Introduce a scheduler job to delete old files that may accumulate over time #510
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@@ -59,6 +59,15 @@ component directory to the ``BIRDHOUSE_EXTRA_CONF_DIRS`` variable in your local | |
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| * component location: ``optional-components/scheduler-job-deploy_raven_testdata`` | ||
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| * Automatically remove old files | ||
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| * Removes files generated by other components that may accumulate over time and are not manage automatically by those components. | ||
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| * Currently supports removing WPS output files from the ``finch``, ``raven``, and ``hummingbird`` components as well as log files | ||
| from the ``thredds`` component. | ||
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| * component location: ``optional-components/scheduler-job-clean_old_files`` | ||
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Member
There was a problem hiding this comment. Should be in the optional-components' README. Should also include mentions of the specific per-service configuration variables, just to provide insights that there are options to enable/disable them individually, and further options to control their cron/cleanup/fs-meta strategies.
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There was a problem hiding this comment. All of the optional scheduler jobs are documented here and in env.local.example (for configuration options). If we want to improve the documentation for all these jobs that's fine but we should do so for all, not just one, and maybe in a different PR.
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There was a problem hiding this comment. Since it is an optional component, it should be described in The documentation does not need to be explicit about all combinations of component/variables, but should at least indicate some guidance about configuring available options. Notably cron config with atime/mtime conditions on a per-component basis is not that obvious for users that didn't participate in this PR's discussions. Reading only the For example: (from the perspective of a new user):
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All these questions are covered in the documentation in env.local.example and the README file birdhouse-deploy/birdhouse/env.local.example Lines 209 to 218 in af633e4 birdhouse-deploy/birdhouse/components/README.rst Lines 66 to 67 in af633e4 I can either come back to this PR at a later date when I have time to write more extensive documentation or we can include this now and I'll write more documentation in general for the scheduler jobs as a separate PR. I don't really have a preference so if you'd like to wait to merge this PR until more documentation is in place I'll leave it for now.
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There was a problem hiding this comment. A copy-paste is sufficient with quotes for the code elements. I prefer actual docs because it is easier to navigate and read by users. If I point a user to this env file, they will nope-out immediately.
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Yes this clearly solve the duplicate docs problem but might render the tracking of what config var changed (added, renamed, delete) harder for the simple user. Example with JupyterHub, I had to If we take the simple road of simply referencing the config var doc to the proper This one single file can also be diffed to find out when a new config var has been added, renamed or deleted. But with only the reference to the Both (one single file for easy browsing vs generated docs) have pros and cons. I do not have a strong opinion on either of those approaches.
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There was a problem hiding this comment. Thinking more about this duplicate doc problem, how about
Honesly, when reading docs I can infer a lot but just looking at the example usage. I will actually read the full documentation only when my inference from the example do not work as intended. And I think when updating docs, we tend to update the wording to clarify explanation much more frequently than changing the example. Because when changing the example, we basically change the format of the expected value, that means code change and variable meaning change, which happen much less frequently.
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There was a problem hiding this comment. I don't think we really have super diligent and lengthy documentation in most cases in env files. Most places where there are more details is typically because of specific gotchas that are important to highlight contextually in that place, or that support examples, both of which are more relevant with the variable (or others around involved with it). If we add more verbose documentation or explanations to further guide users, then I think those should be only in the README. The few example/comments should be self-explanatory as much as possible in env files. There can also be "see https://..." comments pointing at README to facilitate navigation/information retrieval. About
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There was a problem hiding this comment. Ok... There are a lot of improvements that can be made to the documentation. I think we all agree on that. However I think that the question of how to organize the README files is separate from how to organize default.env and env.local.example. For the README files, yes we should keep the info from components and optional components in their respective READMEs. And I am happy to start that by putting the documentation relevant to this PR in the optional components. A separate PR(s) will have to be made to update the documentation for the other components. For example, the auto deploy info is still in components even though it is nowadays scheduler job in optional components.
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There was a problem hiding this comment. Agreed. Only focus on the current components edited/added within this PR. |
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| * Automatically backup files | ||
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| * automatically backs up application data, user data, representative data, and logs to a restic repository (default) or a docker volume | ||
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| config.yml |
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| # this file intentionally contains no content and is mounted to the scheduler directory if a clean_old_files job is not enabled. |
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| #!/bin/sh | ||
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| ################################################################ | ||
| # Example call to delete all files in /tmp last modified longer | ||
| # than 20 days ago | ||
| # | ||
| # $ sh clean-old-files.sh 20 mtime /tmp | ||
| ################################################################## | ||
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| AGE="$1" | ||
| MODE="$2" | ||
| LOCATION="$3" | ||
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| ACCEPTABLE_MODES='|mtime|ctime|atime|' | ||
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| if ! echo "$AGE" | grep -q '^[0-9][0-9]*$'; then | ||
| >&2 echo "AGE argument set to '${AGE}'. It must be an unsigned integer" | ||
| exit 1 | ||
| fi | ||
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| if [ "${ACCEPTABLE_MODES#*"|${MODE}|"}" = "${ACCEPTABLE_MODES}" ]; then | ||
| >&2 echo "MODE argument set to '${MODE}'. It must be one of 'mtime', 'ctime', or 'atime'" | ||
| exit 1 | ||
| fi | ||
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| if [ -z "${LOCATION}" ]; then | ||
| >&2 echo "LOCATION argument is blank or unset. It must refer to a path on disk." | ||
| exit 1 | ||
| fi | ||
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| echo "Removing files in ${LOCATION} that have a ${MODE} value greater than ${AGE} days" | ||
| find "${LOCATION}" -type f "-${MODE}" +"${AGE}" -print -delete |
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| - name: clean_old_files_finch | ||
| comment: clean old WPS output files generated by Finch | ||
| schedule: '${FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY}' | ||
| command: 'sh /clean-old-files.sh "${FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}" "${FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}" /wps_outputs/finch' | ||
| dockerargs: >- | ||
| --rm --name scheduler-job-clean_old_files_finch | ||
| --volume ${COMPOSE_DIR}/optional-components/scheduler-job-clean_old_files/clean-old-files.sh:/clean-old-files.sh:ro | ||
| --volume "${COMPOSE_PROJECT_NAME}_wps_outputs:/wps_outputs:rw" | ||
| image: '${SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE}' | ||
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There was a problem hiding this comment. Given it's an unattended cron job, where is this logging to so we can debug if something goes wrong? Can log to
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There was a problem hiding this comment. I actually have a question about that.... Now that we are making more use of the scheduler to run additional jobs, why are we writing additional logs to
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That is fine for regular service container (1 service, 1 container) but here if all the jobs all log to the same scheduler container we can have interleaving log if jobs runtime happen to overlap. Even without overlap, it will make searching for the desired log harder because all the jobs logs to the same place. With each separate job logging to separate file, we avoid the search for the desired job log problem and the possible overlap problem. The more jobs we have, the more likely the problems will happen. So I much prefer each job to its own separate log file. |
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| services: | ||
| scheduler: | ||
| volumes: | ||
| - ./optional-components/scheduler-job-clean_old_files/${__SCHEDULER_JOB_CLEAN_OLD_FILES_FINCH_CONFIG_LOC:-blank.config.yml}:/scheduler-job-configs/clean_old_files_finch.yml:ro} |
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| - name: clean_old_files_hummingbird | ||
| comment: clean old WPS output files generated by Hummingbird | ||
| schedule: '${HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY}' | ||
| command: 'sh /clean-old-files.sh "${HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}" "${HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}" /wps_outputs/hummingbird' | ||
| dockerargs: >- | ||
| --rm --name scheduler-job-clean_old_files_hummingbird | ||
| --volume ${COMPOSE_DIR}/optional-components/scheduler-job-clean_old_files/clean-old-files.sh:/clean-old-files.sh:ro | ||
| --volume "${COMPOSE_PROJECT_NAME}_wps_outputs:/wps_outputs:rw" | ||
| image: '${SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE}' |
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| services: | ||
| scheduler: | ||
| volumes: | ||
| - ./optional-components/scheduler-job-clean_old_files/${__SCHEDULER_JOB_CLEAN_OLD_FILES_HUMMINGBIRD_CONFIG_LOC:-blank.config.yml}:/scheduler-job-configs/clean_old_files_hummingbird.yml:ro} |
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| - name: clean_old_files_raven | ||
| comment: clean old WPS output files generated by Raven | ||
| schedule: '${RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY}' | ||
| command: 'sh /clean-old-files.sh "${RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}" "${RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}" /wps_outputs/raven' | ||
| dockerargs: >- | ||
| --rm --name scheduler-job-clean_old_files_raven | ||
| --volume ${COMPOSE_DIR}/optional-components/scheduler-job-clean_old_files/clean-old-files.sh:/clean-old-files.sh:ro | ||
| --volume "${COMPOSE_PROJECT_NAME}_wps_outputs:/wps_outputs:rw" | ||
| image: '${SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE}' |
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| services: | ||
| scheduler: | ||
| volumes: | ||
| - ./optional-components/scheduler-job-clean_old_files/${__SCHEDULER_JOB_CLEAN_OLD_FILES_RAVEN_CONFIG_LOC:-blank.config.yml}:/scheduler-job-configs/clean_old_files_raven.yml:ro} |
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| - name: clean_old_files_thredds | ||
| comment: clean old log files generated by Thredds | ||
| schedule: '${THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY}' | ||
| command: 'sh /clean-old-files.sh "${THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS}" "${THREDDS_LOGS_DELETE_FILES_TIME_MODE}" /thredds' | ||
| dockerargs: >- | ||
| --rm --name scheduler-job-clean_old_files_thredds | ||
| --volume ${COMPOSE_DIR}/optional-components/scheduler-job-clean_old_files/clean-old-files.sh:/clean-old-files.sh:ro | ||
| --volume "thredds_persistence:/thredds:rw" | ||
| image: '${SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE}' |
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| services: | ||
| scheduler: | ||
| volumes: | ||
| - ./optional-components/scheduler-job-clean_old_files/${__SCHEDULER_JOB_CLEAN_OLD_FILES_THREDDS_CONFIG_LOC:-blank.config.yml}:/scheduler-job-configs/clean_old_files_thredds.yml:ro} |
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| export SCHEDULER_JOB_CLEAN_OLD_FILES_DOCKER=alpine # alpine contains find with -ctime -mtime and -atime options (busybox based containers do not) | ||
| export SCHEDULER_JOB_CLEAN_OLD_FILES_VERSION=3.21 | ||
| export SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE='${SCHEDULER_JOB_CLEAN_OLD_FILES_DOCKER}:${SCHEDULER_JOB_CLEAN_OLD_FILES_VERSION}' | ||
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| export FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS= # unset by default if this job is enabled this must be set to an integer | ||
| export FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE=atime | ||
| export FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY="5 4 * * 0" # weekly on Sunday at 4:05 | ||
| export FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED=false | ||
| export __SCHEDULER_JOB_CLEAN_OLD_FILES_FINCH_CONFIG_LOC='$( [ "${FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && echo "config/finch/config.yml" )' | ||
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| export HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS= # unset by default if this job is enabled this must be set to an integer | ||
| export HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE=atime | ||
| export HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY="10 4 * * 0" # weekly on Sunday at 4:10 | ||
| export HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED=false | ||
| export __SCHEDULER_JOB_CLEAN_OLD_FILES_HUMMINGBIRD_CONFIG_LOC='$( [ "${HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && echo "config/hummingbird/config.yml" )' | ||
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| export RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS= # unset by default if this job is enabled this must be set to an integer | ||
| export RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE=atime | ||
| export RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY="15 4 * * 0" # weekly on Sunday at 4:15 | ||
| export RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED=false | ||
| export __SCHEDULER_JOB_CLEAN_OLD_FILES_RAVEN_CONFIG_LOC='$( [ "${RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && echo "config/raven/config.yml" )' | ||
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| export THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS= # unset by default if this job is enabled this must be set to an integer | ||
| export THREDDS_LOGS_DELETE_FILES_TIME_MODE=mtime | ||
| export THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY="20 4 * * 0" # weekly on Sunday at 4:20 | ||
| export THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED=false | ||
| export __SCHEDULER_JOB_CLEAN_OLD_FILES_THREDDS_CONFIG_LOC='$( [ "${THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && echo "config/thredds/config.yml" )' | ||
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| export DELAYED_EVAL=" | ||
| $DELAYED_EVAL | ||
| SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE | ||
| __SCHEDULER_JOB_CLEAN_OLD_FILES_FINCH_CONFIG_LOC | ||
| __SCHEDULER_JOB_CLEAN_OLD_FILES_HUMMINGBIRD_CONFIG_LOC | ||
| __SCHEDULER_JOB_CLEAN_OLD_FILES_RAVEN_CONFIG_LOC | ||
| __SCHEDULER_JOB_CLEAN_OLD_FILES_THREDDS_CONFIG_LOC | ||
| " | ||
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| OPTIONAL_VARS=" | ||
| $OPTIONAL_VARS | ||
| \$FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS | ||
| \$FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE | ||
| \$FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY | ||
| \$HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS | ||
| \$HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE | ||
| \$HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY | ||
| \$RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS | ||
| \$RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE | ||
| \$RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY | ||
| \$THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS | ||
| \$THREDDS_LOGS_DELETE_FILES_TIME_MODE | ||
| \$THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_FREQUENCY | ||
| " | ||
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| VARS=" | ||
| $VARS | ||
| \$SCHEDULER_JOB_CLEAN_OLD_FILES_IMAGE | ||
| " |
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| if ! echo "${BIRDHOUSE_EXTRA_CONF_DIRS}" | grep -q 'scheduler[[:space:]]*$'; then | ||
| log WARN 'The scheduler-job-clean_old_files component is enabled but the scheduler component is not. This WILL cause problems. Please disable the scheduler-job-clean_old_files component.' | ||
| fi | ||
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| _acceptable_modes='|mtime|ctime|atime|' | ||
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| if [ "${FINCH_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && ! echo "${BIRDHOUSE_EXTRA_CONF_DIRS}" | grep -q 'finch[[:space:]]*$'; then | ||
| echo "$FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS" | grep -q '^[0-9][0-9]*$' || log WARN "FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS variable must be an integer not '${FINCH_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}'. Please set this variable to an integer or disable the finch file cleaning job. This job will not run properly!" | ||
| [ "${_acceptable_modes#*"${FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}"}" = "${_acceptable_modes}" ] && log WARN "FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE variable must be one of 'mtime', 'atime', or 'ctime' not '${FINCH_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}'. Please set this variable to a valid option or disable the finch file cleaning job. This job will not run properly!" | ||
| fi | ||
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Collaborator
There was a problem hiding this comment. Can this be refactored to a function like |
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| if [ "${HUMMINGBIRD_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && ! echo "${BIRDHOUSE_EXTRA_CONF_DIRS}" | grep -q 'hummingbird[[:space:]]*$'; then | ||
| echo "$HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS" | grep -q '^[0-9][0-9]*$' || log WARN "HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS variable must be an integer not '${HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}'. Please set this variable to an integer or disable the hummingbird file cleaning job. This job will not run properly!" | ||
| [ "${_acceptable_modes#*"${HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}"}" = "${_acceptable_modes}" ] && log WARN "HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE variable must be one of 'mtime', 'atime', or 'ctime' not '${HUMMINGBIRD_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}'. Please set this variable to a valid option or disable the hummingbird file cleaning job. This job will not run properly!" | ||
| fi | ||
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| if [ "${RAVEN_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && ! echo "${BIRDHOUSE_EXTRA_CONF_DIRS}" | grep -q 'raven[[:space:]]*$'; then | ||
| echo "$RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS" | grep -q '^[0-9][0-9]*$' || log WARN "RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS variable must be an integer not '${RAVEN_WPS_OUTPUTS_DELETE_FILES_OLDER_THAN_DAYS}'. Please set this variable to an integer or disable the raven file cleaning job. This job will not run properly!" | ||
| [ "${_acceptable_modes#*"${RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}"}" = "${_acceptable_modes}" ] && log WARN "RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE variable must be one of 'mtime', 'atime', or 'ctime' not '${RAVEN_WPS_OUTPUTS_DELETE_FILES_TIME_MODE}'. Please set this variable to a valid option or disable the raven file cleaning job. This job will not run properly!" | ||
| fi | ||
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| if [ "${THREDDS_SCHEDULER_JOB_CLEAN_OLD_FILES_ENABLED}" = "true" ] && ! echo "${BIRDHOUSE_EXTRA_CONF_DIRS}" | grep -q 'thredds[[:space:]]*$'; then | ||
| echo "$THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS" | grep -q '^[0-9][0-9]*$' || log WARN "THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS variable must be an integer not '${THREDDS_LOGS_DELETE_FILES_OLDER_THAN_DAYS}'. Please set this variable to an integer or disable the thredds file cleaning job. This job will not run properly!" | ||
| [ "${_acceptable_modes#*"${THREDDS_LOGS_DELETE_FILES_TIME_MODE}"}" = "${_acceptable_modes}" ] && log WARN "THREDDS_LOGS_DELETE_FILES_TIME_MODE variable must be one of 'mtime', 'atime', or 'ctime' not '${THREDDS_LOGS_DELETE_FILES_TIME_MODE}'. Please set this variable to a valid option or disable the thredds file cleaning job. This job will not run properly!" | ||
| fi | ||
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