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CHANGELOG.md

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Changelog for ebi_eva_common_pyutils

0.6.11 (unreleased)

  • Nothing changed yet.

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.