
+                parambuf << "<cctk:RealParameter rdf:about=\"#Parameters/"
+                         << pdata->thorn << "/" << pdata->name << "\">" << endl
+                         << "\t<cctk:hasName>" << fullname
+                         << "</cctk:hasName>" << endl
+                         << "\t<cctk:hasValue>" << value
+                         << "</cctk:hasValue>" << endl
+                         << "</cctk:RealParameter>" << endl;
+//            }
+            }
+            break;
+
+            case PARAMETER_KEYWORD:
+            {
+              const char* const value = *static_cast<const char*const*>(pvalue);
+//            if (pdata->n_set > 0 or Util_StrCmpi (pdata->defval, value)) {
+                parambuf << "<cctk:KeywordParameter rdf:about=\"#Parameters/"
+                         << pdata->thorn << "/" << pdata->name << "\">" << endl
+                         << "\t<cctk:hasName>" << fullname
+                         << "</cctk:hasName>" << endl
+                         << "\t<cctk:hasValue>" << clean (value)
+                         << "</cctk:hasValue>" << endl
+                         << "</cctk:KeywordParameter>" << endl;
+//            }
+            }
+            break;
+
+            case PARAMETER_STRING:
+            {
+              const char* const value = *static_cast<const char*const*>(pvalue);
+//            if (pdata->n_set > 0 or strcmp (pdata->defval, value)) {
+                parambuf << "<cctk:StringParameter rdf:about=\"#Parameters/"
+                         << pdata->thorn << "/" << pdata->name << "\">" << endl
+                         << "\t<cctk:hasName>" << fullname
+                         << "</cctk:hasName>" << endl
+                         << "\t<cctk:hasValue>" << clean (value)
+                         << "</cctk:hasValue>" << endl
+                         << "</cctk:StringParameter>" << endl;
+//            }
+            }
+            break;
+
+            default: assert (0 and "invalid parameter type");
+
+          } // switch (pdata->type)
+
+          free (fullname);
+        } // loop over all parameters of this thorn
+      } // if (is_active)
+
+      msgbuf << "</cctk:Thorn>" << endl;
+
+    } // loop over all thorns
+
+    // FIXME: is there some better method for concatenation ??
+    msgbuf << endl << parambuf.str();
+
+    //
+    // close the RDF/XML document
+    //
+    msgbuf << endl << "</rdf:RDF>" << endl;
   }
 
 
@@ -80,19 +326,15 @@ namespace Formaline
   ~ rdf ()
   {
     DECLARE_CCTK_PARAMETERS;
-    
+
     string const socket_script = "socket-client.pl";
     string const socket_data = "socket-data";
-    
-    
-    
+
+
+
     // Write the data
-    msgbuf
-<< "</form:Simulation>" << endl
-<< endl
-<< "</rdf:RDF>" << endl;
     string const msgstr = msgbuf.str();
-    
+
     ostringstream databuf;
     databuf << "POST HTTP/1.0 200\r\n"
             << "Content-Type: text/xml\r\n"
@@ -102,19 +344,19 @@ namespace Formaline
             << "\r\n"
             << "\r\n";
     string const datastr = databuf.str();
-    
+
     ostringstream datafilenamebuf;
     datafilenamebuf << out_dir << "/" << socket_data;
     string const datafilenamestr = datafilenamebuf.str();
     char const * const datafilename = datafilenamestr.c_str();
-    
+
     ofstream datafile;
     datafile.open (datafilename, ios::out);
     datafile << datastr;
     datafile.close ();
-    
-    
-    
+
+
+
     // Write the script
     ostringstream scriptbuf;
     scriptbuf
@@ -178,19 +420,19 @@ namespace Formaline
 << "}" << endl
 << endl;
     string const scriptstr = scriptbuf.str();
-    
+
     ostringstream scriptfilenamebuf;
     scriptfilenamebuf << out_dir << "/" << socket_script;
     string const scriptfilenamestr = scriptfilenamebuf.str();
     char const * const scriptfilename = scriptfilenamestr.c_str();
-    
+
     ofstream scriptfile;
     scriptfile.open (scriptfilename, ios::out);
     scriptfile << scriptstr;
     scriptfile.close ();
-    
-    
-    
+
+
+
     // Check that the file name is sane
     if (! is_clean_for_shell (scriptfilename))
     {
@@ -202,9 +444,9 @@ namespace Formaline
         return;
       }
     }
-    
-    
-    
+
+
+
     // Make the script executable
     ostringstream chmodbuf;
     chmodbuf << "chmod a+x " << scriptfilenamestr
@@ -212,9 +454,9 @@ namespace Formaline
     string const chmodstr = chmodbuf.str();
     char const * const chmod = chmodstr.c_str();
     system (chmod);
-    
-    
-    
+
+
+
     bool my_use_relay_host = use_relay_host;
     char const * my_relay_host = 0;
     if (my_use_relay_host)
@@ -250,7 +492,7 @@ namespace Formaline
           // Don't know a good relay host; try without
           my_use_relay_host = false;
         }
-        
+
         if (verbose)
         {
           if (my_use_relay_host)
@@ -265,7 +507,7 @@ namespace Formaline
         }
       }
     }
-    
+
     if (my_use_relay_host)
     {
       // Check that the relay host name is sane
@@ -280,9 +522,9 @@ namespace Formaline
         }
       }
     }
-    
-    
-    
+
+
+
     char cwd[10000];
     if (my_use_relay_host)
     {
@@ -297,7 +539,7 @@ namespace Formaline
           return;
         }
       }
-      
+
       // Check that the current directory name is sane
       if (! is_clean_for_shell (cwd))
       {
@@ -314,9 +556,9 @@ namespace Formaline
     {
       cwd[0] = '\0';
     }
-    
-    
-    
+
+
+
     // Send the data
     ostringstream cmdbuf;
     if (my_use_relay_host)
@@ -331,7 +573,7 @@ namespace Formaline
     }
     string const cmdstr = cmdbuf.str();
     char const * const cmd = cmdstr.c_str();
-    
+
     int const ierr = system (cmd);
     if (ierr != 0)
     {
@@ -342,20 +584,20 @@ namespace Formaline
         CCTK_WARN (1, "Failed to send data to the rdf");
       }
     }
-    
-    remove (datafilename);
+
+//    remove (datafilename);
     remove (scriptfilename);
   }
 
 
-
   void rdf::
   store (char const * const key,
          bool const value)
   {
+#if 0
     ostringstream valuebuf;
     valuebuf << (value ? "true" : "false");
-    
+
     string node;
     list<string> const keys = parse (key, node);
     string indent_string (NUM_INDENT_SPACES, ' ');
@@ -378,6 +620,7 @@ namespace Formaline
       msgbuf << indent_string << "</form:" << * lsi << ">" << endl;
     }
     msgbuf << endl;
+#endif
   }
 
 
@@ -386,9 +629,10 @@ namespace Formaline
   store (char const * const key,
          CCTK_INT const value)
   {
+#if 0
     ostringstream valuebuf;
     valuebuf << value;
-    
+
     string node;
     list<string> const keys = parse (key, node);
     string indent_string (NUM_INDENT_SPACES, ' ');
@@ -411,6 +655,7 @@ namespace Formaline
       msgbuf << indent_string << "</form:" << * lsi << ">" << endl;
     }
     msgbuf << endl;
+#endif
   }
 
 
@@ -419,10 +664,11 @@ namespace Formaline
   store (char const * const key,
          CCTK_REAL const value)
   {
+#if 0
     int const prec = numeric_limits<CCTK_REAL>::digits10;
     ostringstream valuebuf;
     valuebuf << setprecision(prec) << value;
-    
+
     string node;
     list<string> const keys = parse (key, node);
     string indent_string (NUM_INDENT_SPACES, ' ');
@@ -445,6 +691,7 @@ namespace Formaline
       msgbuf << indent_string << "</form:" << * lsi << ">" << endl;
     }
     msgbuf << endl;
+#endif
   }
 
 
@@ -453,9 +700,13 @@ namespace Formaline
   store (char const * const key,
          char const * const value)
   {
+#if 0
+    // don't store keys with empty string values
+    if (not *value) return;
+
     ostringstream valuebuf;
     valuebuf << value;
-    
+
     string node;
     list<string> const keys = parse (key, node);
     string indent_string (NUM_INDENT_SPACES, ' ');
@@ -479,6 +730,7 @@ namespace Formaline
       msgbuf << indent_string << "</form:" << * lsi << ">" << endl;
     }
     msgbuf << endl;
+#endif
   }
 
 
@@ -488,7 +740,7 @@ namespace Formaline
     const
   {
     ostringstream buf;
-  
+
     for (string::const_iterator p = txt.begin(); p != txt.end(); ++ p)
     {
       switch (* p)
@@ -498,12 +750,12 @@ namespace Formaline
       default: buf << * p;
       }
     }
-  
+
     return buf.str();
   }
 
 
-  
+
   static bool
   is_clean_for_shell (char const * const str)
   {
@@ -531,9 +783,9 @@ namespace Formaline
     }
     return true;
   }
-  
-  
-  
+
+
+#if 0
   static list<string>
   parse (char const * const key, string& node)
   {
@@ -550,7 +802,7 @@ namespace Formaline
     node = str.substr (p);
     return strs;
   }
-  
-  
-  
+#endif
+
+
 } // namespace Formaline