update mysql_fixes.sh

chown recursively

add sudo for chmod on send_migration_file

update jira config sample

go_log_rotate.sh go_mk_atlassian_supportzip.sh

new sql for missing groups

update jira config sample

updates to upgrade process

add check for cmdline action in go_upgrade_app

updates for general docker runs

.gitignore

@@ -13,4 +13,6 @@ output
 *.sample
 *.csv
 *.tsv
+
+# log files
 *.log

Dockerfile

@@ -11,7 +11,7 @@ COPY requirements.txt ./
 COPY jira_cleanup jira_cleanup/
 COPY wiki_cleanup wiki_cleanup/
 RUN python -m pip install -r /srv/requirements.txt
-RUN ln -s /home/.netrc /root/.netrc
-RUN ln -s /home/.atlassian-tools-config.ini /root/.atlassian-tools-config.ini
+#RUN ln -s /home/.netrc /root/.netrc
+#RUN ln -s /home/.atlassian-tools-config.ini /root/.atlassian-tools-config.ini
 
 CMD ["bash"]

bin/fix_app_config.sh

@@ -67,6 +67,7 @@ fi
 # See also:
 # https://confluence.atlassian.com/confkb/how-to-adjust-the-session-timeout-for-confluence-126910597.html
 # https://confluence.atlassian.com/jirakb/change-the-default-session-timeout-to-avoid-user-logout-in-jira-server-604209887.html
+# TODO - Is this needed anymore after change to SSO via CiLogon?
 WEB_XML=''
 if [[ $APP_NAME == 'jira' ]] ; then
   WEB_XML="$APP_INSTALL_DIR"/atlassian-jira/WEB-INF/web.xml

bin/fix_vgs.sh

@@ -6,8 +6,9 @@ YES=0
 NO=1
 VERBOSE=$YES
 DEBUG=$YES
+APP_NAME=jira
 
-VGS=( vg_pgsql vg_backups vg_confluence )
+VGS=( vg_pgsql vg_backups vg_$APP_NAME )
 
 ECHO=
 [[ $DEBUG -eq $YES ]] && ECHO=echo

bin/go_log_rotate.sh

@@ -0,0 +1,88 @@
+#!/usr/bin/bash
+
+# See also: https://jira.ncsa.illinois.edu/browse/SVC-24653
+
+
+###
+# Global Variables
+###
+YES=0
+NO=1
+LOG_DIR=/var/log
+ARCHIVE_DIR=/backups/old_logs
+MAX_ARCHIVE_AGE=30 #days
+DATE=$(date +%Y%m%d_%H%M%S)
+VERBOSE=$YES
+DEBUG=$NO
+#DEBUG=$YES
+
+
+###
+# Functions
+###
+
+die() {
+  echo "ERROR: ${*}" 1>&2
+  exit 99
+}
+
+
+force_rotate_logs() {
+  echo "${FUNCNAME[0]} ..."
+  local _vopts _dopts
+  [[ $VERBOSE -eq $YES ]] && {
+    set -x
+    _vopts+=( '-v' )
+  }
+  [[ $DEBUG -eq $YES ]] && _dopts+=( '-d' )
+  /usr/sbin/logrotate -f ${_vopts[@]} ${_dopts[@]} /etc/logrotate.conf
+  echo "${FUNCNAME[0]} OK"
+}
+
+
+archive_logs() {
+  echo "${FUNCNAME[0]} ..."
+  local _vopts
+  [[ $VERBOSE -eq $YES ]] && {
+    set -x
+    _vopts+=( '-v' )
+  }
+  [[ $DEBUG -eq $YES ]] && _dopts+=( '-d' )
+  local _tgz="${ARCHIVE_DIR}"/"${DATE}".tgz
+  local _tmp=$( mktemp -p "${ARCHIVE_DIR}" )
+  >"${_tmp}" find "${LOG_DIR}" -type f \
+    -name '*.[0-9]' \
+    -o -name '*.gz' \
+    -o -regextype egrep -regex '.*-[0-9]{8}'
+  if [[ $DEBUG -eq $YES ]] ; then
+    echo "DEBUG - files that would have been archived:"
+    cat "${_tmp}"
+  elif [[ -s "${_tmp}" ]] ; then
+    tar -zcf "${_tgz}" ${_vopts[@]} -T "${_tmp}" --remove-files
+  fi
+  rm "${_tmp}"
+  echo "${FUNCNAME[0]} OK"
+}
+
+
+clean_old_logs() {
+  echo "${FUNCNAME[0]} ..."
+  [[ $VERBOSE -eq $YES ]] && set -x
+  local _action='-delete'
+  [[ $DEBUG -eq $YES ]] && _action='-print'
+  find "${ARCHIVE_DIR}" -type f -mtime +${MAX_ARCHIVE_AGE} $_action
+  echo "${FUNCNAME[0]} OK"
+}
+
+
+###
+# MAIN
+###
+
+[[ $VERBOSE -eq $YES ]] && set -x
+
+force_rotate_logs
+
+archive_logs
+
+clean_old_logs

bin/go_mk_atlassian_supportzip.sh

@@ -0,0 +1,89 @@
+#!/usr/bin/bash
+
+# See also: https://jira.ncsa.illinois.edu/browse/SVCPLAN-5454
+
+
+###
+# Global Variables
+###
+YES=0
+NO=1
+CHOME=/srv/confluence/home
+CAPP=/srv/confluence/app
+DATE=$(date +%Y%m%d_%H%M%S)
+SUPPORTZIP=/root/${DATE}.support.zip
+CPUZIP=/root/${DATE}.cpu_usage.zip
+VERBOSE=$NO
+
+
+###
+# Functions
+###
+
+die() {
+  echo "ERROR: ${*}" 1>&2
+  exit 99
+}
+
+
+get_confluence_pid() {
+  [[ $VERBOSE -eq $YES ]] && set -x
+  local _pid=$( systemctl show -p MainPID --value confluence )
+  local _cmd=$( ps -p $_pid -o comm= )
+  local _usr=$( ps -p $_pid -o user= )
+  [[ "$_cmd" != "java" ]] && die "Unknown command '$_cmd' for pid '$_pid' ... expected 'java'"
+  [[ "$_usr" != "confluence" ]] && die "Unknown user '$_usr' for pid '$_pid' ... expected 'confluence'"
+  echo "$_pid"
+}
+
+
+dump_cpu_threads() {
+  # Get Thread dumps and CPU usage information
+  [[ $VERBOSE -eq $YES ]] && set -x
+  echo "Dump CPU Threads (this will take a few minutes) ..."
+  local _tempdir=$( mktemp -d )
+  pushd "$_tempdir"
+  for i in $(seq 6); do
+    top -b -H -p $CONF_PID -n 1 > conf_cpu_usage.$(date +%s).txt
+    kill -3 $CONF_PID
+    sleep 10
+  done
+  echo "... Dump CPU Threads OK"
+
+  echo "Make CPU Threads zip ..."
+  zip -q $CPUZIP conf_cpu_usage.*.txt
+  echo "... Make CPU Threads zip OK"
+
+  popd
+  rm -rf "$_tempdir"
+}
+
+
+mk_support_zip() {
+  [[ $VERBOSE -eq $YES ]] && set -x
+  echo "Make support zip (this will also take a minute) ..."
+  zip -q $SUPPORTZIP \
+    ${CHOME}/confluence.cfg.xml \
+    ${CHOME}/logs/* \
+    ${CAPP}/logs/* \
+    ${CAPP}/conf/server.xml \
+    ${CAPP}/bin/setenv.sh
+  echo "... Make support zip OK"
+}
+
+###
+# MAIN
+###
+
+[[ $VERBOSE -eq $YES ]] && set -x
+
+CONF_PID=$( get_confluence_pid )
+
+dump_cpu_threads
+
+mk_support_zip
+
+echo
+echo "Atlassian support files:"
+ls -l /root/${DATE}*.zip
+echo

bin/go_upgrade_app.sh

@@ -22,13 +22,18 @@ ABLEMENT=''
 ###
 
 
-run_installer() {
+assert_app_installed() {
   [[ -d "${APP_INSTALL_DIR}"/bin ]] || die "app install dir '$APP_INSTALL_DIR/bin' not found"
+}
 
+assert_installer_exists() {
   [[ -z "$INSTALLER" ]] && INSTALLER=$( get_installer )
 
   [[ -f "$INSTALLER" ]] || die "Installer file not found; '$INSTALLER' "
+}
+
 
+run_installer() {
   /usr/bin/chmod +x "${INSTALLER}"
   "${INSTALLER}"
 }
@@ -40,11 +45,14 @@ print_usage() {
 ${_prg}
   Upgrade the Atlassian app specified in config file '$CFG'
 SYNOPSYS
-  ${_prg} [OPTIONS] <--start|--finish> [installer_file.bin]
-OPTIONS
-  -h --help Print this help and exit
+  ${_prg} [OPTIONS] <--start | --finish>
+
+USAGE
   --start  Start an upgrade (stop services, install upgrade, etc.)
   --finish Finish an upgrade (re-enable services, re-enable notifications, etc.)
+
+OPTIONS
+  -h --help Print this help and exit
 ENDHERE
 }
 
@@ -73,10 +81,12 @@ while [[ $# -gt 0 ]] && [[ $ENDWHILE -eq 0 ]] ; do
   shift
 done
 
-INSTALLER="$1"
-
 if [[ $ACTION == 'start' ]] ; then
 
+  INSTALLER=$( get_installer )
+  assert_app_installed
+  assert_installer_exists
+
   "${BIN}"/backup_config_files.sh
 
   "${BIN}"/set_services.sh $ABLEMENT
@@ -99,6 +109,10 @@ elif [[ $ACTION == 'finish' ]] ; then
 
   "${BIN}"/set_services.sh $ABLEMENT
 
+  "${BIN}"/set_web_access.sh $ABLEMENT
+
+else
+  die "Missing one of '--start' | '--finish'"
 fi
 
 echo "Elapsed time: '$SECONDS' seconds."

bin/restore_config_files.sh

@@ -16,7 +16,7 @@ FILES=(
 for f in "${FILES[@]}" ; do
   tgt_dir=$( dirname "$f" )
   reference=$( find "$tgt_dir" -type f -print -quit )
-  cp "${BACKUP_DIR}/${f}" "${f}"
+  cp "${BACKUP_DIR}/${f}" "${f}"        #BACKUP_DIR defined in config.sh
   chmod --reference="$reference" "$f"
   chown --reference="$reference" "$f"
 done

conf/config.sh-confluence-sample

@@ -5,6 +5,9 @@ NO=1
 #
 #
 
+VERBOSE=$YES
+DEBUG=$YES
+
 # These must be set or scripts will refuse to run
 # If no changes needed, set them the same
 IPADDR_OLD=
@@ -15,23 +18,13 @@ HOSTNAME_NEW=$HOSTNAME_OLD
 
 # path to jira / confluence home & install dirs
 APP_NAME=confluence
-APP_HOME_DIR=/srv/confluence/home
-APP_INSTALL_DIR=/srv/confluence/app
-
-# Jira/Confluence DB names
-# If no changes needed, set them the same
-# (if both are the same, no updates will be attempted)
-# TODO - can be removed once all databases are local
-DB_NAME_OLD=
-DB_NAME_NEW=$DB_NAME_OLD
+APP_HOME_DIR=/srv/$APP_NAME/home
+APP_INSTALL_DIR=/srv/$APP_NAME/app
 
 # arrays of service names
-SYSTEM_SERVICES_TO_STOP=( puppet telegraf $APP_NAME )
+SYSTEM_SERVICES_TO_STOP=( puppet telegraf xcatpostinit1 $APP_NAME )
 PUPPET_SERVICES_TO_STOP=( telegraf )
 
-VERBOSE=$YES
-DEBUG=$YES
-
 #
 #
 ### END OF USER CONFIGURABLE SECTION

conf/config.sh-jira-sample

@@ -5,6 +5,9 @@ NO=1
 #
 #
 
+VERBOSE=$YES
+DEBUG=$YES
+
 # These must be set or scripts will refuse to run
 # If no changes needed, set them the same
 IPADDR_OLD=
@@ -15,24 +18,21 @@ HOSTNAME_NEW=$HOSTNAME_OLD
 
 # path to jira / confluence home & install dirs
 APP_NAME=jira
-APP_HOME_DIR=/usr/services/jirahome
-APP_INSTALL_DIR=/usr/services/jira-standalone
+APP_HOME_DIR=/srv/${APP_NAME}/home
+APP_INSTALL_DIR=/srv/${APP_NAME}/app
 
 # Jira/Confluence DB names
 # If no changes needed, set them the same
 # (if both are the same, no updates will be attempted)
 # TODO - can be removed once all databases are local
-DB_NAME_OLD=
+DB_NAME_OLD=confluencedb
 DB_NAME_NEW=$DB_NAME_OLD
 
 # arrays of service names
 # TODO - remove CRASHPLAN when no longer appropriate
-SYSTEM_SERVICES_TO_STOP=( puppet telegraf crashplan $APP_NAME )
+SYSTEM_SERVICES_TO_STOP=( puppet telegraf crashplan xcatpostinit1 $APP_NAME )
 PUPPET_SERVICES_TO_STOP=( telegraf )
 
-VERBOSE=$YES
-DEBUG=$YES
-
 #
 #
 ### END OF USER CONFIGURABLE SECTION