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Use already calculated node embeddings if available
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+73
-15
lines changed

5 files changed

+73
-15
lines changed

‎cypher/Node_Embeddings/Node_Embeddings_0a_Query_Calculated.cypher‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
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// Query already calculated and written node embeddings on nodes with label in parameter $dependencies_projection_node including a communityId and centrality. Variables: dependencies_projection_node, dependencies_projection_write_property
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3+
MATCH (codeUnit)
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WHERE $dependencies_projection_node IN LABELS(codeUnit)
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AND codeUnit[$dependencies_projection_write_property] IS NOT NULL
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// AND codeUnit.notExistingToForceRecalculation IS NOT NULL // uncomment this line to force recalculation
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OPTIONAL MATCH (artifact:Java:Artifact)-[:CONTAINS]->(codeUnit)
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WITH *, replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
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OPTIONAL MATCH (projectRoot:Directory)<-[:HAS_ROOT]-(proj:TS:Project)-[:CONTAINS]->(codeUnit)
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WITH *, last(split(projectRoot.absoluteFileName, '/')) AS projectName
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RETURN DISTINCT
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coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
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,coalesce(codeUnit.name, replace(last(split(codeUnit.fileName, '/')), '.jar', '')) AS shortCodeUnitName
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,coalesce(artifactName, projectName) AS projectName
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,coalesce(codeUnit.communityLeidenId, 0) AS communityId
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,coalesce(codeUnit.centralityPageRank, 0.01) AS centrality
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,codeUnit[$dependencies_projection_write_property] AS embedding
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ORDER BY communityId

‎cypher/Node_Embeddings/Node_Embeddings_1d_Fast_Random_Projection_Stream.cypher‎

Lines changed: 11 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,14 @@ CALL gds.fastRP.stream(
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YIELD nodeId, embedding
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WITH gds.util.asNode(nodeId) AS codeUnit
1111
,embedding
12-
OPTIONAL MATCH (artifact:Artifact)-[:CONTAINS]->(codeUnit)
13-
RETURN DISTINCT coalesce(codeUnit.fqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
14-
,coalesce(codeUnit.communityLeidenId, 0) AS communityId
15-
,coalesce(codeUnit.centralityPageRank, 0.01) AS centrality
16-
,replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
17-
,embedding
12+
OPTIONAL MATCH (artifact:Java:Artifact)-[:CONTAINS]->(codeUnit)
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WITH *, replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
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OPTIONAL MATCH (projectRoot:Directory)<-[:HAS_ROOT]-(proj:TS:Project)-[:CONTAINS]->(codeUnit)
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WITH *, last(split(projectRoot.absoluteFileName, '/')) AS projectName
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RETURN DISTINCT
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coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
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,coalesce(codeUnit.name, replace(last(split(codeUnit.fileName, '/')), '.jar', '')) AS shortCodeUnitName
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,coalesce(artifactName, projectName) AS projectName
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,coalesce(codeUnit.communityLeidenId, 0) AS communityId
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,coalesce(codeUnit.centralityPageRank, 0.01) AS centrality
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,embedding

‎cypher/Node_Embeddings/Node_Embeddings_2d_Hash_GNN_Stream.cypher‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,9 +14,14 @@ CALL gds.beta.hashgnn.stream(
1414
YIELD nodeId, embedding
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WITH gds.util.asNode(nodeId) AS codeUnit
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,embedding
17-
OPTIONAL MATCH (artifact:Artifact)-[:CONTAINS]->(codeUnit)
18-
RETURN DISTINCT coalesce(codeUnit.fqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
17+
OPTIONAL MATCH (artifact:Java:Artifact)-[:CONTAINS]->(codeUnit)
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WITH *, replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
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OPTIONAL MATCH (projectRoot:Directory)<-[:HAS_ROOT]-(proj:TS:Project)-[:CONTAINS]->(codeUnit)
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WITH *, last(split(projectRoot.absoluteFileName, '/')) AS projectName
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RETURN DISTINCT
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coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
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,coalesce(codeUnit.name, replace(last(split(codeUnit.fileName, '/')), '.jar', '')) AS shortCodeUnitName
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,coalesce(artifactName, projectName) AS projectName
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,coalesce(codeUnit.communityLeidenId, 0) AS communityId
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,coalesce(codeUnit.centralityPageRank, 0.01) AS centrality
21-
,replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
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,embedding

‎cypher/Node_Embeddings/Node_Embeddings_3d_Node2Vec_Stream.cypher‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,14 @@ CALL gds.node2vec.stream(
1010
YIELD nodeId, embedding
1111
WITH gds.util.asNode(nodeId) AS codeUnit
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,embedding
13-
OPTIONAL MATCH (artifact:Artifact)-[:CONTAINS]->(codeUnit)
14-
RETURN DISTINCT coalesce(codeUnit.fqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
13+
OPTIONAL MATCH (artifact:Java:Artifact)-[:CONTAINS]->(codeUnit)
14+
WITH *, replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
15+
OPTIONAL MATCH (projectRoot:Directory)<-[:HAS_ROOT]-(proj:TS:Project)-[:CONTAINS]->(codeUnit)
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WITH *, last(split(projectRoot.absoluteFileName, '/')) AS projectName
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RETURN DISTINCT
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coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
19+
,coalesce(codeUnit.name, replace(last(split(codeUnit.fileName, '/')), '.jar', '')) AS shortCodeUnitName
20+
,coalesce(artifactName, projectName) AS projectName
1521
,coalesce(codeUnit.communityLeidenId, 0) AS communityId
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,coalesce(codeUnit.centralityPageRank, 0.01) AS centrality
17-
,replace(last(split(artifact.fileName, '/')), '.jar', '') AS artifactName
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,embedding

‎jupyter/NodeEmbeddings.ipynb‎

Lines changed: 28 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -108,6 +108,28 @@
108108
" return pd.DataFrame([r.values() for r in records], columns=keys)"
109109
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "bd1d9775",
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"metadata": {},
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"outputs": [],
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"source": [
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"def query_first_non_empty_cypher_to_data_frame(*filenames : str, parameters: typ.Optional[typ.Dict[str, typ.Any]] = None):\n",
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" \"\"\"\n",
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" Executes the Cypher queries of the given files and returns the first result that is not empty.\n",
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" If all given file names result in empty results, the last (empty) result will be returned.\n",
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" By additionally specifying \"limit=\" the \"LIMIT\" keyword will appended to query so that only the first results get returned.\n",
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" \"\"\"\n",
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" result=pd.DataFrame()\n",
125+
" for filename in filenames:\n",
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" result=query_cypher_to_data_frame(filename, parameters)\n",
127+
" if not result.empty:\n",
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" print(\"The results have been provided by the query filename: \" + filename)\n",
129+
" return result\n",
130+
" return result"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
@@ -177,7 +199,8 @@
177199
" empty_result = pd.DataFrame(columns=[\"codeUnitName\", 'projectName', 'communityId', 'centrality', 'embedding'])\n",
178200
" return empty_result\n",
179201
"\n",
180-
" embeddings = query_cypher_to_data_frame(cypher_file_name, parameters)\n",
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" existing_embeddings_query_filename=\"../cypher/Node_Embeddings/Node_Embeddings_0a_Query_Calculated.cypher\"\n",
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" embeddings = query_first_non_empty_cypher_to_data_frame(existing_embeddings_query_filename, cypher_file_name, parameters=parameters)\n",
181204
" display(embeddings.head()) # Display the first entries of the table\n",
182205
" return embeddings"
183206
]
@@ -210,7 +233,7 @@
210233
" # and the code unit and artifact name of the query above as preparation for the plot\n",
211234
" node_embeddings_for_visualization = pd.DataFrame(data = {\n",
212235
" \"codeUnit\": embeddings.codeUnitName,\n",
213-
" \"artifact\": embeddings.artifactName,\n",
236+
" \"artifact\": embeddings.projectName,\n",
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" \"communityId\": embeddings.communityId,\n",
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" \"centrality\": embeddings.centrality,\n",
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" \"x\": [value[0] for value in two_dimension_node_embeddings],\n",
@@ -316,7 +339,8 @@
316339
" \"dependencies_projection\": \"java-package-embeddings-notebook\",\n",
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" \"dependencies_projection_node\": \"Package\",\n",
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" \"dependencies_projection_weight_property\": \"weight25PercentInterfaces\",\n",
319-
" \"dependencies_projection_embedding_dimension\":\"64\" \n",
342+
" \"dependencies_projection_write_property\": \"embeddingsFastRandomProjection\",\n",
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" \"dependencies_projection_embedding_dimension\":\"64\"\n",
320344
"}\n",
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"embeddings = create_node_embeddings(\"../cypher/Node_Embeddings/Node_Embeddings_1d_Fast_Random_Projection_Stream.cypher\", java_package_embeddings_parameters)\n"
322346
]
@@ -396,6 +420,7 @@
396420
" \"dependencies_projection\": \"typescript-module-embeddings-notebook\",\n",
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" \"dependencies_projection_node\": \"Module\",\n",
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" \"dependencies_projection_weight_property\": \"lowCouplingElement25PercentWeight\",\n",
423+
" \"dependencies_projection_write_property\": \"embeddingsFastRandomProjection\",\n",
399424
" \"dependencies_projection_embedding_dimension\":\"64\" \n",
400425
"}\n",
401426
"embeddings = create_node_embeddings(\"../cypher/Node_Embeddings/Node_Embeddings_1d_Fast_Random_Projection_Stream.cypher\", typescript_module_embeddings_parameters)\n"

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