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fixing dataset bug for collections response #354

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fixing dataset bug for collections response #354

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fbd4454
fixing dataset bug for collections response
costero-e Jul 10, 2024
06f44b8
Merge branch 'master' into develop
costero-e Jul 10, 2024
4132683
api version automatically generated
Jul 10, 2024
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2 changes: 1 addition & 1 deletion beacon/api_version.yml
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
api_version: v2.0-399a0d3
api_version: v2.0-4ee99e2
10 changes: 5 additions & 5 deletions beacon/db/cohorts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ def get_individuals_of_cohort(entry_id: Optional[str], qparams: RequestParams, d
limit = 100
idq="id"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_analyses_of_cohort(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand All @@ -94,7 +94,7 @@ def get_analyses_of_cohort(entry_id: Optional[str], qparams: RequestParams, data
limit = 100
idq="biosampleId"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_variants_of_cohort(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand All @@ -119,7 +119,7 @@ def get_variants_of_cohort(entry_id: Optional[str], qparams: RequestParams, data
limit = 100
idq="caseLevelData.biosampleId"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset

def get_runs_of_cohort(entry_id: Optional[str], qparams: RequestParams, dataset: str):
collection = 'cohorts'
Expand All @@ -143,7 +143,7 @@ def get_runs_of_cohort(entry_id: Optional[str], qparams: RequestParams, dataset:
limit = 100
idq="biosampleId"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_biosamples_of_cohort(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand All @@ -169,7 +169,7 @@ def get_biosamples_of_cohort(entry_id: Optional[str], qparams: RequestParams, da
limit = 100
idq="id"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_filtering_terms_of_cohort(entry_id: Optional[str], qparams: RequestParams):
Expand Down
10 changes: 5 additions & 5 deletions beacon/db/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ def get_variants_of_biosample(entry_id: Optional[str], qparams: RequestParams, d
limit = 100
idq="caseLevelData.biosampleId"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_variants_of_dataset(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand Down Expand Up @@ -143,7 +143,7 @@ def get_variants_of_dataset(entry_id: Optional[str], qparams: RequestParams, dat
limit = 100

count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_biosamples_of_dataset(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand All @@ -169,7 +169,7 @@ def get_biosamples_of_dataset(entry_id: Optional[str], qparams: RequestParams, d
limit = 100
idq="id"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_individuals_of_dataset(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand All @@ -194,7 +194,7 @@ def get_individuals_of_dataset(entry_id: Optional[str], qparams: RequestParams,
limit = 100
idq="id"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def filter_public_datasets(requested_datasets_ids):
Expand Down Expand Up @@ -239,7 +239,7 @@ def get_runs_of_dataset(entry_id: Optional[str], qparams: RequestParams, dataset
limit = 100
idq="biosampleId"
count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
return schema, count, dataset_count, docs
return schema, count, dataset_count, docs, dataset


def get_analyses_of_dataset(entry_id: Optional[str], qparams: RequestParams, dataset: str):
Expand Down
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