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nexus2json_mapper

https://github.com/kit-data-manager/nexus2json_mapper

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ✓
    Institutional organization owner
    Organization kit-data-manager has institutional domain (www.scc.kit.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.6%) to scientific vocabulary

Keywords

cli
Last synced: 4 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: kit-data-manager
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 98.6 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Topics
cli
Created about 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Citation Codemeta

README.md

APE-HE NeXus File to JSON Document Converter

Description:

This script is designed to automate the tasks of extracting metadata from NeXus (.nxs) files generated by the Advanced Photoelectric Effect - High Energy (APE-HE) experiment, and the mapping of extracted metadata to a predifined JSON schema to generate a structured JSON document. The NeXus file is parsed using the Python library H5py, which allows to efficiently navigate and manipulate HDF5-based files like NeXus.

The current script processes individual NeXus files and zipped NeXus files from APE-HE experiments, transforming the extracted metadata into a structured JSON format or zipped JSON files suitable for storage.

Inputs:

  • Path to the Schema file (.json): A JSON schema that defines the desired structure of the output document.
  • Path to the NeXus file (.nxs) or zipped NeXus files (.zip): A NeXus file containing experimental metadata and data.
  • Name of the output file (.json) for a single NeXus file input or (.zip) for zipped NeXus files input: The desired name of the output file where the metadata document will be saved.

Output:

A structured JSON file containing the extracted metadata aligned with the schema.

How to execute the script:

  • For single NeXus file: python NexusMapping_cmdline.py <path_to_schema.json> <path_to_NeXus_file.nxs> <output_document.json>
  • For zipped NeXus files: python NexusMapping_cmdline.py <path_to_schema.json> <path_to_zipped_NeXus_files.zip> <output_document.zip>

Owner

  • Name: KIT Data Manager
  • Login: kit-data-manager
  • Kind: organization
  • Email: webmaster@datamanger.kit.edu
  • Location: Karlsruhe, Germany

Generic software and recommendations for FAIR research data management by DEM.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
type: software
title: APE-HE mapper
abstract: APE-HE Mapper extracts metadata from APE-HE (Advanced Photoelectric Effect
  – High Energy) experimental neXus output into a consistent JSON format that follows
  a schema.
version: v0.1.1
keywords:
  - APE-HE
  - neXus
  - metadata
authors:
  - given-names: Gabin Thibaut
    orcid: https://orcid.org/0000-0002-6745-3464
    family-names: Oumbe Tekam
  - given-names: Irene
    orcid: https://orcid.org/0000-0002-9576-8615
    family-names: Modolo
  - given-names: Dario
    orcid: https://orcid.org/0000-0001-9199-6373
    family-names: De Angelis
  - given-names: Rossella
    orcid: https://orcid.org/0000-0003-2534-0063
    family-names: Aversa
contact:
  - given-names: Gabin Thibaut
    orcid: https://orcid.org/0000-0002-6745-3464
    family-names: Oumbe Tekam
license: Apache-2.0
repository-code: https://github.com/kit-data-manager/Nexus2Json_Mapper

CodeMeta (codemeta.json) 

{
  "@context": [
    "https://doi.org/10.5063/schema/codemeta-2.0",
    "https://w3id.org/software-iodata",
    "https://raw.githubusercontent.com/jantman/repostatus.org/master/badges/latest/ontology.jsonld",
    "https://schema.org",
    "https://w3id.org/software-types"
  ],
  "@type": "SoftwareSourceCode",
  "author": [
    {
      "@type": "Person",
      "givenName": "Gabin Thibaut",
      "familyName": "Oumbe Tekam",
      "@id": "https://orcid.org/0000-0002-6745-3464",
      "identifier": "https://orcid.org/0000-0002-6745-3464"
    }
  ],
  "name": "APE-HE mapper",
  "description": "APE-HE Mapper extracts metadata from APE-HE (Advanced Photoelectric Effect  High Energy) experimental neXus output into a consistent JSON format that follows a schema.",
  "version": "v0.1.1",
  "keywords": [
    "APE-HE",
    "neXus",
    "metadata"
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Gabin Thibaut",
      "familyName": "Oumbe Tekam",
      "@id": "https://orcid.org/0000-0002-6745-3464",
      "identifier": "https://orcid.org/0000-0002-6745-3464"
    }
  ],
  "license": [
    "https://spdx.org/licenses/Apache-2.0"
  ],
  "codeRepository": "https://github.com/kit-data-manager/Nexus2Json_Mapper",
  "contributor": [
    {
      "@type": "Person",
      "givenName": "Irene",
      "familyName": "Modolo",
      "@id": "https://orcid.org/0000-0002-9576-8615",
      "identifier": "https://orcid.org/0000-0002-9576-8615"
    },
    {
      "@type": "Person",
      "givenName": "Dario",
      "familyName": "De Angelis",
      "@id": "https://orcid.org/0000-0001-9199-6373",
      "identifier": "https://orcid.org/0000-0001-9199-6373"
    },
    {
      "@type": "Person",
      "givenName": "Rossella",
      "familyName": "Aversa",
      "@id": "https://orcid.org/0000-0003-2534-0063",
      "identifier": "https://orcid.org/0000-0003-2534-0063"
    }
  ]
}

GitHub Events

Total
  • Release event: 1
  • Issues event: 1
  • Push event: 15
Last Year
  • Release event: 1
  • Issues event: 1
  • Push event: 15

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 23
  • Total Committers: 1
  • Avg Commits per committer: 23.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 23
  • Committers: 1
  • Avg Commits per committer: 23.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
gabinoumbe o****n@y****r 23

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • sabrineChe (1)
Pull Request Authors
Top Labels
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enhancement (1)
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