Add bootstrap installer and a Docker controller Makefile

dev/local/.dockerignore

@@ -0,0 +1,6 @@
+# Ignore everything by default
+*
+# Don't ignore repos dir
+!repos
+# Ignore everything to do with git
+**/*.git

dev/local/Makefile

@@ -0,0 +1,136 @@
+# Docker control panel for delphi-epidata development
+#
+# Usage: make <command> [pdb=1] [test-subdir=<test-subdir>]
+#
+# Assumes you have installed your environment using
+# delphi-epidata/dev/local/install.sh.
+#
+# Checks for the delphi-net bridge and creates if it doesn't exist.
+#
+# Creates all prereq images (delphi_database, delphi_python) only if they don't
+# exist. If you need to rebuild a prereq, you're probably doing something
+# complicated, and can figure out the rebuild command on your own.
+# 
+# 
+# Commands:
+#            
+#   web:     Stops currently-running delphi_web_epidata instances, if any.
+#            Rebuilds delphi_web_epidata image.
+#            Runs image in the background and pipes stdout to a log file.
+# 
+#   db:      Stops currently-running delphi_database_epidata instances, if any.
+#            Rebuilds delphi_database_epidata image.
+#            Runs image in the background and pipes stdout to a log file.
+#            Blocks until database is ready to receive connections.
+# 
+#   python:  Rebuilds delphi_web_python image. You shouldn't need to do this
+#            often; only if you are installing a new environment, or have
+#            made changes to delphi-epidata/dev/docker/python/Dockerfile.
+#
+#   all:     Runs the commands 'web' 'db' and 'python'.
+#
+#   test:    Runs test and integrations in delphi-epidata. If test-subdir 
+#            optional arg is provided, then only the tests in that subdir
+#            are run.
+#
+#   clean:   Cleans up dangling Docker images.
+#
+# 
+# Optional arguments:
+#   pdb=1         Drops you into debug mode upon test failure, if running tests.
+#   test-subdir=  Only runs tests in the directory provided here, e.g.
+#                 repos/delphi/delphi-epidata/tests/acquisition/covidcast
+
+
+# Set optional argument defaults
+ifdef pdb
+	override pdb=--pdb
+else
+	pdb=
+endif
+
+ifdef test-subdir
+else
+	test-subdir=repos/delphi/delphi-epidata/tests repos/delphi/delphi-epidata/integrations
+endif
+
+# Set your shell here
+SHELL:=/bin/sh
+
+# Get the Makefile's absolute path: https://stackoverflow.com/a/324782/4784655
+# (if called from symlink, the path is the location of the symlink)
+NOW:=$(shell date "+%Y-%m-%d")
+CWD:=$(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+LOG_WEB:=$(CWD)docker-logs/delphi_web_epidata_$(NOW).log
+LOG_DB:=$(CWD)docker-logs/delphi_database_epidata_$(NOW).log
+
+
+.PHONY=web
+web:
+	@# Stop container if running
+	@-docker ps | grep delphi_web_epidata && docker stop delphi_web_epidata
+
+	@# Setup virtual network if it doesn't exist
+	@-docker network ls | grep delphi-net || docker network create --driver bridge delphi-net
+
+	@# Build the web_epidata image
+	@cd repos/delphi/delphi-epidata;\
+	docker build -t delphi_web_epidata -f ./devops/Dockerfile .;\
+	cd ../../../
+
+	@# Run the web server
+	@docker run --rm -p 127.0.0.1:10080:80 \
+		--env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" \
+		--env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" \
+		--network delphi-net --name delphi_web_epidata \
+		delphi_web_epidata >$(LOG_WEB) 2>&1 &
+
+.PHONY=db
+db:
+	@# Stop container if running
+	@-docker ps | grep delphi_database_epidata && docker stop delphi_database_epidata
+
+	@# Only build prereqs if we need them
+	@-docker images delphi_database | grep delphi || \
+		docker build -t delphi_database -f repos/delphi/operations/dev/docker/database/Dockerfile .
+
+	@# Build the database_epidata image
+	@docker build -t delphi_database_epidata \
+		-f repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile .
+
+	@# Run the database
+	@docker run --rm -p 127.0.0.1:13306:3306 \
+		--network delphi-net --name delphi_database_epidata \
+		delphi_database_epidata >$(LOG_DB) 2>&1 &
+
+	@# Block until DB is ready
+	@while true; do \
+		sed -n '/Temporary server stopped/,/mysqld: ready for connections/p' $(LOG_DB) | grep "ready for connections" && break; \
+		tail -1 $(LOG_DB); \
+		sleep 1; \
+	done
+
+.PHONY=py
+py:
+	@# Build the python image
+	@docker build -t delphi_python \
+	-f repos/delphi/operations/dev/docker/python/Dockerfile .
+
+	@docker build -t delphi_web_python \
+	-f repos/delphi/delphi-epidata/dev/docker/python/Dockerfile .
+
+.PHONY=all
+all: web db py
+
+.PHONY=test
+test: 
+	@docker run -i --rm --network delphi-net \
+		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata,target=/usr/src/app/repos/delphi/delphi-epidata,readonly \
+		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata/src,target=/usr/src/app/delphi/epidata,readonly \
+		--env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" \
+		--env "FLASK_SECRET=abc" \
+		delphi_web_python python -m pytest --import-mode importlib $(pdb) $(test-subdir) | tee -a output.txt
+
+.PHONY=clean
+clean:
+	docker images -f "dangling=true" -q | xargs docker rmi >/dev/null 2>&1

dev/local/install.sh

@@ -1,9 +1,26 @@
 #!/bin/bash
+# Bootstrap delphi-epidata
+#
+# Downloads the repos needed for local delphi-epidata development into current dir 
+# and provides a Makefile with Docker control commands.
 
-mkdir -p driver/repos/delphi driver-logs/delphi_database_epidata driver-logs/delphi_web_epidata
-cd driver/repos/delphi
+mkdir -p repos/delphi
+cd repos/delphi
 git clone https://github.com/cmu-delphi/operations
 git clone https://github.com/cmu-delphi/delphi-epidata
 git clone https://github.com/cmu-delphi/utils
+git clone https://github.com/cmu-delphi/flu-contest
+git clone https://github.com/cmu-delphi/nowcast
+git clone https://github.com/cmu-delphi/github-deploy-repo
 cd ../../
-ln -s repos/delphi/delphi-epidata/dev/local/epidata-refresh.sh
+
+mkdir -p repos/undefx
+cd repos/undefx
+git clone https://github.com/undefx/py3tester
+git clone https://github.com/undefx/undef-analysis
+cd ../../
+
+mkdir -p docker-logs
+
+ln -s repos/delphi/delphi-epidata/dev/local/Makefile
+ln -s repos/delphi/delphi-epidata/dev/local/.dockerignore

docs/epidata_development.md

@@ -7,10 +7,16 @@ nav_order: 4
 
 ## Quickstart
 
+In the directory where you want to work run the following
+
 ```
 $ curl "https://raw.githubusercontent.com/cmu-delphi/delphi-epidata/dev/dev/local/install.sh" | bash
-$ cd driver
-$ [sudo] ./epidata-refresh.sh database web python
+$ [sudo] make all
+$ make test
+# To drop into debugger on error
+$ make test pdb=1
+# To test only a subset of tests
+$ make test test-subdir=repos/delphi/delphi-epidata/integrations/acquisition
 ```
 (sudo requirement depends on your Docker installation and operating system)