Add webapp

app.py

@@ -0,0 +1,304 @@
+from flask import (
+    Flask,
+    render_template,
+    request,
+)
+from kgcl.model.kgcl import (
+    NodeRename,
+    NodeObsoletion,
+    NodeUnobsoletion,
+    NodeDeletion,
+    NodeMove,
+    NodeDeepening,
+    NodeShallowing,
+    EdgeCreation,
+    EdgeDeletion,
+    PredicateChange,
+    NodeCreation,
+    ClassCreation,
+    NewSynonym,
+    RemovedNodeFromSubset,
+)
+
+import os
+from kgcl.apply.graph_transformer import apply_patch
+
+# from kgcl.diff.example_kgcl_operations import generate_diff
+import rdflib
+from kgcl.grammar.parser import parse
+
+import diff.diff_2_kgcl_single as single
+from diff.diff_2_kgcl_single import SingleTripleChangeSummary
+import diff.diff_2_kgcl_existential as existential
+from diff.diff_2_kgcl_existential import ExistentialChangeSummary
+import diff.diff_2_kgcl_triple_annotation as annotation
+from diff.diff_2_kgcl_triple_annotation import TripleAnnotationChangeSummary
+
+# from diff.example_kgcl_operations import generate_diff
+from render_kgcl import render
+
+
+def generate_diff():
+    pass
+
+
+app = Flask(__name__)
+
+
+# we could store changes in a data base - do we want to
+@app.route("/", methods=["POST", "GET"])
+def index():
+    examples = [
+        "rename",
+        "nodeCreation",
+        "nodeDeletionByLabel",
+        "nodeDeletionById",
+        "obsoleteByLabel",
+        "obsoleteById",
+        "unobsoleteById",
+        "nodeDeepening",
+        "nodeShallowing",
+        "move",
+        "edgeCreation",
+        "edgeDeletion",
+        "addExistential",
+        "addSubsumptionAxiom",
+        "annotatedEdgeCreation",
+        "annotatedEdgeDeletion",
+        "changeRelationship",
+        "createSynonym",
+        "deleteExistential",
+        "deleteSubsumptionAxiom",
+    ]
+
+    if request.method == "POST":
+
+        if "apply_changes" in request.form:
+
+            # get input graph from form
+            graph = request.form["graph"]
+
+            # get input kgcl statements from form
+            kgcl = request.form["kgcl"]
+
+            kgcl_transformation(graph, kgcl)
+
+        if "load_example" in request.form:
+            select = request.form.get("comp_select")
+            example = str(select)
+
+            f = open("examples/kgcl/" + example + "/graph.nt", "r")
+            graph = f.read()
+            f.close()
+
+            f = open("examples/kgcl/" + example + "/kgcl", "r")
+            kgcl = f.read()
+            f.close()
+
+            kgcl_transformation(graph, kgcl)
+
+        # parse KGCL input
+        kgcl_model = parse(kgcl)
+
+        # prepare parsed
+        kgcl_model_rendering = ""
+        for o in kgcl_model:
+            kgcl_model_rendering += render(o) + "\n"
+
+        # load transformed graph
+        f = open("examples/kgcl/tmp/transformation.nt", "r")
+        transformation = f.read()
+        f.close()
+
+        return render_template(
+            "index.html",
+            inputGraph=graph,
+            inputKGCL=kgcl,
+            parsedKGCL=kgcl_model_rendering,
+            outputGraph=transformation,
+            examples=examples,
+        )
+
+    else:
+        # load rename example by default
+
+        # load graph
+        f = open("examples/kgcl/rename/graph.nt", "r")
+        graph = f.read()
+        f.close()
+
+        # load kgcl
+        f = open("examples/kgcl/rename/kgcl", "r")
+        kgcl = f.read()
+        f.close()
+
+        kgcl_transformation(graph, kgcl)
+
+        # parse KGCL input
+        kgcl_model = parse(kgcl)
+
+        # prepare parsed
+        kgcl_model_rendering = ""
+        for o in kgcl_model:
+            kgcl_model_rendering += render(o) + "\n"
+
+        # load transformed graph
+        f = open("examples/kgcl/tmp/transformation.nt", "r")
+        transformation = f.read()
+        f.close()
+
+        # return render_template("index.html", examples=examples)
+        return render_template(
+            "index.html",
+            inputGraph=graph,
+            inputKGCL=kgcl,
+            parsedKGCL=kgcl_model_rendering,
+            outputGraph=transformation,
+            examples=examples,
+        )
+
+
+@app.route("/diff", methods=["POST", "GET"])
+def diff():
+
+    examples = [
+        "rename",
+        "classCreation",
+        "obsoletion",
+        "unobsoletion",
+        "move",
+        "edgeCreation",
+        "edgeDeletion",
+    ]
+
+    # initialise variables
+    graph1 = ""
+    graph2 = ""
+    kgcl = ""
+
+    if request.method == "POST":
+
+        if "generate_diff" in request.form:
+            graph1 = request.form["graph1"]
+            graph2 = request.form["graph2"]
+
+            kgcl_diff(graph1, graph2)
+
+        if "load_example_diff" in request.form:
+            select = request.form.get("comp_select")
+            example = str(select)
+
+            f = open("examples/diff/" + example + "/graph1.nt", "r")
+            graph1 = f.read()
+            f.close()
+
+            f = open("examples/diff/" + example + "/graph2.nt", "r")
+            graph2 = f.read()
+            f.close()
+
+            kgcl_diff(graph1, graph2)
+
+        f = open("examples/kgcl/tmp/patch.kgcl", "r")
+        kgcl = f.read()
+        f.close()
+
+        return render_template(
+            "diff.html",
+            examples=examples,
+            kgclDiff=kgcl,
+            inputGraph1=graph1,
+            inputGraph2=graph2,
+        )
+    else:
+        # load rename by default
+        example = "rename"
+
+        f = open("examples/diff/" + example + "/graph1.nt", "r")
+        graph1 = f.read()
+        f.close()
+
+        f = open("examples/diff/" + example + "/graph2.nt", "r")
+        graph2 = f.read()
+        f.close()
+
+        kgcl_diff(graph1, graph2)
+
+        f = open("diff/stats/all", "r")
+        kgcl = f.read()
+        f.close()
+
+        return render_template(
+            "diff.html",
+            examples=examples,
+            kgclDiff=kgcl,
+            inputGraph1=graph1,
+            inputGraph2=graph2,
+        )
+
+
+# def parse(input):
+#     return parsing.parse(input)
+
+
+def kgcl_transformation(graph, kgcl):
+    # store graph as file
+    f = open("examples/kgcl/tmp/graph.nt", "w")
+    f.write(graph)
+    f.close()
+
+    # store kgcl statements
+    f = open("examples/kgcl/tmp/kgcl", "w")
+    f.write(kgcl)
+    f.close()
+
+    # parse KGCL input
+    parsed_statements = parse(kgcl)
+
+    # load input graph from file
+    g = rdflib.Graph()
+    g.load("examples/kgcl/tmp/graph.nt", format="nt")
+
+    # transform graph
+    apply_patch(parsed_statements, g)
+
+    # save graph
+    # TODO: get text representation of graph without writing to a file
+    g.serialize(destination="examples/kgcl/tmp/transformation.nt", format="nt")
+
+
+def kgcl_diff(graph1, graph2):
+    # store graph as file
+    f = open("examples/kgcl/tmp/graph1.nt", "w")
+    f.write(graph1)
+    f.close()
+
+    f = open("examples/kgcl/tmp/graph2.nt", "w")
+    f.write(graph2)
+    f.close()
+
+    # generate diff
+    # load graphs
+    g1 = rdflib.Graph()
+    g2 = rdflib.Graph()
+    g1.load("examples/kgcl/tmp/graph1.nt", format="nt")
+    g2.load("examples/kgcl/tmp/graph2.nt", format="nt")
+
+    # compute diff
+    existential_summary = existential.generate_atomic_existential_commands(g1, g2)
+    triple_annotation_summary = annotation.generate_triple_annotation_commands(g1, g2)
+    single_triple_summary = single.generate_thin_triple_commands(g1, g2)
+
+    # get KGCL commands
+    kgcl_commands = existential_summary.get_commands()
+    kgcl_commands += triple_annotation_summary.get_commands()
+    kgcl_commands += single_triple_summary.get_commands()
+
+    # write KGCL commands
+    with open("examples/kgcl/tmp/patch.kgcl", "w") as f:
+        for k in kgcl_commands:
+            f.write(k)
+            f.write("\n")
+
+
+if __name__ == "__main__":
+    app.run(debug=True)

examples/diff/classCreation/graph2.nt

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+<http://purl.obolibrary.org/obo/UBERON_0017671> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .

examples/diff/edgeCreation/graph2.nt

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+<http://purl.obolibrary.org/obo/UBERON_0005875> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_4000142> .

examples/diff/edgeDeletion/graph1.nt

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+<http://purl.obolibrary.org/obo/UBERON_0005875> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_4000142> .

examples/diff/move/graph1.nt

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+<http://purl.obolibrary.org/obo/UBERON_0005875> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_0005879> .

examples/diff/move/graph2.nt

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+<http://purl.obolibrary.org/obo/UBERON_0005875> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_4000142> .

examples/diff/obsoletion/graph1.nt

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+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2000/01/rdf-schema#label> "metaplastic ossification" .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_0005879> .

examples/diff/obsoletion/graph2.nt

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+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2000/01/rdf-schema#label> "obsolete metaplastic ossification" .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2002/07/owl#deprecated> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .

examples/diff/rename/graph1.nt

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+<http://purl.obolibrary.org/obo/UBERON_0007176> <http://www.w3.org/2000/01/rdf-schema#label> "superior angle of scapula" .

examples/diff/rename/graph2.nt

@@ -0,0 +1 @@
+<http://purl.obolibrary.org/obo/UBERON_0007176> <http://www.w3.org/2000/01/rdf-schema#label> "inferior angle of scapula" .

examples/diff/unobsoletion/graph1.nt

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+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2000/01/rdf-schema#label> "obsolete metaplastic ossification" .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2002/07/owl#deprecated> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .

examples/diff/unobsoletion/graph2.nt

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+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/2000/01/rdf-schema#label> "metaplastic ossification" .
+<http://purl.obolibrary.org/obo/UBERON_4000142> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .

examples/kgcl/addExistential/kgcl

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+add <http://example.org/subject> SubClassOf <http://example.org/predicate> some <http://example.org/object>

examples/kgcl/addSubsumptionAxiom/kgcl

@@ -0,0 +1 @@
+add <http://example.org/subclass> SubClassOf <http://example.org/superclass>

examples/kgcl/annotatedEdgeCreation/kgcl

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+create edge <<<http://example.org/subject> <http://example.org/predicate> <http://example.org/object>>> <http://example.org/annotationPredicate> <http://example.org/annotation>

examples/kgcl/annotatedEdgeDeletion/graph.nt

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+_:N21088129e79d457c952ec747c2124281 <http://example.org/annotationPredicate> <http://example.org/annotation> .
+_:N21088129e79d457c952ec747c2124281 <http://www.w3.org/2002/07/owl#annotatedProperty> <http://example.org/predicate> .
+_:N21088129e79d457c952ec747c2124281 <http://www.w3.org/2002/07/owl#annotatedSource> <http://example.org/subject> .
+_:N21088129e79d457c952ec747c2124281 <http://www.w3.org/2002/07/owl#annotatedTarget> <http://example.org/object> .
+_:N21088129e79d457c952ec747c2124281 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Axiom> .

examples/kgcl/annotatedEdgeDeletion/kgcl

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+delete edge <<<http://example.org/subject> <http://example.org/predicate> <http://example.org/object>>> <http://example.org/annotationPredicate> <http://example.org/annotation>

examples/kgcl/changeRelationship/graph.nt

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+<http://example.org/subclass> <http://example.org/partOf> <http://example.org/superclass> .

examples/kgcl/changeRelationship/kgcl

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+change relationship between <http://example.org/subclass> and <http://example.org/superclass> from <http://example.org/partOf> to <http://example.org/hasPart>

examples/kgcl/createSynonym/graph.nt

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+<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://www.w3.org/2000/01/rdf-schema#label> "Bacteria" .

examples/kgcl/createSynonym/kgcl

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+create synonym 'Virus' for <http://purl.obolibrary.org/obo/NCBITaxon_2>
+create exact synonym 'Eubacteria' for <http://purl.obolibrary.org/obo/NCBITaxon_2>
+create related synonym 'Disease' for <http://purl.obolibrary.org/obo/NCBITaxon_2>
+create narrow synonym 'Bacterium' for <http://purl.obolibrary.org/obo/NCBITaxon_2>
+create broad synonym 'Infection'@en for <http://purl.obolibrary.org/obo/NCBITaxon_2>

examples/kgcl/deleteExistential/graph.nt

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+_:Ndb451c3aad3841c88d7042f29b20bea8 <http://www.w3.org/2002/07/owl#onProperty> <http://example.org/predicate> .
+_:Ndb451c3aad3841c88d7042f29b20bea8 <http://www.w3.org/2002/07/owl#someValuesFrom> <http://example.org/object> .
+_:Ndb451c3aad3841c88d7042f29b20bea8 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction> .
+<http://example.org/subject> <http://www.w3.org/2000/01/rdf-schema#subClassOf> _:Ndb451c3aad3841c88d7042f29b20bea8 .

examples/kgcl/deleteExistential/kgcl

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+delete <http://example.org/subject> SubClassOf <http://example.org/predicate> some <http://example.org/object>

examples/kgcl/deleteSubsumptionAxiom/graph.nt

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+<http://example.org/targetClass> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://example.org/A> .

examples/kgcl/deleteSubsumptionAxiom/kgcl

@@ -0,0 +1 @@
+delete <http://example.org/targetClass> SubClassOf <http://example.org/A>

examples/kgcl/edgeCreation/kgcl

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+create edge <http://example.org/subject> <http://example.org/predicate> <http://example.org/object>

examples/kgcl/edgeDeletion/graph.nt

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+<http://example.org/subject> <http://example.org/predicate> <http://example.org/object> .

examples/kgcl/edgeDeletion/kgcl

@@ -0,0 +1 @@
+delete edge <http://example.org/subject> <http://example.org/predicate> <http://example.org/object>

examples/kgcl/move/graph.nt

@@ -0,0 +1 @@
+<http://example.org/targetClass> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://example.org/A> .

examples/kgcl/move/kgcl

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+move <http://example.org/targetClass> from <http://example.org/A> to <http://example.org/B>

examples/kgcl/nodeCreation/kgcl

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+create node <http://purl.obolibrary.org/obo/NCBITaxon_2> 'Bacteria'
+create <http://purl.obolibrary.org/obo/NCBITaxon_4>

examples/kgcl/nodeDeepening/graph.nt

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+<http://example.org/targetClass> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://example.org/superclass> .
+<http://example.org/subclass> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://example.org/superclass> .

examples/kgcl/nodeDeepening/kgcl

@@ -0,0 +1 @@
+deepen <http://example.org/targetClass> from <http://example.org/superclass> to <http://example.org/subclass>

examples/kgcl/nodeDeletionById/graph.nt

@@ -0,0 +1,4 @@
+<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://www.w3.org/2000/01/rdf-schema#label> "Bacteria" .
+<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/OBI_0100026> .
+<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
+<http://purl.obolibrary.org/obo/OBI_0100026> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .

examples/kgcl/nodeDeletionById/kgcl

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+delete <http://purl.obolibrary.org/obo/NCBITaxon_2>