Date	Files / Description
2013/02/20	Change so remaining download lock files are removed between update retries
2013/02/20	etc/runPrisma
2013/02/18	Change to improve robustness to errors during the unpack/pretranslation phase
2013/02/18	icarus/lion/prisma/pretransPhase.i
2013/01/21	Fix for a problem with cached file listings if prismacheck is used as a standalone program
2013/01/21	icarus/workflows/coreCheckClasses.i
2013/01/09	Fix for a crash in usage reporting if no files are downloaded during a prisma run
2013/01/09	icarus/lion/prisma/printUsageReport.i
2013/01/07	Fix for a problem in the Prisma reports calender if the current month does not have any reports
2013/01/07	icarus/lion/prisma/generateCalendar.i
2012/12/17	Fix for a problem where the prisma installer would hang
2012/12/17	icarus/lion/prisma/generateCalendar.i
2012/12/17	Fix for crashes in srscheck caused by recent code changes for SRS Prisma
2012/12/17	icarus/workflows/coreCheckClasses.i
2012/12/17	Implementented a more accurate estimate for actual download times in the usage report - taking parallel downloads in account
2012/12/17	icarus/lion/prisma/printUsageReport.i
2012/12/10	A large number of improvements and some fixes for SRS Prisma. See README.PRISMA.201212 for full details. Please use the prisma.latest_update.tar.gz archive to install the updates
2012/12/10	etc/runPrisma etc/prismaDownloadProgressCheck icarus/workflows/coreCheckClasses.i icarus/workflows/moveIndicesPhase.i icarus/util/classAttic/Class_PrismaLibResourceUsage_577213218.i icarus/workflows/moveData.i
2012/05/16	Change to prevent prisma from hanging on gibberish in the command timing records
2012/05/16	icarus/lion/prisma/prismatime.i
2012/04/30	Fixed some usage/options display issues for the -help option
2012/04/30	etc/runPrisma
2012/02/29	Change so SRS Prisma will not descend into all subdirectories during recursive downloads if it is clear from the wanted filename patterns that a path can never match those patterns. When applying this update also update the dbsnp.it and dbsnplocation.it files, otherwise prisma will not be able to download dbsnp data
2012/02/29	icarus/lion/prisma/remoteConnection.i
2012/02/29	Fix for a problem where Prisma would try to re-index dependent databases without first having linked the online data to teh offline directories
2012/02/29	icarus/lion/prisma/pretransPhase.i icarus/lion/prisma/localcopyPhase.i icarus/workflows/buildPhase.i
2012/02/29	Fix for a problem where prisma would not index data files in the correct order if only a few fields need re-indexing
2012/02/29	icarus/workflows/checkLocalFiles.i icarus/workflows/coreCheckClasses.i
2012/02/29	Fixes for various problems where SRS would build unneccesary virtual link sets, or would not move them online
2012/02/29	icarus/workflows/linkPhase.i icarus/workflows/getSystemLibs.i
2011/12/16	Fix for a problem where partial link databases for uniprot_trembl where not removed during indexing due too a removal command which was too long for the shell (resulting in an "Argument list too long" error
2011/12/16	icarus/workflows/linkPhase.i
2011/11/03	Added a new option (-novirtual), which will exclude virtual libraries from checking. This is useful in combination with the -nolinks option during first time updates
2011/11/03	etc/runPrisma icarus/workflows/getSystemLibs.i icarus/workflows/srsCheckClasses.i icarus/lion/prisma/prismaCheckMain.i icarus/lion/prisma/prismaCheckClasses.i icarus/workflows/srsCheckMain.i
2011/11/03	Change to ensure that (memory intensive) sort operations are done sequentially and not simultaneously
2011/11/03	icarus/workflows/buildPhase.i
2011/11/03	Change which should result in better parallization if there are multiple unpack commands
2011/11/03	icarus/lion/prisma/pretransPhase.i
2011/11/03	Fix for a problem in srscheck which occurs if the -L option is used in combination with -nolinks
2011/11/03	icarus/workflows/moveData.i
2011/11/03	Fix for a problem with makefile target names when using srscheck with libraries which have dependencies
2011/11/03	icarus/workflows/srsCheckMain.i
2011/11/03	Fix to ensure that all links for relational databases with a staticlinks setting are build
2011/11/03	icarus/workflows/getSystemLibs.i icarus/workflows/linkPhase.i
2011/10/07	Fix for a problem where srscheck correctly detects offline data files which need indexing, but then fails to use the offline settings in the resulting indexing and data move commands
2011/10/07	icarus/workflows/moveData.i icarus/workflows/srsCheckMain.i
2011/08/15	Fix for a problems where prisma would time-out on or misinterpret symbolic links on remote download sites
2011/08/15	icarus/lion/prisma/remoteConnection.i
2011/08/15	Made some changes to the building of links for virtual databases, so a few unnecessay files are no longer build
2011/08/15	icarus/workflows/linkPhase.i
2011/08/12	Some changes so srscheck knows abou database depedencies. This means that databases which share data files (like emblnewfiles/emblnew, refseqfiles/refseqnew or uniseq/uniest) can be indexed in the same srsheck/srsdo run
2011/08/12	icarus/workflows/moveData.i icarus/workflows/srsCheckMain.i icarus/workflows/moveIndicesPhase.i
2011/08/11	Fixes for some problems in prisma, where it would loose track of index files created, or datafiles to be installed, occuring within database dependencies when prisma is used to re-index databases locally. Also a few other minor corrections
2011/08/11	icarus/lion/prisma/checkDependentDbs.i icarus/lion/prisma/movePrismaData.i icarus/lion/prisma/remoteConnection.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/pretransPhase.i icarus/lion/prisma/reformatPhase.i
2011/08/08	Fixes for several issues with srscheck (and also prisma), which in some circomstances could result in srscheck not detecting valid on-line data files, warnings for duplicate targets when running srsdo or prisma, and some wrong link dependencies when multiple links exist between libraries
2011/08/08	icarus/workflows/coreCheckClasses.i icarus/workflows/buildPhase.i icarus/workflows/linkPhase.i
2011/08/03	Fix for a problem where srscheck might not find valid online files
2011/08/03	icarus/workflows/coreCheckClasses.i
2011/06/07	Conversion information needed for old usage objects after extending usage recording in prisma
2011/06/07	icarus/util/classAttic/Class_PrismaLibResourceUsage_2429876272.i icarus/util/classAttic/Class_PrismaResourceUsage_1123318200.i
2011/05/19	Change so the main dates on the prisma reports refer to the date a prisma run was started, and no longer to the date the report was generated (but we still mention the generation date)
2011/05/19	icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/decisionReport.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/printReformatPages.i
2011/05/19	Change to include the display of cpu/walltime and dowload size and time in the prisma usage reports
2011/05/19	icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/cpuslots.il icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/setReportPhase.i icarus/lion/prisma/prismatime.i
2011/05/19	Change to reduce the amount of STDOUT when downloading large files, and a change to allow for a odd behaviour of the ls command on SELinux systems
2011/05/19	icarus/lion/prisma/remoteConnection.i
2011/05/19	Fix for a problem with sending reports by Email in some configurations
2011/05/19	etc/runPrisma icarus/lion/prisma/printMainPage.i
2011/04/20	Fix for a problem where srscheck or prisma might not detect valid online datafiles
2011/04/20	icarus/workflows/coreCheckClasses.i
2011/04/08	Fix for a problem where srscheck and prisma might not find the current datafiles if the indices are missing
2011/04/08	icarus/workflows/coreCheckClasses.i icarus/workflows/coreCheckClasses.i
2011/04/08	Fix for an email problem if reporting is invoked using the reportPrisma command
2011/04/08	icarus/lion/prisma/printMainPage.i
2011/03/29	Fix for a problem where fasta/blast file generation result in duplicates if a fasta file generated by a previous Prisma run is still present in an offline location when a new Prisma run is started
2011/03/29	icarus/lion/prisma/reformatPhase.i
2011/03/28	Fix for a problem where fasta data generated during the Prisma Reformat phase could end up in the STDOUT of a command instead of in a datafile
2011/03/28	icarus/lion/prisma/reformatPhase.i
2011/03/23	Change so srscheck and Prisma will keep the file order for multiple files of the original indexing job in cases where only a few fields are (re-)indexed.
2011/03/23	icarus/workflows/coreCheckClasses.i icarus/workflows/buildPhase.i
2011/03/21	Removed a debug print statement
2011/03/21	icarus/lion/prisma/prismastatus.is
2011/03/01	Change so one cannot activate on obsolete feature image generation feature which we had in provious version of SRS/Prisma
2011/03/01	icarus/lion/prisma/configurePrisma.i
2011/03/01	Fix for a potential crash during the generation of the usage report image if all commands timed during a prisma run have take very little time to complete
2011/03/01	icarus/lion/prisma/cpuslots.il
2011/03/01	Fix for a problem with sending Emails during reporting and monitoring of a prisma run
2011/03/01	icarus/lion/prisma/printMainPage.i icarus/lion/prisma/prismaRunWatcher.i
2011/03/01	We added the collection of timing information to the various checking steps in prisma, so the usage report can show how much time is spend in these stages. Added more timestamps in the debug output, which should help troubleshooting. Removed some duplication of tasks which was occuring between update rounds in prisma.
2011/03/01	icarus/lion/prisma/reformatPhase.i icarus/lion/prisma/prismadata.i icarus/workflows/coreCheckClasses.i etc/runPrisma icarus/lion/prisma/prismaCheckMain.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/inspectClasses.i
2011/03/01	We implemented a new mechanism for staging the index merge steps for large databases, which should greatly reduce the number of partial index files which accumulates in the offline index directory. This can be controlled via a new -mergeThreads command line option available to both srscheck and runPrisma. For a full explanation see README.mergethreads
2011/03/01	icarus/lion/prisma/remoteConnection.i icarus/workflows/srsCheckClasses.i icarus/lion/prisma/checkRemoteFiles.i icarus/workflows/srsCheckMain.i icarus/workflows/buildPhase.i
2011/03/01	We made some changes to the prisma status database to prevent duplicate ID errors occuring during a prisma run
2011/03/01	icarus/lion/prisma/prismastatus.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/prismastatus.is icarus/lion/prisma/prismaview.i icarus/lion/prisma/prismaInvalidate.i
2010/11/01	Extend the method for estimating the uncompressed file size for remote data by using existing local data as a guide to zip archives
2010/11/01	icarus/lion/prisma/checkRemoteFiles.i
2010/11/01	Fix so the inspection part of prisma will not crash if a tool is not part of a group
2010/11/01	icarus/lion/prisma/inspectReport.i
2010/10/26	Fix for a problem with dependent databases which are updated by mirroring, where SRS/Prisma might try to index the data before the downloading of the data has finished.
2010/10/26	icarus/lion/prisma/pretransPhase.i
2010/09/22	Change so prisma will print out a warning during the checking phase if a subdirectory cannot be accessed while traversing a directory tree
2010/09/22	icarus/lion/prisma/remoteConnection.i
2010/09/21	Change to allow for somewhat more flexibility in specifying non-standard fasta and blast converters
2010/09/21	icarus/lion/prisma/reformatPhase.i
2010/09/20	Change which allows the use of database dependencies for libraries which are updateded by mirroring, so they can be scheduled later in the update cycle
2010/09/20	icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/checkDependentDbs.i
2010/07/21	Change to allow for a %d placeholder in an updateCheckCommand
2010/07/21	icarus/lion/prisma/checkRemoteFiles.i
2010/07/21	Fix so prisma will not stop an update if a subdirectory is inaccessible during a recursive download
2010/07/21	icarus/lion/prisma/remoteConnection.i
2010/03/29	Fix for a daylight saving time problem (Dates would be one day out of sync with their day names) with the calendar in the prisma report.
2010/03/29	icarus/lion/prisma/generateCalendar.i
2010/02/17	Fixes for several problems with non-standard link names
2010/02/17	icarus/workflows/moveIndicesPhase.i icarus/workflows/linkPhase.i
2009/12/10	Fix for a problem where SRS or prisma has problems linking/removing/installing datafiles where the file names contain non standard characters. Note that this not cover cases where the filename contains a ?, *, [, ] or single quote
2009/12/10	icarus/workflows/srsCheckMain.i icarus/workflows/coreCheckClasses.i icarus/lion/prisma/movePrismaData.i icarus/lion/prisma/localcopyPhase.i icarus/workflows/moveData.i
2009/12/07	Added an extra safety in our new method of estimating uncompressed file sizes to prevent problems when files grow a lot between releases
2009/12/07	icarus/lion/prisma/checkRemoteFiles.i
2009/12/07	Fix for an access problem for the geneseq download site
2009/12/07	icarus/lion/prisma/remoteConnection.i icarus/lion/prisma/remoteConnection.i
2009/12/04	Fixed a problem with building links for databases with mixed case database names
2009/12/04	icarus/lion/prisma/setReportPhase.i icarus/lion/prisma/moveLibs.i icarus/workflows/linkPhase.i
2009/12/04	Some improvements to the usage report: we make clearer on which nodes failures occur (these node names are now in red), and we now display all failures (previously we only displayed them if they had a runtime of more than one minute). Note that short processes which failed may still be invisible as they can be hidden by subsequent successfull processes in the graph
2009/12/04	icarus/lion/prisma/cpuslots.il
2009/12/03	Fix for a LONG to INT overflow which could cause wrong sizes/times to be reported in the usage reports
2009/12/03	icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaCheckClasses.i
2009/11/03	Fixed an issue with some proxies, and an error reporting issue which could cause a crash
2009/11/03	icarus/lion/prisma/remoteConnection.i
2009/10/21	Implemented a better way of estimating the size of uncompressed datafiles, using older versions of those files (if available) as a template. This should ensure more evenly distributed part sizes when indexing large databases in parts
2009/10/21	icarus/lion/prisma/checkRemoteFiles.i
2009/10/21	Small change to correct a proxy setting for wgetPrisma
2009/10/21	icarus/lion/prisma/remoteConnection.i
2009/08/24	Implemented a new way of removing partial index files after index merging, in order to prevent performence problems due to NFS congestion
2009/08/24	icarus/workflows/linkPhase.i icarus/lion/prisma/prismaCheckMain.i icarus/workflows/srsCheckMain.i icarus/workflows/buildPhase.i
2009/06/29	Change to ensure internal links (ie links within a database) are moved online by prisma
2009/06/29	icarus/lion/prisma/moveLibs.i
2009/05/21	Chanage to fix a problem with calculating partsizes if the partsize is set to very hight values
2009/05/21	icarus/workflows/linkPhase.i icarus/workflows/buildPhase.i
2009/05/21	Improved the removal of symlinked index (and other srs files) from the off-line index directory. They could be left in the off-line index directory after a crash, and a subsequent srscheck or prisma run could try to install them in the online index directory, resulting in self-referential links. The removal of these links at teh start of a run (during the check phase for a library) should prevent this.
2009/05/21	icarus/workflows/coreCheckClasses.i icarus/workflows/srsCheckMain.i icarus/workflows/getSystemLibs.i
2009/05/11	Fix for a problem when detecting a time window for installing new data
2009/05/11	icarus/lion/prisma/checkTimeWindow.i
2009/04/23	Change so we will not use a username and password for anonymous http access, as this can cause problems with some proxy servers
2009/04/23	icarus/lion/prisma/remoteConnection.i
2009/04/23	Fix for a problem where prisma would not run reformat commands with the -forceReformat option if there is nothing else to update
2009/04/23	icarus/lion/prisma/prismaCheckMain.i
2009/02/24	Two major changes in prisma reporting. We now also report the results of the remote checking in the main prisma report page (previously this was in other files, making it difficult to see if there was a problem with access to remote sites), and we now sort the entries in the report so that failures and errors are at the top of the various lists, so you no longer have to scroll through the entire report to find problems
2009/02/24	icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/checkRemoteFiles.i icarus/lion/prisma/dbSync.i icarus/lion/prisma/prismastatus.is icarus/lion/prisma/prismadata.i icarus/lion/prisma/setReportPhase.i icarus/lion/prisma/qualityReport/indicesTest.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/qualityReport/checkidsize.i icarus/lion/prisma/report_resources/images/check_completed.gif icarus/lion/prisma/report_resources/images/check_compErrors.gif icarus/lion/prisma/report_resources/images/local_copy2_failed.gif icarus/lion/prisma/report_resources/images/check_failed.gif icarus/lion/prisma/report_resources/images/local_copy2_compErrors.gif icarus/lion/prisma/report_resources/images/local_copy2_running.gif icarus/lion/prisma/report_resources/images/local_copy2_completed.gif icarus/lion/prisma/report_resources/images/local_copy2_waiting.gif icarus/lion/prisma/report_resources/images/local_copy2_white.gif icarus/lion/prisma/report_resources/images/local_copy2_skipped.gif icarus/lion/prisma/qualityReport/checkindexsize.i icarus/lion/prisma/report_resources/images/check_white.gif
2009/02/11	Fix for a problem where the usage history in the prisma reports would not display statistics (CPU etc) of previous prisma runs. Note that prisma will start to build up a usage history after applying this fix
2009/02/11	icarus/lion/prisma/printUsageReport.i
2009/02/11	fix for a spurious error thrown by rm during the archiving of prisma reports
2009/02/11	icarus/lion/prisma/prismaArchive.i
2008/12/09	Fix for an issue where prisma sometimes would build link-indices on-line
2008/12/09	icarus/workflows/linkPhase.i
2008/11/20	Fix for a problem where in some cases a missing offline data directory could cause prisma to crash
2008/11/20	icarus/lion/prisma/movePrismaData.i
2008/11/13	Changes to make maintenance easier by reducing the number of changes made to these files when ensembl, prisma or emboss are installed. In order to reduce the risk of system confusion about what changes have been made by these packages, we would recommend to first uninstall these packages by running "srspackage -remove srsprisma/emboss/EnsemblRD" (whatever is appropriate in your situation), update srsgen.i and srsdb.i (in you SRSSITE directory), and then reinstalling the packages. For prisma this is done by running "srspackage -install $SRSLION/packages/srsprisma.ip" (make sure you get the latest version of this file). For ensembl this is done by running "srspackage -install $SRSLION/packages/ensembl.ip". For emboss this is done by running "srssetup -emboss" - but see also the notes on upgrading to EMBOSS 6. After applying this update all these packages do is setting the enabled:y flag for the relevant libraries in srsdb.i file, and no changes are made to srsgen.i.
2008/11/13	icarus/lion/packages/srsprisma.ip
2008/11/11	Added a new feature in prisma reports: the usage report will now contain a graph showing the usage of each cpu slot during a prisma run. This can be useful in locating bottlenecks during data processing
2008/11/11	icarus/lion/prisma/cpuslots.il icarus/lion/prisma/prismaGui.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/report_resources/wz_tooltip.js
2008/11/11	Added an option to runPrisma to ignore data move scheduling conditions (-ignoreMoveDataConditions), and improved verbosity indicating why prisma is waiting with moving data online
2008/11/11	icarus/lion/prisma/checkTimeWindow.i icarus/lion/prisma/checkTimeWindow.i icarus/lion/prisma/checkTimeWindow.i
2008/11/11	Change so srscheck and prisma will remove symbolic links in the offline index directory when checking on a library. This will prevent the srsbuild process from writing to these links, and will also prevent these links being moved online, which could result in these files ending up being self-referential links
2008/11/11	icarus/workflows/coreCheckClasses.i
2008/11/11	fixes for some minor tool testing issues in prisma reports
2008/11/11	icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/srsinspect.i icarus/lion/prisma/toolsTestSets.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/PrismaToolsTestDb/testdata.is icarus/lion/prisma/PrismaToolsTestDb/testdb.i icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata icarus/lion/prisma/qualityReport/toolTests.i icarus/lion/prisma/PrismaToolsTestDb/testdb/distmat.testdata
2008/10/02	change so the prisma test databases no longer show up in the web interface
2008/10/02	icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2008/09/04	Fix for a problem where prisma would not honour all timewindows for data installation
2008/09/04	icarus/lion/prisma/checkTimeWindow.i
2008/08/08	Fix for a problem where prisma would not pick up an update scheduled to run on Sundays
2008/08/08	icarus/lion/prisma/prismaCheckClasses.i
2008/04/18	Change so prisma will honour a defaultBatchCommand if no specific batch command is defined for a task
2008/04/18	icarus/lion/prisma/prismaCheckClasses.i
2008/04/17	Fix for a problem where prisma would not execute a reformat command for a dependend library when the -forceReformat option is specified
2008/04/17	icarus/lion/prisma/checkDependentDbs.i
2008/04/09	Change so the fileCountTolerance used by srscheck and prisma is also applied if the nunber of files decreases
2008/04/09	icarus/workflows/checkLocalFiles.i
2008/04/01	Change so the prisma installation procedure will no longer hardcode the full path to the icarus include files for the prisma test databases in srsdb.i
2008/04/01	icarus/lion/packages/srsprisma.ip
2008/03/27	Fix for a problem with recursive traversion of directories on a remote ftp site
2008/03/27	icarus/lion/prisma/remoteConnection.i
2008/03/27	Fix to ensure we remove old content from the current report directory, and an extra check so prisma will not accidentally wipe out all prisma directories
2008/03/27	icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/prismaCheckMain.i
2008/03/26	Fix to ensure we remove old content from the prisma reports
2008/03/26	icarus/lion/prisma/prismaCheckMain.i
2008/03/10	Workaround for a case where the calender generation mechanism gets confused by daylight savings time
2008/03/10	icarus/lion/prisma/generateCalendar.i
2008/02/28	Fixes for various minor inconsistencies with images in prisma reports
2008/02/28	icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/report_resources/images/bwfavicon.ico icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/report_resources/images/backMainPage_up.png icarus/lion/prisma/printMainPage.i icarus/lion/prisma/report_resources/images/backMainPage_down.png icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/report_resources/images/UsageReport_up.png icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/report_resources/images/QuickReference.gif icarus/lion/prisma/report_resources/images/QualityReport_up.png icarus/lion/prisma/inspectReport.i icarus/lion/prisma/report_resources/images/PrismaReport_up.png icarus/lion/prisma/report_resources/images/DecisionReport_up.png icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/report_resources/images/viewReport_up.png icarus/lion/prisma/report_resources/images/toolsTest_up.png icarus/lion/prisma/prismaGuiCal.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/report_resources/images/loadersTest_up.png icarus/lion/prisma/decisionReport.i
2008/01/29	Fix for a problem with dependent databases when a local re-indexing is done
2008/01/29	icarus/lion/prisma/localcopyPhase.i
2007/12/20	Added SRSFLAGS setting preservation for use with integrated config file updates
2007/12/20	etc/runPrisma
2007/12/12	Fixes for some issues when complete offline data/index sets are found by srscheck or prisma. SRS would not remove obsolete online data files, and would also try to use obsolete filenames from the off-line data directory for link index building. We also added additional integrity checking for the offline data/index sets found.
2007/12/12	icarus/workflows/moveIndicesPhase.i icarus/workflows/coreCheckClasses.i icarus/workflows/checkLocalFiles.i
2007/11/14	Fixed a problem with keeping remote file timestamps
2007/11/14	icarus/lion/prisma/dbSync.i
2007/10/09	Fix for problem regarding CPU timimngs returning a non interger value during reporting phase
2007/10/09	icarus/lion/prisma/prismaCheckClasses.i
2007/09/26	fix for a problem when reconfiguring prisma meta update settings
2007/09/26	icarus/lion/prisma/configurePrisma.i
2007/09/19	Added fix to keep SRSPRISMADATE sane when updating config files in a prisma run
2007/09/19	etc/runPrisma
2007/09/17	Change to make sure the timestamp on indices/caches/sortsets are set when they are moved on line. This prevents srs from wanting to rebuild those when there is no need for it. This was happening in cases where the non-default mod timestamp is used for checking
2007/09/17	icarus/workflows/moveIndicesPhase.i
2007/08/24	Fixed a problem for keeping remote file dates after downloads when keepFileDates is set
2007/08/24	icarus/lion/prisma/dbSync.i
2007/07/31	Added wsrefresh/clearCache.sh as default post installation command. Note that this will only be picked up with a fresh new installation of prisma
2007/07/31	icarus/lion/prisma/configurePrisma.i etc/conf/templ-prisma
2007/07/26	Removal of partial indices could couse I/O bottlenecks in some circumstances. To prevent this prisma will now use a batch queueing system (if configured) to distribute these tasks
2007/07/26	icarus/workflows/buildPhase.i
2007/06/20	Fix for a problem where in some cases prisma would not build link indices for a newly indexed database
2007/06/20	icarus/workflows/linkPhase.i
2007/06/15	Another fix to increase stability for quality report generation
2007/06/15	icarus/lion/prisma/inspectReport.i
2007/06/15	Change so prisma will pick up the correct Email address used for anonymous logins from the prisma config file
2007/06/15	icarus/lion/prisma/dbSync.i
2007/05/25	Change to fix a problem with databases dependencies. This fix is required if you use prisma to update the kegg genome and genes dataabses
2007/05/25	icarus/lion/prisma/pretransPhase.i
2007/05/25	various fixes which will makin the tool testing by prisma more stable
2007/05/25	icarus/lion/prisma/srsinspect.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/toolsTestSets.i icarus/lion/prisma/tokenTest.i icarus/lion/prisma/qualityReport/toolTests.i
2007/04/16	Fix for the inclusion of a wrong include file
2007/04/16	icarus/lion/prisma/configUpdate/resolveConfigConflicts.i icarus/lion/prisma/configUpdate/resolveConfigConflicts.i icarus/lion/prisma/configUpdate/importConfigFile.i
2007/03/29	Correction for a bug in srsinspect which could cause crashes if EMBOSS is enabled
2007/03/29	icarus/lion/prisma/inspectReport.i
2007/03/29	Fix to prevent srsinspect from trying to apply rdb specific tests on virtual rdb libraries (these tests do not apply in that case)
2007/03/29	icarus/lion/prisma/qualityReport/rdbTests.i icarus/lion/prisma/qualityReport/rdbTests.i
2007/03/26	Correction for a spelling error which caused srscheck and prisma to crash
2007/03/26	icarus/workflows/moveIndicesPhase.i
2007/03/20	Changes needed to handle multiple links between two databases. It is safe to apply this update now, but some functionality regarding multiple links between two databases will also require updates binaries. These will be available soon (patch release 8.2.0.2)
2007/03/20	icarus/workflows/moveIndicesPhase.i icarus/workflows/linkPhase.i
2007/03/19	Fixes needed to create fieldcache files
2007/03/19	icarus/workflows/coreCheckClasses.i icarus/workflows/buildPhase.i
2007/02/27	Added check to allows srs admins to exclude specific configuration files from being updated by listing them in a file in SRSETC/conf called cuExcludefiles.txt Create and populate this file to make use of this functionality
2007/02/27	icarus/lion/prisma/configUpdate/dbSyncConfig.i
2007/02/23	Added check to allows srs admins to exclude specific configuration files from being updated
2007/02/23	icarus/lion/prisma/configUpdate/dbSyncConfig.i
2007/02/19	Removed icaIsDebug parameter - no longer useable
2007/02/19	icarus/workflows/srsCheckMain.i
2007/02/16	Fix for a problem when using the -user mode of srscheck, resulting in indexfilenames fused to the directory name
2007/02/16	icarus/workflows/coreCheckClasses.i
2007/02/07	Fix needed to merge partial fieldCache files
2007/02/07	icarus/workflows/buildPhase.i
2007/01/09	Fix for a problem with symbolic links, which could caus problems when downloading pdb data
2007/01/09	icarus/lion/prisma/remoteConnection.i
2007/01/04	fix for srscheck/srsdo/srscheck reporting that virtual libs need rebuilding
2007/01/04	icarus/workflows/moveIndicesPhase.i
2006/12/19	Fixes for image locations in reporting phase of configuration update
2006/12/19	icarus/lion/prisma/configUpdate/configUpdateReport.i
2006/12/19	Fixes for inspection report phase of the prisma run
2006/12/19	icarus/lion/prisma/inspectReport.i
2006/12/19	More fixes for images in reports
2006/12/19	icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/dumpTarget.i
2006/12/18	Removal of tableFormat definition
2006/12/18	icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2006/12/15	Fixes for correct location of image locations
2006/12/15	icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/tracePhase.i icarus/lion/prisma/generateKey.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaview.i icarus/lion/prisma/prismaPage.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/prismaTreeImage.i icarus/lion/prisma/prismaGuiCal.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/decisionReport.i
2006/12/15	More fixes for image locations
2006/12/15	icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/generateKey.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/prismaImage.i
2006/11/24	Changes so prisma will use the new downloads.biowisdomsrs.com address for downloading parser updates. Note that you will have to re-configure prisma for this change to take effect, or edit SRSETC/conf/prisma
2006/11/24	icarus/lion/prisma/importPrismaProperties.i etc/conf/templ-prisma icarus/lion/prisma/testRemoteConnection.i
2006/11/02	Fixed a problem where prisma would not detect local files with unusual owner/group names
2006/11/02	icarus/lion/prisma/remoteConnection.i
2006/11/01	Fix for problem with sendmail location not being picked up correctly
2006/11/01	icarus/lion/prisma/printMainPage.i
2006/10/04	Fix for image locations on prisma report pages
2006/10/04	icarus/lion/prisma/dumpTarget.i
2006/10/03	Fix to correctly replace EOL character with when creating html-ised report files
2006/10/03	icarus/lion/prisma/prismaPage.i
2006/10/03	Minor fix for image links when you drill down to some report pages
2006/10/03	icarus/lion/prisma/dumpTarget.i
2006/10/03	Reversal of minor fix for image links when you drill down to some report pages
2006/10/03	icarus/lion/prisma/dumpTarget.i
2006/10/02	updated README file
2006/10/02	README.prisma
2006/09/29	Fixed a problem where configurePrisma would not accept empty strings as answers for a few specialized options
2006/09/29	icarus/lion/prisma/configurePrisma.i
2006/09/29	Fixed some problems which occur when prisma is not using the default location for reports
2006/09/29	icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/report_resources/images/successWithErrors.gif icarus/lion/prisma/report_resources/images/bw_logo.gif etc/runPrisma icarus/lion/prisma/printMovePages.i icarus/lion/prisma/configurePrisma.i icarus/lion/prisma/report_resources/images/backMainPage_up.png icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/report_resources/images/UsageReport_up.png icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/report_resources/images/UsageReport_down.png icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/report_resources/images/SRSPrisma.gif icarus/lion/prisma/report_resources/images/QualityReport_up.png icarus/lion/prisma/report_resources/images/QualityReport_down.png icarus/lion/prisma/inspectReport.i icarus/lion/prisma/report_resources/images/PrismaReport_up.png icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/report_resources/images/PrismaReport_down.png icarus/lion/prisma/tracePhase.i icarus/lion/prisma/report_resources/images/DecisionReport_up.png icarus/lion/prisma/generateKey.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/report_resources/images/DecisionReport_down.png icarus/lion/prisma/report_resources/images/help_center.gif icarus/lion/prisma/prismaPage.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/prismaTreeImage.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/decisionReport.i icarus/lion/prisma/report_resources/images/suggested_action.gif icarus/lion/prisma/prismaArchive.i
2006/09/19	Added fix to check if member libraries have been updated or just virtual, if just virtual, omit adding additional targets to ensure correct synchronisation of moving libraries online
2006/09/19	icarus/workflows/moveIndicesPhase.i
2006/09/08	Change needed to handle to building of static link indices for relational databases
2006/09/08	icarus/workflows/linkPhase.i
2006/09/01	Added fix to avoid srscheck/srsdo/srscheck reporting that virtual libraries need building when they've just been built
2006/09/01	icarus/workflows/moveIndicesPhase.i
2006/08/21	Change so we do not try to build sort sets for virtual libraries of which the members are relational libraries
2006/08/21	icarus/workflows/getSystemLibs.i
2006/08/18	Added a warning about the need to add usernames and passwords for automatic parser updates to SRSETC/conf/prisma
2006/08/18	icarus/lion/prisma/configurePrisma.i
2006/08/18	Corrected the default download settings for automatic parser updates. Note that you will still have to edit SRSETC/conf/prisma to set username and passwords
2006/08/18	etc/conf/templ-prisma
2006/08/18	Correction for a situation where the update config script would throw an error whent trying to detect a running visad server on sytems where /bin/sh is not equivalent to /bin/bash
2006/08/18	etc/updateConfigFiles.sh
2006/08/18	Correction for an error which caused the correct value of SRSROOT not to be inserted in prep_srs_offline.sh during installation
2006/08/18	icarus/lion/prisma/configUpdate/templ-prep_srs_offline.sh
2006/07/14	Changed logo gif to BioWisdom
2006/07/14	icarus/lion/prisma/configUpdate/configUpdateReport.i
2006/06/22	Fix for a problem where prisma would not download files from subdirectories
2006/06/22	icarus/lion/prisma/remoteConnection.i