output in alignment api and sssom

main.ipynb

@@ -5,8 +5,8 @@
    "execution_count": 1,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-05-05T16:58:30.285996286Z",
-     "start_time": "2023-05-05T16:58:27.520729058Z"
+     "end_time": "2023-07-19T08:57:37.490880538Z",
+     "start_time": "2023-07-19T08:57:35.005710556Z"
     }
    },
    "outputs": [],
@@ -38,8 +38,8 @@
    "execution_count": 2,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-05-05T16:58:33.643656486Z",
-     "start_time": "2023-05-05T16:58:30.289546804Z"
+     "end_time": "2023-07-19T08:57:46.777266756Z",
+     "start_time": "2023-07-19T08:57:37.493551556Z"
     }
    },
    "outputs": [],
@@ -51,24 +51,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-05-04T23:11:23.647059226Z",
-     "start_time": "2023-05-04T23:08:45.535290656Z"
+     "end_time": "2023-07-19T09:00:31.330783432Z",
+     "start_time": "2023-07-19T08:57:46.780973332Z"
     }
    },
    "outputs": [
     {
      "data": {
+      "text/plain": "  0%|          | 0/21 [00:00<?, ?it/s]",
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "dc8966ab2d924576890dd6f0598da481",
        "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "  0%|          | 0/21 [00:00<?, ?it/s]"
-      ]
+       "version_minor": 0,
+       "model_id": "4d5d3d0f0d60477d840af6d66d63615a"
+      }
      },
      "metadata": {},
      "output_type": "display_data"
@@ -88,13 +86,13 @@
       "Loading o1\n",
       "Loading o2\n",
       "0\n",
-      "ontology iterations: 1804, (0.0, 0, 0.0), aligns: 0, po1: 22, po2: 41\n",
+      "ontology iterations: 1804, (0, 0, 0.0), aligns: 0, po1: 22, po2: 41\n",
       "----------------------------------------------------------------------------------------------------\n",
       "cmt.owl Conference.owl\n",
       "Loading o1\n",
       "Loading o2\n",
       "3\n",
-      "ontology iterations: 7552, (0.25, 0.3333333333333333, 0.28571428571428575), aligns: 3, po1: 59, po2: 64\n",
+      "ontology iterations: 7552, (0.3333333333333333, 0.3333333333333333, 0.3333333333333333), aligns: 3, po1: 59, po2: 64\n",
       "----------------------------------------------------------------------------------------------------\n",
       "cmt.owl iasted.owl\n",
       "Loading o1\n",
@@ -166,13 +164,13 @@
       "Loading o1\n",
       "Loading o2\n",
       "2\n",
-      "ontology iterations: 3068, (0.6666666666666666, 1.0, 0.8), aligns: 2, po1: 59, po2: 26\n",
+      "ontology iterations: 3068, (1.0, 1.0, 1.0), aligns: 2, po1: 59, po2: 26\n",
       "----------------------------------------------------------------------------------------------------\n",
       "Conference.owl edas.owl\n",
       "Loading o1\n",
       "Loading o2\n",
       "3\n",
-      "ontology iterations: 6400, (0.6666666666666666, 0.6666666666666666, 0.6666666666666666), aligns: 3, po1: 64, po2: 50\n",
+      "ontology iterations: 6400, (1.0, 0.6666666666666666, 0.8), aligns: 3, po1: 64, po2: 50\n",
       "----------------------------------------------------------------------------------------------------\n",
       "cmt.owl edas.owl\n",
       "Loading o1\n",
@@ -190,7 +188,7 @@
       "Loading o1\n",
       "Loading o2\n",
       "3\n",
-      "ontology iterations: 3328, (0.5, 0.3333333333333333, 0.4), aligns: 3, po1: 64, po2: 26\n",
+      "ontology iterations: 3328, (1.0, 0.3333333333333333, 0.5), aligns: 3, po1: 64, po2: 26\n",
       "----------------------------------------------------------------------------------------------------\n",
       "confOf.owl edas.owl\n",
       "Loading o1\n",
@@ -203,7 +201,7 @@
       "Loading o2\n",
       "4\n",
       "ontology iterations: 4608, (1.0, 0.5, 0.6666666666666666), aligns: 4, po1: 64, po2: 36\n",
-      "iterations: 74590, (0.6857142857142857, 0.5217391304347826, 0.5925925925925927)\n"
+      "iterations: 74590, (0.8275862068965517, 0.5217391304347826, 0.64)\n"
      ]
     }
    ],
@@ -213,23 +211,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 4,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-05-04T23:13:14.075532740Z",
-     "start_time": "2023-05-04T23:13:13.788604059Z"
+     "end_time": "2023-06-01T13:30:47.366350949Z",
+     "start_time": "2023-06-01T13:30:46.430444165Z"
     }
    },
    "outputs": [
     {
-     "ename": "NameError",
-     "evalue": "name 'results' is not defined",
+     "ename": "TypeError",
+     "evalue": "'float' object is not iterable",
      "output_type": "error",
      "traceback": [
       "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
-      "\u001B[0;31mNameError\u001B[0m                                 Traceback (most recent call last)",
-      "Cell \u001B[0;32mIn[1], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m p, r, f \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mzip\u001B[39m(\u001B[38;5;241m*\u001B[39m\u001B[43mresults\u001B[49m)\n\u001B[1;32m      3\u001B[0m x \u001B[38;5;241m=\u001B[39m np\u001B[38;5;241m.\u001B[39marange(\u001B[38;5;241m0.0\u001B[39m, \u001B[38;5;241m1\u001B[39m, \u001B[38;5;241m0.01\u001B[39m)\n\u001B[1;32m      5\u001B[0m plt\u001B[38;5;241m.\u001B[39mplot(x, p, label\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mprecision\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
-      "\u001B[0;31mNameError\u001B[0m: name 'results' is not defined"
+      "\u001B[0;31mTypeError\u001B[0m                                 Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[4], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m p, r, f \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mzip\u001B[39;49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mresults\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m      3\u001B[0m x \u001B[38;5;241m=\u001B[39m np\u001B[38;5;241m.\u001B[39marange(\u001B[38;5;241m0.0\u001B[39m, \u001B[38;5;241m1\u001B[39m, \u001B[38;5;241m0.01\u001B[39m)\n\u001B[1;32m      5\u001B[0m plt\u001B[38;5;241m.\u001B[39mplot(x, p, label\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mprecision\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
+      "\u001B[0;31mTypeError\u001B[0m: 'float' object is not iterable"
      ]
     }
    ],

main.py

+from sentence_transformers import SentenceTransformer
+from models import Finbank
+import random
+import torch
+import numpy as np
+from property_matching import PropertyMatcher
+from tqdm.auto import tqdm
+from property_matching import most_common_pair
+import matplotlib.pyplot as plt
+import argparse
+import rdflib
+import tempfile
+from urllib import parse, request
+from om.ont import get_namespace
+
+
+def parse_arguments():
+    arg_parser = argparse.ArgumentParser(description='LD similarity.')
+
+    arg_parser.add_argument('source', help='Source ontology path.')
+    arg_parser.add_argument('target', help='Target ontology path.')
+    arg_parser.add_argument('--output', dest='output', default='./output', help='Folder to save the results.')
+    arg_parser.add_argument('--format', dest='format', default='align', choices=['align', 'sssom'], help='Output format.')
+
+    return arg_parser.parse_args()
+
+
+def toAlignFormat(aligns, onto1, onto2, location1, location2):
+    data = ["""<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<rdf:RDF xmlns='http://knowledgeweb.semanticweb.org/heterogeneity/alignment#'
+         xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+         xmlns:xsd='http://www.w3.org/2001/XMLSchema#'
+         xmlns:align='http://knowledgeweb.semanticweb.org/heterogeneity/alignment#'>"""]
+
+    data.append(f"""    <Alignment>
+        <xml>yes</xml>
+        <level>0</level>
+        <type>**</type>
+        <onto1>
+            <Ontology rdf:about="{onto1}">
+                <location>{location1}</location>
+            </Ontology>
+        </onto1>
+        <onto2>
+            <Ontology rdf:about="{onto2}">
+                <location>{location2}</location>
+            </Ontology>
+        </onto2>""")
+
+    for (entity1, entity2), confidence in aligns.items():
+        data.append(f"""        <map>
+            <Cell>
+                <entity1 rdf:resource="{entity1}"/>
+                <entity2 rdf:resource="{entity2}"/>
+                <relation>=</relation>
+                <measure rdf:datatype="http://www.w3.org/2001/XMLSchema#float">{confidence}</measure>
+            </Cell>
+        </map>""")
+
+    data.append("""    </Alignment>
+</rdf:RDF>""")
+
+    return '\n'.join(data)
+
+def ssom(aligns):
+    lines = ['subject_id\tpredicate_id\tobject_id\tmapping_justification\tconfidence']
+    for (entity1, entity2), confidence in aligns.items():
+        lines.append(f"{entity1}\tskos:exactMatch\t{entity2}\tsemapv:LexicalMatching\t{confidence}")
+
+    return "\n".join(lines)
+
+if __name__ == '__main__':
+    args = parse_arguments()
+    wm = Finbank('/home/guilherme/Documents/kg/fin.bin')
+    model = SentenceTransformer('sentence-transformers/all-MiniLM-L6-v2')
+    property_matcher = PropertyMatcher(wm, model)
+
+    o1 = rdflib.Graph().parse(args.source)
+    o2 = rdflib.Graph().parse(args.target)
+
+    p, it = property_matcher.match_ontologies(o1, o2, 0.65)
+
+
+
+    # Parser
+
+
+    if args.format == 'sssom':
+        result = ssom(p)
+        suffix = '.tsv'
+    else:
+        result = toAlignFormat(p, get_namespace(o1), get_namespace(o2), args.source, args.target)
+        suffix = '.rdf'
+
+    with tempfile.NamedTemporaryFile('w', prefix='alignment_', suffix=suffix, delete=False) as out_file:
+        out_file.write(result)
+
+        print(parse.urljoin("file:", request.pathname2url(out_file.name)))

property_matching.py

@@ -14,6 +14,7 @@ from collections import Counter
 from tqdm.auto import tqdm
 import math
 
+
 def get_type_h(e, g, ml=1):
     if type(e) is Literal:
         return [e.datatype]
@@ -283,9 +284,6 @@ def get_prop(e, g, p):
     return s, objc
 
 
-
-
-
 def build_tf_models(o1, o2):
     a_entities = set(filter(lambda x: is_property(x, o1), o1.subjects()))
     b_entities = set(filter(lambda x: is_property(x, o2), o2.subjects()))
@@ -380,7 +378,6 @@ class PropertyMatcher:
                     sim = 0
                 label_confidence = sim
 
-
         if sim_weights:
             conf = []
             if 0 in sim_weights:
@@ -403,7 +400,6 @@ class PropertyMatcher:
         if tr is not None:
             trm = [[0, 0] for _ in tr]
 
-
         for r, k1, k2 in tqdm(list(onts(base, ref))):
 
             print('-' * 100)
@@ -457,7 +453,8 @@ class PropertyMatcher:
 
                     trm[i][0] += len(pa.intersection(cp))
                     trm[i][1] += len(cp)
-                    print(f'ontology iterations: {oi}, {metrics(len(pa.intersection(cp)), len(cp), current_total)}, aligns: {current_total}, po1: {len(a_entities)}, po2: {len(b_entities)}')
+                    print(
+                        f'ontology iterations: {oi}, {metrics(len(pa.intersection(cp)), len(cp), current_total)}, aligns: {current_total}, po1: {len(a_entities)}, po2: {len(b_entities)}')
 
             # for a1, a2 in pa.intersection(p):
             #     print(colored('✓', 'green'), get_n(a1, o1), get_n(a2, o2))
@@ -471,8 +468,9 @@ class PropertyMatcher:
             #     print(colored('X', 'red'), get_n(d1, o1), get_n(a1, o1), get_n(r1, o1), colored('<>', 'green'),
             #           get_n(d2, o2), get_n(a2, o2), get_n(r2, o2))
 
-            # print(
-            #     f'ontology iterations: {oi}, {metrics(current_correct, current_pred, current_total)}, aligns: {current_total}, po1: {len(a_entities)}, po2: {len(b_entities)}')
+            print(
+                f'ontology iterations: {oi}, {metrics(current_correct, current_pred, current_total)}, aligns: {current_total}, po1: {len(a_entities)}, po2: {len(b_entities)}')
+
         print(f'iterations: {iterations}, {metrics(correct, pred, total)}')
         if tr is not None:
             res = []
@@ -540,6 +538,4 @@ class PropertyMatcher:
                         pm[iv1] = (iv2, sim)
                         pm[iv2] = (iv1, sim)
 
-
         return p, iterations
-