Upgrading CHT Core from 3.6.0 to 3.9.0 using medic-OS

waok2 · June 25, 2021, 5:18am

Trying to upgrade to CHT 3.9.0 from 3.6.0, using this guide (cht-infrastructure/docs/3.9_CHT_Upgrade.md at main · medic/cht-infrastructure · GitHub). After going through the process(attached link), when i check the admin panel I can see an upgrade has been initiated but instead of 3.9.0 i can see 3.2.1 (see attached screenshot). Also it has already taken 18 hours with no success. What could be the issue.
Also does the number of docs also affect how long the upgrade will take?

nyika · June 25, 2021, 5:50am

Hi @waok2 ,
Kindly share what the tail of horticulturalist logs at /srv/storage/horticulturalist/log/horticulturalist.log say. Also please make sure you installed new packages in step 5 of the guide you quoted.

waok2 · June 25, 2021, 6:20am

Thanks,
yeah i went through step five, below are the logs requested

2021-06-25T06:03:27.091Z horti:debug _design/:staged:medic-client 2021-06-25T06:03:27.091Z horti:debug _design/:staged:medic-sms 2021-06-25T06:03:37.409Z horti:debug View indexer progress
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waok2 · June 25, 2021, 6:20am

I also found this error on the logs

2021-06-25T02:24:33.849Z horti:debug View indexer progress
2021-06-25T02:24:33.849Z horti:debug _design/:staged:medic-client [0%]
2021-06-25T02:24:33.849Z horti:debug _design/:staged:medic-sms [9%]
2021-06-25T02:24:33.849Z horti:debug _design/:staged:medic [0%]
FATAL
{ FetchError: invalid json response body at http://localhost:5984/medic/_design/:staged:medic/_view/contacts_by_depth?limit=1 reason: Unexpected token < in JSON at position 0
at /srv/software/horticulturalist/node_modules/node-fetch/lib/index.js:241:32
at
at process._tickCallback (internal/process/next_tick.js:188:7)
message: ‘invalid json response body at http://localhost:5984/medic/_design/:staged:medic/_view/contacts_by_depth?limit=1 reason: Unexpected token < in JSON at position 0’,
type: ‘invalid-json’ }
[2021-06-25 02:24:47] Starting Horticulturalist 0.12.7 daemon in Medic OS mode
2021-06-25T02:24:47.352Z horti:debug Running pre-boot checks
2021-06-25T02:24:47.505Z horti:debug Pre-boot checks OK
[2021-06-25 02:24:47] Doing install to medic:medic:3.2.1
2021-06-25T02:24:47.551Z horti:debug Bootstrapping upgrade doc
2021-06-25T02:24:48.017Z horti:stage Horticulturalist deployment of ‘medic:medic:3.2.1’ initialising
[2021-06-25 02:24:48] Deploying new build: medic:medic:3.2.1
2021-06-25T02:24:48.362Z horti:stage Pre-deploy cleanup
2021-06-25T02:24:48.672Z horti:debug Clear existing staged DBs
2021-06-25T02:24:48.778Z horti:debug Deleting staged ddocs: [“_design/:staged:medic”,“_design/:staged:medic-admin”,“_design/:staged:medic-client”,“_design/:staged:medic-conflicts”,“_design/:staged:medic-scripts”,“_design/:staged:medic-sms”]
2021-06-25T02:24:49.184Z horti:debug Starting compact and view cleanup
2021-06-25T05:36:47.586Z horti:stage Downloading and staging install
2021-06-25T05:36:47.797Z horti:debug Downloading medic:medic:3.2.1, this may take some time…
2021-06-25T05:36:52.708Z horti:debug Got medic:medic:3.2.1, staging
2021-06-25T05:37:00.671Z horti:debug Staged as _design/:staged:medic
2021-06-25T05:37:00.672Z horti:stage Extracting ddocs
2021-06-25T05:37:00.802Z horti:debug Storing staged: [“_design/:staged:medic-admin”,“_design/:staged:medic-client”,“_design/:staged:medic-conflicts”,“_design/:staged:medic-scripts”,“_design/:staged:medic-sms”,“_design/:staged:medic”]
2021-06-25T05:37:15.123Z horti:stage Warming views
2021-06-25T05:37:15.205Z horti:debug Got 6 staged ddocs
[2021-06-25 05:37:15] Beginning view warming
2021-06-25T05:37:25.281Z horti:debug View indexer progress
2021-06-25T05:37:25.281Z horti:debug _design/:staged:medic [0%]
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nyika · June 25, 2021, 6:39am

So the instance is currently warming views. And it indeed installed 3.2.1 which is strange. I have a hunch that you probably skipped step 4 or you selected the wrong version to upgrade to. Please share the contents of /srv/scripts/horticulturalist/postrun/horticulturalist . For now, You have to wait till the view warming is done. Ensure that you follow the steps and upgrade through the web view.

waok2 · June 25, 2021, 6:43am

thanks, (for step 4 i did as instructed (this is after updating the docker-compose file and building the container a new )
this is the contents of /srv/scripts/horticulturalist/postrun/horticulturalist

#!/bin/sh

source ‘/boot/include/utility’
source ‘/boot/include/logger’

bootstrap()
{
local self=“realpath "$0"”
local base=“dirname -- "$self"”

source “$base/…/env” &&
merge_environment /srv || return 255

If bootstrapping is already done, do nothing

if [ -f “$BOOTSTRAP_COMPLETE_FILE” ]; then
info “Horticulturalist has already bootstrapped”
return 0
fi

If bootstrapping is already disabled, do nothing

if [ “$DOCKER_HORTI_BOOTSTRAP_DISABLED” ]; then
warn “Horticulturalist bootstraping is disabled”
return 0
fi

wait_for_file “$COUCH_PASSWD_FILE” &&
local passwd=“cat "$COUCH_PASSWD_FILE"” &&

source “$base/…/…/medic-core/env” &&
merge_environment /srv ‘path-only’ &&

info ‘Horticulturalist is now bootstrapping’ &&

export COUCH_NODE_NAME=‘couchdb@127.0.0.1’ &&
export COUCH_URL=“http://${PACKAGE_NAME}:${passwd}@localhost:5984/medic” &&

local script=“src/index.js” &&
local run_cmd=“‘which node’ ‘$script’ --medic-os --install=3.2.1 --no-daemon” &&

if [ “$DOCKER_HORTI_BOOTSTRAP” ]; then
run_cmd=“$run_cmd=‘$DOCKER_HORTI_BOOTSTRAP’”
info “Horticulturalist is bootstrapping to ‘$DOCKER_HORTI_BOOTSTRAP’”
fi

local command_line=“cd ‘$PACKAGE_SOFTWARE’ && exec $run_cmd” &&

su -c “$command_line” “$HORTICULTURALIST_USER”
>> “$PACKAGE_STORAGE/logs/horticulturalist.log” 2>&1 &&

touch “$BOOTSTRAP_COMPLETE_FILE” &&
info ‘Horticulturalist bootstrapping complete’
}

bootstrap “$@”
exit “$?”

nyika · June 25, 2021, 7:01am

Indeed you did not run the steps as seen. The script has version 3.2.1 . Once view warming is done. Please run the steps listed and ensure that you have a new version of this script. Then do an upgrade. Step 4 output may not allow you to run step 5, you will need to open a new terminal to execute it. If you follow the steps diligently that file should look like the one below.

#!/bin/sh

source '/boot/include/utility'
source '/boot/include/logger'

bootstrap()
{
  local self="`realpath "$0"`"
  local base="`dirname -- "$self"`"

  source "$base/../env" &&
  merge_environment /srv || return 255

  # If bootstrapping is already done, do nothing
  if [ -f "$BOOTSTRAP_COMPLETE_FILE" ]; then
    info "Horticulturalist has already bootstrapped"
    return 0
  fi

  # If bootstrapping is already disabled, do nothing
  if [ "$DOCKER_HORTI_BOOTSTRAP_DISABLED" ]; then
    warn "Horticulturalist bootstraping is disabled"
    return 0
  fi

  wait_for_file "$COUCH_PASSWD_FILE" &&
  local passwd="`cat "$COUCH_PASSWD_FILE"`" &&
  \
  source "$base/../../medic-core/env" &&
  merge_environment /srv 'path-only' &&
  \
  info 'Horticulturalist is now bootstrapping' &&
  \
  export COUCH_NODE_NAME='couchdb@127.0.0.1' &&
  export COUCH_URL="http://${PACKAGE_NAME}:${passwd}@$DOCKER_NETWORK_NAME:5984/medic" &&
  \

  local script="src/index.js" &&
  local run_cmd="'`which node`' '$script' --medic-os --complete-install --no-daemon" &&

  \
  if [ "$DOCKER_HORTI_BOOTSTRAP" ]; then
    run_cmd="$run_cmd='$DOCKER_HORTI_BOOTSTRAP'"
    info "Horticulturalist is bootstrapping to '$DOCKER_HORTI_BOOTSTRAP'"
  fi
  \
  local command_line="cd '$PACKAGE_SOFTWARE' && exec $run_cmd" &&
  \
  su -c "$command_line" "$HORTICULTURALIST_USER" \
    >> "$PACKAGE_STORAGE/logs/horticulturalist.log" 2>&1 &&
  \
  touch "$BOOTSTRAP_COMPLETE_FILE" &&
  info 'Horticulturalist bootstrapping complete'
}

bootstrap "$@"
exit "$?"

waok2 · June 25, 2021, 7:09am

this is actually the second attempt(staging instance) going through the steps, I will do it once more with this in mind,
Thank you

waok2 · June 25, 2021, 9:02am

Hi, i started the process a new from a snapshot, went through the steps one by one confirming ,
from horticulturalist/logs i get this error

FATAL
Error: Cannot locate app db
at dbs.app.info.catch (/srv/software/horticulturalist/node_modules/horticulturalist/src/checks.js:4:62)
at
at process._tickCallback (internal/process/next_tick.js:188:7)
[2021-06-25 08:43:08] Starting Horticulturalist 0.13.1 daemon in Medic OS mode
2021-06-25T08:43:08.299Z horti:debug Running pre-boot checks
FATAL
Error: Cannot locate app db
at dbs.app.info.catch (/srv/software/horticulturalist/node_modules/horticulturalist/src/checks.js:4:62)
at
at process._tickCallback (internal/process/next_tick.js:188:7)
[2021-06-25 08:43:13] Starting Horticulturalist 0.13.1 daemon in Medic OS mode
2021-06-25T08:43:13.784Z horti:debug Running pre-boot checks
FATAL
Error: Cannot locate app db
at dbs.app.info.catch (/srv/software/horticulturalist/node_modules/horticulturalist/src/checks.js:4:62)
at
at process._tickCallback (internal/process/next_tick.js:188:7)
[2021-06-25 08:43:19] Starting Horticulturalist 0.13.1 daemon in Medic OS mode
2021-06-25T08:43:19.228Z horti:debug Running pre-boot checks

Session terminated, terminating shell… …terminated.

nyika · June 25, 2021, 9:05am

Couchdb is down. Please ensure that CouchDB is running. You can do that by running /boot/svc-restart medic-core couchdb inside the container

waok2 · June 25, 2021, 9:12am

did that , though no change;

waok2 · June 25, 2021, 9:22am

found out the problem is the connection to the database, still looking on how i can solve this(this could be from the medic-os docker compose file) (logs are UTC/GMT +0)

ap.afterConnect [as oncomplete] (net.js:1186:14)',
[2021-06-25 08:39:38] [message]: ‘connect ECONNREFUSED 127.0.0.1:5984’,
[2021-06-25 08:39:38] code: ‘ECONNREFUSED’,
[2021-06-25 08:39:38] errno: ‘ECONNREFUSED’,
[2021-06-25 08:39:38] syscall: ‘connect’,
[2021-06-25 08:39:38] address: ‘127.0.0.1’,
[2021-06-25 08:39:38] port: 5984 }
[2021-06-25 08:39:40] Node Environment Options: ‘–max_old_space_size=20000’
[2021-06-25 08:39:40] Node Version: 8.11.4 in production mode
[2021-06-25 08:39:40] 2021-06-25 08:39:40 ERROR: UNCAUGHT EXCEPTION!
[2021-06-25 08:39:40] 2021-06-25 08:39:40 ERROR: Error: { Error: connect ECONNREFUSED 127.0.0.1:5984
[2021-06-25 08:39:40] at Object._errnoException (util.js:992:11)
[2021-06-25 08:39:40] at _exceptionWithHostPort (util.js:1014:20)
[2021-06-25 08:39:40] at TCPConnectWrap.afterConnect [as oncomplete] (net.js:1186:14)
[2021-06-25 08:39:40] [stack]: ‘Error: connect ECONNREFUSED 127.0.0.1:5984\n at Object._errnoException (util.js:992:11)\n at _exceptionWithHostPort (util.js:1014:20)\n at TCPConnectWrap.afterConnect [as oncomplete] (net.js:1186:14)’,
[2021-06-25 08:39:40] [message]: ‘connect ECONNREFUSED 127.0.0.1:5984’,
[2021-06-25 08:39:40] code: ‘ECONNREFUSED’,
[2021-06-25 08:39:40] errno: ‘ECONNREFUSED’,
[2021-06-25 08:39:40] syscall: ‘connect’,
[2021-06-25 08:39:40] address: ‘127.0.0.1’,
[2021-06-25 08:39:40] port: 5984 }
[2021-06-25 08:39:42] Node Environment Options: ‘–max_old_space_size=20000’
[2021-06-25 08:39:42] Node Version: 8.11.4 in production mode
[2021-06-25 08:39:42] 2021-06-25 08:39:42 ERROR: UNCAUGHT EXCEPTION!
[2021-06-25 08:39:42] 2021-06-25 08:39:42 ERROR: Error: { Error: connect ECONNREFUSED 127.0.0.1:5984
[2021-06-25 08:39:42] at Object._errnoException (util.js:992:11)
[2021-06-25 08:39:42] at _exceptionWithHostPort (util.js:1014:20)
[2021-06-25 08:39:42] at TCPConnectWrap.afterConnect [as oncomplete] (net.js:1186:14)
[2021-06-25 08:39:42] [stack]: ‘Error: connect ECONNREFUSED 127.0.0.1:5984\n at Object._errnoException (util.js:992:11)\n at _exceptionWithHostPort (util.js:1014:20)\n at TCPConnectWrap.afterConnect [as oncomplete] (net.js:1186:14)’,
[2021-06-25 08:39:42] [message]: ‘connect ECONNREFUSED 127.0.0.1:5984’,
[2021-06-25 08:39:42] code: ‘ECONNREFUSED’,
[2021-06-25 08:39:42] errno: ‘ECONNREFUSED’,
[2021-06-25 08:39:42] syscall: ‘connect’,
[2021-06-25 08:39:42] address: ‘127.0.0.1’,
[2021-06-25 08:39:42] port: 5984 }
root@medic-os:/srv/storage/medic-api/logs#

nyika · June 25, 2021, 9:25am

Please ensure that the haproxy container is running through docker ps Alternatively restart all processes by running docker-compose down then docker-compose up -d

waok2 · June 25, 2021, 10:24am

none seems to solve this

nyika · June 25, 2021, 4:35pm

Not sure what this means, unfortunately. Are you running this in the container?

waok2 · June 26, 2021, 6:54am

yeah, it is a container, (using medic-os compose file)

nyika · June 28, 2021, 7:50am

Let me try to detail the steps you need to run.
First, you need to ensure that you have updated your docker-compose file with the latest 3.9 image medicmobile/medic-os:cht-3.9.0-rc.2

Then follow these steps:

Log into the medic-os container

docker exec -it medic-os /bin/bash

Stop all services

/boot/svc-stop medic-core nginx openssh && /boot/svc-stop medic-sentinel && /boot/svc-stop medic-couch2pg && /boot/svc-stop medic-rdbms && /boot/svc-stop horticulturalist && /boot/svc-stop medic-api && /boot/svc-stop medic-core couchdb && rm -rf /srv/storage/horticulturalist/.horticulturalist.lock

Download a new version of horticulculatist. This is the most crucial step.

/boot/package-remove horticulturalist && /boot/package-install /mnt/startup/packages/horticulturalist-v01260-x64.vpkg

Stop Horticulturalist ( the previous step will auto-start it) . You need to open a new terminal to your container as detailed in step 1

/boot/svc-stop horticulturalist

Update the script to allow updates through the API.

sed -i 's/--install=3.9.0/--complete-install/g' /srv/scripts/horticulturalist/postrun/horticulturalist

Update the medic-core scripts

/boot/package-remove medic-core && /boot/package-install /mnt/startup/packages/medic-core-v30000-x64.vpkg

Start all services


/boot/svc-start medic-core couchdb && /boot/svc-start medic-api && /boot/svc-start medic-sentinel && /boot/svc-start horticulturalist

waok2 · July 27, 2021, 12:50pm

Got unblocked on this, i was using the wrong docker image for haproxy , please use (https://raw.githubusercontent.com/medic/cht-core/master/docker-compose.yml).