molgenis
MOLGENIS - for scientific data: management, exploration, integration and analysis.
LGPL-3.0 License
Stars
111
Committers
55
Ecosystems:
Java,
JavaScript
molgenis
- MOLGENIS v2.0
Published by jjettenn almost 8 years ago
Features
- Transactional metadata editing:
- Edit existing attributes and entities in your application
- Add attributes to existing entities at runtime
- Delete attributes and entities at runtime
- Removing packages, including all underlying entities and attributes is now supported
- New attribute type ONE_TO_MANY:
- Specify a ONE_TO_MANY relationship between two attributes, which supports back referencing
- General performance improvements
- Importer speed has been increased
- VCF importing speed has been increased to 20.000 variants / second
- Massive Mapping service performance improvements
- L1, L2 and L3 caches
Breaking changes
- Not compatible with MOLGENIS version 1.21.5 or below
- MySQL is no longer supported, PostGreSQL v9.6.0 or higher is required
Bugfixes
Bugs which were present in MOLGENIS v1.21.5 and are fixed in this release:
- #5254 Other Data explorer filters are ignored when using filters for MREF types
- #5524 Aggregates view attribute selection not remembered
- #5301 Importing OWL ontology requires internet access
- #4602 Date and DateNillable always use the DefaultValue, even when there is a value present
- #2830 User can see import jobs of other users
- #5431 Updating entity with id with dot char fails
- #4635 adding a value in the xmref select box does not select this value
- #4101 mail preferences should be settings
- #4926 Building MOLGENIS with empty local Maven repository fails
- #4894 Missing ID attribute is not caught during validation
- #4873 Sorting on computed attributes in table exception
- #4847 Batch update rest api V2 fails
- #4755 Starting entity names with an underscore prevents importing
- #4753 Adding new source entity is slow
- #4710 Molgenis-HTTP status 404
- #4701 VcfRepository.iterator() returns iterators with unpredictable behaviour
- #4652 When compiling the Molgenis-app in Eclipse the downloading of the maven-metadata.xml times out.
- #4641 File download broken
- #5006 Error executing JavaScript script with alert
- #4965 URL validation fails on valid URLs
- #4640 Firefox complains when updating entity with attribute of type File
- #4597 Support upload of files > 150MB
- #4589 Support updating of a single attribute of an entity
- #4333 Duplicate chrom-pos combinations in VCF upload result in cryptic error message
- #4248 Filter on full name Ontology_OntologyTerm results in multiple results
- #4142 When adding a row through the API that invalidates "validationExpression" it returns Unknown error, should be more informative
- #4090 Cannot select items in dataexplorer with small view width
- #4087 Non-super users need READ permission on "entities" to use Mapping Service
- #4082 No spinner when using mapping-service
- #4011 Import error when running annotators
- #3986 The base package is not filtered out of the list of packages shown in the Model Registry
- #3950 RepositoryValidationDecorator only returns first missing ref
- #3911 When trying to import big questionnaire as a user, I get permission errors
- #3888 Cannot add entities with File type attributes if I don't have permissions for the FileMeta entity
- #3776 Mapping Service algorithm editing is slow
- #3709 FreemarkerTemplate entities read from MySQL instead of Elasticsearch
- #3707 Failing snpEff will not roll back the adding of metadata
- #3630 Creating an integrated dataset after mapping two entities either fails, or takes a very long time
- #3368 Importing an entity with the same name but different casing will result in a locked importer
- #3304 When setting ROOT logging to ALL, the app is completely broken and restarting will not help anymore
- #3296 Resolve VcfUtils FIXMEs
- #3284 Remove DefaultEntityValidator uniques
- #2614 GAF list --- after validation error after pushing the back button.
- #1838 Jenkins reverse proxy set up is broken
- #3008 xhyperlink and xhyperlinknillable should not apply URL validation
molgenis
- MOLGENIS v1.21.5
Published by dennishendriksen almost 8 years ago
Features
- Improved Gavin annotation results (updated genome-wide MAF threshold)
Bugfixes
| Issue | Description |
|---|---|
| #4926 | Building MOLGENIS with empty local Maven repository fails |
| #5152 | Mapping service: increase amount of source attributes for an attribute mapping |
Download
molgenis
- MOLGENIS v1.0.2-BBMRI
Published by fdlk about 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 |
|---|---|
| #5152 | Attribute 'sourceAttributeMetaDatas' of entity 'AttributeMapping' cannot have more than 255 characters |
molgenis
- MOLGENIS v1.22.2-ROW-LEVEL-SECURITY
Published by fdlk about 8 years ago
This is a new release of the row-level-security branch in which the following bug was fixed:
Bugfixes
| issue | contents |
|---|---|
| #5152 | Attribute 'sourceAttributeMetaDatas' of entity 'AttributeMapping' cannot have more than 255 characters |
molgenis
- MOLGENIS v1.21.4
Published by mark-de-haan about 8 years ago
Bugfixes
| issue | contents |
|---|---|
| #5015 | Can't create filter for XREF/MREFs with integer ID in data item selection of data explorer |
| #5016 | Can't select wizard in data item filters of data explorer if the entity has an attribute with fieldType FILE. |
| #5017 | Can't expand empty reference attribute fields if behind an expanded MREF |
| #5028 | When setting lookupAttribute as false, it is still present in the dropdown menu |
| #5165 | When importing, lookupAttributes get stored in the entities repository but not in the EntityMetaData POJO |
molgenis
- MOLGENIS v 1.21.3
Published by fdlk over 8 years ago
Features
M4194 As freemarkertemplate developer I want to set custom headers before/after jquery
Download on maven central repository
molgenis
- MOLGENIS v1.21.2
Published by mark-de-haan over 8 years ago
Features
Updated GAVIN algorithm
Bugfixes
Xref and Mref labels now properly reflect the selected language
molgenis
- MOLGENIS v1.17.1
Published by mark-de-haan over 8 years ago
Fixed migration from 1.16.2 to 1.17.0
When an attribute in a compound is also a lookup attribute, migration would fail
Download on maven central repository
molgenis
- MOLGENIS v1.21.0 - do not use
Published by fdlk over 8 years ago
This version contained a bug in the migration from v1.19.0 to v1.21.0 and should not be used.
Please use v1.21.1 instead.
molgenis
- MOLGENIS v1.21.1
Published by fdlk over 8 years ago
Features
Gavin plugin + app
Annotator 'update' functionality
New versions of SnpEff Annotator and Gavin Annotator
Improved VCF writing
Bugfixes
| issue | contents |
|---|---|
| #4828 | When editing attribute mapping for RD-Connect I get a freemarker error |
| #4691 | ImportApi check if repo exists based on filename, which is nonsense for EMX |
| #4776 | Elasticsearch index rebuild calls wrong delete method |
| #4596 | Selecting from tables with lots of data and multiple MREFs is very slow |
| #4711 | When uploading a file with many attributes, I get a Duplicate key attributes error even when there are no duplicate keys |
| #4757 | Error notification without logging |
| #4756 | Running the CADD annotator results in nullpointer for missing REF attribute in source entity |
| #4478 | Direct basic IN queries to decorated repo |
| #4728 | Elasticsearch EQUALS query with null value incorrect |
| #4836 | File Ingester import job progress message doesn't show error if import fails |
| #4837 | Selecting annotators as a user results in a permission error |
| #4838 | I can no longer set permissions for a group |
| #4840 | When annotating as a normal user, I do not see the progress bar |
| #4843 | Opening the tag wizard gives error |
| #4845 | Inspecting a row in the results table in the attribute mapping view throws an error |
| #4846 | As user I am unable to use the SnpEff annotator |
| #4857 | As Gavin user I'ld like to update the entityname from ccgg to gavin for the annotator resource |
| #4871 | JobExecution entities should have a weak reference to MolgenisUser |
Download on maven central repository
molgenis
- BBMRI Release for Promise Link
Published by mark-de-haan over 8 years ago
molgenis
- CmdLineAnnotator 1.20.0
Published by bartcharbon over 8 years ago
This release is CmdLineAnnotator only, there is no 1.20.0 webapplication.
Features
| pull request | contents |
|---|---|
| - | Implemented feature request #4694: Annotators lack an 'update' functionality |
| - | Updated Genotype-IO to 1.0.3 |
| - | Implement new version of SnpEff Annotator, add Gavin Annotator, refactor VCF writing |
| - | Added test for getPedigree function in VcfUtils |
Bugfixes
| pull request | contents |
|---|---|
| - | Fix #4756 Running the CADD annotator results in nullpointer for missing REF attribute in source entity |
| - | Fix #4739 OMIM annotator returns results within square brackets. Added missing columns to OMIM output |
| - | Fix for #4693: CADD annotator is not multi-allelic |
molgenis
- MOLGENIS v1.19.0
Published by fdlk over 8 years ago
Features
| pull request | contents |
|---|---|
| #4667 | M4094 As SORTA user I want to merge sorta code so I can upload using other format |
| #4709 | M3415 As user I want to be able to delete script parameters |
| #4695 | Get like and not like query working for rsql queries |
| #4692 | Reintroduce old annotator: OMIM |
Bugfixes
| pull request | contents |
|---|---|
| #4696 | Fix #4693 CADD annotator is not multi-allelic |
| #4687 | Fix #4586 GoNL annotator writes non-standard separators and missing values |
| #4686 | Fix #4593 GoNL annotator crashes on a certain SNV |
| #4684 | Fix #4413 Menu overlaps top of page content |
| #4681 | Fix #4670 OwnedEntity changes ownership of owned entities to SYSTEM when inserting as System (also fixed in 1.16.3) |
| #4679 | Fix #4123 Failed login prevents the login dialog from being closed |
| #4678 | Fix #4598 add *.vcf.zip support |
| #4671 | Fix #4541 Data duplication with add/update, error in file (also fixed in 1.16.3) |
| #4664 | Fix #4663 Inconsistent check for length password |
| #4648 | Fix #4647 JDBC decimal type maps to BigInteger |
| #4730 | Fix #4729 MySqlRepository not QUERYABLE but answers queries |
| #4726 | Fix #4725 Updating MREF attrs for ref entity int attribute |
| #4714 | Fix #4713: AUTO id columns overwrite specified id value |
molgenis
- MOLGENIS v1.16.3
Published by fdlk over 8 years ago
Bugfixes
| pull request | contents |
|---|---|
| - | Fix #4541 Data duplication with add/update, error in file |
| - | Fix #4670 OwnedEntity changes ownership of owned entities to SYSTEM when inserting as System |
| - | Fix #4642 Decimal attributes cannot be set to non-integer values in chrome |
molgenis
- MOLGENIS v1.18.0
Published by mark-de-haan over 8 years ago
Features
| pull request | contents |
|---|---|
| #4592 | M4016 For long running processes (annotators, importers, downloads, mapping service) we have a progress bar that can run in the background |
| #4585 | M4036 As RD-connect and BBMRI-ERIC I want to automatic ingest of Excel/CSV file |
| #4578 | M4068 A MOLGENIS style matching the RD-connect styling |
| #4565 | Remove unused molgenis-data dependencies |
| #4560 | Data API stream with fetch operation |
| #4532 | M3372 As data manager I want to import via web service |
| #4656 | Comprehensible error message when foreign keys constraints are too long |
Bugfixes
| pull request | contents |
|---|---|
| #4604 | Fix #4315 Forms occasionally eat up some of the letters that you've typed |
| #4584 | Fix #4583 molgenis-core-ui's node_modules is not cleaned by maven clean target |
| #4580 | Fix #4510 If I copy my entity when annotating and the annotation fails, the created entity is not removed |
| #4571 | Fix #4564 CaseInsensitiveLinkedHashMap is buggy |
| #4570 | Fix #4569 Repository validation fails for self-referencing entities |
| #4568 | Fix #4567 REST update in case of empty mref |
| #4563 | Fix #4334 Buttons the data explorer show their technical names |
| #4562 | Fix #4561 Elasticsearch transactional count with query fails when deleted docs |
| #4559 | Fix #4558 MREF field value conversion does not convert |
| #4557 | Fix format README enumeration for setting the RuntimeProperty |
| #4555 | Fix #4553 Molgenis doesn't like localhost URL |
| #4550 | Fix #4546 VCF import without samples does not report import count |
| #4549 | Fix #4548 Cannot serialize entities using gson |
| #4540 | Fix #4539 DefaultEntityMetaData copy constructor sets fullName instead of simpleName |
| #4537 | Fix #4535 Resetting your password leads to unusable molgenis |
| #4536 | Fix #4336 InMemoryRepository findAll() includes nulls |
| #4534 | Fix #4449 Unable to retrieve XREF values for a single ID through the python REST API. |
| #4531 | Fix #3884 Build time listed in the footer is not Europe/Amsterdam timezone. |
| #4528 | Fix #4429 =like= operator broken in v2 REST api |
| #4527 | Fix #4504 Deleting entities isn't logged |
| #4550 | Fix #4546 VCF import without samples does not report import count |
| #4526 | Fix #3915, #3915 Multiple password reset messages |
| #4525 | Fix #4529 CmdLineAnnotator delivery is always being created when doing a clean install |
| #4665 | Fix #4510 If I copy my entity when annotating and the annotation fails, the created entity is not removed |
| #4662 | Fix #4617: When hitting "tab" immediately after typing the focus switches back to previous field |
| #4655 | Fix #4626: when there are failing annotators the job status is SUCCESS |
| #4660 | Fix #4624: importByUrl returns content-type application/json but is raw text |
| #4658 | Fix #4594 Pagination functionality in the Data Explorer is broken |
| #4657 | Fix #4649 Validation broken |
| #4655 | Fix #4619 Can not annotate as a normal user |
| #4654 | Fix #4643 lookupAttribute is missing |
| #4653 | Fix #4641 File download broken |
| #4651 | Fix #4642 decimal attributes cannot be set to non-integer values in chrome |
| #4650 | Fix #4608 importer reports index within the batch instead of actual line number on fail |
| #4637 | Fix #4630 Tagwizard edit tag error |
| #4614 | Fix #4613 Babel alias path resolver breaks the webpack build on build server |
molgenis
- MOLGENIS v1.17.0
Published by mark-de-haan over 8 years ago
Features
| pull request | contents |
|---|---|
| #4467 | Asynchronous annotators and progress bars |
| #4419 | M3933 Remove AttributeMetaData.isIdAtrribute, isLabelAttribute, isLookupAttribute |
| #4407 | M3494 Modular javascript to get proper frontend dependency management |
Bugfixes
| pull request | contents |
|---|---|
| #4486 | Fix #4481 Table row inspect error for non-superuser |
| #4484 | Fix #4441 REST api login error response message inconsistent |
| #4483 | Fix #4448 Status 500 instead of 40x when not authorized |
| #4482 | Fix #4444 Model registry model details view broken |
| #4480 | Fix #4479 PartialEntity doesn't retrieve attributes not included in the fetch |
| #4476 | Fix #4475 Tape testing for windows |
| #4471 | Fix #4470 No results finding owned entities by id with fetch |
| #4466 | Fix #4465 The ID attribute is no longer a lookUp attribute |
| #4460 | Fix #4459 Updating entities with unchanged readonly mref attributes |
| #4455 | Fix #4433 When doing an add / update the importer throws an error |
| #4454 | Fix #4453 EmbeddedElasticSearch test keeps writing to the same directory, eventually causing Jenkins to fail tests |
| #4446 | Fix #4445 EMX entity id import not unique by default |
| #4439 | Fix #4437: When an uploaded VCF has multiple SNPs with a '.' in its ID column, it will trigger duplicate key entry |
| #4438 | Fix #4431 Uploading a VCF will throw an error |
| #4428 | Fix #3850 Selecting computed ref entities in table displays empty modal |
| #4427 | Fix #4321 Newline missing for expanded categoricalmrefs in table |
| #4426 | Fix #3693 Table attribute expand not working if attribute in compound |
| #4423 | Fix #4422: Model registry UML viewer broken in chrome |
| #4418 | Fix #4412 Cannot delete all OntologyTerm entities (unit tests) |
| #4414 | Fix #4412 Cannot delete all OntologyTerm entities |
| #4408 | Fix #4337 Using other themes than the molgenis theme, will cause a glyphicon not found error |
| #4401 | Fix #1384 Excel sheets with merged regions handling |
| #4400 | Fix #3959 REST API entity attribute update performance |
| #4398 | Fix #4397 migration of molgenisUser from older molgenis versions |
| #4396 | Fix #4351 Requirement Last name and First name fields |
| #4395 | Fix #4355 #3965 #4368 + small vcf import entity/attribute name improvements/checks |
| #4393 | Fix #4388 Mysql library is included in the distribution |
| #4514 | Fix #4515 ConcurrentModificationException when running the annotators |
| #4513 | Fix #4495 Duplicate key error when importing emx_deep_nesting.xlsx |
| #4509 | Fix #4473 Repository validator does not validate ref attribute value + fix integration tests |
| #4503 | Fix integration test by adding null checks in mysqlRepo and EntityToSourceConverter |
molgenis
- MOLGENIS v1.16.2
Published by bartcharbon over 8 years ago
Bugfixes
| pull request | contents |
|---|---|
| - | Fix #4397 migration of molgenisUser from older molgenis versions |
| - | Fix #4412 Cannot delete all OntologyTerm entities |
molgenis
- MOLGENIS v1.16.1
Published by mark-de-haan over 8 years ago
Bugfixes
| pull request | contents |
|---|---|
| #4389 | Fix #4388 Mysql library is included in the distribution |
molgenis
- MOLGENIS v1.16.0
Published by mark-de-haan over 8 years ago
Features
| pull request | contents |
|---|---|
| #4339 | M3857 Data API integration tests |
| #4338 | M3777 As Mapping Service user I can update an existing entity |
| #4317 | M3990 Improve VCF commandline annotation performance |
| #4316 | M3913 Streaming data API |
| #4335 | M3824 Remove JPA and generators |
| #4326 | Use VCF filename as default |
| #4329 | Permission settings for editing metadata |
Bugfixes
| pull request | contents |
|---|---|
| #4341 | Fix #4340: Catalog table doesn't add tbody element between table and table rows. |
| #4313 | Fix #4312: Fetch behavior for references is inconsistent |
| #4311 | Fix #4291 Google sign in creates a redirectloop for inactive user |
| #4309 | Fix #4238 403 when user with inherited import rights imports an entity (for which it has no permissions) |
| #4305 | Fix #4296: Aggregates with threshold smaller than rendered wrong |
| #4302 | Fix #4297: nonobvious ref and alt not working for GoNL |
| #4365 | Fix #4350 Error merging datasets with Merge plugin |
| #4364 | Fix #4357 Migration from 1.14 to 1.15 to 1.16 fails |
| #4363 | Fix #4346 Error! The attribute 'superuser' of entity 'MolgenisUser' can not be null |
| #4362 | Fix #4356 Account info not saved |
| #4361 | Fix #4349 replace UserPermissions in PermissionManagerServiceImpl uses iterable instead of stream |
| #4379 | Fix #4378 Map tab in the mapping service single attribute mapping is empty |
| #4374 | Fix #4372 MappingService - Please contact the administrator |
| #4373 | Fix #4370 and #4371 Entity reports (table) no longer work |
| #4360 | Fix #4348 rebuildIndexElasticSearchEntity uses iterable instead of stream to delete |
| #4359 | Fix #4353 ImportWriter uses iterable instead of stream |
Breaking changes
- JPA has been removed, along with its code generators
- The data API now uses streams
molgenis
- MOLGENIS v1.15.0
Published by mark-de-haan almost 9 years ago
Features
| pull request | contents |
|---|---|
| #4285 | MOLGENIS now has multi language support |
| #4267 | MOLGENIS now supports Google signup and signin |
Bugfixes
| pull request | contents |
|---|---|
| #4292 | Fix #4298 Permission name must be uppercase |
| #4290 | Fix #4289 ResourceUtils - NullPointerException is thrown |
| #4281 | Fix #4185 EMX with self-references import failure |
| #4279 | Fix #4278 Elasticsearch transactional sync issues |
| #4277 | Fix #4276 Navigating to a menu when the session is expired throws a freemarker error instead of redirecting you to the login modal |
| #4271 | Fix #4270 MysqlRepository find executed twice when no results |
| #4269 | Fix #4268 Elasticsearch findOne with query executes query twice |
| #4301 | Fix #4294 Some nillable attributes does not have an N/A option |
| #4300 | Fix #4295 NullPointerException while uploading |
| #4292 | Fix #4298 When logging in as a non admin user, I get 'No count permission on entity languages' |
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