Some progress on fixing tests

Author: ludovicc

CHANGELOG

@@ -0,0 +1,14 @@
+
+# Changelog
+
+## 0.4.0 - 2017-12-01
+
+* Update names of environment variables used to connect to the database, to align with other languages / runtime environments
+
+## 0.3.0 - 2017-11-30
+
+* Use RPostgreSQL instead of RJDBC to connect to the database
+
+## Version 0.1. - 2015-11
+
+* Initial version

CHANGELOG.md

@@ -15,7 +15,7 @@
 #'      IN_DB_PASSWORD : Password for the database connection for input data
 #'      IN_DB_SCHEMA   : Optional schema by default for the database connection for input data
 #' @param query The SQL query to execute on the input database, defaults to the value of environment parameter PARAM_query
-#' @param inFormat Hint for the exact shape of the data stored in the database. Possible values are INTERMEDIATE_RESULTS, OTHER. Defaults to the value of environment parameter IN_FORMAT
+#' @param inFormat Hint for the exact shape of the data stored in the database. Possible values are PARTIAL_RESULTS, OTHER. Defaults to the value of environment parameter IN_FORMAT
 #' @param conn The connection to the database, default to global variable in_conn
 #' @export
 fetchData <- function(

R/fetchData.R

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+## TODO: not functional anymore
+
 # Develop on a simulated Federation
 
 WORK_DIR="$(pwd)"
@@ -79,7 +81,7 @@ $DOCKER run -v $WORK_DIR:/home/docker/data:rw \
     -e IN_JDBC_URL=jdbc:postgresql://indb:5432/postgres \
     -e IN_JDBC_USER=postgres \
     -e IN_JDBC_PASSWORD=test \
-    -e IN_FORMAT=INTERMEDIATE_RESULTS \
+    -e IN_FORMAT=PARTIAL_RESULTS \
     -e OUT_JDBC_DRIVER=org.postgresql.Driver \
     -e OUT_JDBC_JAR_PATH=/usr/lib/R/libraries/postgresql-9.4-1201.jdbc41.jar \
     -e OUT_JDBC_URL=jdbc:postgresql://outdb:5432/postgres \

data

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+## TODO: not functional anymore
+
 WORK_DIR="$(pwd)"
 
 if groups $USER | grep &>/dev/null '\bdocker\b'; then

dev-federation.sh

@@ -37,7 +37,7 @@ services:
       - db
 
   sample_data_db_setup:
-    image: "hbpmip/sample-data-db-setup:0.4.0"
+    image: "hbpmip/sample-data-db-setup:0.4.1"
     container_name: "sample-data-db-setup"
     environment:
       FLYWAY_DBMS: postgresql

dev.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+## TODO: not functional anymore
+
 WORK_DIR="$(pwd)"
 shift
 

dev/docker-compose.yml

@@ -11,6 +11,8 @@ if test $count -gt 0; then
   exit 1
 fi
 
+./tests/test.sh
+
 select_part() {
   local choice=$1
   case "$choice" in
@@ -56,6 +58,8 @@ git pull --tags
 
 updated_version=$(bumpversion --dry-run --list patch | grep current_version | sed -r s,"^.*=",,)
 
+./tests/test.sh
+
 git push
 git push --tags
 

dist.sh

@@ -2,7 +2,7 @@ FROM hbpmip/r-base-build:3.4.2-2
 
 COPY tests/test_local_dataset/testthat.R /src/tests/
 COPY tests/test_local_dataset/testthat/ /src/tests/testthat/
-COPY CHANGELOG DESCRIPTION LICENSE NAMESPACE README.md /src/rmipadaptor/
+COPY CHANGELOG.md DESCRIPTION LICENSE NAMESPACE README.md /src/rmipadaptor/
 COPY R/ /src/rmipadaptor/R/
 COPY man/ /src/rmipadaptor/man/
 

man/fetchData.Rd

@@ -34,7 +34,7 @@ function _cleanup() {
   $DOCKER_COMPOSE rm -f > /dev/null 2> /dev/null | true
   exit $error_code
 }
-trap _cleanup EXIT INT TERM
+#trap _cleanup EXIT INT TERM
 
 echo "Starting the databases..."
 $DOCKER_COMPOSE up -d db
@@ -53,4 +53,4 @@ $DOCKER_COMPOSE run r_test_local_dataset
 
 echo
 # Cleanup
-_cleanup
+#_cleanup

man/saveResults.Rd

@@ -7,7 +7,7 @@ test_that("We save the fact that there was an error", {
     Sys.setenv(JOB_ID = job_id);
     Sys.setenv(NODE = "local");
     Sys.setenv(PARAM_query = "select * from brain_feature");
-    Sys.setenv(OUT_FORMAT = "INTERMEDIATE_RESULTS");
+    Sys.setenv(OUT_FORMAT = "PARTIAL_RESULTS");
     Sys.setenv(ERROR_FILE = "/tmp/errors.txt");
     Sys.setenv(OUTPUT_FILE = "/tmp/output.txt");