def _category_values(category, repo):
if category in repo.categories:
values = repo.category_values(category)
return jsonify(values), 200
else:
text = f"Metadata category: '{category}' does not exist."
return jsonify(text=text, error=404), 404
def dataset_detail(dataset):
resources = get_resources()
dataset_key = 'datasets'
detail_key = '__dataset_detail__'
if dataset_key not in resources:
return jsonify({}), 404
detail = resources[dataset_key].get(dataset)
if detail is None:
return jsonify({'message': f"{dataset} not found"}), 404
return jsonify({dataset: detail[detail_key]}), 200
def available():
resources = get_resources()
escape = {schema.metadata_kw}
dataset_key = 'datasets'
detail_key = '__dataset_detail__'
if dataset_key not in resources:
return jsonify({}), 200
datasets = {}
for k, v in resources[dataset_key].items():
if k in escape:
continue
datasets[k] = v.get(detail_key)
return jsonify(datasets), 200
def _plot_alpha_percentiles_querybuilder(alpha_metric, percentiles, query,
repo, sample_id, alpha_repo_getter):
matching_ids = _filter_ids(repo, alpha_repo_getter(), alpha_metric, query,
sample_id)
if len(matching_ids) <= 1:
return jsonify(text='Did not find more than 1 ID\'s matching '
'request. Plot would be nonsensical.'), 422
alpha_summary, sample_diversity = _get_alpha_info(
alpha_metric,
matching_ids,
percentiles,
sample_id,
alpha_repo_getter,
)
chart = _plot_percentiles_plot(alpha_metric, alpha_summary,
sample_diversity)
return jsonify(**chart.to_dict()), 200
def _plot_alpha_percentiles_querybuilder(alpha_metric, percentiles, query,
repo, sample_id):
error_code, error_response, matching_ids = _filter_ids(
repo, alpha_metric, query, sample_id)
# TODO ideally these would raise an exception lower in the stack and
# then be handled by an exception handler, but for now they are clunky
# to refactor due to execution flow interruption
if error_response:
return error_response, error_code
if len(matching_ids) <= 1:
return jsonify(text='Did not find more than 1 ID\'s matching '
'request. Plot would be nonsensical.'), 422
alpha_summary, sample_diversity = _get_alpha_info(alpha_metric,
matching_ids,
percentiles, sample_id)
chart = _plot_percentiles_plot(alpha_metric, alpha_summary,
sample_diversity)
return jsonify(**chart.to_dict()), 200
def _filter_sample_ids(query, repo, alpha_metric, taxonomy):
matching_ids = repo.sample_id_matches(query)
matching_ids, error_code, error_response = _filter_matching_ids(
matching_ids,
TaxonomyRepo,
'resources',
taxonomy,
'resource',
)
matching_ids, error_code, error_response = _filter_matching_ids(
matching_ids,
AlphaRepo,
'available_metrics',
alpha_metric,
'metric',
error_response=error_response,
error_code=error_code,
)
if error_response:
return error_response, error_code
return jsonify(sample_ids=matching_ids), 200
def categories():
repo = _get_repo()
return jsonify(repo.categories), 200
def get_metadata_values_alt(body, dataset, cat):
repo = _get_repo_alt(dataset)
# check all categories are valid
metadata = _get_metadata_values(body, cat, repo)
return jsonify(metadata.values.tolist()), 200
def _validate_query(dict_, repo):
categories = set(repo.categories)
for id_ in dict_:
if id_ not in categories:
text = f"Metadata category: '{id_}' does not exist."
return jsonify(text=text, error=404), 404
def categories_alt(dataset):
repo = _get_repo_alt(dataset)
return jsonify(repo.categories), 200