Merge b6c30fd into 1f48235

.dockerignore

@@ -0,0 +1,11 @@
+alembic
+tests
+trailblazer.egg-info
+.pytest_cache
+.github
+.editorconfig
+.gitignore
+.gitlint.yaml
+.pre-commit-config.yaml
+DEPLOYMENT.md
+

Dockerfile

@@ -0,0 +1,26 @@
+FROM python:3.7-slim
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_TREADS=1
+ENV GUNICORN_BIND="0.0.0.0:5000"
+ENV GUNICORN_TIMEOUT=400
+
+WORKDIR /home/src/app
+COPY . /home/src/app
+
+RUN pip install -r requirements.txt
+RUN pip install -e .
+
+EXPOSE 5000
+
+RUN useradd worker
+RUN chown -R worker:worker /home/src
+USER worker
+
+CMD gunicorn \
+  --workers=$GUNICORN_WORKERS \
+  --bind=$GUNICORN_BIND \
+  --threads=$GUNICORN_TREADS \
+  --timeout=$GUNICORN_TIMEOUT \
+  trailblazer.server.app:app
+

README.md

@@ -1,9 +1,8 @@
 # Trailblazer [![Coverage Status][coveralls-image]][coveralls-url]
 
-### Automate, monitor, and simplify running the [MIP][mip] analysis pipeline
+### Monitor the progress of analysis workflows submitted to SLURM
 
 Trailblazer is a tool that aims to provide:
-
 - a Python interface to interact with MIP in an automated fashion
 - a limited command line interface to simplify running MIP using an opinionated setup
 

docker-compose.yml

@@ -0,0 +1,42 @@
+version: '3.8'
+
+services:
+  mysql-server:
+    image: mysql:5.6
+    container_name: trailblazer-database
+    restart: always
+    volumes:
+      - ../testing/tb_dump:/docker-entrypoint-initdb.d:rw
+    ports:
+      - '3306'
+    environment:
+      MYSQL_ROOT_PASSWORD: rootpass
+      MYSQL_USER: user
+      MYSQL_PASSWORD: userpass
+      MYSQL_DATABASE: trailblazer-stage
+    networks:
+      - trailblazer-network
+
+  trailblazer:
+    image: mropat/trailblazer
+    container_name: trailblazer-api
+    environment:
+      SQLALCHEMY_DATABASE_URI: "mysql+pymysql://user:userpass@mysql-server:3306/trailblazer-stage"
+      SCOPE: "DEVELOPMENT"
+      GUNICORN_WORKERS: "3"
+      GUNICORN_BIND: "0.0.0.0:5000"
+      GUNICORN_TIMEOUT: "400"
+    ports:
+      - 7076:5000
+    networks:
+      - trailblazer-network
+    depends_on:
+      - mysql-server
+
+networks:
+  trailblazer-network:
+    driver: bridge
+    ipam:
+      driver: default
+
+

requirements.txt

@@ -15,7 +15,9 @@ Flask-SQLAlchemy==2.1
 Flask-CORS
 Flask-Reverse-Proxy
 google-auth
+gunicorn
 
 # misc
 pymysql
 python-dateutil
+cryptography

trailblazer-pod.yaml

@@ -0,0 +1,83 @@
+# Generation of Kubernetes YAML is still under development!
+#
+# Save the output of this file and use kubectl create -f to import
+# it into Kubernetes.
+#
+# Created with podman-2.0.6
+apiVersion: v1
+kind: Pod
+metadata:
+  creationTimestamp: "2020-11-29T09:43:55Z"
+  labels:
+    app: trailblazer-pod
+  name: trailblazer-pod
+spec:
+  containers:
+  - name: trailblazer-stage-db
+    env:
+    - name: MYSQL_PASSWORD
+      value: userpass
+    - name: MYSQL_ROOT_PASSWORD
+      value: rootpass
+    - name: MYSQL_USER
+      value: user
+    - name: MYSQL_DATABASE
+      value: trailblazer-stage
+    image: docker.io/library/mysql:5.6
+    ports:
+    - contrinerPort: 3306
+    resources: {}
+    securityContext:
+      allowPrivilegeEscalation: true
+      capabilities: {}
+      privileged: false
+      readOnlyRootFilesystem: false
+      seLinuxOptions: {}
+    volumeMounts:
+    - mountPath: /docker-entrypoint-initdb.d
+      name: home-admin-Documents-CG-testing-tb_dump
+    workingDir: /
+
+  - name: trailblazer-api
+    env:
+    - name: GUNICORN_TREADS
+      value: "1"
+    - name: GUNICORN_BIND
+      value: 0.0.0.0:5000
+    - name: SCOPE
+      value: DEVELOPMENT
+    - name: GUNICORN_TIMEOUT
+      value: "400"
+    - name: SQLALCHEMY_DATABASE_URI
+      value: mysql+pymysql://user:userpass@localhost:3306/trailblazer-stage
+    - name: GUNICORN_WORKERS
+      value: "1"
+    image: docker.io/mropat/trailblazer:latest
+    ports:
+    - containerPort: 5000
+      hostPort: 7076
+      protocol: TCP
+    resources: {}
+    securityContext:
+      allowPrivilegeEscalation: true
+      capabilities: {}
+      privileged: false
+      readOnlyRootFilesystem: false
+      runAsGroup: 1000
+      runAsUser: 1000
+      seLinuxOptions: {}
+    workingDir: /home/src/app
+
+  volumes:
+  - hostPath:
+      path: /home/admin/Documents/CG/testing/tb_dump
+      type: Directory
+    name: home-admin-Documents-CG-testing-tb_dump
+status: {}
+---
+metadata:
+  creationTimestamp: null
+spec: {}
+status:
+  loadBalancer: {}
+

trailblazer/cli/core.py

@@ -1,7 +1,6 @@
 import logging
-
+import os
 import click
-import coloredlogs
 import ruamel.yaml
 from dateutil.parser import parse as parse_date
 
@@ -16,15 +15,14 @@
 @click.group()
 @click.option("-c", "--config", type=click.File())
 @click.option("-d", "--database", help="path/URI of the SQL database")
-@click.option("-l", "--log-level", default="INFO")
 @click.version_option(trailblazer.__version__, prog_name=trailblazer.__title__)
 @click.pass_context
-def base(context, config, database, log_level):
+def base(context, config, database):
     """Trailblazer - Monitor analyses"""
-    coloredlogs.install(level=log_level)
-
     context.obj = ruamel.yaml.safe_load(config) if config else {}
-    context.obj["database"] = database or context.obj.get("database")
+    context.obj["database"] = database or os.environ.get(
+        "SQLALCHEMY_DATABASE_URI", "sqlite:///:memory:"
+    )
     context.obj["trailblazer"] = Store(context.obj["database"])
 
 

trailblazer/server/api.py

@@ -1,9 +1,10 @@
 import datetime
+import os
+
 from dateutil.parser import parse as parse_datestr
 from flask import abort, g, Blueprint, jsonify, make_response, request
 from google.auth import jwt
 from typing import Dict
-import subprocess
 import multiprocessing
 
 from trailblazer.server.ext import store
@@ -24,6 +25,8 @@ def before_request():
     """Authentication that is run before processing requests to the application"""
     if request.method == "OPTIONS":
         return make_response(jsonify(ok=True), 204)
+    if os.environ.get("SCOPE") == "DEVELOPMENT":
+        return
     auth_header = request.headers.get("Authorization")
     if auth_header:
         jwt_token = auth_header.split("Bearer ")[-1]

trailblazer/server/app.py

@@ -1,21 +1,18 @@
 # -*- coding: utf-8 -*-
 import os
-
-import coloredlogs
 from flask import Flask
 from flask_cors import CORS
 from flask_reverse_proxy import FlaskReverseProxied
 
 from trailblazer.server import api, ext
 
-coloredlogs.install(level="INFO")
 app = Flask(__name__)
 
 SECRET_KEY = "unsafe!!!"
 TEMPLATES_AUTO_RELOAD = True
-SQLALCHEMY_DATABASE_URI = os.environ["SQLALCHEMY_DATABASE_URI"]
-SQLALCHEMY_POOL_RECYCLE = 7200
-SQLALCHEMY_TRACK_MODIFICATIONS = "FLASK_DEBUG" in os.environ
+SQLALCHEMY_DATABASE_URI = os.environ.get("SQLALCHEMY_DATABASE_URI", "sqlite:///:memory:")
+SQLALCHEMY_POOL_RECYCLE = os.environ.get("SQLALCHEMY_POOL_RECYCLE", 7200)
+SQLALCHEMY_TRACK_MODIFICATIONS = os.environ.get("FLASK_DEBUG", False)
 
 app.config.from_object(__name__)