Ricgraph

The following improvements have been made to Ricgraph.

Ricgraph general:
- Improvements and clarifications of the Makefile. Added a target to empty the Neo4j Community graph database.

Ricgraph (these also apply to the harvest scripts):
- Improved command line parameter handling.
- Improved reading from the Ricgraph initialization file.
- Added calls to normalize the data harvested. Some of these calls are in ricgraph/ricgraph.py, others are in the harvest scripts.

Harvest scripts:
- OpenAlex and Pure: Changed the years to harvest research results from: from 2021-2024 to 2022-2025.
- Yoda-DataCite harvest can now harvest multiple organizations by specifying a command line parameter. This required changes in some batch_harvest scripts and in the Ricgraph initialization file (see Upgrading below).

Documentation:
- Clarified documentation to describe more easy install procedures, both for Ricgraph install for a single user and for Ricgraph install for a server.
- Restructured documentation.
- Added several presentations, and an Innovation project involving six students at University of Applied Sciences, Utrecht.

Upgrading:
- Re-install Ricgraph. It is advisable to remove all of your existing files and directories, except for ricgraph.ini, before you re-install Ricgraph.
- Recreate your Ricgraph initialization file from ricgraph.ini-sample, and use the values from your previous ricgraph.ini version. This is due to the changes in harvesting of Yoda-DataCite. Read more about the [Ricgraph initialization file](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_install_configure.md#ricgraph-initialization-file).
- You only need to reharvest your sources if you upgrade from version v2.4 and earlier.

The following improvements have been made to Ricgraph.

Ricgraph general:
- You can now use Ricgraph by installing and using its Podman container. A container is like a small box that holds an application and everything it needs to run, such as files and settings. This makes installation of Ricgraph much simples. [Read more](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_containerized.md).
- The [Makefile](https://github.com/UtrechtUniversity/ricgraph/blob/main/Makefile) has been fully rewritten.
- Ricgraph now contains a script to delete personal data from Ricgraph, if requested by someone.

Ricgraph Explorer:
- On a page with two tabbed tables, these now behave correctly.

Ricgraph:
- More graceful handling of an empty or not (yet) existing graph database.
- Ricgraph has a call to delete nodes.

Documentation:
- Extended and clarified documentation.

Upgrading:
- If you upgrade from any Ricgraph version, you will need to re-install Ricgraph 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:
- 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.