emso-metadata-harmonizer 1.0.2a0

Toolbox for creating/assessing EMSO-compliant NetCDF datasets and integrate them into ERDDAP services

Metadata Harmonizer Toolbox

This repository contains a set of tools that can be used to create NetCDF files, integrate them into an ERDDAP server and to ensure the compliance with the EMSO Metadata Specifications. The tools provided here are:

• emh.generate_dataset(): creates EMSO-compliant NetCDF files from .csv and .yaml files
• emh.erddap_config(): integrates NetCDF files into an ERDDAP server
• emh.metadata_report(): check the compliance of a dataset with the specifications.

In order to create and publish an EMSO-compliant dataset, the typical workflow is:

1. Prepare CSV data and YAML metadata
2. Generate EMSO-compliant NetCDF files using generate_dataset()
3. Integrate datasets into your ERDDAP deployment using erddap_config()
4. Validate metadata and operational compliance using metadata_report()

Installation

To install as a PyPi package:

pip3 install emso_metadata_harmonizer

🛠 NetCDF Generator

To generate a NetCDF dataset from data (csv) and metadata (yaml) files:

import emso_metadata_harmonizer as emh

emh.generate_dataset(["data.csv"], ["meta.yaml"], output="dataset.nc")

Full example with data and metadata from the example 2

import emso_metadata_harmonizer as emh
import urllib

# Download data and metadata from the example 2 in the metadata-harmonizer repository
data_url = "https://raw.githubusercontent.com/emso-eric/metadata-harmonizer/refs/heads/develop/examples/02/SBE16.csv"
meta_url = "https://raw.githubusercontent.com/emso-eric/metadata-harmonizer/refs/heads/develop/examples/02/meta.yaml"
urllib.request.urlretrieve(data_url, "data.csv")
urllib.request.urlretrieve(meta_url, "meta.yaml")

# Generate dataset from one data file
emh.generate_dataset(["data.csv"], ["meta.yaml"], "dataset.nc")

To generate a dataset from multiple data files:

import emso_metadata_harmonizer as emh
import urllib

# Generate dataset from multiple data files
data1_url = "https://raw.githubusercontent.com/emso-eric/metadata-harmonizer/refs/heads/develop/examples/02/SBE16.csv"
data2_url = "https://raw.githubusercontent.com/emso-eric/metadata-harmonizer/refs/heads/develop/examples/02/SBE37.csv"
meta_url = "https://raw.githubusercontent.com/emso-eric/metadata-harmonizer/refs/heads/develop/examples/02/meta.yaml"
urllib.request.urlretrieve(data1_url, "data1.csv")
urllib.request.urlretrieve(data2_url, "data2.csv")
urllib.request.urlretrieve(meta_url, "meta.yaml")

emh.generate_dataset(["data.csv", "data2.csv"], ["meta.yaml"], "dataset2.nc")

⚙️ ERDDAP Configurator

The ERDDAP Configurator (erddap_config()) helps prepare ERDDAP dataset definitions for NetCDF files, reducing manual work editing ERDDAP’s XML configurations. It reads NetCDF metadata and generates XML chunk required to register a new dataset.

import emso_metadata_harmonizer as emh

emh.erddap_config("dataset.nc", "MyDatasetIdentifier", "/path/to/dataset/files")

To automatically append a new dataset into an existing ERDDAP deployment, the path to the datasets.xml file should be passed via the datasets_xml_file parameter.

import emso_metadata_harmonizer as emh

emh.erddap_config("dataset.nc", "MyDatasetIdentifier", "/path/to/dataset/files", datasets_xml_file="path/to/datasets.xml")

📈 Metadata Report

The metadata reporting tool assesses the level of compliance of an ERDDAP or NetCDF dataset with the EMSO Metadata Specifications. To test a dataset, use the following syntax:

import emso_metadata_harmonizer as emh
emh.metadata_report("dataset.nc")

Logging

By default, the tool will print quite some logging information. To silence it:

import logging
logging.getLogger("emso_metadata_harmonizer").setLevel(logging.WARN)

Contact info

• author: Enoc Martínez
• version: v1.0.0
• organization: Universitat Politècnica de Catalunya (UPC)
• contact: [e-mail]