https://github.com/bihealth/reev - v0.6.0

0.6.0 (2024-02-08)

Features

• bump rfl to fix strucvar parsing (#434) (#437) (715f05c)
• bump rfl to integrate plotly-based clinvar landscape (#430) (#436) (6194541)
• Change API status code for nor found ACMG ratings (#388) (#419) (ab294cd)
• Change API status code for not found bookmarks (#387) (#418) (9229358)
• Cleanup module Declarations (#458) (#459) (0f22245)
• Improvements in Literature highlighting (#427) (#431) (2d64ddb)
• integrate reev-frontend-lib as git submodule (#412) (#435) (28bc7f2)
• make home page work on mobile (360x800) resolution (#304) (#457) (23109be)
• make left-side navigation bar sticky (#439) (#441) (f25548e)

Bug Fixes

• bump rfl for gene-clinvar plot coloring (#445) (#449) (9765fe2)
• bump rfl to display correct MMSplice score (#444) (#452) (ecefe37)
• bump rfl to fix non-coding splice display (#446) (#451) (c5dd0f1)
• bump rfl to remove issue with sequenceInfo store (#447) (#450) (1d15de5)
• Fix initial superuser setup (#460) (#461) (98e6d91)
• fixing InterVar display issues after lookup failure (#443) (#448) (fec70e3)
• preventing infinite loop in ACMG predictions (#453) (212cfaf)
• resolving issues with caseInfo storage and API (#454) (#456) (2f3ea9d)

- TypeScript
Published by varfish-bot over 2 years ago

https://github.com/bihealth/reev - v0.5.0

0.5.0 (2024-02-02)

Features

• Add sorting to PanelApp (#397) (#409) (2ebdcc8)
• cleanup front-end tests (#355) (#363) (161da9e)
• Disable "server" buttons for anonymous users (#391) (#392) (bfabd6e)
• enable user feedback after fixing it on the server (#358) (a6c436f)
• Frontest test cleanup (#364) (#382) (15a565d)
• improved validation for writing bookmarks etc. (#365) (#367) (d6e0413)
• integrate AlphaMissense display in scores (#375) (385b584)
• integrate new gnomAD v4 data (#374) (fdaa808)
• integrate PanelApp in gene details card (#373) (c7c7ea8)
• Literature higlight in dark mode (#407) (#415) (2ec6845)
• more robust backend code and cleanup in tests (#354) (#356) (5306196)
• Provide linkouts for PanelApps (#408) (#414) (57f6938)
• Rounded corners for Vega plots (#394, #405) (#406) (84dfd86)
• use integrated gene-wise conditions data from annonars (#389) (#390) (7e377c9)
• Use Seqvar and LinearStrucvar whenever possible (#366) (#378) (c35ae0f)
• using links for home view examples (#349) (#353) (e0e73ee)

Bug Fixes

• ACMG criteria can not be saved to the server (#379) (#386) (8359dff)
• Adjust colors of highlightings in dark mode (#393) (#402) (5329a6b)
• adjusting VariantValidator API (#292) (#376) (63b9275)
• Expantion of MMSplice and SpliceAI scores properly handle Infinity scores (#381) (#383) (8e3efc1)
• Loading the ACMG criteria from intervar (#384) (0fefba5)
• make PDF documentation build and remove some WIP docs (#368) (#423) (c6b17f3)
• more robust handling of async sessions (#360) (#361) (86510e8)
• more robust handling of InterVar result (#362) (25c825f)
• properly handle undefined pubtator abstracts (#359) (970b400)
• Replace acmgSf data with hgnc one in PanelApp (#416) (#417) (d308661)
• resolve issues with example links on home view (#350) (#351) (714bcea)

- TypeScript
Published by varfish-bot over 2 years ago

https://github.com/bihealth/reev - v0.4.0

0.4.0 (2023-12-27)

Features

• deprecation warning for PP3strong + PM1strong (#324) (#341) (09129ae)
• enable Sentry user feedback (#343) (f4af00d)
• improve HPO lookup result quality with latest viguno (#338) (#346) (84d2c7b)
• integrate with PubTator 3 API (#312) (#347) (096cc85)

Bug Fixes

• properly display MANE transcripts (#293) (#348) (7eb5085)

Reverts

• disable sentry feedback again (#344) (50129d6)

Documentation

• documenting ClinVar submission feature (#334) (#345) (0bdeba6)

- TypeScript
Published by varfish-bot over 2 years ago

https://github.com/bihealth/reev - v0.3.0

0.3.0 (2023-12-22)

Features

• add conflict display between PVS1 and PM4/PP3 (#290) (#320) (223d904)
• additional Jump to IGV button (#297) (#299) (38c5668)
• adjust landing and static pages to NAR WSI requirements (#303) (#306) (39aad72)
• allow storing case information in local storage (#247) (#339) (bec6084)
• Allow users to save acmg criteria on the server (#98) (#237) (8738ca4)
• change default presentation of ACMG criteria (#287) (#300) (454135f)
• Consistency in UI design on static pages (#219) (#283) (2bafecb)
• Display all MMSplice and SpliceAI Scores (#296) (#310) (2ebb15b)
• document acmg seq vars (#248) (#249) (ae73ca7)
• enable sentry user feedback and releases (#329) (#331) (8be007c)
• implementing ClinVar upload (#99) (#270) (d4d949e)
• Integrate cada prio web service (#213) (#220) (283209f)
• integrating sentry (#240) (#246) (732cff6)
• link out from app to documentation (#308) (#311) (bb630a0)
• Merge all static information pages into one view (#263) (#264) (61bab0b)
• more consistent UI design on gene details page (#216) (#278) (52c8a45)
• more consistent UI design on seqvar details page (#217) (#279) (b040108)
• more consistent UI design on strucvar details page (#218) (#280) (b5330af)
• more integrated search component (#258) (120128f)
• more streamlined query parsing (#257) (#259) (374377a)
• Move scores card above population frequencies card (#294) (#301) (2db9647)
• Refurbishing design of Profile page (#214) (#256) (61a59d3)
• refurbishing gene details page (#229) (#230) (40daa26)
• refurbishing sequence variant details page (#244) (#255) (8f67c86)
• refurbishing SV details page (#236) (#239) (0d8dd34)
• restrict upgrade/downgrade of AMCG seqvar criteria (#291) (#321) (fabc262)
• updating profile to comply with OrcID requirements (#225) (#226) (23053f3)

Bug Fixes

• adjusting front-end to latest annonars changes (#224) (#228) (ce8ab52)
• Drop PP5 and BP6 criteria (#289) (#319) (a328f3a)
• fix blipping seqvar ACMG card (#266) (#269) (aa186c3)
• make clinvar impact table more robust, ignore labels (#234) (d3df9d7)
• make gray backround also work with dark theme (#276) (#282) (2b161f7)
• make querying for HGNC ID go to the gene (#327) (#333) (e73cf71)
• Make seqvar ACMG criterias upper case (#288) (#317) (0bfd3c0)
• make UI consistent on homepage (#215) (#277) (f81a48f)
• message when SpliceAI prediction unavailable (#268) (c2516e0)
• OMIM id extraction for link-out (#260) (#267) (f394b00)
• Present hpo terms on seqvar page (#286) (#298) (a61b57e)
• properly handle anonymous sessions in clinvarsub card (#328) (#335) (a61f864)
• properly handler errors / empty results from InterVar (#322) (#336) (6782a4f)
• properly urlencode arguments to dotty API call (#323) (#325) (699c654)
• Support for low-res displays (#285) (#295) (bdf7583)
• using text-no-wrap on ClinvarImpact table (#233) (e7cbaa7)
• vega plot background colors in dark mode (#284) (#337) (cb0cac1)

Documentation

• Documentation of tutorial (#305) (3bc8312)
• filling the application's manual (#309) (#315) (c21e888)
• initial version of quickstart tutorial (#274) (#275) (51c6d4f)

- TypeScript
Published by varfish-bot over 2 years ago

https://github.com/bihealth/reev - v0.2.0

0.2.0 (2023-11-15)

Features

• Allow user to store case information with their account (#94, #179) (#178) (3301d74)
• Allow users to bookmark variants and genes (#95) (#173) (162ae13)
• Case specific data functionality (#93) (#175) (247d9b1)
• implement user email verification workflow (#177) (#184) (27c7d98)
• Integration of Matomo (#43) (#180) (0bf5869)
• Switch to vuetify cards for ui (#165) (#171) (a7e2853)
• towards complete integration of OrcID setup (#96) (#176) (3bef5e9)
• Update Info in About (#209) (#210) (0ff3d21)

Bug Fixes

• Allow dynamically load components (#181) (#192) (15c6007)
• Close db connection on startup (#205) (#211) (e8ed6be)
• Close db connection on startup (#205) (#212) (1c2b913)
• Docker build (#191) (2d8a218)
• Docs are rendered properly (#201) (#202) (2119aa6)
• Documentation of APIs (#201) (#206) (fe56f4a)
• Fix documentation in production (#201) (#207) (6973d0e)
• Jinja2 in PIpfile (#204) (e97a151)
• Matomo records (#187) (69ca50c)
• Path in docs (#208) (c12088c)
• Proper matomo url (#183) (#186) (9de2ffd)
• Rebuild docker container (#198) (6003f45)
• vue-matomo module declaration (#182) (21f292f)

Documentation

• Add documentation for caseinfo and utils (#199) (#200) (187cba8)
• collect information for seqvar assessment in manual (#188) (#189) (4db354a)
• document database and rule sets for ACMG prediction (#190) (#193) (cae06de)
• explaining implementation of ACMG 2020 CNV assessment (#195) (#196) (a8f2f21)

- TypeScript
Published by varfish-bot over 2 years ago

https://github.com/bihealth/reev - v0.1.0

0.1.0 (2023-10-19)

Features

• Acknowledgements in about view (#42) (#44) (abd439d)
• ACMG rating of sequence/small variants (#54) (#60) (83540c2)
• Adapt ACMG Rating for multiple sources of info (#65) (#66) (54a2d88)
• Add support for commas in numbers in search Queries (#147) (#157) (d241329)
• Add tool for ACMG assessment of CNVs (#59) (#74) (195003b)
• adding support for login with OpenIDC (#50) (#87) (0ed6e19)
• adjust to annonars v0.24.0 clinvar output (#154) (#166) (08c2374)
• catch-all route in FastAPI allows for deep links in prod (#25) (#26) (454f211)
• Change title (#159) (dfbe284)
• Conflicting evidences in ACMG SV criteria (#120) (061e03f)
• Create Acmg Criteria component (#70) (#73) (7c463f1)
• create initial database setup for project (#49) (#80) (863c046)
• create pages for red tape (#156) (#158) (a604845)
• Default Footer implementation (#33) (#35) (ef6549a)
• Finish integration of genome browser (#102) (#104) (a2f8282)
• Gene-wide variation landscape (#67) (#105) (2ce7de2)
• Implement gene search functionality and gene information page (#11) (#14) (644a2d4)
• Implementation of reverse proxies for varfish-docker-compose-ng (#10) (#12) (c3884a4)
• Implementation of search for general entries (#20) (#37) (eb7b907)
• Improve ACMG rating of sequence/small variants (#64) (#63) (507ad2c)
• integrate dotty to allow querying for HGVS variants (#101) (#110) (781f383)
• Integrate new GTEx and clinvar information as done for VarFish (#61) (#62) (d836edb)
• integration of meahri 0.8.0 (#56) (#103) (b2411a6)
• Link-outs in SV detail page (#143) (#155) (17171a7)
• new SearchBar with vuetify Toolbars (#17) (#34) (6043aec)
• proper LS-RI-AAI and OrcID login buttons (#163) (#164) (3fa85f7)
• put the current version into docker image and display (#28) (#29) (586af7e)
• Retrieval of affected genes in SV from mehari (#56) (#107) (d16af74)
• setup initial support for local login (#48) (#82) (afead65)
• SV Details View (#55) (#75) (4681e30)
• Update ACMG criteria for CNVs (#76) (#114) (0b572f6)

Bug Fixes

• Add keydown entry to text-field in search bar (#144) (#148) (65dcbdc)
• Add linkout for genes in SV page (#152) (#153) (bc062d8)
• Add support for large displays (#113) (#128) (555fae4)
• Add type definitions (#68) (#71) (607af69)
• adjust default backend service ports for prod (#27) (655e549)
• Change redirection method in genes entrypoint (#161) (#162) (903aa5f)
• Consequences display (#116) (#129) (d4c5e3f)
• Correctly present CADD missing scores (#125) (#133) (3251722)
• database credential access in Docker build (#90) (2d8f3ca)
• Display 0 instead of Nan (#119) (#130) (80901c4)
• Display of clinvar variants in variation landscape (#118) (#127) (b3ab2b3)
• entrypoint.sh in Docker build (#88) (81bfd43)
• fixes to .python-version, docs, .gitignore (#8) (9cf42a4)
• fixing favicon in production (#31) (f1be9fd)
• genotype calls are removed from SV details page (#142, #150) (#151) (5123958)
• Input assembly arg for dotty (#141) (#145) (f349e39)
• Linkout to UCSC (#121) (#132) (7f9c1e4)
• login URL generation (#91) (044e5f3)
• make OAuth2 work with ORCID (#92) (c069ff5)
• menu links for details page and tests (#160) (ad59e9b)
• Non existing variants are not handled gracefully (#109) (#112) (22b2001)
• Present Clinvar information (#124) (#134) (11bfc24)
• properly setup vite build & backend server (#21) (#22) (5459db5)
• properly setup vite proxy for development (#85) (63ec6ac)
• Remove 1000 suffix in genome browser coordinates (#146) (#149) (a4de33c)
• Revel score for nonsense variant (#126) (#139) (d501d98)
• Search works only from second time (#23, #24) (#30) (4ca6249)
• Update link to variant validator (#122) (#131) (eb971cb)
• Update scores for lollipops clinvar plot (#137) (#138) (bc251d3)
• write git version to VERSION in CI (#32) (0649cfe)

Documentation

• adding alembic-upgrade notes to quickstart (#84) (43779bf)
• adding missing community standards (#5) (#6) (aa0a237)

- TypeScript
Published by varfish-bot over 2 years ago