Skip to content

fetch multiple genomes with in operator #28

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jun 14, 2023
Merged

fetch multiple genomes with in operator #28

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions src/ensembl/production/metadata/api/genome.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -126,19 +126,19 @@ def fetch_genomes(self, genome_id=None, genome_uuid=None, assembly_accession=Non
# These options are in order of decreasing specificity,
# and thus the ones later in the list can be redundant.
if genome_id is not None:
genome_select = genome_select.filter(Genome.genome_id == genome_id)
genome_select = genome_select.filter(Genome.genome_id.in_(genome_id))

elif genome_uuid is not None:
genome_select = genome_select.filter(Genome.genome_uuid == genome_uuid)
genome_select = genome_select.filter(Genome.genome_uuid.in_(genome_uuid) )

elif assembly_accession is not None:
genome_select = genome_select.filter(Assembly.accession == assembly_accession)
genome_select = genome_select.filter(Assembly.accession.in_(assembly_accession))

elif ensembl_name is not None:
genome_select = genome_select.filter(Organism.ensembl_name == ensembl_name)
genome_select = genome_select.filter(Organism.ensembl_name.in_(ensembl_name))

elif taxonomy_id is not None:
genome_select = genome_select.filter(Organism.taxonomy_id == taxonomy_id)
genome_select = genome_select.filter(Organism.taxonomy_id.in_(taxonomy_id))

with self.metadata_db.session_scope() as session:
session.expire_on_commit = False
Expand Down Expand Up @@ -275,13 +275,13 @@ def fetch_genome_datasets(self, genome_id=None, genome_uuid=None, unreleased_dat
dataset_source = check_parameter(dataset_source)

if genome_id is not None:
genome_select = genome_select.filter(Genome.genome_id == genome_id)
genome_select = genome_select.filter(Genome.genome_id.in_(genome_id))

if genome_uuid is not None:
genome_select = genome_select.filter(Genome.genome_uuid == genome_uuid)
genome_select = genome_select.filter(Genome.genome_uuid.in_(genome_uuid))

if dataset_uuid is not None:
genome_select = genome_select.filter(Dataset.dataset_uuid == dataset_uuid)
genome_select = genome_select.filter(Dataset.dataset_uuid.in_(dataset_uuid))

if unreleased_datasets:
genome_select = genome_select.filter(GenomeDataset.release_id.is_(None)) \
Expand Down