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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[1.5.8] - 2024-10-14

  • initial release for WS294

[1.5.7b] - 2024-03-22

  • fix release for WS293

[1.5.7] - 2024-03-22

  • initial release for WS293

[1.5.6] - 2024-03-22

  • initial release for WS292

[1.5.5] - 2024-01-09

  • initial release for WS291

[1.5.4b] - 2023-10-15

  • hotfix release for WS290

[1.5.4] - 2023-10-15

  • initial release for WS290

[1.5.3] - 2023-07-01

  • initial release for WS289

[1.5.2] - 2023-03-01

  • initial release for WS288

[1.5.1] - 2022-12-13

  • initial release for WS287

[1.5.0] - 2022-08-21

  • Removed Dockerrun.aws.json file, converted to docker-compose.yaml
  • fixed .ebextensions for AWS Linux 2 compatibility - Perl modules, proxy timeout (moved to .platform)
  • overall upgrade to AWS Linux 2
  • small changes on Dockerfile

[1.4.9] - 2022-08-04

  • Pulling in fixes for the expression pattern widget

[1.4.8] - 2022-06-12

  • We all grok what's happening now; version bump only

[1.4.7] - 2022-06-12

  • fixing collision with prior pr

[1.4.6] - 2022-06-12

  • initial release for WS285

[1.4.5] - 2022-03-06

  • initial release for WS284

[1.4.4] - 2021-12-13

  • fix for Log4j security volnurability to 2.5 by adding LOG4J_FORMAT_MSG_NO_LOOKUPS=True

[1.4.3] - 2021-11-30

  • initial release for WS283
  • Fixes for changes to the schema for VEP

[1.4.2] - 2021-08-23

  • initial release for WS282

[1.4.1] - 2021-05-28

  • initial release for WS281

[1.4.0] - 2021-06-15

  • fixing molecular details widget predicted CDS bug

[1.3.9] - 2021-06-01

  • Adding VEP results to genetics widget

[1.3.8] - 2021-05-30

  • Fix moldecular details bug

[1.3.7] - 2021-05-21

  • Adding amino acid diagrams on molecular details widget

[1.3.6] - 2021-05-12

  • Adding VEP results to transcrips on variant molecular detail widget

[1.3.5] - 2021-03-08

  • Initial WS280 release
  • CORS implemented

[1.3.4] - 2020-12-14

  • Initial WS279 release
  • Finished all remaining endpoints

[1.3.3] - 2020-10-16

  • Initial WS278 release

[1.3.2] - 2020-07-14

  • Minor changes for releasing data hotfix WS277.1

[1.3.1] - 2020-06-26

  • Initial WS277 release

[1.3.0] - 2020-06-23

  • changing RDS host

[1.2.9] - 2020-06-03

  • Fixing rare 500 error for homology widget

[1.2.8] - 2020-05-11

  • Compute counts for variations for strains and avoid returning large number of variations

[1.2.7] - 2020-05-01

  • Fix for protein widget 500 error when location of motif is not in db
  • small change for interactions core

[1.2.6] - 2020-04-22

  • pre-production hotix
  • adding non-coding transcripts to sequences table on gene page

[1.2.5] - 2020-04-21

  • pre-production hotfix

[1.2.4] - 2020-04-17

  • Initial WS276 release
  • Bug fixes for interactions
  • Protein Motif Details and Overview Widgets
  • Homology-group Overview widget

[1.2.3] -2020-03-06

  • Fixing 500 error when gene does not have an associated protein in the homology widget

[1.2.2] -2020-03-02

  • Fix for bug for public-name found during caching

[1.2.1] - 2020-02-26

  • Removing Protein overview and motif details widget

[1.2.0] - 2020-02-24

  • release for WS275
  • contains protein overview and motif details widget
  • contains GOTerm page associations widget
  • contains gene Homology widet!

[1.1.0] - 2019-12-19

  • release for WS274
  • retrieve protein homology data
  • retrieve data for interaction venn
  • fix the display of premature stop codon
  • fix life-stage description/definiton WormBase/website#7463
  • fix typo in all_labs representative column

[1.0.2] - 2019-10-24

  • release for WS273
  • stop merging annotations for interactions

[1.0.1] - 2019-09-29

  • release for WS272

[1.0.0] - 2019-06-19

  • created several of the entity level widgets
  • first release for WS271

[0.9.9] - 2019-06-19

  • Fix MTGE transcript bug found by user

[0.9.8] - 2019-06-13

  • releasing PCR-oligo sequences widget
  • fixing a couple bugs with variation molecular details widget

[0.9.7] - 2019-05-25

  • Fixing bugs

[0.9.6] - 2019-05-20

  • fixing handling of multiple 5 prime and/or 3 prime utr on transcripts and cds sequence pages

[0.9.5] - 2019-05-18

  • fix for #6490 (off by one error with variation molecular details widget)

[0.9.4] - 2019-05-16

  • fixed minor issues with #6437 and #7112

[0.9.3] - 2019-05-15

  • Adding logic for when there is not enough room for 2000 bp padding on either side

[0.9.2] - 2019-05-13

  • Fix missing 5 prime UTR in spliced transcript sequence caused by typo

[0.9.1] - 2019-05-10

  • Adding in pseudogene, transcript and CSD widgets

[0.9.0] - 2019-04-22

  • First release for WS270

[0.8.4] - 2019-04-08

  • Hotfix for ASSEMBLIES.json

[0.8.3] - 2019-03-20

  • Fixing when the clond is MTCE for a variations clone

[0.8.2] - 2019-03-20

  • Fixing reverse complement for C

[0.8.1] - 2019-02-25

  • Fixing a couple things with the variation molecular details widget

[0.8.0] - 2019-02-22

  • New disease wigets
  • First WS269 release

[0.7.4] - 2019-01-16

  • Hot fix for when there is a variation with and insertion and a deletion

[0.7.3] - 2019-01-15

  • Fix for when there are no primer pairs in gene reagents widget

[0.7.2] - 2019-01-10

  • Fix for variations that are not in sequence database for molecular details widget

[0.7.1] - 2019-01-10

  • Adding Sibyls hotfix for gene descriptions

[0.7.0] - 2019-01-03

  • Adding variation mulecular-details widget

[0.6.4] - 2018-12-21

  • Adding fix for Interactions schema change

[0.6.3] - 2018-12-17

  • Preping for WS268 release

[0.6.2] - 2018-11-01

  • Preping for WS267 release

[0.6.1] - 2018-08-23

  • Small changes
  • first release for WS266

[0.6.0] - 2018-07-05

  • Adding endpoints for interaction widgets
  • Adding detailed disease model table

[0.5.2] - 2018-06-08

  • Fixing issue with variation

[0.5.1] - 2018-05-16

  • Fixing issue with missing sequence for Fosmids

[0.5.0] - 2018-05-10

  • Adding endpoints for WS264 release

[0.4.1] - 2018-03-07 - Hotfix

  • Fixing 500 errors for gene page expression widget

[0.4.0] - 2018-02-24

  • first release with autoscaling
  • several new urls added

[0.3.9] - 2018-01-26 - Hotfix

  • Commenting out lineage widget - causing d2c to crash
  • Fixing issue with rnai overview widget from laboratory pack-obj bug

[0.3.8] - 2018-01-26

  • fixed 500 errors from pcr_oligo page

[0.3.7] - 2018-01-26

  • fixed 500 was till persisting final fix
  • adding merged into data for variation overview widget

[0.3.6] - 2018-01-26

  • fixed 500 error on variation/locations widgets where variations were merged

[0.3.5] - 2018-01-26

  • fixed 500 error on gene-class/overview widget

[0.3.4] - 2018-01-09

  • make idempotent

[0.3.3] - 2018-01-09

  • Tested and fixed nginx configuration file

[0.3.2] - 2018-01-09

  • Fixing location of nginx configuration file

[0.3.1] - 2018-01-09

  • Adding in extened-proxy-timout.config for EB

[0.3.0] - 2018-01-09

  • Added a significant number of enpoints for WS262 release

[0.2.4] - 2017-11-03

  • changing JVM and datomic memory settings

[0.2.3] - 2017-10-25

  • uncommenting phenotype variation widget

[0.2.2] - 2017-10-23

  • Adding phenotype widgets
  • Adding association widgets
  • Adding expresion cluster widgets
  • Adding some other ones as well

[0.2.1] - 2017-09-13

  • Fix for rearrangement overview widget 500 error

[0.2.0] - 2017-08-16

  • 11 more overview widgets
  • all location widgets

[0.1.8] - 2017-07-25

  • Fix bug in utility functions that affects links to papers
  • Fix bug in expression widget image display

[0.1.7] - 2017-07-05

  • Minor Bug fixes

[0.1.6] - 2017-06-19

  • Includes fixes by Matt for the gene interaction widget
  • commenting out the person widget

[0.1.5] - 2017-06-11

  • Half of the Overview widgets
  • Gene pages Disease widget
  • Ontology widgets

[0.1.4] - 2017-05-31

  • Gene interactions widget.
  • Phenotype widgets

[0.1.3] - 2017-03-31

  • Gene page widgets added: sequences, expression, phenotype-graph, reagents and location.
  • Person page widgets added: laboratory, overview, publications, tracking.
  • All exteranla links.

[0.1.2] - 2017-02-07

  • swagger UI will now display validator badge.

[0.1.1] - 2017-02-01

  • Split up code into new structure.
  • Refactored (compojure-api) routing code.
  • Sort swagger API endpoint listings.
  • Removed unused code.
  • Code QA with lein eastwood.

[0.1.0] - 2017-01-29

  • New routing using compojure-api
  • Automated API listing using swagger (compojure-api)

[0.0.15] - 2017-01-25

  • Added env variable to eb config.

[0.0.14] - 2017-01-25

  • upgrade-to-datomic-0.9.5554
  • Fix-require-widgets-for-side-effects
  • Added sequence feature widget
  • Added gene ontology widget

[0.0.1] - 2016-07-26

  • Externals links URL for the gene page