removing incomplete and unworking graph_digest_benchmark example

1 files changed, 0 insertions, 167 deletions

diff --git a/examples/graph_digest_benchmark.py b/examples/graph_digest_benchmark.py
deleted file mode 100644
index f5bfd02e..00000000
--- a/examples/graph_digest_benchmark.py
+++ /dev/null
@@ -1,167 +0,0 @@
-#!/usr/bin/env python
-
-"""
-This benchmark will produce graph digests for all of the
-downloadable ontologies available in Bioportal.
-"""
-
-
-from rdflib import Namespace, Graph
-from rdflib.compare import to_isomorphic
-from six.moves.urllib.request import urlopen
-from six.moves import queue
-import sys
-import csv
-
-from io import StringIO
-from collections import defaultdict
-
-
-from multiprocessing import Process, Semaphore, Queue
-
-
-bioportal_query = """
-PREFIX metadata: <http://data.bioontology.org/metadata/>
-
-select distinct ?ontology ?title ?download where {
-    ?ontology a metadata:Ontology;
-              metadata:omvname ?title;
-              metadata:links ?links.
-    ?links metadata:Ontology ?download.
-    filter(regex(?download, "/download"))
-}
-"""
-
-stat_cols = [
-    "id",
-    "ontology",
-    "download_url",
-    "tree_depth",
-    "color_count",
-    "individuations",
-    "prunings",
-    "initial_color_count",
-    "adjacent_nodes",
-    "initial_coloring_runtime",
-    "triple_count",
-    "graph_digest",
-    "to_hash_runtime",
-    "canonicalize_triples_runtime",
-    "error",
-]
-
-
-def files_benchmark(ontologies, output_file, threads):
-    w = open(output_file, "w")
-    writer = csv.DictWriter(w, stat_cols)
-    writer.writeheader()
-    tasks = Queue()
-    finished_tasks = Queue()
-    dl_lock = Semaphore(4)
-    task_count = len(ontologies)
-
-    def worker(q, finished_tasks, dl_lock):
-        try:
-            while True:
-                stats = q.get()
-                og = Graph()
-                try:
-                    og.load(stats["download_url"])
-                    print(stats["ontology"], stats["id"])
-                    ig = to_isomorphic(og)
-                    graph_digest = ig.graph_digest(stats)
-                    finished_tasks.put(stats)
-                except Exception as e:
-                    print("ERROR", stats["id"], e)
-                    stats["error"] = str(e)
-                    finished_tasks.put(stats)
-        except queue.Empty:
-            pass
-
-    for i in range(int(threads)):
-        print("Starting worker", i)
-        t = Process(target=worker, args=[tasks, finished_tasks, dl_lock])
-        t.daemon = True
-        t.start()
-    for download in ontologies:
-        stats = defaultdict(str)
-        stats.update(
-            {
-                "id": download.split("/")[-1].split(".")[0],
-                "ontology": download.split("/")[-1].split(".")[0],
-                "download_url": download,
-            }
-        )
-        tasks.put(stats)
-    tasks.close()
-    written_tasks = 0
-    while written_tasks < task_count:
-        stats = finished_tasks.get()
-        # print "Writing", stats['ontology']
-        writer.writerow(stats)
-        w.flush()
-        written_tasks += 1
-
-
-def bioportal_benchmark(apikey, output_file, threads):
-    metadata = Namespace("http://data.bioontology.org/metadata/")
-    url = "http://data.bioontology.org/ontologies?apikey=%s" % apikey
-    ontology_graph = Graph()
-    print(url)
-    ontology_list_json = urlopen(url).read()
-    ontology_graph.parse(StringIO(ontology_list_json), format="json-ld")
-    ontologies = ontology_graph.query(bioportal_query)
-    w = open(output_file, "w")
-    writer = csv.DictWriter(w, stat_cols)
-    writer.writeheader()
-    tasks = Queue()
-    finished_tasks = Queue()
-    dl_lock = Semaphore(4)
-    task_count = len(ontologies)
-
-    def worker(q, finished_tasks, dl_lock):
-        try:
-            while True:
-                stats = q.get()
-                og = Graph()
-                try:
-                    try:
-                        dl_lock.acquire()
-                        og.load(stats["download_url"] + "?apikey=%s" % apikey)
-                    finally:
-                        dl_lock.release()
-                    print(stats["ontology"], stats["id"])
-                    ig = to_isomorphic(og)
-                    graph_digest = ig.graph_digest(stats)
-                    finished_tasks.put(stats)
-                except Exception as e:
-                    print("ERROR", stats["id"], e)
-                    stats["error"] = str(e)
-                    finished_tasks.put(stats)
-        except:
-            pass
-
-    for i in range(int(threads)):
-        print("Starting worker", i)
-        t = Process(target=worker, args=[tasks, finished_tasks, dl_lock])
-        t.daemon = True
-        t.start()
-    for ontology, title, download in ontologies:
-        stats = defaultdict(str)
-        stats.update({"id": ontology, "ontology": title, "download_url": download})
-        tasks.put(stats)
-    tasks.close()
-    written_tasks = 0
-    while written_tasks < task_count:
-        stats = finished_tasks.get()
-        # print "Writing", stats['ontology']
-        writer.writerow(stats)
-        w.flush()
-        written_tasks += 1
-
-
-if __name__ == "__main__":
-    if len(sys.argv) > 4:
-        files_benchmark(sys.argv[1:-2], sys.argv[-2], sys.argv[-1])
-    else:
-        bioportal_benchmark(sys.argv[1], sys.argv[2], sys.argv[3])