diff --git a/canto-docker-initd b/canto-docker-initd index aaca5cc7d7dc81867b56d0a996ca0f7a6f4ce27b..862f0c8a4b221945d002686ceff0f0132daeb621 100644 --- a/canto-docker-initd +++ b/canto-docker-initd @@ -7,7 +7,7 @@ action=$1 port=$2 WORKERS=5 -CANTO_SPACE='/data/export/canto-space' +CANTO_SPACE='/data/export/canto-project/canto-space' PID_PATH=import_export/canto.pid diff --git a/canto-test-docker-initd b/canto-test-docker-initd index 611757c92cb04cf888d370fd32b49b25292f3289..fa3c3cea43044c279573c24d0e1252ea8a9781b6 100644 --- a/canto-test-docker-initd +++ b/canto-test-docker-initd @@ -7,7 +7,7 @@ action=$1 port=$2 WORKERS=5 -CANTO_SPACE='/data/export/canto-space-testing' +CANTO_SPACE='/data/export/canto-project/canto-space-testing' PID_PATH=import_export/canto-test.pid diff --git a/canto.service b/canto.service index 5cf3caad08d576733081353d736144933be12fd6..d57fce8c8c578cce7ddaeff8175825dc738ed296 100644 --- a/canto.service +++ b/canto.service @@ -3,8 +3,8 @@ Wants=network-online.target After=network-online.target [Service] -ExecStart=/data/export/canto-space/canto/script/canto_start_docker --no-tty +ExecStart=/data/export/canto-project/canto-space/canto/script/canto_start_docker --no-tty WorkingDirectory=/data/export/canto-space/ [Install] -WantedBy=default.target \ No newline at end of file +WantedBy=default.target diff --git a/canto/canto_deploy.yaml b/canto/canto_deploy.yaml index 57bab910531fa01ea59f0ec6cecbcc03d407647f..7189a83f1f41f25fb10771cd5002f97939a06e52 100644 --- a/canto/canto_deploy.yaml +++ b/canto/canto_deploy.yaml @@ -15,18 +15,18 @@ annotation_figure_field: 0 # disable deletion buttons on genotype management page? show_quick_deletion_buttons: 0 -# this will define Canto's internal SQL database (track.sqlite3 and files for all curation sessions) to the the 'data' sub-folder of 'canto-space' (/data/export/canto-space/data), which is where all data should reside. -# Here filepaths are relative. Have an initial '/' in '/data/track.sqlite3' and '/data' below, otherwise track.sqlite3 and the data will appear in '/data/export/canto-space/canto/data' rather than in '/data/export/canto-space/data'. +# this will define Canto's internal SQL database (track.sqlite3 and files for all curation sessions) to the the 'data' sub-folder of 'canto-space' (<filepath>/canto-space/data), which is where all data should reside. +# Here, filepaths are somewhat relative. Please have an initial '/' in both '/data/track.sqlite3' and '/data' below, otherwise track.sqlite3 and the curation data will be added to a new 'data' folder at '<filepath>/canto-space/canto/data', rather than to the existing 'data' sub-folder of 'canto-space' at '<filepath>/canto-space/data'. Model::TrackModel: connect_info: -# this sets the path (and name) of the sqlite3 file (track.sqlite3), which queries curation sessions within canto -# make sure it does include the initial '/', otherwise curation session will be misplaced in '/data/export/canto-space/canto/data' -# Make sure the folder where the SQL database 'track.sqlite3' lives (/data in /data/track.sqlite3) matches the data_directory value (/data) +# this sets the path (and name) of the sqlite3 file 'track.sqlite3', which queries curation sessions within canto +# as mentioned above, make sure it does include the initial '/', otherwise 'track.sqlite3' will be misplaced in a new 'data' folder at '<filepath>/canto-space/canto/data' +## Make sure the folder where the SQL database 'track.sqlite3' lives (/data in /data/track.sqlite3) matches the data_directory value mentioned below (/data) - dbi:SQLite:dbname=/data/track.sqlite3 schema_class: Canto::TrackDB # this sets the path to the 'data' sub-folder of 'canto-space', which is where all curation data should reside. -# make sure it does include the initial '/', otherwise curation session will be misplaced in '/data/export/canto-space/canto/data' -# and make sure the folder where the SQL database 'track.sqlite3' lives (/data/track.sqlite3) matches the data_directory value (/data) +# as mentioned above, make sure it does include the initial '/', otherwise curation session will be misplaced in a new folder '<filepath>/canto-space/canto/data' rather than in the existing 'data' sub-folder of 'canto-space' +## Make sure the folder where the SQL database 'track.sqlite3' lives (/data/track.sqlite3) matches this data_directory value (/data) data_directory: /data #Database to connect to - 'connect_info:' bit is the only part that needs changes on a weekly basis diff --git a/canto_running_log.sh b/canto_running_log.sh index 34d63e9448e550aa70c27a0a74d31e86235798e6..b6869a56be55eddb560878dbe685606d95e39f0b 100755 --- a/canto_running_log.sh +++ b/canto_running_log.sh @@ -3,7 +3,7 @@ #this script prints all the activity log messages from the running canto-server container into the file 'canto_running.log' in the 'logs' sub-folder of 'canto-space' # Define canto-space root -CANTOSPACE="/data/export/canto-space" +CANTOSPACE="/data/export/canto-project/canto-space" # Define logs folder inside canto-space LOGS="logs" diff --git a/canto_weekly.service b/canto_weekly.service index e3ec6b11967f48e8dc724a56e8c63d188f93af23..35f3f4fa13d6f3fb41b63fa4672242851740c3fe 100644 --- a/canto_weekly.service +++ b/canto_weekly.service @@ -4,8 +4,8 @@ After=network-online.target Wants=network-online.target [Service] -WorkingDirectory=/data/export/canto-space -ExecStart=/data/export/canto-space/weekly_routine.sh +WorkingDirectory=/data/export/canto-project/canto-space +ExecStart=/data/export/canto-project/canto-space/weekly_routine.sh [Install] -WantedBy=default.target \ No newline at end of file +WantedBy=default.target diff --git a/canto_weekly_export.service b/canto_weekly_export.service index 04ce8fedce6201b36b1b501bfb723ec7cf7e1353..eb89e77418f72f73bc9ccbb2ffbdd14ca0af9c11 100644 --- a/canto_weekly_export.service +++ b/canto_weekly_export.service @@ -4,8 +4,8 @@ After=network-online.target Wants=network-online.target [Service] -WorkingDirectory=/data/export/canto-space -ExecStart=/data/export/canto-space/weekly_export.sh +WorkingDirectory=/data/export/canto-project/canto-space +ExecStart=/data/export/canto-project/canto-space/weekly_export.sh [Install] -WantedBy=default.target \ No newline at end of file +WantedBy=default.target diff --git a/weekly_export.sh b/weekly_export.sh index 83f14e8cbe7c353a6e960707c1cb62ff4b4fe6de..d24b7d6ff57757a5777b2a0b01d6121253403087 100755 --- a/weekly_export.sh +++ b/weekly_export.sh @@ -3,7 +3,7 @@ # This script exports data from canto - to be set to run automatically on Wednesdays noon. # Define canto-space root in flybase-vm -CANTOSPACE="/data/export/canto-space" +CANTOSPACE="/data/export/canto-project/canto-space" # Define logs folder inside canto-space LOGS="logs" diff --git a/weekly_routine.sh b/weekly_routine.sh index 4d56744139a3cca15bac6541f2fb0bd679c39d64..954cfd430aae996213d8990dddd69f0817d9e7c4 100755 --- a/weekly_routine.sh +++ b/weekly_routine.sh @@ -1,9 +1,9 @@ #!/bin/bash -# weekly routine on Sunday pm /Monday am. This script should be run from /data/export/canto-space +# weekly routine on Sunday pm /Monday am. This script should be run from 'canto-space' # Define canto-space root -CANTOSPACE="/data/export/canto-space" +CANTOSPACE="/data/export/canto-project/canto-space" # Define logs folder inside canto-space LOGS="logs" @@ -77,8 +77,7 @@ function restart_canto() # Canto restart # Get Container ID from output - DOCKERNAME=$(docker ps -a --filter status=running | awk '$2 ~ /pombase\/canto-base/ { print $1 }') - if docker restart "${DOCKERNAME}"; then + if docker restart canto; then log "Canto restarted successfully" else log "Canto failed to restart sucessfully!"