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#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
"""Test suite for the remote.py module."""
from socket import gaierror
from cogent.util.unit_test import TestCase, main
from qiime.remote import (_get_cleaned_headers,
_get_spreadsheet_headers,
_export_spreadsheet,
_extract_spreadsheet_key_from_url,
load_google_spreadsheet,
raise_gdata_not_found_error,
GoogleSpreadsheetConnectionError,
GoogleSpreadsheetError)
try:
from gdata.spreadsheet.service import SpreadsheetsService
except ImportError:
SpreadsheetsService = raise_gdata_not_found_error
class RemoteTests(TestCase):
"""Tests for the remote.py module."""
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.url1 = url1
self.url2 = url2
self.url3 = url3
self.spreadsheet_key = '0AnzomiBiZW0ddDVrdENlNG5lTWpBTm5kNjRGbjVpQmc'
self.worksheet_name = 'Fasting_Map'
self.worksheet_id = 'od7'
self.exp_mapping_lines = exp_mapping_lines
def getClient(self):
"""Returns a spreadsheet client if there's an Internet connection.
Returns None if no connection.
"""
client = SpreadsheetsService()
try:
client.GetWorksheetsFeed(self.spreadsheet_key, visibility='public',
projection='basic')
except gaierror:
client = None
return client
def test_load_google_spreadsheet(self):
"""Test retrieves a Google Spreadsheet. Will fail if no Internet connection."""
# Test without naming a worksheet.
obs = load_google_spreadsheet(self.spreadsheet_key,
worksheet_name=None)
self.assertEqual(obs, self.exp_mapping_lines)
# Test with naming a worksheet.
obs = load_google_spreadsheet(self.spreadsheet_key,
worksheet_name='Fasting_Map')
self.assertEqual(obs, self.exp_mapping_lines)
def test_load_google_spreadsheet_invalid_input(self):
"""Test correctly raises errors on various bad inputs. Will fail if no Internet connection."""
# Bad worksheet name.
self.assertRaises(GoogleSpreadsheetError, load_google_spreadsheet,
self.spreadsheet_key, worksheet_name='foo')
def test_extract_spreadsheet_key_from_url(self):
"""Test correctly extracts a key from a URL."""
# Pass various URLs with different key/value combos.
obs = _extract_spreadsheet_key_from_url(self.url1)
self.assertEqual(obs, self.spreadsheet_key)
obs = _extract_spreadsheet_key_from_url(self.url2)
self.assertEqual(obs, self.spreadsheet_key)
obs = _extract_spreadsheet_key_from_url(self.url3)
self.assertEqual(obs, self.spreadsheet_key)
# Pass a key directly.
obs = _extract_spreadsheet_key_from_url(self.spreadsheet_key)
self.assertEqual(obs, self.spreadsheet_key)
# Pass 'key=<key>'.
obs = _extract_spreadsheet_key_from_url('key=' + self.spreadsheet_key)
self.assertEqual(obs, self.spreadsheet_key)
def test_get_spreadsheet_headers(self):
"""Test reading the header line from a spreadsheet. Will fail if no Internet connection."""
client = self.getClient()
if client:
exp = ['#SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Treatment', 'DOB', 'Description']
obs = _get_spreadsheet_headers(client, self.spreadsheet_key,
self.worksheet_id)
self.assertEqual(obs, exp)
else:
raise GoogleSpreadsheetConnectionError("Cannot execute test "
"without an active Internet connection.")
def test_export_spreadsheet(self):
"""Test exporting spreadsheet as TSV. Will fail if no Internet connection."""
client = self.getClient()
if client:
exp = [['#SampleID', 'DOB'],
['#Example mapping file for the QIIME analysis package. '
'These 9 samples are from a study of the effects of exercise '
'and diet on mouse cardiac physiology (Crawford, et al, '
'PNAS, 2009).'], ['PC.354', '20061218'],
['PC.355', '20061218'], ['PC.356', '20061126'],
['PC.481', '20070314'], ['PC.593', '20071210'],
['PC.607', '20071112'], ['PC.634', '20080116'],
['PC.635', '20080116'], ['PC.636', '20080116']]
obs = _export_spreadsheet(client, self.spreadsheet_key,
self.worksheet_id, ['#SampleID', 'DOB'])
self.assertEqual(obs, exp)
else:
raise GoogleSpreadsheetConnectionError("Cannot execute test "
"without an active Internet connection.")
def test_export_spreadsheet_invalid_input(self):
"""Test exporting spreadsheet with bad input raises errors. Will fail if no Internet connection."""
client = self.getClient()
if client:
# Nonexisting header.
self.assertRaises(GoogleSpreadsheetError, _export_spreadsheet,
client, self.spreadsheet_key, self.worksheet_id,
['#SampleID', 'Foo'])
else:
raise GoogleSpreadsheetConnectionError("Cannot execute test "
"without an active Internet connection.")
def test_get_cleaned_headers(self):
"""Test correctly converts headers to Google's representation."""
# Some duplicates.
exp = ['foo', 'foo_2', 'foo_3', 'foo_4', 'fooo', 'foo_5', 'foo_6',
'foo_7', 'foo_8', 'foo_9', 'f2oo456', 'foo_10']
obs = _get_cleaned_headers(
['foo', 'Foo', 'FOO', 'F_oO', 'F:Oo_o', '123foo', '#Foo',
'123foo', ' 123Foo', 'f O\tO#', ' f2\too456', '456 foo'])
self.assertEqual(obs, exp)
# All unique.
exp = ['foo', 'bar']
obs = _get_cleaned_headers(['Fo#o', 'bar'])
self.assertEqual(obs, exp)
# Header consisting of only special characters and header that is
# blank.
self.assertRaises(GoogleSpreadsheetError, _get_cleaned_headers,
['Foo', '___', 'BAR'])
self.assertRaises(GoogleSpreadsheetError, _get_cleaned_headers,
['Foo', '', 'BAR'])
url1 = 'https://docs.google.com/spreadsheet/ccc?key=0AnzomiBiZW0ddDVrdENlNG5lTWpBTm5kNjRGbjVpQmc#gid=1'
url2 = 'https://docs.google.com/spreadsheet/pub?key=0AnzomiBiZW0ddDVrdENlNG5lTWpBTm5kNjRGbjVpQmc&output=html'
url3 = 'https://docs.google.com/spreadsheet/pub?key=0AnzomiBiZW0ddDVrdENlNG5lTWpBTm5kNjRGbjVpQmc&output=html#gid=1'
exp_mapping_lines = """#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tTreatment\tDOB\tDescription
#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
PC.354\tAGCACGAGCCTA\tYATGCTGCCTCCCGTAGGAGT\tControl\t20061218\tControl_mouse_I.D._354
PC.355\tAACTCGTCGATG\tYATGCTGCCTCCCGTAGGAGT\tControl\t20061218\tControl_mouse_I.D._355
PC.356\tACAGACCACTCA\tYATGCTGCCTCCCGTAGGAGT\tControl\t20061126\tControl_mouse_I.D._356
PC.481\tACCAGCGACTAG\tYATGCTGCCTCCCGTAGGAGT\tControl\t20070314\tControl_mouse_I.D._481
PC.593\tAGCAGCACTTGT\tYATGCTGCCTCCCGTAGGAGT\tControl\t20071210\tControl_mouse_I.D._593
PC.607\tAACTGTGCGTAC\tYATGCTGCCTCCCGTAGGAGT\tFast\t20071112\tFasting_mouse_I.D._607
PC.634\tACAGAGTCGGCT\tYATGCTGCCTCCCGTAGGAGT\tFast\t20080116\tFasting_mouse_I.D._634
PC.635\tACCGCAGAGTCA\tYATGCTGCCTCCCGTAGGAGT\tFast\t20080116\tFasting_mouse_I.D._635
PC.636\tACGGTGAGTGTC\tYATGCTGCCTCCCGTAGGAGT\tFast\t20080116\tFasting_mouse_I.D._636
"""
if __name__ == "__main__":
main()
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