Release notes for BinBase versions

Release Notes - BinBase -  version 3.3

• [BINBASE-272] - add publications to the website
• [BINBASE-237] - we need to provide support to set one configuration for a column
• [BINBASE-241] - bellerophon needs to show which database and which application server it's using right now
• [BINBASE-243] - bellerophon anotated specs view needs more features
• [BINBASE-244] - bellerophon it needs to be possible to filter more views
• [BINBASE-248] - if we export a class all related samples are exported and not only the visible ones
• [BINBASE-258] - maven build system does not work anymore since yesterday morning
• [BINBASE-264] - binbase scheduler url problem
• [BINBASE-287] - system crashes during netcdf replacement
• [BINBASE-288] - check cache updata times, they don't seem to work corretly
• [BINBASE-294] - local cluster node - hangs when an exception occures
• [BINBASE-296] - null pointer exception during periodical start of a node
• [BINBASE-298] - shiaz rocks cluster creates problems
• [BINBASE-311] - binbase installer does set the right setupx url
• [BINBASE-247] - anotation views needs filter
• [BINBASE-252] - retention index correction
• [BINBASE-253] - binbase runtime monitor views should be sortable for easier management
• [BINBASE-260] - improve simialrity search
• [BINBASE-261] - highlight bins which are found in any selected library
• [BINBASE-262] - link bins in exports to webgui
• [BINBASE-269] - there needs to be a way to install binbase cluster support without the internet
• [BINBASE-282] - logging categories
• [BINBASE-284] - it needs to be possible to see the actual samples of a result and not only the classes it was created from
• [BINBASE-285] - show a progress monitor during result creation
• [BINBASE-293] - create a service which checks the queue all 5 mintues and starts a node in case it's not empty
• [BINBASE-195] - provide a way to track locks
• [BINBASE-230] - it must be possible to find all standards from C4 - C30
• [BINBASE-246] - summarize massspec
• [BINBASE-250] - we need to add a filter to filter views by similarity
• [BINBASE-251] - create an espter to log4j appender
• [BINBASE-263] - simple nist matcher
• [BINBASE-266] - we need a file based cache which just stores the cached objects in a directory of our choice
• [BINBASE-267] - cache needs to be updated once a night
• [BINBASE-278] - write a parser which find a pegasus massspecs in a file
• [BINBASE-279] - simplified usage of the webgui
• [BINBASE-259] - All bins as NIST MSP file format
• [BINBASE-312] - update logo to reflect binbase 3.3

Release Notes - BinBase -  version 3.2

no notes, internal release only

Release Notes - BinBase -  version 3.1

• [BINBASE-202] - provide a datafile implementaion which works on a fixed array instead of a vector
• [BINBASE-212] - binbase module tests are failing right now, related to deployment problems
• [BINBASE-163] - we need to find out why the multi module compiling does not work
• [BINBASE-180] - we need to recalculate samples from time to time to keep statistics up to date
• [BINBASE-189] - binbase web gui - massspecs need to be rendered as integer and not as double
• [BINBASE-201] - we get exceptions from the cluster after a while
• [BINBASE-206] - exportet results are off, somehow related to the export, the import seems to be fine
• [BINBASE-209] - ear deployment doesnt work right now
• [BINBASE-218] - webgui does not work for some strange reasons
• [BINBASE-207] - reduce the amount of logging for the simple cache
• [BINBASE-208] - provide profiles for reduced build times and remove wait times during test builds
• [BINBASE-181] - update binbase once in a week tool needed
• [BINBASE-215] - integrate setupx connection into the installer

Version binbase version 3.0 - first open source version

• [BINBASE-108] - create postgres compatible schema
• [BINBASE-120] - get these modules running - http://www.eclipse.org/articles/article.php?file=Article-Eclipse-and-Maven2/index.html
• [BINBASE-122] - class loading problem
• [BINBASE-130] - login dialog does not work
• [BINBASE-131] - hibernate model threws exceptions related to that two threads try to modify a session at the same time
• [BINBASE-133] - creating comments does not work
• [BINBASE-134] - cant create reference classes
• [BINBASE-136] - not possible to cassify bins
• [BINBASE-140] - product needs to be packed as a rcp
• [BINBASE-141] - login wizard throws a Null pointer exception during authentification
• [BINBASE-143] - deadlock it happends from time to time that a deadlock occures
• [BINBASE-144] - graphs dont work since they are missing some awt libraries in the rcp package
• [BINBASE-149] - bellerophon crashes when view is closed and repopended afterwards with a dead lock
• [BINBASE-150] - we need a menu to create a ri correction standard
• [BINBASE-151] - we need a menu to define ion ratios
• [BINBASE-96] - we need to write a hibernate and sql implementaion + test cases
• [BINBASE-98] - externalize all sql statements
• [BINBASE-99] - write sql statement tester and compiler
• [BINBASE-109] - hibernate interface does not work with posgres, we need to adjust all tables to the new table names
• [BINBASE-111] - development cluster fails with serialisation error
• [BINBASE-121] - figure out how to pack a project
• [BINBASE-132] - creating and deleting of bin groups does not work
• [BINBASE-137] - provide tests for client side
• [BINBASE-138] - provide tests for server side
• [BINBASE-139] - we got a problem with the used factory on the jboss application server
• [BINBASE-145] - nullpointer exception happens sometimes
• [BINBASE-147] - ant tasks needed to configure jmx bean
• [BINBASE-152] - we need a progress monitor when we delete object or so
• [BINBASE-155] - need to be possible to import samples using bellerophon
• [BINBASE-159] - integration with cluster status is missing
• [BINBASE-167] - binbase client needs jmx with stored key
• [BINBASE-168] - we needs a services to maintains a collections of valid keys
• [BINBASE-170] - query bins by id
• [BINBASE-171] - show species to bins
• [BINBASE-172] - show organ to bin
• [BINBASE-173] - show similar bins
• [BINBASE-176] - show similar bins to selected bin
• [BINBASE-177] - show meta informations to selected bins
• [BINBASE-179] - results of the compound ejb needs to be cached
• [BINBASE-188] - partial info needed in case of an empty cache
• [BINBASE-11] - install vmware management console
• [BINBASE-14] - svn is not working
• [BINBASE-19] - adapt the generated shell script so that the initialisation of the cluster works
• [BINBASE-89] - Tests keep failing - http://bender.fiehnlab.ucdavis.edu:8085/browse/BCI-DEF-2
• [BINBASE-91] - http://bender.fiehnlab.ucdavis.edu:8085/browse/BDI-DEF-4
• [BINBASE-92] - hibernate session refuses connection because matrix task starts to many connections
• [BINBASE-93] - communication exception in binbase service tests
• [BINBASE-101] - netcdf replacement is off, it looks like it wont substract the background noise
• [BINBASE-103] - hibernate unstable connections
• [BINBASE-105] - only use one glibc version, not a mix of severals
• [BINBASE-106] - last commit broke build CLS-15
• [BINBASE-107] - fix or remove failing tests in binbase project
• [BINBASE-110] - postgres atomated test are failing
• [BINBASE-113] - hibernate factory does not work stable after it was open for several times
• [BINBASE-114] - fix failing tests in bba
• [BINBASE-117] - nullpointer exceptio in BinBaseupdate Tool
• [BINBASE-123] - experiment progress view does not render informations correct
• [BINBASE-124] - samples showing progress for up to 120% instead of 100%
• [BINBASE-125] - experiment progress stops at 75% instead of 100%
• [BINBASE-142] - BBA build keeps faling thanks to a test case
• [BINBASE-146] - binbase installer nedded
• [BINBASE-154] - the isntaller keeps installing the test database script
• [BINBASE-160] - date format error, was not discovered by tests
• [BINBASE-161] - calculation of sample progress is off
• [BINBASE-162] - bin generation does not work in one case
• [BINBASE-165] - make binbase maven 2.0.9 compatible, needed for newer java apis
• [BINBASE-182] - make it possible that normal user can use bellerophon
• [BINBASE-184] - cluster service - sub jobs don't work!
• [BINBASE-185] - method in webservice needed to list available database for external tools
• [BINBASE-187] - update meta informations does not work anymore
• [BINBASE-88] - Spectral Similarity Matrix
• [BINBASE-94] - we need to remove hibernate from the experiment creation and replace it with standard sql
• [BINBASE-95] - clusterservice - scp instead of download
• [BINBASE-112] - binbase needs to be able to recycle bin and spectra ids.
• [BINBASE-118] - print formated sql for prepared statements in the debug mode
• [BINBASE-119] - integrate binbase statistic service in the binbase core system
• [BINBASE-126] - binbase sample progress needs to be improved to show 33% and not 33.3333333333333333333333333%
• [BINBASE-127] - provide junit test to test hibernate classes
• [BINBASE-9] - write automated test system for integration tests
• [BINBASE-84] - create utilities to import and extract a neutral schema from the database
• [BINBASE-85] - Retention Index of Each Binbase ID
• [BINBASE-86] - simple ant based installer needed for cluster service
• [BINBASE-87] - additional features needed
• [BINBASE-90] - it needs to be possible to specify the precision of doubles in matrixes.
• [BINBASE-104] - statement cache needed
• [BINBASE-115] - config files and sql files need to be located on the application server
• [BINBASE-128] - ant task needed to create users for the authentifcation service
• [BINBASE-129] - provide possibility to create users using the jmx console
• [BINBASE-135] - we need an installer for the cluster service
• [BINBASE-148] - jmx bean needs to render sop as string so we can look at it
• [BINBASE-164] - provide basic spring support for the hibernate beans
• [BINBASE-166] - secure webservices with dynamic keys
• [BINBASE-169] - binbase web gui needed
• [BINBASE-175] - bellerophon needs some new features
• [BINBASE-178] - provide some form of caching
• [BINBASE-183] - we need a small installer to setup a new database
• [BINBASE-186] - add a webservice to return all available information of a bin
• [BINBASE-1] - install continuum
• [BINBASE-2] - install artifactory
• [BINBASE-3] - install svn system
• [BINBASE-4] - install postgresql
• [BINBASE-5] - install oracle
• [BINBASE-6] - create backup and mirror server for the testserver
• [BINBASE-7] - install binbase in subversion
• [BINBASE-8] - test complete functionality on the test server
• [BINBASE-10] - installing rocks cluster on test server
• [BINBASE-12] - install jboss 4.0.3SP1 version
• [BINBASE-13] - install maven2
• [BINBASE-15] - proxy forwarding for maven so we can access it over apache
• [BINBASE-16] - create repository config file for codehause and eclipse repsitoeries
• [BINBASE-17] - artifactory - wont fetch sources anymore
• [BINBASE-18] - equniox fetching does not work, version conflict
• [BINBASE-20] - create default schema and import it into the test database -> oracle
• [BINBASE-21] - write cluster integration test
• [BINBASE-22] - test if we can use cargo for integration tests
• [BINBASE-23] - test if we can use dbunit for database testing
• [BINBASE-24] - install rocks cluster
• [BINBASE-25] - install oracle database
• [BINBASE-26] - install postgresql database
• [BINBASE-27] - we need a way to wait till a specific job is done on the cluster
• [BINBASE-28] - central configuration interface is needed
• [BINBASE-29] - try basic development cluster installation with vmware
• [BINBASE-30] - switch to jboss 4.2.0GA
• [BINBASE-31] - finding a solution for the ejb jar conflict
• [BINBASE-32] - log4j problem with client communication
• [BINBASE-33] - install a virtual gateway to allow us to route
• [BINBASE-34] - jmx object not found problem
• [BINBASE-35] - switch cluster servie too ejb3.1 for some test's since this is the new standard
• [BINBASE-36] - understand the use of java anotations to provide generic code
• [BINBASE-37] - class not found bug in application server
• [BINBASE-38] - nullpointer exception when web application is enabled
• [BINBASE-39] - for soem reason the jboss tries to register a queue more than once
• [BINBASE-40] - development cluster has no access to the internet, but needs it to fetch libraries
• [BINBASE-41] - cluster needs logging configuration
• [BINBASE-42] - for some reasons it is not possible to finish cluster sub jobs
• [BINBASE-43] - write integration tests for the cluster api which is able too...
• [BINBASE-44] - sar and ear combined
• [BINBASE-45] - simplify culster service result handling
• [BINBASE-46] - provide possibility to delete all registered handlers
• [BINBASE-47] - test is very unstable for fetching the errorlog
• [BINBASE-48] - started with moving bci to maven
• [BINBASE-49] - writing bci integeration test prior of migrating to ejb 3.0
• [BINBASE-50] - jboss doesnt listen do right address
• [BINBASE-51] - jboss installation
• [BINBASE-52] - scheduler needed
• [BINBASE-53] - central configuration
• [BINBASE-54] - converting binbase project to maven
• [BINBASE-56] - convert bibase runtime monitor to maven
• [BINBASE-57] - convert setupx connector to maven
• [BINBASE-58] - how to define that an ejb is packaged as ejb3
• [BINBASE-59] - ava.lang.RuntimeException: Illegal @PersistenceUnit on javax.persistence.EntityManager edu.ucdavis.genomics.metabolomics.binbase.cluster.ejb.LockingServiceBean.manager :There is no default persistence unit in this deployment.
• [BINBASE-60] - ejb calls only work if we put the archivename in front
• [BINBASE-61] - locking is instable with ejb's 3.0
• [BINBASE-62] - create ejb3 base webservices
• [BINBASE-63] - generate reports for samples for easy access
• [BINBASE-64] - binbase change replacement
• [BINBASE-65] - reports for bins similaritys
• [BINBASE-66] - remove quotes from binbase
• [BINBASE-67] - test if we can use ddlutils for migrating the data
• [BINBASE-68] - ejbCreate methods dont work anymore
• [BINBASE-69] - move binbase to maven
• [BINBASE-70] - replace cargo with our own implementation
• [BINBASE-71] - we need a binbase setupx version
• [BINBASE-72] - binbase repository
• [BINBASE-73] - remove ftp server dependencie from binbase
• [BINBASE-74] - binbase exports only 0s
• [BINBASE-75] - continous integreation system keeps failing
• [BINBASE-76] - change netcdf replacement so it works with a range of uniquemasses
• [BINBASE-77] - compiling fails because of missing dependency
• [BINBASE-78] - binbase matrix for bins
• [BINBASE-79] - binbase new similarity
• [BINBASE-80] - create use case diagramm for binbase - setupx
• [BINBASE-81] - bdi = we need to remove the dependency to an application server in the tests
• [BINBASE-82] - write example how to use the api to import/export data
• [BINBASE-83] - write example how to provide a meta dataprovider
• [BINBASE-97] - switch to postgres sql
• [BINBASE-100] - make it possible to build clusterservice without binbase parts
• [BINBASE-102] - Similarity matrix of Fiehn library against Fiehn Library
• [BINBASE-116] - write a test to simulate the cluster on the local pc