Feat/al2 updates

.secrets.baseline

@@ -136,7 +136,7 @@
         "filename": "bin/settings.py",
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_verified": false,
-        "line_number": 43
+        "line_number": 54
       }
     ],
     "docs/local_dev_environment.md": [
@@ -354,5 +354,5 @@
       }
     ]
   },
-  "generated_at": "2024-04-22T20:07:28Z"
+  "generated_at": "2024-08-12T21:26:18Z"
 }

Dockerfile

@@ -1,65 +1,87 @@
-# To run:
-# - Create and fill out `creds.json`:
-# {
-#   "fence_host": "",
-#   "fence_username": "",
-#   "fence_password": "",
-#   "fence_database": "",
-#   "db_host": "",
-#   "db_username": "",
-#   "db_password": "",
-#   "db_database": "",
-#   "gdcapi_secret_key": "",
-#   "indexd_password": "",
-#   "hostname": ""
-# }
-# - Build the image: `docker build . -t sheepdog -f Dockerfile`
-# - Run: `docker run -v /full/path/to/creds.json:/var/www/sheepdog/creds.json -p 81:80 sheepdog`
-# To check running container: `docker exec -it sheepdog /bin/bash`
-
-FROM quay.io/cdis/python:python3.9-buster-2.0.0
+ARG AZLINUX_BASE_VERSION=master
+
+# Base stage with python-build-base
+FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base
+
+# Comment this in, and comment out the line above, if quay is down
+# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base
 
 ENV appname=sheepdog
+ENV POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1
+
+WORKDIR /${appname}
+
+# create gen3 user
+# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000
+RUN groupadd -g 1000 gen3 && \
+    useradd -m -s /bin/bash -u 1000 -g gen3 gen3  && \
+    chown -R gen3:gen3 /$appname && \
+    chown -R gen3:gen3 /venv
+
+
+# Builder stage
+FROM base AS builder
+
+
+RUN yum install -y gcc gcc-c++ make postgresql-devel 
+
+RUN dnf install python3-devel -y
+
+USER gen3
+
+
+RUN python -m venv /venv
+
+COPY poetry.lock pyproject.toml /${appname}/
+
+RUN pip install poetry && \
+    poetry install -vv --only main --no-interaction
+
+COPY --chown=gen3:gen3 . /$appname
+
+# Run poetry again so this app itself gets installed too
+RUN poetry install --without dev --no-interaction
+
+RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \
+    && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py
+
+# Final stage
+FROM base
+
+COPY --from=builder /venv /venv
+COPY --from=builder /$appname /$appname
+
+# install nginx
+RUN yum install nginx postgresql-devel -y
+
+# allow nginx to bind to port 80
+RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx
 
-RUN pip install --upgrade pip poetry
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential libffi-dev musl-dev gcc libxml2-dev libxslt-dev \
-    curl bash git vim
+# chown nginx directories
+RUN chown -R gen3:gen3 /var/log/nginx
 
-RUN mkdir -p /var/www/$appname \
-    && mkdir -p /var/www/.cache/Python-Eggs/ \
-    && mkdir /run/nginx/ \
-    && ln -sf /dev/stdout /var/log/nginx/access.log \
-    && ln -sf /dev/stderr /var/log/nginx/error.log \
-    && chown nginx -R /var/www/.cache/Python-Eggs/ \
-    && chown nginx /var/www/$appname
+# pipe nginx logs to stdout and stderr
+RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log
 
-EXPOSE 80
+# create /var/lib/nginx/tmp/client_body to allow nginx to write to fence
+RUN mkdir -p /var/lib/nginx/tmp/client_body
+RUN chown -R gen3:gen3 /var/lib/nginx/
 
-WORKDIR /$appname
+# copy nginx config
+COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf
 
-# copy ONLY poetry artifact, install the dependencies but not indexd
-# this will make sure than the dependencies is cached
-COPY poetry.lock pyproject.toml /$appname/
-RUN poetry config virtualenvs.create false \
-    && poetry install -vv --no-root --no-dev --no-interaction \
-    && poetry show -v
 
-# copy source code ONLY after installing dependencies
-COPY . /$appname
-COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
-COPY ./bin/settings.py /var/www/$appname/settings.py
-COPY ./bin/confighelper.py /var/www/$appname/confighelper.py
+# Switch to non-root user 'gen3' for the serving process
+USER gen3
 
-# install sheepdog
-RUN poetry config virtualenvs.create false \
-    && poetry install -vv --no-dev --no-interaction \
-    && poetry show -v
+RUN source /venv/bin/activate
 
-RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \
-    && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONIOENCODING=UTF-8
 
-WORKDIR /var/www/$appname
+WORKDIR /var/www/${appname}
 
-RUN ls
-CMD /dockerrun.sh
+CMD ["/sheepdog/dockerrun.bash"]
+# CMD ["gunicorn", "-c", "/sheepdog/deployment/wsgi/gunicorn.conf.py"]

README.md

@@ -22,7 +22,7 @@ import sheepdog
 import datamodelutils
 from dictionaryutils import dictionary
 from gdcdictionary import gdcdictionary
-from gdcdatamodel import models, validators
+from gen3datamodel import models, validators
 
 dictionary.init(gdcdictionary)
 datamodelutils.validators.init(validators)

bin/confighelper.py

@@ -49,6 +49,6 @@ def load_json(file_name, app_name, search_folders=None):
     """
     actual_files = find_paths(file_name, app_name, search_folders)
     if not actual_files:
-        return None
+        return {}
     with open(actual_files[0], "r") as reader:
         return json.load(reader)

bin/settings.py

@@ -1,6 +1,6 @@
 from sheepdog.api import app, app_init
-from os import environ
-import confighelper
+import os
+from . import confighelper
 
 APP_NAME = "sheepdog"
 
@@ -22,39 +22,52 @@ def load_json(file_name):
 
 # Signpost: deprecated, replaced by index client.
 config["SIGNPOST"] = {
-    "host": environ.get("SIGNPOST_HOST") or "http://indexd-service",
+    "host": os.environ.get("SIGNPOST_HOST", "http://indexd-service"),
     "version": "v0",
     "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")),
 }
 config["INDEX_CLIENT"] = {
-    "host": environ.get("INDEX_CLIENT_HOST") or "http://indexd-service",
+    "host": os.environ.get("INDEX_CLIENT_HOST") or "http://indexd-service",
     "version": "v0",
     "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")),
 }
 config["FAKE_AUTH"] = False
 config["PSQLGRAPH"] = {
-    "host": conf_data["db_host"],
-    "user": conf_data["db_username"],
-    "password": conf_data["db_password"],
-    "database": conf_data["db_database"],
+    "host": conf_data.get("db_host", os.environ.get("PGHOST", "localhost")),
+    "user": conf_data.get("db_username", os.environ.get("PGUSER", "sheepdog")),
+    "password": conf_data.get("db_password", os.environ.get("PGPASSWORD", "sheepdog")),
+    "database": conf_data.get("db_database", os.environ.get("PGDB", "sheepdog")),
 }
 
 config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}")
-config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % tuple(
-    [
-        conf_data.get(key, key)
-        for key in ["fence_username", "fence_password", "fence_host", "fence_database"]
-    ]
+
+fence_username = conf_data.get(
+    "fence_username", os.environ.get("FENCE_DB_USER", "fence")
+)
+fence_password = conf_data.get(
+    "fence_password", os.environ.get("FENCE_DB_PASS", "fence")
+)
+fence_host = conf_data.get("fence_host", os.environ.get("FENCE_DB_HOST", "localhost"))
+fence_database = conf_data.get(
+    "fence_database", os.environ.get("FENCE_DB_DATABASE", "fence")
+)
+config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % (
+    fence_username,
+    fence_password,
+    fence_host,
+    fence_database,
 )
 
-config["USER_API"] = "https://%s/user" % conf_data["hostname"]  # for use by authutils
+config["USER_API"] = "https://%s/user" % conf_data.get(
+    "hostname", os.environ.get("CONF_HOSTNAME", "localhost")
+)  # for use by authutils
 # use the USER_API URL instead of the public issuer URL to accquire JWT keys
 config["FORCE_ISSUER"] = True
-config["DICTIONARY_URL"] = environ.get(
+config["DICTIONARY_URL"] = os.environ.get(
     "DICTIONARY_URL",
     "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json",
 )
 
 app_init(app)
 application = app
-application.debug = environ.get("GEN3_DEBUG") == "True"
+application.debug = os.environ.get("GEN3_DEBUG") == "True"

bin/setup_psqlgraph.py

@@ -3,7 +3,7 @@
 import logging
 from sqlalchemy import create_engine
 
-from gdcdatamodel.models import *
+from gen3datamodel.models import *
 from psqlgraph import create_all, Node, Edge
 
 

bin/setup_transactionlogs.py

@@ -5,7 +5,7 @@
 
 import argparse
 from sqlalchemy import create_engine
-from gdcdatamodel.models.submission import Base
+from gen3datamodel.models.submission import Base
 
 
 def setup(host, port, user, password, database, use_ssl=False):

deployment/nginx/nginx.conf

@@ -0,0 +1,44 @@
+user gen3;
+worker_processes auto;
+error_log /var/log/nginx/error.log notice;
+pid /var/lib/nginx/nginx.pid;
+
+# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic.
+include /usr/share/nginx/modules/*.conf;
+
+events {
+    worker_connections 1024;
+}
+
+http {
+    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+
+    access_log  /var/log/nginx/access.log  main;
+
+    sendfile            on;
+    tcp_nopush          on;
+    keepalive_timeout   65;
+    types_hash_max_size 4096;
+
+    include             /etc/nginx/mime.types;
+    default_type        application/octet-stream;
+
+    # Load modular configuration files from the /etc/nginx/conf.d directory.
+    # See http://nginx.org/en/docs/ngx_core_module.html#include
+    # for more information.
+    include /etc/nginx/conf.d/*.conf;
+
+    server {
+
+        listen 80;
+        server_name localhost;
+
+        location / {
+            proxy_pass http://127.0.0.1:8000;
+            proxy_set_header Host $host;
+            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        }
+    }
+}

deployment/wsgi/gunicorn.conf.py

@@ -0,0 +1,17 @@
+# /sheepdoog/bin/settings.py
+wsgi_app = "bin.settings:application"
+bind = "0.0.0.0:8000"
+workers = 4
+preload_app = False
+user = "gen3"
+group = "gen3"
+timeout = 300
+keepalive = 2
+keepalive_timeout = 5
+
+import random
+import time
+
+
+def pre_fork(server, worker):
+    time.sleep(random.uniform(0, 2))

deployment/wsgi/wsgi.py

@@ -0,0 +1 @@
+from sheepdog.api import app as application

dockerrun.bash

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" &
+sleep 30
+nginx -g 'daemon off;'

docs/local_dev_environment.md

@@ -195,7 +195,7 @@ For convenience, the minimal usage looks like the following:
 import datamodelutils
 from dictionaryutils import dictionary
 from gdcdictionary import gdcdictionary
-from gdcdatamodel import models, validators
+from gen3datamodel import models, validators
 from flask import Flask
 import sheepdog