Keywords

Research in context graph, Ricgraph, Ricgraph Explorer, Ricgraph REST API, Data enrichment, Data harvesting, Data linking, Enrichment, Graph, Graph database, Harvest, Harvest data, Harvester, Knowledge graph, Linked data, Metadata, Utrecht University, Visualization

Ricgraph known bugs

1 Error while emptying Ricgraph with Neo4j

While deleting nodes and edges in Ricgraph you might get a Python error, similar to:

Deleting all nodes and edges in Ricgraph...

Transaction failed and will be retried in [number]s (The allocation of an extra [number] MiB 
  would use more than the limit [number] MiB. Currently using [number] MiB. 
  dbms.memory.transaction.total.max threshold reached)

Traceback (most recent call last):
  File "[path]/harvest/harvest_pure_to_ricgraph.py", 
    line 729, in <module> rcg.empty_ricgraph()
  File "[path]/ricgraph/ricgraph.py", line [number], in empty_ricgraph
    _graph.execute_query('MATCH (node) DETACH DELETE node', database_=GRAPHDB_NAME)
  […]
  [module].errors.TransientError: [General.MemoryPoolOutOfMemoryError] 
    The allocation of an extra 2.0 MiB would use more than the limit 716.8 MiB. Currently 
    using 715.0 MiB. dbms.memory.transaction.total.max threshold reached.

This is caused by the free-to-use version of Neo4j, which does not have a statement similar to DROP [database]. If you empty the graph database, it needs to delete every node and edge and this fails when there are a lot of nodes and edges. This happens when you use Neo4j Desktop, and might happen sometimes when you are using Neo4j Community Edition.

1.1 Solution for Neo4j Community Edition

Read Empty a Neo4j Community Edition database.

1.2 Solution for Neo4j Desktop

You can do the following for Neo4j Desktop and Ricgraph:

  1. Start Neo4j Desktop if it is not running yet.
  2. Move your mouse to “Project” in the left column. A red trash can icon appears. Click it to remove the database. Confirm.
  3. The text “No projects found” will appear. Create a project by clicking the button “+ New Project”.
  4. The text “Project” appears with the text “Add a DBMS to get started”. Click on the “+ Add” button next to it and select “Local DBMS”. Leave the name as it is (“Graph DBMS”) and fill in a password. Choose an easy to type and short one since the DBMS will only be accessible from your own machine. Click “Create”. Also, insert the password in field graphdb_password in the Ricgraph initialization file.
  5. Ready.
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