def setUp(self):
self.ont = Ontology('test_data/ontology.owl')
self.doc = Documenter(self.ont)
self.longMessage = True
class TestLabelMap(unittest.TestCase):
"""
Tests the LabelMap class.
"""
def setUp(self):
self.ont = Ontology('test_data/ontology.owl')
self.lm = LabelMap(self.ont)
def test_makeMap(self):
"""
Tests that making a label map from an ontology and its imports closure
works as expected.
"""
# Define all IRI/label pairings in the main test ontology.
testpairs = [
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0001',
'label': 'test object property 1'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0020',
'label': 'test data property 1'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0030',
'label': 'annotation property 1'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0010',
'label': 'test class 1'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0011',
'label': 'test class 2'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_0012',
'label': 'test class 3'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_8000',
'label': 'test individual 1'
},
{
'iri': 'http://purl.obolibrary.org/obo/OBTO_8001',
'label': 'test individual 2'
}
]
# Check all labels in the main, directly loaded ontology.
for testpair in testpairs:
self.assertEqual(
testpair['iri'], str(self.lm.lookupIRI(testpair['label'])),
)
# Check all labels in the imported OWL file.
self.assertEqual(
str(self.lm.lookupIRI('imported test class 1')),
'http://purl.obolibrary.org/obo/OBITO_0001'
)
def test_add_lookupIRI(self):
"""
Tests both add() and lookupIRI().
"""
# Test basic lookup without a root IRI string.
self.assertEqual(
'http://purl.obolibrary.org/obo/OBTO_0001',
str(self.lm.lookupIRI('test object property 1'))
)
# Test lookup of an invalid label.
with self.assertRaisesRegexp(
InvalidLabelError,
'The provided label, "invalid label", does not match'
):
self.lm.lookupIRI('invalid label')
#
# Test using a root IRI string to check the value of a retrieved IRI.
#
# First use a matching root IRI string.
self.assertEqual(
'http://purl.obolibrary.org/obo/OBTO_0001',
str(self.lm.lookupIRI(
'test object property 1', 'http://purl.obolibrary.org/obo/OBTO_')
)
)
# Then use an incorrect root IRI string.
with self.assertRaisesRegexp(
InvalidLabelError, 'The provided IRI root, .*, does not match'
):
self.lm.lookupIRI(
'test object property 1',
'http://purl.obolibrary.org/obo/OBLAH_'
)
#
# Test handling of ambiguous labels.
#
# Add an ambiguous label. This should raise a warning.
with LogCapture() as lc:
self.lm.add(
'test class 1',
IRI.create('http://purl.obolibrary.org/obo/OBITO_0200')
)
# Don't use LogCapture's check() method here because it doesn't support
# substring matching.
self.assertTrue(
'The label "test class 1" is used for more than one IRI in the ontology' in str(lc)
)
# Attempt to dereference an ambiguous label. This should raise an
# exception.
with self.assertRaisesRegexp(
AmbiguousLabelError, 'Attempted to use an ambiguous label'
):
self.lm.lookupIRI('test class 1')
# Attempt to dereference an ambiguous label with an IRI root string.
# This should work without error.
self.assertEqual(
str(self.lm.lookupIRI('test class 1', 'http://purl.obolibrary.org/obo/OBTO_')),
'http://purl.obolibrary.org/obo/OBTO_0010'
)
# Attempt to dereference an ambiguous label with an IRI root string
# that is non-unique. This should raise an exception.
with self.assertRaisesRegexp(
AmbiguousLabelError, 'Attempted to use an ambiguous label'
):
self.lm.lookupIRI(
'test class 1', 'http://purl.obolibrary.org/obo/'
)
# Attempt to dereference an ambiguous label with an IRI root string
# that is invalid. This should raise an exception.
with self.assertRaisesRegexp(
InvalidLabelError, 'The IRI root <.*> did not match any entities'
):
self.lm.lookupIRI(
'test class 1', 'http://invalid.root/iri/'
)
def test_update_notification(self):
"""
Verifies that LabelMap correctly follows changes to its source
ontology.
"""
# The new label should not yet exist.
with self.assertRaisesRegexp(
InvalidLabelError, 'The provided label, ".*", does not match'
):
self.lm.lookupIRI('new test class')
# Create a new class and give it a label.
newclass = self.ont.createNewClass('OBTO:0013')
newclass.addLabel('new test class')
# The LabelMap should automatically have the new label.
self.assertEqual(
'http://purl.obolibrary.org/obo/OBTO_0013',
str(self.lm.lookupIRI('new test class'))
)
class Test_Documenter(unittest.TestCase):
"""
Tests the Documenter class.
"""
def setUp(self):
self.ont = Ontology('test_data/ontology.owl')
self.doc = Documenter(self.ont)
self.longMessage = True
def test_parseDocSpec(self):
"""
This method tests the results of _parseDocSpec() by converting the
returned Document objects to a string representation and checking the
string.
"""
# Define test values and results for valid specifications.
testvals = [
{
'docspec': '',
'expected': ''
},
{
'docspec': ' \n',
'expected': ''
},
# Only a title.
{
'docspec': '# Document title',
'expected': '# Document title'
},
# Several headings and other non-entities text.
{
'docspec':
"""
# Document title
---
## Classes
- not an entities entry
""",
'expected':
"""
# Document title
---
## Classes
- not an entities entry
"""
},
# Multiple non-empty document sections.
{
'docspec':
"""
## Properties
- ID: OBTO:'test data property 1'
## Classes
- ID: OBTO:0010
- ID: OBTO:0011
""",
'expected':
"""
## Properties
Entities:
IRI: http://purl.obolibrary.org/obo/OBTO_0020
OBO ID: OBTO:0020
Label: test data property 1
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
IRI: http://purl.obolibrary.org/obo/OBTO_0011
OBO ID: OBTO:0011
Label: test class 2
"""
},
# Multi-level nested child specifications.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
children:
- ID: OBTO:0010
children:
- ID: OBTO:0012
- ID: OBTO:0011
- ID: OBTO:0090
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0012
OBO ID: OBTO:0012
Label: test class 3
IRI: http://purl.obolibrary.org/obo/OBTO_0011
OBO ID: OBTO:0011
Label: test class 2
IRI: http://purl.obolibrary.org/obo/OBTO_0090
OBO ID: OBTO:0090
Label:
"""
},
# Values of "descendants" that do not result in entity retrieval.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: none
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
"""
},
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: 0
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
"""
},
# Single-level automatic descendants retrieval.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: 1
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
IRI: http://purl.obolibrary.org/obo/OBTO_0011
OBO ID: OBTO:0011
Label: test class 2
IRI: http://purl.obolibrary.org/obo/OBTO_0012
OBO ID: OBTO:0012
Label: test class 3
"""
},
# Multi-level automatic descendants retrieval.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: all
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0091
OBO ID: OBTO:0091
Label:
IRI: http://purl.obolibrary.org/obo/OBTO_0011
OBO ID: OBTO:0011
Label: test class 2
IRI: http://purl.obolibrary.org/obo/OBTO_0012
OBO ID: OBTO:0012
Label: test class 3
"""
},
# Multi-level automatic descendants retrieval with filtering.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: all
filter_by_label: " 1"
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
"""
},
# Multi-level automatic descendants retrieval with both label and
# IRI filtering.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: all
filter_by_label: " 1"
filter_by_IRI: "OBITO_"
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
"""
},
# Multiple mixed Markdown and entities sections.
{
'docspec':
"""
# Document title.
Markdown paragraph.
## Classes
- ID: OBITO:0001
Another Markdown *paragraph*.
* a
* list
## Properties
- ID: OBTO:'test data property 1'
A final Markdown paragraph.
""",
'expected':
"""
# Document title.
Markdown paragraph.
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Another Markdown *paragraph*.
* a
* list
## Properties
Entities:
IRI: http://purl.obolibrary.org/obo/OBTO_0020
OBO ID: OBTO:0020
Label: test data property 1
A final Markdown paragraph.
"""
},
# Including literal '^- .*' in a Markdown section.
{
'docspec':
r"""
- text
-- text
\- text
\\- text
\\\- text
## Classes
- ID: OBITO:0001
""",
'expected':
r"""
- text
-- text
- text
\- text
\\- text
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
"""
},
# Test UTF-8 unicode support.
{
'docspec':
"""
# Document title
## Greek alpha: \xce\xb1
Other text.
""",
'expected':
u"""
# Document title
## Greek alpha: \u03b1
Other text.
"""
}
]
# Add some extra classes to the test ontology hierarchy. After the
# additions, the class structure should now be as follows:
#
# OBTO:0090
# OBITO:0001
# |--- OBTO:0010
# | |--- OBTO:0091
# |--- OBTO:0011
# |--- OBTO:0012
newclass = self.ont.createNewClass('OBTO:0090')
newclass = self.ont.createNewClass('OBTO:0091')
newclass.addSuperclass('OBTO:0010')
for testval in testvals:
result = unicode(self.doc._parseDocSpec(testval['docspec']))
#print result
# When testing the result, remove the leading newline from the
# expected results string.
self.assertEqual(testval['expected'],
result,
msg='Input specification:"""{0}"""'.format(
testval['docspec']))
# Create a cycle in the descendant relationships by making OBITO:0001 a
# subclass of OBTO:0091, and make a polyhierarchy by making OBTO:0010 a
# subclass of OBTO:0011. The class structure should look like this:
#
# OBTO:0090
# OBITO:0001
# |--- OBTO:0010
# | |--- OBTO:0091
# | |--- OBITO:0001
# |--- OBTO:0011
# | |--- OBTO:0010
# | |--- OBTO:0091
# | |--- OBITO:0001
# |--- OBTO:0012
newclass.addSubclass('OBITO:0001')
ent = self.ont.getExistingClass('OBTO:0011')
ent.addSubclass('OBTO:0010')
# Run new multi-level descendants tests to make sure the cycle doesn't
# "trap" the algorithms and that the polyhierarchy is handled
# correctly.
testvals = [
# Multi-level automatic descendants retrieval.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: all
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0091
OBO ID: OBTO:0091
Label:
Children:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
IRI: http://purl.obolibrary.org/obo/OBTO_0011
OBO ID: OBTO:0011
Label: test class 2
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0091
OBO ID: OBTO:0091
Label:
Children:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
IRI: http://purl.obolibrary.org/obo/OBTO_0012
OBO ID: OBTO:0012
Label: test class 3
"""
},
# Multi-level automatic descendants retrieval with filtering. This
# also tests duplicate deletion.
{
'docspec':
"""
## Classes
- ID: OBITO:0001
descendants: all
filter_by_label: " 1"
""",
'expected':
"""
## Classes
Entities:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBTO_0010
OBO ID: OBTO:0010
Label: test class 1
Children:
IRI: http://purl.obolibrary.org/obo/OBITO_0001
OBO ID: OBITO:0001
Label: imported test class 1
"""
}
]
for testval in testvals:
result = unicode(self.doc._parseDocSpec(testval['docspec']))
#print result
self.assertEqual(testval['expected'], result)
# Test error conditions to make sure they are handled correctly.
testvals = [
# Missing entity ID.
{
'docspec': """
## Classes
- descendants: 1
""",
'errorstr': 'No entity ID was provided'
},
# Invalid ID.
{
'docspec': """
## Classes
- ID: OBTO:INVALID
""",
'errorstr': 'No entity with the ID ".*" could be found'
},
# Invalid "descendants" values.
{
'docspec': """
## Classes
- ID: OBTO:0010
descendants: invalid
""",
'errorstr': 'Invalid value for "descendants" directive'
},
{
'docspec': """
## Classes
- ID: OBTO:0010
descendants: -1
""",
'errorstr': 'Invalid value for "descendants" directive'
},
]
for testval in testvals:
with self.assertRaisesRegexp(DocumentationSpecificationError,
testval['errorstr']):
self.doc._parseDocSpec(testval['docspec'])
def setUp(self):
ont = Ontology('test_data/ontology.owl')
self.rman = ReasonerManager(ont)
class _TestOntologyEntity:
"""
Defines tests that apply to all ontology entities. This class should not
be instantiated directly; only its subclasses that target specific ontology
entities should be run. To help reinforce this, _TestOntologyEntity does
not inherit from unittest.TestCase. All subclasses of _TestOntologyEntity
should inherit from unittest.TestCase and treat _TestOntologyEntity as a
sort of "mixin" class that provides standard testing routines.
"""
# Annotation IRIs.
LABEL_IRI = IRI.create('http://www.w3.org/2000/01/rdf-schema#label')
COMMENT_IRI = IRI.create('http://www.w3.org/2000/01/rdf-schema#comment')
def setUp(self):
self.test_ont = Ontology('test_data/ontology.owl')
self.owlont = self.test_ont.getOWLOntology()
# A test entity instance, OWL API object, and IRI should be provided by
# child classes by calling _setEntityObject().
self.t_ent = None
self.t_owlapiobj = None
self.t_entIRI = None
def _setEntityObject(self, entityobj):
self.t_ent = entityobj
self.t_owlapiobj = self.t_ent.getOWLAPIObj()
self.t_entIRI = self.t_ent.getIRI()
def _checkAnnotation(self, annot_propIRI, valuestrs):
"""
Checks that the test entity is the subject of an annotation axiom with
the specified property and value(s).
"""
if isinstance(valuestrs, basestring):
strlist = [valuestrs]
else:
strlist = valuestrs
# Check that the entity has the required annotation and that the text
# value is correct.
annotvals = self.t_ent.getAnnotationValues(annot_propIRI)
self.assertEqual(sorted(strlist), sorted(annotvals))
def test_addDefinition(self):
defstr = 'A new definition.'
self.t_ent.addDefinition(defstr)
# Test that the definition annotation exists and has the correct value.
self._checkAnnotation(self.t_ent.DEFINITION_IRI, defstr)
def test_getDefinitions(self):
# Test the case of no definitions.
self.assertEqual(0, len(self.t_ent.getDefinitions()))
# Test a single definition.
self.t_ent.addDefinition('Definition 1.')
defvals = self.t_ent.getDefinitions()
self.assertEqual(['Definition 1.'], defvals)
# Test multiple definitions.
self.t_ent.addDefinition('Definition 2.')
defvals = self.t_ent.getDefinitions()
self.assertEqual(['Definition 1.', 'Definition 2.'], sorted(defvals))
def test_addLabel(self):
labelstr = 'term label!'
self.t_ent.addLabel(labelstr)
# Test that the label annotation exists and has the correct value.
self._checkAnnotation(self.LABEL_IRI, labelstr)
# Check a label string enclosed in single quotes.
self.t_ent.addLabel("'another label'")
self._checkAnnotation(self.LABEL_IRI, ['another label', labelstr])
def test_getLabels(self):
# Test the case of no labels.
self.assertEqual(0, len(self.t_ent.getLabels()))
# Test a single label.
self.t_ent.addLabel('Label 1')
labelvals = self.t_ent.getLabels()
self.assertEqual(['Label 1'], labelvals)
# Test multiple labels.
self.t_ent.addLabel('Label 2')
labelvals = self.t_ent.getLabels()
self.assertEqual(['Label 1', 'Label 2'], sorted(labelvals))
def test_addComment(self):
commentstr = 'A useful comment.'
self.t_ent.addComment(commentstr)
# Test that the comment annotation exists and has the correct value.
self._checkAnnotation(self.COMMENT_IRI, commentstr)
def test_getComments(self):
# Test the case of no comments.
self.assertEqual(0, len(self.t_ent.getComments()))
# Test a single comment.
self.t_ent.addComment('Comment 1.')
vals = self.t_ent.getComments()
self.assertEqual(['Comment 1.'], vals)
# Test multiple comments.
self.t_ent.addComment('Comment 2.')
vals = self.t_ent.getComments()
self.assertEqual(['Comment 1.', 'Comment 2.'], sorted(vals))
def test_addAnnotation(self):
annotprop_iri = IRI.create('http://purl.obolibrary.org/obo/OBTO_0030')
annot_txt = 'Test annotation text.'
self.t_ent.addAnnotation(annotprop_iri, annot_txt)
self._checkAnnotation(annotprop_iri, annot_txt)
def test_getAnnotationValues(self):
# Test the case of no annotations.
self.assertEqual(0,
len(self.t_ent.getAnnotationValues(self.LABEL_IRI)))
# Test a single annotation value.
self.t_ent.addLabel('A label!!')
annotvals = self.t_ent.getAnnotationValues(self.LABEL_IRI)
self.assertEqual(['A label!!'], annotvals)
# Test multiple annotation values.
commentvals = ['Comment 1', 'Comment 2']
for commentval in commentvals:
self.t_ent.addComment(commentval)
annotvals = self.t_ent.getAnnotationValues(self.COMMENT_IRI)
self.assertEqual(sorted(commentvals), sorted(annotvals))
def test_hash(self):
"""
Tests that entities will behave as expected when they are hashed. Two
entity instances that point to the same ontology entity should produce
equal hashes.
"""
# Get another instance of the same entity.
entcpy = self.test_ont.getExistingEntity(self.t_entIRI)
# Verify that the instances are not the same.
self.assertFalse(self.t_entIRI is entcpy)
# Check the hash values.
self.assertEqual(hash(self.t_ent), hash(entcpy))
self.assertEqual(hash(self.t_owlapiobj), hash(entcpy.getOWLAPIObj()))
# Check the equality operator.
self.assertTrue(self.t_ent == entcpy)
# Check the inequality operator.
self.assertFalse(self.t_ent != entcpy)
def setUp(self):
self.ont = Ontology('test_data/ontology.owl')
self.doc = Documenter(self.ont)
class Test_HTMLWriter(unittest.TestCase):
"""
Tests the HTMLWriter class.
"""
def setUp(self):
self.ont = Ontology('test_data/ontology.owl')
self.doc = Documenter(self.ont)
self.hw = HTMLWriter()
def test_getUniqueValue(self):
coll = ['a', 'b', 'b-1', 'c-']
testvals = [{
'text': '',
'expected': '-1'
}, {
'text': 'd',
'expected': 'd'
}, {
'text': 'a',
'expected': 'a-1'
}, {
'text': 'b',
'expected': 'b-2'
}, {
'text': 'c-',
'expected': 'c--1'
}]
for testval in testvals:
self.assertEqual(testval['expected'],
self.hw._getUniqueValue(testval['text'], coll))
def test_getIDText(self):
# String conversion tests.
testvals = [
{
'text': '',
'expected': '-1'
},
{
'text': '- -- \t\n',
'expected': '-'
},
{
'text': 'will-not_be-changed',
'expected': 'will-not_be-changed'
},
{
'text': '(w*&il|}[]l be\tch@anged',
'expected': 'will-be-changed'
},
{
'text': 'Case-Will-Change',
'expected': 'case-will-change'
},
{
# Includes a unicode lower-case Greek alpha.
'text': unicode('unicode: \xce\xb1', 'utf-8'),
'expected': 'unicode-'
}
]
for testval in testvals:
self.assertEqual(testval['expected'],
self.hw._getIDText(testval['text'], set()))
# Test unique ID generation.
usedIDs = {
'ida', 'idb', 'idb-1', 'idc', 'idc-2', 'idd', 'idd-1', 'idd-2'
}
testvals = [{
'text': 'ide',
'expected': 'ide'
}, {
'text': 'ida',
'expected': 'ida-1'
}, {
'text': 'idb',
'expected': 'idb-2'
}, {
'text': 'idc',
'expected': 'idc-1'
}, {
'text': 'idd',
'expected': 'idd-3'
}]
for testval in testvals:
self.assertEqual(testval['expected'],
self.hw._getIDText(testval['text'], usedIDs))
def _printResultsComparison(self, expected, result):
"""
Prints a line-by-line comparison of an expected text string and a
result text string.
"""
for e_line, r_line in zip(expected.splitlines(), result.splitlines()):
if e_line != r_line:
print 'MISMATCH:'
print 'exp: "{0}"\nres: "{1}"'.format(e_line, r_line)
def test_write(self):
testvals = [
# A document specification that includes two Markdown sections with
# h2 headers, separated by an entities section, followed by another
# entities section. One of the h2 headers has content that will
# generate an ID that conflicts with a reserved ID, to verify that
# reserved IDs are properly preserved.
{
'docspec':
"""
# Test documentation
## First h2 header
## main
## Properties
- ID: OBTO:0020
## Classes
- ID: OBITO:0001
descendants: 1
""",
'expected':
"""
<!doctype html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
<head>
<meta charset="utf-8" />
<title>Test documentation</title>
<link rel="stylesheet" type="text/css" href="documentation_styles.css" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
<script src="navtree.js"></script>
</head>
<body>
<nav id="toc">
<h1>Table of Contents</h1>
<div id="toc_buttons">
<div id="expand_all" class="top_toc_button">expand all</div>
<div id="collapse_all" class="top_toc_button">collapse all</div>
</div>
<ul>
<li><a href="#first-h2-header">First h2 header</a>
</li>
<li><a href="#main-1">main</a>
</li>
<li><a href="#properties">Properties</a>
<ul>
<li><a href="#test-data-property-1">test data property 1</a></li>
</ul>
</li>
<li><a href="#classes">Classes</a>
<ul>
<li><a href="#imported-test-class-1">imported test class 1</a>
<ul>
<li><a href="#test-class-1">test class 1</a></li>
<li><a href="#test-class-2">test class 2</a></li>
<li><a href="#test-class-3">test class 3</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</nav>
<main>
<h1>Test documentation</h1>
<h2 id="first-h2-header">First h2 header</h2>
<h2 id="main-1">main</h2>
<h2 id="properties">Properties</h2>
<ul class="entity_list">
<li>
<h3 id="test-data-property-1">test data property 1</h3>
<p>OBO ID: OBTO:0020</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0020</p>
</li>
</ul>
<h2 id="classes">Classes</h2>
<ul class="entity_list">
<li>
<h3 id="imported-test-class-1">imported test class 1</h3>
<p>OBO ID: OBITO:0001</p>
<p>IRI: http://purl.obolibrary.org/obo/OBITO_0001</p>
<ul class="entity_list">
<li>
<h3 id="test-class-1">test class 1</h3>
<p>OBO ID: OBTO:0010</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0010</p>
</li>
<li>
<h3 id="test-class-2">test class 2</h3>
<p>OBO ID: OBTO:0011</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0011</p>
</li>
<li>
<h3 id="test-class-3">test class 3</h3>
<p>OBO ID: OBTO:0012</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0012</p>
</li>
</ul>
</li>
</ul>
</main>
</body>
</html>"""
},
# A document specification that includes UTF-8 non-ASCI text.
{
'docspec':
"""
## UTF-8 Greek alpha: \xce\xb1
""",
'expected':
"""
<!doctype html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
<head>
<meta charset="utf-8" />
<title></title>
<link rel="stylesheet" type="text/css" href="documentation_styles.css" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
<script src="navtree.js"></script>
</head>
<body>
<nav id="toc">
<h1>Table of Contents</h1>
<div id="toc_buttons">
<div id="expand_all" class="top_toc_button">expand all</div>
<div id="collapse_all" class="top_toc_button">collapse all</div>
</div>
<ul>
<li><a href="#utf-8-greek-alpha-">UTF-8 Greek alpha: \xce\xb1</a>
</li>
</ul>
</nav>
<main>
<h2 id="utf-8-greek-alpha-">UTF-8 Greek alpha: \xce\xb1</h2>
</main>
</body>
</html>"""
}
]
self.doc.setWriter(HTMLWriter())
for testval in testvals:
docspec = testval['docspec']
expected = testval['expected']
strbuf = StringIO.StringIO()
self.doc.document(docspec, strbuf)
result = strbuf.getvalue()
strbuf.close()
#self._printResultsComparison(expected[1:], result)
self.assertEqual(expected[1:], result)
# Create a cycle in the descendant relationships by making OBITO:0001 a
# subclass of OBTO:0010, and make a polyhierarchy by making OBTO:0012 a
# subclass of OBTO:0011. The class structure should look like this:
#
# OBTO:0090
# OBITO:0001
# |--- OBTO:0010
# | |--- OBITO:0001
# |--- OBTO:0011
# | |--- OBTO:0012
# |--- OBTO:0012
ent = self.ont.getExistingClass('OBTO:0010')
ent.addSubclass('OBITO:0001')
ent = self.ont.getExistingClass('OBTO:0011')
ent.addSubclass('OBTO:0012')
# Make sure the cycle doesn't "trap" the documentation generating
# algorithms and that the polyhierarchy is handled correctly.
docspec = """
## Classes
- ID: OBITO:0001
descendants: all
"""
expected = """
<!doctype html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
<head>
<meta charset="utf-8" />
<title></title>
<link rel="stylesheet" type="text/css" href="documentation_styles.css" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
<script src="navtree.js"></script>
</head>
<body>
<nav id="toc">
<h1>Table of Contents</h1>
<div id="toc_buttons">
<div id="expand_all" class="top_toc_button">expand all</div>
<div id="collapse_all" class="top_toc_button">collapse all</div>
</div>
<ul>
<li><a href="#classes">Classes</a>
<ul>
<li><a href="#imported-test-class-1">imported test class 1</a>
<ul>
<li><a href="#test-class-1">test class 1</a>
<ul>
<li><a href="#imported-test-class-1">imported test class 1</a></li>
</ul>
</li>
<li><a href="#test-class-2">test class 2</a>
<ul>
<li><a href="#test-class-3">test class 3</a></li>
</ul>
</li>
<li><a href="#test-class-3">test class 3</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</nav>
<main>
<h2 id="classes">Classes</h2>
<ul class="entity_list">
<li>
<h3 id="imported-test-class-1">imported test class 1</h3>
<p>OBO ID: OBITO:0001</p>
<p>IRI: http://purl.obolibrary.org/obo/OBITO_0001</p>
<ul class="entity_list">
<li>
<h3 id="test-class-1">test class 1</h3>
<p>OBO ID: OBTO:0010</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0010</p>
<ul class="entity_list">
<li>
<h3>imported test class 1</h3>
<p>OBO ID: OBITO:0001</p>
<p>IRI: http://purl.obolibrary.org/obo/OBITO_0001</p>
</li>
</ul>
</li>
<li>
<h3 id="test-class-2">test class 2</h3>
<p>OBO ID: OBTO:0011</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0011</p>
<ul class="entity_list">
<li>
<h3 id="test-class-3">test class 3</h3>
<p>OBO ID: OBTO:0012</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0012</p>
</li>
</ul>
</li>
<li>
<h3>test class 3</h3>
<p>OBO ID: OBTO:0012</p>
<p>IRI: http://purl.obolibrary.org/obo/OBTO_0012</p>
</li>
</ul>
</li>
</ul>
</main>
</body>
</html>"""
strbuf = StringIO.StringIO()
self.doc.document(docspec, strbuf)
result = strbuf.getvalue()
strbuf.close()
#self._printResultsComparison(expected[1:], result)
self.assertEqual(expected[1:], result)