def setup_items(self):
self.table = ReferenceTable()
self.author1 = Author(lastname="FirstLast",
firstname="FirstFirst",
initials="FirstInitials")
self.author2 = Author(lastname="SecondLast",
firstname="SecondFirst",
initials="SecondInitials")
self.pmid = "123456"
self.pmc = "PMC12345"
self.url = "http://www.google.com"
self.journal = "Test journal"
self.year = "1987"
self.title = "Test title"
self.doi = "Test doi"
self.reference = Reference(pmid=self.pmid,
pmc=self.pmc,
doi=self.doi,
url=self.url,
year=self.year,
title=self.title,
journal=self.journal,
authors=[self.author1, self.author2])
def test_annotation_property(self):
reference = Reference()
reference.pmc = "1234"
reference.pmid = "54321"
reference.doi = "5555"
assert Annotation("pubmed", reference.pmid) in reference.annotation
assert Annotation("pmc", reference.pmc) in reference.annotation
assert Annotation("doi", reference.doi) in reference.annotation
def test_saving_changes(self):
reaction = Reaction()
reference = Reference()
model = Model()
evidence = Evidence(entity=reaction)
evidence.add_reference(reference)
widget = EvidenceDisplayWidget()
model.all_evidences[evidence.internal_id] = evidence
assert evidence in reaction.evidences
assert evidence.internal_id in model.all_evidences
assert reference in evidence.references
# Set reaction and model to widget
widget.set_item(reaction, model)
assert widget.dataTable.rowCount() == 1
# Remove evidence copy from data table
widget.dataTable.setRowCount(0)
# Setup new evidence item
new_evidence = Evidence()
new_evidence.assertion = "Catalyzed by"
new_evidence.entity = reaction
reference = Reference()
new_evidence.add_reference(reference, reciprocal=False)
# Test the setup i.e. that items are only linked in a one way (evidence -> item) fashion
assert new_evidence not in reaction.evidences
assert new_evidence not in reference.linked_items
# Add new reference to widget table
widget.dataTable.update_row_from_item(new_evidence)
assert widget.dataTable.rowCount() == 1
assert widget.dataTable.item(0).link is new_evidence
# Action - Save evidences
widget.save_state()
# Check that old instance is detached from all links
assert evidence not in reaction.evidences
assert len(evidence.references) == 0
# Old evidence still kept alive by this test
old_id = evidence.internal_id
assert old_id in model.all_evidences
evidence = None
gc.collect()
assert old_id not in model.all_evidences
# Check that new evidence is linked properly
assert new_evidence in reaction.evidences
assert new_evidence.internal_id in model.all_evidences
def test_full_example(self):
""" Test that a minimal evidence example is parsed correctly """
xml_tree = ET.fromstring(full_evidence)
model = Model()
reaction = Reaction("Test")
target_item = Gene("target_id")
reference = Reference("ref_id")
model.add_reaction(reaction)
model.add_gene(target_item)
model.add_reference(reference)
assert len(model.all_evidences) == 0
assert len(reaction.evidences) == 0
parse_evidences_from_xml(xml_tree, model)
assert len(model.all_evidences) == 1
assert len(reaction.evidences) == 1
evidence = list(reaction.evidences)[0]
assert evidence.entity is reaction
assert evidence.target is target_item
assert evidence.assertion == "Catalyzed by"
assert evidence.eco == "ECO:0000000"
assert len(evidence.references) == 1
assert list(evidence.references)[0] is reference
assert evidence.comment == "test comment"
def addItemSlot(self):
reference = Reference()
dialog = ReferenceEditDialog(reference)
status = dialog.exec_()
if status:
self.dataTable.update_row_from_item(reference)
self.model.add_reference(reference)
def get_reference(self):
if self.information is None:
return None
try:
doi = self.information.ids["doi"]
except KeyError:
doi = None
try:
pmc = self.information.ids["pmc"]
except KeyError:
pmc = None
if self.information.journal.pubdate is not None:
year = str(self.information.journal.pubdate.year)
else:
year = None
return Reference(authors=self.information.authors,
title=self.information.title,
journal=self.information.journal.name,
abstract="",
pmid=self.pmid,
doi=doi,
pmc=pmc,
year=year)
def test_copy_evidence(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
# Create copy
copy = evidence.copy()
# Check the correctness of the copy
assert evidence.entity is copy.entity
assert evidence.target is copy.target
assert evidence.eco == copy.eco
assert evidence.assertion == copy.assertion
assert evidence.comment == copy.comment
assert evidence.references == copy.references
assert evidence.references is not copy.references
# Check that the copy is not linked
assert copy not in entity.evidences
assert copy not in reference.linked_items
assert copy not in target.evidences
def setup_items(self):
self.first_author = Author(lastname="FirstLastname",
firstname="FirstFirstname",
initials="FirstInitials")
self.second_author = Author(lastname="SecondLastname",
firstname="SecondFirstname",
initials="SecondInitials")
self.authors = [self.first_author, self.second_author]
self.test_pmid = "123456"
self.test_pmc = "PMC12345"
self.test_doi = "10.1016/j.chemosphere.2016.03.102"
self.test_url = "http://google.com"
self.test_year = "1999"
self.test_title = "Test title"
self.test_journal = "Test journal"
self.test_ref_id = "Test_id"
self.reference = Reference(id=self.test_ref_id,
pmid=self.test_pmid,
pmc=self.test_pmc,
doi=self.test_doi,
url=self.test_url,
year=self.test_year,
title=self.test_title,
journal=self.test_journal,
authors=self.authors)
self.model = Model("Test")
self.model.references[self.reference.id] = self.reference
def test_evidence_init(self):
entity = Reaction()
target = Gene("id2")
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
# Check proper linking
assert evidence.entity is entity
assert evidence in entity.evidences
assert evidence.target is target
assert evidence in target.evidences
# Check attributes
assert evidence.assertion == assertion
assert evidence.eco == eco
assert evidence.comment == comment
# Check id is set
assert type(evidence.internal_id) is str
assert evidence.internal_id != ""
# Check the references
assert reference in evidence.references
assert evidence in reference.linked_items
def setup_items(self):
self.model = Model()
self.testcase = ModelTest(description="test_description")
self.reaction1 = Reaction(id="r1")
self.testsetting1 = ReactionSetting(self.reaction1,
upper_bound=1000.,
lower_bound=0.,
objective_coefficient=0.)
self.testcase.add_setting(self.testsetting1)
self.reaction3 = Reaction(id="r3")
self.outcome = Outcome(self.reaction3, value=100., operator="greater")
self.testcase.add_outcome(self.outcome)
self.reference = Reference(id="test_refid")
self.testcase.add_reference(self.reference)
self.model.add_reactions([self.reaction1, self.reaction3])
self.model.references[self.reference.id] = self.reference
self.model.tests.append(self.testcase)
self.model.setup_tests_table()
self.root = Element("root", nsmap={None: ge_ns})
add_tests_to_xml(self.root, self.model)
def setup_complete_model(self):
self.model = Model("model")
# Setup reaction1
self.metabolite = Metabolite("m1")
self.reaction = Reaction("r1")
self.gene = Gene("g1")
self.reaction.add_child(self.gene)
self.model.add_genes((self.gene,))
self.reaction.add_metabolites({self.metabolite: -1})
self.model.add_reactions((self.reaction,))
# Setup reaction2
self.metabolite2 = Metabolite("m2")
self.reaction2 = Reaction("r2")
self.gene2 = Gene("g2")
self.genegroup = GeneGroup()
self.genegroup.add_child(self.gene2)
self.reaction2.add_child(self.genegroup)
self.model.add_genes((self.gene2,))
self.reaction2.add_metabolites({self.metabolite2: 1})
self.model.add_reactions((self.reaction2,))
# Setup evidences
self.evidence = Evidence(assertion="Catalyzes")
self.evidence.set_entity(self.gene)
self.evidence.set_target(self.reaction)
self.reference = Reference()
self.model.add_reference(self.reference)
self.evidence.add_reference(self.reference)
self.model.add_evidence(self.evidence)
# Setup test case
self.testcase = ModelTest()
reaction_setting = ReactionSetting(self.reaction, 1000., -1000., 0.)
gene_setting = GeneSetting(gene=self.gene2, activity=False)
outcome = Outcome(self.reaction2, 0., "greater")
self.testcase.add_outcome(outcome)
self.testcase.add_setting(gene_setting)
self.testcase.add_setting(reaction_setting)
self.model.add_test(self.testcase)
self.reference2 = Reference()
self.model.add_reference(self.reference2)
self.testcase.add_reference(self.reference2)
self.model.setup_tables()
def setup_empty_dialog(self):
self.model = Model()
self.evidence = Evidence()
self.entity = Gene("g1")
self.assertion = "Catalyzing reaction"
self.target = Reaction("r1")
self.eco = "ECO:0000250"
self.comment = "Similarity to XY"
self.reference = Reference()
self.dialog = EditEvidenceDialog()
def parse_references(model_node, model=None, progress=None):
reference_list_node = model_node.find(ge_listOfReferences)
if reference_list_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading references...")
progress.setRange(0, len(reference_list_node))
elif progress.wasCanceled():
return
references = []
for i, reference_node in enumerate(
reference_list_node.iterfind(ge_reference)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_reference = Reference(id=reference_node.get("id"),
year=reference_node.get("year"),
title=reference_node.get("title"),
journal=reference_node.get("journal"),
url=reference_node.get("url"))
author_list_node = reference_node.find(ge_listOfAuthors)
if author_list_node is not None:
authors = []
for child in author_list_node.iterfind(ge_author):
authors.append(
Author(firstname=child.get("firstname"),
lastname=child.get("lastname"),
initials=child.get("initials")))
new_reference.authors = authors
annotation = annotate_element_from_xml(reference_node)
if annotation:
for x in annotation:
if x.collection == "pubmed":
new_reference.pmid = x.identifier
elif x.collection == "pmc":
new_reference.pmc = x.identifier
elif x.collection == "doi":
new_reference.doi = x.identifier
if model is None:
references.append(new_reference)
else:
model.add_reference(new_reference)
return references
def test_equality(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
assert evidence.copy() == evidence
def test_addition_of_optional_attributes_only_when_set(self):
root = Element("root")
reference = Reference()
model = Model("Testmodel")
model.references[reference.id] = reference
add_references(root, model)
reference_node = root.find("/".join([ge_listOfReferences, ge_reference]))
assert reference_node is not None
assert reference_node.get("url") is None
assert reference_node.find(ge_listOfAuthors) is None
assert reference_node.get("year") is None
assert reference_node.get("title") is None
assert reference_node.get("journal") is None
assert reference_node.get("id") == reference.id
assert reference_node.find(sbml3_annotation) is None
def test_override_entity(self):
entity = Reaction()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment)
evidence.add_reference(reference)
new_reaction = Reaction()
evidence.set_entity(new_reaction)
# Check disconnection of old reaction
assert evidence.entity is new_reaction
assert evidence not in entity.evidences
def test_inequality(self, attribute, new_value):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
new_copy = evidence.copy()
setattr(new_copy, attribute, new_value)
assert new_copy != evidence
assert not new_copy == evidence
def test_inequality_reference(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
new_copy = evidence.copy()
new_copy.remove_all_references()
assert new_copy != evidence
assert not new_copy == evidence
def test_delete_links(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
evidence.delete_links()
assert evidence.entity is None
assert len(evidence.references) == 0
assert evidence not in entity.evidences
assert evidence not in target.evidences
def test_override_target(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
new_gene = Gene()
evidence.set_target(new_gene)
# Check disconnection of old reaction
assert evidence.target is new_gene
assert evidence not in target.evidences
def setup_evidence(self):
self.reaction = Reaction("r_id")
self.gene = Gene("g_id")
self.target = Gene("g_id2")
self.model = Model("test id")
self.reference = Reference()
self.model.add_gene(self.gene)
self.model.add_gene(self.target)
self.model.add_reactions([self.reaction])
self.model.add_reference(self.reference)
# Set type
self.assertion = "Catalyzed by"
self.eco = "ECO:0000000"
self.comment = "test"
self.evidence = Evidence(entity=self.reaction, eco=self.eco,
assertion=self.assertion, comment=self.comment, target=self.target)
self.evidence.add_reference(self.reference)
self.model.all_evidences[self.evidence.internal_id] = self.evidence
self.root = Element("root", nsmap={None: ge_ns})
def test_setup_links(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence()
evidence.entity = entity
evidence.target = target
evidence.eco = eco
evidence.assertion = assertion
evidence.comment = comment
evidence.add_reference(reference, reciprocal=False)
assert evidence not in entity.evidences
assert evidence not in reference.linked_items
assert evidence not in target.evidences
evidence.setup_links()
assert evidence in entity.evidences
assert evidence in reference.linked_items
assert evidence in target.evidences
class TestReferenceTable:
@pytest.fixture(autouse=True)
def setup_items(self):
self.table = ReferenceTable()
self.author1 = Author(lastname="FirstLast",
firstname="FirstFirst",
initials="FirstInitials")
self.author2 = Author(lastname="SecondLast",
firstname="SecondFirst",
initials="SecondInitials")
self.pmid = "123456"
self.pmc = "PMC12345"
self.url = "http://www.google.com"
self.journal = "Test journal"
self.year = "1987"
self.title = "Test title"
self.doi = "Test doi"
self.reference = Reference(pmid=self.pmid,
pmc=self.pmc,
doi=self.doi,
url=self.url,
year=self.year,
title=self.title,
journal=self.journal,
authors=[self.author1, self.author2])
def test_setup(self):
assert issubclass(ReferenceTable, ElementTable)
assert self.table.rowCount() == 0
assert self.reference.pmid == self.pmid
assert self.reference.pmc == self.pmc
assert self.reference.doi == self.doi
assert self.reference.url == self.url
assert self.reference.year == self.year
assert self.reference.title == self.title
assert self.reference.journal == self.journal
assert self.reference.authors[0] is self.author1
assert self.reference.authors[1] is self.author2
def test_row_from_item(self):
return_value = self.table.row_from_item(self.reference)
assert len(return_value) == len(self.table.header)
for x in return_value:
assert isinstance(x, LinkedItem)
assert x.link is self.reference
assert return_value[0].text() == self.reference.reference_string()
assert return_value[1].text() == self.title
assert return_value[2].text() == self.journal
assert return_value[3].text() == self.year
assert return_value[4].text() == self.pmid
assert return_value[5].text() == self.pmc
assert return_value[6].text() == self.doi
assert return_value[7].text() == self.url
def test_update_row_from_item(self):
assert self.table.rowCount() == 0
self.table.update_row_from_item(self.reference)
assert self.table.rowCount() == 1
assert self.table.item(0,
0).text() == self.reference.reference_string()
assert self.table.item(0, 1).text() == self.title
assert self.table.item(0, 2).text() == self.journal
assert self.table.item(0, 3).text() == self.year
assert self.table.item(0, 4).text() == self.pmid
assert self.table.item(0, 5).text() == self.pmc
assert self.table.item(0, 6).text() == self.doi
assert self.table.item(0, 7).text() == self.url
def test_get_item_from_row(self):
self.table.update_row_from_item(self.reference)
assert self.table.item_from_row(0) is self.reference
def test_get_items(self):
self.table.update_row_from_item(self.reference)
assert self.table.get_items() == [self.reference]
def setup_items(self):
self.test = ModelTest()
self.outcome1 = Outcome()
self.reaction_setting = ReactionSetting()
self.gene_setting = GeneSetting()
self.reference1 = Reference()
def init_objects(self):
self.reference1 = Reference("test_abbrev", "name")
self.reference2 = Reference("test_abbrev", "name")
self.empty_reference = Reference()
class TestReference:
@pytest.fixture(autouse=True)
def init_objects(self):
self.reference1 = Reference("test_abbrev", "name")
self.reference2 = Reference("test_abbrev", "name")
self.empty_reference = Reference()
def test___init__(self):
""" Test the default values of empty reference """
assert self.empty_reference.authors == []
assert self.empty_reference.pmid == ""
assert self.empty_reference.pmc == ""
assert self.empty_reference.abstract == ""
assert self.empty_reference.doi == ""
assert self.empty_reference.title == ""
assert self.empty_reference.year == ""
assert self.empty_reference.url == ""
assert self.empty_reference.journal == ""
def test_author_string1(self):
""" Check that empty string is returned if no author is set """
assert self.empty_reference.reference_string() == ""
def test_author_string2(self):
""" Test correct string for single author """
self.empty_reference.authors = [Author("Family", "First", "Initials")]
self.empty_reference.year = "2015"
assert self.empty_reference.reference_string(
) == "Family Initials, 2015"
def test_author_string3(self):
""" Test correct string for two authors """
self.empty_reference.authors = [
Author("FamilyFirst", "", "InitialsFirst"),
Author("FamilySecond", "", "InitialsSecond")
]
self.empty_reference.year = "2015"
expected = "FamilyFirst InitialsFirst and FamilySecond InitialsSecond, 2015"
assert self.empty_reference.reference_string() == expected
def test_author_string4(self):
""" Test correct string for 3 authors """
self.empty_reference.authors = [
Author("Family1", "", "Initials1"),
Author("Family2", "", "Initials2"),
Author("Family3", "", "Initials3")
]
self.empty_reference.year = "2015"
expected = "Family1 Initials1 et al., 2015"
assert self.empty_reference.reference_string() == expected
def test_annotation_property(self):
reference = Reference()
reference.pmc = "1234"
reference.pmid = "54321"
reference.doi = "5555"
assert Annotation("pubmed", reference.pmid) in reference.annotation
assert Annotation("pmc", reference.pmc) in reference.annotation
assert Annotation("doi", reference.doi) in reference.annotation
