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Robo 3T?
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Based on these requirements, I'd recommend CosmosDB using the MongoDB mode. You will be able to query and structure in a similar manor as a SQL store, and you'll likely have a bunch of Mongo tools you could leverage when building the app (Object Document Mappers (ODM -- Mongoid https://github.com/mongodb/mongoid , etc...), tooling (Robomongo https://robomongo.org , etc..) and other related Mongo tools).
Beyond development experience and tooling, administration and scaling is much simpler with CosmosDB. You can replicate to multiple regions (read replicas), and have an ordered list of failover regions.
Tables would be like writing assembly when using CosmosDB is like using a high-level language.
I'm connecting to MongoDB via this desktop client over SSH. Are you sure it's about executing bash? When you log in to SFTP via Filezilla, you're not executing bash (I think) and an email is still sent. When using a database client it's not.
I had issues too. Windows was easy enough, Ubuntu server was easier, OS X not quite so easy (maybe this is where some of the undue Mongo hate springs from, I dunno).
Back to the OP's question, everyone's just about covered the local dev stuff. With regards to mongo, 1 thing I recall that stumped me for a while was actually connecting to the server for the first time - it's like riding a bike in that you'll do it once and never forget how to fix any of the problems you come across. The default mongo install does provide a web-GUI that's OK for administration, but even better is a tool like robomongo (https://robomongo.org/) that's now known as Robo 3T that's visual and is very easy to work with (it's a viewer for your database, and you can run queries against it using the tool).
If you need any help getting setup, just reply with some specific issues you're having and error messages and I'll also do what I can to assist.
Get a decent mongo GUI tool like robo3t or studio3t. These tools have built in script editors to make it easier to write and save js that you want to run.
Also your question needs better clarification. If you just want to run a .js file, you can run mongo localhost somefile.js