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test_biom_validator.py
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/
test_biom_validator.py
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#!/usr/bin/env python
from unittest import TestCase, main
from biom_validator import valid_format_url, valid_rows,\
valid_columns, valid_data, valid_datetime,\
valid_sparse_data, valid_dense_data, \
valid_shape, valid_matrix_type, valid_matrix_element_type,\
valid_biom, valid_type, valid_generated_by, valid_format, \
valid_metadata
import json
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2012, The BIOM-Format Project"
__credits__ = ["Daniel McDonald", "Jose Clemente", "Greg Caporaso",
"Jai Rideout", "Justin Kuczynski", "Andreas Wilke",
"Tobias Paczian", "Rob Knight", "Folker Meyer",
"Sue Huse"]
__url__ = "http://biom-format.org"
__license__ = "GPL"
__version__ = "1.1.0"
__maintainer__ = "Daniel McDonald"
__email__ = "daniel.mcdonald@colorado.edu"
__status__ = "Development"
class ParserTests(TestCase):
def setUp(self):
self.min_sparse_otu = json.loads(min_sparse_otu)
self.rich_sparse_otu = json.loads(rich_sparse_otu)
self.rich_dense_otu = json.loads(rich_dense_otu)
self.min_dense_otu = json.loads(min_dense_otu)
def test_valid_biom(self):
"""validates a table"""
self.assertEqual(valid_biom(self.min_sparse_otu), None)
self.assertEqual(valid_biom(self.rich_sparse_otu), None)
def test_valid_format_url(self):
"""validates format url"""
table = self.min_sparse_otu
self.assertEqual(valid_format_url(table), None)
table['format_url'] = 'foo'
self.assertRaises(ValueError, valid_format_url, table)
def test_valid_format(self):
"""Should match format string"""
table = self.min_sparse_otu
self.assertEqual(valid_format(table), None)
table['format'] = 'foo'
self.assertRaises(ValueError, valid_format, table)
def test_valid_type(self):
"""Should be valid table type"""
table = self.min_sparse_otu
self.assertEqual(valid_type(table), None)
table['type'] = 'otu table' # should not be case sensitive
self.assertEqual(valid_type(table), None)
table['type'] = 'Pathway table'
self.assertEqual(valid_type(table), None)
table['type'] = 'Function table'
self.assertEqual(valid_type(table), None)
table['type'] = 'Ortholog table'
self.assertEqual(valid_type(table), None)
table['type'] = 'Gene table'
self.assertEqual(valid_type(table), None)
table['type'] = 'Metabolite table'
self.assertEqual(valid_type(table), None)
table['type'] = 'OTU table'
self.assertEqual(valid_type(table), None)
table['type'] = 'Taxon table'
self.assertEqual(valid_type(table), None)
table['type'] = 'foo'
self.assertRaises(ValueError, valid_type, table)
def test_valid_generated_by(self):
"""Should have some string for generated by"""
table = self.min_sparse_otu
self.assertEqual(valid_generated_by(table), None)
table['generated_by'] = None
self.assertRaises(ValueError, valid_generated_by, table)
def test_valid_nullable_id(self):
"""Should just work."""
pass
def test_valid_metadata(self):
"""Can be nullable or an object"""
table = self.min_sparse_otu
table['rows'][2]['metadata'] = None
self.assertEqual(valid_metadata(table['rows'][2]), None)
table['rows'][2]['metadata'] = {10:20}
self.assertEqual(valid_metadata(table['rows'][2]), None)
table['rows'][2]['metadata'] = ""
self.assertRaises(ValueError, valid_metadata, table['rows'][2])
table['rows'][2]['metadata'] = "asdasda"
self.assertRaises(ValueError, valid_metadata, table['rows'][2])
table['rows'][2]['metadata'] = [{'a':'b'},{'c':'d'}]
self.assertRaises(ValueError, valid_metadata, table['rows'][2])
def test_valid_matrix_type(self):
"""Make sure we have a valid matrix type"""
self.assertEqual(valid_matrix_type(self.min_dense_otu), None)
self.assertEqual(valid_matrix_type(self.min_sparse_otu), None)
table = self.min_dense_otu
table['matrix_type'] = 'spARSe'
self.assertRaises(ValueError, valid_matrix_type, table)
table['matrix_type'] = 'sparse_asdasd'
self.assertRaises(ValueError, valid_matrix_type, table)
def test_valid_matrix_element_type(self):
"""Make sure we have a valid matrix type"""
min_sparse_otu = self.min_sparse_otu
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = u'int'
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = 'float'
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = u'float'
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = 'str'
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = u'str'
self.assertEqual(valid_matrix_element_type(min_sparse_otu), None)
min_sparse_otu['matrix_element_type'] = 'obj'
self.assertRaises(ValueError, valid_matrix_element_type, min_sparse_otu)
min_sparse_otu['matrix_element_type'] = u'asd'
self.assertRaises(ValueError, valid_matrix_element_type, min_sparse_otu)
def test_valid_datetime(self):
"""Make sure we have a datetime stamp"""
min_sparse_otu = self.min_sparse_otu
self.assertEqual(valid_datetime(min_sparse_otu), None)
min_sparse_otu['date'] = "1999-11-11T10:11:12"
self.assertEqual(valid_datetime(min_sparse_otu), None)
min_sparse_otu['date'] = "10-11-1999 10:11:12"
self.assertEqual(valid_datetime(min_sparse_otu), None)
min_sparse_otu['date'] = "10-11-1asdfasd:12"
self.assertRaises(ValueError, valid_datetime, min_sparse_otu)
def test_valid_sparse_data(self):
"""Takes a sparse matrix field and validates"""
table = self.min_sparse_otu
self.assertEqual(valid_sparse_data(table), None)
# incorrect type
table['matrix_element_type'] = 'float'
self.assertRaises(ValueError, valid_sparse_data, table)
# not balanced
table['matrix_element_type'] = 'int'
table['data'][5] = [0,10]
self.assertRaises(ValueError, valid_sparse_data, table)
# odd type for index
table['data'][5] = [1.2,5,10]
self.assertRaises(ValueError, valid_sparse_data, table)
def test_valid_dense_data(self):
"""Takes a dense matrix field and validates"""
table = self.min_dense_otu
self.assertEqual(valid_dense_data(table), None)
# incorrect type
table['matrix_element_type'] = 'float'
self.assertRaises(ValueError, valid_dense_data, table)
# not balanced
table['matrix_element_type'] = 'int'
table['data'][1] = [0,10]
self.assertRaises(ValueError, valid_dense_data, table)
# bad type in a field
table['data'][1] = [5, 1, 0, 2.3, 3, 1]
self.assertRaises(ValueError, valid_dense_data, table)
def test_valid_shape(self):
"""validates shape information"""
self.assertEqual(valid_shape(self.min_sparse_otu), None)
self.assertEqual(valid_shape(self.rich_sparse_otu), None)
bad_shape = self.min_sparse_otu.copy()
bad_shape['shape'] = ['asd',10]
self.assertRaises(ValueError, valid_shape, bad_shape)
def test_valid_rows(self):
"""validates rows: field"""
table = self.rich_dense_otu
self.assertEqual(valid_rows(table), None)
table['rows'][0]['id'] = ""
self.assertRaises(ValueError, valid_rows, table)
table['rows'][0]['id'] = None
self.assertRaises(ValueError, valid_rows, table)
del table['rows'][0]['id']
self.assertRaises(AttributeError, valid_rows, table)
table['rows'][0]['id'] = 'asd'
table['rows'][0]['metadata'] = None
self.assertEqual(valid_rows(table), None)
# since this is an OTU table, metadata is a required key
del table['rows'][0]['metadata']
self.assertRaises(AttributeError, valid_rows, table)
def test_valid_columns(self):
"""validates table:columns: fields"""
table = self.rich_dense_otu
self.assertEqual(valid_columns(table), None)
table['columns'][0]['id'] = ""
self.assertRaises(ValueError, valid_columns, table)
table['columns'][0]['id'] = None
self.assertRaises(ValueError, valid_columns, table)
del table['columns'][0]['id']
self.assertRaises(AttributeError, valid_columns, table)
table['columns'][0]['id'] = 'asd'
table['columns'][0]['metadata'] = None
self.assertEqual(valid_columns(table), None)
# since this is an OTU table, metadata is a required key
del table['columns'][0]['metadata']
self.assertRaises(AttributeError, valid_columns, table)
def test_valid_data(self):
"""validates data: fields"""
# the burden of validating data is passed on to valid_sparse_data
# and valid_dense_data
table = self.rich_sparse_otu
self.assertEqual(valid_data(table), None)
table['matrix_type'] = 'foo'
self.assertRaises(AttributeError, valid_data, table)
rich_sparse_otu = """{
"id":null,
"format": "Biological Observation Matrix v0.9",
"format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
{"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
{"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}},
{"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
{"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
],
"columns":[
{"id":"Sample1", "metadata":{
"BarcodeSequence":"CGCTTATCGAGA",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample2", "metadata":{
"BarcodeSequence":"CATACCAGTAGC",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample3", "metadata":{
"BarcodeSequence":"CTCTCTACCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample4", "metadata":{
"BarcodeSequence":"CTCTCGGCCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample5", "metadata":{
"BarcodeSequence":"CTCTCTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample6", "metadata":{
"BarcodeSequence":"CTAACTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}}
],
"matrix_type": "sparse",
"matrix_element_type": "int",
"shape": [5, 6],
"data":[[0,2,1],
[1,0,5],
[1,1,1],
[1,3,2],
[1,4,3],
[1,5,1],
[2,2,1],
[2,3,4],
[2,5,2],
[3,0,2],
[3,1,1],
[3,2,1],
[3,5,1],
[4,1,1],
[4,2,1]
]
}"""
min_sparse_otu = """{
"id":null,
"format": "Biological Observation Matrix v0.9",
"format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "sparse",
"matrix_element_type": "int",
"shape": [5, 6],
"data":[[0,2,1],
[1,0,5],
[1,1,1],
[1,3,2],
[1,4,3],
[1,5,1],
[2,2,1],
[2,3,4],
[2,5,2],
[3,0,2],
[3,1,1],
[3,2,1],
[3,5,1],
[4,1,1],
[4,2,1]
]
}"""
rich_dense_otu = """{
"id":null,
"format": "Biological Observation Matrix v0.9",
"format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
{"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
{"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}},
{"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
{"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
],
"columns":[
{"id":"Sample1", "metadata":{
"BarcodeSequence":"CGCTTATCGAGA",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample2", "metadata":{
"BarcodeSequence":"CATACCAGTAGC",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample3", "metadata":{
"BarcodeSequence":"CTCTCTACCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"gut",
"Description":"human gut"}},
{"id":"Sample4", "metadata":{
"BarcodeSequence":"CTCTCGGCCTGT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample5", "metadata":{
"BarcodeSequence":"CTCTCTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}},
{"id":"Sample6", "metadata":{
"BarcodeSequence":"CTAACTACCAAT",
"LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
"BODY_SITE":"skin",
"Description":"human skin"}}
],
"matrix_type": "dense",
"matrix_element_type": "int",
"shape": [5,6],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
}"""
min_dense_otu = """ {
"id":null,
"format": "Biological Observation Matrix v0.9",
"format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"type": "OTU table",
"generated_by": "QIIME revision XYZ",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "dense",
"matrix_element_type": "int",
"shape": [5,6],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
}"""
if __name__ == '__main__':
main()