Ricgraph

The following improvements have been made to Ricgraph.

Ricgraph general:
- Modifications for a new Ricgraph logo.

Ricgraph Explorer:
- Added the possibility to show a customised text on the home page.
- Added the version number of Ricgraph in the footer.
- Added the possibility to show a privacy statement or a privacy measures document in the footer.
- Added a list that contains all possible values of the *name* field that contain personal data in a Ricgraph node. This is shown in the Statistics section of the Home page, and it can be queried using the REST API call get_ricgraph_list().
- REST API call /organization/information_persons_results now has a *name_want* and *category_want* field that let you specify what to return.
- New REST API call /organization/enrich with similar parameters as /organization/information_persons_results.
- Added *name_want* and *category_want* to /person/enrich. Updated documentation to reflect this.
- Minor changes in the user interface.

Harvest scripts:
- During harvesting OpenAlex, also *ROR* identifiers are being added to Ricgraph, they will be connected to *ORGANIZATION_NAME*.

Upgrading:
- If you upgrade from any Ricgraph version, you will need to [re-install Ricgraph](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md) and re-use your previous Ricgraph initialization file. You only need to reharvest your sources if you upgrade from version v2.4 and earlier. It is advisable to remove all of your existing files and directories, except for ricgraph.ini, before you re-install Ricgraph.

The following improvements have been made to Ricgraph.

Ricgraph general:
- _ricgraph.py_ in directory _ricgraph_ has been converted to Python package _ricgraph_ in the Python Package Index (PyPI) and can be found at https://pypi.org/project/ricgraph.
- Added a bash script _update_version.bash_ to propagate a new version number to various files that contain a version number (such as Makefile, CITATION.cff, __init__.py, etc).

Upgrading:
- If you upgrade from any Ricgraph version, you will need to [re-install Ricgraph](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md) and re-use your previous Ricgraph initialization file. You only need to reharvest your sources if you upgrade from version v2.4 and earlier. It is advisable to remove all of your existing files and directories, except for ricgraph.ini, before you re-install Ricgraph.

The following improvements have been made to Ricgraph.

Ricgraph general:
- Created scripts to import and export nodes and edges from/to csv files.
- The Makefile has been extended and improved. There are more targets and it runs on more Linux editions.
- Created a *maintenance_scripts* directory.
- Renamed directory *export_ricgraph_examples* to *import_export*.

Ricgraph:
- Ricgraph now has a call to merge nodes.
- Renamed confusing function name *cypher_merge_edge()* to *cypher_create_edge_if_not_exists()*.
- Renamed confusing function name *cypher_merge_node()* to *cypher_update_node_properties()*.

Harvest scripts:
- For all harvest scripts: modification so the organization abbreviation is always uppercase, regardless of the input of the user.
- Added research output types *Model*, *Registered report* and *Retraction*.
- OpenAlex and Yoda-DataCite harvest scripts: now organizations of every author are added to Ricgraph. If an author works for multiple organizations, all of these are added. For OpenAlex, this might produce erroneous results since for some authors the organizations they are connected to are not always correct.
- Research Software Directory harvest script: now the organization of every author is added to Ricgraph. If this author works for multiple organizations, these will not be added due to the method this is implemented in the RSD REST API output.
- Pure harvest script: now the organization of a person with an endDate at an organization in the future will be added to Ricgraph (up until now it was assumed that in such a case the field 'endDate' would not be present).
- Added a batch script to harvest Delft University of Technology sources, a batch script to harvest Utrecht University sources, and an example batch script that harvest sources (Yoda-DataCite, Research Software Directory) that do not need an API key.

Documentation:
- Added a [documentation table of contents](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_toc_documentation.md) and [documentation index](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_index_documentation.md).
- Extended and clarified documentation.

Upgrading:
- If you upgrade from any Ricgraph version, you will need to [re-install Ricgraph](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md), re-use your previous Ricgraph initialization file, and reharvest your sources. This is due to the many changes. It is advisable to remove all of your existing files and directories, except for ricgraph.ini, before you re-install Ricgraph.

The following improvements have been made to Ricgraph.

Structural changes:
- Ricgraph now has a [Makefile](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md#ricgraph-makefile). A Ricgraph installation involves a number of steps. This Makefile makes installation of (parts of) Ricgraph easier, since it automates a number of these steps.
- Now, you can also use the Nginx webserver for Ricgraph. It was already possible to use the Apache webserver.

Documentation:
- Added Ricgraph presentations: among other things, a general Ricgraph presentation and a presentation about Enriching Pure data (both with DOIs).
- Added Ricgraph newsletters.
- Various clarifications.

Upgrading:
- If you upgrade from Ricgraph v2.3, you do not need to re-install or reharvest.

The following improvements have been made to Ricgraph.

Structural changes:
- Ricgraph now has a REST API. You can use the Ricgraph REST API to get data from Ricgraph, or to execute predefined queries in Ricgraph and Ricgraph Explorer. The advantage of a REST API is that your code is not dependent on any Ricgraph code. Ricgraph Explorer has a button that shows the documentation and allow you to try out REST API calls. [Read more about this REST API](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_restapi.md).
- Ricgraph now uses a different type of index if you use Neo4j as graph database backend. This results in a much faster harvesting process and much faster queries.
- Ricgraph has a main Ricgraph website on www.ricgraph.eu. Alternative sites are www.ricgraph.nl and www.ricgraph.com. The code and the final published website are in a separate GitHub repository [Website for Ricgraph - Research in context graph](https://github.com/UtrechtUniversity/ricgraph-website).
- Ricgraph uses a new WSGI/ASGI webserver gunicorn. This is required for the REST API.

Ricgraph Explorer:
- Some pages now show histograms, e.g. of the types of research results to which a person has contributed, or the skills in a (sub-)organization.
- It is possible to adjust the maximum number of results from a query, and the maximum number of rows in a table.

Ricgraph:
- Changes to use the Neo4j elementId() function call instead of deprecated id() in neo4j. However, for memgraph, elementId() does not exist and id() should be used.

Harvest scripts:
- The harvest scripts for Pure and OpenAlex now harvest (as default) the years 2021 - 2024, this used to be 2020 - 2023.
- OpenAlex has defined new research result types. These have been added to the harvest script for OpenAlex.

Documentation:
- Documentation for the REST API, including installation instructions.
- Various clarifications.

Upgrading:
- If you upgrade from any Ricgraph version, you will need to [re-install Ricgraph](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md), re-use your previous Ricgraph initialization file, and reharvest your sources. This is due to the many changes. It is advisable to remove all of your existing files and directories, except for ricgraph.ini, before you re-install Ricgraph.
- If you don't use at least Python 3.9, you will need to upgrade to at least this Python version.

This release is the same as [Ricgraph v2.1](https://github.com/UtrechtUniversity/ricgraph/releases/tag/v2.1), except for these minor changes:
- Some mentions have been added.
- CITATION.cff is now correctly formatted (as was not the case in v2.1, which confused some metadata harvesters).

Please read the [Release notes of Ricgraph v2.1](https://github.com/UtrechtUniversity/ricgraph/releases/tag/v2.1) to read what you have to do when upgrading Ricgraph.