Version 1.4.0 Added scripts to git

.Renviron

@@ -10,8 +10,8 @@
 #R_CONFIG_ACTIVE=keycloak_test
 #R_CONFIG_ACTIVE=keycloak_devel
 #R_CONFIG_ACTIVE=sa_admin
-#R_CONFIG_ACTIVE=sa_trainee
-R_CONFIG_ACTIVE=sa_expert
+R_CONFIG_ACTIVE=sa_trainee
+#R_CONFIG_ACTIVE=sa_expert
 #R_CONFIG_ACTIVE=test
 #R_CONFIG_ACTIVE=sa_random_trainee
 #R_CONFIG_ACTIVE=sa_consensus

.gitignore

@@ -21,7 +21,6 @@ letsencrypt
 log
 dev
 testthat*.rds
-scripts/
 covr/
 *.gcno
 *.gcda

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: anomanor
 Title: Anorectal Manometry Inter-Rater Agreement
-Version: 1.3.6
-Date/Publication:	2024-10-11
+Version: 1.4.0
+Date/Publication:	12.01.2025
 Author: Dieter Menne
 Authors@R: c(
     person("Dieter", "Menne", email="[email protected]",

R/app_server.R

@@ -539,10 +539,11 @@ app_server = function(input, output, session) {
 
   # ----------- when to update network edges ---------------------------
   update_network = reactive({
-    req(!is.null(rvalues$expert_classification))
+    req(classification_phase())
+    req(rvalues$expert_classification)
     req( (app_groups == "experts" && g$config$show_results_to_experts) ||
-          app_user == 'x_consensus' )
-    req(rvalues$finalized || app_user == 'x_consensus' )
+          app_user == 'x_consensus' ||
+          (app_groups == "trainees" && rvalues$finalized ))
     list(
          classification_phase(),
          record(),
@@ -554,6 +555,7 @@ app_server = function(input, output, session) {
   # ----------- update network edges ---------------------------
   observeEvent(update_network(), {
     # edges is internal package global data
+    browser()
     cp = classification_phase()
     cm = classification_method()
     req(cp, cm)

inst/config.yml

@@ -18,7 +18,7 @@ default:
 
 sa_trainee:
   app_user: caesar
-  app_groups: trainee
+  app_groups: trainees
 
 sa_admin:
   app_user: anton

scripts/backup_volumes.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+#########################################################################
+#Name: backup-docker-volumes.sh
+#Subscription: This Script backups docker volumes to a backup directory
+##by A. Laub
+#andreas[-at-]laub-home.de
+#
+#License:
+#This program is free software: you can redistribute it and/or modify it
+#under the terms of the GNU General Public License as published by the
+#Free Software Foundation, either version 3 of the License, or (at your option)
+#any later version.
+#This program is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+#or FITNESS FOR A PARTICULAR PURPOSE.
+# https://www.laub-home.de/wiki/Docker_Backup_und_Restore_-_eine_kleine_Anleitung
+#########################################################################
+#Set the language
+export LANG="en_US.UTF-8"
+#Load the Pathes
+export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+# set the variables
+
+# Where to store the Backup files?
+BACKUPDIR=/backup/volumes
+
+# How many Days should a backup be available?
+DAYS=10
+
+# Timestamp definition for the backupfiles (example: $(date +"%Y%m%d%H%M") = 20200124-2034)
+TIMESTAMP=$(date +"%Y%m%d%H%M")
+
+# Which Volumes you want to backup?
+# Volumenames separated by space
+VOLUME="anomanor_shiny_anomanor_keycloak anomanor_data"
+# you can use "$(docker volume ls  -q)" for all volumes
+#VOLUME=$(docker volume ls -q)
+# you can filter all Volumes with grep (include only) or grep -v (exclude) or a combination
+# to do a filter for 2 or more arguments separate them with "\|"
+# example: $(docker volume ls -q |grep 'project1\|project2' | grep -v 'database')
+# to use volumes with name project1 and project2 but not database
+#VOLUME=$(docker volume ls -q |grep 'project1\|project2' | grep -v 'database')
+#VOLUME=$(docker volume ls -q | grep -v 'mailcowdockerized\|_db')
+
+# if you want to use memory limitation. Must be supported by the kernel.
+#MEMORYLIMIT="-m 35m"
+
+### Do the stuff
+echo -e "Start $TIMESTAMP Backup for Volumes:\n"
+if [ ! -d $BACKUPDIR ]; then
+	mkdir -p $BACKUPDIR
+fi
+
+for i in $VOLUME; do
+	echo -e " Backup von Volume:\n  * $i";
+	docker run --rm \
+        -v $BACKUPDIR:/backup \
+        -v $i:/data:ro \
+	-e TIMESTAMP=$TIMESTAMP \
+	-e i=$i	${MEMORYLIMIT} \
+	--name volumebackup \
+        alpine sh -c "cd /data && /bin/tar -czf /backup/$i-$TIMESTAMP.tar.gz ."
+        #debian:stretch-slim bash -c "cd /data && /bin/tar -czf /backup/$i-$TIMESTAMP.tar.gz ."
+	# dont delete last old backups!
+        OLD_BACKUPS=$(ls -1 $BACKUPDIR/$i*.tar.gz |wc -l)
+	if [ $OLD_BACKUPS -gt $DAYS ]; then
+		find $BACKUPDIR -name "$i*.tar.gz" -daystart -mtime +$DAYS -delete
+	fi
+done
+echo -e "\n$TIMESTAMP Backup for Volumes completed\n"

scripts/clean_ano_logs.sql

@@ -0,0 +1,17 @@
+-- delete from ano_logs where message like 'Session%';
+delete from ano_logs where message like 'Rendered%';
+delete from ano_logs where message like '%re-authenticate%';
+-- delete from ano_logs where message like 'Initial%';
+-- delete from ano_logs where message like 'Inserted%';
+delete from ano_logs where message like '%user test%';
+delete from ano_logs where message like 'Both%';
+delete from ano_logs where message like '0%';
+delete from ano_logs where message like 'Session start user anomanor%';
+delete from ano_logs where message like 'Session ended user anomanor%';
+delete from ano_logs where message like 'Executed%';
+delete from ano_logs where message like '%anton%';
+delete from ano_logs where message like 'Initially copied%';
+delete from ano_logs where message like '%since last history%';
+delete from ano_logs where message like 'Startup%';
+delete from ano_logs where message like '%history%';
+delete from ano_logs where message like 'Updated hi%';

scripts/coverage.R

@@ -0,0 +1,8 @@
+# https://github.com/r-lib/covr/issues/448#issuecomment-797738022
+options(covr.gcov =  "C:/rtools40/mingw64/bin/gcov.exe")
+cov = covr::package_coverage(line_exclusions = c(
+  "R/run_app.R",
+  "R/app_config.R"
+#  "R/keycloak.R"
+) )
+covr::report(cov, file = "./covr/coverage-report.html")

scripts/docker_get_data_volume_info.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+
+echo "List of all volumes:"
+echo 
+
+#Loop over all the data volumes
+for docker_volume_id in $(docker volume ls -q)
+do
+	echo "(Un)named volume: ${docker_volume_id}"
+
+	#Obtain the size of the data volume by starting a docker container
+	#that uses this data volume and determines the size of this data volume	
+	docker_volume_size=$(docker run --rm -t -v ${docker_volume_id}:/volume_data alpine sh -c "du -hs /volume_data | cut -f1" ) 
+
+	echo "    Size: ${docker_volume_size}"
+
+	#Determine the number of stopped and running containers that
+	#have a connection to this data volume
+	num_related_containers=$(docker ps -a --filter=volume=${docker_volume_id} -q | wc -l)
+
+	#If the number is non-zero, we show the information about the container and the image
+	#and otherwise we show the message that are no connected containers
+	if (( $num_related_containers > 0 )) 
+	then
+		echo "    Connected containers:"
+		docker ps -a --filter=volume=${docker_volume_id} --format "{{.Names}} [{{.Image}}] ({{.Status}})" | while read containerDetails
+		do
+			echo "        ${containerDetails}"
+		done
+	else
+		echo "    No connected containers"
+	fi
+
+	echo
+done

scripts/insert_x_consensus.sql

@@ -0,0 +1,9 @@
+DELETE FROM classification where user = 'x_consensus';
+
+INSERT INTO classification
+(user, record, method, finalized, protocol_phase, classification_phase, classification, comment)
+ SELECT 'x_consensus' as user, record, method, 0 as finalized, 'consensus' as protocol_phase, classification_phase, classification, max(n)
+ FROM expert_classification
+ GROUP BY classification_phase, record, method
+ ORDER BY record, method, classification_phase;
+

scripts/remove_test_records.sql

@@ -0,0 +1,4 @@
+PRAGMA foreign_keys = 1;
+DELETE FROM classification WHERE record in
+     ('500613_ib', '000278_ib', '402865_ib', '404485_ib', '412011_ib');
+DELETE FROM user where [group] = 'admins';

scripts/workspace.code-workspace

@@ -0,0 +1,24 @@
+{
+	"folders": [
+		{
+			"path": "..\\..\\..\\..\\..\\..\\tmp"
+		}
+	],
+  "settings": {
+    "sqltools.connections": [
+      {
+        "previewLimit": 50,
+        "driver": "SQLite",
+        "name": "naperge",
+        "database": "${workspaceFolder:naperg}/server/prisma/dev.db"
+      }
+    ],
+    "git.ignoreLimitWarning": true,
+    "python.pythonPath": "python"
+  },
+  "extensions": {
+    "recommendations": [
+      "platformio.platformio-ide"
+    ]
+  }
+}