Python Package for DataHerb: create, search, and load datasets.

Related tags

Data Analysispythondatadata-miningdatabasedatasetdata-analysis
Overview


Markdownify
The Python Package for DataHerb

A DataHerb Core Service to Create and Load Datasets.

Install

pip install dataherb

Documentation: dataherb.github.io/dataherb-python

The DataHerb Command-Line Tool

Requires Python 3

The DataHerb cli provides tools to create dataset metadata, validate metadata, search dataset in flora, and download dataset.

Search and Download

Search by keyword

dataherb search covid19
# Shows the minimal metadata

Search by dataherb id

dataherb search -i covid19_eu_data
# Shows the full metadata

Download dataset by dataherb id

dataherb download covid19_eu_data
# Downloads this dataset: http://dataherb.io/flora/covid19_eu_data

Create Dataset Using Command Line Tool

We provide a template for dataset creation.

Within a dataset folder where the data files are located, use the following command line tool to create the metadata template.

dataherb create

Upload dataset to remote

Within the dataset folder, run

dataherb upload

UI for all the datasets in a flora

dataherb serve

Use DataHerb in Your Code

Load Data into DataFrame

# Load the package
from dataherb.flora import Flora

# Initialize Flora service
# The Flora service holds all the dataset metadata
use_flora = "path/to/my/flora.json"
dataherb = Flora(flora=use_flora)

# Search datasets with keyword(s)
geo_datasets = dataherb.search("geo")
print(geo_datasets)

# Get a specific file from a dataset and load as DataFrame
tz_df = pd.read_csv(
  dataherb.herb(
      "geonames_timezone"
  ).get_resource(
      "dataset/geonames_timezone.csv"
  )
)
print(tz_df)

The DataHerb Project

What is DataHerb

DataHerb is an open-source data discovery and management tool.

  • A DataHerb or Herb is a dataset. A dataset comes with the data files, and the metadata of the data files.
  • A Herb Resource or Resource is a data file in the DataHerb.
  • A Flora is the combination of all the DataHerbs.

In many data projects, finding the right datasets to enhance your data is one of the most time consuming part. DataHerb adds flavor to your data project. By creating metadata and manage the datasets systematically, locating an dataset is much easier.

Currently, dataherb supports sync dataset between local and S3/git. Each dataset can have its own remote location.

What is DataHerb Flora

We desigined the following workflow to share and index open datasets.

DataHerb Workflow

The repo dataherb-flora is a demo flora that lists some datasets and demonstrated on the website https://dataherb.github.io. At this moment, the whole system is being renovated.

Development

  1. Create a conda environment.
  2. Install requirements: pip install -r requirements.txt

Documentation

The source of the documentation for this package is located at docs.

References and Acknolwedgement

  • dataherb uses datapackage in the core. datapackage is a python library for the data-package standard. The core schema of the dataset is essentially the data-package standard.
Comments
  • would you like to take a look at our api?

    would you like to take a look at our api?

    I come across this repo and found it very similar to our API, though much more mature. https://github.com/Glacier-Ice/data-sci-api

    we have problems in creating a standard of dataset collection and API documentation for end-users

    is there a way we can collaborate?

    opened by Stockard 4
  • Format search results for better ux

    Format search results for better ux

    The current search result shows too much information. It would be good to format the result into a way that is easier to read and get the id if needed.

    enhancement 
    opened by emptymalei 1
  • use rapidfuzz instead of fuzzywuzzy

    use rapidfuzz instead of fuzzywuzzy

    FuzzyWuzzy is GPLv2 licensed which would force you to licence the whole project under GPLv2. I had the same problem on one of my projects and so I wrote rapidfuzz which is implementing the same algorithm but is based on a version of fuzzywuzzy that was MIT Licensed and is therefor MIT Licensed aswell, so it can be used in here without forcing a License change. As a nice bonus it is fully implemented in C++ and comes with a few Algorithmic improvements making it faster than FuzzyWuzzy.

    opened by maxbachmann 1
  • Use One File for Each Herb in Flora

    Use One File for Each Herb in Flora

    Is it better to have one file for each herb in flora?

    Situition

    Currently, the flora is defined in a single json file.

    • It becomes hard to read. This is not fitting into the human-readable principle.
    • It becomes hard to manage. We are currently sorting everything in the big file. When we have a problem, the whole flora will be unusable.

    Solution

    Use separate files for herbs.

    Simply Copy dataherb.json

    • Copy dataherb.json to workdir/{id}/dataherb.json or {id}.json will work.

      • Using folders allows us to put in more files. For example, we can take datapackage content out to make it more managable.

    • Build the flora from all these files.

    • [x] Implement this new structure.

    Ready for a Demo repo of flora

    In this way, we can put up a repo for open datasets easily and allow users to add more easily.

    Possible creating process

    • Create package directly on GitHub by uploading the dataherb.json file.

      • But there should be a validation process to avoid duplicate id.

    • [ ] Setup a demo repo as demo flora.

    enhancement 
    opened by emptymalei 0
  • Overhaul: New Core Management, Local Indexing Webpage, Flexible Flora Database

    Overhaul: New Core Management, Local Indexing Webpage, Flexible Flora Database

    This is a completely new era of Dataherb.

    New Stuff

    • Supporting S3 as source
    • Serve whole flora as webpages with search
    • User config for flora
    • Multiple flora on one machine

    We also redesigned the core.

    opened by emptymalei 0
  • Add dataset using the URL of a remote repo

    Add dataset using the URL of a remote repo

    We don't only upload datasets, we might also want to load datasets from remote.

    Here we propose to add the option to add datasets using the URL.

    • Build a Herb from remote data
    • Option to add metadata only or download everything.
      • Adding metadata only will only add data to the flora
      • Thus we can not find the dataset folder with the corresponding id.
      • This can be used to decide if a dataset is metadata only or fully downloaded.
    opened by emptymalei 0
  • Sync Flora Metafolder

    Sync Flora Metafolder

    Managing flora using command line

    Version control of the flora is not really hard. We just get into the folder and use git.

    But it would be much easier if we can simply run dataherb sync flora

    Approaches:

    enhancement 
    opened by emptymalei 0
Releases(0.1.6)

  • 0.1.6(Feb 10, 2022)

    Fixed

    • Command line tool dataherb configure -l now only opens the folder.
    • Command line too dataherb download will also display where the dataset is downloaded to. This makes it easier for the user to find the downloaded dataset.
    Source code(tar.gz)
    Source code(zip)

  • 0.1.5(Aug 12, 2021)

    Using Dedicated Folders for Herbs

    In the previous versions, we can only use a single file to host all the flora metadata. It will become unmanageable and hard to read as the number of herbs grows. (#14)

    In this version, we introduce a new structure for the flora metadata. Each herb is getting its own folder! This structure makes it easier for us to read and manage by hand. It is also better for version-controling your flora.

    (🌱 Best wishes to your herbs in their own pots. )

    Source code(tar.gz)
    Source code(zip)

  • 0.1.4(Aug 7, 2021)

  • 0.1.3(Aug 7, 2021)

  • 0.0.5(Mar 14, 2020)

  • 0.0.3(Feb 23, 2020)

    dataherb command line tool now automatically finds the data files and generate part of the metadata based on the files. CSV files are automatically parsed.

    Source code(tar.gz)
    Source code(zip)

  • 0.0.2(Feb 16, 2020)

Owner
DataHerb
Get datasets in a blink of an eye | Experimenting with simple modular small dataset discovery
DataHerb
GitHub Repository https://dataherb.github.io/dataherb-python
LynxKite: a complete graph data science platform for very large graphs and other datasets.

LynxKite is a complete graph data science platform for very large graphs and other datasets. It seamlessly combines the benefits of a friendly graphical interface and a powerful Python API.

124 Dec 14, 2022
PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

Burn Research 4 Oct 13, 2022
PyIOmica (pyiomica) is a Python package for omics analyses.

PyIOmica (pyiomica) This repository contains PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets.

G. Mias Lab 13 Jun 29, 2022
Geospatial data-science analysis on reasons behind delay in Grab ride-share services

Grab x Pulis Detailed analysis done to investigate possible reasons for delay in Grab services for NUS Data Analytics Competition 2022, to be found in

Keng Hwee 6 Jun 07, 2022
MDAnalysis is a Python library to analyze molecular dynamics simulations.

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

MDAnalysis 933 Dec 28, 2022
DefAP is a program developed to facilitate the exploration of a material's defect chemistry

DefAP is a program developed to facilitate the exploration of a material's defect chemistry. A large number of features are provided and rapid exploration is supported through the use of autoplotting

6 Oct 25, 2022
Port of dplyr and other related R packages in python, using pipda.

Unlike other similar packages in python that just mimic the piping syntax, datar follows the API designs from the original packages as much as possible, and is tested thoroughly with the cases from t

179 Dec 21, 2022
Random dataframe and database table generator

Random database/dataframe generator Authored and maintained by Dr. Tirthajyoti Sarkar, Fremont, USA Introduction Often, beginners in SQL or data scien

Tirthajyoti Sarkar 249 Jan 08, 2023
Spectral Analysis in Python

SPECTRUM : Spectral Analysis in Python contributions: Please join https://github.com/cokelaer/spectrum contributors: https://github.com/cokelaer/spect

Thomas Cokelaer 280 Dec 16, 2022
Datashredder is a simple data corruption engine written in python. You can corrupt anything text, images and video.

Datashredder is a simple data corruption engine written in python. You can corrupt anything text, images and video. You can chose the cha

2 Jul 22, 2022
An ETL Pipeline of a large data set from a fictitious music streaming service named Sparkify.

An ETL Pipeline of a large data set from a fictitious music streaming service named Sparkify. The ETL process flows from AWS's S3 into staging tables in AWS Redshift.

1 Feb 11, 2022
PySpark bindings for H3, a hierarchical hexagonal geospatial indexing system

h3-pyspark: Uber's H3 Hexagonal Hierarchical Geospatial Indexing System in PySpark PySpark bindings for the H3 core library. For available functions,

Kevin Schaich 12 Dec 24, 2022
Python Kalman filtering and optimal estimation library. Implements Kalman filter, particle filter, Extended Kalman filter, Unscented Kalman filter, g-h (alpha-beta), least squares, H Infinity, smoothers, and more. Has companion book 'Kalman and Bayesian Filters in Python'.

FilterPy - Kalman filters and other optimal and non-optimal estimation filters in Python. NOTE: Imminent drop of support of Python 2.7, 3.4. See secti

Roger Labbe 2.5k Dec 30, 2022
Additional tools for particle accelerator data analysis and machine information

PyLHC Tools This package is a collection of useful scripts and tools for the Optics Measurements and Corrections group (OMC) at CERN. Documentation Au

PyLHC 3 Apr 13, 2022
scikit-survival is a Python module for survival analysis built on top of scikit-learn.

scikit-survival scikit-survival is a Python module for survival analysis built on top of scikit-learn. It allows doing survival analysis while utilizi

Sebastian Pölsterl 876 Jan 04, 2023
yt is an open-source, permissively-licensed Python library for analyzing and visualizing volumetric data.

The yt Project yt is an open-source, permissively-licensed Python library for analyzing and visualizing volumetric data. yt supports structured, varia

The yt project 367 Dec 25, 2022
Sentiment analysis on streaming twitter data using Spark Structured Streaming & Python

Sentiment analysis on streaming twitter data using Spark Structured Streaming & Python This project is a good starting point for those who have little

Himanshu Kumar singh 2 Dec 04, 2021
Bigdata Simulation Library Of Dream By Sandman Books

BIGDATA SIMULATION LIBRARY OF DREAM BY SANDMAN BOOKS ================= Solution Architecture Description In the realm of Dreaming, its ruler SANDMAN,

Maycon Cypriano 3 Jun 30, 2022
PyPDC is a Python package for calculating asymptotic Partial Directed Coherence estimations for brain connectivity analysis.

Python asymptotic Partial Directed Coherence and Directed Coherence estimation package for brain connectivity analysis. Free software: MIT license Doc

Heitor Baldo 3 Nov 26, 2022
Creating a statistical model to predict 10 year treasury yields

Predicting 10-Year Treasury Yields Intitially, I wanted to see if the volatility in the stock market, represented by the VIX index (data source), had

10 Oct 27, 2021