def testInvertingNameTranslator():
outputFromAPI = {
"panthera tigris": ["panthera tigris", ["panthera tigris"]],
"ursus":
["ursus", ["ursus arctos", "ursus maritimus", "ursus americanus"]],
"blackbird": ["blackbird", ["turdus merula"]],
}
mca = MedeinaCumulativeApplication("dir")
expected = (
{
"panthera tigris": "panthera tigris",
"turdus merula": "blackbird",
"ursus americanus": "ursus",
"ursus arctos": "ursus",
"ursus maritimus": "ursus",
},
[
"panthera tigris",
"ursus arctos",
"ursus maritimus",
"ursus americanus",
"turdus merula",
],
)
assert mca.invertNameTranslation(outputFromAPI) == expected
def testOutputMatrix():
def orderTuples(itms):
return list(
map(lambda x: (x[0], x[1]) if x[0] < x[1] else (x[1], x[0]), itms))
def toHashable(listOfLists):
return list(map(lambda x: tuple(x), listOfLists))
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec1", "Spec2"),
("Spec5", "Spec6"),
]
expected = [
("Spec5", "Spec6"),
("Spec4", "Spec3"),
("Spec3", "Spec2"),
("Spec2", "Spec1"),
]
matrixOut, labelOrder = mca.to_matrix()
crushed = []
matrixOut = matrixOut.tolist()
for kr, row in enumerate(matrixOut):
for kc, col in enumerate(row):
if col == 1:
crushed.append((labelOrder[kr], labelOrder[kc]))
crushed = list(set(orderTuples(crushed)))
unittest.TestCase().assertCountEqual(
list(set(orderTuples(mca.interactionStore))), crushed)
def testOutputGraphOriginal():
def orderTuples(itms):
return list(
map(lambda x: (x[0], x[1]) if x[0] < x[1] else (x[1], x[0]), itms))
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec1", "Spec2"),
("Spec5", "Spec6"),
]
mca.scientificToUser = {
"Spec1": "USpec1",
"Spec2": "USpec2",
"Spec3": "USpec3",
"Spec4": "USpec4",
"Spec5": "USpec5",
"Spec6": "USpec6",
}
expected = [
("USpec1", "USpec2"),
("USpec2", "USpec3"),
("USpec3", "USpec4"),
("USpec5", "USpec6"),
]
unittest.TestCase().assertCountEqual(
orderTuples(mca.to_graph_original().edges), orderTuples(expected))
def testOutputListWithUserMapping():
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec1", "Spec2"),
("Spec5", "Spec6"),
]
mca.scientificToUser = {
"Spec1": "USpec1",
"Spec2": "USpec2",
"Spec3": "USpec3",
"Spec4": "USpec4",
"Spec5": "USpec5",
"Spec6": "USpec6",
}
expectedOne = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec5", "Spec6"),
]
expectedTwo = [
("USpec1", "USpec2"),
("USpec2", "USpec3"),
("USpec3", "USpec4"),
("USpec5", "USpec6"),
]
expected = list(zip(expectedOne, expectedTwo))
unittest.TestCase().assertCountEqual(mca.to_list_original(), expected)
def testIndexingOfSpeciesMixed(patch_apiCall):
class TempWebClass:
def __init__(self):
self.taxa = {
1: {
"family": "A"
},
2: {
"family": "B"
},
3: {
"family": "C"
},
}
self.stringNames = {
"panthera tigris": 1,
"ursus arctos": 2,
"turdus merula": 3,
}
translatedSpecies = [
("ursus americanus", {
"family": "D"
}),
("ursus maritimus", {
"family": "E"
}),
]
WebObj = TempWebClass()
patch_apiCall.return_value = translatedSpecies
mca = MedeinaCumulativeApplication("dir")
data = [
"panthera tigris",
"ursus arctos",
"ursus maritimus",
"ursus americanus",
"turdus merula",
]
expected = {
"panthera tigris": {
"family": "A"
},
"ursus arctos": {
"family": "B"
},
"turdus merula": {
"family": "C"
},
"ursus americanus": {
"family": "D"
},
"ursus maritimus": {
"family": "E"
},
}
assert mca.indexSpeciesWithTaxaData(data, WebObj) == expected
APISpeciesInput, strictParam = patch_apiCall.call_args[0]
assert strictParam == False
assert set(APISpeciesInput) == set(["ursus americanus", "ursus maritimus"])
def testStringMappingDecision():
class TempWebClass:
def __init__(self):
self.taxa = {}
self.stringNames = {}
WebObj = TempWebClass()
WebObj.taxa = {1: {"family": "felidae"}, 2: {"family": "canidae"}}
WebObj.stringNames = {"puma concolor": 1, "turdus merula": 2}
mca = MedeinaCumulativeApplication("dir")
expected = {1: "puma concolor", 2: "turdus merula"}
assert mca.determineAppropriateStringMapper(WebObj, "species") == expected
expected = {1: "felidae", 2: "canidae"}
assert mca.determineAppropriateStringMapper(WebObj, "family") == expected
def testHandlingSingleInteractionDataWritingDiffNamesBlank():
mca = MedeinaCumulativeApplication("dir")
mca.linkEvidence = {("S2", "S1"): [1, 3], ("S3", "S1"): [4]}
mca.links = {1: {"dId": 2}, 2: {"dId": 1}, 3: {"dId": 1}, 4: {"dId": 2}}
mca.datasets = {1: {}, 2: {}}
mca.stringNames = {1: "Spec1", 2: "Spec2", 3: "Spec3", 4: "Spec4"}
mca.interactionWeb = {IDTRACKER: 5, 2: {1: [1, 3], 3: [2]}, 3: {1: [4]}}
evidencingIDs = []
invertedLinkIndex = mca.buildLinkIndex()
fileDumpStruct = mca.handleSingleInteractionEvidence(
evidencingIDs, invertedLinkIndex, "S2", "S1")
assert fileDumpStruct == []
def testBuildingTaxaBasedInteractionsSmall():
WebObj = getSupportingSmallWebObj()
mca = MedeinaCumulativeApplication("dir")
expected = {
"acinonyx jubatus": {
"panthera leo": [4]
},
"panthera tigris": {
"acinonyx jubatus": [3],
"puma concolor": [2]
},
"puma concolor": {
"ursus arctos": [1]
},
}
assert mca.buildTaxaBasedInteractions(WebObj, "species") == expected
def testOutputList():
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec1", "Spec2"),
("Spec5", "Spec6"),
]
expected = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec5", "Spec6"),
]
unittest.TestCase().assertCountEqual(mca.to_list(), expected)
def testHandlingOfNonExceptedSpeciesInvalid():
WebObj = getSupportingInvalidNamesWebObj()
WebObj.taxaExceptions = {}
mca = MedeinaCumulativeApplication("dir")
expected = []
speciesWithTaxa = {
"ursus arctos": {
"family": "",
"species": "ursus arctos"
},
"": {
"family": "ursus",
"species": "ursus maritimus"
},
"": {
"family": "felidae",
"species": ""
},
}
assert mca.handleNonExceptionSpecies(WebObj, speciesWithTaxa,
"species") == expected
assert IDTRACKER in WebObj.interactions
def testHandlingOfNonExceptedSpeciesSmall():
WebObj = getSupportingSmallWebObj()
WebObj.taxaExceptions = {}
mca = MedeinaCumulativeApplication("dir")
speciesWithTaxa = {
"panthera tigris": {
"family": "felidae",
"species": "panthera tigris"
},
"acinonyx jubatus": {
"family": "felidae",
"species": "acinonyx jubatus"
},
"panthera leo": {
"family": "felidae",
"species": "panthera leo"
},
}
interactions = mca.handleNonExceptionSpecies(WebObj, speciesWithTaxa,
"species")
expected = [
("panthera tigris", "acinonyx jubatus"),
("acinonyx jubatus", "panthera leo"),
]
assert interactions == expected
speciesWithTaxa = {
"ursus arctos": {
"family": "ursus",
"species": "ursus arctos"
},
"ursus maritimus": {
"family": "ursus",
"species": "ursus maritimus"
},
}
interactions = mca.handleNonExceptionSpecies(WebObj, speciesWithTaxa,
"family")
expected = []
assert interactions == expected
def testOutputMatrixOriginal():
def orderTuples(itms):
return list(
map(lambda x: (x[0], x[1]) if x[0] < x[1] else (x[1], x[0]), itms))
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [
("Spec1", "Spec2"),
("Spec2", "Spec3"),
("Spec3", "Spec4"),
("Spec1", "Spec2"),
("Spec5", "Spec6"),
]
mca.scientificToUser = {
"Spec1": "USpec1",
"Spec2": "USpec2",
"Spec3": "USpec3",
"Spec4": "USpec4",
"Spec5": "USpec5",
"Spec6": "USpec6",
}
crushed = []
matrixOut, labelOrder = mca.to_matrix_original()
matrixOut = matrixOut.tolist()
for kr, row in enumerate(matrixOut):
for kc, col in enumerate(row):
if col == 1:
crushed.append((labelOrder[kr], labelOrder[kc]))
crushed = list(set(orderTuples(crushed)))
expected = [
("USpec1", "USpec2"),
("USpec2", "USpec3"),
("USpec3", "USpec4"),
("USpec5", "USpec6"),
]
unittest.TestCase().assertCountEqual(orderTuples(expected), crushed)
def testBuildingLinkIndex():
mca = MedeinaCumulativeApplication("dir")
mca.linkEvidence = {("Spec1", "Spec2"): [1, 2], ("Spec3", "Spec4"): [3]}
mca.stringNames = {1: "Spec1", 2: "Spec2", 3: "Spec3", 4: "Spec4"}
mca.interactionWeb = {IDTRACKER: 5, 2: {1: [1, 3, 5], 3: [6]}, 3: {1: [2]}}
linkIndex = mca.buildLinkIndex()
assert linkIndex == {
1: ("Spec2", "Spec1"),
2: ("Spec3", "Spec1"),
3: ("Spec2", "Spec1"),
}
assert IDTRACKER in mca.interactionWeb
def testHandlingOfNonExceptedSpeciesLarge():
WebObj = getSupportingLargeWebObj()
WebObj.taxaExceptions = {}
mca = MedeinaCumulativeApplication("dir")
speciesWithTaxa = {
"ursus arctos": {
"family": "ursus",
"species": "ursus arctos"
},
"vulpes vulpes": {
"family": "canidae",
"species": "vulpes vulpes"
},
"canis lupus": {
"family": "canidae",
"species": "canis lupus"
},
"ursus maritimus": {
"family": "ursus",
"species": "ursus maritimus"
},
"panthera tigris": {
"family": "felidae",
"species": "panthera tigris"
},
"felis catus": {
"family": "felidae",
"species": "felis catus"
},
"panthera onca": {
"family": "felidae",
"species": "panthera onca"
},
}
interactions = mca.handleNonExceptionSpecies(WebObj, speciesWithTaxa,
"species")
expected = [
("ursus arctos", "panthera tigris"),
("vulpes vulpes", "ursus arctos"),
("vulpes vulpes", "panthera onca"),
("canis lupus", "ursus maritimus"),
("ursus maritimus", "ursus arctos"),
("ursus maritimus", "panthera tigris"),
("felis catus", "vulpes vulpes"),
]
assert interactions == expected
speciesWithTaxa = {
"ursus arctos": {
"family": "ursus",
"species": "ursus arctos"
},
"ursus maritimus": {
"family": "ursus",
"species": "ursus maritimus"
},
}
interactions = mca.handleNonExceptionSpecies(WebObj, speciesWithTaxa,
"family")
expected = [
("ursus arctos", "ursus arctos"),
("ursus arctos", "ursus maritimus"),
("ursus maritimus", "ursus arctos"),
("ursus maritimus", "ursus maritimus"),
]
assert interactions == expected
def testIndexingOfSpeciesAllExisting(patch_apiCall):
class TempWebClass:
def __init__(self):
self.taxa = {
1: {
"family": "A"
},
2: {
"family": "B"
},
3: {
"family": "C"
},
4: {
"family": "D"
},
5: {
"family": "E"
},
}
self.stringNames = {
"panthera tigris": 1,
"ursus arctos": 2,
"turdus merula": 3,
"ursus americanus": 4,
"ursus maritimus": 5,
}
translatedSpecies = [
("panthera tigris", True, {
"nkdakda": "A"
}),
("ursus arctos", True, {
"adssakd": "B"
}),
("turdus merula", True, {
"dasdsa": "C"
}),
("ursus americanus", True, {
"dassakdsa": "D"
}),
("ursus maritimus", True, {
"odsksa": "E"
}),
]
WebObj = TempWebClass()
patch_apiCall.return_value = translatedSpecies
mca = MedeinaCumulativeApplication("dir")
data = [
"panthera tigris",
"ursus arctos",
"ursus maritimus",
"ursus americanus",
"turdus merula",
]
expected = {
"panthera tigris": {
"family": "A"
},
"ursus arctos": {
"family": "B"
},
"turdus merula": {
"family": "C"
},
"ursus americanus": {
"family": "D"
},
"ursus maritimus": {
"family": "E"
},
}
assert mca.indexSpeciesWithTaxaData(data, WebObj) == expected
patch_apiCall.assert_not_called()
def testInteractionsToNodes():
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [("S1", "S2"), ("S2", "S3"), ("S2", "S2")]
unittest.TestCase().assertCountEqual(mca.interactionsToNodes(),
["S1", "S2", "S3"])
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = []
unittest.TestCase().assertCountEqual(mca.interactionsToNodes(), [])
mca = MedeinaCumulativeApplication("dir")
mca.interactionStore = [("S2", "S2")]
unittest.TestCase().assertCountEqual(mca.interactionsToNodes(), ["S2"])
def testBuildingTaxaBasedInteractionsLarge():
WebObj = getSupportingLargeWebObj()
mca = MedeinaCumulativeApplication("dir")
expected = {
"acinonyx jubatus": {
"puma concolor": [20, 15],
"vulpes vulpes": [33]
},
"canis latrans": {
"puma concolor": [12]
},
"canis lupus": {
"ursus maritimus": [10]
},
"felis catus": {
"vulpes vulpes": [25]
},
"helarctos malayanus": {
"lynx rufus": [7, 21],
"panthera tigris": [18],
"puma concolor": [19],
},
"lynx rufus": {
"felis catus": [13, 16],
"panthera onca": [22],
"vulpes zerda": [17],
},
"panthera onca": {
"panthera leo": [8, 9]
},
"panthera tigris": {
"panthera leo": [26, 31],
"puma concolor": [4, 5, 6],
"ursus americanus": [32],
},
"puma concolor": {
"ursus arctos": [1]
},
"ursus americanus": {
"lynx rufus": [39],
"panthera onca": [40],
"panthera tigris": [35, 36, 37],
"ursus maritimus": [11],
},
"ursus arctos": {
"panthera tigris": [2, 3]
},
"ursus maritimus": {
"panthera tigris": [38],
"ursus arctos": [34]
},
"vulpes vulpes": {
"canis latrans": [29],
"panthera onca": [28],
"puma concolor": [27],
"ursus americanus": [30],
"ursus arctos": [14],
},
"vulpes zerda": {
"vulpes vulpes": [23, 24]
},
}
assert mca.buildTaxaBasedInteractions(WebObj, "species") == expected
expected = {
"canidae": {
"canidae": [29, 23, 24],
"felidae": [12, 28, 27],
"ursus": [10, 14, 30],
},
"felidae": {
"canidae": [33, 25, 17],
"felidae": [4, 5, 6, 26, 31, 20, 15, 8, 9, 22, 13, 16],
"ursus": [1, 32],
},
"ursus": {
"felidae": [2, 3, 38, 35, 36, 37, 40, 39, 7, 21, 19, 18],
"ursus": [34, 11],
},
}
assert mca.buildTaxaBasedInteractions(WebObj, "family") == expected
def testBuildingTaxaBasedInteractionsInvalid():
WebObj = getSupportingInvalidNamesWebObj()
mca = MedeinaCumulativeApplication("dir")
expected = {"panthera tigris": {"puma concolor": [2]}}
assert mca.buildTaxaBasedInteractions(WebObj, "species") == expected
assert IDTRACKER in WebObj.interactions