ricgraph 2.10__tar.gz → 2.11__tar.gz

{ricgraph-2.10/ricgraph.egg-info → ricgraph-2.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ricgraph
-Version: 2.10
+Version: 2.11
 Summary: Ricgraph - Research in context graph
 Author: Rik D.T. Janssen
 Project-URL: Website, https://www.ricgraph.eu
@@ -122,7 +122,7 @@ The items surrounded by the red line are the solution to this use case.
 
 <img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
 
-### Main contributions of Ricgraph
+## Main contributions of Ricgraph
 
 * Ricgraph can store many types of items in a single graph.
 * Ricgraph harvests multiple source systems into a single graph.
@@ -130,7 +130,7 @@ The items surrounded by the red line are the solution to this use case.
 * Ricgraph facilitates reasoning about items because it infers new relations between items.
 * Ricgraph can be tailored for an application area.
 
-### Read more about Ricgraph
+## Read more about Ricgraph
 
 For a gentle introduction in Ricgraph, read the reference publication: 
 Rik D.T. Janssen (2024). Ricgraph: A flexible and extensible graph to explore research in
@@ -144,3 +144,11 @@ To use Ricgraph, installing the [Ricgraph package from PyPI](https://pypi.org/pr
 is not sufficient. Please read the
 installation instructions in the Ricgraph GitHub repository.
 
+## Contact
+
+Ricgraph has been created and is being maintained by
+Rik D.T. Janssen from Utrecht University in the Netherlands. 
+You can find contact details at
+[his Utrecht University employee page](https://www.uu.nl/staff/DTJanssen).
+He also has an ORCID profile on
+[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).

{ricgraph-2.10 → ricgraph-2.11}/README-PyPI.md

@@ -97,7 +97,7 @@ The items surrounded by the red line are the solution to this use case.
 
 <img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
 
-### Main contributions of Ricgraph
+## Main contributions of Ricgraph
 
 * Ricgraph can store many types of items in a single graph.
 * Ricgraph harvests multiple source systems into a single graph.
@@ -105,7 +105,7 @@ The items surrounded by the red line are the solution to this use case.
 * Ricgraph facilitates reasoning about items because it infers new relations between items.
 * Ricgraph can be tailored for an application area.
 
-### Read more about Ricgraph
+## Read more about Ricgraph
 
 For a gentle introduction in Ricgraph, read the reference publication: 
 Rik D.T. Janssen (2024). Ricgraph: A flexible and extensible graph to explore research in
@@ -119,3 +119,11 @@ To use Ricgraph, installing the [Ricgraph package from PyPI](https://pypi.org/pr
 is not sufficient. Please read the
 installation instructions in the Ricgraph GitHub repository.
 
+## Contact
+
+Ricgraph has been created and is being maintained by
+Rik D.T. Janssen from Utrecht University in the Netherlands. 
+You can find contact details at
+[his Utrecht University employee page](https://www.uu.nl/staff/DTJanssen).
+He also has an ORCID profile on
+[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).

{ricgraph-2.10 → ricgraph-2.11}/README.md

@@ -22,6 +22,11 @@ We use color=#4c1 (green), that color is used by the 'repo status' badge.
 Documentation about the Podman badges can be found here: https://github.com/eggplants/ghcr-badge.
 --->
 
+> Read the [Tutorial](docs/ricgraph_tutorial.md#tutorial-ricgraph---research-in-context-graph).
+> Go to the [Documentation website](https://docs.ricgraph.eu).
+> Consult the [Table of contents](docs/ricgraph_toc_documentation.md#table-of-contents-ricgraph-documentation), 
+> or the [Index](docs/ricgraph_index_documentation.md#index-ricgraph-documentation).
+
 <img alt="Ricgraph logo" src="docs/images/ricgraph_logo.png" width="30%"> 
 
 <!---
@@ -34,12 +39,6 @@ to remove everything up and including these lines. Do not modify the text in it.
 
 # Ricgraph - Research in context graph
 
-[Read the Tutorial Ricgraph](docs/ricgraph_tutorial.md#tutorial-ricgraph---research-in-context-graph).
-Go to the [documentation website for Ricgraph](https://docs.ricgraph.eu).
-
-[Table of contents of Ricgraph documentation](docs/ricgraph_toc_documentation.md#table-of-contents-ricgraph-documentation) and 
-[Index of Ricgraph documentation](docs/ricgraph_index_documentation.md#index-ricgraph-documentation).
-
 ## What is Ricgraph?
 
 Ricgraph, also known as Research in context graph, enables the exploration of researchers, 
@@ -54,8 +53,36 @@ relations that are not present in any of the separate source systems.
 It is flexible and extensible, and can be
 adapted to new application areas.
 
-Throughout this documentation, we illustrate how Ricgraph works by applying 
-it to the application area research information. 
+Currently, there are people working on the following extensions for Ricgraph:
+
+* [BackToPure](https://github.com/UtrechtUniversity/backtopure)
+  is a tool designed to enhance an organization's
+  [Research Information System Pure](https://www.elsevier.com/solutions/pure)
+  by enriching its content. BackToPure can identify items
+  (such as publications, data sets or software)
+  that exist in other external sources but are missing from the organization's Pure,
+  and then insert (enrich) those items into Pure.
+  The result is a more complete overview of research at that organization.
+  Status: experimental stage (beta).
+* A chatbot that allows you to "talk" to Ricgraph. You can formulate questions in
+  plain English, such as "Please give me the research results of the Geosciences
+  faculty of Utrecht University?"
+  or "With what organizations does that faculty collaborate?".
+  It uses a local Large Language Model.
+  Status: planning stage (pre-alpha).
+* A project that uses
+  [AI and Large Language Models to cluster and visualize large amounts of research
+  information](https://docs.ricgraph.eu/docs/ricgraph_pubs_pres_news_use_ment.html#ricgraph-projects-with-students).
+  It assigns *topics* to publications,
+  data sets, and software. By selecting a number of topics, research results are
+  grouped, and possibly experts on these topics can be found.
+  Status: planning stage (pre-alpha).
+* A tool that helps Pure administrators to clean up "external organizations" in Pure.
+  Status: planning stage (pre-alpha).
+
+Throughout this documentation, we illustrate how Ricgraph works by applying
+it to the application area research information.
+
 
 ## Motivation
 
@@ -120,7 +147,7 @@ The items surrounded by the red line are the solution to this use case.
 <img src="docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
 
 
-### Main contributions of Ricgraph
+## Main contributions of Ricgraph
 
 * Ricgraph can store many types of items in a single graph.
 * Ricgraph harvests multiple source systems into a single graph.
@@ -128,65 +155,6 @@ The items surrounded by the red line are the solution to this use case.
 * Ricgraph facilitates reasoning about items because it infers new relations between items.
 * Ricgraph can be tailored for an application area.
 
-### How to use Ricgraph (very short)
-
-* [Install and configure Ricgraph](docs/ricgraph_install_configure.md#install-and-configure-ricgraph).
-* Start harvesting data, see [Ricgraph harvest scripts](docs/ricgraph_harvest_scripts.md#ricgraph-harvest-scripts).
-* Use [Ricgraph Explorer](docs/ricgraph_explorer.md#ricgraph-explorer),
-  the exploration tool for Ricgraph. 
-* Use the [Ricgraph REST API](docs/ricgraph_restapi.md#ricgraph-rest-api),
-  the REST API for Ricgraph.
-* Optional: modify code to fit Ricgraph to your specific use case.
-
-For more details, read the remainder of this documentation.
-  
-### Read more about Ricgraph
-
-For a gentle introduction in Ricgraph, read the reference publication: 
-Rik D.T. Janssen (2024). Ricgraph: A flexible and extensible graph to explore research in
-context from various systems. *SoftwareX*, 26(101736).
-[https://doi.org/10.1016/j.softx.2024.101736](https://doi.org/10.1016/j.softx.2024.101736).
-
-For a further introduction, you might want to read these two presentations:
-
-* A general presentation about Ricgraph, presenting Ricgraph in a visual manner: 
-  [https://doi.org/10.5281/zenodo.12634234](https://doi.org/10.5281/zenodo.12634234).
-* A presentation explaining how to enrich 
-  the [Research Information System Pure](https://www.elsevier.com/solutions/pure)
-  (and other source systems) using Ricgraph 
-  and [BackToPure](https://github.com/UtrechtUniversity/BackToPure):
-  [https://doi.org/10.5281/zenodo.12634658](https://doi.org/10.5281/zenodo.12634658).
-  This presentation explains that after harvesting several Pure systems 
-  (from different institutions)  and other source systems,
-  such as [OpenAlex](https://openalex.org), 
-  one can enrich its own Pure _A_ by using information in other source
-  systems, not present in one's own Pure _A_.
-  
-To learn more about Ricgraph,
-[read why Ricgraph has been developed](#why-ricgraph).
-This is followed by
-[Ricgraph in bullet points](#ricgraph-in-bullet-points). There is also
-[a section with next steps you might want to take](#next-steps),
-including [further information about 
-Ricgraph](#further-information-about-ricgraph),
-an [explanation how to install Ricgraph and harvest 
-data](#steps-to-take-if-you-would-like-to-install-ricgraph-and-harvest-data),
-an [explanation how to use Ricgraph](#steps-to-take-if-you-would-like-to-use-ricgraph), 
-and [information about extending Ricgraph](#read-this-in-case-you-would-like-to-extend-ricgraph).
-Of course there are 
-[videos we have made to demonstrate Ricgraph](docs/ricgraph_example_use_videos.md#ricgraph-videos),
-and there is an overview of the 
-[publications](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-publications),
-[presentations](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-presentations),
-[newsletters](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-newsletters)
-(to subscribe, go to [Ricgraph Contact](#contact)),
-[use](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-use), and
-[mentions](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-mentions)
-of Ricgraph.
-
-You can also use the [Table of contents of Ricgraph documentation](docs/ricgraph_toc_documentation.md#table-of-contents-ricgraph-documentation) 
-or the [Index of Ricgraph documentation](docs/ricgraph_index_documentation.md#index-ricgraph-documentation).
-
 ## Why Ricgraph?
 
 Ricgraph can answer questions like:
@@ -225,6 +193,9 @@ exploration tool for Ricgraph:
   clicking on a number in one of these
   two tables to find the nodes corresponding to that number. 
 
+If you would like to get this information programmatically, you can use
+the [Ricgraph REST API](https://docs.ricgraph.eu/docs/ricgraph_restapi.html#ricgraph-rest-api).
+
 With Ricgraph, you can get metadata from objects from any source system you’d like. 
 You run the harvest script for that
 system, and data will be imported in Ricgraph and will be 
@@ -232,19 +203,18 @@ combined automatically with data which is already there.
 Ricgraph provides harvest scripts for the systems mentioned above. 
 Scripts for other sources can be written easily.
 
-In the remainder of this text, Ricgraph is described in the use case of
-showing people, organizations and research outputs in relation to each other
-in a university context.
-
 ## Examples
 
-See the figures below for example graphs that show how Ricgraph works.
+See the figures below for example graphs that show how Ricgraph works. In this section, we use the following
+symbols and colors.
+
+|                            symbols for type of object                             |                                colors for source system                                 |
+|:---------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------:|
+| <img alt="Symbols for type of object." src="docs/images/symbols.jpg" width="20%"> | <img alt="Colors for source system." src="docs/images/colors-vertical.jpg" width="20%"> |
 
-|                                         one person with several research outputs                                         |                            symbols for type of object                             |                                colors for source system                                 |
-|:------------------------------------------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------:|
-| <img alt="One person with several research outputs." src="docs/images/one-person-with-research-outputs.jpg" width="33%"> | <img alt="Symbols for type of object." src="docs/images/symbols.jpg" width="33%"> | <img alt="Colors for source system." src="docs/images/colors-vertical.jpg" width="33%"> |
 
-This figure shows one person *A* using a
+The following figure shows one person with several research outputs.
+It shows one person *A* using a
 [*person-root* node, a node which "represents" a person](docs/ricgraph_details.md#person-root-node-in-ricgraph)
 as it is called
 in Ricgraph.
@@ -260,21 +230,24 @@ and
 the software package is from the
 [Research Software Directory](https://research-software-directory.org) (in blue).
 
+<img alt="One person with several research outputs." src="docs/images/one-person-with-research-outputs.jpg" width="25%">
 
-|                                           several persons with several research outputs                                            |                                    one person with several identifiers and research outputs                                     |
-|:----------------------------------------------------------------------------------------------------------------------------------:|:-------------------------------------------------------------------------------------------------------------------------------:|
-| <img alt="Several persons with several research outputs." src="docs/images/several-persons-with-research-outputs.jpg" width="40%"> | <img alt="One person with several identifiers and research outputs." src="docs/images/identifiers-and-outputs.jpg" width="50%"> |
-
-The left part of this figure shows several persons having several research outputs
-(the symbols) and
+The following figure shows several persons with several research outputs (the symbols) and
 how these are related (i.e. which person contributed to which research output).
 It also shows from which source system these research outputs have originated
 (using different colors).
-The right part shows one person having several identifiers and several research outputs.
+
+<img alt="Several persons with several research outputs." src="docs/images/several-persons-with-research-outputs.jpg" width="35%"> 
+
+The following figure shows one person having several identifiers and several research outputs.
 This person has two different ORCIDs, one ISNI, one SCOPUS_AUTHOR_ID, and two FULL_NAMEs (which differ
 in spelling). These identifiers have also been obtained from different source systems, as their color indicates.
 
-More examples can be found in [Ricgraph details](docs/ricgraph_details.md#implementation-details).
+<img alt="One person with several identifiers and research outputs." src="docs/images/identifiers-and-outputs.jpg" width="25%">
+
+The following figure shows how three persons have contributed to one research output.
+
+<img alt="Three persons with one research output." src="docs/images/three-persons-one-research-output.jpg" width="15%">
 
 ## Ricgraph in bullet points
 
@@ -295,14 +268,8 @@ More examples can be found in [Ricgraph details](docs/ricgraph_details.md#implem
   relation between two objects.
 * Ricgraph and Ricgraph Explorer are written in Python. You can use two different
   [graph database backends](https://en.wikipedia.org/wiki/Graph_database):
-  * [Neo4j](https://neo4j.com) (either Neo4j Desktop or Neo4j Community Edition);
-  * [Memgraph](https://memgraph.com).
-* Metadata of an object are stored as "properties"
-  in a node, i.e. as information associated with a node.
-  For example, a node may store two properties, *name = PET* and
-  *value = cat*. Another node may store *name = FULL_NAME* and *value = John Doe*.
-  Then the edge between those two nodes means that the person with FULL_NAME John Doe
-  has a PET which is a cat. Ricgraph can store any number of properties in a node.
+  [Neo4j](docs/ricgraph_backend_neo4j.md#ricgraph-with-neo4j-graph-database-backend) and
+  [Memgraph](docs/ricgraph_backend_memgraph.md#ricgraph-with-memgraph-graph-database-backend).
 * The objective of Ricgraph is to get metadata from
   objects from a source system in a process called "harvesting".
   That means that e.g. persons and publications
@@ -315,30 +282,19 @@ More examples can be found in [Ricgraph details](docs/ricgraph_details.md#implem
   the data repository [Yoda](https://www.uu.nl/en/research/yoda),
   the [Research Software Directory](https://research-software-directory.org), and 
   for the [Utrecht University staff pages](https://www.uu.nl/staff/search).
-* Ricgraph can be used as an ID resolver. It can, given an identifier of a person,
+* Ricgraph is an ID resolver. It can, given an identifier of a person,
   easily find other identifiers of that person. When new identifiers are found when
   harvesting from new systems,
   they will be added automatically. 
-* Ricgraph can check the consistency of information harvested. For example, ORCIDs and ISNIs
-  are supposed to refer to one person, so every node representing such an identifier should have
-  only one edge. This can be checked easily.
-  An example script is included.
-* Ricgraph can enrich information in its own graph by using information from other systems. 
-  For example,
-  if a person has an ORCID, but not a Scopus Author ID,
-  [OpenAlex](https://openalex.org) can be used
-  to find the missing Scopus Author ID. An example script is included.
 * Ricgraph can enrich a source system based on information that is present in one
-  source system, but not in another source system. See the use case above.
+  source system, but not in another source system. 
+  See the [librarian use case](#use-case-for-a-librarian) above.
 
 ## Next steps
 
-[Table of contents of Ricgraph documentation](docs/ricgraph_toc_documentation.md#table-of-contents-ricgraph-documentation) and
-[Index of Ricgraph documentation](docs/ricgraph_index_documentation.md#index-ricgraph-documentation).
-
 ### Further information about Ricgraph
 
-* Read the full documentation of Ricgraph on
+* Explore the full documentation of Ricgraph on
   [https://docs.ricgraph.eu](https://docs.ricgraph.eu).
 * For a gentle introduction in Ricgraph, read the reference publication:
   Rik D.T. Janssen (2024). Ricgraph: A flexible and extensible graph to explore research in
@@ -367,10 +323,11 @@ More examples can be found in [Ricgraph details](docs/ricgraph_details.md#implem
   [use](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-use), and
   [mentions](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-mentions)
   of Ricgraph.
-* Look at the [videos we have made to demonstrate Ricgraph](docs/ricgraph_example_use_videos.md#ricgraph-videos).
-* Read more about [Ricgraph details](docs/ricgraph_details.md#implementation-details),
-  such as example graphs, person identifiers and the *person-root* node.
-* You might want to [compare Ricgraph to other systems](docs/ricgraph_comparison.md#ricgraph-comparison).
+* The Ricgraph main website is www.ricgraph.eu.
+  Alternative sites are www.ricgraph.nl and www.ricgraph.com.
+  These are generated using the 
+  [ricgraph-documentation](https://github.com/UtrechtUniversity/ricgraph-documentation)
+  GitHub repository.
 
 ### Steps to take if you would like to install Ricgraph and harvest data
 
@@ -387,28 +344,35 @@ More examples can be found in [Ricgraph details](docs/ricgraph_details.md#implem
 
 ### Steps to take if you would like to use Ricgraph
 
-* First, install Ricgraph (see above).
 * Use [Ricgraph Explorer](docs/ricgraph_explorer.md#ricgraph-explorer),
   the exploration tool for Ricgraph. 
 * Use the [Ricgraph REST API](docs/ricgraph_restapi.md#ricgraph-rest-api),
   the REST API for Ricgraph.
-
-### Read this in case you would like to extend Ricgraph
-
-* Start writing scripts, see [Ricgraph script writing](docs/ricgraph_script_writing.md#ricgraph-script-writing).
-
-### Ricgraph website
-Ricgraph has a main Ricgraph website on www.ricgraph.eu. 
-Alternative sites are www.ricgraph.nl and www.ricgraph.com.
-The sources for this website are on GitHub in repository
-[https://github.com/UtrechtUniversity/ricgraph-website](https://github.com/UtrechtUniversity/ricgraph-website).
+* You can also [write your own harvest scripts](docs/ricgraph_script_writing.md#ricgraph-script-writing),
+  or modify any part of the Ricgraph code.
 
 ## Contact
-Ricgraph has been created and is being maintained by 
-[Rik D.T. Janssen from Utrecht University in the Netherlands](https://www.uu.nl/staff/DTJanssen)
-[(ORCID 0000-0001-9510-0802)](https://orcid.org/0000-0001-9510-0802).
+Ricgraph has been created and is being maintained by
+Rik D.T. Janssen from Utrecht University in the Netherlands.
+You can find contact details at
+[his Utrecht University employee page](https://www.uu.nl/staff/DTJanssen).
+He also has an ORCID profile on
+[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).
 You can contact him for presentations, demos and workshops.
 
+He is also very interested in working together on projects involving Ricgraph.
+Ricgraph is a flexible platform that brings
+together information from multiple systems into a single graph.
+It allows users to analyze this information and explore how it relates
+to other types of information.
+We could work together on use cases applying Ricgraph to
+research information, such as exploring collaborations or
+analyzing how people or organizations contribute to research results.
+We could also explore entirely different domains.
+Any application that involves representing and analyzing
+interconnected information as nodes and relations in a graph,
+regardless of the field, is of interest.
+
 About three to four times a year we send out a 
 newsletter.
 [Please click here to subscribe to it. Your email program will open with
@@ -418,10 +382,12 @@ We also have a
 [newsletter archive](docs/ricgraph_pubs_pres_news_use_ment.md#ricgraph-newsletters). 
 
 If you like Ricgraph, please give it a GitHub Star by clicking on the top right 
-*Star* button on this page. If you have any suggestions or improvements, 
-please let me know by creating a GitHub *Issue* at the top left of this page. 
+*Star* button on the Ricgraph GitHub page
+[https://github.com/UtrechtUniversity/ricgraph](https://github.com/UtrechtUniversity/ricgraph).
+If you have any suggestions or improvements, 
+please let me know by creating a GitHub *Issue* at the top left of that page. 
 
 <!-- Do not change the lines below. The version number will be
      modified by script maintenance/update_version.bash -->
 This README.md file is part of the 
-documentation for version 2.10 of Ricgraph - Research in context graph.
+documentation for version 2.11 of Ricgraph - Research in context graph.

{ricgraph-2.10 → ricgraph-2.11}/pyproject.toml

@@ -7,7 +7,7 @@ packages = ["ricgraph"]
 
 [project]
 name = "ricgraph"
-version = "2.10"
+version = "2.11"
 authors = [
   { name="Rik D.T. Janssen" },
 ]

{ricgraph-2.10 → ricgraph-2.11}/ricgraph/ricgraph.py

@@ -123,7 +123,7 @@ __package__ = 'Ricgraph'
 # __version__ should be placed here instead of in __init__.py.
 # If not here, it cannot be found when executing something like
 # PYTHONPATH=../ricgraph ../bin/python ricgraph_explorer.py
-__version__ = '2.10'
+__version__ = '2.11'
 
 
 # ########################################################################
@@ -153,6 +153,12 @@ nodes_cache_key_element_id = {}
 # Cache size. 'nodes_cache_key_element_id' will be emptied if it has this number of elements.
 MAX_NODES_CACHE_KEY_ID = 15000
 
+# In merge_two_nodes(node_merge_from, node_merge_to), we are constructing a list of
+# all the nodes that are to be merged with node_merge_to, to add to property _history
+# in that node. This value restricts the length of that list (to prevent property
+# values that are too long).
+MAX_NR_HISTORYITEMS_TO_ADD = 100
+
 
 # These counters are used to count the number of accesses to the
 # graph database backend.
@@ -683,17 +689,20 @@ def cypher_merge_nodes(node_merge_from_element_id: str,
                                  result_transformer_=Result.value,
                                  database_=ricgraph_databasename())
 
-    # If merge_node_from does not have neighbors, it will not be deleted.
-    # Do another Cypher query to be sure it is gone.
-    cypher_delete_node(node_element_id=node_merge_from_element_id)
+    if len(nodes) == 0:
+        # If merge_node_from does not have neighbors, len(nodes) will be 0.
+        # Also, it will not have been deleted. The merge has been done.
+        # Do another Cypher query to be sure it is gone.
+        cypher_delete_node(node_element_id=node_merge_from_element_id)
+        node_merge_to_properties['_history'].append('Merged two nodes of which the merged from did not have neighbors.')
+        node = cypher_update_node_properties(node_element_id=node_merge_to_element_id,
+                                             node_properties=node_merge_to_properties)
+        return node
 
     nr_edges = ricgraph_nr_edges_of_node(node_element_id=node_merge_to_element_id)
     graphdb_nr_reads += 2 * nr_edges        # Approximation: edges are in two directions.
     graphdb_nr_updates += 2 * nr_edges      # Approximation: edges are in two directions.
-    if len(nodes) == 0:
-        return None
-    else:
-        return nodes[0]
+    return nodes[0]
 
 
 def cypher_create_edge_if_not_exists(left_node_element_id: str, right_node_element_id: str) -> None:
@@ -1611,12 +1620,18 @@ def update_node_value(name: str, old_value: str, new_value: str) -> Union[Node,
 
     time_stamp = datetimestamp()
     node = read_node(name=lname, value=loldvalue)
-    if node is None:
+    newnode = read_node(name=lname, value=lnewvalue)
+    if node is None and newnode is None:
         # Node we want to change does not exist.
+        print('update_node_value(): Error: both of the nodes do not exist.')
         return None
 
-    newnode = read_node(name=lname, value=lnewvalue)
-    if newnode is not None:
+    if node is None and newnode is not None:
+        # Node we want to change does not exist,
+        # but newnode does, we don't do anything.
+        return newnode
+
+    if node is not None and newnode is not None:
         # The node we want to change to does already exist.
         # So this happens to be a merge of two nodes.
         merged_node = merge_two_nodes(node_merge_from=node,
@@ -1802,8 +1817,14 @@ def merge_two_nodes(node_merge_from: Node, node_merge_to: Node) -> Union[Node, N
         # Done.
         return node_merge_to
 
-    if node_merge_from is None or node_merge_to is None:
-        print('merge_two_nodes(): Error: one or both of the nodes is None - cannot be found.')
+    if node_merge_from is not None and node_merge_to is None:
+        print('merge_two_nodes(): Error: it seems that you are trying to move a node')
+        print('  to another node. This is not supported.')
+        print('  You might want to use update_node_value().')
+        return None
+
+    if node_merge_from is None and node_merge_to is None:
+        print('merge_two_nodes(): Error: both of the nodes do not exist.')
         return None
 
     if node_merge_from['name'] != node_merge_to['name'] \
@@ -1836,23 +1857,27 @@ def merge_two_nodes(node_merge_from: Node, node_merge_to: Node) -> Union[Node, N
 
     count += 1
     what_happened = time_stamp + '-' + format(count, '02d') + ': '
-    what_happened += 'Start of history of the deleted node.'
+    what_happened += '--- Start of history of the deleted node.'
     node_merge_to_properties['_history'].append(what_happened)
 
     for history in node_merge_from['_history']:
         count += 1
         what_happened = time_stamp + '-' + format(count, '02d') + ': '
+        if count >= MAX_NR_HISTORYITEMS_TO_ADD:
+            what_happened += 'List truncated, too many history lines for _history.'
+            node_merge_to_properties['_history'].append(what_happened)
+            break
         what_happened += history
         node_merge_to_properties['_history'].append(what_happened)
 
     count += 1
     what_happened = time_stamp + '-' + format(count, '02d') + ': '
-    what_happened += 'End of history of the deleted node.'
+    what_happened += '--- End of history of the deleted node.'
     node_merge_to_properties['_history'].append(what_happened)
 
     count += 1
     what_happened = time_stamp + '-' + format(count, '02d') + ': '
-    what_happened += 'These were the neighbors of the deleted node, '
+    what_happened += '--- These were the neighbors of the deleted node, '
     what_happened += 'now merged with the neighbors of this node:'
     node_merge_to_properties['_history'].append(what_happened)
 
@@ -1866,12 +1891,16 @@ def merge_two_nodes(node_merge_from: Node, node_merge_to: Node) -> Union[Node, N
         for node in neighbornodes:
             count += 1
             what_happened = time_stamp + '-' + format(count, '02d') + ': '
+            if count >= MAX_NR_HISTORYITEMS_TO_ADD:
+                what_happened += 'List truncated, too many history lines for _history.'
+                node_merge_to_properties['_history'].append(what_happened)
+                break
             what_happened += '"' + str(node['_key']) + '" '
             node_merge_to_properties['_history'].append(what_happened)
 
     count += 1
     what_happened = time_stamp + '-' + format(count, '02d') + ': '
-    what_happened += 'End of list of neighbors of the deleted node.'
+    what_happened += '--- End of list of neighbors of the deleted node.'
     node_merge_to_properties['_history'].append(what_happened)
 
     count += 1

{ricgraph-2.10 → ricgraph-2.11/ricgraph.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ricgraph
-Version: 2.10
+Version: 2.11
 Summary: Ricgraph - Research in context graph
 Author: Rik D.T. Janssen
 Project-URL: Website, https://www.ricgraph.eu
@@ -122,7 +122,7 @@ The items surrounded by the red line are the solution to this use case.
 
 <img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
 
-### Main contributions of Ricgraph
+## Main contributions of Ricgraph
 
 * Ricgraph can store many types of items in a single graph.
 * Ricgraph harvests multiple source systems into a single graph.
@@ -130,7 +130,7 @@ The items surrounded by the red line are the solution to this use case.
 * Ricgraph facilitates reasoning about items because it infers new relations between items.
 * Ricgraph can be tailored for an application area.
 
-### Read more about Ricgraph
+## Read more about Ricgraph
 
 For a gentle introduction in Ricgraph, read the reference publication: 
 Rik D.T. Janssen (2024). Ricgraph: A flexible and extensible graph to explore research in
@@ -144,3 +144,11 @@ To use Ricgraph, installing the [Ricgraph package from PyPI](https://pypi.org/pr
 is not sufficient. Please read the
 installation instructions in the Ricgraph GitHub repository.
 
+## Contact
+
+Ricgraph has been created and is being maintained by
+Rik D.T. Janssen from Utrecht University in the Netherlands. 
+You can find contact details at
+[his Utrecht University employee page](https://www.uu.nl/staff/DTJanssen).
+He also has an ORCID profile on
+[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).