Trying to add PMID and PMCID to citations

[andrewsu]

Checks

• I have searched the docs, existing issues, and existing discussions for answers first.

Link to your website repo

https://github.com/SuLab/sulab.org/tree/pmid_test

Version of Lab Website Template you are using

1.2.1

Description

In this commit, SuLab/sulab.org@aaedd81, I'm trying to add the PMID and PMCID to the citation template. (Ignore the other commits on that branch -- those were meant to go to main.)

I successfully updated _cite/util.py to parse that info from manubot, and I confirmed that information shows up in the citations.yaml file. Example here:

- id: doi:10.1101/2023.05.01.538993
  title: 'DrugMechDB: A Curated Database of Drug Mechanisms'
  authors:
  - Adriana Carolina Gonzalez-Cavazos
  - Anna Tanska
  - Michael D. Mayers
  - Denise Carvalho-Silva
  - Brindha Sridharan
  - Patrik A. Rewers
  - Umasri Sankarlal
  - Lakshmanan Jagannathan
  - Andrew I. Su
  publisher: Cold Spring Harbor Laboratory
  PMID: '37205439'
  PMCID: PMC10187194
  date: '2023-05-02'
  link: https://doi.org/gtrg2f
  orcid: 0000-0002-7792-0150
  mike-mayers-list: true
  plugin: sources.py
  file: sources.yaml
  image: https://www.biorxiv.org/content/biorxiv/early/2023/05/03/2023.05.01.538993/F1.large.jpg
  buttons:
  - type: pdf
    link: pdf/Gonzalez-Cavazos_2023.pdf

I thought I could get that to show up based on a quick addition to _includes/citation.html (referencing citation.PMID and citation.PMCID):

      <div class="citation-details">
        <span class="citation-publisher">
          {{- citation.publisher | default: "[no publisher info]" -}}
        </span>
        &nbsp;·&nbsp;
        <span class="citation-date">
          {{- citation.date | default: "[no date info]" | date: "%d %b %Y" -}}
        </span>
        &nbsp;·&nbsp;
        <span class="citation-id">
          {{- citation.id | default: "[no id info]" -}}
        </span>
        &nbsp;·&nbsp;
        <span class="citation-pmid">
          {{- citation.PMID | default: "[no pmid info]" -}}
        </span>
        &nbsp;·&nbsp;
        <span class="citation-pmcid">
          {{- citation.PMCID | default: "[no pmcid info]" -}}
        </span>
      </div>

but clearly I'm missing something...

If someone can get me pointed in the right direction, that'd be appreciated!

[vincerubinetti]

You almost have it, you just need to add those fields to the list component. See this page of the docs:

https://greene-lab.gitbook.io/lab-website-template-docs/advanced/custom-components

[andrewsu]

Perfect, thank you! (and apologies for missing this in the docs!)