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mizgra

PyPI PyPI - Python Version Docker Image Size (latest by date)

Converts Mizar ESX MML mathematical data to property graph formats - GraphML, YARS-PG. Produce files ready to import to various graph databases, including Neo4j. Supports external RDF data in various formats.

To save output to file, add > /path/to/output.graphml to the end of the command, e.g.:

mizgra /path/to/esx_mml /path/to/mml.lar -m /path/to/metadata.xml -c /path/to/CSVs -cv > mmlkg.graphml

Read more about the MMLKG project at the MMLKG website.

Run mizgra

There are several ways to run mizgra. You can install it from PyPI, run it using Docker, or run it from the source. Choose the most convenient way for you.

PyPI

  1. Install mizgra:
pip install mizgra
  1. Run mizgra:
mizgra [ESXMML] [MMLLAR]

Docker from Docker Hub

  1. Pull Docker image from Docker Hub:
docker pull lszeremeta/mizgra
  1. Run Docker container:
docker run --rm -v /path/to/esx/and/mml.lar:/app/input lszeremeta/mizgra /app/input/esx_mml /app/input/mml.lar

Docker from source

  1. Build Docker image:
docker build -t mizgra .
  1. Run Docker container:
docker run --rm -v /path/to/esx/and/mml.lar:/app/input mizgra /app/input/esx_mml /app/input/mml.lar

Python from source

  1. Clone this repository and go to its directory:
git clone [email protected]:lszeremeta/mizgra.git
cd mizgra
  1. Install requirements:
pip install -r requirements.txt
  1. Run mizgra:
python -m mizgra [ESXMML] [MMLLAR]

Recommended usage

Mizgra requires two arguments:

  • ESXMML: Path to the ESX MML files directory. You can download it from esx_files repository.
  • MMLLAR: Path to the mml.lar file. You can download it from esx_files repository.

Metadata and CSV relations are recommended. To include them, use -m and -c arguments. You can generate metadata with statistics using metadata_gen and CSV relations using csvrelgen.

To save the output to a file, add > /path/to/output.graphml to the end of the command.

Example:

mizgra /path/to/esx_mml /path/to/mml.lar -m /path/to/metadata.xml -c /path/to/CSVs -cv > mmlkg.graphml

See Usage for more details.

Usage

usage: mizgra [-h] [-v] [-o OUTPUT]
              [-s {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...]]
              [-d {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...]]
              [-m METADATA] [-c CSV [CSV ...]] [-cv] [-r RDF] [-rf {json-ld,hext,n3,nquads,nt,trix,turtle,xml}]
              ESXMML MMLLAR

To see all options in your version use -h or --help:

mizgra -h

Informative arguments

  • -h, --help: Show help message and exit.
  • -v, --version: Show program version and exit.

Required arguments

  • ESXMML: Path to the ESX MML files directory. You can download it from esx_files repository.
  • MMLLAR: Path to the mml.lar file. You can download it from esx_files repository.

Output preference arguments

  • -o OUTPUT, --output OUTPUT: Output format (graphml, yarspg; default: graphml).
  • -s {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...], --show {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...]: Show only selected outputs; by default, all possible results are shown, excluding those that are disabled by default ( local-ref-relations, usages-relations, and broader-relations; handled by CSV relations). To show disabled outputs, specify them directly with -s/--show option. It's recommended to use CSV relations.
  • -d {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...], --disable {filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} [{filenames,nodes,metadata,member-relations,local-ref-relations,usages-relations,broader-relations,csv-relations,rdf-relations} ...]: Disable selected outputs (local-ref-relations, usages-relations, and broader-relations are disabled by default; handled by CSV relations).

External data arguments

  • -m METADATA, --metadata METADATA: Path to the metadata file. If not specified, metadata without dataset statistics will be included. You can generate a full metadata file using: https://github.com/domel/metadata_gen
  • -c CSV, --csv CSV: Paths to the CSV files/directories with relations. You can generate it using: https://github.com/arturkornilowicz/csvrelgen
  • -cv, --csv-validate: Validates CSV files by several checks before reading to minimize the possibility of CSV errors; turned off by default.
  • -r RDF, --rdf RDF: Path to the RDF data file; for URLs or files with not standard extensions may be needed to specify format using -rf.
  • -rf {json-ld,hext,n3,nquads,nt,trix,turtle,xml}, --rdf-format {json-ld,hext,n3,nquads,nt,trix,turtle,xml}: RDF data file format, specify if not detected automatically

Examples

Convert ESX MML data to GraphML format:

mizgra /path/to/esx_mml /path/to/mml.lar > graph.graphml

Convert ESX MML data to YARS-PG format:

mizgra /path/to/esx_mml /path/to/mml.lar -o yarspg > graph.yarspg

Convert ESX MML data to GraphML format, showing only metadata and member-relations:

mizgra /path/to/esx_mml /path/to/mml.lar -s metadata member-relations > graph.graphml

Convert ESX MML data to GraphML format and include external metadata:

mizgra /path/to/esx_mml /path/to/mml.lar -m /path/to/metadata.xml > graph.graphml

Convert ESX MML data to GraphML format and include RDF data in Turtle format:

mizgra /path/to/esx_mml /path/to/mml.lar -r /path/to/external.ttl -rf turtle > graph.graphml

Convert ESX MML data to GraphML format, include CSV data from selected directory, validate CSV files:

mizgra /path/to/esx_mml /path/to/mml.lar -c /path/to/external -cv > graph.graphml

Convert ESX MML data to GraphML format and include CSV data:

mizgra /path/to/esx_mml /path/to/mml.lar -c /path/to/external.csv > graph.graphml

Convert ESX MML data to GraphML format and include CSV data from multiple files and directories:

mizgra /path/to/esx_mml /path/to/mml.lar -c /path/to/external1.csv /path/to/external2 /path/to/external3.csv > graph.graphml

Contribution

Would you like to improve this project? Great! We are waiting for your help and suggestions. If you are new to open source contributions, read How to Contribute to Open Source.

License

Distributed under MIT License.

This project contains a sample external RDF data file (rdf_data.nt), prepared by Dominik Tomaszuk (@domel) and available under the CC-BY 4.0 License. The base for the query was developed using Wikidata, which is available under the Creative Commons CC0 License. While it also includes references to DBpedia and YAGO (whose data are on Creative Commons Attribution-ShareAlike 3.0 License), Dominik Tomaszuk only retrieved non-data links from these sources. The structure of this file is entirely different than the above datasets.