From de5028d823675f5d020da2d5eeee0922804fc265 Mon Sep 17 00:00:00 2001
From: noerw <noerw@gmx.de>
Date: Mon, 14 Aug 2017 20:02:04 +0200
Subject: [PATCH] add aggregated boxes metadata to monitor

---
 tools/monitor/Dockerfile                      | 19 ++++++----------
 tools/monitor/analyze.R                       |  3 +++
 tools/monitor/crontab                         |  9 +++++++-
 tools/monitor/docker-entry.sh                 |  5 -----
 tools/monitor/get-boxes.R                     | 22 +++++++++++++++++++
 .../monitor/{osem-monitor.R => get-counts.R}  |  6 ++---
 6 files changed, 42 insertions(+), 22 deletions(-)
 delete mode 100644 tools/monitor/docker-entry.sh
 create mode 100644 tools/monitor/get-boxes.R
 rename tools/monitor/{osem-monitor.R => get-counts.R} (72%)

diff --git a/tools/monitor/Dockerfile b/tools/monitor/Dockerfile
index 11b0610..8fc8190 100644
--- a/tools/monitor/Dockerfile
+++ b/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"]
diff --git a/tools/monitor/analyze.R b/tools/monitor/analyze.R
index 2f1d65f..11b8563 100644
--- a/tools/monitor/analyze.R
+++ b/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$time), unit = 'mins'), 0)
+
+plot(measurements~time, ts)
+plot(measurements_per_minute~time, ts)
diff --git a/tools/monitor/crontab b/tools/monitor/crontab
index dd7ed62..5ccb99f 100644
--- a/tools/monitor/crontab
+++ b/tools/monitor/crontab
@@ -1 +1,8 @@
-*/10 * * * * cd /script/data && /usr/bin/Rscript --save --restore ../osem-monitor.R > rscript.log
+#!/bin/sh
+
+# once every 15 mins
+*/15 * * * * cd /script/data && /usr/bin/Rscript --save --restore ../get-counts.R > get-counts.log 2>&1 
+
+# mondays, 12:02
+#(may not run simultanously, to avoid override of .RData save)
+2 12 * * 1 cd /script/data && /usr/bin/Rscript --save --restore ../get-boxes.R > get-boxes.log
diff --git a/tools/monitor/docker-entry.sh b/tools/monitor/docker-entry.sh
deleted file mode 100644
index c11598a..0000000
--- a/tools/monitor/docker-entry.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-# start cron
-cron -f -l 0
-
diff --git a/tools/monitor/get-boxes.R b/tools/monitor/get-boxes.R
new file mode 100644
index 0000000..d49a9b8
--- /dev/null
+++ b/tools/monitor/get-boxes.R
@@ -0,0 +1,22 @@
+library(magrittr)
+library(opensensmapr)
+library(sf)
+
+if (is.null(as.list(environment())$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)
diff --git a/tools/monitor/osem-monitor.R b/tools/monitor/get-counts.R
similarity index 72%
rename from tools/monitor/osem-monitor.R
rename to tools/monitor/get-counts.R
index 513d6b8..faf430d 100644
--- a/tools/monitor/osem-monitor.R
+++ b/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)