Skip to content

CHANGELOG.md

Latest commit

 

History

History
270 lines (148 loc) · 5.23 KB

CHANGELOG.md

File metadata and controls

270 lines (148 loc) · 5.23 KB

Changelog for ebi_eva_common_pyutils

0.8.4 (unreleased)

  • Nothing changed yet.

0.8.3 (2026-02-19)

  • Add option to limit assembly and sequence to genbank

0.8.2 (2026-02-05)

  • Add property for QC duplicate SS acc in accessioning pipeline properties

0.8.1 (2026-02-04)

  • Remove hard-coded accessioning job name from Spring properties generator
  • Set default readPreference to "primary" for accessioning properties

0.8.0 (2025-12-19)

  • Remove internal Nextflow classes
  • Handle ENA errors when detecting patch assembly

0.7.4 (2025-08-07)

  • Prevent multiple configs from sharing the same content
  • Update biosamples communicator to not retry 404s

0.7.3 (2025-06-19)

  • Fix requirement.txt inclusion

0.7.2 (2025-06-19)

  • Enable overwrite on existing config path.
  • Update lxml

0.7.1 (2025-05-21)

  • Make sure all loggers are debug by default

0.7.0 (2025-04-14)

  • Deprecate the AAP Authentication method

0.6.17 (2025-03-28)

  • Fix the spreadsheet module

0.6.16 (2025-03-28)

  • New function to get the version of the EVA metadata template

0.6.15 (2025-03-26)

  • Change the scientific name retrieval to first check in Ensembl then NCBI

0.6.14 (2025-03-05)

  • Bugfix for connection string

0.6.13 (2025-03-05)

  • Update spring properties to use mongo connection string with retryWrites=true

0.6.12 (2025-01-21)

  • Added new properties in clustering job to run clustering qc duplicate rs accession job

0.6.11 (2024-11-15)

  • Added hikari max-pool-size connection property to the method that generate property for spring jobs

0.6.10 (2024-08-06)

  • Allow text to be returned from biosamples communicators

0.6.9 (2024-07-29)

  • Add get methods to Contig alias client

0.6.8 (2024-07-12)

  • Add biosamples communicators

0.6.7 (2024-05-15)

  • Remove the instance id and add required dummy cutoff day for accessioning and clustering

0.6.6 (2024-04-15)

  • Allow NCBI function ot use API key

0.6.5 (2024-04-02)

  • Ensure that the port forwarding command is running before returning the process.

0.6.4 (2024-03-21)

  • Update Mongodb client to use mongosh instead of the legacy mongo.

0.6.3 (2024-02-22)

  • Variable log level when running a command

0.6.2 (2023-10-30)

  • Resolve patch assemblies to proper assembly code. See here.

0.6.1 (2023-10-09)

  • Added functionality to update config (Writable Config)

0.6.0 (2023-10-05)

  • Refactor to separate functions made for internal EVA use
  • Check Ensembl rapid release for supported assemblies
  • Scientific name fixes

0.5.7 (2023-08-21)

  • Metadata: use scientific name when no common name is available

0.5.6 (2023-06-26)

  • Fix log duplication in stdout
  • SpringProperties generation: Support release automation and provide empty mongo username/password when missing

0.5.5 (2023-06-02)

  • Include multiple mongos hosts during Spring properties generation

0.5.4 (2023-05-22)

  • Add job tracker properties to accession import job

0.5.3 (2023-05-07)

  • Add spring properties generation option for variant load and accession import jobs

0.5.2 (2023-03-03)

  • Add new spring properties generation options

0.5.1 (2022-12-21)

  • Script to archive directories
  • Get accession database from settings in properties generator

0.5 (2022-11-15)

  • Client for contig alias API
  • Default read/write concerns for mongo clients
  • Utilities for printing tables, generating properties files, scientific names

0.4 (2022-10-04)

  • New functions to create assemblies in the metadata databases

0.3.22 (2022-07-27)

  • New option in Nextflow.join_pipeline to keep the two pipeline independent

0.3.21 (2022-05-27)

  • New function to retrieve contig alias credentials.
  • New functions to search NCBI taxonomy info

0.3.20 (2022-01-26)

  • New function to get count service credentials from maven profile.

0.3.19 (2022-01-14)

  • New function to add File handler to the logging configuration.

0.3.18 (2021-10-07)

  • Bugfix in retrieval of assembly/taxonomy code.

v0.3.17 (2021-09-28)

  • New function to retrieve the variant warehouse database name even if it does not exist already

v0.3.16 (2021-08-06)

  • Add function to normalise species scientific name

v0.3.15 (2021-07-09)

  • Refactor & add functionality for accessing database credentials.