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Database Schemas
The database actually consists of several distinct schemas. Each schema serves a different set of functions:
- DESCINFO2. Records configuration of parameters, templates, value lists, and users for the descriptive information eco-system.
- LIMS. The sample catalog and repository of experimental results against those samples. Includes a catalog of files (ASMAN) associated with those samples.
- OPS. Repository of drilling operations information. Bathymetry and navigation content was removed from here as of Subic Bay Tie-up 353P Oct 23, 2014. The content is time and activity based, not sample based. Other workflows manage the bulk of this data outside Oracle. What is recorded here is a small subset of the total operational content we keep.
- TRANSFER.
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- Contains the scripts and tables for data transfer and cleanup processes you will be running.
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Cleaning Process Architecture
End-of-expedition processing leaves data in LIMSin LIMS, TRANSFER. That content may be removed. The beginning-of-expedition processing removes that content. The procedures to conduct the removal are owned by the TRANSFER schemathe TRANSFER schema.
An Annoyance: Monitoring for Archive Log Space Filling
Oracle treats the changes resulting from end-of-expedition processing just like any other transactions. Due to the size of these transactions it is likely that the 100GiB reserved for archive logging will be consumed. When this occurs, the database blocks all activity until archive log space is freed. All attempts at new transactions will receive the message message ORA-00257: archiver stuck.As an Oracle sysdba user, apply this command--via
This method of releasing the archiver assumes there is actually some spare space on the system. Via a DBA account--to increase the amount of archive log space available:alter system set db_recovery_file_dest_size=1000G scope=memory;
The ODA systems carry plenty of disk. The above will get Oracle back up and running with enough breathing room for you to connect and do the following.
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- Must be logged into this page and monitoring the database before the archive logger blocks. If the archive logger is already blocked current experience indicates that OEM is not effecteffective. Direct host login to RMAN becomes necessary.
- The OEM times out your login in about 10/15 minutes. If running out of archive log space is still a real concern with a terabyte of disk, refresh the page frequently.
- Until MCS and developers become more comfortable with the backup process, it is preferable to increase archive log space by the alter system commands above.
- The OEM provides email alerts that trigger on thresholds (e.g. percentage of archive log space filled). Notification settings are determined by the OEM manager.
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Repeat asmanRepeat asman_catalog_delete for delete for as many catalogs as you desire to remove. Confirm removal by re-running the survey script. Commit when done.
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This is the big one. Monitor archive logs. Start it in a stable environment that you know won't be rebooted in anywhere from 6-20 hours. Check on it using SQL to count sample/test/result rows, or watch it via Monitor Sessions in SQLDeveloper. With curr
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Some expeditions are continuations or extensions of previous work. For convenience, the science party may require a local copy of previous samples and analytical content.If small amounts of legacy material is brought out for re-sampling, re-analysis, it is easiest to just re-catalog the material in LIMS with SampleMaster.Legacy data are available online and are already on ship. For most purposes there is not really a requirement for the legacy Janus content to be migrated to LIMS.Should the migration requirement be real: a tool exists to do so. However, Janus2Lims is so infrequently used it will require modification to be made functional for the need. So plan ahead.
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For new participants and staff to experience and practice using integrated shipboard systems, it is helpful to have some data to play with. The same is required for development that continues between expeditions.
Records are de facto accumulated against an expedition/project called TEST 999. After awhile it is helpful to clean out tests and results. Be judicious and selective. Ask around: is anyone using this data? For example, sometimes end-user testing or development is in progress that of which you may not have been aware of. Once you have go-ahead, it is often sufficient to clean out tests and results. Unless specifically testing sample cataloging we prefer to avoid the effort of recreating a complete and representative set of samples. These clean out scripts should only be used in the scenario where samples are being preserved [curatorial tests and results], but science data [non-curatorial] tests and results are being removed.
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