diff --git a/.gitignore b/.gitignore index 944de4f..2714466 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# private Google secret +example_data/example_google_client_secret.json + ### https://raw.github.com/github/gitignore/160d27e2bebf784c4f4a1e070df057f3868b62bc/Python.gitignore # Byte-compiled / optimized / DLL files diff --git a/example_data/config_example.yml b/example_data/config_example.yml index fb8d07a..4c2999c 100644 --- a/example_data/config_example.yml +++ b/example_data/config_example.yml @@ -4,6 +4,7 @@ 'description': 'Example Google Spreadsheet for cell metadata' 'url': 'https://docs.google.com/spreadsheets/d/15OKOC48WZYFUQvYl9E7qEsR6AjqE4_BW7qcCsjJAD6w' 'client_id_filename': 'example_data/example_google_client_id.json' + 'client_secret_filename': 'example_data/example_google_client_secret.json' 'sheet': 'cells' 'cells': 'rows' 'example_sheet_tsv': diff --git a/test/io/count_table_csv_parser.py b/test/io/count_table_csv_parser.py index 2ce7db7..0d43b19 100755 --- a/test/io/count_table_csv_parser.py +++ b/test/io/count_table_csv_parser.py @@ -11,11 +11,11 @@ # NOTE: an env variable for the config file needs to be set when # calling this script print('Parsing example TSV count table') - from singlet.io.csv import parse_counts_table + from singlet.io import parse_counts_table table = parse_counts_table('example_table_tsv') print('Done!') print('Parsing example TSV count table (split)') - from singlet.io.csv import parse_counts_table + from singlet.io import parse_counts_table table = parse_counts_table('example_table_tsv_split') print('Done!') diff --git a/test/io/samplesheet_csv_parser.py b/test/io/samplesheet_csv_parser.py index d450c7f..0f3cbca 100755 --- a/test/io/samplesheet_csv_parser.py +++ b/test/io/samplesheet_csv_parser.py @@ -10,12 +10,10 @@ # NOTE: an env variable for the config file needs to be set when # calling this script - from singlet.io.csv import parse_samplesheet + from singlet.io import parse_samplesheet print('Parsing example TSV sample sheet') - table = parse_samplesheet( - 'example_data/example_sample_table - sequenced.tsv', - 'tsv') + table = parse_samplesheet('example_sheet_tsv') #TODO: check it's correct print('Done!')