1. replacing log references to "${JSONIMPORTFILE}" with "/import_export/import-fbrfs.json", so that the filename is explicit rather than a "." when the file is empty.

2. remove 'CURATEDPAPERLISTFILE' (./fbrf_input_list.tsv) and 'JSONIMPORTFILE' (/import_export/import-fbrfs.json) while archiving, so that the files cannot be re-used in a following epicycle.

Revert "Update weekly_routine.sh"

See merge request !10

This reverts commit 30a813e1

merging vitor_testing into testing

See merge request !9

Revert "Update weekly_routine.sh"

See merge request !8

This reverts commit becfec8b

Revert "Update weekly_routine.sh"

See merge request !7

This reverts commit 4e6210f8

commenting out line 273, so that an empty file is not created and the rest of the scripts uses an old, non-empty file. just for testing.

testing using full filepath instead of 'here' (.) for CURATEDPAPERLISTFILE (i.e. fbrf_input_list.tsv)

#test working directory is working properly by calling pwd

Replacing most './' with CANTOSPACE variable (i.e ${CANTOSPACE}/)

Revert "Update weekly_routine.sh - testing replacing 'here' marks (./) with the full filepath from root."

This reverts commit 884e76e8

Testing

See merge request !6

bit was missing so no scripts would execute.

Comprehensive SOP document for the installation, setup, configuration and use of canto for phenotype curation 

Should be Wed not Weds

Added systemd files to support weekly_export.sh
Added usage_notes.txt to list troubleshooting commands

Adding the label for the publication-level notes section in session/publication front page (external_notes to canto, but internal notes to FlyBase)

This script prints all the activity log from the running canto-server container into the file 'canto_running.log' in the 'logs' sub-folder of 'canto-space'

The command line that add the mock "FlyBase Curator" user now includes a fake value for the ORCID field

Renames 'canto_weekly.log' to 'canto_weekly_update.log', and routes it to the new sub-folder 'logs' 

routes logfile to newly create sub-folder 'logs'
removes if loop to stop/start canto

Update starting-pack.sh - added step to create a 'logs' sub-directory of 'canto-space', where log files will live. 

a) changing docker ps search for DOCKERNAME variable
b) removing . from CURATEDPAPERLISTFILE variable
c) changing JSONARCHIVE variable from "import-fbrfs_json_$(date +"%Y-%m-%d")" into import-fbrfs_$(date +"%Y-%m-%d").json

reconciling with branch vitor_testing1

reconciling with changes in vitor_testing1

Too difficult to merge the branch so I've pulled in various files by hand.

Changed echo to log