diff --git a/README.md b/README.md index 2f88ce4..d2e8fb7 100644 --- a/README.md +++ b/README.md @@ -51,31 +51,15 @@ This repository contains the necessary files to deploy the OMOP database using K | VOCAB_PG_PASSWORD | Password of the administration user of the database | mysecretpassword *(must be the same as in database service)* | | VOCAB_PG_SCHEMA | Schema where the vocabulary will be loaded | omopcdm | -3. In order to load the vocabularies when the database is ready, the [vocab_loader](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/blob/main/vocab_script/scripts/vocab_loader.sh) script is used. This script uses the CSV files downloaded from [OHDSI ATHENA](https://athena.ohdsi.org/vocabulary/list) and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea). To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/vocab_script/files) folder. Don't change the files names, because the script uses them to load the vocabularies. +3. In order to load the vocabularies when the database is ready, the [vocab_loader]() script is used. This script uses the CSV files downloaded from [OHDSI ATHENA]() and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea). To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files]() folder. Don't change the files names, because the script uses them to load the vocabularies. -4. When everything is ready, you must execute the [docker-compose.yaml](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/docker-compose.yaml) using this command: +4. When everything is ready, you must execute the [docker-compose.yaml]() using this command: ```bash docker compose up -d ``` -### Bare Kubernetes -This method is for a vanilla Kubernetes cluster without any additional software. If you want to deploy the OMOP database in a Kubernetes cluster with Istio, you can use the [Istio Kubernetes](#istio-kubernetes) deployment method. - -1. Clone this repository: - - ```bash - git clone https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy.git - ``` - -2. In Kubernetes you should change all args variables and environment variables to the values you want. These are displayed in this format: - - ```yaml - env: - - name: VARIABLE_NAME - value: VARIABLE_VALUE - ``` The variables used and its locations are: @@ -104,9 +88,9 @@ The variables used and its locations are: **THIS VARIABLES SHOULD BE PUT ON THE ARGS SECTION AND THE ENV SECTION** -3. In order to load the vocabularies when the database is ready, the [vocab_loader](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/blob/main/vocab_script/scripts/vocab_loader.sh) script is used. This script uses the CSV files downloaded from [OHDSI ATHENA](https://athena.ohdsi.org/vocabulary/list) and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea) To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/vocab_script/files) folder. Don't change the files names, because the script uses them to load the vocabularies. +3. In order to load the vocabularies when the database is ready, the [vocab_loader]() script is used. This script uses the CSV files downloaded from [OHDSI ATHENA](https://athena.ohdsi.org/vocabulary/list) and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea) To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files]() folder. Don't change the files names, because the script uses them to load the vocabularies. -4. When everything is ready, you must execute the [kubernetes.yaml](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/kubernetes.yaml) using this command: +4. When everything is ready, you must execute the [kubernetes.yaml]() using this command: ```bash kubectl apply -f kubernetes/bare-kubernetes/001_OMOP-Secrets.yaml @@ -171,10 +155,10 @@ This tutorial deploys a new namespace called Datamesh, with a policy that only a **THIS VARIABLES SHOULD BE PUT ON THE ARGS SECTION AND THE ENV SECTION** -4. In order to load the vocabularies when the database is ready, the [vocab_loader](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/blob/main/vocab_script/scripts/vocab_loader.sh) script is used. This script uses the CSV files downloaded from [OHDSI ATHENA](https://athena.ohdsi.org/vocabulary/list) and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea). To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/vocab_script/files) folder. Don't change the files names, because the script uses them to load the vocabularies. +4. In order to load the vocabularies when the database is ready, the [vocab_loader]() script is used. This script uses the CSV files downloaded from [OHDSI ATHENA](https://athena.ohdsi.org/vocabulary/list) and its part of [OHDSI BROADSEA repository](https://github.com/OHDSI/Broadsea). To load the vocabularies, you must download the CSV files from ATHENA and put them in the [vocab_script/files]() folder. Don't change the files names, because the script uses them to load the vocabularies. -5. When everything is ready, you must execute the [kubernetes.yaml](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/tree/main/kubernetes.yaml) using this command: +5. When everything is ready, you must execute the [kubernetes.yaml]() using this command: ```bash kubectl apply -f kubernetes/istio/001_datamesh.yaml @@ -212,4 +196,4 @@ See the License for the specific language governing permissions and limitations under the License. ``` -See [LICENSE](https://gitlab.lst.tfo.upm.es/idea4rc/omop-deploy/-/blob/main/LICENSE) for details. +See [LICENSE](./LICENSE) for details. diff --git a/vocab_script/files/THIS_FOLDER.md b/vocab_script/files/THIS_FOLDER.md deleted file mode 100644 index 87265e2..0000000 --- a/vocab_script/files/THIS_FOLDER.md +++ /dev/null @@ -1,3 +0,0 @@ -# What should be in this folder - -In this folder you should include the vocab files that you want to use inside the database. The files should be CSVs in order to work with the script.