Merge branch 'master' into feat/aquanavi-geomap

Author: andreishket

docker-compose.yml

@@ -237,6 +237,7 @@ services:
       RENV_PATHS_CACHE: /renv/cache
       PYTHONIOENCODING: "utf-8"
       R_ALTMETRIC_APIKEY: "${R_ALTMETRIC_APIKEY}"
+      R_CROSSREF_APIMAIL: "${R_CROSSREF_APIMAIL}"
     restart: unless-stopped
     volumes:
       - ./local_dev/renv/cache:/renv/cache

local_dev/dev.env

@@ -5,6 +5,7 @@ library("plyr")
 mlog <- getLogger("metrics")
 
 apikey_altmetric <- Sys.getenv("R_ALTMETRIC_APIKEY")
+email_crossref <- Sys.getenv("R_CROSSREF_APIMAIL")
 
 enrich_metadata_metrics <- function(metadata, metrics_sources=c("altmetric", "crossref")) {
   start.time <- Sys.time()
@@ -96,7 +97,18 @@ add_citations <- function(metadata) {
 
   cc <- tryCatch(
     {
-      cr_citation_count(doi = valid_dois, async = TRUE)
+      cc_list <- list()
+      for (doi in valid_dois) {
+      tryCatch({
+        count <- cr_citation_count(doi = doi, key = email_crossref)
+        cc_list <- append(cc_list, list(count))
+      }, error = function(err) {
+        mlog$debug(gsub("[\r\n]", "", paste(err, doi, sep = " ")))
+        cc_list <- append(cc_list, list(list(doi = doi, count = NA)))
+      })
+      Sys.sleep(0.1)  # to avoid hitting rate limits
+      }
+      cc <- do.call(rbind.fill, cc_list)
     },
     error = function(err) {
       mlog$debug(gsub("[\r\n]", "", paste(err, doi, sep = " ")))