fixes, better db checks andtolerance

README.md

@@ -62,16 +62,20 @@ The defaults are set up to run against a postgres database on the localhost at p
 
 ## Install, start and load: 
   - set environment variables for the database (PG* in the case of postgres) and the URL for htting the server (HAPI_R4)
-    - `$ source profile.sh`
+    - `$ source bin/profile.sh`
   - fetch the HAPI CLI,  a `ROOT.war` of the server, the aehrc fhir-owl converter and the TimsUI content
     - `$ bin/install.sh`
   - start the server
-    - `$ config/start-hapi.sh`
+    - `$ bin/start-hapi.sh`
   - load the vocabularies
     - `$ bin/loaders.sh`
   - test with the Jupyter notebooks available at https://github.com/HOT-Ecosystem/TSDemoBoard
     - assuming defaults, the `BASE_URL` there should be set in accord with values here, `BASE_URL =\"http://localhost:8001/fhir/"`
   - test also with the TimsUI, installed as part of this installation, accessable at http://<server>:8001/static/index.html
+  - track server's progress by following the log
+    - `tail -f hapi.log`
+  - When necessary, stop with script that will stop all hapi servers on this server.
+    - `$ bin/stop-hapi.sh`
 
 ### Running things manually
 This project is set up to run things automatically. However, it is possible to run some things manually, which may be useful for troubleshooting.

bin/install.sh

@@ -11,6 +11,7 @@ cd $TIMS_DIR/hapi
 # DOWNLOAD the static content from TimsUI, put in $TIMS_DIR/static-files
 if [[ ! -f TimsUI.tar ]] ; then
     wget -q https://github.com/HOT-Ecosystem/TimsUI/releases/download/Jan_Connectathon/TimsUI_Jan_Connectathon.tar 2> /dev/null
+    mv TimsUI_Jan_Connectathon.tar TimsUI.tar
     mkdir $TIMS_DIR/static-files
     cd $TIMS_DIR/static-files
     tar xvf  $TIMS_DIR/hapi/TimsUI.tar
@@ -63,7 +64,7 @@ fi
 #fi
 # Edit application.yaml to point to $TIMS_DIR/static-files, and copy at the same time
 cd $TIMS_DIR
-cat $TIMS_DIR/hapi/application_pg.yaml | sed  "s|XXstatic-filesXX|$TIMS_DIR/static-files/|g" >> $TIMS_DIR/hapi/application.yaml
+cat $TIMS_DIR/hapi/application_pg.yaml | sed  "s|XXstatic-filesXX|$TIMS_DIR/static-files/|g" > $TIMS_DIR/hapi/application.yaml
 
 cd $TIMS_DIR/hapi
 

bin/start-hapi.sh

@@ -1,13 +1,20 @@
 #!/usr/bin/env bash
-set -euo pipefail
+set -uo pipefail
 
-env | grep PG_ 
+env | grep PG 
 if (( $? )) ; then
-    echo "ERROR:missing PG_* environment variables used in the applicaiton.yaml"
-    echo "These are distinct from the PG variables postgres uses that do not have underscores."
+    echo "ERROR:missing PG* environment variables used in the application.yaml"
     exit 1
 fi
 
+psql -lqt | awk '{ print $1 }' | grep  $PGDATABASE
+if (( $? )) ; then
+    echo "INFO: databse \"$PGDATABASE\" does not exist, creating."
+    createdb $PGDATABASE
+else
+    echo "INFO: found databse \"$PGDATABASE\"."
+fi
+
 # RUN
 exec java -Xmx10G -jar "${TIMS_DIR}/hapi/ROOT.war" --spring.config.location="${TIMS_DIR}/hapi/" >> ${TIMS_DIR}/hapi.log &