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Progress of the XML Definitions and Libraries working group

Progress of the XML Definitions and Libraries working group. Martyn Winn CCP4 group CCLRC Daresbury Laboratory. Membership of the XML Working Group. Martyn Winn (coordinator) Airlie McCoy Fei Long Graeme Winter Steven Ness Charles Ballard Paul Emsley Ronan Keegan Daniel Rolfe.

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Progress of the XML Definitions and Libraries working group

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  1. Progress of the XML Definitions and Libraries working group Martyn Winn CCP4 group CCLRC Daresbury Laboratory M.D.Winn, York, March 28th 2006

  2. Membership of the XML Working Group Martyn Winn (coordinator) Airlie McCoy Fei Long Graeme Winter Steven Ness Charles Ballard Paul Emsley Ronan Keegan Daniel Rolfe M.D.Winn, York, March 28th 2006

  3. What have we done? Web pages at: http://www.ccp4.ac.uk/automation/xml_wp/ (id/password = automation/pychart) Contains: Provisional remit and plans of the group Samples of current XML Some source code for writing / reading XML Email discussions June/July CSE Forum set up in November 2005 but not used. No meeting of full Working Group. Meeting with Avi Naim on 20/10/2005 M.D.Winn, York, March 28th 2006

  4. Provisional remit of XML Working Group • Scope: • Define XML for communication between CCP4 programs and potentially with non-CCP4 programs. • Exclude XML used entirely within a single program or package. • XML may or may not be relevant for communication to other domains, e.g. for deposition. Desirable, but that is not at the moment our priority. • Many CCP4 programs already use XML. Aim to draw together these efforts to produce "CCP4 XML". As with CCP4 "standards" for file formats, keyworded input, documentation, etc. the "CCP4 XML" standard is a strong recommendation that we hope will be adopted by most developers. • We aim to provide: • A style guide for XML (inc. when to use XML) • Schemas for the content of XML files (inc. complex data types) • Tools for writing and parsing XML files, for a variety of languages. M.D.Winn, York, March 28th 2006

  5. Steven Ness - XML for Crank Changes for Fortran source code: scaleit, wilson, professs, crossec, phistats Code is in “CCP4-auto” branch of CVS, and on XML-WP web site. Keyword XMLOUT. Can specify exactly what to write out - default is minimal output. E.g. scaleit - 20 possible XML sections, default is 3 of them. M.D.Winn, York, March 28th 2006

  6. Garib/Alexei/Fei - XML from Refmac • Refmac writes XML at end of refinement, including R factors • Activated by XMLOUT on command line. • ARP/wARP write XML file with extra restraints which Refmac can process • MMASS uses XML files internally to relay information required for decision making in process M.D.Winn, York, March 28th 2006

  7. Airlie - XML from Phaser XML output activated by -xml switch. Phaser 1.3.2: contains: cell, symmetry, solution files, etc. Extended for Phaser 2.0 M.D.Winn, York, March 28th 2006

  8. Graeme - DNA / XIA-DP Changes for Fortran source code: mosflm, sortmtz, scala, truncate Code is in main branch of CVS, and in 6.0. Uses XML-writing code in libccp4f Command line DNAOUT. Uses table/list/item hierarchy. M.D.Winn, York, March 28th 2006

  9. Ronan - XML from MrBUMP • Schema for input and output from MrBUMP. Available on XML-WP web site, but out-of-date. Demonstration only! • WSDL file for MrBUMP input available at: • http://clyde.dl.ac.uk/ehtpxWS/BulkMRcluster.xml • Used to auto-generate web service call for portal version of MrBUMP. • But serves as more general definition of MrBUMP input. M.D.Winn, York, March 28th 2006

  10. Dan - Happy • XML input to HAPPy process • http://www.ccp4.ac.uk/HAPPy/docshow.php?doc=design/input.html • Intermediate XML files from HAPPy python objects • information extracted for summary tables • read back in for re-start (TODO) • Writing XML using object write method, and core XML writing class • Reading XML using object read method, and xml.dom.minidom • Example application for creating input XML file • Not using program XML output (yet) because only few quantities required. M.D.Winn, York, March 28th 2006

  11. Avi Naim - Bioxhit • Meeting at DL on 20/10/2005 • http://www.ebi.ac.uk/~naima/bioxhit/bioxhit_at_ebi.html • Includes: • initial version of style guide • suggested crystallographic data types <xsd:complexType> • recommended XML checker • (linked from CCP4 XML site) M.D.Winn, York, March 28th 2006

  12. Where now? • XML is being used by pipeline developers. • Developers are talking to each other, but efforts otherwise independent. • No major overlap yet in XML content. • Variety of XML tools being used. • Top-down imposition of data model may hinder progress. • Feeling that inter-package communication will not be difficult. • Encourage sharing of tools and XML datatypes. M.D.Winn, York, March 28th 2006

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