Merge pull request #833 from OpenKnowledgeMaps/dev

Altmetric API key

Author: chreman

docker-compose.yml

@@ -236,6 +236,7 @@ services:
       LANG: "en_US.UTF-8"
       RENV_PATHS_CACHE: /renv/cache
       PYTHONIOENCODING: "utf-8"
+      R_ALTMETRIC_APIKEY: "${R_ALTMETRIC_APIKEY}"
     restart: unless-stopped
     volumes:
       - ./local_dev/renv/cache:/renv/cache

local_dev/searchflow-container/Dockerfile

@@ -6,12 +6,12 @@ RUN a2enmod rewrite
 
 RUN apt-get update && apt-get install -y \
     curl libsqlite3-dev libonig-dev libxml2-dev \
-    gconf-service libasound2 libatk1.0-0 libatk-bridge2.0-0 libc6 libcairo2 libcups2 \
-    libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgconf-2-4 libgdk-pixbuf2.0-0 \
+    libasound2 libatk1.0-0 libatk-bridge2.0-0 libc6 libcairo2 libcups2 \
+    libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgdk-pixbuf-2.0-0 \
     libglib2.0-0 libgtk-3-0 libnspr4 libpango-1.0-0 libpangocairo-1.0-0 libstdc++6 \
     libx11-6 libx11-xcb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxext6 \
     libxfixes3 libxi6 libxrandr2 libxrender1 libxss1 libxtst6 ca-certificates \
-    fonts-liberation libappindicator1 libnss3 lsb-release xdg-utils wget
+    fonts-liberation libnss3 lsb-release xdg-utils wget
 
 RUN docker-php-ext-install pdo pdo_sqlite mbstring xml fileinfo
 

server/preprocessing/other-scripts/metrics.R

@@ -4,6 +4,7 @@ library("plyr")
 
 mlog <- getLogger("metrics")
 
+apikey_altmetric <- Sys.getenv("R_ALTMETRIC_APIKEY")
 
 enrich_metadata_metrics <- function(metadata, metrics_sources=c("altmetric", "crossref")) {
   start.time <- Sys.time()
@@ -36,7 +37,8 @@ get_altmetrics <- function(dois) {
   for (doi in valid_dois) {
     tryCatch(
       {
-        metrics <- altmetric_data(altmetrics(doi = doi, apikey = ""))
+        metrics <- altmetric_data(altmetrics(doi = doi, apikey = apikey_altmetric))
+        Sys.sleep(0.1)  # to avoid hitting rate limits
         results <- rbind.fill(results, metrics)
       },
       error = function(err) {