From fd4f9f9232322ff61e493390bfdb0d695c9289a3 Mon Sep 17 00:00:00 2001 From: mjdupont12 Date: Fri, 20 Dec 2024 11:53:43 -0500 Subject: [PATCH] =code review fixes --- docs/migrating_to_18.md | 13 +++++++------ docs/object-store.md | 14 ++++++++------ etc/bento.env | 2 +- etc/bento_deploy.env | 4 ++-- etc/bento_dev.env | 4 ++-- etc/default_config.env | 4 ++-- py_bentoctl/other_helpers.py | 4 ++-- 7 files changed, 24 insertions(+), 21 deletions(-) diff --git a/docs/migrating_to_18.md b/docs/migrating_to_18.md index ecb6fee8..749290fc 100644 --- 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 index 85655080..1b0a6d7a 100644 --- 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 \ No newline at end of file +```bash +BENTO_MINIO_ROOT_USER=root # (default value, could be change) +BENTO_MINIO_ROOT_PASSWORD=secure-password +``` \ No newline at end of file diff --git a/etc/bento.env b/etc/bento.env index 17d12c1c..01bffbbb 100644 --- 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 index a0d35234..1e767453 100644 --- 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.${BENTOV2_DOMAIN} # --------------------------------------------------------------------- @@ -81,7 +81,7 @@ BENTOV2_KATSU_APP_SECRET= # TODO: SET ME WHEN DEPLOYING! # Reference BENTO_REFERENCE_DB_PASSWORD= # TODO: SET ME WHEN DEPLOYING! -# minio +# MinIO BENTO_MINIO_ROOT_PASSWORD= # TODO: SET ME WHEN DEPLOYING! # HTTPS Certificates -------------------------------------------------- diff --git a/etc/bento_dev.env b/etc/bento_dev.env index 56fa654c..6f06f5d1 100644 --- a/etc/bento_dev.env +++ b/etc/bento_dev.env @@ -33,7 +33,7 @@ BENTOV2_PORTAL_DOMAIN=portal.${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 index 8260050e..a53fc062 100644 --- 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 index 15dcfc3f..dfcba00e 100644 --- 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 {}),