=code review fixes

bento-platform · Dec 20, 2024 · fd4f9f9 · fd4f9f9
1 parent c4cbe0c
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diff --git a/docs/migrating_to_18.md b/docs/migrating_to_18.md
@@ -19,25 +19,26 @@ TODO
   above location, or copy `branding.png` to `branding.lightbg.png`
 
 
-## 3. Enabling minio
+## 3. Enabling MinIO
 
-Enable minio by setting the feature flag in local.env
+Enable MinIO by setting the feature flag in local.env
 ```bash
 BENTO_MINIO_ENABLED='true'
 ```
 
-After enabling the Minio feature flag for the first time, 
+After enabling the MinIO feature flag for the first time, 
 you must initialize the Docker networks, mounted directories and certs.
 ```bash
 ./bentoctl.bash init-certs -f
-./bentoctl.bash init-docker # new network for minio
+./bentoctl.bash init-docker # new network for MinIO
 ./bentoctl.bash init-dirs 
 ```
 
 Also set root user and password in local.env:
-BENTO_MINIO_ROOT_USER=root (default value, could be change)
+```bash
+BENTO_MINIO_ROOT_USER=root # (default value, could be change)
 BENTO_MINIO_ROOT_PASSWORD=secure-password
-
+```
 
 TODO
 

diff --git a/docs/object-store.md b/docs/object-store.md
@@ -1,23 +1,25 @@
 # Bento object store
 
-![Minio service logs querying](./img/minio_object_store.png)
+![MinIO service logs querying](./img/minio_object_store.png)
 
 ## Configuration
 
-Enable minio by setting the feature flag in local.env
+Enable MinIO by setting the feature flag in local.env
 
 ```bash
 BENTO_MINIO_ENABLED='true'
 ```
 
-After enabling the Minio feature flag for the first time, 
+After enabling the MinIO feature flag for the first time, 
 you must initialize the Docker networks, mounted directories and certs.
 ```bash
 ./bentoctl.bash init-certs -f
-./bentoctl.bash init-docker # new network for minio
+./bentoctl.bash init-docker # new network for MinIO
 ./bentoctl.bash init-dirs 
 ```
 
 Also set root user and password in local.env:
-BENTO_MINIO_ROOT_USER=root (default value, could be change)
-BENTO_MINIO_ROOT_PASSWORD=secure-password
+```bash
+BENTO_MINIO_ROOT_USER=root # (default value, could be change)
+BENTO_MINIO_ROOT_PASSWORD=secure-password
+```
diff --git a/etc/bento.env b/etc/bento.env
@@ -473,7 +473,7 @@ BENTO_PROMTAIL_IMAGE=grafana/promtail
 BENTO_PROMTAIL_IMAGE_VERSION=3.1.2
 BENTO_PROMTAIL_CONTAINER_NAME=${BENTOV2_PREFIX}-promtail
 
-# Minio
+# MinIO
 BENTO_MINIO_IMAGE=quay.io/minio/minio
 BENTO_MINIO_IMAGE_VERSION=RELEASE.2024-12-13T22-19-12Z
 BENTO_MINIO_CONTAINER_NAME=${BENTOV2_PREFIX}-minio

diff --git a/etc/bento_deploy.env b/etc/bento_deploy.env
@@ -37,7 +37,7 @@ BENTOV2_PORTAL_DOMAIN=portal.${BENTOV2_DOMAIN}
 BENTOV2_AUTH_DOMAIN=bentov2auth.local
 # Unused if cBioPortal is disabled:
 BENTOV2_CBIOPORTAL_DOMAIN=cbioportal.${BENTOV2_DOMAIN}
-# Unused if Minio is disabled
+# Unused if MinIO is disabled
 BENTO_MINIO_DOMAIN=minio.${BENTOV2_DOMAIN}
 # ---------------------------------------------------------------------
 
@@ -81,7 +81,7 @@ BENTOV2_KATSU_APP_SECRET=  # TODO: SET ME WHEN DEPLOYING!
 # Reference
 BENTO_REFERENCE_DB_PASSWORD=  # TODO: SET ME WHEN DEPLOYING!
 
-# minio
+# MinIO
 BENTO_MINIO_ROOT_PASSWORD= # TODO: SET ME WHEN DEPLOYING!
 
 # HTTPS Certificates --------------------------------------------------

diff --git a/etc/bento_dev.env b/etc/bento_dev.env
@@ -33,7 +33,7 @@ BENTOV2_PORTAL_DOMAIN=portal.${BENTOV2_DOMAIN}
 BENTOV2_AUTH_DOMAIN=bentov2auth.local
 # Unused if cBioPortal is disabled:
 BENTOV2_CBIOPORTAL_DOMAIN=cbioportal.${BENTOV2_DOMAIN}
-# Unused if Minio is disabled
+# Unused if MinIO is disabled
 BENTO_MINIO_DOMAIN=minio.${BENTOV2_DOMAIN}
 # ---------------------------------------------------------------------
 
@@ -82,7 +82,7 @@ BENTO_REFERENCE_DB_PASSWORD=devpassword456
 # BENTO_CBIOPORTAL_DATABASE_PASSWORD=somepassword  Required for CBIOPORTAL
 # BENTO_CBIOPORTAL_DATABASE_ROOT_PASSWORD=somepassword  Required for CBIOPORTAL
 
-# minio
+# MinIO
 BENTO_MINIO_ROOT_PASSWORD=devpassword789
 
 # Development settings ------------------------------------------------

diff --git a/etc/default_config.env b/etc/default_config.env
@@ -46,7 +46,7 @@ BENTOV2_PORTAL_DOMAIN=portal.${BENTOV2_DOMAIN}
 BENTOV2_AUTH_DOMAIN=bentov2auth.local
 # Unused if cBioPortal is disabled:
 BENTOV2_CBIOPORTAL_DOMAIN=cbioportal.${BENTOV2_DOMAIN}
-# Unused if Minio is disabled
+# Unused if MinIO is disabled
 BENTO_MINIO_DOMAIN=minio.${BENTOV2_DOMAIN}
 # ---------------------------------------------------------------------
 
@@ -110,7 +110,7 @@ BENTOV2_KATSU_DB_PASSWORD=
 BENTO_CBIOPORTAL_DATABASE_PASSWORD=
 BENTO_CBIOPORTAL_DATABASE_ROOT_PASSWORD=
 
-# minio
+# MinIO
 BENTO_MINIO_ROOT_PASSWORD=
 
 # Development settings ------------------------------------------------

diff --git a/py_bentoctl/other_helpers.py b/py_bentoctl/other_helpers.py
@@ -147,7 +147,7 @@ def init_self_signed_certs(force: bool):
             "dir": auth_certs_dir,
         },
 
-        # Minio
+        # MinIO
         **({"minio": {
             "var": "BENTO_MINIO_DOMAIN",
             "priv_key_name": "minio_privkey1.key",
@@ -240,7 +240,7 @@ def init_dirs():
         **({"auth": "BENTOV2_AUTH_VOL_DIR"} if not c.BENTOV2_USE_EXTERNAL_IDP else {}),
         #  - cBioPortal
         **({"cbioportal": "BENTO_CBIOPORTAL_STUDY_DIR"} if c.BENTO_FEATURE_CBIOPORTAL.enabled else {}),
-        #  - minio
+        #  - MinIO
         **({"minio": "BENTO_MINIO_DATA_DIR"} if c.BENTO_FEATURE_MINIO.enabled else {}),
         #  - Monitoring: Grafana/Loki
         **({"grafana": "BENTO_GRAFANA_LIB_DIR"} if c.BENTO_FEATURE_MONITORING else {}),