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udpated fetch this
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AlexanderPico committed Sep 9, 2024
1 parent 33e7e40 commit f19fff3
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Showing 3 changed files with 1 addition and 6 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/daily_figure_fetch.yml
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Expand Up @@ -46,7 +46,7 @@ jobs:
run: |
sudo apt-get update
sudo apt-get install libcurl4-openssl-dev
Rscript -e 'install.packages(c("rentrez", "xml2", "httr", "yaml", "stringr", "dplyr","lubridate"))'
Rscript -e 'install.packages(c("rentrez", "xml2", "httr", "yaml", "stringr", "lubridate"))'
- name: Run R Script to Fetch Figures
run: Rscript scripts/fetch_figures_v2.R || true #commit files even if R crashes
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3 changes: 0 additions & 3 deletions scripts/LOCAL_fetch_figures_v2.R
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Expand Up @@ -19,7 +19,6 @@
# - httr: for making HTTP requests
# - yaml: for reading config and writing metadata
# - stringr: for string manipulation
# - dplyr: for data manipulation
# - lubridate: for date manipulation
#
# Usage:
Expand All @@ -46,7 +45,6 @@ if (!requireNamespace("xml2", quietly = TRUE)) install.packages("xml2")
if (!requireNamespace("httr", quietly = TRUE)) install.packages("httr")
if (!requireNamespace("yaml", quietly = TRUE)) install.packages("yaml")
if (!requireNamespace("stringr", quietly = TRUE)) install.packages("stringr")
if (!requireNamespace("dplyr", quietly = TRUE)) install.packages("dplyr")
if (!requireNamespace("lubridate", quietly = TRUE)) install.packages("lubridate")

library(rentrez)
Expand All @@ -55,7 +53,6 @@ library(httr)
library(yaml)
library(tools)
library(stringr)
library(dplyr)
library(lubridate)

# Logging function
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2 changes: 0 additions & 2 deletions scripts/fetch_figures_v2.R
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Expand Up @@ -19,7 +19,6 @@
# - httr: for making HTTP requests
# - yaml: for reading config and writing metadata
# - stringr: for string manipulation
# - dplyr: for data manipulation
# - lubridate: for date manipulation
#
# Usage:
Expand Down Expand Up @@ -48,7 +47,6 @@ library(httr)
library(yaml)
library(tools)
library(stringr)
library(dplyr)
library(lubridate)

# Logging function
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