Experiments with Remote Access to Scientific Data using HDF5 Kun Yan Robert E. McGrath NCSA May 15, 2002

Today’s Talk 1.Background 2.Experiments with JSP, XML, HDF4, HDF5, etc. 3.Experiments with CORBA, Java, HDF5 4.Discussion

Acknowledgements Kun Yan conducted these experiments as a Research Assistant at NCSA. This report is based upon work supported in part by a Cooperative Agreement with NASA under NASA grants NAG and NCC Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Aeronautics and Space Administration. Other support provided by NCSA and other sponsors and agencies.

Java Native Interface HDF Library and File H5view, etc C Java C Applet Java CORBA Server Other App. Other App. C++ Any Client/RemoteServer/Local Java Server Platform Web browser HTML XML Java Any Java Native Interface Java C Distributed Product Demonstrated in Research Should work, but not demonstrated

2. Experiments with JSP Experiments with JSP, XML, XSL, etc. –Web access to Data and services. –Demonstration of browsing HDF5 datasets Generate HTML or XML Convert data from HDF4 to HDF5 on demand

Tomcat is a standalone web server that supports the Servlet and JSP specifications. developed under the Jakarta project at the Apache Software Foundation. integrated into the J2EE Reference Implementation. Tomcat 4.x (Catalina, Servlet 2.3, JSP 1.2) Tomcat 3.3

JavaServer Pages JavaServer Pages TM (JSP TM ) technology rapidly develop and easily maintain, dynamic web pages uses XML-like tags and Java scriptlets application logic can reside in server- based resources

The Flow of a Request

beans request response client JSP DB data lib XSL XML beans Xalan.jar Xerces.jar HTML response How JSP and Beans Work together Application

3. Experiments with CORBA Created a demonstration CORBA server that reads HDF5 –Written in C++, linked directly to HDF5 library. Created a pure-java client –No CORBA required on the client –Can be used from an applet within a standard Web browser

Technology used Orbacus (C++) (free, full source) Java 1.3 or above HDF , HDF5 C++ interface

HDF5 CORBA Experiment -- Design Diagram CORBA Object Hierarchy

HDF5 CORBA Experiment – IDL File 1.module HDF5{ 2. struct ObjInfo{ 3. long oid; 4. long fid; 5. long type; 6. string name; 7. long numOfMembers; 8. }; typedef sequence Sizes; 11. struct DatasetInfo{ 12. string name; 13. long numOfDim; 14. Sizes dimSizes; 15. Sizes dimMaxSizes; 16. long dataTypeClass; 17. long dataTypeSize; 18. long long storageSize; 19. }; struct DatatypeInfo{ 22. string name; 23. long type; 24. long size; 25. }; 26. interface H5Obj{ 27. void getObjInfo(out ObjInfo obji); 28. void getNumAttributes(out long attrNum); 29. void openAttributes (out long attr); 30. }; interface H5DatasetObj:H5Obj{ 33. void getDatasetInfo(out DatasetInfo dsinfo); 34. long long getStorageSize(); 35. }; interface H5GroupObj:H5Obj{ 38. ObjInfo getGMember(in long fid, in string gName, in long index); 39. void openGroup(in string gName, out H5GroupObj h5gobj); 40. void getDatasetInfo(in string dsName, out DatasetInfo dsinfo); 41. void openDataset(in string dsName, out H5DatasetObj h5ds); 42. void getDataTypeInfo(in string ttName, out DatatypeInfo dtinfo); 43. }; interface H5FileObj{ 46. void getTOC(out ObjInfo obji); 47. void openRootGroup(out H5GroupObj h5gobj); 48. }; interface H5FileAccess{ 51. void openH5File(in string fileName, out H5FileObj h5fobj); 52. void numOfGMembers(in long fileId, in string gName, out long gNum); 53. string closeH5File(in long fileId); 54. }; };

HDF5 CORBA Experiment -- Design Diagram C++ Servant Object Hierarchy H5FileAccessH5FileObj H5Obj H5GroupObj H5DatasetObj H5FileAccess_impl H5::H5File poa_ openFile: closeFile: H5FileObj_impl H5::H5File ObjInfo poa_ getTOC openRootGroup setFileName: H5GroupObj_impl H5::H5Group poa_ openGroup getGMembers openDataset: getDatasetInfo: getDatatypeInfo: H5Obj_impl ObjInfo poa_ getObjInfo setObjName: H5DatasetObj_impl H5::H5Daraset DatasetInfo getDatasetInfo getStorageSize

HDF5 CORBA Experiment -- How to Use the Client Applet Select file name from drop-down list (file resides corba server side) Select Flags and Access Property of the selected file Click on “open file” to open the file Click on “get file TOC” to get the file object info Click on “open root” to open the root group Click on “get group TOC” to get the root group object info Click on “iterate group” to get the group member’s info of the root and each subgroup Input dataset name including path, then click on “get dataset” to get the dataset object –Click on “get dataset TOC” to get the dataset object info –Click on “get storage size” to get the storage size of the opened dataset object Input dataset name including path, then click on “get dataset info” to get object info of the given dataset Input datatype name including path, then click on “get datatype info” to get object info of the given datatype

URLs JSP experiments:

4. Discussion

Java Native Interface HDF Library and File H5view, etc C Java C Applet Java CORBA Server Other App. Other App. C++ Any Client/RemoteServer/Local Java Server Platform Web browser HTML XML Java Any Java Native Interface Java C Distributed Product Demonstrated in Research Should work, but not demonstrated

HDF5 CORBA Experiment -- User Interface

HDF5 CORBA Experiment -- Examples of Object Info window

Other HDF Tools

Viewer/ Editor Generator Source code ASCII HDF5 file XML HDF5 file Java HDF4 h4toh5 HDF4

Dumper HDF DDL HDF5 file XML Non-Java (C) h4toh5 HDF4 file HDF5 h5toh4 HDF5 file HDF4 gif2hdf GIF file HDF5 fp2hdf flat file HDF5 H4 to H5 LIbrary

Silly XMLTricks Netcdf to HDF5, via XML using XSL netcdf ncxdump nc.xml netcdf.dtd h5.xml xalan nctoh5.xsl h5gen hdf5

URLs JSP experiments: