MOLGENIS - for scientific data: management, exploration, integration and analysis.
LGPL-3.0 License
Published by jjettenn almost 8 years ago
Bugs which were present in MOLGENIS v1.21.5 and are fixed in this release:
Published by dennishendriksen almost 8 years ago
Issue | Description |
---|---|
#4926 | Building MOLGENIS with empty local Maven repository fails |
#5152 | Mapping service: increase amount of source attributes for an attribute mapping |
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:
issue | contents |
---|---|
#5152 | Attribute 'sourceAttributeMetaDatas' of entity 'AttributeMapping' cannot have more than 255 characters |
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:
issue | contents |
---|---|
#5152 | Attribute 'sourceAttributeMetaDatas' of entity 'AttributeMapping' cannot have more than 255 characters |
Published by mark-de-haan about 8 years ago
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 |
Published by fdlk over 8 years ago
M4194 As freemarkertemplate developer I want to set custom headers before/after jquery
Published by mark-de-haan over 8 years ago
Updated GAVIN algorithm
Xref and Mref labels now properly reflect the selected language
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
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.
Published by fdlk over 8 years ago
Gavin plugin + app
Annotator 'update' functionality
New versions of SnpEff Annotator and Gavin Annotator
Improved VCF writing
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 |
Published by mark-de-haan over 8 years ago
Published by bartcharbon over 8 years ago
This release is CmdLineAnnotator only, there is no 1.20.0 webapplication.
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 |
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 |
Published by fdlk over 8 years ago
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 |
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 |
Published by fdlk over 8 years ago
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 |
Published by mark-de-haan over 8 years ago
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 |
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 |
Published by mark-de-haan over 8 years ago
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 |
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 |
Published by bartcharbon over 8 years ago
pull request | contents |
---|---|
- | Fix #4397 migration of molgenisUser from older molgenis versions |
- | Fix #4412 Cannot delete all OntologyTerm entities |
Published by mark-de-haan over 8 years ago
pull request | contents |
---|---|
#4389 | Fix #4388 Mysql library is included in the distribution |
Published by mark-de-haan over 8 years ago
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 |
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 |
Published by mark-de-haan almost 9 years ago
pull request | contents |
---|---|
#4285 | MOLGENIS now has multi language support |
#4267 | MOLGENIS now supports Google signup and signin |
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' |