Add the msi_json_objops microservice

Makefile

@@ -1,4 +1,4 @@
-MSI_JSON_UTILS = msi_json_arrayops
+MSI_JSON_UTILS = msi_json_arrayops msi_json_objops
 MSI_ADMIN_UTILS = msi_unmount
 
 MAKEFLAGS += --no-print-directory

msi_json_objops/Makefile

@@ -0,0 +1,12 @@
+GCC = g++
+
+INC=-I/usr/include/irods/ -I/usr/include/irods/boost/ -I/usr/include/irods/jansson/src
+
+all: libmsi_json_objops
+
+libmsi_json_objops:
+ ${GCC} ${INC} -DRODS_SERVER -fPIC "-Wl,-E" -shared -g -Wno-deprecated -rdynamic -o $@.so $@.cpp /usr/lib/libirods_client.a /usr/lib/irods/externals/libjansson.a
+
+
+clean:
+ @rm -f ./*.so

msi_json_objops/README.md

@@ -0,0 +1,32 @@
+# msi_json_objops
+
+Add/set/get/rm element of a given JSON object.
+
+### Copyright and license
+
+This microservice has kindly been provided by the Donders Institute for
+Brain, Cognition and Behaviour.
+
+Copyright (c) 2016, Radboud University, Nijmegen, The Netherlands
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADV

msi_json_objops/libmsi_json_objops.cpp

@@ -0,0 +1,140 @@
+// =-=-=-=-=-=-=-
+#include "apiHeaderAll.hpp"
+#include "msParam.hpp"
+#include "reGlobalsExtern.hpp"
+#include "irods_ms_plugin.hpp"
+#include "reFuncDefs.hpp"
+#include "jansson.h"
+
+// =-=-=-=-=-=-=-
+// STL/boost Includes
+#include <string>
+#include <iostream>
+#include <vector>
+#include <boost/algorithm/string.hpp>
+
+extern "C" {
+ // =-=-=-=-=-=-=-
+ int msi_json_objops_impl(msParam_t* json_str, msParam_t* kvp, msParam_t* ops, ruleExecInfo_t* rei) {
+ using std::cout;
+ using std::endl;
+ using std::string;
+
+ char *null_cstr = new char[5];
+ char *true_cstr = new char[5];
+ char *false_cstr = new char[6];
+
+ strcpy(null_cstr, "null");
+ strcpy(true_cstr, "true");
+ strcpy(false_cstr, "false");
+
+ // input type check
+ const char *inJsonStr = parseMspForStr( json_str );
+ const char *inOps = parseMspForStr( ops );
+ if( ! inJsonStr || ! inOps) {
+ cout << "msi_json_objops - invalid input for string" << endl;
+ return SYS_INVALID_INPUT_PARAM;
+ }
+
+ if (kvp == NULL || kvp->inOutStruct == NULL ||
+ kvp->type == NULL || strcmp(kvp->type, KeyValPair_MS_T) != 0) {
+ cout << "msi_json_objops - invalid input for key-value pairs" << endl;
+ return SYS_INVALID_INPUT_PARAM;
+ }
+
+ keyValPair_t *inKVP;
+ inKVP = (keyValPair_t*) kvp->inOutStruct;
+
+ string strOps(inOps); 
+
+ json_error_t error;
+ json_t *root;
+
+ // try to make initial inJsonStr if it's an empty string 
+ if ( strcmp(inJsonStr, "") == 0 ) {
+ inJsonStr = "{}";
+ }
+
+ // try to load JSON object
+ root = json_loads(inJsonStr, 0, &error);
+ if ( ! root ) {
+ cout << "msi_json_objops - invalid json document" << endl;
+ json_decref(root);
+ return SYS_INVALID_INPUT_PARAM;
+ }
+
+ for (int ik=0; ik<inKVP->len; ik++) {
+
+ char* inKey = inKVP->keyWord[ik];
+ char* inVal = inKVP->value[ik];
+
+ json_t *jval;
+ if (strcmp(inVal, null_cstr) == 0) {
+ jval = json_null();
+ } else {
+ jval = json_loads(inVal, 0, &error);
+ if ( ! jval ) jval = json_string(inVal);
+ }
+
+ // try to find objects in the key
+ json_t *data = json_object_get(root, inKey);
+
+ if ( strOps == "get" ) {
+ if ( json_is_null(data) ) {
+ inKVP->value[ik] = null_cstr;
+ } else if ( json_is_true(data) ) {
+ inKVP->value[ik] = true_cstr;
+ } else if ( json_is_false(data) ) {
+ inKVP->value[ik] = false_cstr;
+ } else if ( json_is_string(data) ) { 
+ const char* val_str = json_string_value(data);
+ char *val_cstr = new char[strlen(val_str) + 1];
+ strcpy(val_cstr, val_str);
+ inKVP->value[ik] = val_cstr;
+ } else {
+ inKVP->value[ik] = json_dumps(data,0);
+ }
+ } else if ( strOps == "add" ) {
+ if (json_is_array( data )) {
+ json_array_append_new(data, jval);
+ } else {
+ json_object_set_new(root, inKey, jval);
+ }
+ } else if ( strOps == "set" ) {
+ json_object_set_new(root, inKey, jval);
+ } else if ( strOps == "rm" ) {
+ if ( data ) {
+ if ( json_is_array( data ) ) {
+ size_t i_match = json_array_size(data);
+ for( int i=0; i<json_array_size(data); i++ ) {
+ json_t *ov = json_array_get(data, i);
+ if ( json_equal(ov, jval) ) { i_match = i; break; }
+ }
+ if ( i_match < json_array_size(data) ) json_array_remove(data, i_match);
+ } else if ( json_equal(data, jval) ) {
+ json_object_del(root, inKey);
+ }
+ }
+ }
+ }
+
+ kvp->inOutStruct = (void *) inKVP;
+ kvp->type = (char *) strdup(KeyValPair_MS_T);
+
+ fillStrInMsParam(json_str, json_dumps(root, 0));
+
+ json_decref(root);
+
+ // Done
+ return 0;
+ }
+
+ irods::ms_table_entry* plugin_factory() {
+ irods::ms_table_entry* msvc = new irods::ms_table_entry(3);
+
+ msvc->add_operation("msi_json_objops_impl", "msi_json_objops");
+
+ return msvc;
+ }
+
+} // extern "C"

msi_json_objops/msi_json_objops_test.r

@@ -0,0 +1,42 @@
+myTestRule {
+
+ *json_str = "";
+
+ ## build JSON object from key-value pairs
+ msiString2KeyValPair("", *kvp);
+ msiAddKeyVal(*kvp, 'type', 'DATA_SHARING');
+ msiAddKeyVal(*kvp, 'collId', '12345');
+ msiAddKeyVal(*kvp, 'title', 'DICOM 原生資料備份');
+ msiAddKeyVal(*kvp, 'creatorList', '["U505173-ru.nl","hurngchunlee-icloud.com"]');
+ msiAddKeyVal(*kvp, 'associatedPublication', '[{"type":"PMID", "id":"654321"}]');
+
+ *ec = errorcode( msi_json_objops(*json_str, *kvp, "add") );
+ writeLine("stdout", *json_str);
+
+ ## modify JSON object (add/set/get/rm)
+ msiString2KeyValPair("", *kvp);
+ msiAddKeyVal(*kvp, 'associatedPublication', '{"type":"arXiv", "id":"xyz/123"}');
+ *ec = errorcode( msi_json_objops(*json_str, *kvp, "add") );
+ writeLine("stdout", *json_str);
+
+ msiString2KeyValPair("", *kvp);
+ msiAddKeyVal(*kvp, 'associatedPublication', '{"type":"PMID", "id":"654321"}');
+ *ec = errorcode( msi_json_objops(*json_str, *kvp, "rm") );
+ writeLine("stdout", *json_str);
+
+ msiString2KeyValPair("", *kvp);
+ msiAddKeyVal(*kvp, 'creatorList', '["hurngchunlee-icloud.com","U505173-ru.nl"]');
+ *ec = errorcode( msi_json_objops(*json_str, *kvp, "set") );
+ writeLine("stdout", *json_str);
+
+ msiString2KeyValPair("", *kvp);
+ msiAddKeyVal(*kvp, 'creatorList', '');
+ msiAddKeyVal(*kvp, 'associatedPublication', '');
+ msiAddKeyVal(*kvp, 'collId', '');
+ msiAddKeyVal(*kvp, 'title', '');
+ #msiAddKeyVal(*kvp, 'associatedPublication', '');
+ *ec = errorcode( msi_json_objops(*json_str, *kvp, "get") );
+ writeLine("stdout", str(*kvp));
+}
+OUTPUT ruleExecOut
+