The citations are not showing up

[Srihitha-l]

In the _data folder I created a new file called sources-2019.yaml. I used sources.yaml as a template and filled in my citation information accordingly. But for some reason the citation won't show up.

[vincerubinetti]

Please link to the repo where you are experiencing problems. I won't be able to help you if I can't see more details about the problem.

[Srihitha-l]

I am runnning everything locally, I don't have a github with my files.

[vincerubinetti]

Okay, are you running it via Docker or the more lengthy non-Docker method:
https://greene-lab.gitbook.io/lab-website-template-docs/getting-started/preview-your-site#on-your-computer-locally

Please paste any console log error messages that you are seeing.

Please zip and attach your folder to this discussion so I can see it.

[Srihitha-l]

I am using the non-Docker method, but it is a bit different than the one provided in the template. I just do bundle install and then bundle exec jekyll serve. I chose this method because I already had ruby and Jekyll installed on my mac.

[vincerubinetti]

Then that is why it is not updating. The auto-cite process is contained in the _cite/cite.py python script that needs to be run. The standard docker container runs this part for you. And if you're not using the docker approach, the docs right below it give you instructions on how to run it "manually" (e.g. when you already have ruby and jekyll installed) and include steps for running the auto-cite process. What you are doing is not part of the documentation. Also in the future, please provide as much detail as possible when you post a discussion.

[vincerubinetti]

You also have other issues. Here is your sources-2019.yaml:

- id: .
  title: 'Bi-Directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature'
  authors:
  - Arjun Magge
  - Davy Weissenbacher
  - Abeed Sarker
  - Matthew Scotch
  - Graciela Gonzalez-Hernandez
  type: paper
  date: 'January 2019'
  description: Magge A, Weissenbacher D, Sarker A, Scotch M, Gonzalez G. Bi-Directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature. Proceedings of the Pacific Symposium on Biocomputing (PSB 2019). 2019; 100-111. Hawaii, USA.
  link: https://www.researchgate.net/publication/329240570_Bi-directional_Recurrent_Neural_Network_Models_for_Geographic_Location_Extraction_in_Biomedical_Literature
  
- id: doi:10.1007/s13181-019-00699-x
  title: Can Reddit Reveal Unique Facets of Suboxone Use and Misuse?
  authors:
  - Rachel Graves
  - Jeanmarie Perrone
  - Jennifer Love
  - Abeed Sarker
  description: R Graves, J Perrone, J Love, Abeed Sarker. Can Reddit Reveal Unique Facets of Suboxone Use and Misuse? Proceedings of the ACMT Annual Summit [meeting abstract]. 2019. San Francisco, USA. doi:10.1007/s13181-019-00699-x.
  date: 'March 2019'
  type: paper

# you're providing an id here, which makes Manubot generate the title, authors, publisher, date, and link, but then you're manually specifying the authors and date which overrides what Manubot generates automatically. are you sure you need to do this? you could remove title, authors, and date... unless you observe that the info Manubot is generating is not accurate in some way.

- id: doi:10.1007/s13181-019-00699-x
  title: Sentiment, Themes, and Analyses in Tweets about Suboxone
  authors:
  - Rachel Graves
  - Jeanmarie Perrone
  - Jennifer Love
  - Abeed Sarker
  description: J Love, J Perrone, R Graves, Abeed Sarker. Sentiment, Themes, and Analyses in Tweets about Suboxone. Proceedings of the ACMT Annual Summit [meeting abstract]. 2019; 58-59. San Francisco, USA. doi https://doi.org/10.1007/s13181-019-00699-x.
  date: 'March 2019'
  type: paper

You have two papers with the same id, so they will get merged together and fields will get overwritten. You also have an id: .. If you don't have an id for a paper and are filling its citation details in manually, just leave the id field absent.

The dates you've put it are also not the expected format (YYYY-MM-DD), and may cause issues with how your citations are sorted by date and how the date is displayed.

[Srihitha-l]

Installing the proper packages to run it manually made it work. Thank you. I somehow missed the non-docker instructions. I changed the date format in the citations.html file. Which is why the date formats are different in the file.