DateFiles / Description
2017-07-03 Fix for a problem with recursive mirroring if multiple remote directories are specified
icarus/lion/prisma/remoteConnection.i
2017-06-23 Removed the escaping of backticks in unpackcommands, as this was causing instability. You may have to review unpackCommands which use backticks in an environment where you also use a batch queue system to ensure that they work as expected
icarus/lion/prisma/pretransPhase.i
2017-05-31 Fix for some spurious warnings during the check phase of srscheck and Prisma
icarus/workflows/getSystemLibs.i
2017-05-30 A number of fixes/improvements for SRS Prisma: Improved stability when using batch queues, Fixed a reporting issus for the check phase, where remote site check problems weher not reported in the Prisma Reports, Fixed a number of problems which where Prisma would show error messages, where actually nothing was wrong
icarus/workflows/coreCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/pretransPhase.i
icarus/workflows/linkPhase.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/moveLibs.i
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/setReportPhase.i
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/generateCalendar.i
icarus/workflows/buildPhase.i
2016-04-14 Improved date checking when comparing file date stamps with those on a remote location in cases where datafiles are not unpacked
icarus/lion/prisma/dbSync.i
2015-12-23 Fixed some issues with chunk and chunksize parallelization
icarus/workflows/linkPhase.i
icarus/workflows/buildPhase.i
2015-11-25 Fixes for problems with dealing with compressed data files and some other bugs
icarus/lion/prisma/checkRemoteFiles.i
icarus/workflows/buildPhase.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/coreCheckClasses.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/linkPhase.i
2015-10-27 Improved stability of the code for drawing the Prisma CPU slot usage image
icarus/lion/prisma/cpuslots.il
2015-08-13 fix for a problem with creating blast indices from file which is already in fasta format
icarus/lion/prisma/reformatPhase.i
2015-03-25 Fix for errors thrown during the removal of partial link indices
icarus/workflows/linkPhase.i
2015-01-23 Fix for a problem induced by the new virtual library defintions for the 2015 release of Medline
icarus/workflows/buildPhase.i
icarus/lion/prisma/analyseLibs.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/linkPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/getSystemLibs.i
2014-12-08 Update for SRS Prisma and srscheck which includes
  • A new -p option which allows you to include parent/dependent libraries on the command line without having to specify all of them, like "runPrisma -l embl" to update all libraries involved in the EMBL virtual library
  • A significant speedup during the check phase for very large libraries, like the WGS sections of EMBL/GenBank/DDBJ
  • Improved statbility in cases where the exit status of Sun Grid Engine qrsh does not reliably reflect a failure
  • Fix for an issue with the removal of partial .mergeinf files during the merge phase
  • A few other minor bug fixes
icarus/workflows/buildPhase.i
icarus/lion/prisma/analyseLibs.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/srsCheckMain.i
icarus/lion/prisma/prismaArchive.i
etc/runPrisma
icarus/workflows/linkPhase.i
icarus/workflows/getSystemLibs.i
icarus/workflows/srsCheckClasses.i
icarus/lion/prisma/prismaArchive.i
2014-08-04 Update for SRS Prisma to handle https connections correctly. Note that differing versions of the shared ssl libaries may mean that you will have to compile the wgetPrisma binaries yourself (the source code is provided in SRSROOT/gnu_src)
icarus/lion/prisma/remoteConnection.i
2014-07-10 Improved stability of data processing by SRS Prisma by catching situations where a batch queue returns a exit status of 0 despite failing to execute a command. This has been seen with SGE
icarus/workflows/buildPhase.i
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/downloadPhase.i
icarus/workflows/linkPhase.i
icarus/lion/prisma/pretransPhase.i
2014-04-14 Fix for a problem with the localcopy command for processing of non-SRS data by SRS Prisma
icarus/workflows/buildPhase.i
2014-03-20 Fix for a problem in srscheck with database dependencies if only link indices are build
icarus/workflows/moveIndicesPhase.i
2014-03-18 Change so srscheck and SRS Prisma will be able to recognize link indices which have become unreadable after an index structure change and then remove and rebuild them.
icarus/workflows/linkPhase.i
2014-03-17 Fix for a problem caused by an = sign in the datafiles for the intact databases. The = sign has a special meaning the the makefiles SRS Prisma generates, and its presence in a file name would break the processing of the makfile, resulting in complete failures of SRS Prisma runs
icarus/lion/prisma/downloadPhase.i
2014-01-28 Change soe SRS Prisma can determine time stamps from file listings which contain a space in the group name, and a fix for a problem with recursive updates using the file (copy) protocol
icarus/lion/prisma/remoteConnection.i
2014-01-28 Change the way the number of download/index chains is calculated, which should allow for a more efficient usage of download and index cpu slots during updates
icarus/lion/prisma/downloadPhase.i
2014-01-28 Fix for a file installation problem if a file is both an indexed SRS database and a FASTA searchable database
icarus/lion/prisma/reformatPhase.i
2014-01-28 Fix for a potential problems with the setting for the maximum number of simultaneous downloads allowed by SRS Prisma
icarus/lion/prisma/dbSync.i
2014-01-13 Fix for a problems with the Prisma test databases if blast is not enabled
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2014-01-09 Fix for a command line option interpretation problems with srsinspect
icarus/lion/prisma/srsinspect.i
2014-01-08 Change so restartPrisma cannot be used if the Prisma job has entered the move phase (at which point it is too late for a restart), and a change so restartPrisma will pick up the original runPrisma command line parameters
etc/runPrisma
etc/restartPrisma
2014-01-08 Removed some tests from the Prisma quality report which are irrelevant for SRS8.4, and improved output for resource and tool tests
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest1.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/qualityReport/resourceObjectCheck.i
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest
icarus/lion/prisma/getappls.i
icarus/lion/prisma/qualityReport/indicesTest.i
2013-12-06 Added a new errorLimit option to our fasta sequence conversion tool, which allows you to set a maximum number of errors allowed before exiting with a fail
icarus/lion/prisma/getFastaSequence.i
2013-12-02 Fix for a problem with srscheck and SRS Prisma when it would detect a discrepance between SRS indices and solr/lucene, call for re-indexing of the database involved, but not move the new indices on-line
icarus/workflows/checkLocalFiles.i
2013-11-29 Change so getFastaSequence.i will print out the entry name in the error output if it cannot retrieve a sequence
icarus/lion/prisma/getFastaSequence.i
2013-10-24 Fix for a problem with Prisma reports for file downloads if files are in subdirectories on the remote site
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/setReportPhase.i
icarus/lion/prisma/printDownloadPages.i
2013-10-02 Fix for a problem in srscheck, where it would try to move virtual library files online before they have been build, occuring when the -force option is usd to rebuild the virtual library
icarus/workflows/moveIndicesPhase.i
2013-09-05 Fix for a problem where prisma would hang on building the prismatimelinks database on some platforms, and removed an unnecessary error message generated by archive checking
icarus/lion/prisma/prismatime.is
icarus/lion/prisma/prismaArchive.i
2013-09-05 Removed some debug prints which were displayed during the remote check phase
icarus/lion/prisma/checkRemoteFiles.i
2013-08-13 Fixed a problem with building fieldCache files for databases which use lucene indices
icarus/workflows/coreCheckClasses.i
2013-08-13 Fixed a problem with database dependencies, which was giving problems for several Kegg databases
icarus/lion/prisma/localcopyPhase.i
2013-08-05 Fix for problems caused by different levels of escaping needed by batchqueues and plain shelld when backticks are used in unPackCommands
icarus/lion/prisma/pretransPhase.i
2013-07-26 Improved the touch option of srscheck (invoked by "srscheck -t") so it will now also touch link indices and the various caches and sortset files which srs uses
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i