Skip to content

Minor Fix for taxid scope #82

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 4 commits into from
Mar 22, 2024
Merged

Minor Fix for taxid scope #82

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f027907
Minor Fix for taxid scope
dpopleton Mar 20, 2024
c8ac2b6
Bugfix for new_homology
dpopleton Mar 21, 2024
3fd7dd6
fixed tests
dpopleton Mar 21, 2024
3d69fdc
Added fix for common name
dpopleton Mar 22, 2024
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
8 changes: 4 additions & 4 deletions src/ensembl/production/metadata/updater/core.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -290,8 +290,8 @@ def get_or_new_organism(self, species_id, meta_session):

# Getting the common name from the meta table, otherwise we grab it from ncbi.
common_name = self.get_meta_single_meta_key(species_id, "species.common_name")
if common_name is None:
taxid = self.get_meta_single_meta_key(species_id, "species.taxonomy_id")
taxid = self.get_meta_single_meta_key(species_id, "species.taxonomy_id")
if common_name is None or common_name == "":

with self.taxonomy_db.session_scope() as session:
common_name = session.query(NCBITaxaName).filter(
Expand Down Expand Up @@ -585,9 +585,9 @@ def get_or_new_genebuild(self, species_id, meta_session, source=None, existing=F
def new_homology(self, meta_session, species_id, genome=None, source=None, dataset_attributes=None, version="1.0"):
if source is None:
production_name = self.get_meta_single_meta_key(species_id, "species.production_name")
db_version = self.get_meta_single_meta_key(species_id, "schema_version")
db_version = self.get_meta_single_meta_key(None, "schema_version")
compara_name = production_name + "_compara_" + db_version
dataset_source = self.get_or_new_source(meta_session, "compara", name="compara_name")
dataset_source = self.get_or_new_source(meta_session, "compara", name=compara_name)
else:
dataset_source = source
dataset_type = meta_session.query(DatasetType).filter(DatasetType.name == "homologies").first()
Expand Down
2 changes: 1 addition & 1 deletion src/tests/databases/core_1/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,4 @@
23 1 genebuild.provider_name test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 assembly.alt_accession GCA_0000012345.3
26 1 schema_version 110
26 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_2/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,4 @@
21 1 genome.genome_uuid test
23 1 genebuild.provider_name test2
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_3/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,4 @@
20 1 strain.type test
23 1 genebuild.provider_name test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_4/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,4 @@
20 1 strain.type test
23 1 genebuild.provider_name test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_5/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,4 @@
20 1 strain.type test
23 1 genebuild.provider_name removed_for_test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_6/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,4 @@
21 1 genome.genome_uuid 90720316-006c-470b-a7dd-82d28f952264
23 1 genebuild.provider_name test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_7/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,5 +21,5 @@
23 1 genebuild.provider_name testfornamenew
24 1 genebuild.start_date 2023-08-Ensembl
25 1 genebuild.havana_datafreeze_date test2
26 1 schema_version 110
26 \N schema_version 110
27 1 assembly.total_coding_sequence_length 8989
2 changes: 1 addition & 1 deletion src/tests/databases/core_8/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,4 @@
20 1 strain.type test
23 1 genebuild.provider_name test
24 1 genebuild.start_date 2023-07-Ensembl
25 1 schema_version 110
25 \N schema_version 110
2 changes: 1 addition & 1 deletion src/tests/databases/core_9/meta.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,4 +22,4 @@
24 1 genebuild.havana_datafreeze_date test2
25 1 assembly.total_genome_length 546
26 1 genebuild.start_date 2023-07-Ensembl
27 1 schema_version 110
27 \N schema_version 110