def test_overlap2():
bdmslist = compare_dirs("./testfiles/overlapmatch1/gold","./testfiles/overlapmatch1/estimated")
resmap = compare_mentions(bdmslist, 0.75)
assert len(resmap) == 10
assert resmap['Species'].tp == 0
assert resmap['Species'].fp == 1
assert resmap['Species'].fn == 1
assert resmap['Sex'].tp == 0
assert resmap['Sex'].fp == 1
assert resmap['Sex'].fn == 1
assert resmap['Endpoint'].tp == 1
assert resmap['Endpoint'].fp == 0
assert resmap['Endpoint'].fn == 0
assert resmap['Groupname'].tp == 0
assert resmap['Groupname'].fp == 1
assert resmap['Groupname'].fn == 1
assert resmap['TimeUnits'].tp == 0
assert resmap['TimeUnits'].fp == 1
assert resmap['TimeUnits'].fn == 1
assert resmap['EndpointMethod'].tp == 0
assert resmap['EndpointMethod'].fp == 1
assert resmap['EndpointMethod'].fn == 1
assert resmap['groupsize'].tp == 0
assert resmap['groupsize'].fp == 1
assert resmap['groupsize'].fn == 1
assert resmap['NewGuessLabel'].tp == 0
assert resmap['NewGuessLabel'].fp == 1
assert resmap['NewGuessLabel'].fn == 0
assert resmap['NewGoldLabel'].tp == 0
assert resmap['NewGoldLabel'].fp == 0
assert resmap['NewGoldLabel'].fn == 1
assert resmap['ALL'].tp == 1
assert resmap['ALL'].fp == 7
assert resmap['ALL'].fn == 7
def test_multi_alloc3():
bdmslist = compare_dirs("./testfiles/multi_alloc/gold","./testfiles/multi_alloc/estimated")
resmap = compare_mentions(bdmslist, 0.01)
assert len(resmap) == 2
assert resmap['Mention1'].tp == 5
assert resmap['Mention1'].fp == 0
assert resmap['Mention1'].fn == 0
assert resmap['ALL'].tp == 5
assert resmap['ALL'].fp == 0
assert resmap['ALL'].fn == 0
def test_grpbasic3_0():
bdmslist = compare_dirs("./testfiles/grpbasic3/test0/gold","./testfiles/grpbasic3/test0/estimated")
comlist = get_mention_mappings(bdmslist, 0.51)
resmap = compare_groups(comlist, 0.51)
assert len(resmap)==2
assert resmap['Equiv'].tp==0
assert resmap['Equiv'].fp==1
assert resmap['Equiv'].fn==0
assert resmap['ALL'].tp==0
assert resmap['ALL'].fp==1
assert resmap['ALL'].fn==0
def test_grpbasic4_1():
bdmslist = compare_dirs("./testfiles/grpbasic4/test1/gold","./testfiles/grpbasic4/test1/estimated")
# gold: groups g1, g2, g3
# est: groups e1, e2
# ov: e1-g1: 0.66, e1-g2: 0.85, e1-g3: 0.66
# ov: e2-g1: 0.00, e2-g2: 0.66, e2-g3: 0.40
# e1-g1, e2-g2 is right, so both links are at 0.66
comlist = get_mention_mappings(bdmslist, 0.51)
resmap = compare_groups(comlist, 0.6)
assert len(resmap)==2
assert resmap['Equiv'].tp==2
assert resmap['Equiv'].fp==0
assert resmap['Equiv'].fn==1
assert resmap['ALL'].tp==2
assert resmap['ALL'].fp==0
assert resmap['ALL'].fn==1
# e1-g1, e2-g2
comlist = get_mention_mappings(bdmslist, 0.51)
resmap = compare_groups(comlist, 0.3)
assert len(resmap)==2
assert resmap['Equiv'].tp==2
assert resmap['Equiv'].fp==0
assert resmap['Equiv'].fn==1
assert resmap['ALL'].tp==2
assert resmap['ALL'].fp==0
assert resmap['ALL'].fn==1
# e1-g2, e2-nil
comlist = get_mention_mappings(bdmslist, 0.51)
resmap = compare_groups(comlist, 0.68)
assert len(resmap)==2
assert resmap['Equiv'].tp==1
assert resmap['Equiv'].fp==1
assert resmap['Equiv'].fn==2
assert resmap['ALL'].tp==1
assert resmap['ALL'].fp==1
assert resmap['ALL'].fn==2
# e1-nill, e2-nil
comlist = get_mention_mappings(bdmslist, 0.51)
resmap = compare_groups(comlist, 0.88)
assert len(resmap)==2
assert resmap['Equiv'].tp==0
assert resmap['Equiv'].fp==2
assert resmap['Equiv'].fn==3
assert resmap['ALL'].tp==0
assert resmap['ALL'].fp==2
assert resmap['ALL'].fn==3
def test_dir_good():
""" test of estimated versus gold directories, should succeed and give outputs """
bdmslist = compare_dirs("./testfiles/dircompare/gold","./testfiles/dircompare/estimated")
resmap = compare_mentions(bdmslist, 0.51)
assert len(resmap)==2
assert resmap['Dose'].tp==4
assert resmap['Dose'].fp==0
assert resmap['Dose'].fn==0
assert resmap['ALL'].tp==4
assert resmap['ALL'].fp==0
assert resmap['ALL'].fn==0
def test_grpbasic3():
bdmslist = compare_dirs("./testfiles/grpbasic/test3/gold","./testfiles/grpbasic/test3/estimated")
comlist = get_mention_mappings(bdmslist, 0.5)
resmap = compare_groups(comlist, 0.75)
assert resmap['TestArticleGroup'].tp==1
assert resmap['TestArticleGroup'].fp==0
assert resmap['TestArticleGroup'].fn==2
assert resmap['Animal'].tp==1
assert resmap['Animal'].fp==0
assert resmap['Animal'].fn==0
assert resmap['Equiv'].tp==0
assert resmap['Equiv'].fp==0
assert resmap['Equiv'].fn==2
assert resmap['ALL'].tp==2
assert resmap['ALL'].fp==0
assert resmap['ALL'].fn==4
def test_grpbasic22():
bdmslist = compare_dirs("./testfiles/grpbasic/test2/gold","./testfiles/grpbasic/test2/estimated")
comlist = get_mention_mappings(bdmslist, 0.5)
resmap = compare_groups(comlist, 0.75) # animal goes away but testarticle still matches
assert resmap['TestArticleGroup'].tp==0
assert resmap['TestArticleGroup'].fp==1
assert resmap['TestArticleGroup'].fn==3
assert resmap['Animal'].tp==0
assert resmap['Animal'].fp==1
assert resmap['Animal'].fn==1
assert resmap['Equiv'].tp==0
assert resmap['Equiv'].fp==0
assert resmap['Equiv'].fn==2
assert resmap['ALL'].tp==0
assert resmap['ALL'].fp==2
assert resmap['ALL'].fn==6
def test_basicmatch():
bdmslist = compare_dirs("./testfiles/basicmatch/gold","./testfiles/basicmatch/estimated")
resmap = compare_mentions(bdmslist, 0.51)
assert len(resmap)==4
assert resmap['Dose'].tp==0
assert resmap['Dose'].fp==1
assert resmap['Dose'].fn==2
assert resmap['GroupName'].tp==2
assert resmap['GroupName'].fp==1
assert resmap['GroupName'].fn==2
assert resmap['Endpoint'].tp==8
assert resmap['Endpoint'].fp==0
assert resmap['Endpoint'].fn==0
assert resmap['ALL'].tp==10
assert resmap['ALL'].fp==2
assert resmap['ALL'].fn==4
def test_multi_overlap3():
bdmslist = compare_dirs("./testfiles/overlap_multiloc/gold","./testfiles/overlap_multiloc/estimated")
resmap = compare_mentions(bdmslist, 0.45)
assert len(resmap) == 6
assert resmap['Mention1'].tp == 0
assert resmap['Mention1'].fp == 1
assert resmap['Mention1'].fn == 1
assert resmap['Mention2'].tp == 1
assert resmap['Mention2'].fp == 0
assert resmap['Mention2'].fn == 0
assert resmap['Mention3'].tp == 1
assert resmap['Mention3'].fp == 0
assert resmap['Mention3'].fn == 0
assert resmap['Mention4'].tp == 1
assert resmap['Mention4'].fp == 0
assert resmap['Mention4'].fn == 0
assert resmap['Mention5'].tp == 1
assert resmap['Mention5'].fp == 0
assert resmap['Mention5'].fn == 0
assert resmap['ALL'].tp == 4
assert resmap['ALL'].fp == 1
assert resmap['ALL'].fn == 1
def test_grpbasic_mention_match():
bdmslist = compare_dirs("./testfiles/grpbasic/testmatch/gold","./testfiles/grpbasic/testmatch/estimated")
comlist = get_mention_mappings(bdmslist, 0.9)
assert len(comlist)==1
assert len(comlist[0])==3
assert len(comlist[0][2])==9
assert "T11" not in comlist[0][2]
assert "T12" not in comlist[0][2]
assert "T13" not in comlist[0][2]
assert comlist[0][2]["T35"] == "T351"
assert comlist[0][2]["T36"] == "T361"
assert comlist[0][2]["T37"] == "T371"
assert comlist[0][2]["T38"] == "T381"
assert comlist[0][2]["T39"] == "T391"
assert "T140" not in comlist[0][2]
assert comlist[0][2]["T50"] == "T501"
assert "T151" not in comlist[0][2]
assert comlist[0][2]["T54"] == "T541"
assert comlist[0][2]["T56"] == "T561"
assert "T157" not in comlist[0][2]
assert comlist[0][2]["T58"] == "T581"
def test_dir_missing_files():
""" test of estimated_mismatch and gold_mismatch, should fail on missing estiamted annotation files """
with pytest.raises(ValueError):
bdmslist = compare_dirs("./testfiles/dircompare/gold_mismatch", "./testfiles/dircompare/estimated_mismatch")
resmap = compare_mentions(bdmslist, 0.51)
