Set up image deployment for seqcolapi

README_seqcolapi.md

@@ -9,35 +9,44 @@ This repository contains:
 
 ### Run locally for development
 
-To run a local server with a **local database**:
-```
-source servers/localhost/dev_local.env
-uvicorn seqcolapi.main:app --reload --port 8100
-```
+First, configure env vars:
+- To run a local server with a **local database**:`source servers/localhost/dev_local.env`
+- To run a local server with **the production database**:`source servers/seqcolapi.databio.org/production.env`
+
+Then, run service:
 
-To run a local server with **the production database**:
 ```
-source servers/seqcolapi.databio.org/production.env
 uvicorn seqcolapi.main:app --reload --port 8100
 ```
 
 ### Running with docker
 
-To build the docker file:
+To build the docker file, from the root of this repository:
 
+First you build the general-purpose image
 
 ```
-docker build --no-cache -t scim .
+docker build -f deployment/dockerhub/Dockerfile -t databio/seqcolapi seqcolapi
+```
+
+Next you build the wrapped image (this just wraps the config into the app):
+
+```
+docker build -f deployment/seqcolapi.databio.org/Dockerfile -t seqcolapi.databio.org deployment/seqcolapi.databio.org
 ```
 
 To run in a container:
 
 ```
-export POSTGRES_PASSWORD=`pass aws/rds_postgres` 
+source deployment/seqcolapi.databio.org/production.env
+docker run --rm -p 8000:80 --name seqcolapi seqcolapi.databio.org
+```
+
+
 docker run --rm -p 8000:8000 --name sccon \
   --env "POSTGRES_PASSWORD" \
   --volume $CODE/seqcolapi.databio.org/config/seqcolapi.yaml:/config.yaml \
-  scim seqcolapi serve -c /config.yaml -p 8000
+  scim 
 ```
 
 To deploy container to dockerhub:

deployment/dockerhub/Dockerfile

@@ -0,0 +1,11 @@
+FROM tiangolo/uvicorn-gunicorn:python3.11-slim
+LABEL authors="Nathan Sheffield"
+RUN pip install https://github.com/databio/yacman/archive/dev.zip
+RUN pip install https://github.com/refgenie/refget/archive/seqcolapi.zip
+
+COPY requirements/requirements-seqcolapi.txt requirements/requirements-seqcolapi.txt
+RUN pip install -r requirements/requirements-seqcolapi.txt --no-cache-dir
+
+COPY . /app/seqcolapi
+
+CMD ["uvicorn", "seqcolapi.main:app", "--host", "0.0.0.0", "--port", "80"]

deployment/seqcolapi.databio.org/Dockerfile

@@ -0,0 +1,3 @@
+FROM databio/seqcolapi
+COPY seqcolapi.yaml /seqcolapi_config.yaml
+ENV SEQCOLAPI_CONFIG /seqcolapi_config.yaml

servers/seqcolapi.databio.org/production.env → deployment/seqcolapi.databio.org/production.env

@@ -6,4 +6,4 @@ export POSTGRES_TABLE="seqcol"
 
 export SEQCOLAPI_PORT="5432"
 export SERVER_ENV="production"
-export SEQCOLAPI_CONFIG="servers/seqcolapi.databio.org/seqcolapi.yaml"
+export SEQCOLAPI_CONFIG="deployment/seqcolapi.databio.org/seqcolapi.yaml"

refget/seqcol.py

@@ -1,6 +1,5 @@
 import henge
 import logging
-import yacman
 
 from itertools import compress
 
@@ -12,26 +11,6 @@
 henge.ITEM_TYPE = "_item_type"
 
 
-class SeqColConf(yacman.YAMLConfigManager):
-    """
-    Simple configuration manager object for SeqColHenge.
-    """
-
-    def __init__(
-        self,
-        entries={},
-        filepath=None,
-        yamldata=None,
-        writable=False,
-        wait_max=60,
-        skip_read_lock=False,
-    ):
-        filepath = yacman.select_config(
-            config_filepath=filepath, config_env_vars=["SEQCOLAPI_CONFIG"], config_name="seqcol"
-        )
-        super(SeqColConf, self).__init__(entries, filepath, yamldata, writable)
-
-
 class SeqColHenge(henge.Henge):
     """
     Extension of henge that accommodates collections of sequences.

seqcolapi/__init__.py

@@ -1,3 +0,0 @@
-import logmuse
-
-logmuse.init_logger("seqcolapi")

seqcolapi/main.py

@@ -1,7 +1,6 @@
 import henge
 import json
 import logging
-import logmuse
 import os
 import sys
 import uvicorn
@@ -17,12 +16,15 @@
 from starlette.staticfiles import StaticFiles
 from typing import Union
 
-from .cli import build_parser
 from .const import *
 from .scconf import RDBDict
 from .examples import *
 
-from refget import SeqColConf, SeqColHenge, format_itemwise
+from refget import SeqColHenge, format_itemwise
+from yacman import select_config, FutureYAMLConfigManager as YAMLConfigManager
+
+class SeqColConf(YAMLConfigManager):
+    pass
 
 global _LOGGER
 
@@ -124,7 +126,7 @@ def create_globals(scconf: yacman.YAMLConfigManager):
 def main(injected_args=None):
     # Entry point for running from console_scripts, installed package
     parser = build_parser()
-    parser = logmuse.add_logging_options(parser)
+    # parser = logmuse.add_logging_options(parser)
     args = parser.parse_args()
     if injected_args:
         args.__dict__.update(injected_args)
@@ -133,10 +135,10 @@ def main(injected_args=None):
         print("No subcommand given")
         sys.exit(1)
 
-    _LOGGER = logmuse.logger_via_cli(args, make_root=True)
+    # _LOGGER = logmuse.logger_via_cli(args, make_root=True)
     _LOGGER.info(f"args: {args}")
     if "config" in args and args.config is not None:
-        scconf = SeqColConf(filepath=args.config)
+        scconf = SeqColConf.from_yaml_file(args.config)
         create_globals(scconf)
         app.state.schenge = schenge
         port = args.port or scconf.exp["server"]["port"]
@@ -149,7 +151,8 @@ def main(injected_args=None):
 if __name__ != "__main__":
     # Entrypoint for running through uvicorn CLI (dev)
     if os.environ.get("SEQCOLAPI_CONFIG") is not None:
-        scconf = SeqColConf()
+        _LOGGER.info(f"Loading config from SEQCOLAPI_CONFIG: {os.environ.get('SEQCOLAPI_CONFIG')}")
+        scconf = SeqColConf.from_yaml_file(os.environ.get('SEQCOLAPI_CONFIG'))
         create_globals(scconf)
         app.state.schenge = schenge
     else:

requirements/requirements-seqcolapi.txt → seqcolapi/requirements/requirements-seqcolapi.txt

@@ -2,7 +2,7 @@ aiofiles
 fastapi
 henge>=0.2.1
 jinja2
-logmuse>=0.2
+pipestat
 psycopg2-binary
 refget
 uvicorn>=0.7.1