pigshare 0.3

Python client for Figshare

=================
Markus Binsteiner
=================

:Author: Markus Binsteiner

.. contents::
1 Pigshare
----------

Python client library and commandline tool for institutional Figshare.

The commandline options are created dynamically from the available api-method wrapper code, which is why some of them might feel a bit clumsy. Also, many of the commands only support values as json-formatted strings. I might change that in the future, but it'd require more complex cli-argparse creation code and I'm not sure whether it's worth it.

1.1 Notes
~~~~~~~~~

So far, I've only tested this on Linux.

1.2 Requirements
~~~~~~~~~~~~~~~~

- python-dev package (for simplejson compilation I think)

- argparse

- setuptools

- restkit

- booby

- simplejson

- parinx

- pyclist

- argcomplete

1.3 Installation
~~~~~~~~~~~~~~~~

1.3.1 Release
^^^^^^^^^^^^^

``(sudo) pip install pigshare
``

1.3.2 Development version from Github
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

``(sudo) pip install https://github.com/UoA-eResearch/pigshare/archive/master.zip
``

1.4 Usage (commandline client)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1.4.1 Connection details
^^^^^^^^^^^^^^^^^^^^^^^^

**pigshare** reads a config file $HOME/.pigshare.conf, in the format:

``[default]
url = https://api.figsh.com/v2
token = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
``

(note, this example uses the staging environment)

**pigshare** supports profiles, so you can have multiple profiles in your config file like for example:

``[default]
url = https://api.figsh.com/v2
token = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
[markus]
url = https://api.figshare.com/v2
token = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
[not_markus_but_somebody_else]
url = https://api.figshare.com/v2
token = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
``

Now, when you call **pigshare** with the **-p** argument, you can switch between different backends/identities:

``pigshare -p markus [command]
``

The command you chose will be using the selected connection parameters.

1.4.2 Features:
^^^^^^^^^^^^^^^

1.4.2.1 Supported
:::::::::::::::::

- creation of articles

- listing of public and private articles

- searching for public and private articles

- updating of articles

- creation of collections

- listing of public and private collections

- searching for public and private collections

- updating of collections

1.4.2.2 Not (yet) supported
:::::::::::::::::::::::::::

- automatically deal with the 10 item limits on some methods

- everything else

1.4.3 General usage
^^^^^^^^^^^^^^^^^^^

Basic usage is displayed via:

``pigshare -h
``

Command specific usage can be displayed via:

``pigshare [command] -h
``

1.4.4 Filtering
^^^^^^^^^^^^^^^

(Sub-)commands that display one or more items can be called using an output filter (the **-o** argument before the sub-command). Depending on the sub-command called only certain fields of the items are available (e.g. **list\ :sub:`articles`\** has only a subset of fields compared to **read\ :sub:`article`\**).

I'd recommend trying out the command you want to run first, and checking which fields are available, then run the command again with the appropriate filter. A command to list all articles and only display the **doi** and **title** of each article would be:

``pigshare -o doi,title list_articles
``

For more advanced filtering, consider piping in the 'full' output of **pigshare** into a tool like jq ( `https://stedolan.github.io/jq/ <https://stedolan.github.io/jq/>`_ ).

1.4.5 Commonly used commands
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

1.4.5.1 Articles
::::::::::::::::

1.4.5.1.1 List articles
'''''''''''''''''''''''

To list all articles and display the **doi**, (internal) **id**, **title**, **url**, and **published\ :sub:`date`\** for each, issue:

``pigshare list_articles
``

To display a table with all articles, but only display **doi** and **title**, you can use:

``pigshare -o doi,title list_articles
``

1.4.5.1.2 Read an article
'''''''''''''''''''''''''

To display the properties of an article, use:

``pigshare read_article [article_id]
``

To display the doi and all tags of a number of articles, use (tags are not part of the 'short' article format that the **list\ :sub:`articles`\** command returns):

``pigshare -o doi,tags read_article [article_id] [article_id] [article_id]
``

1.4.5.1.3 Search for articles
'''''''''''''''''''''''''''''

To list all articles matching a search string, issue:

``pigshare search_articles --search_term [search_term]
``

To display all dois and titles of articles that match a search string:

``pigshare -o doi,title search_articles --search_term [search_term]
``

1.4.5.1.4 List my articles
''''''''''''''''''''''''''

To list all of your own articles:

``pigshare list_my_articles
``

1.4.5.1.5 To create a new article
'''''''''''''''''''''''''''''''''

``pigshare create_article --article '{"title": "Markus test", "custom_fields": {"key1": "value"}}'
``

1.4.5.1.6 Upload one (or more files) for an article
'''''''''''''''''''''''''''''''''''''''''''''''''''

``pigshare upload_new_file --id [article_id] file1 [file2 ... ...]
``

1.4.5.2 Collections
:::::::::::::::::::

Very similar to articles.

1.4.6 Other random example calls:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

``# create new collection
pigshare create_collection --collection '{"title": "Collection markus test", "articles": [2009074,2009075,2009084], "custom_fields": {"test1": "value1"}}'
``

``# add articles to a collection
pigshare add_article --id 2761 --article_ids [2009103,2009106]
``

``# search articles that contain a search_term, display only ids, separated by ',' (useful to copy and paste into 'add_article' command)
pigshare -o id -s ',' search_my_articles --search_term [search_term]
``

``# list all of your personal articles, and add all of them to a collection
for id in `pigshare -o id list_my_articles`; do echo "$id"; pigshare add_article --collection_id 3222 --article_id "$id"; done
``

``# update/overwrite the title and articles connected to a collection
pigshare update_collection --id 2761 --collection '{"title": "Collection markus test changed", "articles": [2009074,2009075]}'
``

``# update/overwrite the categories field in a collection
pigshare update_article --id 2000077 --article '{"categories": [2]}'
``

``# update/overwrite the custom_fields of a collection
pigshare update_article --id 2000077 --article '{"custom_fields": {"field1":"value1"}}'
``

1.5 Usage (Library)
~~~~~~~~~~~~~~~~~~~

TODO




History
-------

0.1.0 (2015-01-11)
---------------------

* First release on PyPI.