1 files changed, 0 insertions, 202 deletions
diff --git a/backend/data/genDbpConflicts.py b/backend/data/genDbpConflicts.py
deleted file mode 100755
index c0d3704..0000000
--- a/backend/data/genDbpConflicts.py
+++ /dev/null
@@ -1,202 +0,0 @@
-#!/usr/bin/python3
-
-import sys, re
-import sqlite3
-
-usageInfo =  f"usage: {sys.argv[0]}\n"
-usageInfo += "Reads DBpedia data from dbpedia/dbpData.db, along with tree-of-life\n"
-usageInfo += "node name data from a sqlite database, and looks for potential\n"
-usageInfo += "conflicts in associating node names with DBpedia-node labels. For\n"
-usageInfo += "example, a node named 'homo sapiens' might have conflicting labels\n"
-usageInfo += "'Homo sapiens', 'homo sapiens (novel)', and 'homo sapiens (song)'.\n"
-usageInfo += "\n"
-usageInfo += "Writes conflict information to file. For each conflict, a line is printed,\n"
-usageInfo += "holding comma-separated DBpedia labels. If the labels include no-parentheses elements,\n"
-usageInfo += "additional tab-indented lines are printed, wholding short-abstracts for those labels.\n"
-if len(sys.argv) > 1:
-	print(usageInfo, file=sys.stderr)
-	sys.exit(1)
-
-dbpDb = "dbpedia/dbpData.db"
-dbFile = "data.db"
-outFile = "conflicts.txt"
-
-# Open dbs
-dbCon = sqlite3.connect(dbFile)
-dbCur = dbCon.cursor()
-dbpCon = sqlite3.connect(dbpDb)
-dbpCur = dbpCon.cursor()
-# Get node names
-print("Reading node names")
-nodeNames = set()
-for row in dbCur.execute("SELECT name from nodes"):
-	nodeNames.add(row[0])
-# Get disambiguation page labels
-print("Reading disambiguation-page labels")
-disambigLabels = set()
-query = "SELECT labels.iri from labels INNER JOIN disambiguations ON labels.iri = disambiguations.iri"
-for (label,) in dbpCur.execute(query):
-	disambigLabels.add(label)
-# Find labels with conflicts
-print("Finding conflicting labels")
-nameVariantRegex = re.compile(r"(.*) \(([^)]+)\)")
-nameToVariants = {}
-iterNum = 0
-for (label,) in dbpCur.execute("SELECT label from labels"):
-	iterNum += 1
-	if iterNum % 1e5 == 0:
-		print(f"Processing line {iterNum}")
-	#
-	if label in disambigLabels:
-		continue
-	name = label.lower()
-	if name in nodeNames:
-		if name not in nameToVariants:
-			nameToVariants[name] = [label]
-		elif label not in nameToVariants[name]:
-			nameToVariants[name].append(label)
-	else:
-		match = nameVariantRegex.fullmatch(name)
-		if match != None:
-			subName = match.group(1)
-			if subName in nodeNames and match.group(2) != "disambiguation":
-				if subName not in nameToVariants:
-					nameToVariants[subName] = [name] # Intentionally ignoring case here
-				elif name not in nameToVariants[subName]:
-					nameToVariants[subName].append(name)
-namesToRemove = set()
-for (name, variants) in nameToVariants.items():
-	if len(variants) == 1:
-		namesToRemove.add(name)
-for name in namesToRemove:
-	del nameToVariants[name]
-print(f"Number of conflicts: {len(nameToVariants)}")
-# Try conflict resolution via taxon-type information
-print("Resolving conflicts using instance-type data")
-taxonTypes = { # Obtained from the DBpedia ontology
-	"http://dbpedia.org/ontology/Species",
-	"http://dbpedia.org/ontology/Archaea",
-	"http://dbpedia.org/ontology/Bacteria",
-	"http://dbpedia.org/ontology/Eukaryote",
-	"http://dbpedia.org/ontology/Plant",
-	"http://dbpedia.org/ontology/ClubMoss",
-	"http://dbpedia.org/ontology/Conifer",
-	"http://dbpedia.org/ontology/CultivatedVariety",
-	"http://dbpedia.org/ontology/Cycad",
-	"http://dbpedia.org/ontology/Fern",
-	"http://dbpedia.org/ontology/FloweringPlant",
-	"http://dbpedia.org/ontology/Grape",
-	"http://dbpedia.org/ontology/Ginkgo",
-	"http://dbpedia.org/ontology/Gnetophytes",
-	"http://dbpedia.org/ontology/GreenAlga",
-	"http://dbpedia.org/ontology/Moss",
-	"http://dbpedia.org/ontology/Fungus",
-	"http://dbpedia.org/ontology/Animal",
-	"http://dbpedia.org/ontology/Fish",
-	"http://dbpedia.org/ontology/Crustacean",
-	"http://dbpedia.org/ontology/Mollusca",
-	"http://dbpedia.org/ontology/Insect",
-	"http://dbpedia.org/ontology/Arachnid",
-	"http://dbpedia.org/ontology/Amphibian",
-	"http://dbpedia.org/ontology/Reptile",
-	"http://dbpedia.org/ontology/Bird",
-	"http://dbpedia.org/ontology/Mammal",
-	"http://dbpedia.org/ontology/Cat",
-	"http://dbpedia.org/ontology/Dog",
-	"http://dbpedia.org/ontology/Horse",
-}
-iterNum = 0
-for (label, type) in dbpCur.execute("SELECT label, type from labels INNER JOIN types on labels.iri = types.iri"):
-	iterNum += 1
-	if iterNum % 1e5 == 0:
-		print(f"Processing line {iterNum}")
-	#
-	if type in taxonTypes:
-		name = label.lower()
-		if name in nameToVariants:
-			del nameToVariants[name]
-		else:
-			match = nameVariantRegex.fullmatch(name)
-			if match != None:
-				name = match.group(1)
-				if name in nameToVariants:
-					del nameToVariants[name]
-print(f"Number of conflicts: {len(nameToVariants)}")
-# Try conflict resolution via category-list
-	# Does a generic-category pass first (avoid stuff like Pan being classified as a horse instead of an ape)
-print("Resolving conflicts using category-list")
-generalCategories = {
-	"species", "genus", 
-	"plant", "fungus", "animal", 
-	"annelid", "mollusc", "arthropod", "crustacean", "insect", "bug", 
-	"fish", "amphibian", "reptile", "bird", "mammal", 
-}
-specificCategories = {
-	"protist", "alveolate", "dinoflagellates", 
-	"orchid", "Poaceae", "fern", "moss", "alga",
-	"bryozoan", "hydrozoan", 
-	"sponge", "cnidarian", "coral", "polychaete", "echinoderm",
-	"bivalve", "gastropod", "chiton",
-	"shrimp", "decapod", "crab", "barnacle", "copepod", 
-	"arachnid", "spider", "harvestman", "mite",
-	"dragonfly", "mantis", "cicada", "grasshopper", "planthopper", 
-		"beetle", "fly", "butterfly", "moth", "wasp",
-	"catfish",
-	"frog",
-	"lizard",
-	"horse", "sheep", "cattle", "mouse",
-}
-namesToRemove = set()
-for (name, variants) in nameToVariants.items():
-	found = False
-	for label in variants:
-		match = nameVariantRegex.match(label)
-		if match != None and match.group(2) in generalCategories:
-			namesToRemove.add(name)
-			found = True
-			break
-	if not found:
-		for label in variants:
-			match = nameVariantRegex.match(label)
-			if match != None and match.group(2) in specificCategories:
-				namesToRemove.add(name)
-				break
-for name in namesToRemove:
-	del nameToVariants[name]
-print(f"Number of conflicts: {len(nameToVariants)}")
-# Find descriptions for plain-named labels
-print("Finding descriptions for plain-named labels")
-labelToDesc = {}
-iterNum = 0
-query = "SELECT label, abstract from labels INNER JOIN abstracts ON labels.iri = abstracts.iri"
-for (label, desc,) in dbpCur.execute(query):
-	iterNum += 1
-	if iterNum % 1e5 == 0:
-		print(f"Processing line {iterNum}")
-	#
-	if label.lower() in nameToVariants:
-		labelToDesc[label] = desc
-print("Finding descriptions for redirect-resolved labels")
-iterNum = 0
-query = "SELECT label, abstract from labels" \
-	" INNER JOIN redirects ON labels.iri = redirects.iri INNER JOIN abstracts ON redirects.target = abstracts.iri"
-for (label, desc,) in dbpCur.execute(query):
-	iterNum += 1
-	if iterNum % 1e5 == 0:
-		print(f"Processing line {iterNum}")
-	#
-	if label.lower() in nameToVariants:
-		labelToDesc[label] = desc
-#
-print("Writing conflict data to file")
-with open(outFile, "w") as file:
-	for (name, variants) in nameToVariants.items():
-		for n in variants:
-			file.write(n + ", ")
-		file.write("\n")
-		for n in variants:
-			if n in labelToDesc:
-				file.write(f"\t{n}: {labelToDesc[n]}\n")
-# Close dbs
-dbCon.close()
-dbpCon.close()