ual-re / ldcoolp-figshare

Python tool using the Figshare API for data curation

About Us

Research Engagement (RE) helps UA faculty, researchers, and students with every stage of their research. We have three functional units:

1. Research Incubator
2. Data Cooperative
3. Scholarly Communications

Members of the Data Cooperative:

GitHub	Name	Role/Title
	Jeff Oliver	Data Science Specialist
	Fernando Rios	Data Management Specialist
	Kiri Carini	GIS Specialist
	Jonathan Ratliff	Research Data Repository Assistant

Experience

Specialty	Tools/Resources
Data Science
Data Management & Publishing
GIS

ldcoolp-figshare's Issues

Add Sphinx documentation and publish to ReadTheDocs

We will host the documentation at ldcoolp-figshare.readthedocs.io.

This is straight forward feature:

• Include a docs/source folder containing documentation.
• Add sphinx-build GitHub actions
• Docstrings update
• Add instructions for using code
• Enable with RTDs.org

Include issue_request from redata-commons

The issue_request function will be included as part of redata-commons. Thus, it's best to import from our library. Note that the figshare library/package that we use is not PyPI packaged, which makes it a bit of a pain.

Prepare code for PyPI packaging

Will need to include:

• requirements.txt
• setup.py
• MANIFEST.in
• Add pypi-publish.yml GitHub Action
• Add API token for PyPI
• Update README.md and docs/source/index.rst

Update URL paths for LD-Cool-P

Since the repo has been migrated (se UAL-RE/LD-Cool-P#175), we need to fix any links to LD-Cool-P

Add .idea to exclude in .gitignore

ldcoolp-figshare should also have the .idea PyCharm settings folder ignored.


Change PyPI API tokens to use team account

The PYPI_TOKEN and TEST_PYPI_TOKEN needs to be updated to use the team account.

Token is saved in team stache folder.

Add CHANGELOG

Use the same template that we did with redata-commons

Add GitHub action to create releases with v* tags

Include a simple Action that triggers on pushed tags prefixed with 'v'



Chore: Add README.md, LICENSE, and .gitignore files

Since we started by migrating code from LD-Cool-P, these files are not included.


Update use of redata.commons to include process option

redata==0.4.1 now has support for the process option, which allows for returning the requests.Response result. Let's now incorporate this in all methods of FigshareInstituteAdmin

See: UAL-RE/redata-commons#18

Update README.md with RTDs information and links

RTDs is published at: https://ldcoolp-figshare.readthedocs.io/en/latest/index.html

Let's update all links. In addition, we should include GitHub badges at the top.


Bug: Minor fixes after PyPI publishing

• Fix description in PyPI
• Fix typo with shields.io badge
  

Reorganize codebase for easier packaging

We should have a folder called ldcoolp_figshare and for the figshare module to be included. We should consider importing FigshareInstituteAdmin in ldcoolp_figshare/__init__.py

For get_curation_list method, allow for pending selection

This API endpoint allows for an optional status input: https://docs.figshare.com/#account_institution_curations


Refactor FigshareInstituteAdmin for general use

Steps include:

• Adding optional input parameter for admin_filter
• Import FigshareInstituteAdmin in __init__.py
• Change from dict input to separate parameters
• Simplify docstrings to remove method description (this is for Sphinx docs)

Remove GitHub badges from RTDs

RTDs builds seem to fail due to inclusion of SVG, such as GitHub badges. Also since these badges are dynamic, they are confusing when someone looks at the docs. We should remove this.


Feature: Incorporate figshare.Figshare into ldcoolp-figshare

We are currently using our forked copy of cognoma's figshare.

In LD-Cool-P this is used in the retrieve module (download_files function) and in development preserve module. Howevr, this code was not made easiy installable with pip. The simplest solution is to add it to ldcoolp-figshare so it's included.

For simplicity, this will be the Figshare class. We might consider renaming main module to curation and create a new main.

Enhancement: update dependencies

Summary

Update dependencies

Objectives

Update its dependencies in requirements.txt and setup.py to the latest stable version.

Proposal

requirement.txt dependencies include:

• redata == 0.6 (after redata-commons upgraded to the latest version]

setup.py dependencies include:

• version = '0.4.0'
• programming language: remove Python 3.7 (line 25, and line 30)
• programming language: add Python 3.10 (line 33)
• changing author to "UAL-RE" and its associated email
• Update PYPI release

init.py include:

• version = "0.4.0"

Changelog:

• v0.4.0:

/docs/source/requirement.txt:

• redata
• sphinx
• sphinx-rtd-theme
• sphix-autodoc-typehints

Review and update needed lines:

• /docs/source/authors.rst
• /docs/source/conf.py
• /docs/source/getting_started.rst

Testing notes

• Testing manual run

Additional notes

This is related to redata-commons Issue 40

Implemented in: TBD

Add method to retrieve ORCID and Figshare account ID for users

See UAL-RE/LD-Cool-P#232 for more details.

The endpoint with the Figshare account and ORCID only requires the ReDATA account id (institution account):
https://docs.figshare.com/#private_account_institution_user