SRS Prisma 4.2 Updates
Latest SRS Prisma 4.2 Updates
| Date | Files / Description |
|---|---|
| 2010/07/21 | Change to allow for a %d placeholder in an updateCheckCommand | 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 | 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. | icarus/lion/prisma/generateCalendar.i |
| 2010/02/17 | Fixes for several problems with non-standard link names | icarus/workflows/linkPhase.i icarus/workflows/moveIndicesPhase.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 | icarus/lion/prisma/localcopyPhase.i icarus/workflows/moveData.i icarus/workflows/srsCheckMain.i icarus/lion/prisma/movePrismaData.i icarus/workflows/coreCheckClasses.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 | icarus/lion/prisma/checkRemoteFiles.i |
| 2009/12/07 | Fix for an access problem for the geneseq download site | 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 | icarus/lion/prisma/moveLibs.i icarus/workflows/linkPhase.i icarus/lion/prisma/setReportPhase.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 | 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 | icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/printUsageReport.i |
| 2009/11/03 | Fixed an issue with some proxies, and an error reporting issue which could cause a crash | 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 | icarus/lion/prisma/checkRemoteFiles.i |
| 2009/10/21 | Small change to correct a proxy setting for wgetPrisma | 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 | icarus/workflows/srsCheckMain.i icarus/lion/prisma/prismaCheckMain.i icarus/workflows/buildPhase.i icarus/workflows/linkPhase.i |
| 2009/06/29 | Change to ensure internal links (ie links within a database) are moved online by prisma | 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 | 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. | icarus/workflows/getSystemLibs.i icarus/workflows/coreCheckClasses.i icarus/workflows/srsCheckMain.i |
| 2009/05/11 | Fix for a problem when detecting a time window for installing new data | 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 | 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 | 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 | icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/setReportPhase.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/checkRemoteFiles.i icarus/lion/prisma/prismadata.i icarus/lion/prisma/dbSync.i icarus/lion/prisma/qualityReport/indicesTest.i icarus/lion/prisma/qualityReport/checkindexsize.i icarus/lion/prisma/report_resources/images/local_copy2_running.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/check_white.gif icarus/lion/prisma/report_resources/images/local_copy2_waiting.gif icarus/lion/prisma/report_resources/images/local_copy2_compErrors.gif icarus/lion/prisma/report_resources/images/check_compErrors.gif icarus/lion/prisma/qualityReport/checkidsize.i icarus/lion/prisma/report_resources/images/local_copy2_completed.gif icarus/lion/prisma/report_resources/images/local_copy2_white.gif icarus/lion/prisma/prismastatus.is icarus/lion/prisma/report_resources/images/check_completed.gif icarus/lion/prisma/report_resources/images/local_copy2_skipped.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 | icarus/lion/prisma/printUsageReport.i |
| 2009/02/11 | fix for a spurious error thrown by rm during the archiving of prisma reports | icarus/lion/prisma/prismaArchive.i |
| 2008/12/09 | Fix for an issue where prisma sometimes would build link-indices on-line | 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 | 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. | 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 | icarus/lion/prisma/prismaGui.i icarus/lion/prisma/report_resources/wz_tooltip.js icarus/lion/prisma/cpuslots.il icarus/lion/prisma/printUsageReport.i |
| 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 | 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 | icarus/workflows/coreCheckClasses.i |
| 2008/11/11 | fixes for some minor tool testing issues in prisma reports | icarus/lion/prisma/toolsTestSets.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/srsinspect.i icarus/lion/prisma/PrismaToolsTestDb/testdb/distmat.testdata icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/qualityReport/toolTests.i icarus/lion/prisma/PrismaToolsTestDb/testdata.is icarus/lion/prisma/PrismaToolsTestDb/testdb.i icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata |
| 2008/10/02 | change so the prisma test databases no longer show up in the web interface | icarus/lion/prisma/PrismaToolsTestDb/testdb.i |
| 2008/09/04 | Fix for a problem where prisma would not honour all timewindows for data installation | 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 | 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 | 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 | 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 | 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 | icarus/lion/packages/srsprisma.ip |
| 2008/03/27 | Fix for a problem with recursive traversion of directories on a remote ftp site | 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 | icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/prismaCheckMain.i |
| 2008/03/26 | Fix to ensure we remove old content from the prisma reports | icarus/lion/prisma/prismaCheckMain.i |
| 2008/03/10 | Workaround for a case where the calender generation mechanism gets confused by daylight savings time | icarus/lion/prisma/generateCalendar.i |
| 2008/02/28 | Fixes for various minor inconsistencies with images in prisma reports | icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/prismaGuiCal.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/decisionReport.i icarus/lion/prisma/report_resources/images/viewReport_up.png icarus/lion/prisma/report_resources/images/backMainPage_down.png icarus/lion/prisma/report_resources/images/loadersTest_up.png icarus/lion/prisma/report_resources/images/QuickReference.gif icarus/lion/prisma/report_resources/images/toolsTest_up.png icarus/lion/prisma/report_resources/images/backMainPage_up.png icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/report_resources/images/UsageReport_up.png icarus/lion/prisma/inspectReport.i icarus/lion/prisma/report_resources/images/DecisionReport_up.png icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/report_resources/images/QualityReport_up.png icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/report_resources/images/PrismaReport_up.png icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/report_resources/images/bwfavicon.ico |
| 2008/01/29 | Fix for a problem with dependent databases when a local re-indexing is done | icarus/lion/prisma/localcopyPhase.i |
| 2007/12/20 | Added SRSFLAGS setting preservation for use with integrated config file updates | 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. | icarus/workflows/coreCheckClasses.i icarus/workflows/checkLocalFiles.i icarus/workflows/moveIndicesPhase.i |
| 2007/11/14 | Fixed a problem with keeping remote file timestamps | icarus/lion/prisma/dbSync.i |
| 2007/10/09 | Fix for problem regarding CPU timimngs returning a non interger value during reporting phase | icarus/lion/prisma/prismaCheckClasses.i |
| 2007/09/26 | fix for a problem when reconfiguring prisma meta update settings | icarus/lion/prisma/configurePrisma.i |
| 2007/09/19 | Added fix to keep SRSPRISMADATE sane when updating config files in a prisma run | 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 | icarus/workflows/moveIndicesPhase.i |
| 2007/08/24 | Fixed a problem for keeping remote file dates after downloads when keepFileDates is set | 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 | etc/conf/templ-prisma icarus/lion/prisma/configurePrisma.i |
| 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 | 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 | icarus/workflows/linkPhase.i |
| 2007/06/15 | Another fix to increase stability for quality report generation | 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 | 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 | icarus/lion/prisma/pretransPhase.i |
| 2007/05/25 | various fixes which will makin the tool testing by prisma more stable | icarus/lion/prisma/toolsTestSets.i icarus/lion/prisma/srsinspect.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/qualityReport/toolTests.i icarus/lion/prisma/tokenTest.i |
| 2007/04/16 | Fix for the inclusion of a wrong include file | 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 | 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) | 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 | 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) | icarus/workflows/moveIndicesPhase.i icarus/workflows/linkPhase.i |
| 2007/03/19 | Fixes needed to create fieldcache files | icarus/workflows/buildPhase.i icarus/workflows/coreCheckClasses.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 | icarus/lion/prisma/configUpdate/dbSyncConfig.i |
| 2007/02/23 | Added check to allows srs admins to exclude specific configuration files from being updated | icarus/lion/prisma/configUpdate/dbSyncConfig.i |
| 2007/02/19 | Removed icaIsDebug parameter - no longer useable | 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 | icarus/workflows/coreCheckClasses.i |
| 2007/02/07 | Fix needed to merge partial fieldCache files | icarus/workflows/buildPhase.i |
| 2007/01/09 | Fix for a problem with symbolic links, which could caus problems when downloading pdb data | icarus/lion/prisma/remoteConnection.i |
| 2007/01/04 | fix for srscheck/srsdo/srscheck reporting that virtual libs need rebuilding | icarus/workflows/moveIndicesPhase.i |
| 2006/12/19 | Fixes for image locations in reporting phase of configuration update | icarus/lion/prisma/configUpdate/configUpdateReport.i |
| 2006/12/19 | Fixes for inspection report phase of the prisma run | icarus/lion/prisma/inspectReport.i |
| 2006/12/19 | More fixes for images in reports | icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/generateCalendar.i |
| 2006/12/18 | Removal of tableFormat definition | icarus/lion/prisma/PrismaToolsTestDb/testdb.i |
| 2006/12/15 | Fixes for correct location of image locations | icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/tracePhase.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/prismaview.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaTreeImage.i icarus/lion/prisma/decisionReport.i icarus/lion/prisma/prismaPage.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/generateKey.i icarus/lion/prisma/prismaGuiCal.i icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/dumpTarget.i |
| 2006/12/15 | More fixes for image locations | icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/prismaImage.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/generateKey.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/dumpTarget.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 | icarus/lion/prisma/importPrismaProperties.i icarus/lion/prisma/testRemoteConnection.i etc/conf/templ-prisma |
| 2006/11/02 | Fixed a problem where prisma would not detect local files with unusual owner/group names | icarus/lion/prisma/remoteConnection.i |
| 2006/11/01 | Fix for problem with sendmail location not being picked up correctly | icarus/lion/prisma/printMainPage.i |
| 2006/10/04 | Fix for image locations on prisma report pages | icarus/lion/prisma/dumpTarget.i |
| 2006/10/03 | Fix to correctly replace EOL character with when creating html-ised report files | icarus/lion/prisma/prismaPage.i |
| 2006/10/03 | Minor fix for image links when you drill down to some report pages | icarus/lion/prisma/dumpTarget.i |
| 2006/10/03 | Reversal of minor fix for image links when you drill down to some report pages | icarus/lion/prisma/dumpTarget.i |
| 2006/10/02 | updated README file | README.prisma |
| 2006/09/29 | Fixed a problem where configurePrisma would not accept empty strings as answers for a few specialized options | icarus/lion/prisma/configurePrisma.i |
| 2006/09/29 | Fixed some problems which occur when prisma is not using the default location for reports | icarus/lion/prisma/tracePhase.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/decisionReport.i icarus/lion/prisma/prismaTreeImage.i icarus/lion/prisma/prismaPage.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/report_resources/images/suggested_action.gif icarus/lion/prisma/report_resources/images/bw_logo.gif icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/report_resources/images/successWithErrors.gif icarus/lion/prisma/report_resources/images/help_center.gif icarus/lion/prisma/report_resources/images/backMainPage_up.png icarus/lion/prisma/report_resources/images/UsageReport_up.png icarus/lion/prisma/inspectReport.i etc/runPrisma icarus/lion/prisma/report_resources/images/UsageReport_down.png icarus/lion/prisma/report_resources/images/SRSPrisma.gif icarus/lion/prisma/report_resources/images/QualityReport_up.png icarus/lion/prisma/generateKey.i icarus/lion/prisma/report_resources/images/QualityReport_down.png icarus/lion/prisma/report_resources/images/PrismaReport_up.png icarus/lion/prisma/report_resources/images/PrismaReport_down.png icarus/lion/prisma/report_resources/images/DecisionReport_up.png icarus/lion/prisma/report_resources/images/DecisionReport_down.png icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/configurePrisma.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printBuildPages.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 | icarus/workflows/moveIndicesPhase.i |
| 2006/09/08 | Change needed to handle to building of static link indices for relational databases | 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 | 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 | 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 | 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 | 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 | 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 | icarus/lion/prisma/configUpdate/templ-prep_srs_offline.sh |
| 2006/07/14 | Changed logo gif to BioWisdom | icarus/lion/prisma/configUpdate/configUpdateReport.i |
| 2006/06/22 | Fix for a problem where prisma would not download files from subdirectories |
| icarus/lion/prisma/remoteConnection.i |
