Closed HLWeil closed 2 years ago
arc init - create an arc directory structure below the current directory (as git init) arc push - push all changes to the specified "upstream" (t.b.d.) arc pull - ... arc check - validate that the current directory is an arc, and output helpful messages towards compliance
arc register - (re-)register all assays and workflows
arc help
arc run - run all workflows
arc investigation
arc assay [c|create] - create a directory assays/
arc assay [rregister]
arc assay [a|add] - create plus register
arc assay [a|move] ...
arc assay [rm|remove]
arc assay edit -- edit assay metadata in Excel or
Some arguments are required and some are not. If required arguments are left out by the user a prompt should be opened where the user can input the missing arguments. Ideally required arguments should be marked (e.g. by an attribute). Also it would be good
Let me point out that in all Unix systems (including macOS), it is the convention that the EDITOR (or less often, VISUAL) environment variable is used to designate the preferred editor. This works with VSCode’s “code” command line interface as well.
On 29. Oct 2020, at 18:11, Lukas Weil notifications@github.com wrote:
Some arguments are required and some are not. If required arguments are left out by the user a prompt should be opened where the user can input the missing arguments. Ideally required arguments should be marked (e.g. by an attribute). Also it would be good
if the texteditor could be opened on a stream instead of a file (check if possible) if the texteditor of choice could be set in a config file — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nfdi4plants/arcCommander/issues/7#issuecomment-718896152, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKFCTTZGYDSFP7ZD25UIGLSNGO5JANCNFSM4TAQWKPQ.
via #13 and #14 we now have the following structure of the arc cli.
arc <top-level-command> <top-level-command-args>
e.g.
arc init
or
arc <object> <subcommand-verb> <subcommand-verb-args>
where <object>
is one of the following:
assay
study
investigation
and <subcommand-verb>
models what to do with the object, e.g
arc study init
will initialize a new empty study in the ARC.
while not all object subcommands support all verbs, here is a list of the verbs and what to expect when they are applicable for an <object>
:
<object>
init : will initialize a new empty <object>
in the ARC.<object>
create will create a new <object>
with the passed arguments in the ARC.<object>
update will update an existing <object>
with the passed arguments.<object>
edit will open an existing <object>
with a text editor. Arguments passed for this verb will be pre-set in the editor.<object>
register will register an existing <object>
in the ARC with the passed arguments.<object>
add is the combination of create/init+update and register, meaning it will create a new <object>
in the ARC and subsequently register it with the passed arguments<object>
remove will remove the <object>
from the ARC's register.<object>
move will move the <object>
from source to target register.<object>
list will print all <object>s
registered in the ARC.<object>
Delete will delete the <object>
.Will close this for now, as the argument structure seems to have stabilized
This issue is meant as a place for discussing possible argument design choices
Argument Query (Asking for fields via text editor prompt)