MOLGENIS - for scientific data: management, exploration, integration and analysis.
LGPL-3.0 License
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Published by fdlk about 6 years ago
Updated documentation is available here.
Published by sidohaakma about 6 years ago
Updated documentation is available here.
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Published by bartcharbon about 6 years ago
Updated documentation is available here.
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Published by dennishendriksen over 6 years ago
Updated documentation is available here.
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 |
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 |
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Published by sidohaakma almost 7 years ago
Updated Negotiator Dialog
Published by mark-de-haan almost 7 years ago
Patch update for negotiator functionality
Pull Request | Content |
---|---|
#6937 & #6933 | Backport Negotiator directory features to 5.2 |
Published by mark-de-haan about 7 years ago
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 |
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 |
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Published by tommydeboer about 7 years ago
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 |
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 |
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 |
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' |
Download the war from Maven central
Published by fdlk over 7 years ago
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 |
You can download the web archive here
Published by mark-de-haan over 7 years ago
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. |
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 |
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 |
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. |
You can download the web archive here
Published by fdlk over 7 years ago
You can download the web archive here
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 |
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 |
Published by fdlk over 7 years ago
Pull Request | Content |
---|---|
#6118 | Fix #5985: Job logs can exceed max log size, disastrous consequences |
Published by mark-de-haan over 7 years ago
You can download the web archive here
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 |
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' |
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
Published by dennishendriksen over 7 years ago
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 |
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 |
Existing 1.x or 2.x versions of MOLGENIS are no longer compatible with 3.0 or higher
Published by fdlk over 7 years ago
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 |
Published by dennishendriksen almost 8 years ago
This bug fix release allows other projects to use the molgenis-das module.
Issue | Description |
---|---|
#4926 | Building MOLGENIS with empty local Maven repository fails |
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:
issue | contents |
---|---|
#4926 | Building MOLGENIS with empty local Maven repository fails |
#5516 | Categorical mref filtering displays dropdown instead of checkboxes |
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:
issue | contents |
---|---|
#4926 | Building MOLGENIS with empty local Maven repository fails |
#5516 | Categorical mref filtering displays dropdown instead of checkboxes |
Published by bartcharbon almost 8 years ago