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Neo4J

This project Neo4J as our graph database.

Importing to Neo4J

Run python load_all_to_neo4j.py to generate a list of GraphML files in graphml_dump/.

The script recreates all components in all repositories. The script takes edge directions into consideration.

Place these files into the import directory of a Neo4J graph database, and run the Cypher query script cypher_scripts/Import_All_Files.cypher. Alternatively, drag and drop the full database dump (neo4j.dump in root directory) into Neo4J.

The attributes available in the database are:

  • type: one of pull_request or issue
  • status: one of merged, closed, or open
  • repository: in user/repo format
  • creation_date: Unix timestamp
  • updated_at: Unix timestamp
  • closed_at: Unix timestamp or 0 if node's status is open.
  • number: node identifier, same as pull request or issue number on GitHub
  • link_type: only for edges; one of fixes, duplicate, or other
  • user: the GitHub username of the user that created the node (or for edges, the comment linking the two nodes)
  • user_url: URL to GitHub page of user
  • url: URL to node's GitHub page; similarly, link_url links to the mentioning issue's GitHub page

Querying

Copy-paste one of the topology pattern scripts in cypher_scripts/ in the Neo4J Browser to return results.

Our queries will visualize both the matches and the components the matches were found in.

Neo4J will match subgraphs separately. For example, if a query is for an issue linked to a pull request, and there is one issue linking to many pull requests, each issue / pull request match is returned separately. Neo4J also may return duplicate nodes if running a collect, so ensure collect(distinct ...) is used instead. This may be salient when returning counts.

Take care when using Neo4J collect statements to collect information about all instances. If used like so, it will return only the distinct IDs within a match:

with i, collect(distinct id(i)) as ids

To get all IDs over all matches, use a subquery call first. The result can then be included into the scope of the remaining query with with.

match (i)
where ...
return collect(distinct id(i)) as ids

Excluding Matches

Some topologies require other topologies to be excluded before they can be matched. For example, matches of Consequence 2 will all contain matches for Consequence 1, so matches of Consequence 2 need to be excluded before querying for Consequence 1 to ensure their results are mutually exclusive.

This can be done by collecting a list of node IDs (Neo4J-assigned) for all known matches of a topology. Because of the way Neo4J's collect works, the query for the excluded topology must be called in the query for the topology to be matched.

  • First, run the match for the excluded topology and collect all node IDs (i.e. return collect(distinct id(i))+collect(distinct id(p)) as exclude_ids)
  • Then, run the match for the topology to be matched, and assert none of its node IDs are in the list of exclude_ids

This technique is used in several queries, including for excluding Dependent PRs from PR Hubs and PR Hubs from Improvements. Note how the pattern dependencies 'chain' into queries: the query for exclusion of Dependent PRs from PR Hubs must also be executed in the Improvements query.

Dependent PR Query Generation

The Dependent PR topology is unique in that Neo4J does not have a feature to match a path of unspecified length while specifying properties of nodes on that path, so queries are generated with a script.

python -m cypher_scripts.generate_pr_stack --size=[size] will generate a query for a stack of the specified size, and save it to cypher_scripts/PR_Stack_Gen.cypher.

The same query generation function is used in cypher_scripts/fetch_all_pr_stack_ids.py to statically fetch all IDs of nodes in a Dependent PR topology. The script prints the set of node IDs, as well as saving them to cypher_scripts/all_ids_dump. This makes the PR Hub and Improvement queries more efficient as the list of IDs can be loaded statically without running many iterations of the Dependent PR subquery.