Index: branches/prototype-v0/zoo-project/zoo-kernel/Makefile.in =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/Makefile.in (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/Makefile.in (revision 873) @@ -78,4 +78,7 @@ 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 @@ -114,13 +117,13 @@ 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} Index: branches/prototype-v0/zoo-project/zoo-kernel/ZOOMakefile.opts.in =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/ZOOMakefile.opts.in (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/ZOOMakefile.opts.in (revision 873) @@ -58,4 +58,9 @@ PYTHON_FILE=@PYTHON_FILE@ +RCFLAGS=@R_CPPFLAGS@ +RLDFLAGS=@R_LDFLAGS@ +R_ENABLED=@R_ENABLED@ +R_FILE=@R_FILE@ + RUBYCFLAGS=@RUBY_CPPFLAGS@ RUBYLDFLAGS=@RUBY_LDFLAGS@ @@ -115,5 +120,5 @@ 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} ${RLDFLAGS} @GETTEXT_LDFLAGS@ @JSON_LDFLAGS@ @XSLT_LDFLAGS@ DATAROOTDIR=@datarootdir@/zoo-project Index: branches/prototype-v0/zoo-project/zoo-kernel/configure.ac =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/configure.ac (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/configure.ac (revision 873) @@ -523,4 +523,40 @@ AC_SUBST([MS_FILE]) AC_SUBST([MS_VERSION]) + +# =========================================================================== +# Detect if R is installed +# =========================================================================== + +AC_ARG_WITH([r], + [AS_HELP_STRING([--with-r=PATH], [To enable python support or Specifies an alternative directory for R installation, disabled by default])], + [R_PATH="$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]) + # =========================================================================== Index: branches/prototype-v0/zoo-project/zoo-kernel/service.c =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/service.c (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/service.c (revision 873) @@ -190,9 +190,25 @@ * 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){ Index: branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.c =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.c (revision 873) +++ branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.c (revision 873) @@ -0,0 +1,403 @@ +/* + * Author : Gérald FENOY + * + * Copyright (c) 2018 GeoLabs SARL + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + +#include "service_internal_r.h" + +void jump_to_toplevel(void){ + fprintf(stderr,"Error occured\n"); + fprintf(stderr,"%s %d \n",__FILE__,__LINE__); + fflush(stderr); + //resetStack(1); + fprintf(stderr,"%s %d \n",__FILE__,__LINE__); + fflush(stderr); +} + +void init_zoo(SEXP conf,SEXP outputs){ + const char* names[]={ + "SERVICE_SUCCEEDEED", + "SERVICE_FAILED", + "conf", + "outputs", + "" + }; + SEXP res = PROTECT(mkNamed(VECSXP, names)); + SET_VECTOR_ELT(res, 0, Rf_ScalarInteger(3)); + SET_VECTOR_ELT(res, 1, Rf_ScalarInteger(4)); + SET_VECTOR_ELT(res, 2, conf); + SET_VECTOR_ELT(res, 3, outputs); + defineVar(install("zoo"),res, R_GlobalEnv); + + static const R_CallMethodDef callMethods[] = { + {"ZOOTranslate", (DL_FUNC) &RTranslate, 1}, + {"ZOOUpdateStatus", (DL_FUNC) &RUpdateStatus, 2}, + {NULL, NULL, 0} + }; + + static R_NativePrimitiveArgType RTranslate_t[] = { + STRSXP + }; + static R_NativePrimitiveArgType RUpdateStatus_t[] = { + VECSXP,STRSXP + }; + + static const R_CMethodDef cMethods[] = { + {"ZOOTranslate", (DL_FUNC) &RTranslate, 1, RTranslate_t}, + {"ZOOUpdateStatus", (DL_FUNC) &RUpdateStatus, 2, RUpdateStatus_t}, + {NULL, NULL, 0, NULL} + }; + + DllInfo *info = R_getEmbeddingDllInfo(); + R_registerRoutines(info, cMethods, callMethods, NULL, NULL); +} + +/** + * Load a R script then run the function corresponding to the service + * by passing the conf, inputs and outputs parameters by reference. + * + * @param main_conf the conf maps containing the main.cfg settings + * @param request the map containing the HTTP request + * @param s the service structure + * @param real_inputs the maps containing the inputs + * @param real_outputs the maps containing the outputs + */ +int zoo_r_support(maps** main_conf,map* request,service* s,maps **real_inputs,maps **real_outputs){ + SEXP pName; + int result=0; + maps* m=*main_conf; + maps* inputs=*real_inputs; + maps* outputs=*real_outputs; + map* tmp0=getMapFromMaps(*main_conf,"lenv","cwd"); + char *ntmp=tmp0->value; + map* tmp=NULL; + int hasToClean=0; + char *r_path, *rpath; + map* cwdMap=getMapFromMaps(*main_conf,"main","servicePath"); + int r_argc = 3; + char *r_argv[] = { "R", "--no-save", "--silent" }; + Rf_initEmbeddedR(r_argc, r_argv); + if(cwdMap!=NULL) + r_path=cwdMap->value; + else{ + if(tmp0!=NULL) + r_path=tmp0->value; + else + r_path=(char*)"."; + } + + tmp=getMap(s->content,"serviceProvider"); + map* mp=getMap(request,"metapath"); + if(tmp!=NULL){ + if(mp!=NULL && strlen(mp->value)>0){ + char *mps=zStrdup(mp->value); + int i,len=strlen(mps); + int j=0; + for(i=0;ivalue)+2)*sizeof(char)); + sprintf(mn,"%s.%s",mps,tmp->value); + pName = mkString(mn); + free(mn); + free(mps); + } + else{ + dumpMap(tmp); + char *tmpStr=(char*)malloc((strlen(r_path)+strlen(tmp->value)+2)*sizeof(char)); + sprintf(tmpStr,"%s/%s",r_path,tmp->value); + pName = mkString(tmpStr); + free(tmpStr); + } + } + else{ + errorException (m, "Unable to parse serviceProvider please check your zcfg file.", "NoApplicableCode", NULL); + return -1; + } + SEXP e; + int errorOccurred; + PROTECT(e = lang2(install("source"), pName)); + R_tryEval(e, R_GlobalEnv, &errorOccurred); + UNPROTECT(1); + if (errorOccurred){ + setMapInMaps(*main_conf,"lenv","message",_("Unable to load your R file")); + return SERVICE_FAILED; + }else{ + result=SERVICE_FAILED; + { + SEXP pValue; + SEXP arg1=RList_FromMaps(m); + SEXP arg2=RList_FromMaps(*real_inputs); + SEXP arg3=RList_FromMaps(*real_outputs); + SEXP r_call; + init_zoo(arg1,arg3); + PROTECT(r_call = lang4(install(s->name), arg1,arg2,arg3)); + int errorOccurred; + + SEXP ret = R_tryEval(r_call, R_GlobalEnv, &errorOccurred); + if (!errorOccurred) { + int *val = INTEGER(ret); + for (int i = 0; i < LENGTH(ret); i++) + if(i==0){ + result=val[i]; + SEXP zooEnv = findVar(install("zoo"), R_GlobalEnv); + if(zooEnv!=NULL){ + SEXP names = Rf_getAttrib(zooEnv, R_NamesSymbol); + int nbKeys=nrows(names); + int i; + for(i=0;iname); + res[i+1]=""; + i++; + tmp=tmp->next; + } + return res; +} + +char** listMapKeys(map* m){ + char** res=NULL; + map* tmp=m; + int i=0; + while(tmp!=NULL){ + if(i==0) + res=(char**)malloc(2*sizeof(char*)); + else + res=(char**)realloc(res,(i+2)*sizeof(char*)); + res[i]=zStrdup(tmp->name); + res[i+1]=""; + i++; + tmp=tmp->next; + } + return res; +} + +/** + * Convert a maps to a R List + * + * @param t the maps to convert + * @return a new SEXP containing the converted maps + * @see RList_FromMap + * @warning make sure to free resources returned by this function + */ +SEXP RList_FromMaps(maps* t){ + maps* tmp=t; + char** keys=listMapsKeys(t); + SEXP res = PROTECT(mkNamed(VECSXP,(const char**) keys)); + free(keys); + int cnt=0; + while(tmp!=NULL){ + SEXP input = RList_FromMap(tmp->content); + SET_VECTOR_ELT(res,cnt,input); + cnt++; + tmp=tmp->next; + } + UNPROTECT(1); + return res; +} + +/** + * Convert a map to a R List + * + * @param t the map to convert + * @return a new SEXP containing the converted maps + * @warning make sure to free resources returned by this function + */ +SEXP RList_FromMap(map* t){ + map* tmp=t; + int hasSize=0; + char** keys=listMapKeys(t); + SEXP res = PROTECT(mkNamed(VECSXP, (const char**)keys)); + free(keys); + int cnt=0; + while(tmp!=NULL){ + SEXP value=mkString(tmp->value); + SET_VECTOR_ELT(res,cnt,value); + cnt++; + tmp=tmp->next; + } + UNPROTECT(1); + return res; +} + +/** + * Convert a R List to a maps + * + * @param t the PyDictObject to convert + * @return a new maps containing the converted PyDictObject + * @warning make sure to free resources returned by this function + */ +maps* mapsFromRList(SEXP t){ + maps* res=NULL; + maps* cursor=NULL; + SEXP names = Rf_getAttrib(t, R_NamesSymbol); + int nbKeys=nrows(names); + int i; + for(i=0;icontent=mapFromRList(value); + cursor->next=NULL; + if(res==NULL) + res=dupMaps(&cursor); + else + addMapsToMaps(&res,cursor); + freeMap(&cursor->content); + free(cursor->content); + free(cursor); + } + return res; +} + +/** + * Convert a R List to a map + * + * @param t the PyDictObject to convert + * @return a new map containing the converted PyDictObject + * @warning make sure to free resources returned by this function + */ +map* mapFromRList(SEXP t){ + map* res=NULL; + SEXP names = Rf_getAttrib(t, R_NamesSymbol); + int nbKeys=nrows(names); + int i; + for(i=0;i 100){ + return R_NilValue; + } + // create a local copy and update the lenv map + conf = mapsFromRList(confdict); + if(status!=NULL){ + maps* tmpMaps=getMaps(conf,"lenv"); + addIntToMap(tmpMaps->content,"status",istatus); + } + else + setMapInMaps(conf,"lenv","status","15"); + _updateStatus(conf); + freeMaps(&conf); + free(conf); + return R_NilValue; +} Index: branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.h =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.h (revision 873) +++ branches/prototype-v0/zoo-project/zoo-kernel/service_internal_r.h (revision 873) @@ -0,0 +1,47 @@ +/* + * Author : Gérald FENOY + * + * Copyright (c) 2009-2010 GeoLabs SARL + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + */ + +#ifndef ZOO_SERVICE_INTERNAL_R_H +#define ZOO_SERVICE_INTERNAL_R_H 1 + +#pragma once + +#include +#include +#include "service_internal.h" +#include "response_print.h" +#include "cgic.h" + +SEXP RList_FromMaps(maps* t); +SEXP RList_FromMap(map* t); + +maps* mapsFromRList(SEXP t); +map* mapFromRList(SEXP t); + +int zoo_r_support(maps**,map*,service*,maps**,maps**); + +SEXP RTranslate(SEXP); +SEXP RUpdateStatus(SEXP,SEXP); + +#endif Index: branches/prototype-v0/zoo-project/zoo-kernel/service_json.c =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/service_json.c (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/service_json.c (revision 873) @@ -89,4 +89,54 @@ } + 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 } Index: branches/prototype-v0/zoo-project/zoo-kernel/service_json.h =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/service_json.h (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/service_json.h (revision 873) @@ -38,4 +38,5 @@ json_object* mapToJson(map*); json_object* mapsToJson(maps*); + json_object* serviceToJson(service*); #ifdef __cplusplus } Index: branches/prototype-v0/zoo-project/zoo-kernel/zoo_service_loader.c =================================================================== --- branches/prototype-v0/zoo-project/zoo-kernel/zoo_service_loader.c (revision 872) +++ branches/prototype-v0/zoo-project/zoo-kernel/zoo_service_loader.c (revision 873) @@ -35,4 +35,8 @@ #ifdef USE_OTB #include "service_internal_otb.h" +#endif + +#ifdef USE_R +#include "service_internal_r.h" #endif @@ -706,4 +710,15 @@ #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) @@ -1711,4 +1726,8 @@ 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); @@ -2548,4 +2567,6 @@ rewind(stdout); + fprintf(stderr,"%s %d %d\n",__FILE__,__LINE__,eres); + if (eres != -1) outputResponse (s1, request_input_real_format, Index: branches/prototype-v0/zoo-project/zoo-services/cgal/voronoi.c =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/cgal/voronoi.c (revision 872) +++ branches/prototype-v0/zoo-project/zoo-services/cgal/voronoi.c (revision 873) @@ -197,4 +197,14 @@ int ns = 0; int nr = 0; + int nf = 0; + Face_iterator fit =T.faces_begin(); + FILE* f=fopen("/tmp/toto.log","w+"); + for ( ; fit !=T.faces_end(); ++fit) { + fprintf(stderr," *** %s %d %d %d\n",__FILE__,__LINE__,nf,fit.info()); + fflush(stderr); + + nf++; + } + fclose(f); Edge_iterator eit =T.edges_begin(); for ( ; eit !=T.edges_end(); ++eit) { @@ -203,4 +213,5 @@ const Pointz p1=tmp->source(); const Pointz p2=tmp->target(); + fprintf(stderr,"P1 %d %d | P2 %d %d\n",p1.x(),p1.y(),p2.x(),p2.y()); #ifdef DEBUG fprintf(stderr,"P1 %d %d | P2 %d %d\n",p1.x(),p1.y(),p2.x(),p2.y()); Index: branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/RVoronoi.zcfg =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/RVoronoi.zcfg (revision 873) +++ branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/RVoronoi.zcfg (revision 873) @@ -0,0 +1,56 @@ +[RVoronoi] + Title = Voronoi Diagram. + Abstract = Computes the edges of Voronoi diagram for a set of data points. + Profile = urn:ogc:wps:1.0.0:voronoi + processVersion = 2 + storeSupported = true + statusSupported = true + serviceProvider = hello.R + serviceType = R + + [InputPoints] + Title = Data points + Abstract = The set of data points. + minOccurs = 1 + maxOccurs = 1 + + + mimeType = text/xml + encoding = UTF-8 + schema = http://schemas.opengis.net/gml/3.1.0/base/feature.xsd + + + mimeType = text/xml + encoding = base64 + schema = http://schemas.opengis.net/gml/3.1.0/base/feature.xsd + + + + + [Result] + Title = Voronoi Diagram. + Abstract = JSON String / GML Entity of the Voronoi Diagram. + + + mimeType = application/json + encoding = UTF-8 + + + mimeType = image/png + useMapserver = true + msStyle = STYLE COLOR 125 0 105 OUTLINECOLOR 0 0 0 WIDTH 0.3 OPACITY 65 END + + + mimeType = text/xml + encoding = base64 + schema = http://schemas.opengis.net/gml/3.1.0/base/feature.xsd + useMapserver = true + + + mimeType = text/xml + encoding = UTF-8 + schema = http://schemas.opengis.net/gml/3.1.0/base/feature.xsd + useMapserver = true + + + Index: branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/failR.zcfg =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/failR.zcfg (revision 873) +++ branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/failR.zcfg (revision 873) @@ -0,0 +1,28 @@ +[failR] + Title = HelloWorld Service in R + Abstract = Output and Hello Wolrd string + processVersion = 2 + storeSupported = true + statusSupported = true + serviceProvider = hello.R + serviceType = R + + [S] + Title = Name + Abstract = The name to display in the hello message + minOccurs = 0 + maxOccurs = 1 + + dataType = string + + + + + [Result] + Title = The resulting string + Abstract = The string created by service. + + dataType = string + + + Index: branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hello.R =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hello.R (revision 873) +++ branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hello.R (revision 873) @@ -0,0 +1,61 @@ +source("minimal.r") + +hellor <- function(a,b,c) { + # Create a useless graph + cars <- c(1,2,3,4,5) + filePath <- paste(a[["main"]][["tmpPath"]],paste("cars",zoo[["conf"]][["lenv"]][["usid"]],".png",sep=""),sep="/") + png(filePath) + plot(cars) + quartzFonts(avenir = c("Avenir Book", "Avenir Black", "Avenir Book Oblique", "Avenir Black Oblique")) + par(family = 'avenir') + title("Hello from R World!") + dev.off() + # Set the result + zoo[["outputs"]][["Result"]][["value"]] <<- paste("Hello",b[["S"]][["value"]],"from the R World! (plot ref:",filePath,")",sep=" ") + # Update the main conf settings + zoo[["conf"]][["lenv"]][["message"]] <<- "Running from R world!" + # Return SERVICE_SUCCEEDEED + return(zoo[["SERVICE_SUCCEEDEED"]]) +} + +failR <- function(conf,inputs,outputs){ + zoo[["conf"]][["lenv"]][["message"]] <<- ZOOTranslate("Failed running from R world!") + return(zoo[["SERVICE_FAILED"]]) +} + +voronoipolygons <- function(x,poly) { + require(deldir) + if (.hasSlot(x, 'coords')) { + crds <- x@coords + } else crds <- x + bb = bbox(poly) + rw = as.numeric(t(bb)) + z <- deldir(crds[,1], crds[,2],rw=rw) + w <- tile.list(z) + polys <- vector(mode='list', length=length(w)) + require(sp) + finalCoordinates <- c() + for (i in seq(along=polys)) { + pcrds <- cbind(w[[i]]$x, w[[i]]$y) + pcrds <- rbind(pcrds, pcrds[1,]) + finalCoordinates[[i]] <- i + polys[[i]] <- Polygons(list(Polygon(pcrds)), ID=as.character(i)) + } + SP <- SpatialPolygons(polys) + voronoi <- SpatialPolygonsDataFrame(SP, data=data.frame(identifier=finalCoordinates)) + return(voronoi) +} + +RVoronoi <- function(conf,inputs,outputs){ + require(rgdal) + require(rgeos) + message(names(inputs[["InputPoints"]])) + message(inputs[["InputPoints"]]) + myGeoData <- readOGR(inputs[["InputPoints"]][["cache_file"]],layer=ogrListLayers(inputs[["InputPoints"]][["cache_file"]])[1], verbose = FALSE); + voronoiData <- voronoipolygons(myGeoData,myGeoData) + filePath <- paste(conf[["main"]][["tmpPath"]],paste("RBuffer_",zoo[["conf"]][["lenv"]][["usid"]],".shp",sep=""),sep="/") + writeOGR(voronoiData, dsn=filePath, layer="Voronoi", driver="ESRI Shapefile", verbose = FALSE) + zoo[["outputs"]][["Result"]][["storage"]] <<- filePath + return(zoo[["SERVICE_SUCCEEDEED"]]) +} + Index: branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hellor.zcfg =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hellor.zcfg (revision 873) +++ branches/prototype-v0/zoo-project/zoo-services/hello-r/cgi-env/hellor.zcfg (revision 873) @@ -0,0 +1,28 @@ +[hellor] + Title = HelloWorld Service in R + Abstract = Output and Hello Wolrd string + processVersion = 2 + storeSupported = true + statusSupported = true + serviceProvider = hello.R + serviceType = R + + [S] + Title = Name + Abstract = The name to display in the hello message + minOccurs = 1 + maxOccurs = 1 + + dataType = string + + + + + [Result] + Title = The resulting string + Abstract = The string created by service. + + dataType = string + + + Index: branches/prototype-v0/zoo-project/zoo-services/utils/status/Makefile =================================================================== --- branches/prototype-v0/zoo-project/zoo-services/utils/status/Makefile (revision 872) +++ branches/prototype-v0/zoo-project/zoo-services/utils/status/Makefile (revision 873) @@ -1,8 +1,8 @@ ZRPATH=../../.. include ${ZRPATH}/zoo-kernel/ZOOMakefile.opts -CFLAGS=-I${INST_INCLUDE} ${ZOO_CFLAGS} ${XML2CFLAGS} ${GDAL_CFLAGS} ${PYTHONCFLAGS} -DLINUX_FREE_ISSUE #-DDEBUG +CFLAGS1=${CFLAGS} -I${INST_INCLUDE} ${ZOO_CFLAGS} ${XML2CFLAGS} ${GDAL_CFLAGS} ${PYTHONCFLAGS} -DLINUX_FREE_ISSUE #-DDEBUG cgi-env/wps_status.zo: service.c - g++ -rdynamic ${CFLAGS} -shared -fpic -o cgi-env/wps_status.zo ./service.c ${GDAL_LIBS} ${XML2LDFLAGS} ${MACOS_LD_FLAGS} ${ZOO_LDFLAGS} ${MACOS_LD_NET_FLAGS} ${XSLT_LDFLAGS} ${FCGI_LDFLAGS} -L${ZRPATH}/zoo-kernel/ -lzoo_service + g++ ${CFLAGS1} -shared -fpic -o cgi-env/wps_status.zo ./service.c ${GDAL_LIBS} ${XML2LDFLAGS} ${MACOS_LD_FLAGS} ${ZOO_LDFLAGS} ${MACOS_LD_NET_FLAGS} ${XSLT_LDFLAGS} ${FCGI_LDFLAGS} -L${ZRPATH}/zoo-kernel/ -lzoo_service install: