clinvar-this 0.18.5

ClinVar Submission via API Made Easy

ClinVar This!

ClinVar Submission via API Made Easy

• Free software: MIT license
• Documentation: https://clinvar-this.readthedocs.io/en/latest/
• Discussion Forum: https://github.com/bihealth/clinvar-this/discussions
• Bug Reports: https://github.com/bihealth/clinvar-this/issues

Getting Started

Documentation

You can find comprehensive documentation here:

• https://clinvar-this.readthedocs.io/en/latest/

A good place to start is:

• "Getting Started" in the documentation

Changelog

0.18.5 (2025-02-28)

Bug Fixes

• downgrade xmltodict to v0.13 because of memory leak regression (#290) (ddddef2)

0.18.4 (2025-02-28)

Bug Fixes

• deal with undefined XRef (#288) (9745f36)

0.18.3 (2024-10-22)

Bug Fixes

• make _uuid4_if_falsy always return str (#272) (038a22e)

0.18.2 (2024-09-07)

Bug Fixes

• adding .pyi files (#261) (a1ae5cb)

0.18.1 (2024-09-07)

Bug Fixes

• losen lower protobuf dependency version (#259) (b963510)

0.18.0 (2024-09-06)

Features

• extract-vars writes thinned-out SCV infos (#240) (#258) (19ecf18)
• xml-to-json can now left-shift variants (#255) (#256) (66671cd)

0.17.1 (2024-07-01)

Bug Fixes

• namespaced string issue from 2207-07-01 (#241) (ab85be8)

0.17.0 (2024-06-07)

⚠ BREAKING CHANGES

• adjust ClinVar XML parsing to cardinality fixes (#233) (#234)

Bug Fixes

• adjust ClinVar XML parsing to cardinality fixes (#233) (#234) (119ab42)

0.16.0 (2024-05-31)

Features

• make compatible with 2024 March 1 schema of ClinVar (#222) (#223) (a7480dd)
• make compatible with 2024 May 15 schema of ClinVar (#221) (#229) (c0d1a4c)

0.15.5 (2024-05-29)

Bug Fixes

• refined (thinned out) extraction of variants (#219) (dc9652c)

0.15.4 (2024-05-28)

Bug Fixes

• quotes in gene-impact report (#217) (e10d4ef)

0.15.3 (2024-05-28)

Bug Fixes

• per-gene report also includes other impact (#216) (4b27718)

Documentation

• more API documentation (#214) (41fc92a)

0.15.2 (2024-05-28)

Bug Fixes

• release as v0.15.2 (#212) (23eb2dc)

0.15.1 (2024-05-28)

Bug Fixes

• properly configure release-please with manifest (#210) (25973e7)

0.15.0 (2024-05-28)

⚠ BREAKING CHANGES

• adjusting to new XML structure with germline/somatic split (#201)

Features

• adjusting to new XML structure with germline/somatic split (#201) (85652be)

0.14.6 (2023-12-15)

Bug Fixes

• include JSON schemas in package (#184) (c3dc65a)

0.14.5 (2023-12-13)

Bug Fixes

• fixing MANIFEST.in for so py.typed are included (#182) (3015b32)

0.14.4 (2023-12-13)

Bug Fixes

• adding missing py.typed files for mypy (#180) (3b5945a)

0.14.3 (2023-12-12)

Bug Fixes

• fixing counter types (#178) (0b23c6b)

0.14.2 (2023-12-12)

Bug Fixes

• resolve dictionary dump enum issue (#176) (a6a6c20)

0.14.1 (2023-12-11)

Bug Fixes

• serialization of counter dict (#174) (06caa81)

0.14.0 (2023-12-11)

Features

• adding async client code via switch to httpx (#167) (#170) (7b76770)
• switch from attrs to pydantic (#166) (#168) (d84db77)
• updating to latest upstream JSON schemas (#173) (f5da1fc)
• write out RCV/VCV version in extract_vars and phenotype_link (#159) (#172) (534cba1)

Bug Fixes

• adding support for "no classification from unflagged records" review status (#171) (f144e74)

0.13.1 (2023-12-04)

Bug Fixes

• pinning python to 3.11 in release for setuptools (#164) (afb6035)

0.13.0 (2023-12-04)

Features

• adapt to ClinVar public XML update (#162) (8d90a36)

0.12.0 (2023-10-18)

Features

• include VCV and title in "clinvar-data extract-vars" (#152) (c3e1bf2)

0.11.0 (2023-10-06)

Features

• Adding Clinvar Accession to TSV input (#146) (1ef8b8f)
• Implement Pubmed IDs in tsv import format (#143) (9473380)
• Support multiple condition types and multiple conditions (#147) (f972356)

Bug Fixes

• mypy linting of tests (#144) (ee1fc5d)

Documentation

• Update docs on file formats and fixing errors (#150) (0b9efc6)

0.10.2 (2023-09-11)

Bug Fixes

• typo accession => accession (#135) (9ac72a2)

0.10.1 (2023-09-11)

Bug Fixes

• properly write out variants to JSONL (#133) (17b7e5c)

0.10.0 (2023-09-08)

Features

• write out HGNC identifier with variants (#130) (#131) (ea33100)

0.9.0 (2023-09-08)

Features

• write assessment to extract variants (#128) (dd72c90)

Bug Fixes

• normalizing molecular consequence (#126) (c2a72cf)

0.8.0 (2023-09-08)

Features

• variant extraction (#124) (c7bb7c9)

0.7.0 (2023-09-07)

Features

• writing out clinical significance in gene-to-phenotype link (#121) (1c65fc6)

0.6.0 (2023-09-07)

Features

• write out organisation and local key to phenotype gene link (#119) (f87facc)

0.5.0 (2023-09-07)

Features

• allow read/write .gz everywhere (#116) (d3b658e)

0.4.1 (2023-09-06)

Bug Fixes

• adding clinvar_data to built package (#114) (4a78256)

0.4.0 (2023-09-06)

Features

• add command to extract gene-to-phenotype links (#104) (#106) (b3b323a)
• adding --version option (#110) (7f3b091)
• adding command to generate per-gene impact report (#102) (#103) (c86a5c7)
• adding missing clinvar measure set (#109) (f0f64e0)
• adding support for parsing ClinVar XML (#99) (#100) (c673f7d)
• command to extract variants per ACMG class and freq. (#107) (#108) (c623f6d)

Bug Fixes

• making conversion more robust, indicate errors (#105) (8333aea)

0.3.0 (2023-09-04)

Features

• removing versioneer in favour of version from release-please (#95) (5b922bb)

Bug Fixes

• using varfish-bot token for release-please (#97) (35fad52)

0.2.1 (2023-03-17)

Bug Fixes

• fixing strucvar export (#84) (1050a67)
• sequence variant export (#82) (0fe3fb9)

0.2.0 (2023-03-15)

Features

• add support for SV TSV files (#75) (#78) (d4fffce)

Documentation

• add badges to readme (#65) (207038c)
• adding file format documentation (#71) (3a04ffd)
• extending docs; getting started from README (#44) (#68) (77892f0)
• updating docs introduction section (#67) (d6c865b)

0.1.0 (2022-12-02)

Features

• add basic config management in CLI (#32) (#33) (c903546)
• add functions for managing batch data (#34, #37) (#35) (0c7e0f9)
• add sphinx-based documentation (#30) (#31) (d10adc5)
• add tests for submission messages (#19) (#22) (b168d47)
• add unit tests for submission messages (#19) (#20) (1c4e11a)
• adding mypy type checking (#11) (#12) (700994a)
• adjust to ClinVar API change (Nov 2022) (#47) (#48) (0e4fb50)
• allow annotation with HPO terms in TSV format (#50) (#56) (0b0da41)
• allow import of extra columns (#53) (#54) (616bfe7)
• completing enums (#23) (#24) (9198983)
• implement api models (#4) (#5) (3690c36)
• implement attrs-based message models (#1) (#2) (f253c24)
• implement enums for submission messages (#14) (#16) (201cbe4)
• implement internal models for submissions (#9) (#26) (be04e40)
• implement minimal TSV format (#17) (#18) (960827d)
• implement models for extra files (#6) (#13) (852e4c6)
• implement models for submission message (#8) (#15) (90afd10)
• implement more columns in TSV (#39) (#55) (6184d76)
• implementing REST clinvar_api.client module (#28) (#29) (829d907)
• store errors from "batch retrieve" (#59) (#60) (67b8b0c)
• write data into profile sub directory (#52) (e699736)

Bug Fixes

• interpret TSV OMIM "not provided" (#57) (#58) (b655097)

Documentation

• add getting started tutorial to README (#45) (#61) (3de084b)