Configuration

All configuration is done by editing the config file.

Config File

By default the pipeline looks for a config file called config.ini, but you can specify any config file with the --config (or -c) flag (e.g. ./papers.py --config my-config-file.ini), it will look in the config folder for a file with that name. This is useful if you want to run multiple instances of the pipeline at the same time on different data sets.

Project Details

The project name sets the main title on the html pages. The short_name sets the file paths for the cache and html outputs.

The colour_hex_primary and colour_hex_secondary allows the sites colour scheme to be changed from one place. The primary colour is the main colour used for the sites top bar and other headings. The secondary colour is used on some charts. These are hex codes (see e.g. https://htmlcolorcodes.com/) and specified without the #.

• header_institution_logo_filename is the address of the image in the top header bar.
• header_institution_name is the title that is displayed when a user hovers over the image.
• header_institution_url is the address the user is taken to when they click on the image.

The side image details can be left blank.

• side_image_filename is the address of the image on the left below the navigation menu.
• side_image_link is the address the user is take to when they click on the image.

Collate

• zotero_get_all flag to force redownloading of the Zotero metadata. (1=force redownload, 0=only download if not in cache). Note that the pipeline will get a list of publications from Zotero every time (regardless of this flag), this just sets if the metadata record should be downloaded.
• use_doi_pubmed_cache flag to force redownloading of DOI and PubMed data (regardless of presence in cache). (1=use cache, 0=force redownload)

Zotero API

• zotero_api_key - Get this from the zotero webpages (see [zotero set up]).
• zotero_collection - Which set of publications you are interested in, get from the URL when you click on a collection in the web interface, might look like VRFSSMRQ.
• zotero_type - Probably 'group'
• zotero_id - The ID of the type above. In the URL, e.g. 811126

Pubmed API

• pubmed_email - Pubmed like to know who is using their API and warn you if you hit usage limits, so put your email here.

Scopus

• scopus_force_citation_update forces the script to ignore the cache and get new citation data.
• scopus_api_key is the API key used for getting citation data from Scopus.
• scopus_citation_max_age_days is the maximum age in days that a citation count can sit in the cache before it is classed as out of date and is overwritten.
• scopus_run_citation is a flag that decides whether or not to allow the add.citations.citations script to run (The EuropePMC citations are retrieved as part of the add.citations.citations script so that is also affected by this flag).

Logging

loglevel set the log level. Can be one of DEBUG, INFO, WARNING, ERROR, CRITICAL.

Metrics

Some calculations on the metrics page require the metrics_study_start_year and metrics_study_current_year need to be set appropriately.

Pages

There are a small number of pages that may not be relevant to you, these can be turned off.

• page_show_author_network - Remove Network link from navigation. (True/False)
• public_facing - There are some pages that are useful for data cleaning and debugging but are not intended for public facing webpages. Setting this to True will not show links to them in the navigation menu. (True/False)

Networks

create_networks - we are starting to do network stuff, but it is very experimental at this stage. The generation of linked networks of authors is computationally intensive, so if you don't want to use it then don't generate it. (True/False)