[Adhoc] Edit oss docs and add broadsea setup (#557)

* edit docs and add broadsea setup
* edit formatting

docs/2-load/8-load-broadsea.md

@@ -0,0 +1,59 @@
+
+# Broadsea-atlasdb
+- Initially, the D2E system does not contain any data
+- This docker container is part of the OHDSI Broadsea set of Docker containers. 
+
+# Configure Patient Database Credentials 
+
+## Add database connection details & credentials
+
+- Login as the new admin user
+- Switch to **Admin Portal**
+- Select **Setup** on top right
+  - URL is now https://localhost:41100/portal/systemadmin/setup
+- Select **Databases** **Configure** button
+- Select **Add database**
+- Add the values from the table below.
+- Click **Save**
+
+
+name | value | note
+--- | --- | ---
+Host | broadsea-atlasdb | PostgreSQL container name /or/ external database FQDN
+Database code | broadsea_atlasdb | display name
+Database name | postgres | actual name
+Vocab schemas | demo_cdm | select from dropdown. `*`
+Extra | {"max": 50, "schema": "demo_cdm", "queryTimeout": 60000, "statementTimeout": 60000, "idleTimeoutMillis": 300000, "connectionTimeoutMillis": 60000, "idleInTransactionSessionTimeout": 300000}
+Admin username | postgres | `*`
+Read username | postgres | `*`
+Admin password | mypass | `*`
+Read password | mypass | `*`
+
+notes:
+- `*` - schema/usernames are the values expected for sample data load steps - do not change 
+
+## Restart Containers
+
+Run the following command to restart the system for the new connection details be provisioned to the data services
+```bash
+yarn start:minerva --force-recreate
+```
+
+# Create a dataset 
+- open https://localhost:41100/portal
+- Login as primary admin as
+- Select **Admin** mode
+- Navigate to **Datasets**
+- Select **Add dataset**
+- Provide the following values in the table below: 
+
+name | value | note
+--- | --- | ---
+Dataset name | eg. Demo
+CDM Schema Option | select 'Use existing schema' from dropdown
+Schema Name field | e.g. demo_cdm | name of the cdm schema that was used for seeding
+Vocab schema name | e.g. demo_cdm
+Data Model Option | omop5-4 [datamodel-plugin]
+PA Config | OMOP_GDM_PA_CONF_DUCKDB
+Type | e.g. DemoDataset
+Token dataset code | e.g. DemoDataset

docs/README.md

@@ -13,6 +13,9 @@ git clone --branch develop https://github.com/alp-os/d2e.git
 ```
 
 - Request docker credentials from [D2E Support](#d2e-support) for authenticating to private docker registry to retrieve resources to run D2E.
+```bash
+docker login -u $ACR_USERNAME -p "$ACR_PASSWORD" $REGISTRY_URL
+```
 
 ## Environment Variables and Credentials Setup 
 - Generate environment variables (Refer [here](./1-setup/environment-variables.md) for more information on the environment variables generated)
@@ -101,8 +104,6 @@ Additional info:
 
 This sections assumes that there is an existing database available. The database should be in a Postgres docker container name or external database with a Fully Qualified Domain Name (FQDN).
 
-If there is no existing databases available, you may consider using a [sample dataset](./2-load/), and perform sub-steps [3](./2-load/3-setup-pg-permissions.md), [4](./2-load/4-setup-db-credentials.md), [6](./2-load/6-load-synpuf1k.md) and [7](./2-load/7-load-vocab.md) to setup the database. Thereafter, you may continue to follow the guide from section [Plugins](#plugins) onwards.
-
 
 - In the Admin Portal, navigate to **Setup** > **Databases** > **Configure** > **Add database**
   > **The expected display is:** ![DatabaseListEmpty](./images/database/DatabaseListEmpty.png)
@@ -115,6 +116,9 @@ If there is no existing databases available, you may consider using a [sample da
 yarn start:minerva --force-recreate; sleep 60
 ```
 
+If there is no existing databases available, you may consider using the following sample database below and continue with the guide from section [Plugins](#plugins) onwards.
+- [Synthetic Public Use Files (SynPUFs)](./2-load/): Perform sub-steps [3](./2-load/3-setup-pg-permissions.md), [4](./2-load/4-setup-db-credentials.md), [6](./2-load/6-load-synpuf1k.md) and [7](./2-load/7-load-vocab.md)
+- broadsea-atlasdb: Refer to the docs [here](/docs/2-load/8-load-broadsea.md)
 
 ## Plugins 
 The Admin portal allows the admin user to manage plugins in the platform, for instance installation, version updates and uninstallation of plugins. 
@@ -157,8 +161,6 @@ This section generates the Data Quality Dashboard based on the dataset of intere
 
   > **The expected result is:** ![dqd-dashboard](./images/dqd/dqd-dashboard-1.png)
 
-- Refer to the Jobs Portal if you
-
 ### Create Cache
 This section provides the steps for setting up the analytics environment.
 - Navigate to the dataset of interest and click **Select Action**.