Appendix

Using ineo as Neo4j Management Software

Install ineo

  • Download and install ineo

    • Citehound relies heavily on a graph database and requires at least 1 running Neo4J server.

    • You can install and manage one or more Neo4J servers locally or over the network (e.g. on a cloud computing provider)

    • However, we have found that certain tasks are made much easier by a Neo4J management software such as ineo and this is why it is recommended here.

Configuration

  • Creating project_base using ineo:

    > ineo create -v 4.4.0 -d project_base

    This will download and configure a new instance based on neo4j (community edition) version 4.4.0.

    Take your time to review the installation because there are some key differences from a default community installation. To do this, go ahead and run:

    > ineo list

    which will most likely reply with something like:

    > instance 'project_base'
  VERSION: 4.4.0
  EDITION: community
  PATH:    /home/someuser/.ineo/instances/project_base
  PORT:    7474
  HTTPS:   7475
  BOLT:    7476

    Warning

    Please take note of the ports that each interface is running on. Especially the BOLT port, because it will be required when onfiguring the NEO4J_BOLT_URL in the next step.

Checking that a Citehound project is active

  • > ineo status project_base

If this replies that project_base is inactive, then start it with:

  • > ineo start project_base

Preserving and re-using project_base

If you have been following up this process using ineo, then project_base is located in ~/.ineo/instances/project_base and it can be compressed with a simple: > zip -r project_base.zip ~/.ineo/instances/project_base/*.

Using project_base as the basis for a new project is as easy as copying between two “instance” directories.

For example, to kickstart a pubmed_project_1 from project_base, all you have to do is:

  1. Ensure that project_base is not running

    • > ineo stop project_base

  2. Drop to a terminal and copy project_base to pubmed_project_1

    > cd ~/.ineo/instances
> mkdir pubmed_project_1
> cp -r project_base/ pubmed_project_1/

    • Now pubmed_project_1 is pre-loaded with everything available in project_base.

  3. Start pubmed_project_1

    • > ineo start pubmed_project_1