ArcCommander Argument design

[HLWeil]

This issue is meant as a place for discussing possible argument design choices

Argument Query (Asking for fields via text editor prompt)

• Add basic query functionality
• Allow user to set preferred text editor (#8)
• For Unix systems, infer editor via EDITOR (or less often, VISUAL) environment variable

[muehlhaus]

Top-level

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

Investigation

arc investigation or arc i subcmd
arc i edit - open editor to edit ISA in YAML (yay!)

Assay

arc assay [c|create] - create a directory assays/, prepopulate it with defaults

arc assay [rregister]

| --update

arc assay [a|add] - create plus register

arc assay [a|move] ...

arc assay [rm|remove]

arc assay edit -- edit assay metadata in Excel or

[HLWeil]

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

[chgarth]

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 ***@***.***> 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 <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKFCTTZGYDSFP7ZD25UIGLSNGO5JANCNFSM4TAQWKPQ>.

[kMutagene]

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.

Subcommand verbs

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>:

• arc <object> init : will initialize a new empty <object> in the ARC.
• arc <object> create will create a new <object> with the passed arguments in the ARC.
• arc <object> update will update an existing <object> with the passed arguments.
• arc <object> edit will open an existing <object> with a text editor. Arguments passed for this verb will be pre-set in the editor.
• arc <object> register will register an existing <object> in the ARC with the passed arguments.
• arc <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
• arc <object> remove will remove the <object> from the ARC's register.
• arc <object> move will move the <object> from source to target register.
• arc <object> list will print all <object>s registered in the ARC.
• arc <object> Delete will delete the <object>.

[HLWeil]

Will close this for now, as the argument structure seems to have stabilized