zotero_tools¶

Programmatic access to Zotero libraries.

documentation of pyzotero: https://pyzotero.readthedocs.io
API key: https://www.zotero.org/settings/keys/new
group id: open the page of the group via https://www.zotero.org/groups and hover over the link to the group settings, the id is the integer after /groups/.

create_zot_client ¶

create_zot_client(
    api_key, library_id, library_type="group"
)

Create a Zotero client bound to a library.

The item methods of the client only operate on this library.

Parameters:

Name	Type	Description	Default
`api_key`	`str`	Zotero API key with read access to the library.	required
`library_id`	`int`	id of the user or group library.	required
`library_type`	`str`	`group` or `user`.	`'group'`

Returns:

Type	Description
`Zotero`	The client.

get_items ¶

get_items(zot, show=False, limit=None)

Get the top level items of the library.

Parameters:

Name	Type	Description	Default
`zot`	`Zotero`	client of the library, see `create_zot_client`.	required
`show`	`bool`	print the items to the console.	`False`
`limit`	`int \| None`	maximal number of items; all items if `None`.	`None`

Returns:

Type	Description
`list[dict[str, Any]]`	The items as returned by the Zotero API.

pmid_from_extra ¶

pmid_from_extra(extra)

Get the PubMed id from the extra field of a Zotero item.

Parameters:

Name	Type	Description	Default
`extra`	`str \| None`	`extra` field with one `key: value` per line, e.g., `PMID: 27267043` and `PMCID: PMC4895977`.	required

Returns:

Type	Description
`str \| None`	The PubMed id or `None`.

create_tag_table ¶

create_tag_table(items, tags_set, tag_prefixes)

Create a table of the items with the selected tags.

A tag is selected if it is in tags_set or starts with one of the tag_prefixes. Every selected tag is a boolean column, which is True for the items with the tag.

Parameters:

Name	Type	Description	Default
`items`	`Iterable[dict[str, Any]]`	items of a library, see `get_items`.	required
`tags_set`	`Iterable[str]`	tags to select.	required
`tag_prefixes`	`Iterable[str]`	prefixes of the tags to select, e.g., `"species:"`.	required

Returns:

Type	Description
`DataFrame`	The table with the columns `key`, `doi`, `pubmed` and one column per
`DataFrame`	selected tag.