986 reference papers

[dmijatovic]

Add reference papers to software edit section

Closes #289
Closes #756
Closes #986

Changes proposed in this pull request:

• The user can add the reference papers used to cite their software.
• The scraper will search for all citations using OpenAlex api.
• List all the citations and which reference paper is cited in the "Referenced by" tab

How to test:

• make start to build app, after app is started you will need to stop it and start it with scrapers. You can use docker compose down && docker compose up -d
• login as rsd-admin in order to be able to edit existing software, otherwise you can create new software items
• select first software from the list, and edit the software.
• rename software to CDK reference test so you can find it easily later,
• navigate to reference papers section
• review no items to show messages and provide improvement suggestions (if any)
• add following CDK reference papers by DOI
  • doi:10.1186/s13321-017-0220-4
  • 10.1186/1758-2946-6-3
  • https://doi.org/10.1021/ci025584y
  • doi:10.1021/ci025584y
• after you added reference papers you should wait ca. 10 min for scrapers to start working or run manually

docker compose exec scrapers java -cp /usr/myjava/scrapers.jar nl.esciencecenter.rsd.scraper.doi.MainCitations

• in the meantime navigate to some other pages. When you get back to reference papers page the count in the tab should show the number of citations scraped
• take another software or create one and try some other reference papers. AFAIK any DOI paper will be scraped for the citations (it does not have to be related to a software at all).

Start screen reference papers page

Added reference papers

Scraper found some citations

PR Checklist:

• Increase version numbers in docker-compose.yml
• Link to a GitHub issue
• Update documentation
• Tests

[jmaassen]

Works well, but I did find a bug:

Papers that have been scraped, and are later added as reference papers in other software do not seem to be scraped themselves. I did the following:

1. Start and empty RSD with scrapers:

make start 
docker compose down --volumes
docker compose up --scale data-generation=0 --scale scrapers=1 --detach

Next, sign in and create a software called "test". Add the following reference paper:

https://doi.org/10.5194/gmd-10-3167-2017

Then run the scraper using

docker compose exec scrapers java -cp /usr/myjava/scrapers.jar nl.esciencecenter.rsd.scraper.doi.MainCitations

The software should now have 11 "referenced by" papers

2. Next, clean up the RSD and start over:

docker compose down --volumes
docker compose up --scale data-generation=0 --scale scrapers=1 --detach

Sign in and create a software called "test1". Add the following reference paper:

https://doi.org/10.5194/gmd-7-267-2014

Then run the scraper using

docker compose exec scrapers java -cp /usr/myjava/scrapers.jar nl.esciencecenter.rsd.scraper.doi.MainCitations

The software should now have 14 "referenced by" papers. Note that this includes the paper we used in step 1

Next, create a software called "test2" and add this first reference paper again:

https://doi.org/10.5194/gmd-10-3167-2017

When adding, this paper shows "OpenAlex" as source.

Run the scrapers again (and again). Regardless of how many times I run the scraper, the "referenced by" count for "test2" remains zero.

[sonarcloud]

[rsd-database] Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[sonarcloud]

[scrapers] Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
7 Code Smells

0.0% Coverage
0.0% Duplication

[sonarcloud]

[rsd-frontend] SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
6 Code Smells

4.0% Coverage
10.0% Duplication

Catch issues before they fail your Quality Gate with our IDE extension SonarLint

[jmaassen]

Works fine with the new fixes