Sage portals require content management of publications, people, data, studies and grants stored in Synapse. This package helps maintain that content with constrained formatting.
[[[[work in-progress]]]]
devtools::install_github('Sage-Bionetworks/porTools')
These are the instructions for installing the dependencies for this project. You will need to have R and RStudio installed on your computer. You will also need to have an account on Synapse.
install.packages('remotes')
remotes::install_cran('rentrez')
remotes::install_cran('librarian')
remotes::install_version('rjson', version='0.2.21')
remotes::install_version('reticulate', version='1.28')
reticulate::install_miniconda()
remotes::install_cran("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org"))
You will want to run this tool via the command line in the terminal.
Rscript ./inst/scripts/query-pubmed-grants.R \
--grant_table syn51209786 \
--parent syn51317180 \
--pub_table syn51407023
There is a github action updated-publications.yaml that runs this script on a schedule. It will automatically run the above command on a monthly basis. The script is ran via the Synapse service user: synapse-service-dpe-team.
Important notes about the github action:
- It will stop after 60 days if there are no pushes to this repository. (This is a Github limitation.)
- Look at the results of the "Query PubMed and upload results" section in each of the executions in the "Actions" tab.
There will be
[1] "All pmids already in the portal"printed at the end if there is no pmids to update.
2023-10-10
- If the grant serial number overlaps with annother for example
UH2AG064706andUH3AG064706then a different call to get the search results must be made and the previously developed functions do not work - Found the NIH library for R is much faster than python