Changeset 873 for branches/prototype-v0/zoo-project/zoo-kernel

Timestamp:

Mar 19, 2018, 3:53:31 PM (7 years ago)

Author:

djay

Message:

Add support for R language and its documentation.

Location:

branches/prototype-v0/zoo-project/zoo-kernel

Files:

• Makefile.in (modified) (2 diffs)
• ZOOMakefile.opts.in (modified) (2 diffs)
• configure.ac (modified) (1 diff)
• service.c (modified) (1 diff)
• service_internal_r.c (added)
• service_internal_r.h (added)
• service_json.c (modified) (1 diff)
• service_json.h (modified) (1 diff)
• zoo_service_loader.c (modified) (4 diffs)

branches/prototype-v0/zoo-project/zoo-kernel/Makefile.in

@@ -78 +78 @@
         g++ ${XML2CFLAGS} ${PYTHONCFLAGS} ${CFLAGS} -c service_internal_python.c
 
+service_internal_r.o: service_internal_r.c service.h
+        g++ ${XML2CFLAGS} ${RCFLAGS} ${CFLAGS} -c service_internal_r.c
+
 service_internal_otb.o: service_internal_otb.c service_internal_otb.h service.h
         g++ ${XML2CFLAGS} ${OTBCFLAGS} ${CFLAGS} -c service_internal_otb.c
@@ -114 +117 @@
         g++ -c ${XML2CFLAGS} ${PYTHONCFLAGS} ${CFLAGS} service_loader.c
 
-zoo_service_loader.o: zoo_service_loader.c service.h version.h ${MS_FILE} ${PYTHON_FILE} ${PHP_FILE} ${JAVA_FILE} ${JS_FILE} ${PERL_FILE} ${RUBY_FILE} ${YAML_FILE} ${OTB_FILE} ${SAGA_FILE} ${MONO_FILE} ${HPC_FILES} ${METADB_FILE}
-        g++ -g -O2 ${JSON_CFLAGS} ${GDAL_CFLAGS} ${XML2CFLAGS} ${CFLAGS} ${MONO_CFLAGS} ${SAGA_CFLAGS} ${OTBCFLAGS} ${PYTHONCFLAGS} ${JAVACFLAGS} ${JSCFLAGS} ${PERLCFLAGS} ${PHPCFLAGS} ${SAGA_ENABLED} ${OTB_ENABLED} ${HPC_ENABLED} ${PYTHON_ENABLED} ${JS_ENABLED} ${PHP_ENABLED} ${PERL_ENABLED} ${JAVA_ENABLED} ${MONO_ENABLED} ${METADB_ENABLED} -c zoo_service_loader.c  -fno-common -DPIC -o zoo_service_loader.o
+zoo_service_loader.o: zoo_service_loader.c service.h version.h ${MS_FILE} ${R_FILE} ${PYTHON_FILE} ${PHP_FILE} ${JAVA_FILE} ${JS_FILE} ${PERL_FILE} ${RUBY_FILE} ${YAML_FILE} ${OTB_FILE} ${SAGA_FILE} ${MONO_FILE} ${HPC_FILES} ${METADB_FILE}
+        g++ -g -O2 ${JSON_CFLAGS} ${GDAL_CFLAGS} ${XML2CFLAGS} ${CFLAGS} ${MONO_CFLAGS} ${SAGA_CFLAGS} ${OTBCFLAGS} ${RCFLAGS} ${PYTHONCFLAGS} ${JAVACFLAGS} ${JSCFLAGS} ${PERLCFLAGS} ${PHPCFLAGS} ${SAGA_ENABLED} ${OTB_ENABLED} ${HPC_ENABLED} ${PYTHON_ENABLED} ${R_ENABLED} ${JS_ENABLED} ${PHP_ENABLED} ${PERL_ENABLED} ${JAVA_ENABLED} ${MONO_ENABLED} ${METADB_ENABLED} -c zoo_service_loader.c  -fno-common -DPIC -o zoo_service_loader.o
 
 libzoo_service.${EXT}: version.h service_internal.o service.o sqlapi.o
         gcc -shared  ${GDAL_CFLAGS} ${DEFAULT_OPTS} -fpic -o libzoo_service.${EXT} ${CFLAGS}  service_internal.o service.o sqlapi.o ${FCGI_LDFLAGS} ${GDAL_LIBS} ${ZOO_LDFLAGS}
 
-zoo_loader.cgi: version.h libzoo_service.${EXT} zoo_loader.c zoo_service_loader.o  ulinet.o service.h lex.sr.o service_conf.tab.o service_conf.y ulinet.o main_conf_read.tab.o lex.cr.o request_parser.o response_print.o server_internal.o caching.o ${MS_FILE} ${PYTHON_FILE} ${PHP_FILE} ${JAVA_FILE} ${JS_FILE} ${PERL_FILE} ${RUBY_FILE} ${YAML_FILE} ${OTB_FILE} ${SAGA_FILE} ${HPC_FILES} ${METADB_FILE} ${JSON_FILE} service_callback.o
+zoo_loader.cgi: version.h libzoo_service.${EXT} zoo_loader.c zoo_service_loader.o  ulinet.o service.h lex.sr.o service_conf.tab.o service_conf.y ulinet.o main_conf_read.tab.o lex.cr.o request_parser.o response_print.o server_internal.o caching.o ${MS_FILE} ${PYTHON_FILE} ${PHP_FILE} ${JAVA_FILE} ${JS_FILE} ${PERL_FILE} ${RUBY_FILE} ${YAML_FILE} ${OTB_FILE} ${R_FILE} ${SAGA_FILE} ${HPC_FILES} ${METADB_FILE} ${JSON_FILE} service_callback.o
         g++ -g -O2 ${JSON_CFLAGS} ${JSCFLAGS} ${PHPCFLAGS}  ${PERLCFLAGS} ${RUBYCFLAGS}  ${JAVACFLAGS} ${XML2CFLAGS} ${PYTHONCFLAGS} ${CFLAGS} -c zoo_loader.c  -fno-common -DPIC -o zoo_loader.o
-        g++  ${JSON_CFLAGS} ${JSCFLAGS} ${SAGA_CFLAGS} ${OTBCFLAGS} ${GDAL_CFLAGS} ${XML2CFLAGS} ${PHPCFLAGS} ${PERLCFLAGS} ${JAVACFLAGS} ${PYTHONCFLAGS} ${CFLAGS} zoo_loader.o zoo_service_loader.o ${MS_FILE} ${PYTHON_FILE}  ${PERL_FILE} ${PHP_FILE}  ${JS_FILE} ${JAVA_FILE} ${YAML_FILE} ${OTB_FILE} ${SAGA_FILE} ${MONO_FILE} ${HPC_FILES} ${METADB_FILE} ${JSON_FILE} service_callback.o response_print.o server_internal.o caching.o request_parser.o ulinet.o lex.cr.o lex.sr.o service_conf.tab.o main_conf_read.tab.o -o zoo_loader.cgi -L. ${LDFLAGS}
+        g++  ${JSON_CFLAGS} ${JSCFLAGS} ${SAGA_CFLAGS} ${OTBCFLAGS} ${GDAL_CFLAGS} ${XML2CFLAGS} ${PHPCFLAGS} ${PERLCFLAGS} ${JAVACFLAGS} ${PYTHONCFLAGS} ${CFLAGS} zoo_loader.o zoo_service_loader.o ${MS_FILE} ${PYTHON_FILE}  ${PERL_FILE} ${PHP_FILE}  ${JS_FILE} ${JAVA_FILE} ${YAML_FILE} ${OTB_FILE} ${SAGA_FILE} ${MONO_FILE} ${HPC_FILES} ${METADB_FILE} ${JSON_FILE} ${R_FILE} service_callback.o response_print.o server_internal.o caching.o request_parser.o ulinet.o lex.cr.o lex.sr.o service_conf.tab.o main_conf_read.tab.o -o zoo_loader.cgi -L. ${LDFLAGS}
 
 zcfg2yaml: zcfg2yaml.c service.h lex.sr.o service_conf.tab.o service_conf.y main_conf_read.tab.o lex.cr.o response_print.o server_internal.o service_internal.o ${MS_FILE} ${YAML_FILE}

branches/prototype-v0/zoo-project/zoo-kernel/ZOOMakefile.opts.in

@@ -58 +58 @@
 PYTHON_FILE=@PYTHON_FILE@
 
+RCFLAGS=@R_CPPFLAGS@
+RLDFLAGS=@R_LDFLAGS@
+R_ENABLED=@R_ENABLED@
+R_FILE=@R_FILE@
+
 RUBYCFLAGS=@RUBY_CPPFLAGS@
 RUBYLDFLAGS=@RUBY_LDFLAGS@
@@ -115 +120 @@
 
 CFLAGS=@SSH2_CPPFLAGS@ @GETTEXT_CFLAGS@ @PROJ_CPPFLAGS@ @RELY_ON_DB@ @DEB_DEF@ -fpic @OPENSSL_CFLAGS@ @UUID_CFLAGS@ ${FCGI_CFLAGS} ${YAML_CFLAGS} ${MACOS_CFLAGS} ${MS_CFLAGS} -I../../thirds/cgic206 -I. -DLINUX_FREE_ISSUE #-DDEBUG #-DDEBUG_SERVICE_CONF
-LDFLAGS=-lzoo_service @SSH2_LDFLAGS@ @PROJ_LDFLAGS@ @DEFAULT_LIBS@ -L../../thirds/cgic206 -lcgic ${GDAL_LIBS} ${XML2LDFLAGS} ${PYTHONLDFLAGS} ${PERLLDFLAGS}  ${PHPLDFLAGS} ${JAVALDFLAGS} ${JSLDFLAGS}  ${FCGI_LDFLAGS} @OPENSSL_LDFLAGS@ @UUID_LDFLAGS@ ${MS_LDFLAGS} ${MACOS_LD_FLAGS} ${MACOS_LD_NET_FLAGS} ${YAML_LDFLAGS} ${OTBLDFLAGS} ${SAGA_LDFLAGS} ${MONO_LDFLAGS} @GETTEXT_LDFLAGS@ @JSON_LDFLAGS@ @XSLT_LDFLAGS@
+LDFLAGS=-lzoo_service @SSH2_LDFLAGS@ @PROJ_LDFLAGS@ @DEFAULT_LIBS@ -L../../thirds/cgic206 -lcgic ${GDAL_LIBS} ${XML2LDFLAGS} ${PYTHONLDFLAGS} ${PERLLDFLAGS}  ${PHPLDFLAGS} ${JAVALDFLAGS} ${JSLDFLAGS}  ${FCGI_LDFLAGS} @OPENSSL_LDFLAGS@ @UUID_LDFLAGS@ ${MS_LDFLAGS} ${MACOS_LD_FLAGS} ${MACOS_LD_NET_FLAGS} ${YAML_LDFLAGS} ${OTBLDFLAGS} ${SAGA_LDFLAGS} ${MONO_LDFLAGS} ${RLDFLAGS} @GETTEXT_LDFLAGS@ @JSON_LDFLAGS@ @XSLT_LDFLAGS@
 
 DATAROOTDIR=@datarootdir@/zoo-project

branches/prototype-v0/zoo-project/zoo-kernel/configure.ac

@@ -523 +523 @@
 AC_SUBST([MS_FILE])
 AC_SUBST([MS_VERSION])
+
+# ===========================================================================
+# Detect if R is installed
+# ===========================================================================
+
+AC_ARG_WITH([r], 
+        [AS_HELP_STRING([--with-r=PATH], [To enable python support or Specifies an alternative directory for R installation,  disabled by default])], 
+        [R_PATH="$withval"; R_ENABLED="-DUSE_R"], [R_ENABLED=""])
+
+if test -z "$R_ENABLED"
+then
+        R_FILE=""
+else
+        R_FILE="service_internal_r.o"
+        # Extract the linker and include flags 
+        R_LDFLAGS="-L$R_PATH/lib/ -lR"
+        R_CPPFLAGS="-I$R_PATH/include/"
+
+        # Check headers file
+        CPPFLAGS_SAVE="$CPPFLAGS"
+        CPPFLAGS="$R_CPPFLAGS"
+        AC_CHECK_HEADERS([RInternals.h],
+                 [], [AC_MSG_ERROR([could not find headers include related to R])])
+
+        # Ensure we can link against libphp
+        #LIBS_SAVE="$LIBS"
+        #LIBS="$R_LDFLAGS"
+        #AC_CHECK_LIB([$LIBS], [R_tryEval], [], [AC_MSG_ERROR([could not find libR])], [])
+        #LIBS="$LIBS_SAVE"
+fi
+
+AC_SUBST([R_CPPFLAGS])
+AC_SUBST([R_LDFLAGS])
+AC_SUBST([R_ENABLED])
+AC_SUBST([R_FILE])
+
 
 # ===========================================================================

branches/prototype-v0/zoo-project/zoo-kernel/service.c

@@ -190 +190 @@
  * Count number of map in a map
  *
- * @param m the maps to count
+ * @param m the map to count
  * @return number of map in a map
  */
 int count(map* m){
   map* tmp=m;
+  int c=0;
+  while(tmp!=NULL){
+    c++;
+    tmp=tmp->next;
+  }
+  return c;
+}
+
+/**
+ * Count number of maps in a maps
+ *
+ * @param m the maps to count
+ * @return number of maps in a maps
+ */
+int maps_length(maps* m){
+  maps* tmp=m;
   int c=0;
   while(tmp!=NULL){

branches/prototype-v0/zoo-project/zoo-kernel/service_json.c

@@ -89 +89 @@
   }
 
+  json_object* elementsToJson(elements* myElements){
+    json_object *res=json_object_new_object();
+    elements* cur=myElements;
+    while(cur!=NULL){
+      json_object *cres=json_object_new_object();
+      json_object_object_add(cres,"content",mapToJson(cur->content));
+      json_object_object_add(cres,"metadata",mapToJson(cur->metadata));
+      json_object_object_add(cres,"additional_parameters",mapToJson(cur->additional_parameters));
+      if(cur->format!=NULL){
+        json_object_object_add(cres,"format",json_object_new_string(cur->format));
+      }
+      if(cur->child==NULL){
+        if(cur->defaults!=NULL)
+          json_object_object_add(cres,"defaults",mapToJson(cur->defaults->content));
+        else
+          json_object_object_add(cres,"defaults",mapToJson(NULL));
+        iotype* scur=cur->supported;
+        json_object *resi=json_object_new_array();
+        while(scur!=NULL){
+          json_object_array_add(resi,mapToJson(scur->content));
+          scur=scur->next;
+        }
+        json_object_object_add(cres,"supported",resi);
+        fprintf(stderr,"%s %d\n",__FILE__,__LINE__);
+        fflush(stderr);
+      }
+      
+      dumpElements(cur->child);
+      json_object_object_add(cres,"child",elementsToJson(cur->child));
+      fprintf(stderr,"%s %d\n",__FILE__,__LINE__);
+      fflush(stderr);
+
+      json_object_object_add(res,cur->name,cres);
+      cur=cur->next;
+    }
+    return res;
+  }
+  
+  json_object* serviceToJson(service* myService){
+    json_object *res=json_object_new_object();
+    json_object_object_add(res,"name",json_object_new_string(myService->name));
+    json_object_object_add(res,"content",mapToJson(myService->content));
+    json_object_object_add(res,"metadata",mapToJson(myService->metadata));
+    json_object_object_add(res,"additional_parameters",mapToJson(myService->additional_parameters));
+    json_object_object_add(res,"inputs",elementsToJson(myService->inputs));
+    json_object_object_add(res,"outputs",elementsToJson(myService->outputs));
+    return res;
+  }
+  
+  
 #ifdef __cplusplus
 }

branches/prototype-v0/zoo-project/zoo-kernel/service_json.h

@@ -38 +38 @@
   json_object* mapToJson(map*);
   json_object* mapsToJson(maps*);
+  json_object* serviceToJson(service*);
 #ifdef __cplusplus
 }

branches/prototype-v0/zoo-project/zoo-kernel/zoo_service_loader.c

@@ -35 +35 @@
 #ifdef USE_OTB
 #include "service_internal_otb.h"
+#endif
+
+#ifdef USE_R
+#include "service_internal_r.h"
 #endif
 
@@ -706 +710 @@
 #endif
 
+#ifdef USE_R
+  if (strncasecmp (r_inputs->value, "R", 6) == 0)
+    {     
+      *eres =
+        zoo_r_support (&m, request_inputs, s1,
+                            &request_input_real_format,
+                            &request_output_real_format);
+    }
+  else
+#endif
+
 #ifdef USE_JAVA
   if (strncasecmp (r_inputs->value, "JAVA", 4) == 0)
@@ -1711 +1726 @@
                                   addNestedOutputs(&s1);
 #endif
+                                  json_object* jobj=serviceToJson(s1);
+                                  const char* jsonStr=json_object_to_json_string_ext(jobj,JSON_C_TO_STRING_PLAIN);
+                                  fprintf(stderr,"*** %s %d %s \n",__FILE__,__LINE__,jsonStr);
+
                                   printDescribeProcessForProcess (zooRegistry,m, doc, n, s1);
                                   freeService (&s1);
@@ -2548 +2567 @@
   rewind(stdout);
 
+  fprintf(stderr,"%s %d %d\n",__FILE__,__LINE__,eres);
+
   if (eres != -1)
     outputResponse (s1, request_input_real_format,