Improve code logic and add fetch genome by ensembl and assembly name

[bilalebi]

JIRA Ticket

https://www.ebi.ac.uk/panda/jira/browse/EA-1090

Changes

Added the possibility to fetch genome by ensembl_name and assembly_name (genebuild_id will be added in the future)

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Update:

Major changes

• Added fetch genome by ensembl name and assembly name
• Remove mutual exclusivity in fetch_genomes() and fetch_sequences()
• Improved fetch_taxonomy_names() to include ncbi_common_name, alternative_names and common_name
• Improved fetch_sequences() to include assembly_uuid
• Added fetch_genome_by_keyword()
• Added and fixed broken tests
• Improved the overall code logic
• Added the possibility to fetch unreleased genomes
• ...

This branch is also used to update the API to be used by ensembl-metadata-service

Related PR:

Ensembl/ensembl-metadata-service#25

[bilalebi]

Thanks @dpopleton for your suggestions, I pushed the required changes

[bilalebi]

Hi @vinay-ebi
Please feel free to take a look at this PR, some of the major changes:

• Added fetch genome by ensembl name and assembly name
• Remove mutual exclusivity in fetch_genomes() and fetch_sequences()
• Improved fetch_taxonomy_names() to include ncbi_common_name, alternative_names and common_name
• Improved fetch_sequences() to include assembly_uuid
• Added fetch_genome_by_keyword()
• Added and fixed broken tests
• Improved the overall code logic
• Added the possibility to fetch unreleased genomes
• ...

NB: I commented 3 out of 4 tests in the updater because they were failing and they need to be fixed based on the changes @dpopleton made in this PR #32 that can be done later

[vinay-ebi]

Hi @vinay-ebi Please feel free to take a look at this PR, some of the major changes:

• Added fetch genome by ensembl name and assembly name
• Remove mutual exclusivity in fetch_genomes() and fetch_sequences()
• Improved fetch_taxonomy_names() to include ncbi_common_name, alternative_names and common_name
• Added fetch_genome_by_keyword()
• Added and fixed broken tests
• Added __repr__ functions in the models
• Improved the overall code logic

NB: I commented 3 out of 4 tests in the updater because they were failing and they need to be fixed based on the changes @dpopleton made in this PR #32 that can be done later

Hi @bilalebi , changes look good to me, let @dpopleton have the final look

[dpopleton]

So a few minor comments. It looks good for the most part. I have not tested it further or checked for conflicts , so I hope you have. :)

All recommendations implemented as requested