Be consistent and safe in our bash options. (#184)

The pipefail option was clearly intended but was not being applied in a lot of cases. DB creation code was wrong; use the postgres docker image's env var intended for this purpose instead.
SAFEHR-data · Dec 14, 2023 · 228d46e · 228d46e
1 parent 09ac04d
commit 228d46e
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Showing 11 changed files with 12 additions and 16 deletions.
diff --git a/bin/run-all-tests.sh b/bin/run-all-tests.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eo pipefail
+set -euxo pipefail
 
 BIN_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 PROJECT_DIR="${BIN_DIR%/*}"

diff --git a/cli/tests/run-tests.sh b/cli/tests/run-tests.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 
 function wait_until_service_healthy() {
     while ! docker ps | grep "$1" | grep -q healthy ;do

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -283,7 +283,7 @@ services:
     environment:
       POSTGRES_USER: ${PIXL_DB_USER}
       POSTGRES_PASSWORD: ${PIXL_DB_PASSWORD}
-      PIXL_DB_NAME: ${PIXL_DB_NAME}
+      POSTGRES_DB: ${PIXL_DB_NAME}
       PGTZ: Europe/London
     env_file:
       - ./docker/common.env

diff --git a/pixl_dcmd/bin/run-tests.sh b/pixl_dcmd/bin/run-tests.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eo pipefail
+set -euxo pipefail
 
 BIN_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
 PACKAGE_DIR="${BIN_DIR%/*}"

diff --git a/pixl_ehr/tests/docker-compose.yml b/pixl_ehr/tests/docker-compose.yml
@@ -75,7 +75,7 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
-      PIXL_DB_NAME: pixl
+      POSTGRES_DB: pixl
       PGTZ: Europe/London
       PIXL_DB_EHR_SCHEMA_NAME: emap_data
     env_file:

diff --git a/postgres/pixl-db_init.sh b/postgres/pixl-db_init.sh
@@ -13,16 +13,12 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-set -o nounset
-
-psql -U "${POSTGRES_USER}" -tc "SELECT 1 FROM pg_database WHERE datname = '${PIXL_DB_NAME}'" |\
-    grep -q 1 | \
-    psql -U "${POSTGRES_USER}" -c "CREATE DATABASE ${PIXL_DB_NAME}"
+set -euxo pipefail
 
 # Create the EHR schema and associated tables
 columns_and_types="mrn text, accession_number text, age integer, sex text, ethnicity text, height real, weight real, gcs integer, xray_report text"
 ehr_create_command="CREATE SCHEMA emap_data AUTHORIZATION ${POSTGRES_USER}
     CREATE TABLE ehr_raw ($columns_and_types)
     CREATE TABLE ehr_anon ($columns_and_types)
 "
-psql -U "${POSTGRES_USER}" --dbname "${PIXL_DB_NAME}" -c "$ehr_create_command"
+psql -U "${POSTGRES_USER}" --dbname "${POSTGRES_DB}" -c "$ehr_create_command"
diff --git a/test/run-system-test.sh b/test/run-system-test.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 BIN_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
 PACKAGE_DIR="${BIN_DIR%/*}"
 cd "${PACKAGE_DIR}/test"

diff --git a/test/scripts/check_entry_in_orthanc_anon.sh b/test/scripts/check_entry_in_orthanc_anon.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 
 # This could be much improved by having more realistic test data some of
 # which actually was persisted

diff --git a/test/scripts/check_entry_in_pixl_anon.sh b/test/scripts/check_entry_in_pixl_anon.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 
 _sql_command="select * from emap_data.ehr_anon"
 _result=$(docker exec -it test-postgres-1 /bin/bash -c \

diff --git a/test/scripts/check_max_storage_in_orthanc_raw.sh b/test/scripts/check_max_storage_in_orthanc_raw.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 
 # This could be much improved by having more realistic test data some of
 # which actually was persisted

diff --git a/test/scripts/insert_test_data.sh b/test/scripts/insert_test_data.sh
@@ -12,7 +12,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-set -eux pipefail
+set -euxo pipefail
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )