Merge pull request #190 from bento-platform/feat/v14/phenov2

feat: Phenopacket V2

README.md

@@ -32,6 +32,7 @@ that make up the Bento platform.
 
 ## Migration documents
 
+* [v14 to v15](./docs/migrating_to_15.md)
 * [v13 to v14](./docs/migrating_to_14.md)
 * [v12 to v13](./docs/migrating_to_13.md)
 * [v2.11 to v12](./docs/migrating_to_12.md)
@@ -631,6 +632,27 @@ Note: the CORS instructions have already been taken care of in the `docker-compo
 
 ![Elasticvue login](docs/img/elasticview_login.png)
 
+
+### Converting Phenopackets
+
+Phenopackets JSON documents can be converted from [V1](https://phenopacket-schema.readthedocs.io/en/1.0.0/toplevel.html) 
+to [V2](https://phenopacket-schema.readthedocs.io/en/2.0.0/toplevel.html) using `bentoctl` and 
+[Phenopacket-tools](https://github.com/phenopackets/phenopacket-tools) as its backend.
+
+For the `bentoctl convert-pheno` command to work, you need to:
+1. [Download](http://phenopackets.org/phenopacket-tools/stable/tutorial.html#download-phenopacket-tools) a Phenopacket-tools release.
+2. Unzip its content and place the .jar file somwhere safe.
+3. Specify the .jar path in `local.env` with the `PHENOTOOL_JAR_PATH` variable
+
+You can then convert a file with:
+```shell
+bentoctl convert-pheno <source> <target>
+```
+
+If the `target` argument is not provided, `bentoctl` will append "_pheno_v2" to the source file's name and save it in its 
+parent directory.
+
+
 <br />
 
 ## Testing

docs/migrating_to_15.md

@@ -0,0 +1,21 @@
+# Migrating to Bento v15
+
+Bento v15 migrates to Phenopackets v2, and as such requires that Phenopackets are updated and re-ingested.
+
+Before updating, perform the following steps:
+
+* Shut down Bento with `./bentoctl.bash stop`
+* Remove the Katsu data volume
+* Remove the WES data volume
+
+Then, update your instance:
+
+```bash
+./bentoctl.bash pull
+```
+
+Finally, restart Bento:
+
+```bash
+./bentoctl.bash start
+```

etc/bento.env

@@ -30,7 +30,7 @@ BENTOV2_GATEWAY_INTERNAL_CERTS_DIR=/usr/local/openresty/nginx/certs
 
 # Gateway
 BENTOV2_GATEWAY_IMAGE=ghcr.io/bento-platform/bento_gateway
-BENTOV2_GATEWAY_VERSION=0.7.1
+BENTOV2_GATEWAY_VERSION=0.8.0
 BENTOV2_GATEWAY_VERSION_DEV=${BENTOV2_GATEWAY_VERSION}-dev
 BENTOV2_GATEWAY_CONTAINER_NAME=${BENTOV2_PREFIX}-gateway
 
@@ -75,7 +75,7 @@ BENTO_AUTH_DB_NETWORK="${BENTOV2_PREFIX}-auth-db-net"
 
 # - Authz service
 BENTO_AUTHZ_IMAGE=ghcr.io/bento-platform/bento_authorization_service
-BENTO_AUTHZ_VERSION=0.4.0
+BENTO_AUTHZ_VERSION=0.5.0
 BENTO_AUTHZ_VERSION_DEV=${BENTO_AUTHZ_VERSION}-dev
 BENTO_AUTHZ_CONTAINER_NAME=${BENTOV2_PREFIX}-authz
 BENTO_AUTHZ_NETWORK=${BENTOV2_PREFIX}-authz-net
@@ -95,7 +95,7 @@ BENTO_AUTHZ_DB_MEM_LIM=1G
 # Web
 BENTO_WEB_CUSTOM_HEADER=
 BENTOV2_WEB_IMAGE=ghcr.io/bento-platform/bento_web
-BENTOV2_WEB_VERSION=3.2.2
+BENTOV2_WEB_VERSION=edge
 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev
 BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web
 BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net
@@ -107,7 +107,7 @@ BENTOV2_WEB_CPUS=2
 
 # Drop-Box
 BENTOV2_DROP_BOX_IMAGE=ghcr.io/bento-platform/bento_drop_box_service
-BENTOV2_DROP_BOX_VERSION=1.0.1
+BENTOV2_DROP_BOX_VERSION=1.1.1
 BENTOV2_DROP_BOX_VERSION_DEV=${BENTOV2_DROP_BOX_VERSION}-dev
 BENTOV2_DROP_BOX_CONTAINER_NAME=${BENTOV2_PREFIX}-drop-box
 BENTO_DROP_BOX_NETWORK=${BENTOV2_PREFIX}-drop-box-net
@@ -121,7 +121,7 @@ BENTOV2_DROP_BOX_CPUS=3
 
 # Service Registry
 BENTOV2_SERVICE_REGISTRY_IMAGE=ghcr.io/bento-platform/bento_service_registry
-BENTOV2_SERVICE_REGISTRY_VERSION=1.2.2
+BENTOV2_SERVICE_REGISTRY_VERSION=1.3.1
 BENTOV2_SERVICE_REGISTRY_VERSION_DEV=${BENTOV2_SERVICE_REGISTRY_VERSION}-dev
 BENTOV2_SERVICE_REGISTRY_CONTAINER_NAME=${BENTOV2_PREFIX}-service-registry
 BENTO_SERVICE_REGISTRY_NETWORK=${BENTOV2_PREFIX}-service-registry-net
@@ -133,7 +133,7 @@ BENTOV2_SERVICE_REGISTRY_CPUS=1
 
 # Notification
 BENTOV2_NOTIFICATION_IMAGE=ghcr.io/bento-platform/bento_notification_service
-BENTOV2_NOTIFICATION_VERSION=3.0.1
+BENTOV2_NOTIFICATION_VERSION=3.1.0
 BENTOV2_NOTIFICATION_VERSION_DEV=${BENTOV2_NOTIFICATION_VERSION}-dev
 BENTOV2_NOTIFICATION_CONTAINER_NAME=${BENTOV2_PREFIX}-notification
 BENTO_NOTIFICATION_NETWORK=${BENTOV2_PREFIX}-notification-net
@@ -163,7 +163,7 @@ BENTOV2_AGGREGATION_CPUS=2
 
 # Event-Relay
 BENTOV2_EVENT_RELAY_IMAGE=ghcr.io/bento-platform/bento_event_relay
-BENTOV2_EVENT_RELAY_VERSION=3.0.2
+BENTOV2_EVENT_RELAY_VERSION=3.1.0
 BENTOV2_EVENT_RELAY_VERSION_DEV=${BENTOV2_EVENT_RELAY_VERSION}-dev
 BENTOV2_EVENT_RELAY_CONTAINER_NAME=${BENTOV2_PREFIX}-event-relay
 BENTO_EVENT_RELAY_NETWORK=${BENTOV2_PREFIX}-event-relay-net
@@ -176,7 +176,7 @@ BENTOV2_EVENT_RELAY_CPUS=1
 
 # WES
 BENTOV2_WES_IMAGE=ghcr.io/bento-platform/bento_wes
-BENTOV2_WES_VERSION=0.11.0
+BENTOV2_WES_VERSION=0.12.2
 BENTOV2_WES_VERSION_DEV=${BENTOV2_WES_VERSION}-dev
 BENTOV2_WES_CONTAINER_NAME=${BENTOV2_PREFIX}-wes
 BENTO_WES_NETWORK=${BENTOV2_PREFIX}-wes-net
@@ -203,7 +203,7 @@ BENTOV2_WES_WORKFLOW_TIMEOUT=172800
 
 # DRS
 BENTOV2_DRS_IMAGE=ghcr.io/bento-platform/bento_drs
-BENTOV2_DRS_VERSION=0.13.0
+BENTOV2_DRS_VERSION=edge
 BENTOV2_DRS_VERSION_DEV=${BENTOV2_DRS_VERSION}-dev
 BENTOV2_DRS_CONTAINER_NAME=${BENTOV2_PREFIX}-drs
 BENTO_DRS_NETWORK=${BENTOV2_PREFIX}-drs-net
@@ -246,7 +246,7 @@ BENTOV2_KATSU_DB_CPUS=4
 
 # Katsu
 BENTOV2_KATSU_IMAGE=ghcr.io/bento-platform/katsu
-BENTOV2_KATSU_VERSION=5.0.0
+BENTOV2_KATSU_VERSION=edge
 BENTOV2_KATSU_VERSION_DEV=${BENTOV2_KATSU_VERSION}-dev
 BENTOV2_KATSU_CONTAINER_NAME=${BENTOV2_PREFIX}-katsu
 BENTO_KATSU_NETWORK=${BENTOV2_PREFIX}-katsu-net
@@ -289,7 +289,7 @@ BENTOV2_GOHAN_DATA_ROOT=${BENTOV2_ROOT_DATA_DIR}/gohan
 
 # -- API
 BENTOV2_GOHAN_API_IMAGE=ghcr.io/bento-platform/gohan-api
-BENTOV2_GOHAN_API_VERSION=4.0.1
+BENTOV2_GOHAN_API_VERSION=pr-57
 BENTOV2_GOHAN_API_VERSION_DEV=${BENTOV2_GOHAN_API_VERSION}-dev
 
 BENTOV2_GOHAN_API_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-api
@@ -369,7 +369,7 @@ BENTO_PUBLIC_TRANSLATED=true
 BENTO_BEACON_CONTAINER_NAME=${BENTOV2_PREFIX}-beacon
 BENTO_BEACON_NETWORK=${BENTOV2_PREFIX}-beacon-net
 BENTO_BEACON_IMAGE=ghcr.io/bento-platform/bento_beacon
-BENTO_BEACON_VERSION=0.11.0
+BENTO_BEACON_VERSION=pr-63
 BENTO_BEACON_VERSION_DEV=${BENTO_BEACON_VERSION}-dev
 BENTO_BEACON_INTERNAL_PORT=${BENTO_STD_SERVICE_INTERNAL_PORT}
 BENTO_BEACON_EXTERNAL_PORT=5000

etc/bento_dev.env

@@ -66,3 +66,7 @@ [email protected]
 # e.g.:
 # BENTOV2_DRS_VERSION=v0.8.0
 # BENTOV2_DRS_VERSION_DEV=v0.8.0-dev
+
+# Path to the Phenopacket-tools jar
+# https://github.com/phenopackets/phenopacket-tools
+PHENOTOOL_JAR_PATH=

py_bentoctl/config.py

@@ -180,3 +180,5 @@ def _get_enabled_services(compose_file: str, filter_out: Tuple[str, ...] = ()) -
 BENTO_ORCHESTRATION_STATE_DB_FILE = os.getenv("BENTO_ORCHESTRATION_STATE_DB", "./.bentoctl.state.db")
 
 MULTI_SERVICE_PREFIXES = ("gohan",)
+
+PHENOTOOL_PATH = os.getenv("PHENOTOOL_JAR_PATH", "")

py_bentoctl/entry.py

@@ -266,6 +266,22 @@ def exec(args):
             fh.init_cbioportal()
 
 
+class ConvertPhenopacket(SubCommand):
+
+    @staticmethod
+    def add_args(sp):
+        sp.add_argument("source", type=str, help="Source Phenopackets V1 JSON document to convert")
+        sp.add_argument("target", nargs="?", default=None, type=str,
+                        help="Optional target file path where to place the converted Phenopackets")
+
+    @staticmethod
+    def exec(args):
+        # import asyncio
+        # TODO: re-convert to async
+        # asyncio.run(oh.convert_phenopacket_file(args.source, args.target))
+        oh.convert_phenopacket_file(args.source, args.target)
+
+
 def main(args: Optional[list[str]] = None) -> int:
     args = args or sys.argv[1:]
 
@@ -323,6 +339,8 @@ def _add_subparser(arg: str, help_text: str, subcommand: Type[SubCommand], alias
     _add_subparser("shell", "Run a shell inside an already-running service container.", Shell, aliases=("sh",))
     _add_subparser("run-as-shell", "Run a shell inside a stopped service container.", RunShell)
     _add_subparser("logs", "Check logs for a service.", Logs)
+    _add_subparser("convert-pheno",
+                   "Convert a Phenopacket V1 JSON document to V2", ConvertPhenopacket, aliases=("conv",))
 
     p_args = parser.parse_args(args)