molgenis
MOLGENIS - for scientific data: management, exploration, integration and analysis.
LGPL-3.0 License
Stars
111
Committers
55
Ecosystems:
Java,
JavaScript
molgenis
- 7.0.0-RELEASE
Published by fdlk about 6 years ago
Documentation
Updated documentation is available here.
Features
- Dynamic decorators.
- EntityType permissions can now be set in bulk by handing out permissions to the package they are in.
- EntityTypes can now be row level secured in the permission manager. This replaces the Owned entity.
- Using the includeCategories flag in a REST query will now add categorical options to the api/v2 attribute metadata response for CATEGORICAL and CATEGORICAL_MREF attributes.
- Mapping service now supports algorithms which want to use values from a referenced entity besides ID values
- Made changes to make searching and filtering in MOLGENIS case-IN-sensitive. Changes are reflected in the following modules:
- XREF / MREF filters in the data explorer
- Searching and filtering is now performed via a SEARCH query instead of a LIKE query.
- Search in settings screen
- XREF / MREF filters in the data explorer
- M5663 As data owner I want to check package permissions when creating packages or entitytypes
- Users cannot be deleted anymore, only disabled.
- Disabled users cannot authenticate nor be used to create an authentication token
- Upgraded the App store, now called the App manager.
- New UI written in Vue
- New backend
- New app zip specifications
- Apps are now described by a config.json file
- Added app search functionality
- Increased performance by implementing different strategy for evaluating javascript validation expressions
- M5796 As dev/ops I want to be able to configure MOLGENIS using only environment variables
- store version in database instead of mutating molgenis-server.properties
- set default application data root to 'user.home/.molgenis'
- generate random one-time use password for admin
- Added group API which makes it possible to add a Group with default Roles, Permissions and Package in one simple step.
- M5811 - Add Security Manager to MOLGENIS. You can manage groups and role memberships in groups. When you create a group, a folder is created implicitly. Members can be MANAGER, EDITOR or VIEWER in this folder-context.
- Data explorer delete button for those who have the proper permission
- M5980 Questionnaire PDF download: optionally include logo, introduction text and pagenumbers
- Importer now has an option to ignore metadata changes when importing EMX
Fixes
- Fix #7542 #7665 #7666 Python tests and documentation fixes
- Fix #7611 EMX import with tags fails when ignoring metadata
- Fix #7615 Deleting all row-level secured data does not delete all data
- Fix #7631 #6930 Deleting 'cascade delete' entity type does not perform cascade delete
- Fix #7588 Editor/viewer cannot view reports in the view tab
- Fix #7543 Vue style plugins are broken when using a 'top'
- Fix #7374 Vulnerability in math.js used in MagmaScript
- Fix #7184 When I upload dataset with wrong mref value I get wrong error message
- Fix #6969 label must be specified when id is hidden
- Fix #7247 lookup attributes must be visible
- Fix #7183 CSV read exception on #values mismatch with #headers
- Fix #6906 Importing an entitytype with several columns with the same name, import without errors
- Fix #6792 When adding a new setting, using it after restart will add a comma to all inputs
- Fix #6729 When adding a compound attribute to a system entity the attribute is added twice
- Fix #7254 Cannot update attributes for an abstract entity that is extended by concrete entity
- Fix "Dataexplorer should be usable without permission on genomebrowser config entities"
- Fix #7280 Importing multiple attributes with the same name doesn't throw an error
- Fix #7297 One-to-many with integer ids retrieval
- Fix #7178 Navigator results might not be up-to-date
- Fix #7302 Search all plugin missing results
- Fix #6945 NPE importing EMX with abtract entity type data
- Fix #7131 Unclear error importing an EMX file twice in ADD mode
- Fix #7336 REST API v2 unknown error instead of not found message
- Fix #7169 When having jobs running as superuser and my account is set to inactive, my jobs still run
- Fix #2691 Infinite EMX import for EMX with deep nested formulas
- Fix #7341 Excel repository assumes case insensitive headers
- Fix #292 Change default FreeMarker number formatting
- Fix #7365 Range type mismatch unclear error
- Fix #7199 Mapping service: do not map to target expressed attribute
- Fix #7335 Metadata manager: error creating file attribute
- EMX metadata parser: validate that compound parent is not itself
- Fix #7379 Import wizard package assignment broken
- Fix #7438: 2FA pincode entry does not acquire focus
- Fix #6418 As data manager user I require that 'label' attribute cannot be nillable
- Fix #7248 Label attribute can be hidden
- Fix #7360 Entities without labels cannot be saved in the metadata manager
- Fix #7455 Can't delete entity with id containing special chars
- Fix #7474 Metadata manager one-to-many attribute creation not possible
- Fix #7440 Invalid range in input in questionnaire results in loss of progress
- Fix #7415 My generated algorithm in mapping service starts with tabs
- Fix #7416 Large text indexing results in exception
- Fix #7496 Mapping service attribute search results incorrect count/results
- Fix #7498 Mappings between molgenis 6 and 7 not compatible
- Fix #7545: SearchAll does not show thrown exceptions
- Fix #7558: Test Questionnaire EMX file is not properly localized
- Fix #7536: Cannot select label in compound
- Fix broken styling for login modal in Vue menu
- Fix #7585 Quick data import fails on dates
- Fix #7666 Python test script UploadZipAndDeleteList.py is broken (this time also for python 3)
Changes
- Removed hierarchical permissions from permission manager controller plugin
- Permissions not accessible through data explorer plugin or REST API
- Remove ontology manager plugin
- Remove gavin and annotators
#7239 Elasticsearch config changes
- Reduce Elasticsearch index size by a factor of ten
- Increase Elasticsearch indexing speed (Travis integration tests finish in 28.5 instead of 40.5 min)
- Split on case transitions: search query 'ontology' matches 'ontologyTerm'
- Split on letter-number transitions: search query 'sample' matches' 'sample123'
- ASCII folding: search query 'role' matches 'rôle', 'strasse' matches 'Straße'
- Ngram tokenization changes: like query 'ring' doesn't match 'String', 'stri' does match 'String'
Breaking changes
- Tomcat 8.5.x required instead of 7.x
- Drop-in upgrade not possible: use a clean install
- Numbers in freemarker are now by default "computer language" (https://freemarker.apache.org/docs/ref_builtins_number.html#ref_builtin_c)
- Upgraded mathjs from 2.1.1 to 4.3.0
- Entities must have a visible label attribute (this may be the id attribute if no label attribute is present)
- Only superusers can use the mapping service
molgenis
- MOLGENIS v6.1.0
Published by sidohaakma about 6 years ago
Documentation
Updated documentation is available here.
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
- 7.1.0-RELEASE
Published by bartcharbon about 6 years ago
Documentation
Updated documentation is available here.
Features
- Parameterized Dynamic Decorators
- Add ICD-10 Expander Decorator
WAR
Download the war from Maven central
molgenis
- MOLGENIS v6.0.0
Published by dennishendriksen over 6 years ago
Documentation
Updated documentation is available here.
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
Download the war from Maven central
molgenis
- MOLGENIS v5.2.2
Published by sidohaakma almost 7 years ago
Updated Negotiator Dialog
molgenis
- MOLGENIS v5.2.1
Published by mark-de-haan almost 7 years ago
Patch update for negotiator functionality
Features
| Pull Request | Content |
|---|---|
| #6937 & #6933 | Backport Negotiator directory features to 5.2 |
molgenis
- MOLGENIS v5.2.0
Published by mark-de-haan about 7 years ago
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
Download the war from Maven central
molgenis
- MOLGENIS v5.1.0
Published by tommydeboer about 7 years ago
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
Download the war from Maven central
molgenis
- MOLGENIS v5.0.1
Published by fdlk over 7 years ago
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
- MOLGENIS v5.0.0
Published by mark-de-haan over 7 years ago
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
- MOLGENIS v4.1.0
Published by fdlk over 7 years ago
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
- MOLGENIS v3.0.2
Published by fdlk over 7 years ago
Bugfixes
| Pull Request | Content |
|---|---|
| #6118 | Fix #5985: Job logs can exceed max log size, disastrous consequences |
molgenis
- MOLGENIS v4.0.0
Published by mark-de-haan over 7 years ago
WAR
You can download the web archive here
Features
| Pull Request | Content |
|---|---|
| #6005 | Underscores in entity names / technical identifiers |
| #5933 | M4720 Unit and integration test robustness improvements |
| #5941 | M3169 Cascading delete |
| #5897 | M4597 App manager plugin |
| #6004 | [GF] Make localization easier to work with for both users and developers |
| #6003 | REST API Integration tests |
| #5994 | Upgrade Guava 19.0 to 21.0 |
| #6009 | Move commandline annotators to separate repo |
Bugfixes
| Pull Request | Content |
|---|---|
| #6083 | Fix #6030 REST-API main page should contain intro text and info when … |
| #6080 | Fix #6040 Importing ontologies as user without permissions on ontolog… |
| #6079 | Fix #6041 I cannot import GroupMember entities |
| #6078 | Fix #6046 Categorical MREFs with default values are imported incorrectly |
| #6076 | Fix #6048 When importing long values, they are capped at max int value |
| #6074 | Fix #6050 Panicked title on warning message if activation link has al… |
| #6072 | Fix #6062 Description of aggregate threshold setting is incorrect |
| #6065 | Fix #6059 Import step 2 options label gives incomplete hint |
| #6007 | Fix README links |
| #5993 | Fix #5996 Table row selector doesn't contain entry for 10 rows |
| #5992 | Fix #5990 NPE deleting non-existing File Meta with REST v1 |
| #5986 | Add 'allow-script-in-comments' to javadoc plugin settings |
| #5973 | Fix #5972 Cmd line annotator doesn't support bgzip input/output |
| #5970 | Fix #5931 Can not import a correct zip of csv/tsv files if a directory is zipped instead of only the files |
| #5968 | Fix #5969: Cannot do clean install nor update mail settings |
| #5967 | Fix #5555: Installation manual should instruct the administrator to c… |
| #5966 | Fix #5320 VCF writer adds bad ";" after INFO field |
| #5963 | Fix #5329 VCF invalid due to missing "." for multi-allelic missing values |
| #5962 | Fix #5954 Build stability warnings building molgenis |
| #5960 | Fix #5917 FAIR datapoint gives nullpointer |
| #5958 | Fix #5953 Upgrading Spring 4.3.4 to 4.3.5/6/7 breaks application |
| #5957 | Fix #5909 Entity type specific repository decoration differences |
| #5949 | Fix #5886 Fileingest running infinitely in case of missing mail settings |
| #5946 | Fix #5940 Removing filter with '>' in the value breaks data explorer |
| #5937 | Fix #5814 Genome browser produces 500 error when processing an abstract entity |
| #5922 | Fix #5908 Unclear error message when adding required attribute |
| #5919 | Fix #5913 Remove setDescription("") from entity type metadata classes |
| #5918 | Fix #5906 Unclear error message deleting ref entity that is in use |
| #5915 | Fix #5907: Import step 2 options label gives incorrect hint |
| #5912 | Fix #3217 Deleting FileMeta doesn't delete corresponding file from file store |
| #5905 | Fix #5888 Restarting application performs indexing actions |
| #5903 | Fix #5885 rest returns all data when 'num' is set to '0' |
molgenis
- MOLGENIS v3.0.1
Published by bartcharbon over 7 years ago
Features
M4307 As col7a1 I need a new solution for homozygous patients in the dataexplorer
Bugfixes
Fix #5940 Removing filter with '>' in the value breaks data explorer
Fix #5950: home page logs nullpointer after clean deploy
molgenis
- MOLGENIS v3.0
Published by dennishendriksen over 7 years ago
Features
| Feature | contents |
|---|---|
| M4585 | Fair data point |
| M4714 | Entity types and packages can be moved to other packages |
| M4832 | REST API v2 endpoint to delete multiple entities |
| #5805 | Improve RSQL readability in URL |
Bugfixes
| issue | contents |
|---|---|
| #3488 | Remove duplicate OntologyService and OntologyServiceImpl |
| #3506 | Ontology tree plugin reports error when loaded |
| #4530 | Integration tests cannot build concurrently |
| #4741 | Resetting your password in the Account plugin will: Error! No READ permission on entity MolgenisUser |
| #4827 | Importer: importing vcf files with uppercase extension not working |
| #4952 | Data explorer: genome browser not displaying all mutations |
| #5223 | The molgenis.addAll(entityName, dataFrame) function in R is extremely slow |
| #5281 | When trying to match full search term with double in dataexplorer search quotes an error occurs |
| #5248 | Create specific immutable classes for QueryRules, to validate values properly |
| #5573 | Sort errors: introduce Elasticsearch technical identifiers |
| #5632 | Non-admin user cannot see entity report |
| #5674 | DATE and DATE_TIME persisted with too much detail in PostgreSQL |
| #5711 | User repository decorator delete issues |
| #5731 | Maven warnings on clean install of parent project |
| #5718 | Error selecting self-referencing entities after update |
| #5721 | EMX label/lookup attribute selection when undefined |
| #5729 | Importer in update mode always reports zero imported entities |
| #5736 | molgenis.R api has garbled formatting |
| #5744 | FDP endpoint doesn't strip parameters from the IRI |
| #5751 | Send queries with nested attribute to index |
| #5757 | Error message incorrect when when trying to delete ref entity |
| #5764 | Restarting MOLGENIS not working |
| #5765 | Entity type delete strange error |
| #5773 | When deleting a row in the EntityType table, I get a RuntimeException: Unknown attribute for column name [fullName] |
| #5781 | Javascript date format will not validate in Mapping service |
| #5789 | Cannot delete an entity in the DataExplorer |
| #5805 | RSQL encodes too many characters, making it harder to read than is strictly necessary |
| #5812 | Cannot filter aggregates |
| #5824 | JavaScript date return value cannot be converted |
| #5826 | Mapping service: date mapping broken |
| #5838 | Data explorer entity select shows name instead of label |
| #5839 | Catalogue: display possible values for CATEGORICAL_MREF data items |
| #5842 | REST API v1 and v2 transactionality |
| #5870 | System attribute meta data can be updated at runtime |
| #5838 | Data explorer entity select shows name instead of label |
Breaking changes
Existing 1.x or 2.x versions of MOLGENIS are no longer compatible with 3.0 or higher
molgenis
- MOLGENIS v2.1.0
Published by fdlk over 7 years ago
Features
- Bookmarkable filters in the data explorer.
- M4755 As BBMRI-ERIC I want to send my selection to negotiator
Bugfixes
| issue | contents |
|---|---|
| #5727 | When having a categorical value in a compound, the expand function of the categorical does not work properly |
| #5780 | Bugs in mapping service resulting in 500 error and broken mapping |
| #5793 | Complex filters through the wizard don't work |
| #5798 | Human readable form of filters sent to negotiator contains url-encoded identifiers |
| #5800 | Negotiator button should have configurable labels |
| #5802 | When not applying filters an error occurs when using the negotiator |
| #5809 | Filtering on two separate MREF attributes with different refentity causes invalid SQL. |
| #4952 | DAS datasource selects first 1000? hits from a chromosome without looking at the position |
molgenis
- MOLGENIS v2.0.1
Published by dennishendriksen almost 8 years ago
This bug fix release allows other projects to use the molgenis-das module.
Bugfixes
| Issue | Description |
|---|---|
| #4926 | Building MOLGENIS with empty local Maven repository fails |
Download
molgenis
- MOLGENIS v1.0.3-BBMRI
Published by dennishendriksen almost 8 years ago
This is the BBMRI app.
It depends on the row-level-security branch of MOLGENIS in which the following bug was fixed:
Bugfixes
| issue | contents |
|---|---|
| #4926 | Building MOLGENIS with empty local Maven repository fails |
| #5516 | Categorical mref filtering displays dropdown instead of checkboxes |
molgenis
- MOLGENIS v1.22.3-ROW-LEVEL-SECURITY
Published by dennishendriksen almost 8 years ago
This is a new release of the row-level-security branch in which the following bug was fixed:
Bugfixes
| issue | contents |
|---|---|
| #4926 | Building MOLGENIS with empty local Maven repository fails |
| #5516 | Categorical mref filtering displays dropdown instead of checkboxes |
molgenis
- v2.1.0-GAVIN SNAPSHOT release for GAVIN
Published by bartcharbon almost 8 years ago
Package Rankings
Top 12.93% on Repo1.maven.org
Badges
Extracted from project README
