Skip to content

Commit

Permalink
Merge 24419b0 into ddafa9d
Browse files Browse the repository at this point in the history
  • Loading branch information
@talavis
talavis committed Aug 5, 2019
2 parents ddafa9d + 24419b0 commit 485f967
Show file tree
Hide file tree
Showing 2 changed files with 29 additions and 28 deletions.
53 changes: 27 additions & 26 deletions backend/modules/browser/lookups.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ def autocomplete(dataset:str, query:str, ds_version:str=None):
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
except AttributeError as err:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err
query = (db.Gene.select(db.Gene.name)
.where(((db.Gene.name.startswith(query)) &
(db.Gene.reference_set == ref_set))))
Expand Down Expand Up @@ -220,9 +220,9 @@ def get_exons_in_transcript(dataset:str, transcript_id:str, ds_version=None):
.where((db.Transcript.transcript_id == transcript_id) &
(db.Gene.reference_set == ref_set))
.get())
except db.Transcript.DoesNotExist:
except db.Transcript.DoesNotExist as err:
logging.info('get_exons_in_transcript({}, {}): unable to retrieve transcript'.format(dataset, transcript_id))
raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data.')
raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data.') from err
wanted_types = ('CDS', 'UTR', 'exon')
features = sorted(list(db.Feature.select().where((db.Feature.transcript == transcript) &
(db.Feature.feature_type in wanted_types)).dicts()),
Expand All @@ -247,14 +247,14 @@ def get_gene(dataset:str, gene_id:str, ds_version:str=None):
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
except AttributeError as err:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err

try:
return db.Gene.select().where((db.Gene.gene_id == gene_id) &
(db.Gene.reference_set == ref_set)).dicts().get()
except db.Gene.DoesNotExist:
raise error.NotFoundError(f'Gene {gene_id} not found in reference data.')
except db.Gene.DoesNotExist as err:
raise error.NotFoundError(f'Gene {gene_id} not found in reference data.') from err


def get_gene_by_dbid(gene_dbid:str):
Expand Down Expand Up @@ -291,8 +291,8 @@ def get_gene_by_name(dataset:str, gene_name:str, ds_version=None):
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
except AttributeError as err:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err

try:
return (db.Gene.select()
Expand All @@ -308,9 +308,9 @@ def get_gene_by_name(dataset:str, gene_name:str, ds_version=None):
(db.Gene.reference_set == ref_set))
.dicts()
.get())
except db.GeneOtherNames.DoesNotExist:
except db.GeneOtherNames.DoesNotExist as err:
logging.info('get_gene_by_name({}, {}): unable to retrieve gene'.format(dataset, gene_name))
raise error.NotFoundError(f'Gene {gene_name} not found in reference data')
raise error.NotFoundError(f'Gene {gene_name} not found in reference data') from err


def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_version:str=None):
Expand All @@ -330,8 +330,8 @@ def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
except AttributeError as err:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err

genes = db.Gene.select().where((db.Gene.reference_set == ref_set) &
(db.Gene.start <= stop_pos) &
Expand Down Expand Up @@ -381,10 +381,10 @@ def get_raw_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_versio
.where(db.VariantTranscripts.variant == variant['id'])
.dicts()]
return variant
except db.Variant.DoesNotExist:
except db.Variant.DoesNotExist as err:
logging.info('get_raw_variant({}, {}, {}, {}, {}, {}): unable to retrieve variant'
.format(dataset, pos, chrom, ref, alt, dataset_version.id))
raise error.NotFoundError(f'Variant {chrom}-{pos}-{ref}-{alt} not found')
raise error.NotFoundError(f'Variant {chrom}-{pos}-{ref}-{alt} not found') from err


def get_transcript(dataset:str, transcript_id:str, ds_version:str=None):
Expand All @@ -404,8 +404,8 @@ def get_transcript(dataset:str, transcript_id:str, ds_version:str=None):
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
except AttributeError as err:
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err
try:
transcript = (db.Transcript
.select(db.Transcript, db.Gene.gene_id)
Expand All @@ -416,9 +416,9 @@ def get_transcript(dataset:str, transcript_id:str, ds_version:str=None):
.get())
transcript['exons'] = get_exons_in_transcript(dataset, transcript_id)
return transcript
except db.Transcript.DoesNotExist:
except db.Transcript.DoesNotExist as err:
logging.info('get_transcript({}, {}): unable to retrieve transcript'.format(dataset, transcript_id))
raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data')
raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data') from err


def get_transcripts_in_gene(dataset:str, gene_id:str, ds_version:str=None):
Expand All @@ -436,16 +436,16 @@ def get_transcripts_in_gene(dataset:str, gene_id:str, ds_version:str=None):
"""
try:
ref_set = db.get_dataset_version(dataset, ds_version).reference_set
except AttributeError:
except AttributeError as err:
logging.warning('get_transcripts_in_gene({}, {}): unable to get referenceset dbid'.format(dataset, gene_id))
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.')
raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err

try:
gene = db.Gene.select().where((db.Gene.reference_set == ref_set) &
(db.Gene.gene_id == gene_id)).dicts().get()
except db.Gene.DoesNotExist:
except db.Gene.DoesNotExist as err:
logging.info('get_transcripts_in_gene({}, {}): unable to retrieve gene'.format(dataset, gene_id))
raise error.NotFoundError(f'Gene {gene_id} not found in reference data')
raise error.NotFoundError(f'Gene {gene_id} not found in reference data') from err

return [transcript for transcript in db.Transcript.select().where(db.Transcript.gene == gene['id']).dicts()]

Expand Down Expand Up @@ -510,9 +510,10 @@ def get_variants_by_rsid(dataset:str, rsid:str, ds_version:str=None):

try:
rsid = int(rsid.lstrip('rs'))
except ValueError:
except ValueError as err:
logging.error('get_variants_by_rsid({}, {}): not an integer after rs'.format(dataset, rsid))
raise error.ParsingError('Not an integer after rs')
raise error.ParsingError('Not an integer after rs') from err

variants = (db.Variant
.select()
.where((db.Variant.rsid == rsid) &
Expand Down
4 changes: 2 additions & 2 deletions backend/modules/browser/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -464,8 +464,8 @@ def parse_region(region:str):
try:
start = int(start)
stop = int(stop)
except ValueError:
raise error.ParsingError(f'Unable to parse region {region} (positions not integers).')
except ValueError as err:
raise error.ParsingError(f'Unable to parse region {region} (positions not integers).') from err

return chrom, start, stop

Expand Down

0 comments on commit 485f967

Please sign in to comment.