Update weekly_routine.sh - reverting to using "${CURATEDPAPERLISTFILE}" instead of "${CANTOSPACE}/import_export/fbrf_input_list.tsv" as input for canto_json_input_maker.pl

This reverts commit 682b9c65

Update weekly_routine.sh - for canto_json_input_maker.pl command, the input filepath has been changed so that it uses here (./) instead of the full filepath ($CANTOSPACE)

moving CURATEDPAPERLISTFILE ("./fbrf_input_list.tsv") to canto-space/import_export immediately after being generated.This is to allow the 'canto_json_input_maker.pl' script to use a defined filepath from root rather than from "./", since "./" has been creating problems.

Update weekly_routine.sh - trying to eliminate the 'the input device is not a TTY' error from docker commands by adding '--non-interactive' to them 

commenting line 270, for testing with a previous FBrf list file.

reinstating CURATEDPAPERLISTFILE="./fbrf_input_list.tsv"

removing # from lines 270, 302, 319
 

testing only using CURATEDPAPERLISTFILE="fbrf_input_list.tsv" , without defining the rest of filepath 

adding full filepath from root to $CURATEDPAPERLISTFILE
commenting lines ' #rm "${CURATEDPAPERLISTFILE}" ' and ' #rm ".${JSONIMPORTFILE}" ' for testing that files are created

reverting the addition of --tty to docker commands

testing --tty in 'docker restart'

Testing adding --tty to all docker commands

This reverts commit 9279042d

for testing - commenting line 270, so that no (empty) CURATEDPAPERLISTFILE="./fbrf_input_list.tsv" is created and a previous file can be used.

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.

This reverts commit 30a813e1

This reverts commit becfec8b

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

bit was missing so no scripts would execute.

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

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

Changed echo to log

This reverts commit 8da0f998

changing docker container image to pombase/canto-base

- Adding missing fi
- Added missing [[ & ]]

- Chaged name of config file dir to camto_support to prevent clash
- Added missing quotes for variable

- Added function check of db in canto_done file has changed since last run. If not then restart Canto and exit.
- Tidied up code ordering to make it more logical
- Create data folder to store some files to keep things tidy. It be sensible to put fbrf_input_list.tsv in there as well.