Merge pull request #72 from PhysiciansDataCollaborative/dev

DerekRoberts · DerekRoberts · commit a9332021265b · 2015-07-30T16:26:54.000-07:00
0.1.2
diff --git a/Makefile b/Makefile
@@ -48,43 +48,43 @@ prod:
 #########################
 
 hubdb:
-	@	sudo mkdir -p $(PATH_MONGO)
-	@	$(call dockerize,hubdb,$(DOCKER_HUBDB_PRODUCTION))
+	@	sudo mkdir -p $(PATH_MONGO_DB) $(PATH_MONGO_DUMP)
+	@	$(call dockerize,hubdb,$(DOCKER_HUBDB_PROD))
 	@	sudo docker exec hubdb /app/mongodb_init.sh > /dev/null
 
 
 hub:
-	@	sudo mkdir -p $(PATH_HUB_SSH_HOST) $(PATH_HUB_SSH_AUTOSSH)
-	@	$(call dockerize,hub,$(DOCKER_HUB_PRODUCTION))
+	@	sudo mkdir -p $(PATH_HUB_AUTHKEYS) $(PATH_HUB_AUTOSSH)
+	@	$(call dockerize,hub,$(DOCKER_HUB_PROD))
 
 
 auth:
 	@	sudo mkdir -p $(PATH_DACS)
-	@	$(call dockerize,auth,$(DOCKER_AUTH_PRODUCTION))
+	@	$(call dockerize,auth,$(DOCKER_AUTH_PROD))
 
 
 dclapi:
 	@	sudo mkdir -p $(PATH_DRUGREF)
-	@	$(call dockerize,dclapi,$(DOCKER_DCLAPI_PRODUCTION))
+	@	$(call dockerize,dclapi,$(DOCKER_DCLAPI_PROD))
 
 
 hapi:
-	@	$(call dockerize,hapi,$(DOCKER_HAPI_PRODUCTION))
+	@	$(call dockerize,hapi,$(DOCKER_HAPI_PROD))
 
 
 viz:
 	@	sudo mkdir -p $(PATH_CERT)
-	@	$(call dockerize,viz,$(DOCKER_VIZ_PRODUCTION))
+	@	$(call dockerize,viz,$(DOCKER_VIZ_PROD))
 
 
 ep-sample:
 	@	sudo mkdir -p $(PATH_EPX_AUTOSSH)
-	@	$(call dockerize,endpoint,$(DOCKER_ENDPOINT_PRODUCTION),0)
+	@	$(call dockerize,endpoint,$(DOCKER_ENDPOINT_PROD),0)
 	@	$(call config_ep,0,cpsid,cpsid,admin,TEST,sample)
 
 
 queries:
-	@	$(call dockerize,queries,$(DOCKER_QI_PRODUCTION))
+	@	$(call dockerize,queries,$(DOCKER_QI_PROD))
 	@	sudo docker logs -f queries
 	@	$(call docker_remove,queries)
 
@@ -107,7 +107,7 @@ ep:
 			echo "Usage: make ep [gID=#] [DOCTOR=#####] [op:JURISDUCTION] [op:ROLE] [op:PASSWORD]"; \
 			echo; \
 		else \
-			$(call dockerize_ep,endpoint,$(DOCKER_ENDPOINT_PRODUCTION),$(gID)); \
+			$(call dockerize_ep,endpoint,$(DOCKER_ENDPOINT_PROD),$(gID)); \
 			$(call config_ep,$(gID),$(DOCTOR),$(ROLE),$(JURISDICTION),$(PASSWORD)); \
 		fi
 
@@ -269,6 +269,7 @@ config-bash:
 				echo "alias r='sudo docker rm -fv'"; \
 				echo "alias s='sudo docker ps -a | less -S'"; \
 				echo "alias m='make'"; \
+				echo "alias gitsubdiffs='find . -maxdepth 1 -mindepth 1 -type d -exec git -C {} status \;'"; \
 			) | tee -a $${HOME}/.bashrc; \
 			echo ""; \
 			echo ""; \
@@ -277,8 +278,8 @@ config-bash:
 		fi
 
 
-config-oc:
-	# Add repository and install owncloud cmd client
+config-backups:
+	# Add repository, install owncloud cmd client and run cronjobs for infrastructure and MongoDB data
 	#
 	@	echo 'deb http://download.opensuse.org/repositories/isv:/ownCloud:/desktop/xUbuntu_14.04/ /' \
 			| sudo tee /etc/apt/sources.list.d/owncloud-client.list
@@ -306,6 +307,11 @@ config-oc:
 				echo 'cd $${SCRIPT_DIR}'; \
 				echo ''; \
 				echo ''; \
+				echo '# Create a MongoDB dump'; \
+				echo '#'; \
+				echo 'sudo docker exec hubdb /app/mongodb_dump.sh';\
+				echo ''; \
+				echo ''; \
 				echo '# Copy non-sensitive MongoDB dumps to ./mongo_partial/'; \
 				echo '#'; \
 				echo 'sudo mkdir -p mongo_partial/'; \
@@ -345,10 +351,17 @@ config-oc:
 	@	if((! sudo test -e /var/spool/cron/crontabs/root )||(! sudo grep --quiet 'oc_backup.sh' /var/spool/cron/crontabs/root )); \
 		then \
 		  ( \
+		    echo ''; \
 		    echo ''; \
 		    echo '# Backup to ownCloud every 30 minutes'; \
 		    echo '#'; \
 		    echo '0,30 * * * * $\${PATH_HOST}/oc_backup.sh'; \
+		    echo ''; \
+		    echo ''; \
+		    echo '# Dump MongoDB nightly for UVic backup'; \
+		    echo '#'; \
+		    echo '15 1 * * * sudo docker exec hubdb /app/mongodb_dump.sh'; \
+		    echo ''; \
 		  ) | sudo tee -a /var/spool/cron/crontabs/root; \
 		fi
 
@@ -437,7 +450,7 @@ define config_ep
 	# Add Hub to known_hosts and receive Endpoint's public key
 	#
 	sudo docker exec ep$1 ssh -p $(PORT_AUTOSSH) -o StrictHostKeyChecking=no autossh@$(URL_HUB) 2> /dev/null || true
-	sudo docker exec ep$1 /app/key_exchange.sh | sudo tee -a $(PATH_HUB_SSH_AUTOSSH)/authorized_keys > /dev/null
+	sudo docker exec ep$1 /app/key_exchange.sh | sudo tee -a $(PATH_HUB_AUTOSSH)/authorized_keys > /dev/null
 
 	# Add Endpoint to the HubDB
 	#
@@ -480,40 +493,31 @@ endef
 include config.env
 
 
-# Set branch defaults
+# Override branch defaults for non-production modes
 #
-ifeq ($(BUILD_MODE), dev)
-	BRANCH_DEFAULT = dev
-else ifeq ($(BUILD_MODE), master)
-	BRANCH_DEFAULT = master
-else
-	BRANCH_DEFAULT = $(RELEASE_VERSION)
+ifneq ($(BUILD_MODE), prod)
+	BRANCH_AUTH ?= $(BUILD_MODE)
+	BRANCH_DCLAPI ?= $(BUILD_MODE)
+	BRANCH_ENDPOINT ?= $(BUILD_MODE)
+	BRANCH_EPXCLOUD ?= $(BUILD_MODE)
+	BRANCH_HAPI ?= $(BUILD_MODE)
+	BRANCH_HUB ?= $(BUILD_MODE)
+	BRANCH_HUBDB ?= $(BUILD_MODE)
+	BRANCH_QI ?= $(BUILD_MODE)
+	BRANCH_VIZ ?= $(BUILD_MODE)
 endif
 
 
 # Append Docker run commands for non-production modes
 #
 ifneq ($(BUILD_MODE), prod)
-	DOCKER_AUTH_PRODUCTION += $(DOCKER_AUTH_DEV_APPEND)
-	DOCKER_DCLAPI_PRODUCTION += $(DOCKER_DCLAPI_DEV_APPEND)
-	DOCKER_ENDPOINT_PRODUCTION += $(DOCKER_ENDPOINT_DEV_APPEND)
-	DOCKER_EPXCLOUD_PRODUCTION += $(DOCKER_ENDPOINT_DEV_APPEND)
-	DOCKER_HAPI_PRODUCTION += $(DOCKER_HAPI_DEV_APPEND)
-	DOCKER_HUB_PRODUCTION += $(DOCKER_HUB_DEV_APPEND)
-	DOCKER_HUBDB_PRODUCTION += $(DOCKER_HUBDB_DEV_APPEND)
-	DOCKER_QI_PRODUCTION += $(DOCKER_QI_DEV_APPEND)
-	DOCKER_VIZ_PRODUCTION += $(DOCKER_VIZ_DEV_APPEND)
+	DOCKER_AUTH_PROD += $(DOCKER_AUTH_JOIN)
+	DOCKER_DCLAPI_PROD += $(DOCKER_DCLAPI_JOIN)
+	DOCKER_ENDPOINT_PROD += $(DOCKER_ENDPOINT_JOIN)
+	DOCKER_EPXCLOUD_PROD += $(DOCKER_ENDPOINT_JOIN)
+	DOCKER_HAPI_PROD += $(DOCKER_HAPI_JOIN)
+	DOCKER_HUB_PROD += $(DOCKER_HUB_JOIN)
+	DOCKER_HUBDB_PROD += $(DOCKER_HUBDB_JOIN)
+	DOCKER_QI_PROD += $(DOCKER_QI_JOIN)
+	DOCKER_VIZ_PROD += $(DOCKER_VIZ_JOIN)
 endif
-
-
-# Use branch defaults where overrides are not provided
-#
-BRANCH_AUTH ?= $(BRANCH_DEFAULT)
-BRANCH_DCLAPI ?= $(BRANCH_DEFAULT)
-BRANCH_ENDPOINT ?= $(BRANCH_DEFAULT)
-BRANCH_EPXCLOUD ?= $(BRANCH_DEFAULT)
-BRANCH_HAPI ?= $(BRANCH_DEFAULT)
-BRANCH_HUB ?= $(BRANCH_DEFAULT)
-BRANCH_HUBDB ?= $(BRANCH_DEFAULT)
-BRANCH_QI ?= $(BRANCH_DEFAULT)
-BRANCH_VIZ ?= $(BRANCH_DEFAULT)
diff --git a/config.env b/config.env
@@ -9,26 +9,9 @@
 BUILD_MODE=prod
 
 
-# Release
-#
-RELEASE_VERSION=0.1.1
-
-
 # Hub external IP/Address (10.0.2.2 for Vagrant/VirtualBox)
 #
-URL_HUB=hub.pdc.io
-
-
-# Notification addresses
-#
-EMAIL_ERRORS=errors@pdc.io
-
-
-# ownCloud backup details
-#
-OWNCLOUD_ID=hub.pdc.io
-OWNCLOUD_PW=
-OWNCLOUD_URL=
+URL_HUB=10.0.2.2
 
 
 # GitHub branch overrides
@@ -37,15 +20,22 @@ OWNCLOUD_URL=
 #
 # (Note: do not leave blank values!)
 #
-#BRANCH_AUTH=master
-#BRANCH_DCLAPI=master
-#BRANCH_ENDPOINT=master
-#BRANCH_EP=master
-#BRANCH_HAPI=master
-#BRANCH_HUB=master
-#BRANCH_HUBDB=master
-#BRANCH_QI=master
-#BRANCH_VIZ=master
+BRANCH_AUTH=0.1.2
+BRANCH_DCLAPI=0.1.1
+BRANCH_ENDPOINT=0.1.2
+BRANCH_EPXCLOUD=0.1.1
+BRANCH_HAPI=0.1.2
+BRANCH_HUB=0.1.1
+BRANCH_HUBDB=0.1.2
+BRANCH_QI=0.1.1
+BRANCH_VIZ=0.1.2
+
+
+# ownCloud backup details
+#
+OWNCLOUD_ID=hub.pdc.io
+OWNCLOUD_PW=<password>
+OWNCLOUD_URL=<https://...>
 
 
 # DACS
@@ -60,6 +50,11 @@ DACS_JURISDICTION=TEST
 PATH_HOST=/pdc/data
 
 
+# Notification addresses
+#
+EMAIL_ERRORS=errors@pdc.io
+
+
 # Node.js
 #
 NODE_TLS_REJECT_UNAUTHORIZED=0
@@ -118,46 +113,47 @@ URL_DCLAPI=http://dclapi:3007
 
 # Host data folders
 #
-PATH_HUB_AUTHKEYS=${PATH_HOST}/hub/etc/ssh
-PATH_HUB_AUTOSSH=${PATH_HOST}/hub/home/autossh/DOTssh
+PATH_HUB_AUTHKEYS=${PATH_HOST}/hub/etc/ssh/
+PATH_HUB_AUTOSSH=${PATH_HOST}/hub/home/autossh/DOTssh/
 PATH_EPX_AUTOSSH=${PATH_HOST}/epx/root/DOTssh/
-PATH_CERT=${PATH_HOST}/cert
-PATH_DACS=${PATH_HOST}/dacs
-PATH_MONGO=${PATH_HOST}/mongo
-PATH_DRUGREF=${PATH_HOST}/drugref
+PATH_CERT=${PATH_HOST}/cert/
+PATH_DACS=${PATH_HOST}/dacs/
+PATH_MONGO_DB=${PATH_HOST}/mongo/db/
+PATH_MONGO_DUMP=${PATH_HOST}/mongo/dump/
+PATH_DRUGREF=${PATH_HOST}/drugref/
 
 
 # DACS
 #
-DACS_KEYFILE=${DACS_STOREDIR}/federations/pdc.dev/federation_keyfile
-DACS_ROLEFILE=${DACS_STOREDIR}/federations/pdc.dev/roles
+DACS_KEYFILE=/etc/dacs/federations/pdc.dev/federation_keyfile
+DACS_ROLEFILE=/etc/dacs/federations/pdc.dev/roles
 
 
 # Containers
 #
-DOCKER_AUTH_PRODUCTION=-v ${PATH_DACS}:${DACS_STOREDIR}/:rw
-DOCKER_AUTH_DEV_APPEND=-p ${PORT_AUTH_M}:${PORT_AUTH_M} -p ${PORT_AUTH_C}:${PORT_AUTH_C}
+DOCKER_AUTH_PROD=-v ${PATH_DACS}:${DACS_STOREDIR}/:rw
+DOCKER_AUTH_SUPPLEMENT=-p ${PORT_AUTH_M}:${PORT_AUTH_M} -p ${PORT_AUTH_C}:${PORT_AUTH_C}
 #
-DOCKER_DCLAPI_PRODUCTION=-v ${PATH_DRUGREF}:/app/drugref/
-DOCKER_DCLAPI_DEV_APPEND=-p ${PORT_DACS}:${PORT_DACS}
+DOCKER_DCLAPI_PROD=-v ${PATH_DRUGREF}:/app/drugref/
+DOCKER_DCLAPI_JOIN=-p ${PORT_DACS}:${PORT_DACS}
 #
-DOCKER_ENDPOINT_PRODUCTION=-v $(PATH_EPX_AUTOSSH):/root/.ssh/:rw
-DOCKER_ENDPOINT_DEV_APPEND=
+DOCKER_ENDPOINT_PROD=-v $(PATH_EPX_AUTOSSH):/root/.ssh/:rw
+DOCKER_ENDPOINT_JOIN=
 #
-DOCKER_EPXCLOUD_PRODUCTION=-v $(PATH_EPX_AUTOSSH):/root/.ssh/:ro
-DOCKER_EPXCLOUD_DEV_APPEND=
+DOCKER_EPXCLOUD_PROD=-v $(PATH_EPX_AUTOSSH):/root/.ssh/:ro
+DOCKER_EPXCLOUD_JOIN=
 #
-DOCKER_HAPI_PRODUCTION=--link auth:auth --link hubdb:hubdb --link dclapi:dclapi
-DOCKER_HAPI_DEV_APPEND=-p ${PORT_HAPI}:${PORT_HAPI}
+DOCKER_HAPI_PROD=--link auth:auth --link hubdb:hubdb --link dclapi:dclapi
+DOCKER_HAPI_JOIN=-p ${PORT_HAPI}:${PORT_HAPI}
 #
-DOCKER_HUB_PRODUCTION=--link hubdb:hubdb -v ${PATH_HUB_AUTOSSH}:/home/autossh/.ssh/:rw -v ${PATH_HUB_AUTHKEYS}:/etc/ssh/:rw -p ${PORT_AUTOSSH}:22 -p ${PORT_HUB_WEB}:3002
-DOCKER_HUB_DEV_APPEND=
+DOCKER_HUB_PROD=--link hubdb:hubdb -v ${PATH_HUB_AUTOSSH}:/home/autossh/.ssh/:rw -v ${PATH_HUB_AUTHKEYS}:/etc/ssh/:rw -p ${PORT_AUTOSSH}:22 -p ${PORT_HUB_WEB}:3002
+DOCKER_HUB_JOIN=
 #
-DOCKER_HUBDB_PRODUCTION=-v ${PATH_MONGO}:/data/:rw
-DOCKER_HUBDB_DEV_APPEND=-p ${PORT_MONGO}:27017
+DOCKER_HUBDB_PROD=-v ${PATH_MONGO_DB}:/data/db/:rw -v ${PATH_MONGO_DUMP}:/data/dump/:rw
+DOCKER_HUBDB_JOIN=-p ${PORT_MONGO}:27017
 #
-DOCKER_QI_PRODUCTION=--link hubdb:hubdb
-DOCKER_QI_DEV_APPEND=
+DOCKER_QI_PROD=--link hubdb:hubdb
+DOCKER_QI_JOIN=
 #
-DOCKER_VIZ_PRODUCTION=--link auth:auth --link hapi:hapi -p 80:${PORT_VIZ} -p 443:${PORT_VIZ} -v ${PATH_CERT}:/app/cert/:ro
-DOCKER_VIZ_DEV_APPEND=-p ${PORT_VIZ}:${PORT_VIZ}
+DOCKER_VIZ_PROD=--link auth:auth --link hapi:hapi -p 443:${PORT_VIZ} -v ${PATH_CERT}:/app/cert/:ro
+DOCKER_VIZ_JOIN=-p ${PORT_VIZ}:${PORT_VIZ}
diff --git a/viz_add.sh b/viz_add.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+#
+#
+set -e -o nounset
+
+
+# Expected input
+#
+# $0 this script
+# $1 Endpoint #
+# $2 Doctor ID
+
+
+# Check parameters
+#
+if([ $# -lt 2 ] || [ $# -gt 3 ])
+then
+        echo ""
+        echo "Unexpected number of parameters."
+        echo ""
+        echo "Usage: viz_add.sh [endpointNumber] [doctorID] [more soon!]"
+        echo ""
+        exit
+fi
+
+
+# Set variables from parameters
+#
+export EP_NUM=$(printf "%04d" ${1})
+export EP_NAME=pdc-${EP_NUM} 
+export DOCTOR=${2}
+
+
+# Add Endpoint to the HubDB
+#
+#sudo docker exec hubdb /app/endpoint_add.sh $1 | grep WriteResult
+
+
+# Get ClinicID (Endpoint's MongoDB ObjectID) and provide it to Auth
+#
+sudo docker exec -ti auth /sbin/setuser app /app/dacs_add.sh \
+        ${DOCTOR} $(sudo docker exec hubdb /app/endpoint_getClinicID.sh ${EP_NUM}) \
+        ${EP_NAME} admin TEST sample
