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Generic openBIS Change Log and Known Issues

Version 13.04.14 (2 December 2015)

Generic

  • (SSDM-2668) PathInfoDatabaseFeedingTask never stops
  • (SSDM-2803) Vulnerable libraries (commons-collections, commons-fileupload) have been patched
  • (SSDM-2805) White and black list of allowed/disallowed Java classes in remote API calls, see API Security (since 13.04.14)
  • (SSDM-2731) Make unarchiving being stopped by the same stop file as archiving

  • (SSDM-2708) Attachments are not indexed when added through sample details view 

Version 13.04.13 (27 October 2015)

Generic

  • (SSDM-1999) Multi data set archiving: Increase performance of sanity check
  • (SSDM-2054) Multi Data Set Archiving Finalizer improvements
  • (SSDM-2260) Unarchiving across multiple archives from any dataset view 
  • (SSDM-2069) Increase performance of multi data set archiving
  • (SSDM-2355) Introduce the dropbox monitor webapp, that shows the status of the running dropboxes
  • (SSDM-2091, SSDM-2329) Do not shuffle recently deleted data sets
  • (SSDM-2433) Providing in API whether a data set has post-registered or not
  • (SSDM-2512) Data Store Server: Allow incoming folder to be on a different disk than the associated incoming share
  • (SSDM-2197) Introduce type specific store shuffler policy

Bug fixes

  • (SSDM-2500) Store shuffler should respect archiving status
  • (SSDM-2090) File leak from service conversations fixed
  • (SSDM-2520) Fixed problems with shutting down DSS
  • (SSDM-1623) Visible parent/child data sets in data set details view for unauthorised users

  • (SSDM-1832) Dataset uploader now works on 13.04 with Java 8

  • (SSDM-2230) Fix a bug where PathInfoDatabaseFeedingTask would operate on data sets which storage has not been confirmed

Version 13.04.12 (11 June 2015)

Generic

  • (SSDM-1277, SSDM-1339) Multi data set archiving: Waiting for replication of TAR archive on strongbox and handle clean up in case of archiving fails.
  • (SSDM-1178) Multi data set archiving: Unarchiving in batch mode.
  • (SSDM-1191) Multi data set archiving: Generic grouping policy for automatic archiving.
  • (SSDM-1930) Multi data set archiving: Log events with read/writing performance measurements.
  • (SSDM-2003) Archiver can pause starting archiving in presents of a pause file.
  • (SSDM-1287, SSDM-1337) Search domain results return entity code and entity type. In case of BLAST search bit score, plain score and evalue are returned.
  • (SSDM-1340, SSDM-1463) Allow to disable a running openBIS instance with etc/nologin.html.

Screening

  • (SSDM-1820) User defined intensity ranges are again 12/16 bit compatible as it was before 13.04.9

Bug fixes

  • (SSDM-1268) Indices not up-to-date in certain situations
  • (SSDM-1326) Labels for overlays can conflict
  • (SSDM-1415) Cannot see overlays from two different datasets, even if they are selected
  • (SSDM-1461) Multi dataset archiver fails to archive datasets with long code
  • (SSDM-1486) Registrator / Modifier fields not updating correctly
  • (SSDM-1799) Thumbnails not used in default view
  • (SSDM-1966) Repeated calls to ingestion service results in "too many files open" exception.
  • (SSDM-1965) It's impossible to call ingestions service from two clients at the same time.
  • (SSDM-1388) Installer can not upgrade if database server is on a different machine.
  • (SSDM-1266) Installer doesn't show an error message if installation script fails (e.g. because unzip tool doesn't exist). 
  • (SSDM-1464) Installer shows database passwords on console.
  • (SSDM-1596) BLAST search doesn't work with special characters and white spaces.
  • (SSDM-2014) Multi Data Set Archiving: Replication mode doesn't allow to do 'Add to Archive'

Version 13.04.11 (8 January 2015)

Generic

  • (SSDM-85, SSDM-579, SSDM-580, SSDM-689, SSDM-949, SSDM-1075, SSDM-1080) Generic search domain API. Support for local BLAST search. For more details see Search Domain Service (since 13.04.11)
  • (SSDM-535) Customizable start page and welcome pages. For more details see Customize Login Page and Welcome Page
  • (SSDM-665) Generic openbis is using screening welcome page in simple mode

  • (SSDM-688) Minimal service.properties for dss has no example for remote postgres server 

  • (SSDM-690) Persist index.html across upgrades
  • (SSDM-716) Authorization failure during archiving
  • (SSDM-768) Fix flaky DSS tests
  • (SSDM-720) DataSet Export to Cifex fails for Container DataSets
  • (SSDM-891) TarArchiver failure/retry should happen per data set + Bug in RsynArchiver sanity check phase fixed
  • (SSDM-772 + SSDM-876)  Link to navigate to a specific sub-tab in the generic web UI
  • (SSDM-258) SOB-147: Aggregation sometimes fails because of "read timed out" (32452, 32453, 32455)
  • (SSDM-912) Archiving: Temp folder used by the sanity check is configurable
  • (SSDM-1324) Introducing multiple processing task queues. Fore more details see Processing Plugins
  • (SSDM-829 + SSDM-947) Global Search: Indicate an ongoing search
  • (SSDM-127) Delete project/experiment/sample/dataset through public APIs

  • (SSDM-937) Reduced database load caused by dataset deletion

  • (SSDM-1195) Mechanism in openBIS to use servlets using the session token

  • Multi-dataset archiving

Generic Bugfix

  • (SSDM-910) Archiving: Session time for large archiving jobs
  • (SSDM-911) Archiving: Archiving jobs couldn't be recovered from command queue after DSS crash or shut down
  • (SSDM-1330) DynamicPropertyEvaluationMaintenanceTask should not clear the command queue

Screening

  • (SSDM-701 + SSDM-713) Optimal image filter does not work for 16-bit grayscale images
  • (SSDM-946) Improvements for images displayed: Single channel images are already colored as in merged images. User-defined scaling always operates on range 0-256.

Version 13.04.10 (10 July 2014)

Generic

  • (SSDM-290) Allow to create/update openBIS databases by database admins
  • (SSDM-238) Add support for SMTP ports other than 25
  • (SSDM-350) Exports of table: User is asked for providing a file name used by the Web browser to save the table content
  • (SSDM-374) Improved memory usage during Excel batch upload
  • (SSDM-360) The installer is now able to upgrade openBIS without postgres superuser credentials
  • (SSDM-394) Log warning to indicate that the dropbox is not specified as rpc dropbox
  • (SSDM-302) OpenBIS can now run with Java 8
  • (SSDM-387) Meta data of container data set added to meta-data.tsv of data sets archived with ZipArchiver or TarArchiver

Generic Bugfix

  • (SSDM-316) Managed properties that define registration form widgets and are assigned to an XML property do not fail during an entity creation with an incorrect _JSON_ value error
  • (SSDM-317) Sample batch registration fails if there is a managed property with batchColumnNames()
  • (SSDM-304) Reporting Plugin tables with entity links don't work for non-instance-admin users
  • (SSDM-400) Trigger reindexing of a data set after setting storage confirmed
  • (SSDM-396) Welcome page does not show scroll bars
  • (SSDM-464) Dropbox fails when an updatable representation of the same entity is requested multiple times from a transaction

Screening Bugfix

  • (SSDM-475) Fix the bug in screening API, when feature vector loader would fail for some non-standard data

Version 13.04.9 (15 May 2014)

Generic

  • (CCS-75) New maintenance task to revoke user access privileges
  • (BIS-655) Improved performance of the API search methods in case the search was done with subcriteria only (no conditions in the main criteria were specified)
  • (BIS-653) Improved Widget for adding controlled vocabulary terms, now allows to add labels and comments
  • (BIS-657) Removed unnecessary error message that was logged upon DSS startup if DSS is not configured to have admin privileges for a database
  • (BIS-636) Biozentrum patch to improve Matlab API from 13.04.6
  • (BIS-664) Mobile client server plugins
  • (BIS-677) Data Set Size Filling Maintenance Task
  • (BIS-686) Deleting pre-staging folder for V1 and V2 of drop box API
  • (SSDM-11) Switch the Strongbox Archiver to use tar
  • (SSDM-12) Control the destination of the archived file based on file size
  • (SSDM-101) Improve the recognition of non-retriable exceptions in dss recovery
  • (SSDM-50) Store last access date for data sets

Generic Bugfix

  • (BIS-660) Data Set Upload GUI gives a timeout message on slow servers
  • (BIS-667) Sample with container data set can no longer be detached from experiment. See Installation and Administrator Guide of the openBIS Server in order to check and fix if such samples had been connected from their experiment.
  • (SSDM-23) Shadowing of files in container data sets with a container as a component didn't worked. Also the file size of the shadowed file instead of the shadowing file has been shown.
  • (BIS-617) JavaDoc missing for code in cisd-base
  • (BIS-688) DemoArchiver causes files to be deleted
  • (CFX-215): OpenBIS LDAP library logs in with correct user and empty password.
  • (SSDM-23) Data set container: Wrong file size for shadowed files and wrong shadowing
  • (SSDM-170) Data Set Metadata Update does not delete properties

Screening

  • (BIS-666) Upgrade bioformats version to 4.4.10

Screening Bugfix

  • (BIS-665) Fix the problem when in some cases user defined filter was not applied
  • (BIS-654) Fix the problem where listing plate properties was returning empty list
  • (BIS-676) Do not abort image merging if component size of some of the images to be merged cannot be determined

Version 13.04.8 (24 January 2014)

Generic

  • (BIS-620) Allow disabling and initialization of master data in core-plugins properties

Bugfixes

  • (BIS-616) ISimpleOpenbisServiceFacade.listSamplesForProjects(List<String>) does not work
  • (BIS-633) Dynamic properties referring to component samples do not work - OTRS BSSE#1033525
  • (BIS-635) Disable master data core plugin should follow the same format
  • (BIS-640) Feature vectors listed via API have wrong plate reference

Version 13.04.7 (09 January 2014)

Generic

  • (BIS-594) Attachment file name max length was increased from 100 to 255 (when upgrading existing installations please execute this SQL script manually on the openbis database).
  • (BIS-602 + CCS-73 / SP-1067) Plate view performance problems fixed.
  • (BIS-573) Fix to dropboxes sometimes failing when multiple datasets are being registered concurrently.
  • (BIS-598) Improve error messages for excel file reader

Proteomics

  • (BIS-588) Info box right of False Discovery Rate combo box explains its meaning.

Bugfixes

  • (BIS-595) Attachments with '&' and other special symbols can be downloaded
  • (BIS-600) Edit forms for Experiment/Sample/Data Set/Material types shown special HTML symbols (like '<' and '&') in escaped form.
  • (BIS-583) Dynamic properties will be recalculated after being evaluated to null

Required Configuration Updates

  • (BIS-594) requires an SQL migration script to be executed manually when upgrading existing installations (see above)

Version 13.04.6 (27 November 2013)

Generic

  • (BIS-556) A default project can be chosen in a user settings dialog
  • (BIS-548) Attachments can be now accessed in dropboxes
  • (BIS-517) GeneralInformationService searchForSamples methods return results sorted by relevance
  • (BIS-557) Better error message when importing images fails
  • (BIS-543) Python scripts can now import modules from the same directory
  • (BIS-544) Speedup of database backup during upgrade process in case of PostgreSQL 9.3
  • (BIS-570)  Update JDBC driver

Proteomics

  • (CCS-62/SP-982) Protein identification database is fed only of prot.xml file is not large than a configurable value.

Bugfixes

  • (BIS-546) Numeric property values are stored in a database in a consistent format which prevents unwanted entries in the property history table with the same value but in a different format
  • (BIS-547) After changing an entity a person was becoming an author of all property values even those he/she hadn't changed them
  • (BIS-551) Field info icons in the user settings dialog were not shown
  • (BIS-555) Width of label section in registration/edit forms increase to avoid overlapping of labels with input fields
  • (BIS-575) Novartis - dynamic properties do not work anymore in 13.04.5
  • (BIS-585) Passwords logged in plaintext in LongRunningThread report
  • (BIS-559) Use default project for experiment batch registration/update
  • (BIS-578) Column index is out of range when listing nodes using PathInfoProviderBasedHierarchicalContent
  • (BIS-586) Cannot consistently create materials with material properties in one transaction
  • (BIS-584) [SOB-138] Registration of many data sets makes openBIS slow
  • (BIS-566) [SOB-127] Fixed behavior of resolution drop down to remember separately the resolution for different windows.

Version 13.04.5 (8 October 2013)

Generic

  • (BIS-499): Matlab API small improvements
  • (BIS-486): Fast checking of already archived data set in zip file based archiver
  • (BIS-506): Zip file based archiver consistency checks
  • (BIS-487): Stand-alone tool for checking the integrity of dataset .zip archives is added to DSS distribution
  • (BIS-506): DistributingArchiver renamed to ZipArchiver
  • (CCS-50): New AS maintenance task for re-evaluation of dynamic properties of samples which refer directly or indirectly to changed materials
  • (BIS-527): The new master data registration page does not prompt on close with unsaved changes
  • (BIS-518): Debug logging of database connections, service calls and long-running invocations can be enabled for AS/DSS at runtime with configure.sh/datastore_server.sh scripts
  • (BIS-539): New methods for operating on controlled vocabulary columns in custom filter scripts
  • (BIS-536): The list of fields in the new master data registration page was not properly refreshed when the tab was closed without saving
  • (BIS-536): Section value could not be cleared for a field when the edit popup was closed by pressing Enter button
  • (BIS-545): Custom columns and filters: New function to get dates and timestamps as strings in a standard format

Bugfixes

  • (BIS-501): Deadlock on Datastore
  • (BIS-490): Reading of some images with bioformats library fails
  • (BIS-300): Database connections are being lost with "idle in transaction" state
  • (BIS-496): Improved performance of the data set uploader startup
  • (BIS-505): Multithreading bugfixes in HDF5 library
  • (BIS-503): Loading of container data sets via Matlab API does not cause any side-effect error messages in the logs
  • (BIS-506): ZipArchiver now logs to notification log if archiving a dataset fails
  • (BIS-515): Long running batch imports (i.e. experiment/sample/dataset/material batch registration/update via web UI, general batch import, dropboxes) should not block concurrent login/logout/browse operations (when upgrading existing installations please execute this SQL script manually on the openbis database).
  • (BIS-523): Updating display settings by multiple threads could lead to a deadlock
  • (BIS-525): DSS start up script didn't showed correct version of the software
  • (BIS-512): Installer file name didn't reflect the correct version of the software distribution
  • (BIS-526): Improve error message when convert utility not found
  • (BIS-530):  Data set code column size was different in openbis and pathinfo databases (when upgrading existing installations please execute this SQL script manually on the pathinfo database).
  • (BIS-504): Fix the problem where the MatlabAPI would download empty datasets when retrying failed download
  • (BIS-531): Too many open files error was occurring because of unreleased resources in dynamic property/managed property/entity validation python scripts
  • (BIS-511): Gaps in ordering of fields in the new master data registration page
  • (BIS-528): Ingestion services now return proper error message if the transaction is rolled back
  • (BIS-535): It is now possible to delete an entity that has a property with a backslash ('\') as a second character
  • (BIS-534): Project information obtained from public APIs now contains the project description
  • (BIS-538): Improved performance of General Batch Import when registering/updating component samples
  • (BIS-540): 16bit thumbnails are not visible in single channel mode

Required Configuration Updates

  • Debug logging of database connections, service calls and long-running invocations requires new log4j configuration files. When upgrading an existing openBIS installation with the installer, those files will not be automatically updated. For the new functionality to work please replace openBIS-server/jetty/etc/log.xml with the content of log.xml  and datastore_server/etc/log.xml with the content of log.xml
  • BIS-515 and BIS-530 bugfixes require SQL migration scripts to be executed manually when upgrading existing installations (see above)

Version 13.04.4 (8 August 2013)

Generic

  • (BIS-476) Improved embedded mode of openBIS Web UI: Session id can be provided as URL parameter. Also registration of samples and editing of entities can be embedded.

Bugfixes

  • (BIS-480) Material properties couldn't be edited in openBIS Web UI.
  • (BIS-465) Evaluation of a new dynamic property script with a test entity always returns (null).
  • (BIS-472) Update/add attachment to a project via dropbox fails.

Version 13.04.3

Was by mistake identical to 13.04.2 and thus has been retracted.

Version 13.04.2 (2 July 2013)

Generic

  • (BIS-428) Archiver for facilities
  • (BIS-447, BIS-460) Data set shuffling for facilities (MappingBasedShareFinder)
  • (BIS-301) iPad App search functionality
  • (BIS-440) Added methods to the dropbox API for managing role assignments

Screening

  • (BIS-416) Add option to specify human-readable labels in image/analysis dataset selection on plate-view

Bugfixes

  • (BIS-464) FTP Server couldn't be configured as a core plugin
  • (BIS-462) Space admin couldn't delete the space he/she created
  • (BIS-463) Space admin couldn't see space created if created by dropbox for him/her
  • (BIS-454) "Valid From Date" column in entity history tabs contained incorrect values (when upgrading existing installations please execute this SQL script manually on the openbis database) 
  • (BIS-448) Fetching parents/children of samples/datasets was failing in dynamic properties script
  • (BIS-451) Successful data set registration was ending up in the unidentified folder
  • (BIS-453) Table export didn't work properly in IE8
  • (BIS-450) Dynamic properties maintenance task didn't work for data sets
  • ( BIS-449) Plugin script couldn't be saved more than once
  • ( BIS-466) Data view didn't work because of expired session

Version 13.04.1 (12 June 2013)

Generic

  • (BIS-378) Data Set Uploader GUI: Sample and Data Set chooser improved.
  • (BIS-345) share-manager.sh command list-shares also lists share which shouldn't be used in shuffling.
  • (BIS-390, BIS-398, BIS-436, BIS-444) Completely reworked GUI to maintain master data. Old GUI can still be accessed enabling it at the user settings.
  • (BIS-366) Added abstraction to create search criteria objects for preforming searches to openbis.js
  • (BIS-382) Batch operation performance improved.
  • (BIS-202) More detailed logging of dropbox operations.
  • (BIS-370, BIS-429) openBIS-KNIME integration improved: new nodes, bugfixes.
  • (BIS-402) Executing reporting and processing plugins in with multi-DSS setup is now possible.
  • (BIS-399) Container information added to MatLab API

Screening

  • (BIS-359) All features list is now always available with preserved ordering of features.
  • (BIS-360, BIS-388) Added methods to list and retrieve feature lists to openbis-screening.js
  • (BIS-413) Improve error message when creating empty feature vector.

Bugfixes

  • (BIS-419) Console-based installer shows proper error messages in case of failed validators (e.g. wrong database passwords)
  • (BIS-384) Authorization leak in API fixed: Ancestors and descendents of samples retrieved from API are filtered out if user has no access rights.
  • (BIS-276, BIS-389) Saving an edited space, vocabulary, vocabulary term, experiment/sample/dataset/material/property type, property type assignment, plugin, custom column/filter,  or user group is no longer be possible if someone else has edited the same item at the same time. Instead an error message will be shown.
  • (BIS-394) Proteomics Annotation Wizard: Connect a biological sample to an MS_INJECTION sample failed sometimes. This has been fixed.
  • (BIS-417) Roles allowed to create spaces are consistent for UI, dropbox and custom import code paths
  • (BIS-395, BIS-415) Fix the problem, where in special cases overlay images couldn't be seen (screening)  
  • (BIS-414) Fixing DynamicPropertyEvaluationMaintenanceTask which wasn't working at all.
  • (BIS-421) Query API: Missing label added to AggregationServiceDescription
  • (BIS-411) Removed occasional errors when starting screening openBIS.
  • (NONE) NGS plugin fixed.
  • (BIS-433) Nested HTML is now shown correctly in dataset views.
  • (BIS-434) Fix the problem that some of the API methods did not work for container feature vector datasets (screening)
  • (BIS-393) Removed too verbose logging from transaction retries in case of deadlock/optimistic locking exception.
  • (BIS-422) Sometimes users were getting errors when saving their display settings.
  • (BIS-437) QueryApiServer returned empty Date/Timestamp columns.
  • (BIS-441) In special situations all thumbnails were generated identical
  • (BIS-445) Fixed links in getting started page.
  • (BIS-404) DssServiceRpcScreening.listAvailableFeatureCodes and IDssServiceRpcScreening.listAvailableFeatures methods did not accept both physical and container data sets.
  • (BIS-391) Java dropbox: ClassNotFound during DSS startup
  • (BIS-374) DSS startup was flaky.
  • (BIS-234) Improve error message in GUI for custom import (502: proxy error)
  • (BIS-448) OTRS: BSSE#1028304 - Dynamic Plugin Error

Metabolomics

  • (BIS-409) Metabolomics distributed as core-plugin.

Internal 

  • (BIS-432) KNIME node .jar and openbis-mobile.jar added to libraries project.
  • (r28789) library updates
  • (BIS-405) ServiceFinder does not return incorrect services any more.
  • (r28774) Application server start-up waiting time increased from 80 seconds to 160 seconds.

Version S153 (28 March 2013)

Generic

  • Users having only observer rights can tag entities with meta-projects.
  • Installer: Default drop box which can be used out-of-the-box by Data Set Registration GUI/CLI application.
  • API: Instance observers can get meta-projects on behalf of another user.
  • PathInfoDatabaseFeedingTask: Improvements as maintenance task in case of a large number of data sets.
  • SecondCopyPostRegistrationTask: Post registration task creating a second copy of the data set
  • DataSetAndPathInfoDBConsistencyCheckTask: Maintenance task for checking correctness of pathinfo database.
  • Making uploading of data sets to CIFEX and deletion of data sets more robust in case of remotely mounted shares.
  • openBIS javascript facade (see openBIS JSON API):
    • separate openbis.js and openbis-screening.js files
    • automatic AS and DSS urls detection
    • support for all the methods from Java APIs (except for methods operating on streams)
    • support for multiple DSSes
    • new methods for generating graphs

Screening

  • Feature vector data sets can be accompanied with automatically created "All" feature list that preserves ordering of features.
  • Improved creating image datasets via dropbox 
  • Fixed problems viewing czi files read by BioFormats

Bugfixes

  • openBIS javascript facade:
    • Long/long values represented as Strings to properly handle all 64bit numbers
    • GeneralInformationService.listDataSetsXXX methods return parents and children collections properly initialized

  • Expired download session message is not handled as a downloadable file any more
  • Path info feeding task could be stuck in a very specific case. This is not possible any more.
  • Ingestion services can now be used even if there are no  dropboxes registered.
  • Embedded well view is initialized correctly in cases of multiple image data sets.
  • Sample batch registration is now able to handle samples from multiple spaces

Version S152 (14 March 2013)

Generic

  • Improved performance of opening of a trash can
  • Improved performance of general batch import
  • Improved performance of experiment browser
  • Added retry of batch operations from UI in case of optimistic-locking failures
  • Added ability to get notified when an upload completes in the session workspace uploader (javascript)
  • Start a graph service by default when the DSS starts.
  • API: Listing and downloading of attachments for projects, experiments, and samples.
  • GUI improvements for predeployed plugins.
  • Manual data set shuffling: More than one data set can be moved by the script.
  • Shares can be configured to be ignored in shuffling.
  • Improved PathInfoDatabaseFeedingTask: It can process hundreds of thousands data sets without potential memory overflow.
  • New version of openBIS KNIME nodes: Adapted to KNIME 2.7.2

Screening

  • Improved performance of fetching feature vector values via api
  • Optimal image rescaling is now done not only for black&white images, but also for "color" images with only one RGB color component.
  • Updated Bioformats library to v4.4.6.

Bugfixes

  • Batch registration/update: An error occurred if a property of data type material with a specific material type has been specified as full material identifiers (i.e. material code and material type code).
  • Table cell editing: After cell editing changes of a table with a huge number of rows it was possible to see the old values when doing quickly an action like sorting, paging exporting.
  • After logout of the user files could be still downloaded from DSS with his/her old session token. 

Version S151 (28 February 2013)

Generic

  • Graph generation made more flexible. See Configuring Graphs and Plots for details (Section "Graphs without common properties file").
  • For every jar file in /lib subdirectory of enabled core plugins a symbolic link is created automatically to DSS /lib folder
  • Admin script for shuffling data sets manually.
  • Master data script: Allow to add/modify terms of existing vocabularies.
  • Data sources (external databases) configuration is now simpler. Instead of requiring a class that contains the version, the DB version can be specified directly using the "version" property.
  • We now use new terminology to refer to certain kinds of extensions to the openBIS functionality. In the past, we have referred to "validation scripts", "managed property scripts", and "dynamic property scripts". It is now possible to implement such extensions in Java, not just in the scripting language Python. Thus, we now use the terminology "validation plugin", "managed property plugin", and "dynamic property plugin". This change in terminology is reflected in the UI.
  • It is possible to get temporary URLs to data sets, where the client can specify the duration of validity of the URL. See the documentation for ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss.

Screening

  • Implement direct loading of existing images in well content view
  • Allow rescaling of color images with only one color component

Bugfixes

  • Custom Import: Template download bug for Firefox fixed. Now always the latest version is downloaded.
  • Headers and columns of grids are properly aligned in Chrome browser.

Version S150 (14 February 2013)

Screening

  • Add new method to API, that allows fetching of transformed thumbnails directly from the store

Generic

  • Add support for configuring the DSS which handles RPC Dropboxes for an openBIS server in a multi-DSS setup. See Installation and Administrators Guide of the openBIS Data Store Server for details.
  • Search for experiment added for openBIS service facade and general information service.
  • Installer improvements: DSS installation only, selective database backup, deselecting pathinfo database possible, database owner/admin checks
  • Added asynchronous batch registration/update of materials
  • Registration of java dropboxes is now done with hot deployment; no symbolic links to DSS lib folder required any more.
  • Add support for providing dynamic and managed properties and validation plugins as hot-deployed Java plugins.
  • Improved performance of sample batch registration and update.
  • Improved SFTP performance when accessing data sets that are located on a different data store.

Bugfixes

  • Attachments with special characters in file name (like '+') couldn't be downloaded.
  • Screening: Well Search could lead to a browser crash if two many results found.
  • Fix custom queries anchored at an openBIS entity when type is specified explicitly.
  • Made it possible to permanently remove data sets that haven't been processed by post processing maintenance tasks yet.
  • Fixed an installer bug that made the installer believe it is doing an update when the installation directory already existed.
  • Experiment batch registration is now possible.

Version S149 (31 January 2013)

Generic

  • Only global cache for files retrieved by a DSS from another DSS. Cache size is kept by remove old data sets from the cache.
  • Performance of batch import/update of samples with validation scripts improved.
  • Authentication caching system added to shorten login times with slow LDAP servers.
  • Change HDF5 file creation code to avoid variable-length strings as they turned out to be detrimental to stability in some setups.

Screening

  • Add color depth to images.
  • Added a check to prevent registration of empty feature vectors.
  • Update Bioformats library to 4.4.5.

Proteomics

  • Registering of data sets of type PROT_RESULT: Experiment code can be specified in search.properties

Bugfixes

  • Specifying dataset path in plugin.properties file of reporting plugins is now possible.
  • Search box results show matching text from metaprojects.
  • File export of grids now contain custom column values for other export types than "for batch update".
  • Fix a timeout exception when copying very large files and directories on slow storage in a dropbox.
  • Fix a disconnect of the SFTP server when trying to download a file that doesn't exist.

Infrastructure

  • Upgrade Jetty to v8.1.8.

Version S148 (17 January 2013)

Generic

  • Emptying trash with lot of samples: performance improved.
  • Export for batch update: performance improved
  • Progress is indicated during all the batch registration/update operations available from the UI.
  • It is possible now to search entities by their perm id: through the API using search criteria, and from the UI level.
  • Global and session-based cache for files retrieved by a DSS from another DSS.
  • Allow possibility of general batch update by non-admin users
  • Dynamic properties, validation scripts: performance update

Screening

Proteomics

  • Code of biological sample appears in abundance columns of protein viewer even if treatment types and values are specified.

Bugfixes

  • Emptying trash when there are a lot of datasets is now possible.
  • Matching text shows up in the search results.  
  • Following regression fixed: Properties of experiments and data sets didn't appear in edit forms.
  • Fixed the bug, when empty directories were left after data registration

Version S147 (19 December 2012)

Generic

  • Flexible way to use DSS data sources also in AS. For more details see Sharing Databases
  • Managed property scripts run now much faster (caching of python interpreters added)

Screening

  • In well content dialog it is possible to set user defined rescaling per each channel
  • Add extraction of metadata to example cellomics dropbox
  • Improve feature vector containers

Version S146 (5 December 2012)

Generic

  • Extended SearchCriteria with ANY_FIELD and ANY_PROPERTY field types
  • Improved presentation of multiline error messages at edit/registration forms
  • Metaprojects:
    • Added a metaproject edit page
    • Improved performance of metaproject browser tree
    • Untagging entities that are not accessible any more is possible
    • Metaproject creation is available from metaproject chooser dialog
  • Samples can be created in dropboxes without specifying codes for them
  • In validation scripts it is possible to ask for a subset of samples of an experiment (instead of just getting all of them). The subset is specified by giving a regular expression to match against sample types.

Bugfixes

  • Couldn't register in a dropbox entities (i.e. experiments, samples, data sets) and metaprojects at the same time.
  • Metaprojects browser tree and metaproject property panel are now refreshed after Tag/Untag operations

Screening

  • User defined heat map scales

Version S145 (21 November 2012)

Generic

  • Dropbox API: v1 and v2 versions of dss api object are now completely separate
  • Dropbox API v2: the read-only methods in transaction are now deprecated. SearchService should be used instead for those.
  • Aggregation services get access to all openbis read-only entities via SearchService

Version S145 (21 November 2012)

Generic

  • Metaprojects:
    • new metaproject browser and metaproject details pages
    • add listing metaproject functionality to search service
    • tagging and untagging entities is possible from all single-entity-type entity browsers.
  • Search service
    • added possibility to get the search service for arbitrary user in dropbox
    • added support for getting properties definitions 
  • Dropbox API: Added support for write access to vocabularies in dropboxes
  • Dropbox API: Support updating of projects.
  • Dropbox API: Add support for uploading attachments for experiments, samples and projects.
  • Aggregation and ingestion services can now be called via the dss rpc service.
  • Reports can contain information about datasets stored in multiple DSS instances.
  • DSS FTP server is able to access datasets in all DSS instances.
  • Public API: Add methods DataSet.getContainerOrNull() and DataSet.knowsContainer() to get to the container dataset of a given dataset.
  • Public API: Add a method IDataSetDss.tryGetInternalPathInDataStore() to get the internal path of a data set in the data store.
  • Consistent updating of modifier and modification timestamp for entities: If a link between two entities is added or removed modifier and modification timestamps are updated for both entities.

Bugfixes

  • Make custom queries work with Oracle data sources.
  • Managed Properties: fixing performance issues.

Screening

  • bugfix: feature codes are now normalized correctly during feature vector data set registration.

Version S144 (7 November 2012)

Generic

  • Metaprojects:
    • added new 'Metaprojects' field to entity registration and edit forms
    • extended entity DTO objects returned by GeneralInformationService with metaproject information
    • addded metaproject functionality to dropboxes
  • Custom Import: added feedback information that data is being uploaded and processed
  • Dropboxes and aggregation servives:  Search service now by default filters the data for the calling user. There is still possibility to access non-filtered search service
  • Aggregation services: content provider by default is only showing data available for the user. There is still possibility to access all datasets by using non-filtered content provider
  • Added vocabularies to search service
  • Managed Properties: function updateFromRegistrationForm is now used for updating managed property from registration form. 

Bugfixes

  • Metaprojects: fixed searchForSamplesOnBehalfOfUser and searchForDataSetsOnBehalfOfUser methods from GeneralInformationService to return proper results when searching by metaprojectsScreening

Screening

  • Images are correctly presented when default transformation is defined.

 

Version S143 (25 October 2012)

Generic

  • Managed Property: The script can tell whether raw values are editable or not.
  • Notify log will be sent to DSS server admin if registration of a data set fails.
  • Optimistic locking failure behavior improved: The failed transaction will be retried.
  • Introduced metaprojects functionality that allows users to tag their entities to mark them as belonging together in a particular context.
  • Added information about a user that is performing an update to updateFromUI and updateFromBatchInput managed properties functions  .
  • Access to files of a data set via aggregation/ingestion services are now automatically checked for sufficient permissions (used to be the responsibility of the script writer).
  • Master data scripts of screening and proteomics split into mandatory and optional parts.

Bugfixes

  • Avoid filling up the DSS log when a buggy item is going to be reprocessed.

Version S142 (11 October 2012)

Generic

  • Jython aggregation services: Add variable userId to execution environment
  • Improved performance of DSS API getDownloadUrlForFileForDataSet() and listFilesForDataSet() methods
  • Improved automatic code generation - regenerate code when a conflict with a manually entered code is detected
  • STORAGE_CONFIRMED field is now available in dataset search for admins
  • Add API method IGeneralInformationService.getDataStoreBaseURLs() to get the right DSS URLs for a list of datasets quickly.
  • GUI: Sample and experiment registration forms support structured managed properties with multiple sections of input fields.
  • Installer: Checks key store passwords. Prevent changing key store passwords if default or existing key store is used.
  • There is a separate highwater mark for recovery data: recovery-haghwater-mark.

Bugfixes

  • The owner of a data set can be changed from a sample to just an experiment in the UI
  • It is possible to create new samples that are parents/children of each other
  • The installer verifies the passwords provided for a keystore.
  • Updating an experiment with large amounts of samples is now much faster.

Screening

  • There is possibility to import features lists for feature vector data sets. Each feature lists consist of several feature codes. All imported lists are visible on the Plate Layout in Choose features list combobox. By selecting one of them, user is narrowing features available in Choose heatmap kind combobox to the ones on the list.

Version S141 (26 September 2012)

Generic

  • Properties related to core plugins have been moved from AS and DSS service.properties to a new properties file inside the core-plugins folder which only configures modules and core-plugins and which is not affected by upgrades.
  • Make that number of parallel database connections configurable.
  • Calculation of dynamic properties for entity or validations of entities, can now access entities related to this entity (parents, children, containers, experiment, etc)
  • It is possible to force validation of selected related entities from the entity validation scripts.
  • Improve parallelization of DSS service calls to make DSS more responsive under high load.
  • Improved CPU and memory performance of updating experiments with many assigned samples.
  • Service conversations:
    • Timeout for conversations between DSS and AS (in both directions) is now configurable via 'server-timeout-in-minutes' property in DSS service.properties (default value is 5 minutes)
    • AS calls long-running DSS methods now via service conversations to avoid timeouts.
  • API: Make the timeout of data streams configurable (used to be hardcoded to 20s).
  • Application monitoring:
    • It's possible to monitor active openbis user sessions. If the number of sessions exceed a specified threshold, a notification log is being sent to the admin. This behavior is controlled by two properties (defined in openbis service.properties file)
      • session-notification-threshold (by default is 0, meaning the feature is switched off)
      • session-notification-delay-period (how much time should pass between two notifications expressed in seconds)
    • It is possible to monitor the usage of database connections. If the number of connections exceed a specified threshold, a notification log is sent out to the admin and detailed logging of requesting and returning database connections is switched on.
  • Dropboxes have now development mode that disables the auto-recovery feature. Use it for a quick feedback loop when developing dropboxes by setting development-mode = true in dropbox plugin.properties.
  • The etc/ capabilities file now supports specifying more than one role per line by separating roles by coma (used to require two lines with the same capability to give that capability to two roles).

Screening

  • Update bioformats library to v4.4.2.
  • Re-enabled support for feature vectors to have arbitrary data set types.

Bugfixes

  • A database connection leak has been fixed which slipped into S140.1 (also fixed in S140.2).
  • Database: Add SELECT grant to the database group openbis_readonly for tables which had previously been forgotten. This make these tables accessible for users writing their own SQL queries.

Version S140 (12 September 2012)

Generic

  • Improved speed of unarchiving of datasets when unarchiving to a DSS share with many datasets.
  • Memory monitoring and logging plugin enabled for DSS and AS by default.
  • Authorization annotations are moved from the public API interface classes to the implementing classes.

  • Ensure openBIS drops non-functional database connections from the pool and only returns functional ones (no loss-of-service after database restart).
  • New scripts check.sh and watchdog.sh to monitor (and if necessary restart) AS.
  • PathInfoDB and DataSetAndPathInfoDBConsistencyCheckProcessingPlugin are enabled by default for new installations.

Bugfixes

  • Saved table cell editings are not reflected when paging or sorting the table has been applied. This is fixed if the user isn't doing paging, sorting etc. faster than the server can refresh the cached data.
  • Fixed a problem when OpenBIS was becoming unresponsive (any operations on samples were blocked) during sample batch update and registration
  • Fixed problems with updating entity relations via API:
    • removing one parent of a data set was removing all parents
    • setting a component's container didn't create the relation
  • Fixed a problem with registration of overview images in case when contained datasets do not have a link to the plate sample

Version S139 (29 August 2012)

Generic

  • Sample types have a new flag 'show parent meta data'. If set the sample details view of such samples will also show the properties of its parents.
  • Automatically generation of sample and experiment codes will use for samples and experiment different sequences which are independent of other sequences used to generate unique codes (as e.g. data set codes and perm IDs).
  • Change of accessing Web Apps: The URL changed from https://my-openbis.domain/<web app name> to https://my-openbis.domain/openbis/webapp/<web app name>.
  • Grids embedded in webapps store their state in the display settings (see openBIS webapps)
  • Entity validation mechanism has been introduced. It allows writing a python script (similiar to the dynamic properties) that is evaluated on each update or creation of a new entity (sample, dataset, material or experiment). Such a script can prevent the update if some condition is not met.

Screening

  • New methods in the API to load base64 encoded images and thumbnails (see openBIS JSON API).
  • It is possible to generate overview images for already registered image data sets. It is also possible to register overview images created outside of openBIS.
  • Processing plugin that triggers registration of overview images for already registered image data sets.

Bugfixes

  • DSS: Plugins using regular expression for the allowed data types have not been recognized in AS when a new data set type matching the regular expression has been registered.

Version S138 (15 August 2012)

Generic

  • GUI: Tables with Experiments or Samples or Data Sets can be exported in a form suitable for batch updates.
  • Webapps:
    • can be embedded in the OpenBIS UI. See the documentation.
    • can upload, download and delete files from session workspace. See the documentation.
  • Added template files for custom import. See the documentation.
  • Add support for storing and retrieving settings for webapps.
  • Processing and reporting plugins can be configured using wildcards in the data set type. See Processing Plugins.

  • The results of an aggregation service can be shown using the openBIS grids in openBIS webapps.

Screening

  • Added a new datasets type - container for feature vector data sets. From now on all new feature vector datasets will be containers.
  • Introduced a new maintenance task ComputeIntensityLevelTransformationsMaintenanceTask. See the documentation
  • If available, transformed overview images will be used in web UI

Version S137 (31 July 2012)

Generic

  • Enabled PathInfoDB (including computing checksums) by default
  • Improved checksum validation when moving a data set to a different share:
    • PathInfoDB precalculated checksums are used during the validation to improve performance
    • validation can be enabled/disabled with a new "verify-checksum" flag
  • Added checksums to the file browser of the data set detail view
  • Exposeed the checksums to the API (ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO)
  • Add support for a session workspace to have files available for any aggregation plugin, reporting plugin and to exchange files with the client
  • Add support for switching on and off the built-in SFTP server and FTP server separately
  • Added an automatic conversion of controlled vocabulary URL templates from a deprecated $term$ format to a recommended ${term} format
  • Enabling new core plugin technology does not require any change to applicationContext.xml anymore
  • Improved the format of the email sent by the DataSetAndPathInfoDBConsistencyCheckProcessingPlugin processing task
  • Improved logging in the DSS for the following cases: reprocess-faulty-datasets = true; the incoming file was deleted before processing completed
  • Made it is impossible to select the two incompatible options "Update existing" and "Generate codes automatically" options at sample batch registration form

Screening

  • Improved the performance of methods in IScreeningOpenbisServiceFacade API which take plate lists as their input
    Introduced a new maintenance task ComputeIntensityLevelTransformationsMaintenanceTask. See the documentation
  • Update bioformats library to 4.4.1

Bugfixes

  • Parents field is no longer cleared when saving an unchanged data set edit form
  • The dynamic query object provided by getDatabaseQuery() in dropboxes used to return a default value (like 0) when primitive value (like an Integer) was SQL NULL in the database
  • Fixed the PathInfoDatabaseChecksumCalculationTask to correctly handle all files when generating checksums (there was one special value that could cause problems).
     

Version S136 (18 July 2012)

Generic

  • Added the ability to register entities (Experiments, Samples, Data Sets, Materials) to aggregation services
  • New processing task that verifies data sets consistency between the data store and the metadata in the PathInfoDB
  • Support writing v2 dropboxes in Java (before S136, only Jython was supported)
  • Robustly handle a file that is deleted from a dropbox while it is being processed
  • More capabilities added for fine-grained authorization of entity relationship changes:
    • ADD_PARENT_TO_DATASET
    • REMOVE_PARENT_FROM_DATASET
    • ADD_CONTAINER_TO_DATASET
    • REMOVE_CONTAINER_FROM_DATASET
  • Improvements for linked datasets:
    • Name of a data management system is displayed in a linked data set details view
    • Full information about a data management system of a linked data set is now returned by the DataSetAPI
  • IGeneralInformationService has now methods which allows a server to ask certain queries on behalf of another user
  • Managed properties can now be represented by either XML or JSON in the database with both formats being accepted on reading
  • Added property hard-link-copy to processing plugins DataSetCopier and DataSetCopierForUsers 
  • Speed up saving on table editing
  • Support ${term} in controlled vocabulary URL templates
  • Implement possibilities to update existing Experiments and Materials  from the transaction.
  • Make it possible to disable checksum veryfing in RsyncArchiver with the property 'verify-checksums' (default is true)

Screening

  • On registration of an image dataset, it is now possible to specify a fixed range transformation by calling setDefaultFixedIntensityRangeForAllImages() or setDefaultFixedIntensityRangeForAllImages() on classes derived from SimpleImageDataConfig

Bugfixes

  • On metadata update in dropboxes, there was a race condition in the optimistic locking check
  • In the aggregation framework openBIS provides a mail client to the aggregration script. This mail client didn't work as expected

Version S135 (4 July 2012)

Generic

  • Performance improvements for bulk updates of samples and data sets via Jython dropboxes.
  • New AS Core Plugins type: dss-data-sources (see Installation and Administrator Guide of the openBIS Server)
  • New AS Core Plugins type: webapps (see openBIS webapps).
  • New kind of data set was introduced: Link Data Set (see Link Data Sets)
  • Menu structure have been improved (more consistent labels and ordering of the labels)
  • Data sources returned by DataSourceQueryService in Jython context are now automatically closed
  • More capabilities added for fine-grained authorization of entity relationship changes:
    • ADD_PARENT_TO_SAMPLE
    • REMOVE_PARENT_FROM_SAMPLE
    • ADD_CONTAINER_TO_SAMPLE
    • REMOVE_CONTAINER_FROM_SAMPLE

Screening

  • Improve speed of well search in certain cases.

Bugfixes

  • DSS dropboxes didn't recover from AS restart
  • ISampleImmutable.getContainedSamples()  (from the DSS dropbox API) would sometimes return misleading information. The ISampleImmutable object now includes a method, ISampleImmutable.canGetContainedSamples(), which returns true if the sample object includes the contained samples. The getContainedSamples() method throws an exception if the samples are not actually available.
  • Shared samples are now visible for all types of users - not only INSTANCE_*
  • Shared samples can now be modified only by INSTANCE_ADMIN users
  • Optimistic locking for sample and dataset updates via DSS have been improved

Version S134 (20. June 2012)

Generic

  • Enabling technologies also for DSS.
  • AS Core Plugins for types maintenance-tasks, query-databases, custom-imports and miscellaneous.
  • Jython dropboxes: Allow more fine-grain authorization when creating/updating spaces, projects, experiments, samples, materials and data sets.
  • Jython dropboxes: Add access to AuthorizationService from transaction, that allows checking if the same user has certain privileges.
  • Possibility to deactivate users was added; deactivated users won't be authorized by application.
  • There is an option to send number of active users to CISD Helpdesk in admin menu.
  • Relationships history was extended to track the history of experiment-project, sample-space, project-space relationships.
  • Property history view was replaced by history view, that shows not only the properties history, but also relationships history.
  • More capabilities added for fine-grained authorization of entity relationship changes:
    • ASSIGN_EXPERIMENT_TO_PROJECT
    • ASSINGN_PROJECT_TO_SPACE,
    • ASSIGN_SAMPLE_TO_EXPERIMENT
    • UNASSIGN_SAMPLE_FROM_EXPERIMENT
    • UNSHARE_SAMPLE
    • ASSIGN_SAMPLE_TO_SPACE
    • SHARE_SAMPLE
    • ASSIGN_DATASET_TO_EXPERIMENT
    • ASSIGN_DATASET_TO_SAMPLE
    Note: defaults for these new capabilities do not match the behavior of previous openBIS versions. To get the old behavior (or any custom behavior) the Capability-Role map file should be used and the SPACE_USER role should be assigned to any of the capabilities listed above.
  • Capability-Role mapping file (etc/capabilities) now supports setting multiple roles per capability.
  • Jython dropbox scripts can get and set the parent identifiers of a sample using:

    public List<String> getParentSampleIdentifiers();
    void setParentSampleIdentifiers(List<String> parentSampleIdentifiers);
  • JSON-RPC support for circular references
  • JSON-RPC support for nested arrays
  • Change h5ar containers to make it impossible that there is a name clash with any file name
  • New version of the jython dropbox api has been introduced. The most important parts are:

Screening

Bugfixes

Version S133 (6. June 2012)

Generic

  • Switching from disabling technologies to enabling technologies.
  • Bundling all client and API distributions in a single package.
  • Specifying type of JSON objects sent to JSON-RPC services is now made consistent. All JSON objects accept @type attribute (@class is still supported but deprecated). See more information on the change in JSON-RPC documentation: openBIS JSON API
  • Aggregation Service Reporting Plugins now support custom objects (not only primitive types and collections) in parameters map when used from JSON context
  • Additionally to last modification date on entities, also the person who did the changes is saved
  • History of relations between experiments, samples and data sets is saved in database (however this information is not available in the UI).
  • Filtering with timestamps supports now "greater than" and "less than"
  • Space admin or higher authorization is now required when changing project of an experiment.
  • Integer properties are stored with a width of 64 bits instead of 32 bits

Screening

Bugfixes

  • Failed archiving can lead to corrupted data sets in archive.
  • Match text is shown when using the search box search

Version S132 (23. May 2012)

Generic

  • AS Maintenance task for feeding a material report database.
  • Jython based Aggregation Service Reporting Plugin
  • Custom Import functionality was added; files can be uploaded to the jython dropbox via web UI.

Screening

  • Screening version of Jython based Aggregation Service Reporting Plugin

  • Space between the tiles in the movie view 

Bugfixes

  • .SHREDDER directories are now deleted also for HDF5 packed datasets.
  • Deletion of data set during shuffling is handled in correct way now.
  • Validation in DataSet uploader was broken (regression).

Version S131 (9. May 2012)

Generic

  • Store optionally CRC32 checksums in pathinfo database.
  • Check checksum of just archived data sets.
  • Location of core plugins folder for AS and DSS is no longer configurable.
  • Properties History tab in details view for Experiments, Materials, Samples and Data Sets.
  • DSS calls AS through service conversation framework when registering a new data set. This removes the problem with socket timeouts.
  • Data set batch update has been extended to support changing experiment, sample, container, parents and file format.
  • Data set are now deleted asynchronously from the data store by a maintenance task.

Screening

  • DSS public API has a new method loadImagesBase64() that returns images as base64 encoded strings. The method can be used also through the JSON RPC API.

  • Added space beetween images in well view

Proteomics

Bugfixes

Version S130 (25. April 2012)

Generic

  • Allow deletion of single deletion sets in trash can view.
  • In case of deletion of non-empty projects the error message tells which experiments are still connected. Also experiments in the trash can are listed.
  • Deletion of data sets can be forbidden for chosen data set types.
  • Location of core plugins folder for AS and DSS is no longer configurable.
  • Making ExperimentBasedArchivingTask more robust against configuration errors. It also sends a notification e-mail on error.
  • Installer allows to specified a different Java key store (and passwords) for SSL certificates.
  • Master data API: New methods allow to register master data even though their are already registered. Thus it is possible to write scripts without producing error messages in such cases.
  • Remove size constraint for master data registration scripts.
  • Create h5ar container archives to speed up listing operation of huge directories in the container.
  • Public API date based searches:
    • Dates are now defined as strings (YYYY-MM-DD) instead of long values.
    • Time zone can be given as an argument.
  • Interface IDataSetImmutable (used in dropboxes) now has additional methods: isContainedDataSet() and getContainerDataSet()

Screening

  • API: ImageRepresentationFormat includes information about transformation applied on overview images.

Proteomics

  • Allow DECOY_ prefix not only directly on the accession number but also for the accession number with database prefix. DECOY_ prefix will be transferred to the actual accession number.

Bugfixes

  • Main data set pattern in the form for editing/registering Data Set Types could be non-valid regular expression. Now, this will be checked and an error message shows the error.
  • Fix a resource leak on database access; this fixes the issue of path info database feeding becoming progressively slower with the number of datasets.
  • Fixed attachment download links in SIMPLE mode.
  • Fixed opening tabs for a data set and a sample with the same primary key.
  • Fixed problem that some datasets couldn't be deleted.
  • Fixed saving transformed overview images also for images containing all channels in single file.
  • Fixed 'Settings' button.
  • Fixed deletion of archived data sets.

Version S129 (11. April 2012)

Generic

  • API: IGeneralInformationService has been extended by a method which allows to control for sample search whether properties, children, all descendants, parents, and/or all ancestors are included.
  • DSS: Material and sample columns of tables created by a reporting plugin can be turned in to columns with links.
  • A new KNIME node allows to download data set files from openBIS to be used in a KNIME workflow.

Screening

  • Playback of a series of images have been improved to minimize the latency.
  • Pace of a playback of a series of images can now be controlled with a new "delay" field.

Proteomics

Bugfixes

  • It is possible to search entities by their PermIDs.
  • Modification date appears in the grids now.
  • Cancel button in sample browser works now.
  • Fixed a problem with disappearing items in "Space/Project" tree when rapidly scrolled.
  • Python scripts are now evaluated in isolated interpreters (globals between dropboxes do not interfere with each other anymore).

Version S128 (28. March 2012)

Generic

  • Improved consistency of contained dataset's behavior
    • When the container dataset is deleted, the contained datasets are also deleted. (It didn't work wihtout the trashcan)
    • When the container dataset's experiment is changed, the contained dataset's experiment is also changed.
  • Possibility to search samples and data sets by their registration and modification dates.

Screening

  • Analysis Summary can be provided by a reporting plugin instead of been calculated by openBIS.
  • By default only the container data set and not the contained data sets will be linked to the plate. 
  • Movie buttons (play, stop, previous frame, next frame) for series of images
Bug Fixes
  • Fixed the "Resolution" combo box in views that show image so that it correctly shows the size of the selected image.

Proteomics

  • More flexible way to refer MS_INJECTION samples in protXML parameter elements.

Bugfixes

  • Trashcan bug fixed.

Version S127 (14. March 2012)

Generic

  • Modularizing DSS plugins: New plugin types See Core Plugins.
  • GUI: Multiple selection in sample chooser for sample parents.
  • GUI: Experiment details view: Sample and data set tab have check box 'only directly connected'. If unchecked all descendent samples and data sets are shown. Also data sets and their descendants are shown if they are connected to one of the descendant samples
  • GeneralInformationService has methods for querying Materials.
  • SearchCriteria for search methods of GeneralInformationService allows to search for dates and date intervals on registration and modification dates.

Screening

  • Field Viewer. It opens up if one clicks on a tile/field image shown in Well Viewer.

Bugfixes

  • Details view of non-screening experiments show 'Plates' instead of 'Samples' and the tabs 'Well Search', 'Library Index' and 'Analysis Summary' which doesn't make sense.
  • Version information not shown in About Box if openBIS Standard Technologies has been used for installation/upgrading.
  • Incorrect layout of project tree view in Experiment Browser in Chrome.

Version S126 (29. February 2012)

Generic

  • Modularizing DSS plugins by introducing core plugins concept. See Core Plugins.
  • DSS: Experiment-based Share Finder allows to shuffle data sets to share associated with certain experiments.
  • DSS: When a data set is moved to another share a CRC checksum check is done in addtion to file size check for asserting that the content has been moved correctly.
  • Speed improvement of SFTP server.
  • Upgraded programing model for jython dropboxes. Added context object and hooks to jython dropboxes for pre and post metadata registration and post storage.
  • Parents column in all tables showing data sets.
  • Performance improvements of indexing.
  • Sample deletion does not automatically delete its children.

Screening

Bugfixes

  • Managed Properties are evaluated when property in batch import file has empty value (LMS-2805)

Version S125 (14. February 2012)

Generic

  • Performance improvements of FTP/SFTP server and GeneralInformationService.getDataSetMetaData().
  • Installer for 'Standard Technologies' (i.e. Screening and Proteomics) which allows to combine screening with proteomics.
  • BaSynthec: Dashboard
  • URL resolver for Sample Registration with filter on sample types.

Screening

Bugfixes

  • XML structured managed properties bug fixed.
  • Matlab API
  • Removing trasnformation in ImageViewer

Version S124 (1. February 2012)

Generic

Screening

Bugfixes

  • Make Path Info DB query robust with respect to duplicate slashes like in original.h5//myimage.tiff. (LMS-2765)
  • Grid column order is no longer lost (LMS-2711)

Version S123 (18. January 2012)

Generic

  • Information about openBIS version moved from the footer to a new About Box accessible from the user menu (LMS-2734)
  • New maintenance task which notifies by e-mail about new data sets registered last week or month (LMS-2717).
  • By default RsyncArchiver do not delete data sets in the archive but only mark them as deleted (LMS-2483).
  • General Batch Import improved by checking correctness of data to be registered. It checks existence of material and sample types and property columns. In addition it checks that referred container samples either already exists or will be registered by the batch import (LMS-2733).

Screening

  • Added support for JSON-RPC protocol for IScreeningApiServer and IDssServiceRpcScreening services (LMS-2736)
  • Material Summary View for all assays do not compute ranks by default; to compute ranks parameter computeRanks=true needs to be added in URL (LMS-2732)

Bugfixes

  • Permlink to material details now accept empty experiment identifier (LMS-2727)
  • Consistent tab naming in sample detail view and sample search (LMS-2724)
  • Improved DSU Downloader - sequenced/notsequenced labels are based on the number of uploaded files (LMS-2722)
  • Auto-opening of the last viewed entity after login doesn't fail when the entity no longer exists (LMS-2723)
  • Trashing stuff which are linked to non-available (i.e. mostly archived) data sets is not allowed. The error message list these data sets (LMS-2725).
  • Searching for parent data sets in case of a huge number of data sets is working correctly (LMS-2731).

Version S122 (22. December 2011)

Generic

  • Added auto-detection of incoming folders for DSS RPC Uploads (includes DSS Upload Clients). The property 'rpc-incoming-dir' is now moot.
  • HTML apps are no longer restricted to user with role INSTANCE_ADMIN.
  • Information about the process of registering data sets is stored in the "log-registrations" folder, making it possible to track the registration process.

Bug Fixes

  • Custom columns couldn't be selected in settings.

Screening

  • API extension: Image sizes common for all images of an experiment are provided.
  • API extension: Retrieving common meta data (like image size) for all images (original ones and thumbnails) existing for a data set.
  • API extension: Retrieving images from data set fulfilling some criteria (like image size).
  • Maintenance task (ch.systemsx.cisd.openbis.dss.etl.ImageSizeFeedingMaintenanceTask) which fills extended imaging db with image and thumbnail sizes of already existing data sets of type HCS_IMAGE*.

Version S121 (8. December 2011)

Generic

  • Add author information to all property values and make this information also go into the property history.
  • Do not set "Evaluation Pending" as the property value of dynamic properties when properties of an entity are updated.
  • Added openBIS logo to our DHTML apps, the DSU downloader, BaSynthec strain viewer and the plate browser.
  • Added cascading deletion for container data sets. Now, when deleting a container data sets all of their contents will be deleted too.
  • Added Refresh button in all pickers in Data Set Upload client.
  • Data Set Upload client registers ad-hoc vocabulary terms on the fly when the terms have been extracted by a metadata extraction script.
  • Generic Batch Import now ignores empty rows in the Excel sheets.
  • Improved speed of Generic Batch Import when uploading samples with specified CURRENT_CONTAINER.
  • Improved speed of listing many materials
  • SFTP server.
  • Making FTP over SSL/TSL more secure.
  • Jython drop box API: Access to data set type property type assignments.
  • Creating links in custom columns is now possible
  • openBIS facade method are automatically retried in case of any communication errors
Bugfixes
  • Fixed bug that would cause a org.springframework.remoting.RemoteAccessException to be shown in the DSS log on certain errors detected in the openBIS application server.
  • Fixed bug that could leave empty directories behind after a transaction rollback in a jython dropbox.
  • Fix a bug that prevented the last version of a property that was deleted to be added to the property history table in some cases.
  • Fixed a bug where database create/update operations were not automatically picked up by the web UI.
  • Materials with integer codes could not be referenced by General Batch Import, because their ids were parsed incorrectly (e.g. 123 was parsed as 123.0).
  • Experiment browser not refreshed upon addition of new projects.

Screening

  • Documentation describing how to publish final HCS data has been written and is available here.
  • Documentation about screening dropboxes has been improved, e.g. the concept of analysis procedure has been explained.
  • Fixed problem that prevented Safari users from logging into the publication portal version of openBIS (the "fix" is to explain the workaround to users on the login page).
  • Improved speed of importing image datasets when using BioFormats library.

Version S120 (23. November 2011)

Generic

Bugfixes
  • Data sets returned from public API always had NULL values for their controlled vocabulary properties
  • bisup.sh fails if the application logs an error immediately after a successful start
  • Confusing error message when deleting Sample types referenced by Trash Can contents.

Screening

  • It has become possible to delete or archive raw image datasets and to keep the thumbnails still available.
    No dropbox changes are required. Functionality is not yet available for already registered datasets.
  • MATLAB PDF documentation is replaced by HTML(Javadoc) of OpenBISScreeningML.

Version S119 (09. November 2011)

Generic

  • FTP Server: Eliminate data set duplicates in child-parent path chains
  • Added new post registration task Hdf5CompressingPostRegistrationTask which asynchronously HDF5-compresses the contents of imported data sets into new "clone" data sets. The task only processes data sets which are part of a container data set. After the execution of the Hdf5CompressingPostRegistrationTask post registration task, the initially imported data set will be overshadowed by the new "clone" data set via the container data set mechanism. This allows having constant URLs pointing immediately after registration point to the non-compressed data set, but then switch to the HDF5 container of the compressed "clone" data set. After this switch is done the original non-compressed data set is deleted.
  • Improved KNIME node for reporting: Data set chooser shows also sample and properties. Filtering and sorting of data sets as well as multi-selection are supported in the chooser.
  • Added support for restricting the set of data set types available to the user in the data set uploader. Restriction can be specified using either a whitelist or a blacklist. See Installation and Administrator Guide of the openBIS Server#DataSetUploadClientCustomizations.
  • Swing Data Set Uploader: jython script can be used to fill up the properties.
  • Swing Data Set Uploader: sample picker shows only experiments having samples, data set picker shows only experiments having data sets.
Distribution
  • Write PID file of openBIS Application Server to openbis.pid on startup.
  • Add script bin/status.sh that prints the status of the server to the console.
  • bisup.sh handles long startup times correctly.
  • Upgrade process aborts if the creation of a database backup fails.
  • bin/env removed from the distribution.
Bug fixes
  • Data set properties no longer shown in the data set grids.
  • Data set file listings break occasionally with Error - Resource 'original;jsessionid=XXXX' does not exist.
  • .dynamic_property_evaluator_queue grows larger than 2GB

Proteomics NEW

  • New openBIS customization for proteomics. Allows to register protein identification data via prot.XML files and list identified proteins (including peptides) in GUI. For more details see openBIS for Proteomics
  • Easy installer for openBIS Proteomics.

PhosphoNetX

  • For all Java package names phosphonetx are replaced by proteomics. This important for all Java code using Proteomics Data API Facade.

Screening

  • Added validation to prevent registering microscopy images when multiple image files map to the same spatio-temporal location in openBIS
  • Added method to the Matlab API to just list the data sets and their files for an experiment.
  • DssServiceRpcScreening.listImageMetadata() API method was speeded up.

Version S118 (27. October 2011)

Generic

New Features
  • New KNIME node for reporting.
  • Extended the experiment based archiver (ExperimentBasedArchivingTask) to have configurable free space providers. The archiver has been change so that it does not try to measure the free space after each archiving operation. Instead, it accepts the average estimated size of data sets (per type) and calculates an approximation of the space freed from an archiving operation. Archiving continues until the estimated free space is enough.
    • Added PostgresPlusFileSystemFreeSpaceProvider that accurately measures the total free space on a hard drive as the sum of the file system free space and the free space within a configured PostgreSQL data source.
Bug Fixes
  • Corrupted search index after changing the experiment of a sample with data sets fixed.
  • Missing time out for Crowd authentication fixed.
  • Broken streaming in JSON API fixed.
  • Jython transaction rollback fails when commit throws an exception in the AS
  • The default staging folder for a Jython dropbox is moved to be inside its corresponding incoming share. The previous default (directly under the store root) was causing problems when shares were mapped to external drive (e.g. NAS).
  • Flood of "Faulty paths ... has been removed manually" messages in the DSS logs

Screening

New Features
  • Add support for Evotec/PerkinElmer Opera Flex files with images
  • Add MATLAB API method loadDataSetsForExperiment to allow listing of data sets for a given experiment.
  • Add information about the transformations for a given image channel to the image metadata DTO.
  • Add Java API method listAvailableFeatures() to get code, label and descriptions of features.
Bug Fixes
  • BioFormats library became a default one to read TIFF images because the standard java library JAI proved to be unstable.
  • a problem which causes that Image Viewer for color adjustment could not start has been fixed.
  • ImageViewer webstart application doesn't start anymore (downgraded to Jetty 7.4.5)

Version S117 (13. October 2011)

Generic

Infrastructure
  • Upgraded Jetty to 7.5.2
New Features
  • FTP Service can be configured to show parent/child data sets as sub-folders of a data set.
  • DSS Generic API has been extended to allow downloading of files also via JSON.
  • Made (SQL) queries available over JSON-RPC.
  • New method listVocabularies() added to IGeneralInformationService to allow retrieving of vocabulary data by JSON clients.
  • IGeneralInformationChangingService is exposed over JSON-RPC.
  • Changed menu structure of openBIS to be task-oriented (as opposed to the previous entity-oriented structure)
  • Material codes can contain arbitrary characters. The feature can be switched on via the property material-relax-code-constraints in the openBIS AS service.properties file.
  • There is a new installation package bundling the generic AS and DSS into a common package. It is recommended that new installations of openBIS use the installation tarball as it defines unified directory structure and upgrade procedures. More details on how to install openBIS with it are available in openBIS setup guide.
Bug Fixes
  • Fixed some circumstances in which the data could get lost in the store if the file system becomes unavailable during registration.
  • Fixed saving of sorting order in grid tables, in some cases it could lead to loss of all settings of grid table.

Screening

New Features
  • error messages have been improved in MatLab API.
  • it is possible to have a link to well without metadata attached.
  • From now on installation tarballs can be used for upgrade. For more details see the updated openBIS setup guide.
Bug Fixes
  • a critical bug which was making the results of 16 bit images transformations incorrect has been fixed

PhosphoNetX

Bug Fixes
  • A maintenance task fixes the bug that PROT_RESULT data sets haven't been linked to their parents.
  • In simple view mode Protein Viewer has links to protein detail views.

Version S116 (29. September 2011)

Generic

  • If you are using online javadoc documentation please note the URL at which you can access it has changed. Each page at svnsis.ethz.ch/doc/something is now available at svnsis.ethz.ch/doc/ openbis /something.
  • openBIS is now compatible with PostgreSQL 9.1; support for PostgreSQL 8.4 is dropped as of this version
New Features
  • Made registration of data sets more robust on unreliable file systems (e.g., NAS).
  • Improved openBIS documentation
  • History of Material/Sample/Experiment/Data Set properties. When a property is updated or deleted the old value will be kept together with a time stamp. The history is currently not accessible. Side-effect: Materials or Vocabulary Terms can not be deleted if they are previous values of some properties of type MATERIAL or CONTROLLED_VOCABULARY, respectively.
  • New automatic archiver which archives whole experiments starting with the oldest one if free disk space is below a threshold.
  • Master Data API now supports the creation of vocabularies and file format types.
Bug Fixes
  • Fixed problems with the Batch Upload Java Web Start client Data Set -> Batch Upload that would cause the error "Port out of range: -1".
  • Data set uploading via API or Batch Upload Java Web Start client problem caused by a non-existing second data store. The non-existing data store has been removed from the database.

Screening

New Features
  • Public API has been extended with a method to fetch complete plates metadata information including the properties of all wells/materials belonging to the plates. See IScreeningOpenbisServiceFacade.getPlateMetadataList(...) for details.
  • MatLab APIhas been improved:
    • loadDataSet() delivers in addition the parent data set codes.
    • A new method has been added which delivers only data set meta data: getDataSetMetaData()
  • One can mark a particular image transformation as a default one. It will be applied automatically when user tries to browse the image and does not choose a different transformation explicitly. It will also cause that the predefined 'Optimal (image)' transformation will not be available automatically. More details here.
  • One can assign any RGB color to each channel, the color will be used to produce merged channel image.
    openBIS can also assign the color matching to the channel's wavelength automatically. More details here.
  • It is possible to extract AS and DSS distributions from the installer distribution (the one which includes a built-in installation program).
  • In the Well Search results there is an additional option to show all the data without restricting it to one analysis procedure. Afterwards some analysis procedures can be still filtered out using standard "Filters" option.
Bug Fixes
  • if tiff files were read by ImageJ library then thumbnails were generated in 8 bits instead of using the original color depth. It caused that image transformations did not work correctly. To fix it for old image datasets one has to register them again to regenerate thumbnails.
  • Shutting down the DSS while importing large image datasets resulted in data sets being copied to the DSS store without having a corresponding record in the openBIS AS database. A symptom of the bug is failure to rollback a transaction immediately after DSS restart.
  • Uploading library materials with gene symbols containing spaces (e.g. " SYMBOL ") resulted in damaged gene symbols where the spaces was replaces by underscores (e.g. "SYMBOL")
  • Images dialogs were displaying channel codes instead of channel labels
  • Images larger than the image dialog were rendered with a double scrollbar on the right side.

Version S115 (15. September 2011)

Generic

New Features
  • AS: Add support for overriding the capability-to-role map in etc/capabilities
  • AS: New option appeared in the Administration menu: 'Global Batch Import'. It allows to import samples and materials from single Excel file.
  • AS: Introduced new Jython API for registering master data. See Jython Master Data Scripts
  • DSS: Jython drop-boxes now have robust support for interacting with alternate databases. See Jython Dropboxes v.1 (Legacy)#Databasequeries
  • GUI: 'Export Data' button for data set detail view. It exports the data set via CIFEX
  • GUI: Force Empty Trash available when clicking on 'Empty Trash' button with alt key pressed.
  • AS+DSS: IGeneralInformationService and IDssServiceRpcGeneric are now accessible via JSON-RPC under the URLs /openbis/rmi-general-information-v1.json and /datastore_server/rmi-dss-api-v1.json correspondingly.
Bug Fixes
  • AS: Entities from the trashcan are visible via various public APIs. Also affects Screening
  • AS: Sending a child data set to the trashcan makes the parent data set no longer accessible
  • GUI: Table cell editing doesn't work for vocabulary terms with labels.
  • GUI: Experiment Detail View is not refreshed automatically when experiment is moved to trash.
  • GUI: Perm-Links: anonymous flag should only be considered when there is no session
  • GUI: Delete button on entity views changed its name 'Delete <<entity name>>', e. g. 'Delete Sample', 'Delete Experiment', etc.
  • GUI: Sample registration form: Space field is automatically filled after an experiment has been chosen

Screening

New Features
  • During datasets registration it is possible to choose a list of custom image transformations which will be available when browsing images in the GUI or fetching images with the API. More details here
  • Now it is possible to use smart autorescaling of all plate images which causes that the conversion to 8 bit color depth looses less much less information and at the same time allows to compare images of one dataset to each other. This option must be switched on in the dropbox for chosen datasets. Consult this page for details.
  • Faster retrieving of images via GUI and API
  • HDF5 Containers use a directory structure that matches the folder container for plate images. In particular, they now include an "original/" directory at the root.

Version S114 (31. August 2011)

Application Server
  • Added HTML output to the Managed Property API. It is possible to define a managed property that displays content as HTML (in addition to tables, which was already available). See Managed Properties#HTMLOutput
  • Made an unofficial variable available to managed property scripts, the propertyPE. The official API greatly limits the information available to a script and sometimes it is necessary to find out more about an entity. See Managed Properties#Unofficial API
  • It is possible to edit managed properties when registering or editing an entity. To enable this, turn on the "Shown in Edit Views" flag of the entity type / property type assignment. This flag can be set when making the assignment or after the fact. When turned on, users will be able to edit the raw value of a managed property when registering or editing an entity.
  • Easier batch upload:
    • batch import of materials and samples has now an 'Update existing' option which causes that new entities are registered and these which already existed before are updated,
    • it is easier to reference materials when using batch import or update of any entity - if the entity has a property of material type and the type of the material is fixed in property type definition, it is enough to mention only material code, specifying the type is no longer necessary,
    • Excel file (*.xls) can be used instead of TSV file,
    • DEFAULT block can be defined with default values of different columns. The block can be defined within single section (and then defaults apply only for this section) or within whole file (at te top of the file), then they apply to all entries in file,
    • artificial column default_space was introduced. In case when the identifier of sample/experiment is missing a SPACE part, value from default_space column,
    • possibility to import of materials of multiple types from single file was added.
  • Batch registration of samples inside experiment registration will use experiment space as default sample space instead of users's home space.
Imaging
  • Big improvement of the performance when showing an image series data set with a lot of images in the Web GUI.
Data Store Server
  • Fixed a crash bug in HDF5 that terminated the DSS when certain files in an HDF5 container were accessed.
  • The logging level for calls to the openBIS listDeletedDataSets and listDataSets methods has been set to DEBUG. This is because these methods are called with high frequency by the DSS, they show up often in the openBIS logs, but don't provide administrators with useful logging information.

Version S113 (18. August 2011)

Application Server
  • Make "trashcan deletion" (aka "logical deletion") fully usable. It is disabled by default but can be enabled by adding the line "enable-trash = true" to the web-client.properties. Make sure the web-client.properties are configured to be used in the service.properties

    # Name of the file that stores Web Client configuration
    web-client-configuration-file = etc/web-client.properties
    
  • WebStart programs (Image Viewer and Dataset Uploader) didn't start up when the server's certificate didn't have a valid chain of trust.
Data Store Server
  • Add the option to release shares of a multi-share data store by adding the line "withdraw-share=true to the share.properties. All datasets stored on a share in state withdrawal are moved to other shares.
  • Jython has been updated to 2.5.2. The new Jython interpreter is no longer able to resolve Java classes by wildcards. So entries in dropbox scripts like

    from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import *
    

    will no longer work. You need to explicitly specify all the classes that should be imported, e.g.:

    from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import BasicDataSetInformation
    from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageFileInfo
    
  • Use streaming mode when putting files into an HDF5 container on dataset registration; now we are no longer limited by server memory on how large files we can process.
  • Fixed a "Too many open files" exception when using the bioformats library to read images.
Screening
  • If several segmentation image datasets are registered for one plate with different analysis procedure, the user can choose from which analysis procedure the datasets should be shown.
  • The bioformats library has been updated to 4.3.1.
  • API methods loadThumbnailImageWellCaching() and loadImageWellCaching() used to hang indefinitely when PlateImageReference referred to a well which has no images at all. Now they return a byte[] of length 0.
  • Augmented the existing putDataSet method (for plates) in the Screening API to make it possible to set parents when uploading a data set. Also added a putDataSet method to the ScreeningAPI that makes it possible to upload a data set to an experiment. Added uploadDataSetForPlateAndParents and uploadDataSetForExperimentAndParents to the Matlab API to take advantage of this feature.
  • Automatically hide tooltips when a well-detail popup is opened.
Infrastructure
  • Check on system startup that daemons are not running as root. DSS and AS now refuse to start up when run by root. Starting the servers as root is strongly discouraged for security reasons and lead commonly to problems with file and database permissions.
  • When calling bin/startup.sh multiple times in the Application Server's installation directory, this used to create processes that were hard to find and to stop afterwards. Now this situation is detected and only ever one process is started.
  • The setting of the truststore (-Djavax.net.ssl.trustStore=etc/openBIS.keystore) has moved from datastore_server.sh to etc/datastore_server.conf to make it survive upgrades. When upgrading to S113 you need to add it to etc/datastore_server.conf if your server relies on this setting to work properly. This is true for all servers that use SSL and rely on the mock SSL certificates we are shipping with openBIS.

Version S112 (4. August 2011)

Application Server
  • IGeneralInformationService: exposed registration details for experiments, samples, data sets and vocabulary terms. The newly available method getRegistrationDetails() provides information about the registration date and the registrator.
Data Store Server
  • Jython Dropbox API extensions: Dropboxes can query and update external databases. See Jython Dropboxes v.1 (Legacy) for details.
  • Usability improvements for DSS Uploader
Screening
  • MATLAB API extensions
    • listAnalysisProcedures(experiment) and listPlates(experiment, analysisProcedure) methods have been added
    • loadDataSet() methods now returns properties
  • Added support for headless installations to the HCS installer

Version S111 (20. July 2011)

Application Server
  • Logical deletion of main entities (experiments, samples & data sets) was introduced:
    • Permanent deletion of the entities is done in 2 steps. Entities are first moved to trash and then the trash can be emptied (currently only by instance admin).
    • Entities are moved to trash with cascade. If one moves an experiment to trash all owned entities - samples and data sets, are trashed together as well. The same goes with samples - children, components and data sets are moved to trash.
    • There is a new view of Trash where the entities are moved when a user deletes them.
    • User who deleted entities can revert the deletions. Instance admin can revert all deletions. The revert operation can be performed both from Trash and from detail view of deleted entities.
    • Entities that are in trash can still be viewed in openBIS. They can't be modified though. All links leading to such entities are crossed out (like EXP1).
Screening
  • All views which show analysis results (Well Search, Material Detail view, Plate Layout) allow to filter the data by the analysis procedure. The new feature works only if one sets the analysis procedure property of the analysis data during registration (property code: $ANALYSIS_PROCEDURE).

Version S110 (6. July 2011)

Application Server
Data Store Server
  • Framework for Jython-based Reporting and Processing Plugins was introduced. For more details, see Jython-based Reporting and Processing Plugins
  • Jython Dropbox API extensions
    • dropboxes can now register materials
    • dropboxes can query external databases via IDataSourceQueryService. The service can be obtained from the "state" variable. It accesses configured DSS data sources by name.
    • added a new callback function (commit_transaction) allowing scripts to handle the successful completion of a transaction
  • Added a new ext-lib folder to the DSS installation. Administrators can place 3rd party libraries (JAR files) in ext-lib. These binaries will be available on the classpath and can be used from DSS and the Jython Dropboxes. The contents of the ext-lib folder will be preserved when updating to the next DSS version.
Screening
  • 'Summary' section in detail view of Material shows now contents from 2 old sections depending on selection of experiment context as in 'Plate Locations' section. One can see feature vectors in all experiments or in a selected experiment.
  • New data set property type ANALYSIS_PROCEDURE introduced for data sets of type HCS_ANALYSIS_WELL* and HCS_IMAGE_SEGMENTATION*. This property can be set in scripts of Jython dropboxes. Queries against IScreeningOpenbisServiceFacade and MatLab API can be restricted to data sets with specified value of this property.

Version S109 (22. June 2011)

Application Server
  • Table Editing improvements: it is now possible to modify properties of all types through the table (including vocabulary, material, date and boolean properties)
  • When deleting samples/experiments/data sets one can decide to delete it permanently (old behaviour) or invalidate it. Invalidated entities are still in the database and in future one will be able to revert such an invalidation. For now invalidated entities are still accessible from UI but links to them are crossed out.
  • Searching for Data Sets is now part of the openBIS public API (IGeneralInformationService)
Data Store Server
  • DSS Client: A new convenience client-side facade was added that encapsulates communication to AS and DSS in a single interface - IOpenbisServiceFacade. Instances of the facade can be constructed by OpenbisServiceFacadeFactory.
  • Simplify servlet configuration for reporting and processing plugins.
  • Added functionality to Jython dropbox to allow easy searching for experiments, samples, and data sets.
Screening
  • The publication view which shows feature vector summaries for all experiments in which the material is present shows now the ranking of each feature for each experiment. It is available if the experiments are restricted to one project.
  • A chosen material property can now be rendered as link which replaces the existing "Show/Show Details" link in various publication-related views.
  • MatLab API extended to handle multiple data sets with different feature vectors.

Version S108 (8. June 2011)

Application Server
  • Table Editing improvements:
    • it is now possible to modify properties of type MULTILINE_VARCHAR
    • table editing mode was introduced - user can modify multiple cells in one go and then decide to save or cancel all changes
  • Breadcrumbs in detail view headers of data sets, samples and experiments:
    • e.g. a breadcrumb for data set contains links to space, project, experiment and sample (optionally) that the data set is attached to
    • links to space and project open experiment browser with the space or project selected, other links work as usual (open detail view of an experiment/sample)
    • it is now possible to browse all experiments in a space by clicking on space in experiment browser's project tree
Data Store Server
  • All DSS client API methods (e.g. listing, downloading data sets) now use filesystem abstraction, which adds support for Container Data Sets and HDF5 container traversal.
  • Added new StandardShareFinder
Screening
  • publication portal has been polished, among other things:
    • the user interface look&feel has been improved
    • missing links between views have been added
    • it's possible to limit the view to assays in one project
  • Registering image container files (like multi-page TIFF) for microscopy

Version S107 (25. May 2011)

Application Server
  • Assigned properties of type REAL, INTEGER, and VARCHAR can be edited directly in tables by double-clicking on the cell.
  • PhosphoNetX: Protein/Peptide Summary table shows protein/peptide counts for decoy and non-decoy proteins.
  • It is possible to add 'Ad Hoc' Vocabulary Terms by power users when filling up the form. For more details, see Ad Hoc Vocabulary Terms
Data Store Server
  • New feature - "Container Data Sets" was introduced. For more details have a look at the guide Container Data Sets.
  • TSV Viewer and other reporting plugins that supported TSV and CSV files are now also supporting XLS and XLSX Excel files.
Screening
  • It is possible in the Jython dropbox to fix colors of each channel (before they were assigned automatically without any influence from the admin user).
    See Extensions chapter in Importing Images Configuration for details.
  • Material Analysis Summary view which presents all the analysis results and images for the material is now available by default (in all view modes). Few bugs in user interface have been fixed.
  • There is a tab in material detail view which shows feature vector summaries for all experiments in which the material is present.

Version S106 (11. May 2011)

Application Server
  • Advanced Search UI extension: it is possible to specify search sub criteria with metadata of: container/parent/child sample, experiment (UI is now as powerful as Search API)
  • Support configuration option ldap.queryTemplate in service.properties to set a template for the LDAP query; this may be necessary to support an OpenLDAP server.
  • debug panel: debug=true URL parameter turns on special mode where a debug panel is put at the bottom of openBIS page; it is useful e.g. for profiling performance of both client and server side of openBIS
Data Store Server
  • Support of graphs & plots in reporting plugins.
Screening
  • MatLab API extended: Uploading/downloading of data sets, setting/getting well properties, loading single tile images.
  • Gene summary view has been extended
    • gene id, its description and a link to the external gene database are available
    • all gene images are displayed in a table, images for one siRNA are grouped in one row
    • images are labeled, so one can see to which siRNA and technical replica the image belongs
  • Assay description is available in assay summary view

Version S105 (27. April 2011)

Application Server
Data Store Server
  • Path info database for faster file browsing inside data sets.
  • Share finder for shuffling and unarchiving recognize speed parameters of shares and speed hints of data sets. The speed hint of a data set is also saved in the database.
  • DSS can now start an internal FTP server providing read-only access to the data store contents.
  • A network timeout parameter has been added to the DSS console client.
  • DSS validation scripts on the WebStart uploader can now access the Python library and can parse Excel files using the Apache POI library.
Screening
  • openBIS can handle all the images which can be opened by BioFormats library.

Version S104 (13. April 2011)

Application Server
  • PhosphoNetX: Showing modified amino-acids in protein and peptide sequences in protein detail view.
  • Home icon was added to welcome tab.
  • Home database instance code is no longer added to sample identifiers.
  • It is possible to traverse content of HDF5 containers in Data View in data set detail view.
  • Bug fixes:
    • users no longer need to manually refresh openBIS in their browsers upon server upgrades
    • unlock search index after server is restarted during indexing operation
    • values int filter combo boxes are escaped in a consistent way
    • user logged in anonymously cannot switch to normal (non-anonymous) mode without logging in
Data Store Server
  • Restartable shuffling maintenance task.
  • PhosphoNetX: Feeding database also with modification fractions.
  • SampleAndDataSetRegistrationHandler now honors sample/data set types configured in service.properties
  • RsyncArchiver: implementation was improved to use rsync both locally and remotely, update of archive doesn't require deletion of the destination folder any more
  • Introduced an abstraction to access files and directories in a data set. The abstraction is currently used only in Data View in Application Server allowing to transparently traverse the filesystem.
Screening
  • Image intensity rescaling application store rescaling configuration also for users having only SPACE_POWER_USER rights.
  • Jython dropboxes can now specify image transformations with the 'convert' command tool. These transformations will be applied every time before diplaying the images in openBIS.
  • Well search displays matching materials in a single row per well (previously there was one row for the combination well+material).
  • There is a new tab in experiment detail view which displays analysis results summary for each gene (or compound) screened in the experiment. For each gene (or compound) one can navigate to the table with detailed analysis results, which contains one feature and all replicated wells per row. New views are useful when it comes to publication of the final screen results.
  • Performance of the "Well Search" has been greatly improved

Version S103 (30. March 2011)

Application Server
  • List of last seen experiments/samples/data sets/materials on the start page.
  • Anonymous login.
  • PhosphoNetX: Data set processing tasks appear as links in the lower left corner of detail views for experiments of type MS_SEARCH and MS_QUANTIFICATION.
  • Last table columns are automatically hidden if number of all visible columns exceeds the limit specified in web client properties (default 50).
  • Managed Properties: support for displaying Unicode characters in tables generated by scripts.
  • Search API: extension of complex queries for samples - it is possible to specify search sub criteria with metadata of a container/parent/child
  • UI Usability: added drag & drop support for table column reordering.
  • Data Set Uploader: A WebStart client program to upload data sets.
  • openbis can be launched in a mode suitable for embedding it inside external web pages.
    This mode is very similar to the 'simple' mode, but:
    • toolbar at the top and footer are not displayed
    • each table has only one button which allows to export it. There are no buttons for filtering, refreshing and changing the settings.
      To lunch openBIS in embedded mode it is enough to add '?viewMode=embedded' to the URL. It can be also configured that embedded mode is the default one.
Data Store Server
  • The thread of a maintenance task did stop when the maintenance task threw an exception (e.g. because it tried to contact the AS and the AS was down); this lead to the maintenance task no longer being executed after the exception until the DSS was restarted
  • Post Registration framework for executing post registration task. Following post registration tasks are implemented: Shuffling (i.e. moving data set to a different share), notification, and archiving.
  • Jython dropboxes can now create spaces and projects on the fly
  • Jython dropboxes can server RPC requests for registering data sets.
Screening
  • up till now when looking for wells with specified materials (e.g. a gene) in "Well Search" window all the results were presented in one table, even if many materials matched the query.
    Now a disambiguation page can be shown on request in such a case. The page allows to choose one interesting material and show data only for it.
  • it is possible to suppress sending notifications when the registered image dataset has some images missing:

      <dropbox>.storage-processor.notify-if-incomplete = true/false
    
  • it is possible to avoid moving datasets which could not be registered to the error directory and leave them in the incoming folder:

      <dropbox>.storage-processor.move-unregistered-datasets-to-error-dir = true/false
    
  • in python dropboxes there is a way to find a smallest plate geometry which contains all images of a plate:

    plate = transaction.createNewSample(sampleIdentifier, "PLATE")
      geometry = factory.figureGeometry(registrationDetails)
      plate.setPropertyValue("$PLATE_GEOMETRY", plateGeometry)
    

Version S102 (16. March 2011)

Application Server
  • PhosphoNetX: Wizard for annotating MS_INJECTION samples
  • Managed properties: links to entities in tables generated for managed properties can now display arbitrary text (by default identifiers are shown)
  • API: it is possible to search for samples using experiment's metadata (e.g. code, type, properties, project's code)
Data Store Server
  • Auto archiving can now be configured to leave the data store contents intact
  • Added rsync archiver
  • Added GUI client for data set upload
Screening
  • a framework to save image transformations for a single image has been established

Version S101 (2. March 2011)

Application Server
  • Usability:
    • Replaced 'Perform' menu in Data Set tables with its Archiving submenu. Moved reporting services to a combo box in section's header (switching between them replaces the table view). Moved processing services to separate menu in section's header.
    • Display last active tab when user logs in (only in 'Normal View Mode' when user entered openbis without history token in URL)
  • Force web browsers to use Standards Mode when displaying openBIS pages (fixes simple view mode history in IE).
  • Migration to GXT 2.2.1
Data StoreServer
  • The symbolic link names created by HierarchicalStorageUpdater are now configurable by a template. The link folder structure was simplified to contain only 4 nested levels (previously they were 10)
  • Jython dropbox improvements
    • added support for setting/getting data set properties
    • registration of multiple datasets by storage processors working with external databases is now possible
Screening
  • well properties are displayed in the Well Search table
  • a dropbox to import image analysis results can be configured in Jython in a very flexible way
  • a dropbox to import image data can be configured to use ImageMagic 'convert' tool to generate thumbnails. The tool has to be installed separately, but is generating thumbnails much faster than the one which is used by default.
  • improved speed of loading data for showing plate layout (all features of a well are loaded when well's tooltip is shown)

Version S100 (16. February 2011)

Application Server
  • Logout, Search and Home buttons are available on the top menu bar in Simple View Mode
  • Fixed problems with stale dynamic property values and lucene search index after performing batch operations.
  • Managed properties:
    • links to entities in tables generated for managed properties are now displayed as identifiers, not permIds
    • batch update is partly supported (with no access to old values of updated properties in the script)
Data StoreServer
  • Data store can be segmented and distributed on many file systems (local and shared ones). Each segment (called share) is a subfolder in the store or a symbolic link to a subfolder somewhere else. A maintenance task ch.systemsx.cisd.etlserver.plugins.SegmentedStoreShufflingTask allows to shuffle data sets from shares associated with drop boxes (so called incoming shares) to other shares if the incoming share is full.
Screening
  • Screening API 1.6 with a bunch of new methods.
  • dataset types for screening have been standardized. See Pending Configuration Changes if you want to start using new types
  • It is possible to select which channels should be merged (before there was only an option to merge all available channels)
  • Well Search can be accessible from the welcome page in Simple View mode (use href=#action=GLOBAL_WELL_SEARCH)
  • Thumbnails can be generated faster on multi-core machines
  • Writing dropboxes for image datasets in python has been greatly simplified and documented
  • Improved speed of loading data for showing plate layout (number of initially loaded features is limited) - IE doesn't warn about long running script any more

Version S99 (2. February 2011)

Application Server
  • Introduced Managed Properties (Documentation) as a new kind of properties that are handled by Jython scripts (Documentation) allowing for:
    • customization of batch import, UI displayed in entity detail views (as tables with support for entity links) and UI for edition of the property
    • handling (parsing/modification) of XML properties in the script using an abstraction - similar to DOM API
Data StoreServer
  • Archives to be uploaded in CIFEX are now assembled using the TrueZIP library. One of the advantages of TrueZIP over the standard JVM is that it can handle archives larger than 2GB.
  • it is possible to configure the dropbox with a Jython script. There is a special version for Screening available as well. Further work on simplifying the configuration will take place in the next script, when the full documentation will be published.

Version S98 (18. January 2011)

Application Server
    • Showing large tables has been speeded up.
Data StoreServer
  • PhosphoNetX:
    • During registration of data sets for an MS_INJECTION sample the sample can be immediately linked to a biological sample.
    • Data sets of type PROT_RESULT can be linked to data sets of a specified experiment
    • Processing/reporting plugin for APMS table report
Screening/Microscopy
  • it can be decided if image datasets in one experiment should have the same channels or not. It is particularly useful for overlay datasets.
  • error handling for overlays has been improved
  • improvements of the viewer for images with timeseries and depth-scans
    (separate sliders, images are loaded only when the slider is moved)
  • support for transparent overlay images
  • possibility of writing screening/microscopy dropboxes in Jython
  • colors adjustments can be done for microscopy datasets as well

Version S97 (4. January 2011)

Application Server
  • Number of visible columns in all tables is limited (default: 50, configurable in web-client.properties).
  • It is possible to export table with all columns (not only the visible ones).
  • Screening and Microscopy:
    • overlays of the images (e.g. showing where the image analysis algorithm has found the nuclei) can be imported and shown on top of the original images. Several overlays in one dataset (as different channels) and several datasets with overlays for one image dataset are supported.
    • Images can be browsed in the detail view of the well or microscopy sample.
  • PhosphoNetX: Protein Viewer performance improved. Loading the data of an already shown table is improved by server-side caching.
Data StoreServer
  • Extended the ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler to allow updating samples and registering data sets with metadata in bulk using a drop box.
  • It's possible to define a script that should be called before data set registration (<incoming-thread>.pre-registration-script = <script-path>). See Installation and Administrators Guide of the openBIS Data Store Server
  • Copying processing task can sent detailed e-mails for each copied data set.

Version S96 (15. December 2010)

Application Server
  • New on attachment grids: Add button for adding an attachment
  • Improved performance of listing big tables 
  • File browser in data set details view: All file links can be copy-pasted into other Web browser because their URL includes session keys. Works only for valid sessions.
  • Character encoding used for import/export files is not dependent on server default settings - it is fixed to UTF-8 
  • Screening
    • Library Upload: user can select one of the following field separators: comma, space, semicolon
    • Plate wells will now always have direct connection with experiment so they become owners of data sets.
Data Store Server
  • DSU: Processing plugin for exporting meta data in SOFT format
  • Added the ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler, a data set handler for registering samples and data sets, with metadata, in bulk using a drop box.
  • Microscopy images support: the "openBIS for Screening" has been extended to support microscopy data.
    • one logical image not connected to the plate can be imported and viewed. All features known from HCS for images of a single well are present: tiles, channels, timepoint series, depth scans series. Image dataset can be attached to any sample.
    • whenever a dataset table is shown there is a new "Overview" column. For microscopy datasets it shows an overview of the image.
    • one can upload a dataset with images not adhering to any naming convention and view them as a series.
  • Screening: depth-scans can be imported and viewed.

Version S95 (1. December 2010)

Application Server
  • Performance improvements: data set batch update, listing of samples.
  • 'Save & Upload Data Set' button added to sample registration/edit form. After saving sample in OpenBIS database, 'Data Set Upload' window is opened with 'Sample' field filled. This feature is only available if cifex data upload has been enabled (AS service.properties: cifex-recipient and cifex-url).
  • Dynamic Properties: support material and vocabulary properties.
  • Renaming of table GROUP in openBIS database schema for meta data to SPACE. Also all foreign keys onto this table are rename from grou_id to space_id.
  • PhosphoNetX: Proteomics Data API has been extended with methods to handle any experiment based on PROT_RESULT data sets not only MS_SEARCH experiments.
  • Screening
    • It is possible to import image analysis results which are not numbers but have text values. In this way e.g. a category can be assigned to each well. The whole plate can be displayed as a clickable heatmap which shows which well belongs to which category.
    • Channel selected in a combo box is stored in user display settings using experiment as the context (both in Plate Layout and in Wells Search).
Data Store Server
  • It's possible to define a script that should be called after successful data set registration (<incoming-thread>.postregistration-script = <script-path>). See Installation and Administrators Guide of the openBIS Data Store Server
  • PhosphoNetX: Renaming DataSetInfoExtractorForSearchExperiment to DataSetInfoExtractorForProteinResults and two properties added to configure experiment type and experiment properties file name.

Version S94 (17. November 2010)

Application Server
  • Support for multiple parents in batch update and import of samples.
  • Improved showing indirectly connected data sets in sample detail view to show also all data sets connected with derived samples.
  • Script editor now allows to test the script on selected entity (sample/experiment/material/data set). The script is also validated.
  • Screening:
    • Image Transformation Framework to define transformations (e.g. color adjustments) on experiment level applied to all images presented.
    • Possibility of storing images of the whole plate compressed in one file. It allows to considerably reduce both the number of files stored in the file system and the needed storage space. Files are stored in HDF5 format.
    • Plate layout can be presented in a form of a heatmap where a value of the chosen feature for each well is visualized. After clicking on a well its images and metadata are presented.
  • PhosphoNetX: Proteomics Data API: Simplifying processing of data sets by providing directly data set codes.

Version S93 (3. November 2010)

Application Server
  • Introduced Dynamic Properties (Documentation) as an alternative to Custom Columns for entities (values are connected with entities - not tables, better viewing performance - the evaluation is done on updates).
  • Registration of experiments in a batch.
  • Batch update of samples and materials was made significantly faster (10-20x).
  • Number of search results is limited to a configurable number - user is informed if his query reaches the limit.
  • PhosphoNetX: Proteomics Data API: listRawDataSamples() delivers also biological experiment with properties as well as all data sets with their properties.
  • CINA Add API call to list experiments.
  • Fixed a bug that prevented some functions of openBIS to work with PostgreSQL 9.0
Data Store Server
  • Fixed an issue on batch updates which lead to data set uploads sporadically failing for openBIS Metabolomics
  • Fixed a bug in the CifexStorageProcessor when interacting with a delegate storage processor
Infrastructure
  • Add list and original checksums for all configuration files in the distribution so that changed configuration files can easily spotted during uprade

Version S92 (20. October 2010)

Application Server
  • Updating materials in a batch.
  • Custom queries:
    • entity type code can be specified as a regular expression (rather that just a single entity type code) to specify to what entity types a given custom query can be applied to
    • it is possible to specify a list of possible values for a parameter of a custom query (Documentation) by means of either:
      • a predefined list (works also in custom filters), e.g.:
        ${query name::query=select distinct identifier from time_series where identifier like 'BBA%'}
      • another SQL query, e.g.:
        ${query name::list=option1,option2,...,optionN}
  • Performance improvement: Sample batch update scales lineraly with number of updated samples.
  • Screening:
    • Added capability to store thumbnails in compressed form in the PlateStorageProcessor
Data Store Server
  • Created new ch.systemsx.cisd.etlserver.hdf5.Hdf5StorageProcessor, a storage processor that stores data sets in an HDF5 container.

Version S91 (6. October 2010)

Application Server
  • Index title and description of attachments for quick search
  • Fix Out Of Memory Exception when searching for a quoted expression in quick search
  • Size of a left panel (properties) in detail view of sample/experiment/material/data set is stored in user's display settings.
  • Default view mode (SIMPLE/NORMAL) of Web Client is now configurable (before normal mode was a fixed default).
  • Custom queries for experiments/samples/materials/data sets can be defined for specific types. Such queries will be presented only for entities of a specified type.
  • XML Schema and XSLT script are now validated against appropriate schemas.
  • Screening:
    • "Well Search" table shows each well content property and feature in a separate column. It allows to e.g. sort the images by the infection index.
    • one can access "Plate Metadata Report" and "Well Search" with a URL
    • fix a bug in the Screening API that would lead to images not being delivered via the API
Data Store Server
  • A new reporting plugin mimics the behavior of the smart view: ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin. It can be used to provide multiple smart views for a data set type.
  • Combination of DSS plugins made possible.
  • In case of registration via CIFEX or API the registrator is added.
  • The ability to retrieve the path of a data set in the store was added to the DSS API and DSS command-line client.
  • BaSysBio:
    • remove unused fields cg and bi_id from the database
    • index for column ControlledGene
    • fix LCA Microscope validation to allow for several data sets providing data for different samples but the same experimental condition

Version S90 (22. September 2010)

Application Server
  • Query_Project Databases: Change default of <database>.creator-minimal-role to INSTANCE_OBSERVER for query databases which contain data from more than one data space (i.e. have <database>.data-space not set)
  • Allow automatically created db role openbis_readonly to login so it can be used for the db query interface.
  • Introduced new data type - XML, for storing structured information in properties (Documentation):
  • Changed the way how batch update of samples/datasets/vocabularies work:
    • To delete a property/field one needs to explicitly specify it in the uploaded file with - DELETE - value in appropriate column.
    • No column or empty value in a column means that no change should be done.
  • Extended expressiveness of filters (also in Cifex) to support numerical comparison and conjunction of conditions:
    • supported numerical comparison operations: <, >, <=, >=, =, !=) with a number immediately after those characters (e.g. <10)
    • conjunction of conditions: separate conditions with ' & ',
      • (old) space separator evaluates alternative of conditions e.g. 'abc bcd' means that an accepted value should contain 'abc' or 'bcd'
      • (new) 'abc & bcd' means that an accepted value whould contain both 'abc' and 'bcd'
  • Web Client can be configured to hide some parts of the default GUI (Documentation)
  • Improved layout of sample, experiment, data set and material Detail View (tabs)
  • Added a method to the service API that permits searching for samples based on metadata.
  • Screening:
    • Simplified way of accessing plate datasets - now all the information are available from the main plate detail view.
    • Well Reviewing Panel shows now not only images for the found genes, but also their feature vectors.
    • Improved layout of Well Content Dialog
    • Changed names of GUI elements (note that "Wells Reviewing Panel" is now called "Wells Search" and "Well Materials" changed to "Library Index")
    • Improved simple view mode support: fixed links to material details, added support for material type preselection in material browser.
Data Store Server
  • Data Set Registration: Registrator can be specified either by an e-mail (CIFEX use case) or an user ID (API use case).
  • BaSysBio: Uploaded TSV files are checked on trailing TAB characters.

Version S89 (7. September 2010)

Application Server
  • Screening
    • sample type OLIGO_WELL has been renamed to SIRNA_WELL, material type and property type OLIGO has been renamed to SIRNA
    • New section Well Materials has been added to experiment detail view. It contains a table with all materials (e.g. genes, siRNAs or compounds) used in an experiment, from all wells in all plates. User can filter by the type of material, his last selection is remembered.
    • API speed improvement: fetching feature vector datasets for a given set of plates became considerably faster
    • plugins which will allow openBIS to integrate with iBRAIN have been written
    • bugfixes
      • a bug which caused that images could not be shown sometimes when too many users were accessing them has been fixed
      • you can see the magnified image with all channels merged (before just one channel was shown)
    • GENEs are now identified uniquely by Library ID. Previously imported genes with the same Library ID have been merged and the codes have been stored as the value of GENE_SYMBOLS property.
    • Plate Reviewing Panel allows to search for genes not only by gene symbol, but also by gene id. You can also specify any properties as a search criteria, e.g. part of the description - in such a case uncheck "Exact Matches Only" option.
Data Store Server
  • BaSysBio:
    • New database schema which makes it easier to write SQL queries.
  • DSU: Additional files (apart from srf files) are attached to each ILLUMINA_FLOW_LANE sample data set. Afterwards DATA_TRANSFERRED property of the sample is set to the current date.

Version S88 (24. August 2010)

Application Server
  • Support for maintenance tasks also on application server side using the same configuration as in DSS.
  • Screening
    • Support for storing and showing time series of images has been added.
    • Support for merged view of up to 6 channels.
    • Other improvements:
      • Feature vector names are replaced by label and codes. If not specified codes are normalized labels.
      • Channel names are replaced by label and codes. If not specified codes are normalized labels.
      • New API has a minor version 2 as a consequence of changes from feature names to labels/codes.
      • "Dummy" wells are no longer automatically created in OpenBIS when dataset is registered.
Data Store Server
  • Plasmids
    • OpenBIS is now integrated with PlasMapper (registering a data set of type SEQ_FILE, holding a plasmid sequence, will additionaly generate and store an image with a Graphic Map of the sequence)
  • BaSysBio: New *_TIME_SERIES data set types which should be used instead of TIME_SERIES because time series data sets are no longer splitted. This also means that no TIME_POINT samples/data sets are created.
  • It's now possible to specify both code and label (<CODE> Label) as the column header in the TSV files. The code can be later used in Custom Column and Custom Filter definitions. If the code is not specified, the label will be normalized (allowed characters:"A-Z0-9_") and used as the code.

Version S87 (11. August 2010)

Application Server
  • Samples can now have multiple parents. This feature is not yet supported in batch import/update of samples.
  • Screening
    • allow to compare gene images across all experiments
    • use Wells Reviewing Panel in material detail view
    • (Plugin configuration) HCSImageFileExtractor allows to specify well geometry (site/tile number - well location mapping).
APIs
  • Screening API, new minor version 2:
    • New method listPlateWells(MaterialIdentifier,boolean)
    • New method listPlateMaterialMapping(List<PlateIdentifier>,MaterialTypeIdentifier)
  • Add OpenBISScreeningML class as an API that is simple to use from Matlab.

Version S86 (27. July 2010)

Application Server
  • A column in TSV file will be ignored by openbis during registration/update of entities if name of the column's header starts with ! (e.g. !fake). Such a column can be used to compute values in other columns that will be stored as sample properties.
  • Template for import of samples has property columns sorted in the same order as the one used in sample registration and detail view.
  • When user issues registration of a new sample in a specific context some of the fields in the registration forms are filled automatically (e.g. when Add Sample button is clicked in Samples section of experiment detail viewer the Experiment and Space fields will be filled)
  • Fixed bugs with permlinks to attachments that have special chars like = or spaces in their file names.
  • Screening: support for plates with compounds, controls, multiple siRNA or genes when siRNA is not used has been added. At the moment non-siRNA screening libraries have to be registered in two steps using material batch upload and sample batch upload.
Data Store Server
  • DynamiX: a plugin to upload the data from DynamiX project has been written

Version S85 (14. July 2010)

Application Server
  • Custom DSS databases which must be accessible by AS will be resolved depending on on the data set. This allows to run more than one DSS with a custom database.
  • new public API started: GeneralInformationService
  • PhosphoNetX: RawData API extended: method added which list all projects a user has USER rights.
Data Store Server
  • BaSysBio: LCA_MIC data sets will be deleted if registration of derived LCA_MIC_TIME_SERIES data sets fail.

Version S84 (30. June 2010)

OpenBIS Application Server
  • In Sample Detail View the derived samples are no longer shown like properties. Now they are shown as a table.
  • Sample deletion speed improved.
  • Improve message of the dialog for exporting data sets via CIFEX.
  • Switch from Tomcat to Jetty 7.
  • PhosphoNetX: Column for identifier of biological experiment added to table behind menu item Utilities -> All MS INJECTION Samples.
  • Sample type selected in sample browsers is saved as display setting.
  • HCS: column showing thumbnails added to Reviewing Panel.
OpenBIS DSS
  • Switch from Jetty 6 to Jetty 7.
  • CLI client: Avoid need for providing password as plain text.
  • PhosphoNetX: Raw Data API delivers also identifier of biological experiment.
  • Screening: Imaging database is used for storing and providing feature vectors.
  • YeastX: MZ_PEAKS is not automatically dropped in migration from database version 004 to 005.

Version S83 (16. June 2010)

OpenBIS Application Server
  • Introduced permlinks for sample and experiment attachments.
  • In all grids it is possible to:
    • filter out rows where a given value appears (put '!' before the value)
    • show rows where the value starts/ends with the specified text (put '^'/'$' at the beginning/end of the text)
  • Improved the way of handling filter values chosen from a combo box - only rows that match exactly the selected text will be shown even if the filter value contains spaces or is a prefix of another value.
  • Added missing links in sample and experiment browser on identifier, and subcode columns. These column are now sorted in the same way as Code column (numerical parts are sorted separately).
  • Huge speed improvement of assigning properties with default values to entity types / release of assignments. Update of search index is performed in a separate, low-priority thread that doesn't affect openBIS performance. On the other hand search index will not be immediately consistent with the state of the database.
  • Improved speed of sample batch update.
  • Added possibility to update of data set properties in batches.
  • openBIS for screening: "Genes Reviewing Panel" has been introduced as the experiment section. It is possible to paste many gene codes and browse images connected to those genes in the experiment quickly. It is no longer necessary to choose the experiment for each gene separately.
  • openBIS for screening: show channel names instead of numbers; this included a change in the class used by the Screening API - PlateImageReference contains now channel name instead of number.
  • Entity (sample/experiment/material/data set) properties in the viewers are stored in the same order as in registration forms.
OpenBIS DSS
  • Added configuration options to RPC-based upload of datasets
  • YeastX: More compact way to store MS peaks in metabol database
  • BaSysBio: Maintenance task for deleting every hour data sets in BaSysBio database which are deleted in openBIS AS
  • HCS: Maintenance task deleting from screening database data sets no longer existing in OpenBIS.
  • CINA: Import CINA bundle data sets.
  • CSB
    • OpenBIS is now accessible through URL: https://openbis-csb.ethz.ch/openbis.
    • It is possible to upload data sets through internal instance of CIFEX.
    • Plasmid subcode uniqueness is preserved even if they are components of different container. It is also possible to use identify such samples by their subcode in identifiers (useful e.g. in sample or data set registration).
    • Added a property holding name of the file stored in a plasmid data set.
Cifex
  • Extended expressiveness of filters to support:
    • Alternatives (by ' ')
    • Negation (by '!')
    • Binding to start of value (by '^')
    • Binding to end of value (by '$')
    • Quoting by single ("'") and double ('"') quotes
    • Escaping of special characters (by '\')

Version S82 (2. June 2010)

OpenBIS Application Server
  • Fixed bugs of custom columns in Query module (disappearing column on SQL change, missing cell values).
  • Confirmation window is not shown when leaving simple view mode.
  • Setup a new instance for CSB group and their plasmids
  • Improved sorting of CODE column in tables - if a code contains a number the number part of the code is sorted separately from the rest of the code
  • PhosphoNetX: Protein Browser only shows primary proteins. Protein details view shows also corresponding indistinguishable proteins.
  • Screening: a special imaging database is used to store information about images. Before file system has been used for this purpose, now it is more efficient.
OpenBIS Data Store Server
  • Added support for upload (put command) using the dss_client.
  • BaSysBio: Preventing upload of data columns already present in the BaSysBio database.
  • BaSysBio: Uploader/Validator for ChIP-chip datasets
Cifex
  • Improved refresh of layout when user resizes browser window - e.g. sizes of tables are refreshed too and scroll bars appear

Version S81 (19. May 2010)

OpenBIS Application Server
  • modules (entity type independent plugins) can now specify a collection of sections that will be added to generic detail view of sample, material, experiment and data set
  • Custom queries can be defined for experiments (also samples, materials and data sets). Those queries should contain a 'magic' parameter '${key}', which will be replaced with the perm id of the experiment. Experiment custom queries will be presented as the additional section in the experiment details view.
  • Extended Query Module - it supports querying multiple external databases and allows for more powerful, configurable authorization on data space level.
  • Improved performance and reliability of database operations: fixed pooling of database connections.
  • List of elements in a combo box (e.g. a filter field) has width auto adjusted to maximum width of all elements the list.
  • Made display settings changes temporary in Simple View Mode. These changes last only as long as http session does. They are not saved in the database and therefore are isolated if more than one person logs in as the same user.
  • Dataset Query results open in a new tab every time they are invoked. Such tabs have unique labels with name of the query and time of getting query results.
  • PhosphoNetX: Improve p-grade API (called Raw Data API) based on new concept for public APIs.

Version S80 (5. May 2010)

OpenBIS Application Server
  • Query API V1.0
  • KNIME plugin for a node based on Query API
  • Metadata panel of entity details views (Experiment, Sample, Data Set) is collapsible.
  • Introduced Simple View Mode in which users can't modify any data and there are no tabs (there is only one view opened, all navigation between views is done using bookmarkable links, clicking on a link replaces current view, browser history back/forward buttons go to previous/next view)
  • Project code in tables and detail views (new) of samples, experiments and data sets are now links to Project detail view.
  • Improved performance of assigning/unassigning property types.
  • Improved performance of operations performed on data sets (processing/reporting/archiving/upload/deletion).
  • openBIS for Screening
    • the public API for HCS specific operations has been developed. Special care was taken to ensure that images download is fast.
    • import of screening libraries has been improved to deal with the cases when similar genes are used in several screens.
OpenBIS Data Store Server
  • PhosphoNetX: Data set copier with destination template. Template parameter ${user} is replaced by user ID.

Version S79 (21. April 2010)

OpenBIS
  • Changed tracking of samples for the DSU project .
  • Archiving module improvements: optional Archiving submenu in data set tables, meaninful messages, renamed labels .
  • Improved performace of displaying views with tables and changing between tabs.
  • Admin console for registering data sets and assigning data set properties
  • Screening: image analysis results can be shown on graphs (heatmaps, scatter plots, histograms)
Data Store Server
  • PhosphoNetX: Extended registration of ms injection data sets and of protein data sets
  • BaSysBio: Registration for LCA MIC and LCA MTP data sets
  • YeastX: Data set archiver cleaning metabol database

Version S78 (7. April 2010)

OpenBIS
  • It is possible to open an experiment/sample/material detail view "in the background" (Alt+Click).
  • GUI Logging Console for debugging and performance measurements
  • PhosphoNetX: Performance improvements of protein view
Data Store Server
  • Added (RPC) service interface to DSS.
  • Created command-line client for listing and downloading files in a data set.

Version S77 (24. March 2010)

OpenBIS
  • Experiment detail view shows experiment properties immediately, even if there are many connected samples and datasets.
  • Distribution contains a client JAR with stripped down to CISD classes which needed for remote invocations of openBIS APIs.
  • It is possible to request archiving and unarchiving of data sets (data set table). The action will performed by the archiver configured to appropriate data store.
  • It is possible to "lock" (also "unlock") data sets (data set table). Locked data sets cannot be archived (also by the auto-archiver).
  • PhosphoNetX: Improved performance of protein viewer.
  • HCS: Registration of plates in QIAGEN-like format can be done directly from OpenBIS GUI (Sample Import -> SampleType:Library).
  • YeastX: performance of showing the chromatograms images has been significantly improved, memory leaks have been detected and fixed.
Data Store Server
  • Maintenance tasks: It is possible to define the time of the first execution (HH:mm).
  • It is possible to define the archiver plugin. Archiving may be triggered manually by openBis user or by auto-archiver (maintenance task).
  • PhosphoNetX: Automatical creation of Search Experiments and Search Samples when a protein identification result data set is registered.

Version S76 (10. March 2010)

OpenBIS
  • PhosphoNetX: Improved performance of protein viewer
Data Store Server
  • TSV plugin has been improved (support for different separators, ignoring comments starting with #)
  • BDS 1.1 format changed: group_code replaced by space_code
  • YeastX: Report Show eicML chromatogram images improved.
  • BaSysBio: E-mail also in case of successful uploading of a time-series data set.
  • BaSysBio: Reporting plugin that allows to extract time series data set properties like TECHNICAL REPLICATE from the TSV files
  • BaSysBio: Processing plugin that allows to update time series data set properties like TECHNICAL REPLICATE taking values from TSV files
  • DSU: Error message improved in case of flow lane appearing twice.
  • CINA: A version of DSS that can import data sets and register experiments and samples
  • Screening: support for opening compressed tiff images has been added

Version S75 (24. February 2010)

OpenBIS
  • "Group" renamed to "Space" .
  • Data set details contains information about the group that connected sample/experiment belongs to.
  • Direct and parameterized SQL Queries for any second PostgreSQL database. Result sets are shown as sortable, filterable, exportable tables.
  • Sample Browser can show samples of all spaces.
  • Improved performances of detail views (sample, experiment, dataset) by not loading of data that is not needed
Data Store Server
  • Generic:
    • Validators allow to check column values uniqness based on chosen parts of the value .
  • BaSysBio:
    • Additional properties extracted from the headers of *TIME_SERIES data sets:
      • TECHNICAL_REPLICATE_CODE
      • BIOLOGICAL_REPLICATE_CODE
      • TIME_SERIES_DATA_SET_TYPE
      • CEL_LOC
      • CG
      • CULTIVATION_METHOD_EXPERIMENT_CODE
      • EXPERIMENT_CODE
      • SCALE
      • TIME_POINT
      • TIME_POINT_TYPE
      • BI_ID
      • VALUE_TYPE

Version S74 (10. February 2010)

OpenBIS
  • User defined global settings for formating real numbers.
  • Allowed description length increased to 2000 characters.
  • openBIS for Screening version: it is possible to see plate images in the dataset detail view as well. Thanks to this fact images can be browsed if more than one dataset with images for one plate exist.
  • Improved support for keyboard navigation in the detailed searches. Enter runs the search.
  • Support Autofill on the OpenBIS login screen in Firefox and IE.
  • Improved layout of column filters - up to 24 filters can be displayed properly per table.
Data Store Server
  • Generic:
    • Extended e-mail notification mechanism about processing task completion. Data sets are grouped by processing statuses.
  • PhosphoNetX:
    • Registration of MS_INJECTION data automatically creates experiment and user if not present.
  • BaSysBio:
    • Time series data sets also stored in a relational database. A maintenance task does this also for already registered data sets.
    • LCA_MTP_TIME_SERIES data sets can be uploaded.
  • YeastX
    • Reporting plug-in that renders chromatograms as graphs
Data Mover
  • Introduced an optional step allowing to perform a transformation before data is moved from the buffer to outgoing directory (as a first use case transformator performing tiff compression was implemented for InfectX).

Version S73 (27. January 2010)

OpenBIS
  • Clickable info icon added to the property fields in the forms, that opens a pop-up containing the property description. It is possible to copy the some parts of the text and use it in the field.
  • Sample search works also with contained samples (e.g. 'PARENT:CONTAINED').
  • Improved data detail viewer:
    • reports are opened in Data View section (the same section where one can browse data set directory)
    • added 'Process' menu with processing plugins assigned to data set type
    • added usage of wildcard characters in 'Main Data Set Pattern' (Data Set Type property) for 'Smart' viewer; regular expressions are still available with regexp: prefix
  • Added online help links for remaining dialogs with functionality that is not trivial and an info icon with a short help message to the top menu.
  • Improved data set details view
  • bugfix:
    • auto applying filters after backspace
    • correct rendering of internal properties
    • improved layout of the forms
  • Support for URLs that link to samples specified by code. E.g., https://sprint-openbis.ethz.ch/openbis/?searchEntity=SAMPLE&code=CL1
  • openBIS for High Content Screening
    • It's possible to export the plate metadata.
  • PhosphoNetX:
    • Protein overview has been moved to experiment details view.
    • All properties of MS_INJECTION samples and their parent biological samples are shown.
    • User can use any processing DSS plugin for processing data sets of chosen MS_INJECTION samples.
    • IRawDataService interface extend to support this choice of DSS plugins.
Cifex
  • It is possible to share files with externally authenticated users that have never logged in (an account is created automatically).
  • Added support for autofill forms on the login page. Works on Firefox 3 and IE 8, does not work on Safari or Chrome.

Version S72 (13. January 2010)

OpenBIS
  • Upgraded to GWT 2.0
  • Extended online help, including adding help to advanced search dialogs and column settings dialogs.
  • Content of data sets can be browsed directly from openbis (data set details window)
  • Batch update of samples extension: if Default Group is selected one doesn't need to specify whole Identifiers for updated samples - it is enough to provide sample Codes.
  • Improved speed of browsing Materials.
  • Global search (the one in top menu) can now search also for Data Sets.
  • Search behaviour is now customizable. User can switch between two search modes:
    • basic mode - new mode in which a '*' wildcard is automatically added at the beginning and at the end of the query text to behave in a similar way as table filters - using a contains search condition; this mode will be used by default for newly created users,
    • wildcard mode - default mode used so far in which no wildcards are added automatically to the query text; this mode will still be used as the default one for old users.
  • User can restore default settings (the ones used by SYSTEM) reverting all changes like showing/hiding columns in a particular browser table. SYSTEM user settings are also used for newly created users as the default settings.
  • Deleting materials is now possible.
  • PhosphoNetX:
    • New remote service (IRawDataService) which allows to query MS_INJECTION samples and to copy data sets of selected MS_INJECTION samples to a preconfigured location.
    • New query: All MS INJECTION Samples
    • Protein detail view also show protein probability
  • openBIS for High Content Screening
    • the performance of browsing the content of plates and displaying images for a selected gene has been significantly improved
    • it is possible now to browse images with all channels merged
    • when browsing images for a selected gene one can change the channels in which all images are displayed with one click
  • YeastX
    • new reports for eicML files are available in openBIS (chromatograms, runs)
Data Store Server
  • New processing plugin for copying (via rsync) data sets to a preconfigured location.
  • New reporting plugin visualizing tsv files as openbis table.
  • Sending an e-mail to the user who initiated Data Set processing upon processing task completion.
Cifex
  • Significant changes to user interface.

Version S71 (21. December 2009)

OpenBIS
  • a pilot version of openBIS customized for High Content Screening has been released. It allows to browse the content of plates, see images for a chosen well and display images for a selected gene acquired in a chosen experiment.
  • Project Detail View has been added. It shows project description and its attachment. The new view is accessible directly from the Experiment Browser, after selecting the project a link is displayed next to project code.
Data Store Server
  • PhosphoNetX: Plugin for registering MS_INJECTION data sets
  • BaSysBio: More validation of time series data sets (unique data column header, correctly chosen experiment, ID validation depending on column header name)
Cifex
  • File name and comment can be updated
  • Migrated to GWT 2.0 (GXT was not changed – still using 2.1)
  • Changed the user interface to use tabs

Version S70 (9. December 2009)

OpenBIS
  • Migrated to GXT 2.1
  • Batch update of vocabulary terms - reordering and modifying old terms as well as inserting new terms in a single operation is possible using uploaded TSV file that has the same format as vocabulary term registration file.
  • Batch update of samples - meta data of multiple samples can be updated at once using an uploaded TSV file that has the same format as batch sample registration (import).
  • Increased the size of Code fields from 40 to 60 chars.
  • Switched the graphics on login page to the new openBIS logo
  • Implemented infrastructure to support Wiki-based online help. We are waiting to resolve some user-interaction questions, but once that happens, online help should be made available to users.
Data Store Server
  • BaSysBio: Storage Processor and Data Column Validator for time series data sets.
  • PhosphoNetX: Deletion maintenance task for proteins for data sets deleted in openBIS.
  • PhosphoNetX: Uploader of protXML files ignores proteins with a false discovery rate larger than 10%.

Version S69 (25. November 2009)

OpenBIS
  • Migrated to GWT 1.7 and GXT 2.0
  • Hide superfluous widgets in the filter toolbar if there are no choices for the user to make
  • bugfix: Update open (sample, experiments, datasets, materials) tabs when new properties are added to the types
  • Tracking of openBIS events for the DSU project
  • bugfix: Keep column headers in sync with the tables when column order is changed
  • bugfix: A dot in the property code no longer causes problems for displaying the property in a table column
Data Store Server
  • Send an email to the uploader of the dataset if it fails validation
  • Data set validation framework supports registration of synonyms for missing values (e.g., - or n/a)

Version S68 (11. November 2009)

OpenBIS
  • bugfix: save display settings even if the user does not logout but just closes the browser
  • there is an option for each sample type to have the sample code created automatically. If this option is chosen, then the sample registration dialog will show the automatically created sample code greyed out. So the user don't have to press the "create sample code" button and she won't be able to insert a different sample code instead of the automatically generated one.
Data Store Server
  • Data Set Invalidation Framework for TAB-separated value (TSV) files
  • DSU: Flow lane validation and version extraction
  • More Flexibility to handle Data Sets Registration via CIFEX: CifexStorageProcessor can wrap any Storage Processor
Data Mover
  • Support calling a 'finish' script after a directory has been copied successfully

Version S67 (28. October 2009)

OpenBIS
  • Instance admin can decide to hide container and parent fields in sample registration and edition forms setting container and derived hierarchy depths to 0.
  • Instance admin can specify order in which assigned property types will be displayed in entity registration and edition forms. Additionally property type assignments can be grouped in sections.
  • Every table column containing a limited set of values can be filtered with auto-filters - the value could be chosen from a list, there is no need of typing it
Data Store Server
  • Reporting framework supports thumbnails of images included into a report.
  • The file with meta-data added to an export of data sets shows also properties of the data set, the experiment, and if present the sample.
  • DSU: Meta data file of flow lanes show property code instead of label.
  • YeastX: datasets containing mzXML data can be now uploaded to openBIS

Version S66 (14. October 2009)

OpenBIS
  • Ability to define custom columns in any table by the openbis power user. The column is defined by an expression which can reference other columns. Standard and custom filters can reference custom columns.
  • Ordering of vocabulary terms (the order in which they appear in combo boxes) is now configurable by the user/admin.
  • Importing TSV files allow row with less number of cells than header line. Missing cells are treated as empty strings.
  • Improved upload of data sets through CIFEX functionality and data set edition (either sample or experiment needs to be specified and when there is no connection with sample dataset parents may be specified)
  • Relaxed business rules concerning sample group in relation to parent/container group - now parent/container sample can be in a different group then the child/component sample.
  • User can search for entity using both code and label of vocabulary term that the entity relates to (before only code was searchable).
  • Tooltips with codes and descriptions are shown for lists of elements in combo boxes where user chooses entity (sample/experiment/...) type or a filter.
  • Client session does not expire as long as user has the browser with openbis opened. When the browser is closed it will expire like it used to do after few hours (currently 12h).
  • Improved custom filters (added reset all filter fields functionality, some bugs fixed).
Data Store Server
  • DSS project for Deep Sequencing Unit (DSU)
  • XML schema validation for YeastX and PhosphoNetX

Version S65 (30. September 2009)

OpenBIS
  • It is possible to edit and delete custom table filters.
  • It is possible to delete all samples/experiments/datasets displayed in a table with 'Delete All' button (even without selecting any table row). Messages and labels in dialogs that are used for these deletion operations were improved.
  • It is possible to click on an identifier of a sample parent/container in sample browsers and as a result quickly navigate to the specific sample details view.
  • Tables are automatically resized when an entity (sample/experiment/...) chooser window is resized.
  • Improved custom filters (numerical values, Math module, predefined functions (toInt, avg, min, max, choose etc), access to column model metadata, arrays)
  • Vocabulary term combo box shows the tooltip containing the code, label and description of the term
  • YeastX specific features: support for metabolomics quantification datasets has been added

Version S64 (16. September 2009)

OpenBIS
  • It is possible to create custom table filters
  • Dataset browsing and searching works much faster
  • Metabolomics quantification data model has been created for YeastX project
  • When user modifies display settings e.g. of a certain table in one tab and then switches to another tab that was already opened before and had the same table kind displayed the table is refreshed with updated settings.
  • Data set edition form is extended to meet new connection possibilities (many parents can be specified, connection with sample is optional).
  • Data set detail view has been improved to show parents and children in separate tables.
  • In sample detail view by default only directly connected data sets are shown but user can toggle to show both directly and indirectly (through dataset ancestors - using parent hierarchy) connected data sets.
Data Store Server
  • Data sets not connected with a sample with any number of parent data sets can be registered.
  • Data sets can no longer be connected with a sample and a parent data set at the same time. Already existing sample links are remove if a data set has at least one parent.

Version S63 (2. September 2009)

OpenBIS
  • display only dataset/sample properties relevant to the entity types present in the dataset/sample browsers (e.g. sample components, experiment datasets)
  • detailed search of samples (similar to detailed search of datasets)
  • allow to add sample/experiment/project/vocabulary/property type directly from their browsers using an 'Add' button (instead of using top menu)
  • allow to register a new person with an email address as Code (@ is an allowed character for person Code)
  • allow to specify experiment in sample registration
  • save user display information about visibility sections sample/attachment/dataset sections for sample/experiment viewers
  • improved functionality of showing data sets related to search results - user can select some result rows or use all displayed rows
  • improved performance of vocabulary terms browser (with statistics)
  • improved performance of simple (top menu) search of samples/experiments/materials
  • improved performance of starting openbis server with no search index generated (or index regenerated)

Version S62 (19. August 2009)

OpenBIS
  • allow to list users belonging to a user groups
  • allow add/delete users from the user groups
  • improved performance of sample browser
  • simplified search (faster saving/editing/indexing)
  • different column setting for samples/data sets belonging to different experiment/sample types (sample viewer and experiment viewer)
  • user properties do not require USER. prefix, internal properties use $ prefix
  • allow to delete all data sets/experiments found with a query (belonging to any of the pages of the grid)
  • allow to delete many entities (samples, experiments, data sets, file format types etc.) "in one go"
  • allow attachments automatically when the sample/experiment/project is deleted
  • improved experiment/sample viewer (sections use wisely the available space and may be switched off)
  • business rule added: data set parent should belong to the same experiment as the child
  • allow add attachments from Internet Explorer
  • improved rendering of columns

Version S61 (5. August 2009)

OpenBIS
  • deletion of projects and groups
  • allow to assign contained samples (/group/container-sample-code:contained-sample-code) to experiments
  • allow to create/delete and browse user groups (authorization groups)
  • dot character allowed in codes
  • longer descriptions (e.g. of sample types) (1000 characters)
  • batch registration (import) of samples of different types (file with sections)
  • allow to specify experiment during sample import (batch registration)
  • labels and descriptions added to vocabulary terms
  • attachments are not indexed anymore
  • allow openBIS to work with H2 database
  • client side validation added to entity type and group registration
  • extended editing of data sets: file format, parent
  • editing of group description

Version S60 (22. Jul 2009)

OpenBIS
  • improved reporting plugin (openbis table with export, many data stores)
  • improved sample edition (editing group, container, parent)
  • sample chooser used for choosing container and parent in sample registration and edition
  • deletion of property types, vocabularies, groups, projects,
  • exporting to Cifex of all data sets from the table allowed
  • edition of sample types: listable, parent and container depth
  • smart table (export, filters) used to show persons, roles, groups and sample components
DSS
  • added a periodic task that re-creates the old hierarchy of data sets (soft links)

Version S59 (08. Jul 2009)

OpenBIS
  • improved performance of systems with large vocabularies
  • improved experiment viewer (space usage, scrolling bars)
  • allow to edit imported entities (samples, experiments,..) with date property in nonstandard format
  • allow to run report generation and processing of data sets (DSS plugins)
  • allow multiline descriptions
  • allow to change mandatory property type assignments to optional and vice versa
  • edit property type (description and label)
  • show the warning message on closing the window only when logged in
DSS
  • added new IStorageProcessor implementation that deletes the files with name not matching specified regular expression (extension of data set upload by CIFEX feature)

Version S58 (24. Jun 2009)

OpenBIS
  • description (sample type, vocabulary etc.) length increased to 250
  • added description and title to attachments
  • vocabulary terms with URL displayed as links
  • allow to upload data sets to OpenBIS via CIFEX
  • allow to show samples and experiments of all types
  • allow to delete and edit file format types
  • allow to delete and edit attachments
  • allow to edit vocabularies
  • Excel date format supported during import
  • unified links (only text works as link, and not the whole cell)
  • add more information to data set details view
  • show the warning when the 'Back' button is pressed in the web browser
  • store user settings for attachment tables
  • allow continue edition after changing business key of the entity
  • allow to easily select all/no columns and filters
  • improved search performance
  • added group role 'POWER_USER'
  • programmatic access to OpenBIS (via HttpInvoker)
  • introduced modules (entity type independent plugins)

Version S57 (10. Jun 2009)

OpenBIS
  • allow deletion of samples and experiments
  • allow complete deletion of datasets
  • template files for sample batch registration available for download
  • registration forms store values for next registration
  • URL template for vocabulary terms
  • TSV parser does not allow empty mandatory columns
  • extended migration of screening data (033-034)
  • improved performance of loading vocabularies
  • small improvements of dataset browser

Version S56 (27. May 2009)

OpenBIS
  • bookmarks to samples and experiments can be created (aka "permlinks")
  • all tables displayed in openbis can be quickly filtered by any column - the 'Columns' button at the bottom of the table allows user to show "quick filters" for the chosen columns.
  • dataset upload specific for YeastX RTD project has been imlemented
  • basic ontology support has been added to openbis
  • the position of all menu buttons has been reviewed and made more coherent

Version S54 (29. April 2009)

OpenBIS
  • Creating new data set types.
  • Unassigning property types.
  • Assigning new samples / unassign existing samples during experiment editing.
  • Register and assign samples specified in the file when registering/editing an experiment.
  • Experiment browser allows to choose the project in a more convenient way from the tree.
  • Components section in sample detail view is shown only when there are any components.
  • In experiment detail-view sample and dataset properties can be displayed.
  • In sample detail view dataset properties can be displayed.
  • Allow entities movement. Now it is possible to:
    • change the sample to which the dataset belongs.
    • change the experiment to which a sample is assigned, even if some datasets have been produced for this sample.
    • change the project to which experiment belongs, even if some datasets have been produced in this experiment.
    • change the group to which the project belongs.
  • Grids display settings are stored for each user in the database, so changing column width or column visibility will be remembered even if the user logs out.
  • Allow deletion of material/sample/experiment/dataset types created by mistake.
  • Edit description of material/sample/experiment/dataset types.
  • Minor GUI improvements and bugfixes.

Version S53 (15. April 2009)

OpenBIS
  • show property types assigned to data set types in property type browser and property type assignment browser
  • allow to specify comment and file name while uploading data sets to Cifex
  • HYPERLINK and MULTILINE_TEXT property types
  • project and sample attachments
  • possibility to generate sample and experiment codes automatically
  • improved directory structure of data set files uploaded to Cifex
DSS
  • improved method of gathering information about data set properties in DSS
  • simplified directory structure in data set store (no group/project/experiment/sample part)
  • marker files are optional

Version S52 (1. April 2009)

  • improved data set search (freshly assigned properties indexed)
  • authorization for data set tables
  • upload data sets to Cifex
  • automatic refresh of the tabs
  • assigning property types to material types
  • data set properties
  • add/delete vocabulary terms
  • links to samples, materials and experiments in GUI

Version S51 (18. March 2009)

  • property types of data type 'material' are suported
  • datasets shown in experiment detail view can be exported to a file
  • datasets can be deleted
  • it's possible to edit properties of a material, sample or experiment
  • it's possible to add new experiment attachments
  • it's possible to change the project to which an experiment belongs
  • it's possible to assign a chosen sample to an experiment or change the assigned experiment in the same group
  • for each vocabulary you can browse or export its terms and terms usage statistics
  • the left-hand side menu has been replaced

DataSetCopier

BIS-460