molgenis

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Bugfixes

• #8132 Copy/Delete/Download jobs not row-level secured
• #8037 Application can boot with NoSuchBeanDefinitionException
• Let metrics classes register themselves at the registry

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Features

• M6492 Permissions API v1
• M6548 As group manager I can assign role to ‘anonymous’ or ‘logged in’ user.
• Removed Index Manager

Bugfixes

• #8481 Header is not sticky in new pages
• #8300 Browser console errors on bootstrap 4 pages when you're not logged in

Upgrade from 7.x

• MOLGENIS requires JDK11.x
• MOLGENIS requires Apache Tomcat 9.x
• MOLGENIS requires PostgreSQL 11.x
• MOLGENIS requires Minio 6.0.x

Migrate from 7.x

See: Migration guide

Release

• Documentation can be found here
• Warfile is available on maven central.
• Updated docker id available in classic dockerfile and experimental flavors.
• For VM installations see: Install MOLGENIS

Features

• M6062 Display App version in app manager and app
• M6619 Non-superuser cannot modify superuser
• M6173 Cancel a running job
• M5393 Attribute type categorical/xref -> categorical_mref/mref update
• M6441 Files API for file upload and download
• M3774 EMX support for auto date/datetime
• M6105 Mapper: Copy algorithms from source when adding new source
• M6537 New scripts-UI implemented
  • Automatically generate script-parameters in form
  • More user friendly UI
• Added new Settings-plugin
  • All the permissions given to the old settingsplugin are removed.
• Default editor in Data Explorer now uses new interface for editing and creating new rows (fixes character eating bug)

Breaking changes

• The Python REST client has moved to its own GitHub repository and is now an official Python package. This means that the client is no longer served by MOLGENIS and that it should be installed using the Python package installer: pip install molgenis-py-client
• Drop support for expressions that have 'string' (or similar) as source attribute type and categorical/xref as target attribute type. Existing expressions must be converted to template expressions, e.g. {"template":"{{biobank.name}}"} instead of biobank.
• The bootstrap version of the static content pages (home, news, background, contact and references) is upgraded to bootstrap 4. This means if you used bootstrap 3 in your pages, you have to migrate the classes to classes that are bootstrap 4 compatible. For more information about migrating bootstrap 3 to bootstrap 4, please read the bootstrap 4 migration page.
• Switch from ajp protocol to http protocol in tomcat to allow maxSwallowSize.

Bugfixes

• #8453 Top logo pushes plugin content down
• #8356 Data row editor shows True/False instead of Yes/No for boolean values
• #8443 context-ui is not a plugin
• #8430 Logo above menu bar does not work on small screen
• Update babel polyfill to latest 6.x version
• #8402 ScriptJob fails when scheduled, succeeds when started manually
• #8378 Importer ignores tags in the database, causing unjustified UnknownTagExceptions
• #8236 Validation expression for date not correct in new forms
• #7669 Several field validations not correct in new Forms
• #7599 In data-row-edit plugin I can not add a new row or edit a row in TypeTest 7.1 bug
• #7670 Forms behaviour on some nullable fields not as expected
• #8269 Attributes of compounds disappear, when using metadata manager
• #7680 Vue forms don't recognise changes in categoricals when editing a row
• #8158 Large metadata manager checkboxes in ie11
• #8293 Mail cannot be sent from MOLGENIS cluster instances
• #8291 Menu manager dataexplorer plugin broken
• #8177 Navigator download writes abstract attributes of existing types
• #7875 Import failing with weird error message when having attribute specified as empty string
• #8046 The importer should be able to import files with only packages
• #8053 When multiple algorithms refer to unknown attributes the algorithms can't be fixed via the mapping service algorithm editor
• #8051 Add source to mapping project with existing sources could result in 500 error
• #8058 CSV header value mismatch (values > headers)
• #7886 JobExecution entity delete allowed for running job
• #8101 Search all link to navigator is broken for top level entity
• #7917 Metadata manager lookup attribute doesn't work
• #8132 Copy/Delete/Download jobs not row-level secured
• #8018 System packages can be moved outside of system package
• #8160 Tag wizard entity type dropdown contains untaggable types
• #5258 An error in an entity report causes the previous one to be shown
• #8170 Sign up failure displays wrong error
• #7634 App setting 'CSS href' ignored in case of Vue plugins
• #3886 User signup doesn't remember country
• Add polyfill to vue menu
• #8052 Validation of a mapping algorithm that refers to an unknown attribute succeeds
• #7935 Default value reference entity type incorrect: improved message
• #7636 (partial fix) Use cookie wall from ui-context in vue pages
• #2898 Script without results extension 400 error
• #6025 LookupAttributeIndex differs depending on the way they are created
• #8273 Broken links behind proxy
• #8194 Broken links in documentation
• #7835 Login redirect incorrect when 403 on logo
• #3154 Error 500 when exceeding the maximum file upload size
• #8283 Improved importer error message when entity id=null
• #8286 Log PostgreSqlExceptionTranslator exceptions of unexpected class
• #8251 Token authentication changes session authentication
• #8292 Account unreachable when 'Forgot password' mail not sent
• #8361 User manager: user activation broken
• #8367 Adding same user to same group in multiple roles is allowed
• #8359 Mapping service algorithm edit search broken
• #8379 Scheduled job timestamp incorrect
• #8404 Settings can return incorrect cached data
• #6402 Google analytics broken
• #8440 Import API tries to make entityType when I try to upload a csv
• #8344 No options for XREF/MREF until you start typing
• #8356 Data row editor shows True/False instead of Yes/No for boolean values
• #8360 New forms do not enforce max long value
• #8352 Data row editor does not enforce maximum string lengths
• #8448 Columns not deleted from database when removing a compound attribute
• #8450 Columns not deleted from database when removing a compound with the Metadata Manager
• #8384 R script executor: Heatmap script can't be executed
• #8324 Can not use swagger ui to test entity endpoint
• #8375 FDP response contains invalid URLs
• #8464 Cannot add new token without first clearing expiration date
• #8469 Double invalid value message when filling out data row
• #8470 Nullable expresion test in data row edit results in error
• #8475 Frontend dependencies are listed using imprecise version
• #8486 Hamburger is always displayed on IE11

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Feature

• Update babel polyfill to latest 6.x version

Bugfix

• Add babel polyfill to vue menu

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Features

• M6167/6168/6169/6256: Navigator: Create, Edit, Move, Copy, Upload and Download resources.
• M6314: Add FeatureInfoPlugin to GenomeBrowser config and make "genomebrowser/tracks" endpoint available

Bugfixes

• #8041 PostgreSql translated exceptions can be too vague
• #8028 Computed values should not be validated
• #6559 Navigator refreshes list of Tables slowly, resulting in laggy behaviour
• #7551 As navigator user I want to quickly create/edit tables and folders
• #7659 Navigator exception message not localized
• #7607 Scripts plugin can't execute JavaScript Magma scripts
• #7908 StackOverflowError when moving a package to its child

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Features

• M6144: Expression templates
• Add metrics for Prometheus monitoring to MOLGENIS
• M6129: Add functions to submit mapping and script jobs and return the execution href
• M5914: Implement a new Captcha (recaptcha) so that it won't be broken by spambots like the current captcha

Bugfixes

• #8023: Vendor bundle is much larger than it needs to be
• #7447: If i click "enable 2fa" but do not finish the form I'm stuck on "/2fa/activation"
• #7862: Ontology-deletion non-practical
• Notify user when fields are invalid on trying to save row (in forms)
• #7922: Python executor errors on windows
• #7956 Job exceptions not logged
• #7948 Job failure progress messages not coded
• #7167 Index job execution user incorrectly set to "admin"
• #7960 SecurityUtils.getCurrentUsername refers to unknown User
• #7985 EntityType.newInstance doesn't copy indexing depth
• #7621 Plugin delete doesn't remove menu entries

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Changes

• Bump molgenis-ui-form in questionnaire from 0.11.4 to 2.1.0
• Fix styling of questionnaire
• Make request body optional when updating entity.attribute via rest api

Bugfixes

• #7914: When I start my questionnaire and go back to start and then start again, my questionnaire does not start
• #7915: When I fill in an out of range number in questionnaire, I can proceed and submit (!)
• #7929 Questionnaire tries range value if missing max or min prop as invalid
• Refactor questionnaire autosave
• Disable chapter navigation while validation is pending

Release

Updated documentation is available here.
Warfile is available on maven central.
Updated docker id available in classic dockerfile and experimental flavors.

Features

• #7899 Max-depth configurable in mapping project

Release

Updated documentation is available here.
Updated docker id available here.

Bugfixes

#7866 Error page when attempting to run bio-bank-explorer app

• Fix Apps server routing

Release

Updated documentation is available here.
Updated docker id available here.

Features

• M6050 Navigator: delete selected items
• M6042 Assign existing questionnaires to the users
• M6114 OpenID connect authentication, runtime configurable
• M6051 Group deletion
• M6119 Give managers access to the user manager
• Added citation to footer

Bugfixes

• #7793 update example EMX example date
• #7728 Navigator tree disappears after highlighting search in internet explorer
• #7751 Mapping service broken if dataexplorer unavailable
• #7752 Computed MREF attribute display error in entity report
• #7755 Group manager can't handle usernames-with-dot
• #3172 Infinite import when ImportRun message is too long
• #7734 Data explorer anonymous issue
• #7766 Metadata manager nullable expression update unsupported
• #7663 Sign up impossible because captcha isn't showing
• #6553 Inactive user can reset and change password
• #7412 Data explorer entered-data lost on click outside of modal
• #7687 EMX documentation: file datatype broken link
• #7771 Metadata manager doesn't allow default value update
• #7739 Import fails on EMX update with one-to-many attributes
• #7713 One-to-many attribute readonly update fails
• #6869 Metadata manager attribute tree render issue
• #7630 Metadata manager cascade delete support
• #7676 Metadata manager undo-all-changes option
• #6928 Attribute.idAttribute update shouldn't be allowed
• #7789 EntityUtils.equals doesn't compare i18n labels/descriptions
• #7792 Metadata manager cannot add/update localized fields
• #7820 Updating readonly attribute type fails
• #5252 Logging out removes query parameters in URL
• #7814 Metadata manager reference to no-reference type update
• #6516 Mail settings username/password are required
• #7821 show non visible attributes in data row edit
• #7831 Mapping service plugin broken when project is broken
• Data-Row-Edit plugin error handing