diff --git a/testing/databaseTest.py b/testing/databaseTest.py index e05b508d488..db68efa839b 100644 --- a/testing/databaseTest.py +++ b/testing/databaseTest.py @@ -294,10 +294,19 @@ def kinetics_checkCorrectNumberofNodesInRules(self, family_name): """ family = self.database.kinetics.families[family_name] expectedNumberNodes = len(family.getRootTemplate()) + tst = [] for label, entries in family.rules.entries.iteritems(): for entry in entries: nodes = label.split(';') - nose.tools.assert_equal(len(nodes), expectedNumberNodes, "Wrong number of groups or semicolons in family {family} rule {entry}. Should be {num_nodes}".format(family=family_name, entry=entry, num_nodes=expectedNumberNodes)) + tst.append((len(nodes), expectedNumberNodes, "Wrong number of groups or semicolons in family {family} rule {entry}. Should be {num_nodes}".format(family=family_name, entry=entry, num_nodes=expectedNumberNodes))) + + boo = False + for item in tst: + if item[0] != item[1]: + boo = True + logging.error(item[2]) + if boo: + raise ValueError("Error occured") def kinetics_checkNodesInRulesFoundInGroups(self, family_name): """ @@ -313,29 +322,65 @@ def kinetics_checkNodesInRulesFoundInGroups(self, family_name): topDescendants.append(nodes) topGroupOrder = ';'.join(topNode.label for topNode in family.getRootTemplate()) - + tst1 = [] + tst2 = [] for label, entries in family.rules.entries.iteritems(): for entry in entries: nodes = label.split(';') for i, node in enumerate(nodes): - nose.tools.assert_true(node in family.groups.entries, "In {family} family, no group definition found for label {label} in rule {entry}".format(family=family_name, label=node, entry=entry)) - nose.tools.assert_true(family.groups.entries[node] in topDescendants[i], "In {family} family, rule {entry} was found with groups out of order. The correct order for a rule should be subgroups of {top}.".format(family=family_name, entry=entry, top=topGroupOrder)) + tst1.append((node in family.groups.entries, "In {family} family, no group definition found for label {label} in rule {entry}".format(family=family_name, label=node, entry=entry))) + tst2.append((family.groups.entries[node] in topDescendants[i], "In {family} family, rule {entry} was found with groups out of order. The correct order for a rule should be subgroups of {top}.".format(family=family_name, entry=entry, top=topGroupOrder))) + boo = False + for i in xrange(len(tst1)): + if not tst1[i][0]: + logging.error(tst1[i][1]) + boo = True + if not tst2[i][0]: + logging.error(tst2[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkGroupsFoundInTree(self, family_name): """ This test checks whether groups are found in the tree, with proper parents. """ family = self.database.kinetics.families[family_name] + tst = [] + tst1 = [] + tst2 = [] + tst3 = [] for nodeName, nodeGroup in family.groups.entries.iteritems(): - nose.tools.assert_false('[' in nodeName or ']' in nodeName, "Group {group} in {family} family contains square brackets [ ] in the label, which are not allowed.".format(group=nodeName, family=family_name)) + tst.append(('[' in nodeName or ']' in nodeName, "Group {group} in {family} family contains square brackets [ ] in the label, which are not allowed.".format(group=nodeName, family=family_name))) ascendParent = nodeGroup + # Check whether the node has proper parents unless it is the top reactant or product node while ascendParent not in family.groups.top and ascendParent not in family.forwardTemplate.products: child = ascendParent ascendParent = ascendParent.parent - nose.tools.assert_true(ascendParent is not None, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=child, family=family_name)) - nose.tools.assert_true(child in ascendParent.children, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=nodeName, family=family_name)) - nose.tools.assert_false(child is ascendParent, "Group {group} in {family} family is a parent to itself".format(group=nodeName, family=family_name)) + tst1.append((ascendParent is not None, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=child, family=family_name))) + tst2.append((child in ascendParent.children, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=nodeName, family=family_name))) + tst3.append((child is ascendParent, "Group {group} in {family} family is a parent to itself".format(group=nodeName, family=family_name))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + for i in xrange(len(tst1)): + if not tst1[i][0]: + logging.error(tst1[i][1]) + boo = True + if not tst2[i][0]: + logging.error(tst2[i][1]) + boo = True + if tst3[i][0]: + logging.error(tst3[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkGroupsNonidentical(self, family_name): """ @@ -346,10 +391,20 @@ def kinetics_checkGroupsNonidentical(self, family_name): family = Database() family.entries = originalFamily.groups.entries entriesCopy = copy(family.entries) + tst = [] for nodeName, nodeGroup in family.entries.iteritems(): del entriesCopy[nodeName] for nodeNameOther, nodeGroupOther in entriesCopy.iteritems(): - nose.tools.assert_false(family.matchNodeToNode(nodeGroup, nodeGroupOther), "Group {group} in {family} family was found to be identical to group {groupOther}".format(group=nodeName, family=family_name, groupOther=nodeNameOther)) + tst.append((family.matchNodeToNode(nodeGroup, nodeGroupOther), "Group {group} in {family} family was found to be identical to group {groupOther}".format(group=nodeName, family=family_name, groupOther=nodeNameOther))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkChildParentRelationships(self, family_name): """ @@ -359,6 +414,7 @@ def kinetics_checkChildParentRelationships(self, family_name): originalFamily = self.database.kinetics.families[family_name] family = Database() family.entries = originalFamily.groups.entries + tst = [] for nodeName, childNode in family.entries.iteritems(): #top nodes and product nodes don't have parents by definition, so they get an automatic pass: if childNode in originalFamily.groups.top or childNode in originalFamily.forwardTemplate.products: continue @@ -373,9 +429,9 @@ def kinetics_checkChildParentRelationships(self, family_name): continue # Check whether the node has proper parents unless it is the top reactant or product node # The parent should be more general than the child - nose.tools.assert_true(family.matchNodeToChild(parentNode, childNode), + tst.append((family.matchNodeToChild(parentNode, childNode), "In {family} family, group {parent} is not a proper parent of its child {child}.".format(family=family_name, parent=parentNode, child=nodeName)) - +) #check that parentNodes which are LogicOr do not have an ancestor that is a Group #If it does, then the childNode must also be a child of the ancestor if isinstance(parentNode.item, LogicOr): @@ -383,8 +439,17 @@ def kinetics_checkChildParentRelationships(self, family_name): while ancestorNode not in originalFamily.groups.top and isinstance(ancestorNode.item, LogicOr): ancestorNode = ancestorNode.parent if isinstance(ancestorNode.item, Group): - nose.tools.assert_true(family.matchNodeToChild(ancestorNode, childNode), - "In {family} family, group {ancestor} is not a proper ancestor of its child {child}.".format(family=family_name, ancestor=ancestorNode, child=nodeName)) + tst.append((family.matchNodeToChild(ancestorNode, childNode), + "In {family} family, group {ancestor} is not a proper ancestor of its child {child}.".format(family=family_name, ancestor=ancestorNode, child=nodeName))) + + boo = False + for i in xrange(len(tst)): + if not tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkSiblingsForParents(self, family_name): """ @@ -397,6 +462,7 @@ def kinetics_checkSiblingsForParents(self, family_name): originalFamily = self.database.kinetics.families[family_name] family = Database() family.entries = originalFamily.groups.entries + tst = [] for nodeName, node in family.entries.iteritems(): #Some families also construct a 2-level trees for the products #(root with all entries down one level) We don't care about this @@ -404,8 +470,16 @@ def kinetics_checkSiblingsForParents(self, family_name): if node in originalFamily.forwardTemplate.products: continue for index, child1 in enumerate(node.children): for child2 in node.children[index+1:]: - nose.tools.assert_false(family.matchNodeToChild(child1, child2), - "In family {0}, node {1} is a parent of {2}, but they are written as siblings.".format(family_name, child1, child2)) + tst.append((family.matchNodeToChild(child1, child2), + "In family {0}, node {1} is a parent of {2}, but they are written as siblings.".format(family_name, child1, child2))) + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkAdjlistsNonidentical(self, database): """ @@ -422,6 +496,7 @@ def kinetics_checkAdjlistsNonidentical(self, database): if product.label not in speciesDict: speciesDict[product.label] = product + tst = [] # Go through all species to make sure they are nonidentical speciesList = speciesDict.values() labeledAtoms = [species.molecule[0].getLabeledAtoms() for species in speciesList] @@ -436,8 +511,16 @@ def kinetics_checkAdjlistsNonidentical(self, database): except KeyError: # atom labels did not match, therefore not a match continue + tst.append((speciesList[i].molecule[0].isIsomorphic(speciesList[j].molecule[0], initialMap), "Species {0} and species {1} in {2} database were found to be identical.".format(speciesList[i].label,speciesList[j].label,database.label))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True - nose.tools.assert_false(speciesList[i].molecule[0].isIsomorphic(speciesList[j].molecule[0], initialMap), "Species {0} and species {1} in {2} database were found to be identical.".format(speciesList[i].label,speciesList[j].label,database.label)) + if boo: + raise ValueError("Error occured") def kinetics_checkRateUnitsAreCorrect(self, database, tag='library'): """ @@ -615,11 +698,21 @@ def kinetics_checkReactantAndProductTemplate(self, family_name): if family.ownReverse: nose.tools.assert_equal(family.forwardTemplate.reactants, family.forwardTemplate.products) else: + tst = [] reactant_labels = [reactant.label for reactant in family.forwardTemplate.reactants] product_labels = [product.label for product in family.forwardTemplate.products] for reactant_label in reactant_labels: for product_label in product_labels: - nose.tools.assert_false(reactant_label==product_label, "Reactant label {0} matches that of product label {1} in a non-reversible family template. Please rename product label.".format(reactant_label,product_label)) + tst.append((reactant_label==product_label, "Reactant label {0} matches that of product label {1} in a non-reversible family template. Please rename product label.".format(reactant_label,product_label))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkCdAtomType(self, family_name): """ @@ -637,7 +730,7 @@ def kinetics_checkCdAtomType(self, family_name): ignore.append(product) ignore.extend(product.children) else: ignore=[] - + tst = [] for entryName, entry in family.groups.entries.iteritems(): #ignore products if entry in ignore: continue @@ -665,11 +758,20 @@ def kinetics_checkCdAtomType(self, family_name): #remove duplicates from correctAtom: correctAtomList=list(set(correctAtomList)) for correctAtom in correctAtomList: - nose.tools.assert_true(atomTypes[correctAtom] in atom.atomType, + tst.append((atomTypes[correctAtom] in atom.atomType, """In family {0}, node {1} is missing the atomtype {2} in atom {3} and may be misusing the atomtype Cd, CO, CS, or Cdd. The following adjList may have atoms in a different ordering than the input file: {4} - """.format(family_name, entry, correctAtom, index+1, entry.item.toAdjacencyList())) + """.format(family_name, entry, correctAtom, index+1, entry.item.toAdjacencyList()))) + + boo = False + for i in xrange(len(tst)): + if not tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkUnimolecularGroups(self,family_name): """ @@ -795,31 +897,41 @@ def getEndFromBackbone(backbone, endLabels): #print outputs + tst = [] if A != []: s = "These end groups have extra labels that their top level end group do not have:"+"\n [root group, error group]" for x in A: s += '\n'+str(x) - nose.tools.assert_true(False,s) + tst.append((False,s)) if B != []: s = "These end groups are missing labels that their top level end group have:"+"\n [root group, error group]" for x in B: s += '\n'+str(x) - nose.tools.assert_true(False,s) + tst.append((False,s)) if C != []: s = "These backbone groups are missing labels that are in the end groups:"+"\n [root group, error group]" for x in C: s += '\n'+str(x) - nose.tools.assert_true(False,s) + tst.append((False,s)) if D != []: s = "These backbone groups are missing labels along the path atoms:"+"\n [root group, error group]" for x in D: s += '\n'+str(x) - nose.tools.assert_true(False,s) + tst.append((False,s)) if E != []: s = "These backbone have end subgraphs that don't match a root:"+"\n [root group, error group]" for x in E: s += '\n'+str(x) - nose.tools.assert_true(False,s) + tst.append((False,s)) + + boo = False + for i in xrange(len(tst)): + if not tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error occured") def kinetics_checkSampleDescendsToGroup(self, family_name): """ @@ -828,6 +940,9 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): """ family = self.database.kinetics.families[family_name] + tst1 = [] + tst2 = [] + tst3 = [] #ignore any products ignore=[] if not family.ownReverse: @@ -857,7 +972,6 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): #If atom has too many benzene rings, we currently have trouble making sample atoms skipped = [] - for entryName, entry in family.groups.entries.iteritems(): if entry in ignore: continue elif isinstance(entry.item, Group): @@ -874,8 +988,9 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): #test accessibility here atoms = sampleMolecule.getLabeledAtoms() match = family.groups.descendTree(sampleMolecule, atoms, strict=True, root = root) - nose.tools.assert_is_not_none(match, "Group {0} does not match its root node, {1}".format(entryName, root.label)) - nose.tools.assert_in(entry, [match]+family.groups.ancestors(match), """In group {0}, a sample molecule made from node {1} returns node {2} when descending the tree. + tst1.append((match, "Group {0} does not match its root node, {1}".format(entryName, root.label))) + if tst1[-1][0] is not None: + tst2.append((entry, [match]+family.groups.ancestors(match), """In group {0}, a sample molecule made from node {1} returns node {2} when descending the tree. Sample molecule AdjList: {3} @@ -891,10 +1006,10 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): entry.item.toAdjacencyList(), "\n\nBackbone Group Adjlist:\n" + backboneSample.label +'\n' if mergesNecessary and root not in backboneRoots else '', backboneSample.item.toAdjacencyList() if mergesNecessary and root not in backboneRoots else '', - match.item.toAdjacencyList())) + match.item.toAdjacencyList()))) except UnexpectedChargeError, e: - nose.tools.assert_true(False, """In family {0}, a sample molecule made from node {1} returns an unexpectedly charged molecule: + tst3.append((False, """In family {0}, a sample molecule made from node {1} returns an unexpectedly charged molecule: Sample molecule AdjList: {2} @@ -905,7 +1020,7 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): entry.item.toAdjacencyList(), "\n\nBackbone Group Adjlist:\n" + backboneSample.label +'\n' if mergesNecessary and root not in backboneRoots else '', backboneSample.item.toAdjacencyList() if mergesNecessary and root not in backboneRoots else '') - ) + )) except ImplicitBenzeneError: skipped.append(entryName) @@ -916,6 +1031,23 @@ def kinetics_checkSampleDescendsToGroup(self, family_name): for entryName in skipped: print entryName + boo = False + for i in xrange(len(tst1)): + if tst1[i][0] is None: + logging.error(tst1[i][1]) + boo = True + for i in xrange(len(tst2)): + if tst2[i][0] not in tst2[i][1]: + logging.error(tst2[i][2]) + boo = True + for i in xrange(len(tst3)): + if not tst3[i][0]: + logging.error(tst3[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") + def general_checkNodesFoundInTree(self, group_name, group): """ This test checks whether nodes are found in the tree, with proper parents. @@ -923,36 +1055,69 @@ def general_checkNodesFoundInTree(self, group_name, group): for nodeName, nodeGroup in group.entries.iteritems(): ascendParent = nodeGroup # Check whether the node has proper parents unless it is the top reactant or product node + tst1 = [] + tst2 = [] + tst3 = [] while ascendParent not in group.top: child = ascendParent ascendParent = ascendParent.parent - nose.tools.assert_true(ascendParent is not None, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=child, group=group_name)) - nose.tools.assert_true(child in ascendParent.children, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=nodeName, group=group_name)) - nose.tools.assert_false(child is ascendParent, "Node {node} in {group} is a parent to itself".format(node=nodeName, group=group_name)) + tst1.append((ascendParent is not None, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=child, group=group_name))) + if tst1[-1] is not None: + tst2.append((child in ascendParent.children, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=nodeName, group=group_name))) + tst3.append((child is ascendParent, "Node {node} in {group} is a parent to itself".format(node=nodeName, group=group_name))) + + boo = False + for i in xrange(len(tst1)): + if not tst1[i][0]: + logging.error(tst1[i][1]) + boo = True + for i in xrange(len(tst2)): + if not tst2[i][0]: + logging.error(tst2[i][1]) + boo = True + if tst3[i][0]: + logging.error(tst3[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") def general_checkGroupsNonidentical(self, group_name, group): """ This test checks whether nodes found in the group are nonidentical. """ entriesCopy = copy(group.entries) + tst = [] for nodeName, nodeGroup in group.entries.iteritems(): del entriesCopy[nodeName] for nodeNameOther, nodeGroupOther in entriesCopy.iteritems(): group.matchNodeToNode(nodeGroup,nodeGroupOther) - nose.tools.assert_false(group.matchNodeToNode(nodeGroup, nodeGroupOther), "Node {node} in {group} group was found to be identical to node {nodeOther}".format(node=nodeName, group=group_name, nodeOther=nodeNameOther)) + tst.append((group.matchNodeToNode(nodeGroup, nodeGroupOther), "Node {node} in {group} group was found to be identical to node {nodeOther}".format(node=nodeName, group=group_name, nodeOther=nodeNameOther))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") def general_checkChildParentRelationships(self, group_name, group): """ This test checks that nodes' parent-child relationships are correct in the database. """ + tst1 = [] + tst2 = [] for nodeName, childNode in group.entries.iteritems(): #top nodes and product nodes don't have parents by definition, so they get an automatic pass: if childNode in group.top: continue parentNode = childNode.parent # Check whether the node has proper parents unless it is the top reactant or product node # The parent should be more general than the child - nose.tools.assert_true(group.matchNodeToChild(parentNode, childNode), + tst1.append((group.matchNodeToChild(parentNode, childNode), "In {group} group, node {parent} is not a proper parent of its child {child}.".format(group=group_name, parent=parentNode, child=nodeName)) +) #check that parentNodes which are LogicOr do not have an ancestor that is a Group #If it does, then the childNode must also be a child of the ancestor @@ -960,9 +1125,23 @@ def general_checkChildParentRelationships(self, group_name, group): ancestorNode = parentNode while ancestorNode not in group.top and isinstance(ancestorNode.item, LogicOr): ancestorNode = ancestorNode.parent - if isinstance(ancestorNode.item, Group): - nose.tools.assert_true(group.matchNodeToChild(ancestorNode, childNode), + if isinstance(ancestorNode.item, Group) and tst1[-1][0]: + tst2.append((group.matchNodeToChild(ancestorNode, childNode), "In {group} group, node {ancestor} is not a proper ancestor of its child {child}.".format(group=group_name, ancestor=ancestorNode, child=nodeName)) +) + + boo = False + for i in xrange(len(tst1)): + if not tst1[i][0]: + logging.error(tst1[i][1]) + boo = True + for i in xrange(len(tst2)): + if not tst2[i][0]: + logging.error(tst2[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") def general_checkSiblingsForParents(self, group_name, group): """ @@ -982,11 +1161,22 @@ def general_checkSiblingsForParents(self, group_name, group): thermo groups B might be a tricyclic and C a bicyclic parent. Currently there is no way to writes a bicyclic group that excludes an analogous tricyclic. """ + tst = [] for nodeName, node in group.entries.iteritems(): for index, child1 in enumerate(node.children): for child2 in node.children[index+1:]: - nose.tools.assert_false(group.matchNodeToChild(child1, child2), - "In {0} group, node {1} is a parent of {2}, but they are written as siblings.".format(group_name, child1, child2)) + tst.append((group.matchNodeToChild(child1, child2), + "In {0} group, node {1} is a parent of {2}, but they are written as siblings.".format(group_name, child1, child2))) + + boo = False + for i in xrange(len(tst)): + if tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") + def general_checkCdAtomType(self, group_name, group): """ This test checks that groups containing Cd, CO, CS and Cdd atomtypes are used @@ -994,7 +1184,7 @@ def general_checkCdAtomType(self, group_name, group): """ targetLabel=['Cd', 'CO', 'CS', 'Cdd'] targetAtomTypes=[atomTypes[x] for x in targetLabel] - + tst = [] for entryName, entry in group.entries.iteritems(): if isinstance(entry.item, Group): for index, atom in enumerate(entry.item.atoms): @@ -1019,11 +1209,20 @@ def general_checkCdAtomType(self, group_name, group): #remove duplicates from correctAtom: correctAtomList=list(set(correctAtomList)) for correctAtom in correctAtomList: - nose.tools.assert_true(atomTypes[correctAtom] in atom.atomType, + tst.append((atomTypes[correctAtom] in atom.atomType, """In group {0}, node {1} is missing the atomtype {2} in atom {3} and may be misusing the atomtype Cd, CO, CS, or Cdd. The following adjList may have atoms in a different ordering than the input file: {4} - """.format(group_name, entry, correctAtom, index+1, entry.item.toAdjacencyList())) + """.format(group_name, entry, correctAtom, index+1, entry.item.toAdjacencyList()))) + + boo = False + for i in xrange(len(tst)): + if not tst[i][0]: + logging.error(tst[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") def general_checkSampleDescendsToGroup(self, group_name, group): """ @@ -1032,6 +1231,9 @@ def general_checkSampleDescendsToGroup(self, group_name, group): """ skipped = [] + tst1 = [] + tst2 = [] + tst3 = [] for entryName, entry in group.entries.iteritems(): try: if isinstance(entry.item, Group): @@ -1050,8 +1252,8 @@ def general_checkSampleDescendsToGroup(self, group_name, group): atoms = sampleMolecule.getLabeledAtoms() match = group.descendTree(sampleMolecule, atoms, strict=True) - nose.tools.assert_is_not_none(match, "Group {0} does not match its root node, {1}".format(entryName, group.top[0])) - nose.tools.assert_in(entry, [match]+group.ancestors(match), """In group {0}, a sample molecule made from node {1} returns node {2} when descending the tree. + tst1.append((match, "Group {0} does not match its root node, {1}".format(entryName, group.top[0]))) + tst2.append((entry, [match]+group.ancestors(match), """In group {0}, a sample molecule made from node {1} returns node {2} when descending the tree. Sample molecule AdjList: {3} @@ -1065,9 +1267,10 @@ def general_checkSampleDescendsToGroup(self, group_name, group): match, sampleMolecule.toAdjacencyList(), entry.item.toAdjacencyList(), - match.item.toAdjacencyList())) + match.item.toAdjacencyList()))) + except UnexpectedChargeError, e: - nose.tools.assert_true(False, """In family {0}, a sample molecule made from node {1} returns an unexpectedly charged molecule: + tst3.append((False, """In family {0}, a sample molecule made from node {1} returns an unexpectedly charged molecule: Sample molecule AdjList: {2} @@ -1075,7 +1278,7 @@ def general_checkSampleDescendsToGroup(self, group_name, group): {3}""".format(group_name, entry.label, e.graph.toAdjacencyList(), - entry.item.toAdjacencyList())) + entry.item.toAdjacencyList()))) except ImplicitBenzeneError: skipped.append(entryName) @@ -1086,5 +1289,21 @@ def general_checkSampleDescendsToGroup(self, group_name, group): for entryName in skipped: print entryName + boo = False + for i in xrange(len(tst1)): + if tst1[i][0] is None: + logging.error(tst1[i][1]) + boo = True + if tst2[i][0] not in tst2[i][1]: + logging.error(tst2[i][2]) + boo = True + for i in xrange(len(tst3)): + if not tst3[i][0]: + logging.error(tst3[i][1]) + boo = True + + if boo: + raise ValueError("Error Occurred") + if __name__ == '__main__': nose.run(argv=[__file__, '-v', '--nologcapture'], defaultTest=__name__)