def test_reports_batch_download_build_header(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
bd._build_header()
assert bd.header == ['File download URL']
def test_reports_batch_download_get_column_to_field_mapping(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
assert list(bd._get_column_to_fields_mapping().items()) == [
('File download URL', ['files.href'])
]
def test_reports_batch_download_generate(index_workbook, dummy_request):
from types import GeneratorType
from encoded.reports.batch_download import BatchDownload
from pyramid.response import Response
dummy_request.environ['QUERY_STRING'] = ('type=Experiment')
bd = BatchDownload(dummy_request)
response = bd.generate()
assert isinstance(response, Response)
assert response.content_type == 'text/plain'
assert response.content_disposition == 'attachment; filename="files.txt"'
assert len(list(response.body)) >= 100
def test_reports_batch_download_build_params(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
dummy_request.json = {'elements': ['/experiments/ENCSR123ABC/']}
bd = BatchDownload(dummy_request)
bd._build_params()
assert len(bd.param_list['field']
) == 5, f'{len(bd.param_list["field"])} not expected'
assert len(bd.param_list['@id']) == 1
def test_reports_batch_download_init_batch_download(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
assert isinstance(bd, BatchDownload)
def test_reports_batch_download_get_encoded_metadata_link_with_newline(
dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
metadata_link = bd._get_encoded_metadata_link_with_newline()
assert metadata_link == (
'"http://localhost/metadata/?type=Experiment'
'&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status%21=archived&files.biological_replicates=2"'
'\n').encode('utf-8')
dummy_request.json = {
'elements': ['/experiments/ENCSR123ABC/', '/experiments/ENCSRDEF567/']
}
bd = BatchDownload(dummy_request)
metadata_link = bd._get_encoded_metadata_link_with_newline()
assert metadata_link == (
'"http://localhost/metadata/?type=Experiment'
'&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status%21=archived&files.biological_replicates=2"'
' -X GET -H "Accept: text/tsv" -H "Content-Type: application/json"'
' --data \'{"elements": ["/experiments/ENCSR123ABC/", "/experiments/ENCSRDEF567/"]}\''
'\n').encode('utf-8')
def test_reports_batch_download_default_params(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
assert bd.DEFAULT_PARAMS == [
('limit', 'all'),
('field', 'files.@id'),
('field', 'files.href'),
('field', 'files.restricted'),
('field', 'files.no_file_available'),
('field', 'files.file_format'),
('field', 'files.file_format_type'),
('field', 'files.status'),
('field', 'files.assembly'),
]
def test_reports_batch_download_build_query_string(dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam')
bd = BatchDownload(dummy_request)
bd._initialize_report()
bd._build_params()
bd._build_query_string()
bd.query_string.deduplicate()
assert str(bd.query_string) == (
'type=Experiment&files.file_type=bigWig'
'&files.file_type=bam&limit=all&field=files.%40id'
'&field=files.href&field=files.restricted'
'&field=files.no_file_available&field=files.file_format'
'&field=files.file_format_type&field=files.status'
'&field=files.assembly&field=files.file_type')
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
bd._initialize_report()
bd._build_params()
bd._build_query_string()
assert str(bd.query_string) == (
'type=Experiment&files.file_type=bigWig'
'&files.file_type=bam&files.replicate.library.size_range=50-100'
'&files.status%21=archived&files.biological_replicates=2'
'&limit=all&field=files.%40id&field=files.href&field=files.restricted'
'&field=files.no_file_available&field=files.file_format'
'&field=files.file_format_type&field=files.status&field=files.assembly'
'&field=files.href&field=files.file_type&field=files.file_type'
'&field=files.replicate.library.size_range&field=files.biological_replicates'
)
def test_reports_batch_download_maybe_add_json_elements_to_metadata_link(
dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
metadata_link = bd._maybe_add_json_elements_to_metadata_link('')
assert metadata_link == ''
dummy_request.json = {'elements': ['/experiments/ENCSR123ABC/']}
bd = BatchDownload(dummy_request)
metadata_link = bd._maybe_add_json_elements_to_metadata_link('')
assert metadata_link == (
' -X GET -H "Accept: text/tsv" -H '
'"Content-Type: application/json" '
'--data \'{"elements": ["/experiments/ENCSR123ABC/"]}\'')
dummy_request.json = {'elements': []}
bd = BatchDownload(dummy_request)
metadata_link = bd._maybe_add_json_elements_to_metadata_link('')
assert metadata_link == ''
dummy_request.json = {
'elements': ['/experiments/ENCSR123ABC/', '/experiments/ENCSRDEF567/']
}
bd = BatchDownload(dummy_request)
metadata_link = bd._maybe_add_json_elements_to_metadata_link('')
assert metadata_link == (
' -X GET -H "Accept: text/tsv" -H '
'"Content-Type: application/json" '
'--data \'{"elements": ["/experiments/ENCSR123ABC/", "/experiments/ENCSRDEF567/"]}\''
)
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2'
'&cart=xyz123')
dummy_request.json = {
'elements': ['/experiments/ENCSR123ABC/', '/experiments/ENCSRDEF567/']
}
bd = BatchDownload(dummy_request)
metadata_link = bd._maybe_add_json_elements_to_metadata_link('')
assert metadata_link == ''
def test_reports_batch_download_should_add_json_elements_to_metadata_link(
dummy_request):
from encoded.reports.batch_download import BatchDownload
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2')
bd = BatchDownload(dummy_request)
assert not bd._should_add_json_elements_to_metadata_link()
dummy_request.json = {'elements': ['/experiments/ENCSR123ABC/']}
bd = BatchDownload(dummy_request)
assert bd._should_add_json_elements_to_metadata_link()
dummy_request.json = {'elements': []}
bd = BatchDownload(dummy_request)
assert not bd._should_add_json_elements_to_metadata_link()
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&files.file_type=bigWig&files.file_type=bam'
'&files.replicate.library.size_range=50-100'
'&files.status!=archived&files.biological_replicates=2'
'&cart=xyz123')
dummy_request.json = {
'elements': ['/experiments/ENCSR123ABC/', '/experiments/ENCSRDEF567/']
}
bd = BatchDownload(dummy_request)
assert not bd._should_add_json_elements_to_metadata_link()