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@mtholder
mtholder committed Apr 13, 2020
1 parent 2c0776a commit 7e40aaa
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68 changes: 34 additions & 34 deletions deploy/push.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ done

# Used by oauth
if [ "x$OPENTREE_PUBLIC_DOMAIN" = x ]; then
echo "Defaulting OPENTREE_PUBLIC_DOMAIN to $OPENTREE_HOST"
echo "Defaulting OPENTREE_PUBLIC_DOMAIN to $OPENTREE_HOST" || exit 1
OPENTREE_PUBLIC_DOMAIN=$OPENTREE_HOST
fi
# WEBAPP_BASE_URL is only needed for defaulting other things
Expand Down Expand Up @@ -144,7 +144,7 @@ ASSH="ssh -i ${ADMIN_IDENTITY}"
# For unprivileged actions to server
OT_USER=$OPENTREE_USER

echo "host=$OPENTREE_HOST, admin=$OPENTREE_ADMIN, pem=$OPENTREE_IDENTITY, controller=$CONTROLLER"
echo "host=$OPENTREE_HOST, admin=$OPENTREE_ADMIN, pem=$OPENTREE_IDENTITY, controller=$CONTROLLER" || exit 1

restart_apache=no

Expand Down Expand Up @@ -204,7 +204,7 @@ EOF
err "Unrecognized command, or component not in OPENTREE_COMPONENTS: $command"
fi
# Default if not a recognized command: treat as component name
docomponent $command
docomponent $command || exit 1
esac
}

Expand All @@ -214,32 +214,32 @@ function docomponent {
component=$1
case $component in
opentree)
push_webapps
push_webapps || exit 1
restart_apache=yes
;;
phylesystem-api | api)
# 'api' option is for backward compatibility
push_phylesystem_api
push_phylesystem_api || exit 1
restart_apache=yes
;;
oti)
push_neo4j oti
push_neo4j oti || exit 1
;;
treemachine)
push_neo4j treemachine
push_neo4j treemachine || exit 1
# restart apache to clear the RAM cache (stale results)
restart_apache=yes
;;
taxomachine)
push_neo4j taxomachine
push_neo4j taxomachine || exit 1
# restart apache to clear the RAM cache (stale results)
restart_apache=yes
;;
smasher)
push_smasher
push_smasher || exit 1
;;
otcetera)
push_otcetera
push_otcetera || exit 1
;;
*)
echo "Unrecognized component: $component"
Expand Down Expand Up @@ -294,19 +294,19 @@ function push_neo4j_db {
err "Usage: $0 -c {configfile} push-db {tarball} {application}"
fi
HEREBALL=downloads/$APP.db.tgz
time rsync -vax -e "${SSH}" $TARBALL "$OT_USER@$OPENTREE_HOST":$HEREBALL
install_neo4j_db $HEREBALL $APP
time rsync -vax -e "${SSH}" $TARBALL "$OT_USER@$OPENTREE_HOST":$HEREBALL || exit 1
install_neo4j_db $HEREBALL $APP || exit 1
}

function install_neo4j_db {
HEREBALL=$1
APP=$2
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-db.sh $HEREBALL $APP $CONTROLLER
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-db.sh $HEREBALL $APP $CONTROLLER || exit 1
}

function index_doc_store {
if [ $DRYRUN = "yes" ]; then echo "[index_doc_store]"; return; fi
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/index-doc-store.sh $OPENTREE_API_BASE_URL $CONTROLLER
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/index-doc-store.sh $OPENTREE_API_BASE_URL $CONTROLLER || exit 1
}

# Component installation
Expand All @@ -327,19 +327,19 @@ function push_webapps {
# N.B. This includes the final domain name, since we'll need different keys for dev.opentreeoflife.org, www.opentreeoflife.org, etc.
keyfile=${OPENTREE_SECRETS}/treeview-GITHUB_CLIENT_SECRET-$OPENTREE_PUBLIC_DOMAIN
if [ -r $keyfile ]; then
rsync -pr -e "${SSH}" $keyfile "$OT_USER@$OPENTREE_HOST":repo/opentree/webapp/private/GITHUB_CLIENT_SECRET
rsync -pr -e "${SSH}" $keyfile "$OT_USER@$OPENTREE_HOST":repo/opentree/webapp/private/GITHUB_CLIENT_SECRET || exit 1
else
echo "** Cannot find GITHUB_CLIENT_SECRET file $keyfile"
echo "** Cannot find GITHUB_CLIENT_SECRET file $keyfile" || exit 1
fi
keyfile=${OPENTREE_SECRETS}/curation-GITHUB_CLIENT_SECRET-$OPENTREE_PUBLIC_DOMAIN
if [ -r $keyfile ]; then
rsync -pr -e "${SSH}" $keyfile "$OT_USER@$OPENTREE_HOST":repo/opentree/curator/private/GITHUB_CLIENT_SECRET
rsync -pr -e "${SSH}" $keyfile "$OT_USER@$OPENTREE_HOST":repo/opentree/curator/private/GITHUB_CLIENT_SECRET || exit 1
else
echo "** Cannot find GITHUB_CLIENT_SECRET file $keyfile"
echo "** Cannot find GITHUB_CLIENT_SECRET file $keyfile" || exit 1
fi

# we’re using the bot for “anonymous” comments in the synth-tree explorer
push_bot_identity
push_bot_identity || exit 1
}

# Utility for all the webapps.
Expand All @@ -349,10 +349,10 @@ function push_bot_identity {
# place an OAuth token for GitHub API by bot user 'opentreeapi'
tokenfile=${OPENTREE_SECRETS}/OPENTREEAPI_OAUTH_TOKEN
if [ -r $tokenfile ]; then
rsync -pr -e "${SSH}" $tokenfile "$OT_USER@$OPENTREE_HOST":.ssh/OPENTREEAPI_OAUTH_TOKEN
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/OPENTREEAPI_OAUTH_TOKEN
rsync -pr -e "${SSH}" $tokenfile "$OT_USER@$OPENTREE_HOST":.ssh/OPENTREEAPI_OAUTH_TOKEN || exit 1
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/OPENTREEAPI_OAUTH_TOKEN || exit 1
else
echo "** Cannot find OPENTREEAPI_OAUTH_TOKEN file $tokenfile"
echo "** Cannot find OPENTREEAPI_OAUTH_TOKEN file $tokenfile" || exit 1
fi
}

Expand All @@ -368,47 +368,47 @@ function push_phylesystem_api {
[ "x$OTI_BASE_URL" != "x" ] || err "OTI_BASE_URL not configured"
[ "x$OTINDEX_BASE_URL" != "x" ] || err "OTINDEX_BASE_URL not configured"

push_bot_identity
push_bot_identity || exit 1

# Place private key for GitHub access
if [ "x$OPENTREE_GH_IDENTITY" = "x" ]; then
echo "Warning: OPENTREE_GH_IDENTITY not specified"
echo "Warning: OPENTREE_GH_IDENTITY not specified" || exit 1
elif [ ! -r $OPENTREE_GH_IDENTITY ]; then
echo "Warning: $OPENTREE_GH_IDENTITY not found"
echo "Warning: $OPENTREE_GH_IDENTITY not found" || exit 1
else
rsync -p -e "${SSH}" "$OPENTREE_GH_IDENTITY" "$OT_USER@$OPENTREE_HOST":.ssh/opentree
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/opentree
rsync -p -e "${SSH}" "$OPENTREE_GH_IDENTITY" "$OT_USER@$OPENTREE_HOST":.ssh/opentree || exit 1
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/opentree || exit 1
fi

# Try to place an OAuth token for GitHub API by bot user 'opentreeapi'
tokenfile=${OPENTREE_SECRETS}/OPENTREEAPI_OAUTH_TOKEN
if [ -r $tokenfile ]; then
rsync -p -e "${SSH}" $tokenfile "$OT_USER@$OPENTREE_HOST":.ssh/OPENTREEAPI_OAUTH_TOKEN
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/OPENTREEAPI_OAUTH_TOKEN
rsync -p -e "${SSH}" $tokenfile "$OT_USER@$OPENTREE_HOST":.ssh/OPENTREEAPI_OAUTH_TOKEN || exit 1
${SSH} "$OT_USER@$OPENTREE_HOST" chmod 600 .ssh/OPENTREEAPI_OAUTH_TOKEN || exit 1
else
echo "****************************\n OAuth token file (${tokenfile}) not found!\n Falling back to any existing token on the server, OR a prompt for manual creation of webhooks.\n****************************"
fi

${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-api.sh "$OPENTREE_HOST" \
$OPENTREE_DOCSTORE $COLLECTIONS_REPO $AMENDMENTS_REPO $FAVORITES_REPO $CONTROLLER $OTI_BASE_URL $OPENTREE_API_BASE_URL $COLLECTIONS_API_BASE_URL $AMENDMENTS_API_BASE_URL $FAVORITES_API_BASE_URL $OPENTREE_DEFAULT_APPLICATION $OTINDEX_BASE_URL
$OPENTREE_DOCSTORE $COLLECTIONS_REPO $AMENDMENTS_REPO $FAVORITES_REPO $CONTROLLER $OTI_BASE_URL $OPENTREE_API_BASE_URL $COLLECTIONS_API_BASE_URL $AMENDMENTS_API_BASE_URL $FAVORITES_API_BASE_URL $OPENTREE_DEFAULT_APPLICATION $OTINDEX_BASE_URL || exit 1
}

function push_neo4j {
APP=$1
if [ $DRYRUN = "yes" ]; then echo "[neo4j app: $APP]"; return; fi
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-neo4j-app.sh $CONTROLLER $APP $FORCE_COMPILE
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-neo4j-app.sh $CONTROLLER $APP $FORCE_COMPILE || exit 1
}

function push_smasher {
if [ $DRYRUN = "yes" ]; then echo "[push_smasher]"; return; fi
echo push_smasher: ${OPENTREE_WEBAPI_BASE_URL}
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-smasher.sh ${CONTROLLER} ${OPENTREE_WEBAPI_BASE_URL}
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-smasher.sh ${CONTROLLER} ${OPENTREE_WEBAPI_BASE_URL} || exit 1
}

function push_otcetera {
if [ $DRYRUN = "yes" ]; then echo "[push_otcetera]"; return; fi
echo push_otcetera:
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-otcetera.sh ${CONTROLLER} ${OPENTREE_WEBAPI_BASE_URL}
${SSH} "$OT_USER@$OPENTREE_HOST" ./setup/install-otcetera.sh ${CONTROLLER} ${OPENTREE_WEBAPI_BASE_URL} || exit 1
}

process_arguments $*
process_arguments $* || exit 1
16 changes: 8 additions & 8 deletions deploy/setup/functions.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -22,13 +22,13 @@ fi
# ---------- Setup TWO VIRTUALENVs ----------
# Set up python env
if [ ! -d venv ]; then
virtualenv venv
virtualenv venv || exit 1
fi
source venv/bin/activate
source venv/bin/activate || exit 1


if [ ! -d venvp3 ]; then
python3 -m venv venvp3
python3 -m venv venvp3 || exit 1
fi


Expand All @@ -39,19 +39,19 @@ function log() {
echo "CONTROLLER shell variable is not set !?"
exit 1
fi
mkdir -p log
(echo `date` $CONTROLLER $OPENTREE_TAG " $*") >>log/messages
mkdir -p log || exit 1
(echo `date` $CONTROLLER $OPENTREE_TAG " $*") >>log/messages || exit
}

# ---------- WORKSPACES ----------

# Temporary locations for things downloaded from web. Can delete this
# after server is up and running.

mkdir -p downloads
mkdir -p downloads || exit 1

REPOS_DIR=repo
mkdir -p $REPOS_DIR
mkdir -p $REPOS_DIR || exit 1

# ---------- SHELL FUNCTIONS ----------

Expand All @@ -62,7 +62,7 @@ function opentree_branch {
#echo Set branch for $1 to be ${OPENTREE_BRANCHES[$1]}
}

. setup/CONFIG
. setup/CONFIG || exit

# Refresh a git repo

Expand Down
28 changes: 14 additions & 14 deletions deploy/setup/install-api.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -22,18 +22,18 @@ FAVORITES_API_BASE_URL=${11}
OPENTREE_DEFAULT_APPLICATION=${12}
OTINDEX_BASE_URL=${13}

. setup/functions.sh
. setup/functions.sh || exit 1

setup/install-common.sh $OPENTREE_DEFAULT_APPLICATION $CONTROLLER
setup/install-common.sh $OPENTREE_DEFAULT_APPLICATION $CONTROLLER || exit 1

echo "Installing API"
echo "Installing API" || exit 1


#Pre installs for normal phylestem-api venv
venv/bin/pip install vine==1.3
venv/bin/pip install vine==1.3 || exit 1
#Force early version of vine in venv to deal with python2 python3 issues
venv/bin/pip install kombu==4.1.0
venv/bin/pip install celery==4.1.0
venv/bin/pip install kombu==4.1.0 || exit 1
venv/bin/pip install celery==4.1.0 || exit 1



Expand All @@ -50,9 +50,9 @@ if ! test -f redis/bin/redis-server ; then
tar xfz "${REDIS_WITH_VERSION}.tar.gz")
fi
if ! test -d redis/work ; then
mkdir -p redis/work
mkdir -p redis/work || exit 1
(cd downloads/${REDIS_WITH_VERSION} ; \
make && make PREFIX="${HOME}/redis" install)
make && make PREFIX="${HOME}/redis" install) || exit 1
fi
fi

Expand All @@ -67,10 +67,10 @@ APPROOT=repo/$WEBAPP
OTHOME=$PWD

# This is required to make "git pull" work correctly
git config --global user.name "OpenTree API"
git config --global user.email api@opentreeoflife.org
git config --global user.name "OpenTree API" || exit 1
git config --global user.email api@opentreeoflife.org || exit 1

echo "...fetching $WEBAPP repo..."
echo "...fetching $WEBAPP repo..." || exit 1
git_refresh OpenTreeOfLife $WEBAPP || true

if [ "${PEYOTL_LOG_FILE_PATH:0:1}" != "/" ]; then
Expand All @@ -80,12 +80,12 @@ fi
git_refresh OpenTreeOfLife peyotl || true
py_package_setup_install peyotl || true

(cd $APPROOT; pip install -r requirements.txt)
(cd $APPROOT/ot-celery; pip install -r requirements.txt ; python setup.py develop)
(cd $APPROOT; pip install -r requirements.txt) || exit 1
(cd $APPROOT/ot-celery; pip install -r requirements.txt ; python setup.py develop) || exit 1

(cd web2py/applications; \
rm -rf ./phylesystem ; \
ln -sf ../../repo/$WEBAPP ./phylesystem)
ln -sf ../../repo/$WEBAPP ./phylesystem) || exit 1

# ---------- DOC STORE ----------

Expand Down
32 changes: 16 additions & 16 deletions deploy/setup/install-common.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -10,35 +10,35 @@ fi
OPENTREE_DEFAULT_APPLICATION=$1
CONTROLLER=$2

. setup/functions.sh
. setup/functions.sh || exit 1

echo "Installing web2py common"
echo "Installing web2py common" || exit 1

bash setup/install-web2py.sh
bash setup/install-web2py.sh || exit 1

echo "...fetching opentree repo..."
echo "...fetching opentree repo..." || exit 1
git_refresh OpenTreeOfLife opentree || true

# requirements list ?

(cd web2py/applications; \
ln -sf ../../repo/$WEBAPP/common ./)
ln -sf ../../repo/$WEBAPP/common ./) || exit 1

# Apply our patches to vanilla web2py 2.8.2
# See comments in each patched file for details.
cp -p repo/opentree/oauth20_account.py web2py/gluon/contrib/login_methods/
cp -p repo/opentree/rewrite.py web2py/gluon/
cp -p repo/opentree/custom_import.py web2py/gluon/
cp -p repo/opentree/oauth20_account.py web2py/gluon/contrib/login_methods/ || exit 1
cp -p repo/opentree/rewrite.py web2py/gluon/ || exit 1
cp -p repo/opentree/custom_import.py web2py/gluon/ || exit 1

TMP=/tmp/tmp.tmp
echo default_application should be "$OPENTREE_DEFAULT_APPLICATION"
echo default_application should be "$OPENTREE_DEFAULT_APPLICATION" || exit 1
sed -e "s+default_application='.*'+default_application='$OPENTREE_DEFAULT_APPLICATION'+" \
repo/opentree/SITE.routes.py >$TMP
cp $TMP web2py/routes.py
rm $TMP
grep default_ web2py/routes.py
repo/opentree/SITE.routes.py >$TMP || exit 1
cp $TMP web2py/routes.py || exit 1
rm $TMP || exit 1
grep default_ web2py/routes.py || exit 1

# Kludge in case OPENTREE_DEFAULT_APPLICATION is set to 'welcome' or (more likely) 'phylesystem'
cp -p repo/opentree/webapp/static/robots.txt web2py/applications/welcome/static/
mkdir -p web2py/applications/phylesystem/static
cp -p repo/opentree/webapp/static/robots.txt web2py/applications/phylesystem/static/
cp -p repo/opentree/webapp/static/robots.txt web2py/applications/welcome/static/ || exit 1
mkdir -p web2py/applications/phylesystem/static || exit 1
cp -p repo/opentree/webapp/static/robots.txt web2py/applications/phylesystem/static/ || exit 1

3 comments on commit 7e40aaa

@jimallman
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I gather this is a hygienic measure, yes? And that we don't trust set -e to do the right thing? Just want to make sure I understand these changes.

@snacktavish
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Yep! basically it was silently failing early on, abut only resulting in errors later, so we wanted to be clear as soon as something goes wrong. I don't know about alternatives like set -e as an option though.

@jimallman
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Gotcha. While set -e looks like a much simpler catch-all solution for errors, the discussion linked above convinces me that it can also lead to confusing behavior. So || exit 1 (as used here) looks like the better way.

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