pyfigshare 0.6

A python package to interact with figshare

Installation

pip install git+https://github.com/DingWB/pyfigshare.git
reinstall
pip uninstall -y pyfigshare &&  pip install git+https://github.com/DingWB/pyfigshare.git

# or
pip install pyfigshare

Usage

(1). setup token

Login to https://figshare.com, create account, click profile -> Applications -> Create Personal Tokens

mkdir -p ~/.figshare
vim ~/.figshare/token
# paste the personal token in ~/.figshare/token

Alternatively, instead paste the token into ~/.figshare/token, one can also pass parameter token to Figshare class.

(2). Create article and upload files onto figshare

figshare upload -h

INFO: Showing help with the command 'figshare upload -- --help'.

NAME
    figshare upload - Upload files or directory to figshare

SYNOPSIS
    figshare upload <flags>

DESCRIPTION
    Upload files or directory to figshare

FLAGS
    -i, --input_path=INPUT_PATH
        Default: './'
        folder name, or single file path, or file pattern passed to glob (should be quote using "", and * must be included).
    --title=TITLE
        Default: 'title'
        article title, if not existed this article, it will be created.
    -d, --description=DESCRIPTION
        Default: 'description'
        article description.
    --token=TOKEN
        Type: Optional[]
        Default: None
        If ~/.figshare/token existed, this paramter can be ignored.
    -o, --output=OUTPUT
        Default: 'figshare.tsv'
        After the uploading is finished, the file id,url and filename will be written into this output file.
    --threshold=THRESHOLD
        Default: 15
        There is only 20 GB availabel for private storage, when uploading a big datasets (>20Gb), if the total quota usage is grater than  this threshold, the article will be published so that the 20GB usaged quata will be reset to 0.
    -c, --chunk_size=CHUNK_SIZE
        Default: 20
        chunk size for uploading [20 MB]
    -l, --level=LEVEL
        Default: 'INFO'
        loguru log level: DEBUG, INFO, WARNING, ERROR

# To use the command line, one have to paste token into ~/.figshare/token
figshare upload -i test_data/ --title test1
figshare upload -i MajorType/ --title MajorType --threshold 13 -c 100 -d "MajorType allc files"
# upload folder test_data onto figshare and give a title "test1"

(3) Get private or public article information

List private or public article file names

figshare list_files 9273710

Listing files for article 9273710:
  16871153 - pone.0220029.s001.pdf
  16871156 - pone.0220029.s002.pdf

List article detail information

figshare Figshare --private False get_article -h

INFO: Showing help with the command 'figshare Figshare --private False get_article -- --help'.

NAME
    figshare Figshare --private False get_article

SYNOPSIS
    figshare Figshare --private False get_article ARTICLE_ID <flags>

POSITIONAL ARGUMENTS
    ARTICLE_ID

FLAGS
    -v, --version=VERSION
        Type: Optional[]
        Default: None
    -p, --private=PRIVATE
        Type: Optional[]
        Default: None

NOTES
    You can also use flags syntax for POSITIONAL ARGUMENTS

figshare Figshare --private False get_article 9273710

(3) delete article

delete article with given article id

figshare Figshare --private True delete_article <article_id>

delete article with given title

figshare Figshare --private True delete_articles_with_title test1

(4) download all files for a given article id

figshare download 9273710 -o downlnoaded_data

Other functions

figshare Figshare --private True -h

INFO: Showing help with the command 'figshare Figshare --private True - -- --help'.

NAME
    figshare Figshare --private True

SYNOPSIS
    figshare Figshare --private True - GROUP | COMMAND | VALUE

GROUPS
    GROUP is one of the following:

     dict_attrs

     list_attrs

     valid_attrs

     value_attrs

COMMANDS
    COMMAND is one of the following:

     author

     complete_upload

     create_article
       Create a new article with attributes (see: https://docs.figsh.com/#private_article_create for detail), for example: { "title": "Test article title", "description": "Test description of article", "is_metadata_record": true, "metadata_reason": "hosted somewhere else", "tags": [ "tag1", "tag2" ], "keywords": [ "tag1", "tag2" ], "references": [ "http://figshare.com", "http://api.figshare.com" ], "related_materials": [ { "id": 10432, "identifier": "10.6084/m9.figshare.1407024", "identifier_type": "DOI", "relation": "IsSupplementTo", "title": "Figshare for institutions brochure", "is_linkout": false } ], "categories": [ 1, 10, 11 ], "categories_by_source_id": [ "300204", "400207" ], "authors": [ { "name": "John Doe" }, { "id": 1000008 } ], "custom_fields": { "defined_key": "value for it" }, "custom_fields_list": [ { "name": "key", "value": "value" } ], "defined_type": "media", "funding": "", "funding_list": [ { "id": 0, "title": "string" } ], "license": 1, "doi": "", "handle": "", "resource_doi": "", "resource_title": "", "timeline": { "firstOnline": "2015-12-31", "publisherPublication": "2015-12-31", "publisherAcceptance": "2015-12-31" }, "group_id": 0 }

     delete_article

     delete_articles_with_title

     delete_file

     download_article

     get_account_info

     get_article

     get_author_id

     get_file_check_data

     get_file_details
       Get the details about a file associated with a given article.

     get_used_quota_private

     initiate_new_upload

     issue_request

     list_article_versions

     list_articles

     list_files

     publish

     raw_issue_request

     search_articles

     update_article

     upload

     upload_file

     upload_folder

     upload_part

     upload_parts

VALUES
    VALUE is one of the following:

     baseurl

     chunk_size
       chunk size for uploading (in Mb), default is 20MB

     max_quota

     private
       whether to read or write private article, set to False if downloading public articles.

     threshold

     token
       if token has already been written to ~/.figshare/token, this parameter can be ignored.

     token_path

More information

https://help.figshare.com/article/how-to-use-the-figshare-api https://colab.research.google.com/drive/13CAM8mL1u7ZsqNhfZLv7bNb1rdhMI64d?usp=sharing#scrollTo=affected-source