1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
#!/usr/bin/python3
import sys, re
import csv, sqlite3
vnamesFile = "eol/vernacular_names.csv"
dbFile = "data.db"
# Read in vernacular-names data
# Note: Canonical-names may have multiple pids
# Note: A canonical-name's associated pids might all have other associated names
nameToPids = {}
pidToNames = {}
canonicalNameToPids = {}
def updateMaps(name, pid, canonical):
if name not in nameToPids:
nameToPids[name] = {pid}
else:
nameToPids[name].add(pid)
if canonical:
if name not in canonicalNameToPids:
canonicalNameToPids[name] = {pid}
else:
canonicalNameToPids[name].add(pid)
if pid not in pidToNames:
pidToNames[pid] = {name}
else:
pidToNames[pid].add(name)
with open(vnamesFile, newline="") as csvfile:
reader = csv.reader(csvfile)
lineNum = 0
for row in reader:
lineNum += 1
if lineNum == 1:
continue
pid = int(row[0])
name1 = re.sub(r"<[^>]+>", "", row[1].lower())
name2 = row[2].lower()
# Add to maps
updateMaps(name1, pid, True)
updateMaps(name2, pid, False)
# Open db connection
dbCon = sqlite3.connect(dbFile)
cur = dbCon.cursor()
# Create 'names' table
cur.execute("CREATE TABLE names(name TEXT, alt_name TEXT, eol_id INT, PRIMARY KEY(name, alt_name))")
# Iterate through 'nodes' table, resolving to canonical-names
usedPids = set()
unresolvedNodeNames = set()
cur2 = dbCon.cursor()
iterationNum = 0
for row in cur2.execute("SELECT name FROM nodes"):
name = row[0]
iterationNum += 1
if iterationNum % 10000 == 0:
print("Loop 1 iteration {}".format(iterationNum))
# If name matches a canonical-name, add alt-name entries to 'names' table
if name in canonicalNameToPids:
pidToUse = 0
for pid in canonicalNameToPids[name]:
if pid not in usedPids:
pidToUse = pid
break
if pidToUse > 0:
usedPids.add(pidToUse)
altNames = {name}
for n in pidToNames[pidToUse]:
altNames.add(n)
for n in altNames:
cur.execute("INSERT INTO names VALUES (?, ?, ?)", (name, n, pidToUse))
elif name in nameToPids:
unresolvedNodeNames.add(name)
# Iterate through unresolved nodes, resolving to vernacular-names
iterationNum = 0
for name in unresolvedNodeNames:
iterationNum += 1
if iterationNum % 10000 == 0:
print("Loop 2 iteration {}".format(iterationNum))
# Add alt-name entries to 'names' table for first corresponding pid
pidToUse = 0
for pid in nameToPids[name]:
if pid not in usedPids:
pidToUse = pid
break
if pidToUse > 0:
usedPids.add(pidToUse)
altNames = {name}
for n in pidToNames[pidToUse]:
altNames.add(n)
for n in altNames:
cur.execute("INSERT INTO names VALUES (?, ?, ?)", (name, n, pidToUse))
dbCon.commit()
dbCon.close()
|
