From 381f00dc1f82a17c17465c2972c164e3426908a1 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Tue, 4 Jun 2024 23:09:48 +0200
Subject: [PATCH] update README and run script to be verbose and show errors

---
 README.md | 80 ++++++++-----------------------------------------------
 run       | 18 +++++--------
 2 files changed, 18 insertions(+), 80 deletions(-)

diff --git a/README.md b/README.md
index 4cd6639..20ef80e 100644
--- a/README.md
+++ b/README.md
@@ -1,74 +1,16 @@
-# OntoPortal docker development environment
-
-This repo contains docker compose and [DIP](https://github.com/bibendi/dip) configuration for running and
-developing OntoPortal stack in 3 different ways:
-
-1. docker-compose.backend_only.yml contains just the backend services required for developing and running API on your local system.  To take advantage of that you would need to run `docker compose -f docker-compose.backend_only.yml up -d`
-2. Run API/ncbo_cron and depenencies in docker using DIP
-3. Run API/ncbo_cron in docker with mounted source code volumes from your local system. This will allow editing files on your local machine while running code inside docker container. 
-
-
-```sh
-# clone this repo
-git clone https://github.com/bioportal/ontoportal_docker.git
-
-# clone ontologies_linked_data repo which is needed for creating solr configsets
-git clone https://github.com/bioportal/ontologies_linked_data.git
-
-# generate configsets:
-cd ontologies_linked_data
-./test/solr/generate_ncbo_configsets.sh
-
-cd ../ontoportal_docker
-
-# install DIP
-bundle install
-
-# export bioportal APIKEY which is needed for importing ontologies from bioportal when provisioning
-cp .env.sample .env
-
-# run provisioning via dip 
-dip provision
+# OntoPortal docker  environment
+See help 
 ```
-
-`dip provision` will:
-- clear existing volumes, i.e removing all data
-- create 4store kb
-- run ncbo_cron rake tasks for creating admin user acccount
-- run bin/ncbo_ontology_import script on ncbo_cron container to import STY
-    ontology from bioportal
-- run ontology pull script
-- process STY ontology
-
-# DIP commands:
-
-list available dip commands
-
-`dip ls`
-
-starts api which you would be able to access on http://localhost:9393
-
-`dip api rackup` 
-
-run ncbo_cron scripts:
-
-`dip cron bundle exe bin/<script>`
-
-For example, to import new ontology from BioPortal, pull and process it you would run:
-```sh
-dip cron bundle exec bin/ncbo_ontology_import --from-apikey ${BP_APIKEY} -o PO --from https://data.bioontology.org --admin-user admin
-dip cron bundle exec bin/ncbo_ontology_pull -o PO
-dip cron bundle exec bin/ncbo_ontology_process -o PO
+./run  -h    
 ```
 
-# API Development
-
-When developing API it is possible to mount the source code from your local directory inside the container so that it runs your latest changes. To do that you need to make changes to dip.yml file and uncomment the line containing `# - docker-compose.dev.yml`.  docker-compose.dev.yml contains overwrights to the docker-compose.yml which mounts your local directory.
-
-to install gems inside the API container you would need to run `dip api bundle install` or `dip api bundle update` to get newer gems
+to know how to run an ontoportal API docker instance
 
-to test your changes you would need to run `dip api test`
-
-# AllegroGraph 
+```                                                                                                 
+Usage: ./run [-k API_KEY] [-u API_URL] [-r IMAGE_REPOSITORY] [-t IMAGE_TAG] [-s STARTER_ONTOLOGY] [--no-provision]
+```
 
-Ontoportal has support for running AllegroGraph as triple store backend.  To change default 4store triple store to AllgegroGraph you would need to rename dip.override.yml.sample to dip.override.yml    
+Example
+```bash
+./run  -k <apikey>-r agroportal -t master  -s STY -u "https://data.bioontology.org"
+```
diff --git a/run b/run
index 7fc0631..d5d9754 100755
--- a/run
+++ b/run
@@ -41,10 +41,6 @@ fi
 echo "Running the Ontoportal API and CRON Setup..."
 
 
-# Step 1: Clone ontologies_linked_data repo
-echo "Cloning ontologies_linked_data repo..."
-git clone --depth=1 https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-
 # Step 4: Install
 echo "Installing  (Docker in Production) dependencies..."
 if ! bundle install; then
@@ -96,15 +92,15 @@ if [ "$PROVISION" = true ]; then
     echo "Running provisioning ..."
     commands=(
         'docker compose down --volumes > /dev/null 2>&1'
-        'docker compose run --rm  4store bash -c "4s-backend-setup ontoportal_kb" > /dev/null 2>&1 '
-        'docker compose run --rm  ncbo_cron bundle exec rake user:create[admin,admin@nodomain.org] > /dev/null 2>&1'
-        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_import --admin-user admin --ontologies $STARTER_ONTOLOGY --from-apikey $API_KEY --from $API_URL' > /dev/null 2>&1 "
-        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_pull -o $STARTER_ONTOLOGY' > /dev/null 2>&1 "
-        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_process -o ${STARTER_ONTOLOGY}' > /dev/null 2>&1"
+        'docker compose run --rm  4store bash -c "4s-backend-setup ontoportal_kb" '
+        'docker compose run --rm  ncbo_cron bundle exec rake user:create[admin,admin@nodomain.org]'
+        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_import --admin-user admin --ontologies $STARTER_ONTOLOGY --from-apikey $API_KEY --from $API_URL'"
+        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_pull -o $STARTER_ONTOLOGY'"
+        "docker compose run --rm  ncbo_cron bundle exec 'bin/ncbo_ontology_process -o ${STARTER_ONTOLOGY}'"
     )
 
     for cmd in "${commands[@]}"; do
-        echo "Run: $cmd"
+        echo "> Run: $cmd"
         if ! eval "$cmd"; then
           echo "Error: Failed to run provisioning .  $cmd"
           exit 1
@@ -117,7 +113,7 @@ fi
 
 
 echo "Running api ..."
-docker compose run --service-ports -d api
+docker compose run --service-ports -d --rm api
 
  # Wait for API to be ready (adjust the sleep time accordingly)
 timeout=300