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CCP4 Database Automation: Usage, Requirements, and Current State of Affairs

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This document outlines the usage, requirements, and current state of affairs concerning the CCP4 database, focusing on automation within CCP4 projects at Daresbury. It highlights various aspects such as data storage, tracking jobs, and knowledge bases associated with software like CCP4i and HAPPy. Topics covered include individual versus central databases, security models, data types, object persistence, and the importance of templates and protocols in the workflow. The document serves as a comprehensive guide for ongoing and future projects in the CCP4 community.

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CCP4 Database Automation: Usage, Requirements, and Current State of Affairs

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  1. “Database” usage and requirements for CCP4 automation CCP4 database meeting

  2. Projects at Daresbury • HAPPy - experimental phasing • DJR, PE, EJD, CCB • XIA-DPA - dataprocessing (other) • GW (DNA) • BMP - molecular replacement • RK, MDW (NDS) • CCP4i • PJB • Data storage • WY, PJB CCP4 database meeting

  3. Tracking Persistence Current state of affairs Project Job Fact Project_id Name Job_id Name Name_id Fact • Database or filesystem • Individual or central • Security models Dingbat dingbat_id dingbat CCP4 database meeting

  4. (Loose) Storage Requirements • Tracking (Jobs) - ccp4i, HAPPy • Data types • Knowledge base - ccp4i • Object persistence - GW • Templates and protocols - eHTPX External view Project Control CCP4 database meeting

  5. Job Tracking • Workflow view • Database or filesystem • Track progress • ccp4i gives good example CCP4 database meeting

  6. HAPPy view • Nodes (actions) • Type: Job, Fork, Decision, Start, End (Container) • Status: Success, Failed, Killed, Running • Time stamps • Human readable notes • Designed to work with ccp4i database. CCP4 database meeting

  7. Data tracking • Meta data (describe file) • URI • Wavelength • Cell • Column names • Source and usage CCP4 database meeting

  8. Knowledge base • Small amounts of data -> xml files, otherwise database • Project and pipeline independent • mmcif definitions at deposition end • Datamodel (?) • HA positions and statistics • x, y, z, occ, anon_occ, b • Sequence • Solvent fraction • MR models CCP4 database meeting

  9. Persistent Objects (databucket) • Project specific (unless common) • Store local state • object orientated database (ZODB) • dingbats • .xml file • HAPPy has HAPPy state object • always in memory • current state and history • persistence required for restart CCP4 database meeting

  10. Protocols and Templates • User preferences • Pathways / Workflow CCP4 database meeting

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