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curedcolumns

CUREd+ metadata tool: generates a list of all the columns in every table in the database.

https://github.com/cured-plus/curedcolumns

Science Score: 44.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

metadata
Last synced: 6 months ago · JSON representation ·

Repository

CUREd+ metadata tool: generates a list of all the columns in every table in the database.

Basic Info
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 4
Topics
metadata
Created almost 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing License Citation

README.md

Tests passing

CUREd+ metadata generator

The CUREd+ metadata generator tool generates a list of all the columns in every table in the database.

The data in the target bucket must be arranged in the following directory structure: <data_set_id>/<table_id>/data/**/*.parquet

This script will generate a CSV file with the following columns:

  • data_set_id
  • table_id
  • column_name
  • data_type

Installation

Ensure Python is installed. (See this tutorial.)

Install AWS command-line interface (CLI). Configure your access key using the aws configure command.

Install this package using the Python package manager:

bash pip install curedcolumns

Usage

The basic usage of this app is to specify the AWS CLI profile and the bucket name you want to inspect.

bash curedcolumns --profile $AWS_PROFILE $AWS_BUCKET --output $OUTPUT_FILE

You should create an AWS profile using the aws configure command.

bash aws configure --profile $AWS_PROFILE

To view the command line options:

```bash $ curedcolumns --help usage: curedcolumns [-h] [-v] [--version] [-l LOGLEVEL] [--prefix PREFIX] [--no-sign-request] [--profile PROFILE] [-d DELIMITER] [-o OUTPUT] [-f] bucket

List all the field names for all the data sets in a bucket on AWS S3 object storage and display the metadata in CSV format. This assumes a folder structure in this layout: //data/*.parquet

positional arguments: bucket S3 bucket location URI

options: -h, --help show this help message and exit -v, --verbose --version Show the version number of this tool -l LOGLEVEL, --loglevel LOGLEVEL --prefix PREFIX Limits the response to keys that begin with the specified prefix. --no-sign-request --profile PROFILE AWS profile to use -d DELIMITER, --delimiter DELIMITER Column separator character -o OUTPUT, --output OUTPUT Output file path. Default: screen -f, --force Overwrite output file if it already exists ```

Example

Use the AWS CLI profile named "clean"

bash curedcolumns --profile clean s3://my_bucket.aws.com

Development

See CONTRIBUTING.md.

Owner

  • Name: CUREd-Plus
  • Login: CUREd-Plus
  • Kind: organization

Citation (CITATION.cff) 

---
authors:
  - given-names: "Joe Salvador Thornhill"
    family-names: Heffer
    affiliation: "University of Sheffield"
    orcid: "https://orcid.org/0000-0001-8733-1117"
cff-version: "1.1.0"
message: "If you use this software, please cite it using these metadata."
...

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 3
  • Delete event: 1
  • Push event: 6
  • Pull request event: 2
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 3
  • Delete event: 1
  • Push event: 6
  • Pull request event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 1
  • Average time to close issues: 26 minutes
  • Average time to close pull requests: 17 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: 26 minutes
  • Average time to close pull requests: 17 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Joe-Heffer-Shef (3)
Pull Request Authors
  • Joe-Heffer-Shef (5)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 22 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
pypi.org: curedcolumns

CUREd+ metadata tool: generates a list of all the columns in every table in the database.

  • Homepage: https://www.sheffield.ac.uk/data-connect
  • Documentation: https://github.com/CUREd-Plus/curedcolumns/blob/main/README.md
  • License: MIT License Copyright (c) 2024 Data Connect Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.1.3
    published about 1 year ago
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 22 Last month
Rankings
Dependent packages count: 10.7%
Average: 35.5%
Dependent repos count: 60.3%
Maintainers (1)
jheffer
Last synced: 7 months ago

Dependencies

pyproject.toml pypi
  • boto3 ==1.*
  • pyarrow ==16.*
.github/workflows/python-publish.yml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish v1.9.0 composite
.github/workflows/test.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite