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Recent Releases of biosamples-v4

biosamples-v4 - v5.3.11

What's Changed

  • don't lowercase attribute names by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/752
  • Bsd 2413 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/753
  • BSD release 5.3.11 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/755

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.3.10...v5.3.11

- Java
Published by dipayan1985 about 1 year ago

biosamples-v4 - v5.3.10

What's Changed

  • new webin get client by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/743
  • add facet fields param to facet endpoint by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/744
  • Preparing for release 5.3.10 by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/745
  • Bsd 2347 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/746
  • BSD release 5.3.10 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/747

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.3.8...v5.3.10

- Java
Published by dipayan1985 about 1 year ago

biosamples-v4 - v5.3.8 - AAP and curationdomains deprecation release

What's Changed

  • Refactoring before deprecating AAP by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/735
  • Remove support for curation domains by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/737
  • Chore/21 biosamples aap auth support deprecation by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/736
  • AAP deprecation final changes, SRA accession related changed for NCBI… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/740
  • better integration test by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/741
  • BSD release 5.3.8 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/742

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.3.7...v5.3.8

- Java
Published by dipayan1985 over 1 year ago

biosamples-v4 - v5.3.7

What's Changed

  • Bsd 2255 biosamples file uploader improvements by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/695
  • BioSamples documentation issue by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/697
  • Post 5.3.2 release by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/696
  • Final fixes for v5.3.6 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/698
  • NCBI domain access control and index prive samples to solr by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/708
  • Use new OLS API to point to ontology links by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/702
  • not building ENA and NCBI ENA Link pipelines by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/711
  • BSD software release 5.3.6 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/712
  • Bsd 2336 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/713
  • Bulk samples submission service return validation errors by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/714
  • Code cleanup and adding MICROBE in front page by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/715
  • ck-45-Add submission errors to bulk submission response by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/718
  • bsd-716: use gitlab environments to maintain deployed environments by @amnonkhen in https://github.com/EBIBioSamples/biosamples-v4/pull/717
  • Code cleanup and adding MICROBE in front page by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/724
  • ENA pipeline BSD authority handling re-introduced by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/726
  • BSD release 5.3.7 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/727

New Contributors

  • @amnonkhen made their first contribution in https://github.com/EBIBioSamples/biosamples-v4/pull/717

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.3.2...v5.3.7

- Java
Published by dipayan1985 over 1 year ago

biosamples-v4 - v5.3.2

What's Changed

  • Fixes post 5.2.21 release by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/687
  • FORBIDDEN message change for BioSamplesAapService by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/688
  • BSD release 5.3.0 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/689
  • Fix AAP auth issues by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/690
  • BSD release 5.3.1 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/691
  • Refactoring 1 2024 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/692
  • Refactoring 1 2024 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/693
  • BSD SW Release 5.3.2 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/694

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.21...v5.3.2

- Java
Published by dipayan1985 over 2 years ago

biosamples-v4 - v5.3.0

What's Changed

  • Fixes post 5.2.21 release by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/687
  • FORBIDDEN message change for BioSamplesAapService by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/688
  • BSD release 5.3.0 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/689

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.21...5.3.0

- Java
Published by dipayan1985 over 2 years ago

biosamples-v4 - v5.2.21

What's Changed

  • Improvements post 5.2.20 release incl, OOM error fix, AAP user sample… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/684
  • BSD bugfix release 5.2.21 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/685

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.20...v5.2.21

- Java
Published by dipayan1985 over 2 years ago

biosamples-v4 - v5.2.20 - major release with software upgrades and ERS accessioning support

What's Changed

  • BSD release 5.2.19 BioSamplesClient fixes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/671
  • Java 17 and SB upgrade by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/672
  • Ers accessioning and other changes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/673
  • ERS accessioning in BSD-fixes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/675
  • Refactoring and minor fixes re ERS accession by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/676
  • Update README.adoc by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/678
  • Bsd 2308 ers accessioning and other changes 2 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/677
  • Compilation errors fix of reintroduced pipelines by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/680
  • final changes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/681
  • ncbi-ena-link to GL CI by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/682
  • BSD software release 5.2.20 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/683

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.19...v5.2.20

- Java
Published by dipayan1985 over 2 years ago

biosamples-v4 - BioSamples release 5.2.19

What's Changed

  • 5.2.19 fixes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/644
  • Release 5.2.19 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/645

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.18...v5.2.19

- Java
Published by dipayan1985 almost 3 years ago

biosamples-v4 - Release 5.2.18

What's Changed

  • 1. clean-up code around cross access control, 2. ENA pipeline: remove… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/638
  • Separating ENA import and NCBI link/ re-fill by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/639
  • clean-up by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/640
  • Fixes foe BSD release 5.2.18 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/641
  • BSD release 5.2.18 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/642
  • BSD release 5.2.18 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/643

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.17...v5.2.18

- Java
Published by dipayan1985 almost 3 years ago

biosamples-v4 - Release 5.2.17

What's Changed

  • add public filter for INSDC status != suppressed by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/630
  • Bsd 2292 taxon importer codon by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/629
  • fix release date/ sample status bug in accessioning of V1 and V2, sam… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/631
  • Adding sample post release action to CI/CD by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/632
  • Fix Gitlab CI file for post release action pipeline by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/633
  • Fix CI/CD for sample post release action by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/634
  • Too large artifact error in CICD by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/635
  • Configure micrometer stackdriver by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/620
  • Stackdriver monitoring by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/636
  • BSD release 5.2.17 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/637

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.16...v5.2.17

- Java
Published by dipayan1985 almost 3 years ago

biosamples-v4 - v5.2.16

What's Changed

  • BSD release 5.2.15 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/612
  • ENA pipeline review, ENA pipeline structured data handling review by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/613
  • CH pipeline back by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/614
  • Add status Id to sample for better tracking by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/615
  • Bug/faceting and filtering issues by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/617
  • Ensure variables are final and immutability if maintained as required by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/616
  • Suppressed sample handling by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/619
  • Add missing ENA external links by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/621
  • SUPPRESSED samples handling in ENA pipeline by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/618
  • Import ENA sample DESCRIPTION by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/623
  • Bsd 2291 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/624
  • BSD-2287-sample-release-pipeline by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/626
  • Pipeline old PR merging (zooma and pipeline exit method name change) by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/627
  • Software release 5.2.16 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/628

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.15...v5.2.16

- Java
Published by dipayan1985 about 3 years ago

biosamples-v4 - v5.2.15

What's Changed

  • Bsd 2264 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/610
  • Bsd 2272 amr duplication issue by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/611

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.14...v5.2.15

- Java
Published by dipayan1985 over 3 years ago

biosamples-v4 - v5.2.14

What's Changed

  • Biovalidator upgrade by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/607
  • Fix AAP submissions where a domain is not specified in the payload bu… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/608
  • Preparing to release v5.2.14 by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/609

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.13...v5.2.14

- Java
Published by dipayan1985 over 3 years ago

biosamples-v4 - v5.2.13

What's Changed

  • Adding new COMPLETEDWITHERRORS status and handling for file upload … by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/594
  • Bsd 2233 biosamples remove curated view by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/596
  • Fetch old sample just once and reuse during submissions/ updates + EN… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/589
  • Software release 5.2.11 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/597
  • BSD-2258-improve V2 APIs by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/598
  • Improvements to pipelines, exceptions by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/599
  • add instant serializers for curami mongo model by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/601
  • Copy-down all qualifying attributes from parent samples to child sample by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/600
  • Bsd 2260 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/602
  • Clean-up by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/603
  • Software release 5.2.12 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/604
  • Clean-up and better API error handling by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/605
  • Software release 5.2.13 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/606

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.10...v5.2.13

- Java
Published by dipayan1985 over 3 years ago

biosamples-v4 - Software release 5.2.10

What's Changed

  • Spring boot 2 and solr upgrade by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/570
  • Bsd 2239 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/586
  • Spring boot 2 and solr upgrade by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/585
  • Bump jsoup from 1.14.2 to 1.15.3 in /webapps/core-v2 by @dependabot in https://github.com/EBIBioSamples/biosamples-v4/pull/588
  • Bump jsoup from 1.14.2 to 1.15.3 in /webapps/core by @dependabot in https://github.com/EBIBioSamples/biosamples-v4/pull/587
  • Bsd 2250 improve pagination regards to memory management by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/590
  • SitemapController limit page size and spotless by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/591
  • Removing unnecessary files by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/592
  • Software release 5.2.10 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/593

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.9...v5.2.10

- Java
Published by dipayan1985 over 3 years ago

biosamples-v4 - 5.2.9 software release

What's Changed

  • Don't fetch un-curated view while checking if sample exists by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/579
  • BSD-2229 and BSD-2231 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/580
  • Fix return type of V2 bulk retrieval client methods, from EntityModel… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/581
  • Add single sample fetch in V2 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/582
  • Integration test fix by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/583
  • BSD Release 5.2.9 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/584

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.8...v5.2.9

- Java
Published by dipayan1985 almost 4 years ago

biosamples-v4 - 5.2.8 software release, incl Spring Boot Upgrade

What's Changed

  • Duplicate accessioning fix by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/555
  • BSD release 5.2.5 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/556
  • Release 5.2.5 release candidate fixes by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/557
  • Master by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/558
  • Setting write concern to 1 to get ACK from one server in the cluster by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/559
  • Bsd 2210 phenopacket improvements to new spec by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/560
  • curationdomain documentation by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/561
  • EBI search pipeline fix by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/562
  • Bump jsoup from 1.8.3 to 1.14.2 in /webapps/core-v2 by @dependabot in https://github.com/EBIBioSamples/biosamples-v4/pull/529
  • Bulk fetch and bulk accession logging improvements by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/564
  • BSD release 5.2.6 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/565
  • Refactoring and clean-up of mainly NCBI pipeline, some excess deps cl… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/566
  • Remove SampleConversionControllerAdvice from commons and put it in ut… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/567
  • Bsd 2221 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/568
  • Fix bug related to curation submission and certification with webin a… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/569
  • Fixes to ENA pipeline by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/571
  • Improvement to NCBI load from ERAPRO where submitter id namespace is … by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/572
  • Bsd 2221 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/573
  • Upgrade to spring boot 2 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/563
  • BSD release 5.2.7 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/574
  • Dev -> Master for 5.2.7 release by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/575
  • BSD-2226+BSD-2227+BSD-2228 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/576
  • Oracle deps downport by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/577
  • BSD release 5.2.8 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/578

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.4...v5.2.8

- Java
Published by dipayan1985 almost 4 years ago

biosamples-v4 - v5.2.4

What's Changed

  • Allow duplicate sample names per submitter for uploader submissions by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/542
  • BioSamples release 5.2.2 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/543
  • Bsd 2178 remove auth provider from api by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/541
  • Bsd 2165 bio samples module restructuring by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/544
  • Bsd 2181 better handling of tax id of samples by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/545
  • Add pubmed info to ENA and NCBI imported samples by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/546
  • change solr private filter date by @theisuru in https://github.com/EBIBioSamples/biosamples-v4/pull/547
  • Bsd refactoring exceptions by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/548
  • BioSamples release 5.2.3 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/549
  • bulk-fetch new API added by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/550
  • Improvements to bulk fetch API and BSD client changes for bulk fetch by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/551
  • BSD Client changes for adding authentication support for bulk-fetch w… by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/552
  • Add new method in BioSamplesClient to call for bulk-fetch with jwt by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/553
  • BSD Release 5.2.4 by @dipayan1985 in https://github.com/EBIBioSamples/biosamples-v4/pull/554

Full Changelog: https://github.com/EBIBioSamples/biosamples-v4/compare/v5.2.1...v5.2.4

- Java
Published by theisuru over 4 years ago

biosamples-v4 - v5.1.10

Release with internal bug fixes

- Java
Published by theisuru over 4 years ago

biosamples-v4 - 5.1.6

File uploader improvements to avoid HTTP 504 gateway timeouts and 408 request timeouts

BioSamples file uploader has gone through some changes for dealing with larger file uploads. Any file upload with over 200 samples are queued and submitters are provided with a submission ID. Submitters can use the submission ID in the View submissions tab and check status of their uploads. Once a submission is searched in the View Submissions tab and if the submission ID is valid then the submitter will get a result json file with the submission status and the sample accessions mapped against sample names.

Submissions can have either of the 3 status, ACTIVE, COMPLETED or FAILED.

ACTIVE status: Submission is waiting to be processed or is being processed

COMPLETED status: Submission has completed, if a submission is in COMPLETED status, it is expected that the samples have been created and accessions generated OR samples have failed validation against minimal validation rules of BioSamples database or samples have failed validation against checklist specified by the submitter while doing the file upload

FAILED status: Submission has failed, the submission might have a failed status of the file uploaded was invalid and BioSamples were not able to parse the file or any technical issue in BioSamples database which has prevented the submission from getting processed

JSON schema-store integration and BioSamples checklist (BSDC) ID space

BioSamples now has a checklist ID space starting from BSDC00001. This is to clearly distinguish between ENA checklists and BioSamples checklists. We have also imported ENA checklists into BioSamples schema-store preserving ENA checklist IDs. ‘checklist’ attribute in the sample will trigger a validation in sample submission time, where the checklist will be retrieved from the schema-store and validated using the Elixir biovalidator.

- Java
Published by dipayan1985 almost 5 years ago

biosamples-v4 - v5.1.3

v5.1.3 Release notes Bug Fixes 1. Elixir biovalidate response format mismatch Due to existence of different versions of Elixir validator, there were some output format errors. Now on BioSamples will only use Elixir biovalidator.

- Java
Published by theisuru about 5 years ago

biosamples-v4 - Release v5.0.7

v5.0.7 Release notes

Bug Fixes:

  1. Re-introduce missing samples/validate endpoint In last release we have removed samples/validate endpoint in favour of validate endpoint. But since most users are using samples/validate we will keep this and deprecate in a future release.

  2. Support both json and hal+json for accept header Validate endpoint did not support hal+json accept header in last release. We will include support for this.

  3. Enable ENA to pre-accession samples using WEBIN authentication instead of AAP ENA will pre-accession samples using a WEBIN super user (prefixed SU-) and the metadata submission will be done by a non super user. During metadata submission we will check if the sample has been accessioned by the ENA registered super user and if yes then we will allow submission by any general webin user who wants to submit metadata against the accession.

- Java
Published by theisuru about 5 years ago

biosamples-v4 - Release v5.0.6

New features

  • Authentication We have added additional authentication support in BioSamples. With this release BioSamples users can authenticate using EBML-EBI’s European Nucleotide Archive (ENA) WEBIN authentication service (https://www.ebi.ac.uk/ena/submit/webin/auth). This is especially useful for users who intend to submit their sample metadata to BioSamples and sequencing data to ENA as shared, identical WEBIN credentials can be used to submit to both BioSamples and ENA. BioSamples continues to support the existing AAP authentication mechanism. AAP authentication is the default mode and current users using AAP authentication to submit sample metadata to BioSamples are not required to do any changes to their submission routines. More information related to authentication could be found here - https://www.ebi.ac.uk/biosamples/docs/guides/authentication
  • Sample search results bulk download A new API enables downloading searching and bulk downloading results up to a maximum of 100,000 samples. The API supports text search and samples filtering. When search results exceed the maximum allowable download size, only the first 100,000 samples will be downloaded. Download buttons were also added to the search user interface. Currently this supports downloading samples as JSON, XML or accession list only.
  • Validation checklist in samples body (similar to existing ENA checklists) Samples are validated at submission time. They are by default validated against the biosamples-minimal (ERC100001) checklist. Users can additionally provide the name of a known checklist in the sample body; when provided, this is also used for validation. If validation fails, the submission will be rejected. This enables users to define their preferred validation checklist at submission time. Please refer to the validation guide to see available checklists. The validation API is also available independently of submission and can be used to validate samples without submitting. We have updated our documentation to reflect these changes in certification and validation.

Bug fixes

  • Link to new ENA browser - Samples having external reference to ENA were using the old ENA browser links. This has now been updated to link to the new ENA browser.

Example: Old link - https://www.ebi.ac.uk/ena/data/view/SAMEA5776016

New link - https://www.ebi.ac.uk/ena/browser/view/SAMEA5776016

- Java
Published by theisuru about 5 years ago

biosamples-v4 - v5.0.5

** v5.0.5 Release notes *** New features Private samples are searchable by authenticated users Previously, private samples were only available for direct retrieval after logging in. This release enables searching of private samples through the API by their owner. The sample search endpoint requires a JWT and returns the private samples the user is authorised for.

*** Bug fixes: Documentation updates Links to deprecated AAP services links have been updated throughout. Furthermore, the documentation has been improved to distinguish between the dev and production authentication services.

- Java
Published by theisuru over 5 years ago

biosamples-v4 - Release v4.2.7

== v4.2.7 Release notes === New features 1. Sample groups API: + Sample group API, which was present in SampleTab is now present in JSON API. But we are in discussion whether there is a real user requirement for this. We will be really happy to hear from users, if they have any use case in mind for sample groups. 2. Sample graph search API, interface and new neo4j dependency: + Sample graph search is an experimental feature, which enables to explore sample to sample and sample to external resource relationships. This is backed by neo4j graph database and therefore now neo4j is introduced as a new dependency. Experimental interface (which will change in future) enables simple relationship queries and lists down the results. 3. Domain transfer from old SampleTab domain to new AAP domain: + Now we have started moving old SampleTab domains to new DSP subs domains. This is done only on user request. Let us know if you need to move your samples from old domains t new AAP domain. 4. Sample relationship source validation and relationship documentation: + In a sample relationship, sample source should equal to the containing sample accession. This is validated at sample submission time. New section is added to the user guide to explain sample relationships. 5. Clearinghouse import: + Now we have all the scripts in place for importing curations from clearinghouse. As a result we have also changed how we curate "not collected" and "not provided" values. This is described in documentation. 6. Improvements to EBI Search Engine data dump pipeline 7. BioSamples support to ENA presentation: External reference to ENA is added to samples submitted through BioSamples, i.e. BioSamples authority samples 8. Improve BioSamples documentation

=== Bug fixes: 1. Remove alt text from h1 tag in UI. Alt text in h1 tag has caused google to wrongly index biosamples in search results. 2. Include missing domain validation when updating samples: + Domain validation in sample update service was missing in the previous version. This has been added in the new version. Now if a user has access to an existing sample, he can update the sample using any domain he has access to. 3. Fix the curation pipeline to retain meaningful attributes having values like “not provided”, “not collected” 4. NCBI Exchange - There are cases of missing SRA accessions in NCBI samples imported to EBI BioSamples. In such cases NCBI samples are cross checked with ENA Oracle database and if SRA accession is found in ENA Oracle database, the NCBI samples are updated with the same 5. There were often failures in updating already private samples in NCBI to private in EBI BioSamples, this has been fixed in this release

=== Notifications * Please note that we will be removing SampleTab format submission support on 1st of July. Please let us know if you have any concerns regarding this.

- Java
Published by theisuru almost 6 years ago

biosamples-v4 - v4.2.0

New features and bug fixes: • Deprecation of SampleTab submission format. • Adding static collection for samples+curations. • Modify applying order for the curation objects. • Add link to sample accession.

- Java
Published by dipayan1985 over 6 years ago

biosamples-v4 - Release v4.1.15

  • Update phenopacket version
  • Add curami pipeline to curate biosamples attributes

- Java
Published by theisuru almost 7 years ago

biosamples-v4 - v4.1.14

4.1.14

  • Add DUO attribute to external reference class
  • Add script to import EGA data
  • Add presto connector as a BioSamples client module

- Java
Published by theisuru about 7 years ago

biosamples-v4 - v4.1.13.1

  • Added API in biosamples-client to utilize JWT tokens
  • Resolved issue where ENA pipeline failed if FIRST_PUBLIC date is not available

- Java
Published by danielvaughan about 7 years ago

biosamples-v4 - v4.1.12

  • Replicate required ENA XML Dump functionality in the ENA pipeline
  • Added an annotation 'submitted via USI' to USI samples
  • Added support for suppressed samples imported through ENA pipeline
  • Added user documentation of JSON schema
  • Added logging and retry logic for re-indexing pipeline
  • Refined ncbi pipeline to check suppressed samples are in Solr index before removing

- Java
Published by theisuru over 7 years ago

biosamples-v4 - v4.1.10

  • Remove the holiday message
  • Fix submit tab link in error pages

- Java
Published by theisuru over 7 years ago

biosamples-v4 - v4.1.9

  • Added a Curation Undo Pipeline to allow for removal of erroneous curations.
  • Fix an issue where long attributes break the sample box UI.

- Java
Published by danielvaughan over 7 years ago

biosamples-v4 - v4.1.8

  • Corrected error in curation pipeline which caused sample characteristics to be removed erroneously
  • Added holiday message

- Java
Published by danielvaughan over 7 years ago

biosamples-v4 - v4.1.7

  • Added libraries to enable applications to use Graylog to allow configuration of aggregated logging
  • Switched to the AAP explore environment at https://explore.api.aai.ebi.ac.uk
  • Updated the default AAP URL used by the BioSamples client
  • Included sampletab template file in the sampletab documentation
  • Included ETAG and Curation Object recipes to the BioSamples cookbook
  • Removed name and API key lookup functionality from SampleTab process

- Java
Published by danielvaughan over 7 years ago

biosamples-v4 - BioSamples v4.1.6

  • Addition of AMR structured data into BioSamples
  • Submission of samples with a relationship not targeting a valid accession now return an error
  • Fixed bug with Phenopacket export not able to extract medatada for Orphanet terms
  • Updated user interface to use the newer version of the EBI visual framework
  • Improved documentation navigation experience adopting a new menu style

- Java
Published by Kerruba over 7 years ago

biosamples-v4 - 4.1.3

Release 4.1.3

  • Additional sample attributes required by ENA are now available including a single, top-level taxId field
  • The export box for a sample is now renamed download and contains a list of serialisations that always download as a file fixing a blocked popups issue in Safari
  • The search results now have an updated look and feel based on feedback from ENA

- Java
Published by Kerruba almost 8 years ago

biosamples-v4 -

  • Expose the BioSchemas markup with enhanced context and Sample ontology code
  • SampleTab submission pipeline has been rewrite for better robustness
  • In the samples results page the sample name and the sample accession are now linking to the single sample page
  • Fix various broken hyperlinks

- Java
Published by Kerruba almost 8 years ago

biosamples-v4 -

New features

GDPR:

  • SampleTab submissions enforce explicit acceptance of the terms of service and the privacy information
  • GDPR notices added throughout ### Other:
  • SampleTab where targets of relationships are neither sample name nor sample accession are now rejected, providing user additional information on the problematic data
  • Bioschema.org entities are exported in BioSamples and available both in the UI - embedded in a script tag - and through the API

Bug fixes

  • Solved issues with wrong header’s hyperlinks
  • Solved issue with resolving relationship by name in SampleTab submissions
  • Solved issue with converting DatabaseURI to external references in SampleTab submissions
  • Improved special characters handling in SampleTab submissions

- Java
Published by Kerruba about 8 years ago

biosamples-v4 -

This is a bug-fix release that addresses the following issues:

  • Inclusion of GDPR notices
  • Update format of the Sitemap file

- Java
Published by Kerruba about 8 years ago

biosamples-v4 -

4.0.6

This is a bugfix release that addresses the following issues:

  • Improves search handling of special characters in facets for searching
  • Improves search handling of special characters in search terms
  • Fix issue with curation link URLs
  • Implemented DataCatalog, Dataset and DataRecord profiles on JSON+LD
  • Add ability to control which curation domains are applied to a sample
  • Updated and improved API documentation
  • Updated and improved SampleTab documentation
  • Fix links to XML and JSON serialisation in the UI
  • Fix bug in handling special characters in SampleTab submission
  • Added export pipeline to JSON file
  • Added copy down pipeline, initially for organism attributes copied over derived from relationships

- Java
Published by afaulconbridge about 8 years ago

biosamples-v4 -

4.0.5

This is a bugfix release that addresses the following issues:

  • Improved consistency of paged search results if any of the samples are added or modified whilst paging
  • Improved search update throughput by using Solr transaction log
  • Updated JSON+LD format to the latest version
  • Correctly accept XML sample groups and their related samples
  • Fix issue related to search query terms not being applied to legacy XML and legacy JSON endpoints.
  • Fix incorrect HAL links on autocomplete endpoint
  • Replace SampleTab submitted relationships by name with accessions. As a consequence, they can now be consistently cross referenced by accession in user interface and API
  • Improved indexing of samples when they are rapidly updated or curated
  • Updated Elixir Deposition Database banner URL
  • Reduce number of Zooma calls by not attempting to map "unknown" or "other" attributes
  • Reduce load on OLS by ensuring Zooma does not requery OLS as any results from OLS would not be used by BioSamples

- Java
Published by afaulconbridge about 8 years ago

biosamples-v4 -

4.0.4

This is a bugfix release that addresses the following issues:

  • Persistence of search terms and filters when using HAL paging links
  • SameAs relation in the legacy JSON API works as intended
  • Removed residual test endpoints from legacy JSON API
  • Details relation in legacy JSON API now correctly resolves
  • Added informative and specific title to webpages
  • Added https://www.elixir-europe.org/platforms/data/elixir-deposition-databases[Elixir Deposition Database] banner

- Java
Published by afaulconbridge over 8 years ago

biosamples-v4 -

4.0.3

This is a bugfix release that addresses the following issues:

  • Forward legacy group URLs /biosamples/groups/SAMEGxxxx to /biosamples/samples/SAMEGxxxxx
  • Missing or malformed update and release date on legacy XML group submission will default to current datetime. It is not recommended that users intentionally rely on this.
  • Index legacy XML group submissions, which was not happening due to an unexpected consequence of the interaction of components.
  • Redirect /biosamples/sample and /biosamples/group URLs in case of typo

- Java
Published by afaulconbridge over 8 years ago

biosamples-v4 -

4.0.2

This is a bugfix release that addresses the following issues:

  • Fix javascript on SampleTab submission and accession
  • Handle load-balanced accessioning
  • Fix for storage of relationships source on new samples

- Java
Published by afaulconbridge over 8 years ago

biosamples-v4 - v4.0.1

4.0.1

This is a bugfix release that addresses the following issues:

  • Fix submission of new unaccessioned samples with relationships by inserting an assigned accession into the source of any relationships that are missing it.
  • Fix curation pipeline of numeric organism iri to "http://purl.obolibrary.org/obo/NCBITaxon+taxId" when it should be "http://purl.obolibrary.org/obo/NCBITaxon"+taxId e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606
  • Allow CORS requests for legacy XML APIs.
  • Updated homepage project sample links to use a filter search rather than a text search.

- Java
Published by afaulconbridge over 8 years ago

biosamples-v4 - v4.0.0

4.0.0 Version 4.0.0 represents a re-architecture and re-engineering of the BioSamples software stack. It is now based on the Java Spring-Boot framework, utilising MongoDB for storage and Solr for indexing and search. Version 4.0.0 follows modern web standards and conventions, while remaining backwards compatible. This will also give us a strong and stable foundation to build more features and improvements from, more reliably and more rapidly.

Highlights include:

Submissions and updates will be available immediately via accession, and will be available via search within a few minutes or less. There is also improved handling of submissions and updates, with fewer errors and better feedback about any problems.

Integration with EBI AAP for login management and access to pre-publication samples, including use of ELIXIR AAI single sign-on accounts.

Separation of submitted sample information from curation of that information, including the ability for 3rd party (re-)curation of samples. Please contact us if you would be interested in more information and/or to supply curation information.

Improved handling of non-alphanumeric characters in attribute types e.g. "geographic location (country and/or sea)". Previous versions stripped these characters e.g. "geographic location country and or sea".

Improved faceting allowing selection of multiple values within same facet, fixed re-use and re-distribution of search URLs. This will be expanded in future with additional facet types where appropriate.

Support and recommend the use of content negotiation to accessing multiple formats at the same URIs. In addition to the content (HTML vs XML vs JSON) this also supports compression and caching through standard mechanisms.

Java client using Spring, and a Spring-Boot starter module for easy use. This is used by BioSamples internally and other teams at EMBL-EBI, so is high performance and battle tested.

Containerisation using Docker and Docker-Compose, which makes it easier to run a local version for client development or for local storage of sample information.

Data content Ontology terms Numeric tax IDs (e.g. 9606) and short ontology terms (e.g. PATO:0000384) are being replaced with full IRIs (e.g. http://purl.obolibrary.org/obo/NCBITaxon9606 and http://purl.obolibrary.org/obo/PATO0000384 ) in many places and eventually everywhere.

Groups will continue to exist for backwards compatibility purposes. However, we are investigating future development to reduce or remove many of these in favour of alternatives such as filtering samples by external link, or delegating grouping of samples to other EMBL-EBI archives such as BioStudies.

JSON /biosamples This is the preferred API for use, and uses the same URIs as the HTML pages, and utilising content negotiation to provide a JSON response. This is designed as a hypermedia as the engine of application state (HATEOS) API and therefore we recommend users do not use specific URLs but rather follow relationships between API endpoints, much like a user would use links between HTML pages. It is similar to the /biosamples/api JSON format, with a few critical differences to improve on various issues users have raised:

added release in full ISO 8601 format including time. The backwards-compatible releaseDate exists but should be considered deprecated and will be removed in a future release.

added update in full ISO 8601 format including time. The backwards-compatible updateDate exists but should be considered deprecated and will be removed in a future release.

removed description as a separate field, is now available as a characteristic.

remove relations rel link; equivalent information is now embedded in sample in relationships and externalReferences lists.

remove sample rel link; with relations now embedded, this link serves no purpose.

added curationLinks rel link.

ordering may be different.

fields are not displayed if empty or null.

characteristic names accurately reflect what was submitted and may now be multiple words and may include non alphanumeric characters (e.g brackets, greek letters, etc). In the /biosamples/api responses characteristic names were always camelCased and with non-alphanumeric characters removed.

external references directly embedded in the samples and the groups.

XML /biosamples/xml We are maintaining this for backwards compatibility. Later in 2018 we will be consulting about future development of this API, with a view to removing it. This is in the context of the improved JSON /biosamples API using content negotiation and several long-standing issues with limitations arising from the XML schema in use. We strongly recommend users switch to the new JSON /biosamples API but nevertheless will be maintaining /biosamples/xml for backwards compatibility, although please note the following differences:

XML element TermSourceREF element Name and element URI are removed.

XML element Property attributes characteristic and comment always false.

elements and attributes may be in different order.

allows only one IRI on attributes, so in rare cases of multiple IRIs will not be complete.

Query parameter query has now a default value of * if none is provided.

Query parameter sort is ignored for the search, due to undefined behaviour and lack of usage.

JSON /biosamples/api This API should be considered deprecated and we will aim to remove it by 2019. Any users of this should move to using the /biosamples URIs to retrieve JSON representations with an improved schema via content negotiation. Further announcements will be made in future for specific updates and deadlines.

ordering may be different from previous versions, and is not guaranteed for future versions.

fields are not displayed if empty or null.

/api/externallinksrelations/{id}/sample and /api/externallinksrelations/{id}/group are removed due to lack of usage.

fixed externalReferences and publications to be nested objects and not JSON strings.

Acknowledgements This release has been made possible with the support of our funders:

EMBL-EBI Core Funds

EC -ELIXIR-EXCELERATE

WT- HIPSCI

IMI - EBiSC

ELIXIR – Meta Data Implementation Study

WT-GA4GH

- Java
Published by afaulconbridge over 8 years ago

biosamples-v4 -

- Java
Published by afaulconbridge over 8 years ago