add aggregated boxes metadata to monitor

tools/monitor/Dockerfile

@@ -1,28 +1,23 @@
 FROM r-base
 
 RUN apt-get update && \
-    apt-get install -y libssl-dev libcurl3-dev cron
+    apt-get install -y libssl-dev libcurl3-dev cron libgdal-dev libgeos-dev libproj-dev libudunits2-dev liblwgeom-dev
 
 # install dependencies
-RUN Rscript -e 'install.packages("httr")'
-RUN Rscript -e 'install.packages("dplyr")'
+RUN Rscript -e 'install.packages("sf")'
 RUN Rscript -e 'install.packages("magrittr")'
-#RUN Rscript -e 'install.packages("readr")'
-
-# install opensensemap package
 RUN Rscript -e 'install.packages("devtools")'
 RUN Rscript -e 'devtools::install_github("noerw/opensensmapR")'
 
-COPY docker-entry.sh /docker-entry.sh
-RUN chmod 0755 /docker-entry.sh
-
 # install crontab
 COPY crontab /crontab
 RUN /usr/bin/crontab /crontab
 
+RUN apt-get clean && apt-get autoremove -y
 
 # install script
-COPY osem-monitor.R /script/osem-monitor.R
-WORKDIR /script/data
+COPY get-counts.R /script/get-counts.R
+COPY get-boxes.R /script/get-boxes.R
 
-CMD ["/docker-entry.sh"]
+WORKDIR /script/data
+CMD ["cron", "-f"]

tools/monitor/analyze.R

@@ -4,3 +4,6 @@ ts = osem_counts_ts
 # compute our own measurements per minute, to check against the provided computation
 ts$measurement_diff = c(diff(ts$measurements), 0)
 ts$measurement_minute = ts$measurement_diff / c(as.numeric(diff(ts$time), unit = 'mins'), 0)
+
+plot(measurements~time, ts)
+plot(measurements_per_minute~time, ts)

tools/monitor/crontab

@@ -1 +1,8 @@
-*/10 * * * * cd /script/data && /usr/bin/Rscript --save --restore ../osem-monitor.R > rscript.log
+#!/bin/sh
+
+# once every 15 mins
+*/15 * * * * cd /script/data && /usr/bin/Rscript --save --restore ../get-counts.R > get-counts.log 2>&1 
+
+# mondays, 12:02
+#(may not run simultanously, to avoid override of .RData save)
+2 12 * * 1 cd /script/data && /usr/bin/Rscript --save --restore ../get-boxes.R > get-boxes.log

tools/monitor/docker-entry.sh

@@ -1,5 +0,0 @@
-#!/bin/sh
-
-# start cron
-cron -f -l 0
-

tools/monitor/get-boxes.R

@@ -0,0 +1,22 @@
+library(magrittr)
+library(opensensmapr)
+library(sf)
+
+if (is.null(as.list(environment())$osem_boxes_ts))
+  osem_boxes_ts = data.frame()
+
+b = osem_boxes()
+
+# only keep aggregated data
+b_agg = data.frame(time = Sys.time(), boxcount = nrow(b))
+b_agg$model = b$model %>% table() %>% as.list() %>% list()
+b_agg$exposure = b$exposure %>% table() %>% as.list() %>% list()
+b_agg$geometry = b %>% osem_as_sf() %>% st_geometry() %>% list()
+b_agg$phenomena = b %>% osem_phenomena() %>% list()
+
+# combine with existing time series
+osem_boxes_ts = rbind(b_agg, osem_boxes_ts)
+
+# cleanup
+rm(b)
+rm(b_agg)

tools/monitor/get-counts.R

@@ -1,6 +1,5 @@
-library(dplyr)
 library(magrittr)
-library(opensensemap)
+library(opensensmapr)
 
 if (is.null(as.list(environment())$osem_counts_ts))
   osem_counts_ts = data.frame()
@@ -8,5 +7,4 @@ if (is.null(as.list(environment())$osem_counts_ts))
 osem_counts_ts = osem_counts() %>%
   list(time = Sys.time()) %>%
   as.data.frame() %>%
-  dplyr::bind_rows(osem_counts_ts)
-
+  rbind(osem_counts_ts)