Latest release

MOLGENIS v6.1.0

@sidohaakma sidohaakma released this May 28, 2018 · 2 commits to 6.1 since this release

Features

  • Mapping service now supports algorithms which want to use values from a referenced entity besides ID values
  • Increased performance by implementing different strategy for evaluating javascript validation expressions

WAR

Download the war from Maven central

MOLGENIS v6.0.0

@dennishendriksen dennishendriksen released this Feb 5, 2018 · 2 commits to 6.0 since this release

Features

Pull Request Content
#6916 #6955 M4944 FDP metadata includes entity type tags
#6790 M5108 Respect size of logo navigation bar
#6816 #6885 M5396 Attribute nullable expressions
#6974 M5470 Beacon interface
#7058 M5514 Localized coded exceptions with improved messages
#6907 M4766 Google analytics improvements for data explorer
#6832 #6833 #6808 M5406 Data explorer packages link to navigator
#6857 M5360 Mapping service allows repairing broken projects due to metadata changes
#6786 M5353 UI metadata label internationalization
#6972 M5206 Remove Google Spreadheet support
#6972 M5206 Remove Galaxy download support
#6882 M5205 Remove Catalogue plugin
#6882 M5205 Remove Pathways plugin
#6882 M5205 Remove Charts from data explorer plugin
#6862 M0000 Swagger: new UI, more endpoints, grouped endpoints in modules
#7086 Added Submit date to questionnaire data on submit
#7083 M5477 upgrade to bootstrap v4.0.0

Bugfixes

Pull Request Content
#7120 Fix #6951 "long" language names causes overlap of dropdown and "help link"
#7102 Fix #6686 Menu font changes between items
#7089 Fix CVE-2014-3558 Hibernate Validator: JSM bypass via ReflectionHelper
#7057 Fix #6836 Inconsistent results getting entities with offset and page size without sort
#7055 Fix #7047 Mapping to entity type with auto id fails
#7023 Fix #7022 Anonymous user can't edit static content
#6999 Fix #6809 Out of memory on complex entity delete by making compound children cascade on delete
#6984 #6968 Fix #6967 MOLGENIS does not run on mac os version 'high sierra'
#6958 Fix #6957 Footer text is displayed on top of navigator buttons
#6949 Fix #6876 The Vue menu shows a sign out button when using a plugin anonymously
#6932 Fix #6922 Scheduled job infinitely pending running with unknown user
#6929 Fix #6923 When altering static content, spans without text are destroyed
#6875 Fix #6874 Authorities updater can't update anonymous token
#6871 Fix #6588 Delete attribute using metadata manager fails
#6860 Fix #6853 EMX with attributes sheet doesn't import data
#6856 Fix #6689 RSQL complex ref filter is incorrectly applied and shown in Data Explorer
#6852 Fix #6650 When executing an R script, only the last output is shown
#6844 Fix #6800 Not able to enter multiple email addresses for scheduled jobs
#6838 Fix #6803 When making a mistake editing the menu json it breaks the entire webapp
#6830 Fix #6807 Error: null when uploading EMX file with an error in it
#6823 Fix #6822 Entity type copy doesn't contain source validation expression
#6820 Fix #6819 Project doesn't compile with Java 9
#6804 #6814 Fix #5602 Can't add required attribute with default value
#6797 Fix #6609 Advanced importer does not show entity fields
#6793 Fix #6732 Genomebrowser broken when using IE10
#6765 Fix #6112 #6635 #6982 Client expression validation of date/time values
#6762 Fix #6727 Import error message unclear for duplicate mref values
#6761 Fix #6528 Upload corrupt .vcf files gives unclear message
#6759 Fix #6566 Hidden attributes in entity type copy not hidden
#6996 #6720 Fix #4737 #4929 #5284 #5539 #5541 #5788 SORTA plugin
#7054 #7007 #6990 #6989 #6947 #6946 #6930 #6835 #6764 Fix #6920 #6935 #6975 #6129 #6100 #6834 documentation
#6980 Fix login with password hash is allowed
#6817 Remove unused insecure session expired method
#6801 Update api client version to include X-request-with header
#6563 Various documentation fixes

WAR

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MOLGENIS v5.2.2

@sidohaakma sidohaakma released this Dec 5, 2017 · 2 commits to 5.2 since this release

Updated Negotiator Dialog

MOLGENIS v5.2.1

@mark-de-haan mark-de-haan released this Nov 20, 2017 · 7 commits to 5.2 since this release

Patch update for negotiator functionality

Features

Pull Request Content
#6937 & #6933 Backport Negotiator directory features to 5.2

MOLGENIS v5.2.0

@mark-de-haan mark-de-haan released this Oct 4, 2017 · 19 commits to 5.2 since this release

Features

Pull Request Content
#6613 Use max-height instead of height to stop blowing up smaller images
#6646 Sort entities by label in data-explorer entity select
#6605 Hide the system packages and entities for non super users in the navigator plugin
#6636 Added questionnaire documentation + example
#6622 Create a link from the dataexplorer to the navigator
#6644 M5269 Filter 'system' entities in entity editor
#6637 M5269 Filter 'system' entities in dataexplorer for non super user
#6630 M5312 Description per plugin
#6588 M5263 As developer I want a testplan and unit tests for the one-click-importer
#6580 M5169 As IBD i want to 'search all' entities

Bugfixes

Pull Request Content
#6760 Fix #6752 One-click importer cannot import decimal data
#6758 Fix Data Explorer <-> BBMRI Negotiator interaction bugs
" Fix #6743 Searching for special characters in the dataexplorer gives results, while the rest api/negotiator does not
" Fix #6618: Search queries with spaces do not get sent to negotiator
" Fix #6737: When I combine search term with filter, list of matching biobanks only matches filter in negotiator
" Fix #6733: Human readable string in negotiator post encodes special characters
#6756 Fix #6745 Data explorer filter roundtrip doesn't work with =in= operator
#6754 Fix #6687: When downloading the content as xlsx of a large table (66.…
#6748 Fix #6747 When typing " in navigator I get error: {}
#6746 Fix #6461 Javascript package versions used in the build should be rep…
#6740 Fix #6713 One-click-importer permission issue
#6738 Fix #6731 System entity type count permission
#6730 Fix #6675 #6716 #6717 #6688 IE9/IE10/IE11 issues
#6722 Fix #6690 Genome browser settings metadata entities have 'Metadata' in their names
#6719 Fix #6706 When an entity is not in a package, it is not shown in the root of the navigator
#6718 Fix #6705 After searching for something in the navigator, the system packages (which are not in the root) are shown
#6715 Fix #6704 Data explorer breaks using browser back/forward
#6707 Fix #6673 Altering ref entity results in broken table
#6700 Fix #6677 When adding a header logo above the menu bar parts of plugins are not clickable
#6698 Fix #6691 File filter does not display add-on OR button on multiselect
#6697 Fix #6693 Tag wizard entity type select broken
#6680 Fix #6670 Genome Browser entities are in the wrong package
#6584 Fix SearchAll link to filtered dataexplorer
#6658 Fix #6611 Footer overlaps mapping service buttons if GA is enabled
#6654 Fix #6465 Clean up flow config.
#6652 Fix #6639 As molgenis server owner I want elasticsearch to automatically reconnect if server is rebooted
#6651 Fix #6575 REST calls with an id that ends with a file extension get swallowed by Spring
#6621 Fix #6505 Users can still sign in with /login when their passwords needs to be reset
#6620 Fix #6571 If 2fa is not enabled I get an empty security tab
#6616 Fix #6615 Appstore does not support apps with vue-router
#6607 Fix #6603 UserAccountController eats up errors when you try to change the language code
#6606 Fix #6601 Async JS tests in metadata editor, and searchall do not use the molgenis-vue-test-utils library
#6604 Fix #6581 Aggregates broken in some ref attribute cases
#6602 Fix #6595 Import wizard occasionally hangs on fast-failing import jobs
#6600 Fix #6583 Index queries fail when index doesn't exist (yet)
#6597 Fix #6596 Throwable.printStackTrace(...) should not be called
#6593 Fix #6592 WebAppInitializer contains MyDAS references
#6591 Fix #6582 Startup NPE on app termination with running jobs
#6590 Fix #6589 Navigator async JS tests are very different from other async tests
#6579 Fix #6578 In the scheduled jobs docs there are no examples for the amazonbucket file ingest and mapping service
#6577 Fix #6576 Default opencpu port number is 80, which conflicts with http protocol
#6778 Fix #6755 Metadata editor is very slow causing saving to be clicked twice giving error message the second time twice giving error message the second time
#6777 Fix #6769 Genome browser tracks of different type show data of one type
#6776 Fix #6773 Filter wizard doesn't remove filters from URL
#6774 Fix #6766 Can't import file other than .xlsx in one-click importer in Safari
#6718 Fix #6705 After searching for something in the navigator, the system packages (which are not in the root) are shown
#6667 Fix #6661: ClientFactory issues

WAR

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MOLGENIS v5.1.0

@tommydeboer tommydeboer released this Aug 28, 2017 · 2 commits to 5.1 since this release

Breaking changes

Pull Request Content Impact
#6431 M4866 R script execution through OpenCPU From this version onward, you will need to install and configure OpenCPU instead of an R executable to be able to run R scripts locally or on your server

Features

Pull Request Content
#6479 M4489: Add Vue menu and footer to vue based plugins
#6504 M5171 Two-factor authentication
#6507 M5121: Expanded theme manager to enable uploading of bootstrap 3 and 4 themes
#6463 M5146 As new apps user I expect bootstrap themes to be applied
#6408 M4302: remove MyDAS and update Dalliance
#6452 M5198 One click importer
#6509 Persisted plugin metadata instead of plugin registry
#6475 Tomcat guide: add Python dependency & version updates
#6455 remove sass, use css instead

Dependency updates

Pull Request Content
#6420 Update Google AutoValue 1.3 to 1.4.1
#6462 Upgrade Spring Security 4.2.0 to 4.2.3 / Spring 4.3.7 to 4.3.10
#6474 Upgrade Elasticsearch 5.4.1 to 5.5.1

Bugfixes

Pull Request Content
#6481 Fix #6480: IndexActionRegisterService forgets the type of the IDs and…
#6476 Fix #6421: @transactional @RunAsSystem wrong Authentication in commitTransaction
#6467 Fix #6363 NPE starting app with Spring TRACE logging
#6520 #6492 EMX importer fails on BOM preventing CSV's to be uploaded in some cases
#6459 Update yarn lockfile to the version created when building with maven.
#6446 Fix IntelliJ Javadoc issues
#6412 rename 'manual' to 'help'

WAR

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MOLGENIS v5.0.1

@fdlk fdlk released this Jul 17, 2017 · 4 commits to 5.0 since this release

Bugfixes

Pull Request Content
#6394 Add deleteList to R API
#6393 Backport fixes #6286, #6374, #6325, #6365, #6327 to 5.0 branch
" #6286 Job's view page refreshing interferes with ability to use the system
" #6374 Able to delete rows referenced in MREF
" #6325 "Unknown table name" when deleting EntityType with references to it
" #6365 Can't delete package for complex EMX
" #6327 Performance severely reduced after importing a model with many entities and attributes

WAR

You can download the web archive here

MOLGENIS v5.0.0

@mark-de-haan mark-de-haan released this Jul 11, 2017 · 13 commits to 5.0 since this release

Breaking changes

Pull Request Content Impact
#6215 M4667 Upgrade embedded Elasticsearch 1.7.3 to standalone 5.4.1 From this version onward, you will need to install and configure a standalone Elasticsearch server to run MOLGENIS.

Features

Pull Request Content
#6238 M4570 Navigator for browsing Packages and EntityTypes
#6288 M4028 Metadata manager for editing and creating metadata
#6271 M3983 Appstore now supports index.html inside a .zip bundle
#6250 M5085 Configurable indexing depth
#6292 Expanded Python API with deleteList() and uploadZip() functions

Bugfixes

Pull Request Content
#6308 Fix #6223 Failing query when searching for many values in an mref
#6228 Fix #6109, #6226 Delete package issues
#6227 Fix #4744 Tooltips stay on screen even after switching tab. blocking parts of the screen
#6225 Fix #6051 Error when trying to tag an entity in the TagWizard
#6247 Fix #6242 MyDas config cannot be found, resulting in stacktrace at startup
#6291 Fix #6290 Travis build verify fails with endPos Table error with module containing a lot of AutoValue classes
#6262 Fix #6261 Using bookmark-able filters with attributes containing 'weird' characters results in errors
#6295 Fix #6248 Always set required JDBC properties
#6293 Fix #3983 Appstore edit form for file type
#6283 fix #6278: Bucket Ingest cannot cope with CSV of TXT files
#6280 Fix #5532 Error editing entity with attribute of type FILE
#6277 Fix #6253 Deleting entity type without read-only attributes fails
-- Fix #4623 Creating a copy of an entity can result in foreign key names that are too long
-- Fix #6330 Download filename has wrong hour format
-- Fix #4354 User with edit permission on home plugin can't edit
-- Fix #6335 Filter operator change doesn't update url
-- Fix #4380 Manual adding and removing tag in tagging service is not working
-- Fix #4375 Automatic generated algorithms for body mass index are not applied
-- Fix #3865 Using " in the Filters or "Search data values" in the data-explorer throws an error

Documentation

Pull Request Content
#6307 Python REST API Client documentation
#6313 Add link to documentation in menu
#6298 Replaced Cargo documentation with Docker documentation
#6284 Documentation for running the platform integration tests.

WAR

You can download the web archive here

MOLGENIS v4.1.0

@fdlk fdlk released this May 29, 2017 · 2 commits to 4.1 since this release

WAR

You can download the web archive here

Features

Pull Request Content
#6153 M5011 As Directory-Negotiator workflow user I want the google search to be included in the request
#6149 M4504 Job scheduling framework
#6142 Add optional packageId argument to importApi
#6123 M4915: As a user I want to be able to programmatically trigger the mapping service from a script
#6116 added update one to python api
#6032 M4691 As developer I want to get the date and datetime data types right so that I prevent DST bugs and allow users to specify exactly what they mean
#6029 M4765 As MOLGENIS user I want to have a persistent URL for each instance of an entity

Bugfixes

Pull Request Content
#6146 Fix #6145 Map tab broken when mapping an XREF with INT ids
#6138 Fix #5983: Mapping to existing entity is broken when existing entity has more than 20.000 rows
#6128 Fix #5985: Job logs can exceed max log size, disastrous consequences
#6127 Fix #6124 Permissions lost when doing something transactional in the …
#6106 Fix #6105: Advanced mapping editor shows entity ID values instead of …
#6094 Fix #5927 Create new user, language code no select is shown
#6070 Fix #6063 MailSettings aren't set at clean install of the app

MOLGENIS v3.0.2

@fdlk fdlk released this Apr 25, 2017 · 2 commits to 3.0 since this release

Bugfixes

Pull Request Content
#6118 Fix #5985: Job logs can exceed max log size, disastrous consequences

molgenis-app-3.0.2.war