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bootstrap_data.sh
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#!/bin/bash
###########################################################
### Init infrastructure
###########################################################
#echo "Starting third-party containers"
#cd config/testbed
#docker-compose -p thirdparty -f compose/third-party.yml up -d pushpin beanstalkd redis mongodb mysql sftp
docker-compose -p testbed -f config/testbed/data.yml up -d --force-recreate sftp irods4
docker-compose -p testbed -f config/testbed/compute.yml up -d --force-recreate ssh slurm htcondor
printf "Waiting for irods4 container to come online..."
sleep 30
until [[ -n "$(docker-compose -p testbed -f config/testbed/data.yml logs irods4 | grep "NOTICE: Agent process")" ]];
do
printf '.'
sleep 2
done
###########################################################
### Init cli tenant
###########################################################
# Add default tenant `agave.dev`
auth-switch -t agave.dev -u testuser -d http://api.example.com -S
###########################################################
### Register systems
###########################################################
SYSTEMS_FOLDER=agave-systems/systems-core/src/test/resources/systems
############### STORAGE - SFTP ######################
systems-addupdate -d -F $SYSTEMS_FOLDER/storage/storage.example.com.json
# set as the default storage system
systems-setdefault -d storage.example.com
# set as the default storage system
if [[ "$(systems-list -D -S --filter=id -v -l 1)" == "storage.example.com" ]]; then
echo "Verified storage.example.com as the default storage system"
else
echo "Failed to set storage.example.com as the default storage system"
fi
############### STORAGE - IRODS ######################
systems-addupdate -d -F $SYSTEMS_FOLDER/storage/irods4.example.com.json
############### EXECUTION - CLI ######################
systems-addupdate -d -F $SYSTEMS_FOLDER/execution/execute.example.com.json
# switch to admin for publishing ops
auth-switch -u dooley -S
# set as the default execution system
systems-publish -d execute.example.com
# return to standard user
auth-switch -u testuser -S
############### EXECUTION - HPC ######################
systems-addupdate -d -F $SYSTEMS_FOLDER/execution/slurm.example.com.json
############### EXECUTION - CONDOR ######################
systems-addupdate -d -F $SYSTEMS_FOLDER/execution/condor.example.com.json
###########################################################
### Move data
###########################################################
#################### Upload data to IRODS ########################
if [[ ! -e 'science-api-samples' ]]; then
git clone https://bitbucket.org/agaveapi/science-api-samples.git
fi
# remove most of the data to speed things up.
if [[ -e 'science-api-samples' ]]; then
find science-api-samples/* -type d | xargs rm -rf
fi
files-mkdir -d -N testuser -S storage.example.com .
files-mkdir -d -N testuser -S irods4-password.example.com .
files-upload -d -v -F science-api-samples -S irods4-password.example.com testuser
#################### Create persistent notifications on the upload folder ########################
# We need the uuid of the uploaded folder, so we'll make a request and pull it out of the metadata link in the hypermedia response
UPLOAD_FOLDER_UUID=$(files-list -d -v -l 1 --filter=_links.metadata -S irods4-password.example.com testuser/science-api-samples | jq -r '.[0]._links.metadata.href' | sed 's/^.*?q=//g' | urldecode | jq -r '.associationIds')
# Create persistent notifications on the UUID of the upload folder we just retrieved.
# these notifications will always fail and get persisted in the failed attempt queue
notifications-addupdate -d -U 'http://httpbin.org/status/500' -E "*" -P -I 0 -R NONE -D 0 -L 0 -S -A $UPLOAD_FOLDER_UUID
#################### Transfer data between system ########################
# First, make a destination folder to keep things clean for later if/when we publish the system
files-mkdir -d -N transferred_data -S storage.example.com testuser
# create a webhook URL just in case we want to watch while things run
IMPORT_REQUESTBIN=$(requestbin-create)
echo "Webhooks for the file transfer will post to $IMPORT_REQUESTBIN"
# transfer the data from the irods system to the compute system
files-import -d -U 'agave://irods4-password.example.com/testuser/science-api-samples' -W "$IMPORT_REQUESTBIN?path=${PATH}&event=${EVENT}" -S storage.example.com testuser/transferred_data
###########################################################
### Register Apps
###########################################################
# Local path to the JSON app descriptions
export APPS_FOLDER=agave-apps/apps-core/src/test/resources/software
# create parent folder for all app assets
files-mkdir -d -N agave/apps -S storage.example.com testuser
################# fork-1.0.0 #################
# upload the app assets and register the app
files-upload -d -F $APPS_FOLDER/fork-1.0.0 -S storage.example.com testuser/agave/apps
apps-addupdate -d -F $APPS_FOLDER/fork-1.0.0/app.json
# create some history for the app
apps-addupdate -d -F $APPS_FOLDER/fork-1.0.0/app.json fork-1.0.0
apps-disable -d fork-1.0.0
apps-enable -d fork-1.0.0
# # share the app with someone
apps-pems-update -d -p READ_EXECUTE -u testshareuser fork-1.0.0
apps-pems-list -d fork-1.0.0
# ################# fork-clone-1.0.0 #################
# # create a copy of this app with a new id
apps-clone -d -n fork-clone -s storage.example.com -e slurm.example.com -v fork-1.0.0
CLONE_APP=$(apps-list -d -v fork-clone-1.0.0)
# update it for a history record
echo "${CLONE_APP}" | apps-addupdate -d -F - fork-clone-1.0.0
# enable and disable
apps-disable -d fork-clone-1.0.0
apps-enable -d fork-clone-1.0.0
################# head-hpc-1.0.0 #################
# upload the app assets and register the app
files-upload -d -F $APPS_FOLDER/head-hpc-1.0.0 -S storage.example.com testuser/agave/apps
apps-addupdate -d -F $APPS_FOLDER/head-hpc-1.0.0/app.json
################# wc-condor-1.0.0 #################
# upload the app assets and register the app
files-upload -d -F $APPS_FOLDER/wc-condor-1.0.0 -S storage.example.com testuser/agave/apps
apps-addupdate -d -F $APPS_FOLDER/wc-condor-1.0.0/app.json
###########################################################
### Publishing Apps and Systems
###########################################################
# switch to admin for publishing ops
auth-switch -u dooley -S
################# publishing systems #################
# create the public app folder
files-mkdir -d -N public -S storage.example.com
systems-publish -d storage.example.com
systems-setdefault -G -d storage.example.com
systems-publish -d execute.example.com
systems-setdefault -G -d storage.example.com
################# publishing fork-1.0.0 #################
# The resulting id will be fork-1.0.0u1
apps-publish -d fork-1.0.0
# The resulting id will be fork-1.0.0u2
apps-publish -d fork-1.0.0
################# publishing fork-clone-1.0.0 #################
# The resulting id will be fork-1.0.0u3.
apps-publish -d -e execute.example.com -n fork fork-clone-1.0.0
# The resulting id will be fork-1.0.0u4
apps-publish -d fork-1.0.0
################# disable older public apps #################
apps-disable -d fork-1.0.0u1
apps-disable -d fork-1.0.0u2
apps-disable -d fork-1.0.0u3
# return to standard user
auth-switch -u testuser -S
###########################################################
### Create metadata
###########################################################
################# system comments #################
export STORAGE_SYSTEM_UUID=$(systems-list -d -v --filter=uuid storage.example.com | jq -r '.uuid')
export EXECUTION_SYSTEM_UUID=$(systems-list -d -v --filter=uuid execute.example.com | jq -r '.uuid')
echo '{"name": "comment", "value":{"owner":"testuser","body": "This might be useful."}, "associatedIds": ["'$EXECUTION_SYSTEM_UUID'","'$STORAGE_SYSTEM_UUID'"]}' | metadata-addupdate -d -F -
################# files comments #################
echo '{"name": "comment", "value":{"owner":"testuser","body": "Created as part of file upload and transfer tests."}, "associatedIds": ["'$UPLOAD_FOLDER_UUID'"]}' | metadata-addupdate -d -F -
################# files comments #################
APP_FORK_1_0_0_UUID=$(apps-list -d -v --filter=uuid fork-1.0.0 | jq -r '.uuid')
APP_FORK_1_0_0_u3UUID=$(apps-list -d -v --filter=uuid fork-1.0.0u3 | jq -r '.uuid')
echo '{"name": "comment", "value":{"owner":"testuser","body": "Accidentally overwritten by the cloned fork app. Disregard this for real usage."}}, "associatedIds": ["'$APP_FORK_1_0_0_UUID'"]}' | metadata-addupdate -d -F -
METADATA_PROJECT_ID=$(echo '{"name": "project", "value":{"owner":"testuser","description": "This is my first project."}}' | metadata-addupdate -d -v -F - | jq -r '.id')
echo '{"name": "project_vote", "value":{"voter":"ryan","is_in_favor": true}, "associatedIds": ["'$METADATA_PROJECT_ID'"]}' | metadata-addupdate -d -v -F -
echo '{"name": "project_vote", "value":{"voter":"rion","is_in_favor": true}, "associatedIds": ["'$METADATA_PROJECT_ID'"]}' | metadata-addupdate -d -v -F -
echo '{"name": "project_vote", "value":{"voter":"rian","is_in_favor": false}, "associatedIds": ["'$METADATA_PROJECT_ID'"]}' | metadata-addupdate -d -v -F -
echo '{"name": "project_vote", "value":{"voter":"ryon","is_in_favor": true}, "associatedIds": ["'$METADATA_PROJECT_ID'"]}' | metadata-addupdate -d -v -F -
###########################################################
### Run Jobs
###########################################################
# create a webhook URL just in case we want to watch while jobs run
export JOBS_REQUESTBIN=$(requestbin-create)
echo "Webhooks for the job submissions will post to $JOBS_REQUESTBIN"
################# generate job request templates #################
# generate the job submission templates from the app descriptions and default values
export JOB_TEMPLATE_FORK_1_0_0=$(jobs-template -d -A -v -C fork-1.0.0)
export JOB_TEMPLATE_FORK_1_0_0_u_4=$(jobs-template -d -A -v -C fork-1.0.0u4)
export JOB_TEMPLATE_HEAD_HPC_1_0_0=$(jobs-template -d -v -A -C head-hpc-1.0.0 | jq --arg rqbin "$JOBS_REQUESTBIN?appId=\${APP_ID}&job_id=\${JOB_ID}&event=\${EVENT}" '.notifications |= [{"url": $rqbin, "event":"*", "persistent":true, "policy":{"retryStrategy":"IMMEDIATE","retryLimit":3,"retryRate":5,"retryDelay":0,"saveOnFailure":true}}]')
export JOB_TEMPLATE_WC_CONDOR_1_0_0=$(jobs-template -d -v -A -C wc-condor-1.0.0 | jq --arg rqbin "$JOBS_REQUESTBIN?appId=\${APP_ID}&job_id=\${JOB_ID}&event=\${EVENT}" '.notifications |= [{"url": $rqbin, "event":"*", "persistent":true, "policy":{"retryStrategy":"IMMEDIATE","retryLimit":3,"retryRate":5,"retryDelay":0,"saveOnFailure":true}}]')
################# run unarchived jobs #################
# vanilla no archive private app job
export JOB_ID_FORK_1_0_0=$(echo $JOB_TEMPLATE_FORK_1_0_0 | jq '.archive |= false' | jobs-submit -d -v -F - | jq -r '.id')
# vanilla no archive public app job
JOB_ID_FORK_1_0_0_u_4=$(echo $JOB_TEMPLATE_FORK_1_0_0_u_4 | jq '.archive |= false' | jobs-submit -d -v -F - | jq -r '.id')
# throw in a few more
for i in {1..9}; do
jobs-resubmit -d $JOB_ID_FORK_1_0_0
jobs-resubmit -d $JOB_ID_FORK_1_0_0_u_4
done
################# run unarchived jobs #################
# archive app to IRODS with default path
JOB_ID_FORK_1_0_0=$(echo "$JOB_TEMPLATE_FORK_1_0_0" | jq '.archiveSystem |= "irods4-password.example.com"' | jobs-submit -d -v -F - | jq -r '.id')
# archive app to IRODS with custom path
JOB_ID_FORK_1_0_0=$(echo "$JOB_TEMPLATE_FORK_1_0_0" | jq '.archiveSystem |= "irods4-password.example.com" | .archivePath |= "testuser/customarchivepath"' | jobs-submit -d -v -F - | jq -r '.id')
################# run a batch of jobs across all apps and systems #################
shuffle_jobs() {
local i tmp size max rand
# $RANDOM % (i+1) is biased because of the limited range of $RANDOM
# Compensate by using a range which is a multiple of the array size.
size=${#jobs_ids[*]}
max=$(( 32768 / size * size ))
for ((i=size-1; i>0; i--)); do
while (( (rand=$RANDOM) >= max )); do :; done
rand=$(( rand % (i+1) ))
tmp=${jobs_ids[i]} jobs_ids[i]=${jobs_ids[rand]} jobs_ids[rand]=$tmp
done
}
# vanilla archived private app job
JOB_ID_FORK_1_0_0_ARCHIVE=$(echo "$JOB_TEMPLATE_FORK_1_0_0" | jobs-submit -d -v -F - | jq -r '.id')
JOB_ID_FORK_1_0_0_u_4_ARCHIVE=$(echo "$JOB_TEMPLATE_FORK_1_0_0_u_4" | jobs-submit -d -v -F - | jq -r '.id')
JOB_ID_HEAD_HPC_1_0_0_ARCHIVE=$(echo "$JOB_TEMPLATE_HEAD_HPC_1_0_0" | jobs-submit -d -v -F - | jq -r '.id')
JOB_ID_WC_CONDOR_1_0_0_ARCHIVE=$(echo "$JOB_TEMPLATE_WC_CONDOR_1_0_0" | jobs-submit -d -v -F - | jq -r '.id')
jobs_ids=()
for i in {1..10}; do
jobs_ids+=($JOB_ID_FORK_1_0_0_ARCHIVE)
jobs_ids+=($JOB_ID_FORK_1_0_0_u_4_ARCHIVE)
jobs_ids+=($JOB_ID_HEAD_HPC_1_0_0_ARCHIVE)
jobs_ids+=($JOB_ID_WC_CONDOR_1_0_0_ARCHIVE)
done
shuffle_jobs
for i in "${jobs_ids[@]}"; do
jobs-resubmit -d $i
done