ricgraph 3.2__tar.gz → 3.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {ricgraph-3.2/ricgraph.egg-info → ricgraph-3.4}/PKG-INFO +35 -92
- {ricgraph-3.2 → ricgraph-3.4}/README-PyPI.md +32 -91
- ricgraph-3.4/README.md +180 -0
- {ricgraph-3.2 → ricgraph-3.4}/pyproject.toml +5 -1
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph.py +18 -13
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_cache.py +36 -14
- ricgraph-3.4/ricgraph/ricgraph_constants.py +513 -0
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_cypher.py +408 -188
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_file.py +15 -4
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_graphdb.py +96 -81
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_harvest.py +214 -136
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_researchinfo.py +20 -22
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_restapi.py +1 -1
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/ricgraph_utils.py +132 -60
- {ricgraph-3.2 → ricgraph-3.4/ricgraph.egg-info}/PKG-INFO +35 -92
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph.egg-info/requires.txt +2 -0
- ricgraph-3.2/README.md +0 -452
- ricgraph-3.2/ricgraph/ricgraph_constants.py +0 -210
- {ricgraph-3.2 → ricgraph-3.4}/LICENSE +0 -0
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph/__init__.py +0 -0
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph.egg-info/SOURCES.txt +0 -0
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph.egg-info/dependency_links.txt +0 -0
- {ricgraph-3.2 → ricgraph-3.4}/ricgraph.egg-info/top_level.txt +0 -0
- {ricgraph-3.2 → ricgraph-3.4}/setup.cfg +0 -0
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Metadata-Version: 2.4
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Name: ricgraph
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Version: 3.
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Version: 3.4
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Summary: Ricgraph - Research in context graph
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Author: Rik D.T. Janssen
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License-Expression: MIT
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Requires-Dist: neo4j>=5.8
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Requires-Dist: numpy
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Requires-Dist: pandas
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Requires-Dist: pymemcache
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Requires-Dist: requests
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Requires-Dist: unidecode
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Requires-Dist: markupsafe
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Dynamic: license-file
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[](https://doi.org/10.5281/zenodo.7524314)
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## What is Ricgraph?
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Ricgraph, also known as Research in context graph, enables the exploration of researchers,
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Ricgraph, also known as Research in context graph, enables the exploration of researchers, teams, their results,
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collaborations, skills, projects, and the relations between these items.
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Ricgraph can store many types of items into a single graph.
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Ricgraph can store many types of items into a single graph.
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These items can be obtained from various systems and from
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multiple organizations. Ricgraph facilitates reasoning about these
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multiple organizations. Ricgraph facilitates reasoning about these
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items because it infers new relations between items,
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relations that are not present in any of the separate source systems.
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relations that are not present in any of the separate source systems.
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It is flexible and extensible, and can be
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adapted to new application areas.
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##
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Ricgraph is
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*research information
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research information, the principle “relations
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### Use case for a journalist
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As a journalist, I want to find researchers with a certain skill S and their publications,
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Example skills can be: *climate change* or *stem cells*.
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The items surrounded by the red line are the solution to this use case.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/journalist-use-case.jpg" alt="Ricgraph use case for a journalist." width="70%">
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### Use case for a librarian
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As a librarian, I want to enrich my local research information system with research results
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from person A that are in other systems (in orange, *RIS2*) but not in
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The items surrounded by the red line are the solution to this use case.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/librarian-use-case.jpg" alt="Ricgraph use case for a librarian." width="75%">
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### Use case for a researcher
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As a researcher A, I want to find researchers from other universities that have
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The items surrounded by the red line are the solution to this use case.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
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## Main contributions of Ricgraph
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* Ricgraph can store many types of items in a single graph.
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* Ricgraph harvests multiple source systems into a single graph.
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* Ricgraph Explorer is the exploration tool for Ricgraph.
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* Ricgraph facilitates reasoning about items because it infers new relations between items.
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* Ricgraph can be tailored for an application area.
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## Read more about Ricgraph
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For a gentle introduction in Ricgraph, read the reference publication:
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Rik D.T. Janssen (2024). *Ricgraph: A flexible and extensible graph to explore research in
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context from various systems*. SoftwareX, 26(101736).
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[https://doi.org/10.1016/j.softx.2024.101736](https://doi.org/10.1016/j.softx.2024.101736).
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You might also want to read the documentation on
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[https://docs.ricgraph.eu](https://docs.ricgraph.eu).
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You can also go to the [Ricgraph GitHub repository](https://github.com/UtrechtUniversity/ricgraph).
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To use Ricgraph, installing the [Ricgraph package from PyPI](https://pypi.org/project/ricgraph)
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is not sufficient. Please read the
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installation instructions in the Ricgraph GitHub repository.
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## Why Ricgraph is unique
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Ricgraph is unique because it allows you to:
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* Explore collaborations between (sub-)organizations with Ricgraph;
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* Explore Open science with Ricgraph;
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* Enhance research information systems with Ricgraph;
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The nice thing
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about Ricgraph is that anyone with Python knowledge can easily extend it,
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so you can use Ricgraph to test your own ideas or to create your own applications.
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You can use Ricgraph either as a standalone tool,
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a number of handy tools.
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Ricgraph has been developed for the application area
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research information
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relations between items from various source systems.
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## More information about Ricgraph
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To learn more about Ricgraph, please go to the
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[Ricgraph website www.ricgraph.eu](https://www.ricgraph.eu).
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If you would like to know more details about Ricgraph, please go to the
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[Ricgraph documentation website docs.ricgraph.eu](https://docs.ricgraph.eu).
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## Contact
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You can find contact details at
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He also has an ORCID profile on
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[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).
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the [Ricgraph contact page](https://www.ricgraph.eu/contact.html).
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## What is Ricgraph?
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Ricgraph, also known as Research in context graph, enables the exploration of researchers,
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teams, their results,
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Ricgraph, also known as Research in context graph, enables the exploration of researchers, teams, their results,
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collaborations, skills, projects, and the relations between these items.
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Ricgraph can store many types of items into a single graph.
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Ricgraph can store many types of items into a single graph.
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These items can be obtained from various systems and from
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multiple organizations. Ricgraph facilitates reasoning about these
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items because it infers new relations between items,
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relations that are not present in any of the separate source systems.
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relations that are not present in any of the separate source systems.
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It is flexible and extensible, and can be
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### Use case for a journalist
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Example skills can be: *climate change* or *stem cells*.
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The items surrounded by the red line are the solution to this use case.
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<!--
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the documentation generated with Quarto, a.o. for the documentation website.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/journalist-use-case.jpg" alt="Ricgraph use case for a journalist." width="70%">
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### Use case for a librarian
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from person A that are in other systems (in orange, *RIS2*) but not in
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The items surrounded by the red line are the solution to this use case.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/librarian-use-case.jpg" alt="Ricgraph use case for a librarian." width="75%">
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so that I can read their publications to find out if we share common research interests.
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The items surrounded by the red line are the solution to this use case.
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<img src="https://raw.githubusercontent.com/UtrechtUniversity/ricgraph/main/docs/images/researcher-use-case.jpg" alt="Ricgraph use case for a researcher." width="35%">
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## Main contributions of Ricgraph
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* Ricgraph can store many types of items in a single graph.
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* Ricgraph harvests multiple source systems into a single graph.
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* Ricgraph Explorer is the exploration tool for Ricgraph.
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* Ricgraph facilitates reasoning about items because it infers new relations between items.
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* Ricgraph can be tailored for an application area.
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## Read more about Ricgraph
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For a gentle introduction in Ricgraph, read the reference publication:
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Rik D.T. Janssen (2024). *Ricgraph: A flexible and extensible graph to explore research in
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context from various systems*. SoftwareX, 26(101736).
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[https://doi.org/10.1016/j.softx.2024.101736](https://doi.org/10.1016/j.softx.2024.101736).
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[https://docs.ricgraph.eu](https://docs.ricgraph.eu).
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You can also go to the [Ricgraph GitHub repository](https://github.com/UtrechtUniversity/ricgraph).
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To use Ricgraph, installing the [Ricgraph package from PyPI](https://pypi.org/project/ricgraph)
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is not sufficient. Please read the
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installation instructions in the Ricgraph GitHub repository.
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## Why Ricgraph is unique
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Ricgraph is unique because it allows you to:
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* Explore collaborations between (sub-)organizations with Ricgraph;
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* Explore Open science with Ricgraph;
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* Enhance research information systems with Ricgraph;
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The nice thing
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about Ricgraph is that anyone with Python knowledge can easily extend it,
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so you can use Ricgraph to test your own ideas or to create your own applications.
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You can use Ricgraph either as a standalone tool,
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or as a component that provides a graph based data structure with
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a number of handy tools.
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Ricgraph has been developed for the application area
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research information
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and it can be used for other application areas that require
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relations between items from various source systems.
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## More information about Ricgraph
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To learn more about Ricgraph, please go to the
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[Ricgraph website www.ricgraph.eu](https://www.ricgraph.eu).
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If you would like to know more details about Ricgraph, please go to the
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[Ricgraph documentation website docs.ricgraph.eu](https://docs.ricgraph.eu).
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## Contact
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Ricgraph has been created and is being maintained by
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You can find contact details at
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[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).
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the [Ricgraph contact page](https://www.ricgraph.eu/contact.html).
|
ricgraph-3.4/README.md
ADDED
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[](https://doi.org/10.5281/zenodo.7524314)
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[](https://doi.org/10.1016/j.softx.2024.101736)
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[](https://doi.org/10.2139/ssrn.5524439)
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[](https://www.ricgraph.eu)
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[](https://docs.ricgraph.eu)
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[](https://github.com/UtrechtUniversity/ricgraph)
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[](https://pypi.org/project/ricgraph)
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[](https://pypistats.org/packages/ricgraph)
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[](https://github.com/UtrechtUniversity/ricgraph/blob/main/docs/ricgraph_containerized.md)
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[](https://github.com/utrechtuniversity/ricgraph/pkgs/container/ricgraph)
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[](LICENSE)
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[](https://www.repostatus.org/#active)
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[](https://github.com/CLARIAH/clariah-plus/blob/main/requirements/software-metadata-requirements.md#15--you-should-express-a-technology-readiness-level)
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[](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32110&r=123)
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<!---
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Note, some lines above end in two spaces, to force a line break but not a paragraph break.
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We use color=#4c1 (green), that color is used by the 'repo status' badge.
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Documentation about the Podman badges can be found here: https://github.com/eggplants/ghcr-badge.
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--->
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> Quick links:
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> [Use Ricgraph](https://www.ricgraph.eu/pilot-project-open-ricgraph-demo-server.html)
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> & [Read news about Ricgraph](https://www.ricgraph.eu/ricgraph-news.html)
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> & Go to the [Documentation website](https://docs.ricgraph.eu)
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> & Consult the [Table of contents](docs/ricgraph_toc_documentation.md#table-of-contents-ricgraph-documentation),
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> or the [Index](docs/ricgraph_index_documentation.md#index-ricgraph-documentation).
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<img alt="Ricgraph logo" src="docs/images/ricgraph_logo.png" width="30%">
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<!---
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The Mark below is used in file
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https://github.com/UtrechtUniversity/ricgraph-documentation/blob/main/Makefile
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to remove everything up and including these lines. Do not modify the text in it.
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--->
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<!--- Mark to remove everything up to here --->
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# Ricgraph - Research in context graph
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## What is Ricgraph?
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Ricgraph, also known as Research in context graph, enables the exploration of researchers, teams, their results,
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collaborations, skills, projects, and the relations between these items.
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Ricgraph can store many types of items into a single graph.
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These items can be obtained from various systems and from
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multiple organizations. Ricgraph facilitates reasoning about these
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items because it infers new relations between items,
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relations that are not present in any of the separate source systems.
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It is flexible and extensible, and can be
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adapted to new application areas.
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## Why Ricgraph is unique
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Ricgraph is unique because it allows you to:
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* [Explore collaborations between (sub-)organizations with
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Ricgraph](https://www.ricgraph.eu/collaborations-with-ricgraph.html).
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* [Explore Open science with Ricgraph](https://www.ricgraph.eu/open-science-with-ricgraph.html).
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* [Enhance research information systems with Ricgraph](https://www.ricgraph.eu/enhancing-with-ricgraph.html).
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The nice thing
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about Ricgraph is that anyone with Python knowledge can easily extend it,
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so you can use Ricgraph to test your own ideas or to create your own applications.
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You can use Ricgraph either as a standalone tool,
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or as a component that provides a graph based data structure with
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a number of handy tools.
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Ricgraph has been developed for the application area
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research information,
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and it can be used for other application areas that require
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relations between items from various source systems.
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## Ricgraph introduction videos
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You may want to watch the following videos about Ricgraph. The left one is a
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short video, only including the Ricgraph use cases. The right one is a more
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extensive one (also including the use cases).
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<table>
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<tr>
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<td style="width:50%;"><b>Ricgraph use cases video (1m30s)</b></td>
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<td style="width:50%;"><b>Ricgraph introduction video including use cases (2m28s)</b></td>
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<tr>
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<td><video src="docs/videos/ricgraph_usecases.mp4" controls width="90%">Ricgraph use cases video (1m30s)</video></td>
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<td><video src="docs/videos/ricgraph_intro_usecases.mp4" controls width="90%">Ricgraph introduction video including use cases (2m28s)</video></td>
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<tr>
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<td>
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<a href="https://docs.ricgraph.eu/docs/videos/ricgraph_usecases.mp4" target="_blank">
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Click to play or download the Ricgraph use cases video</a>.
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</td>
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<td>
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<a href="https://docs.ricgraph.eu/docs/videos/ricgraph_intro_usecases.mp4" target="_blank">
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Click to play or download the Ricgraph introduction video</a>.
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</td>
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</tr>
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</table>
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## More information about Ricgraph
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To learn more about Ricgraph, please go to the
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[Ricgraph website www.ricgraph.eu](https://www.ricgraph.eu).
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If you would like to know more details about Ricgraph, please go to the
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[Ricgraph documentation website docs.ricgraph.eu](https://docs.ricgraph.eu).
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[Use Ricgraph or participate](https://www.ricgraph.eu/pilot-project-open-ricgraph-demo-server.html).
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## Ricgraph in bullet points
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* Read more about [Why Ricgraph is
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unique](https://www.ricgraph.eu/what-is-ricgraph.html#why-ricgraph-is-unique).
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* The philosophy of Ricgraph is that it stores metadata, not the objects the metadata
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refer to. To access an object, a node has a link to that object in
|
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the system it was obtained from.
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* We have chosen a
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graph as a data structure, since it is a logical and efficient
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method to access objects
|
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which are close to objects they have a relation to. For example,
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starting with a person, its research outputs are only one
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step away by following one edge, and other contributors to that research output are
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again one step (edge) away.
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* Ricgraph can be used to store, manipulate and read metadata of any object that
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has a relation to another object,
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as long as every object can be "represented" by at least a *name* and a *value*.
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In Ricgraph, one node represents one object, and an edge represents the
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relation between two objects.
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* Ricgraph and Ricgraph Explorer are written in Python. You can use two different
|
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[graph database backends](https://en.wikipedia.org/wiki/Graph_database):
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[Neo4j](docs/ricgraph_backend_neo4j.md#ricgraph-with-neo4j-graph-database-backend) and
|
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[Memgraph](docs/ricgraph_backend_memgraph.md#ricgraph-with-memgraph-graph-database-backend).
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* The objective of Ricgraph is to get metadata from
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objects from a source system in a process called "harvesting".
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That means that e.g. persons and publications
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can be harvested from one system, data sets from another system, and software from a third system.
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Everything found will be combined into one graph.
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* Ricgraph can harvest from many sources, and you can write your own
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harvesting scripts. Example scripts are included to
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harvest from the [OpenAlex](https://openalex.org),
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the [Research Information System Pure](https://www.elsevier.com/solutions/pure),
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the data repository [Yoda](https://www.uu.nl/en/research/yoda),
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the [Research Software Directory](https://research-software-directory.org), and
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for the [Utrecht University staff pages](https://www.uu.nl/staff/search).
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* Ricgraph is an ID resolver. It can, given an identifier of a person,
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easily find other identifiers of that person. When new identifiers are found when
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harvesting from new systems,
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they will be added automatically.
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## Contact
|
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Ricgraph has been created and is being maintained by
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Rik D.T. Janssen from Utrecht University in the Netherlands.
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You can find contact details at
|
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[his Utrecht University employee page](https://www.uu.nl/staff/DTJanssen).
|
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|
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He also has an ORCID profile on
|
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[ORCID 0000-0001-9510-0802](https://orcid.org/0000-0001-9510-0802).
|
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You can contact him for presentations, demos and workshops.
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For more details, including subscribing to the Ricgraph newsletter and
|
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opportunities for collaboration, read
|
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the [Ricgraph contact page](https://www.ricgraph.eu/contact.html).
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If you like Ricgraph, please give it a GitHub Star by clicking on the top right
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*Star* button on the Ricgraph GitHub page
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[https://github.com/UtrechtUniversity/ricgraph](https://github.com/UtrechtUniversity/ricgraph).
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If you have any suggestions or improvements,
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please let me know by creating a GitHub *Issue* at the top left of that page.
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<!-- Do not change the lines below. The version number will be
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modified by script maintenance/update_version.bash -->
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This README.md file is part of the
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documentation for version 3.4 of Ricgraph - Research in context graph.
|
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# pyproject.toml file to build module ricgraph for PyPI.
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3
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[build-system]
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4
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requires = ["setuptools>=61.0"]
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5
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build-backend = "setuptools.build_meta"
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[project]
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name = "ricgraph"
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version = "3.
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version = "3.4"
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authors = [
|
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{ name="Rik D.T. Janssen" },
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]
|
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[project.urls]
|
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|
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- url_other: other URL for a node, pointing to e.g. the originating record in a source system.
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- year: year of a research
|
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- year: year of a research result.
|
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- source_event: an event to be added to the _source list.
|
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@@ -100,8 +100,8 @@ In the default configuration of Ricgraph, the following properties are included:
|
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from numpy import nan
|
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from pandas import DataFrame, concat, set_option
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from typing import Union
|
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from .ricgraph_constants import PERSON_CATEGORY_PERSON
|
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from .ricgraph_utils import (timestamp, timestamp_posix,
|
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print_records_per_minute,
|
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print_progress)
|
|
@@ -120,7 +120,7 @@ __package__ = 'Ricgraph'
|
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# __version__ should be placed here instead of in __init__.py.
|
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|
# If not here, it cannot be found when executing something like
|
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# PYTHONPATH=../ricgraph ../bin/python ricgraph_explorer.py
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__version__ = '3.
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__version__ = '3.4'
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# ##############################################################################
|
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node_properties[prop_name] = getattr(row, other_name)
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create_update_node(name=row.name, category=row.category,
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create_update_node(name=str(row.name), category=str(row.category),
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value=str(row.value),
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other_properties=node_properties)
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|
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def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
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def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame | None) -> None:
|
|
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"""Create two nodes (called 'node pairs') and two directed edges between those nodes.
|
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This is done for all the nodes passed. The nodes are specified in a DataFrame.
|
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One row in the DataFrame contains two nodes which are to be connected.
|
|
@@ -187,6 +188,8 @@ def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
|
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:param left_and_right_nodepairs: the node pairs in a DataFrame.
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:return: None.
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"""
|
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if left_and_right_nodepairs is None or left_and_right_nodepairs.empty:
|
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return
|
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print('There are ' + str(len(left_and_right_nodepairs)) + ' rows ('
|
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|
+ timestamp() + '), creating nodes and edges for row:')
|
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count = 0
|
|
@@ -203,8 +206,10 @@ def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
|
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if prop_name + '2' == other_name:
|
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|
node_properties[prop_name + '2'] = getattr(row, other_name)
|
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|
-
create_two_nodes_and_edge(name1=row.name1, category1=row.category1,
|
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-
|
|
209
|
+
create_two_nodes_and_edge(name1=str(row.name1), category1=str(row.category1),
|
|
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value1=str(row.value1),
|
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|
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name2=str(row.name2), category2=str(row.category2),
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value2=str(row.value2),
|
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|
**node_properties)
|
|
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|
print_progress(count=count, now=True)
|
|
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|
end_ts = timestamp_posix()
|
|
@@ -214,9 +219,9 @@ def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
|
|
|
214
219
|
return
|
|
215
220
|
|
|
216
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|
|
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217
|
-
def create_nodepairs_and_edges_params(name1:
|
|
218
|
-
name2:
|
|
219
|
-
**other_properties:
|
|
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|
+
def create_nodepairs_and_edges_params(name1: dict | str, category1: dict | str, value1: dict | str,
|
|
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|
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name2: dict | str, category2: dict | str, value2: dict | str,
|
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**other_properties: dict | str) -> None:
|
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"""Create two nodes (called 'node pairs') and two directed edges between those nodes.
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221
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This is done for all the nodes passed. The nodes are specified by values passed to this function.
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Each value can be either a string or a dict containing strings.
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@@ -285,7 +290,7 @@ def create_nodepairs_and_edges_params(name1: Union[dict, str], category1: Union[
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290
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def unify_personal_identifiers(personal_identifiers: DataFrame,
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288
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-
source_event:
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293
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+
source_event: dict | str, history_event: dict | str) -> None:
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"""Unify a collection of personal identifiers (e.g. ORCID, ISNI, etc.).
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290
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That means that every column is unified to every other column.
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The identifiers are specified as columns in a DataFrame.
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@@ -343,9 +348,9 @@ def unify_personal_identifiers(personal_identifiers: DataFrame,
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343
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identifiers.rename(columns={column1: 'value1',
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column2: 'value2'}, inplace=True)
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new_identifiers_columns = {'name1': column1,
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346
|
-
'category1':
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351
|
+
'category1': PERSON_CATEGORY_PERSON,
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347
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'name2': column2,
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348
|
-
'category2':
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+
'category2': PERSON_CATEGORY_PERSON,
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'source_event1': source_event,
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'history_event1': history_event,
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'source_event2': source_event,
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