New front end: Shiny - Githubissues

clnsmth commented 6 years ago

Build Shiny web application for EMLassemblyline.

earnaud commented 5 years ago

I'm really interested in taking part to this project, and I could produce this app to fill the files (and possibly launch make_eml() then).

earnaud commented 5 years ago

I'd like to know, @clnsmth : to upload my first pieces of R-Shiny apps, where would you like them to be located? Thanks.

srearl commented 5 years ago

Hi @clnsmth and @earnaud - very cool, been thinking about this for a while. You might already be headed this way but I might suggest developing the Shiny front-end in a separate package. Best to keep the front-end and EMLassemblyline isolated and call assembly from the Shiny app.

clnsmth commented 5 years ago

Thanks for your interest in contributing to this project @earnaud, and thanks @srearl for these recommendations.

Lately I've been thinking that a full web interface for EMLassemblyline is unnecessary since it would duplicate (or even triplicate) community efforts underway to make nice web-form based EML metadata entry tools. Instead, @earnaud's suggestion for a Shiny interface for editing EMLassemblyline metadata template files would be a big improvement in the workflow of EMLassemblyline users.

What features would be good for this use case to have? Here are a few ideas:

Reads template file content from local environment
Intuitive user editing interface
Support for controlled vocabularies and other external resources (where appropriate)
The application opens on a function call from a users RStudio session and saves results to a local directory

NOTE: The ROpenSci EML project has a Shiny app for editing data table attributes we may want to leverage the great work they've done on that, though EMLassemblyline has not yet been refactored for EML v2.0.0.

@earnaud, if you'd like to develop Shiny apps for EMLassemblyline please work from my fork. There's a major refactoring and upgrade going on over there right now.

earnaud commented 5 years ago

@clnsmth I indeed began to work on current release EMLassembleLine branch, but I'll see your fork. My current shinyApp is focused on being intuitive for the user first. I implemented a kind of template for the metadata fields to fill (with a user-friendly synonym and an example). I'll detail the current features while uploading it. I'm okay with the rest of your goals, and I'll work on it next week. I already saw quickly the Ropensci EML git, but passed on the shinyApp: idem, I'll check it next Monday.

vanderbi commented 5 years ago

A nice feature would be for the attribute editor to have an autocomplete list of standard units for the user to choose from, or the option to create a new one.

From: Colin Smith notifications@github.com Sent: Friday, February 22, 2019 6:13 PM To: EDIorg/EMLassemblyline Cc: Subscribed Subject: Re: [EDIorg/EMLassemblyline] New front end: Shiny (#9)

Thanks for your interest in contributing to this project @earnaudhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_earnaud&d=DwMFaQ&c=lhMMI368wojMYNABHh1gQQ&r=rXMuRfaym1QbEBVEAO21Fw&m=b5uLbfoMxczGJKg95alglW4IyhYzOfsH2YmY1oxANnA&s=SbrmGsevGk-EqBlXS4qlwFqAbxhbHcS6AzlgAa1bRzw&e=, and thanks @srearlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_srearl&d=DwMFaQ&c=lhMMI368wojMYNABHh1gQQ&r=rXMuRfaym1QbEBVEAO21Fw&m=b5uLbfoMxczGJKg95alglW4IyhYzOfsH2YmY1oxANnA&s=C1FlJy5UeJ6GjKD6ypDki85LGEKo4Wi2uyTn8Imf5TE&e= for these recommendations.

Lately I've been thinking that a full web interface for EMLassemblyline is unnecessary since it would duplicate (or even triplicate) community efforts underway to make nice web-form based EML metadata entry tools. Instead, @earnaudhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_earnaud&d=DwMFaQ&c=lhMMI368wojMYNABHh1gQQ&r=rXMuRfaym1QbEBVEAO21Fw&m=b5uLbfoMxczGJKg95alglW4IyhYzOfsH2YmY1oxANnA&s=SbrmGsevGk-EqBlXS4qlwFqAbxhbHcS6AzlgAa1bRzw&e='s suggestion for a Shiny interface for editing EMLassemblyline metadata template files would be a big improvement in the workflow of EMLassemblyline users.

What features do we want this use case to support? Here are a few ideas:

Intuitive user interface
Support for controlled vocabularies and other external resources (where appropriate)
The application opens on a function call from a users RStudio session and saves results to a local directory

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_EDIorg_EMLassemblyline_issues_9-23issuecomment-2D466581377&d=DwMFaQ&c=lhMMI368wojMYNABHh1gQQ&r=rXMuRfaym1QbEBVEAO21Fw&m=b5uLbfoMxczGJKg95alglW4IyhYzOfsH2YmY1oxANnA&s=1rThrkhEMkzqdpiijCvwCQviNKh7IiW2giFy3N9rLC8&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEcjfuerd5jX-2DpPL-2D4GEKDjMp8SY-5FuHJks5vQHm3gaJpZM4UjiTl&d=DwMFaQ&c=lhMMI368wojMYNABHh1gQQ&r=rXMuRfaym1QbEBVEAO21Fw&m=b5uLbfoMxczGJKg95alglW4IyhYzOfsH2YmY1oxANnA&s=9vOZU21W3PXhYN4ZLlXFk_1d9TaeUW0cBqyUzs8yE_c&e=.

earnaud commented 5 years ago

@vanderbi I will try as possible to have such a feature accessible, but I'm thinking about the following possibilities:

units in a scrolling list with categories (SI, derivedSI - e.g. m², physical - e.g. lux , ecological - e.g. individuals count)
units defined on SI and/or ecology (environment light: lux = cd/m², density: count/m²)

Currently, I'm thinking the UI in two parts:

the first one allows the user to enter information (ids, units, ...) to be memorized in files for further uses. To allow future uses, I'll need to think this files to have unique contents (e.g. a 'Personnel' file represents only one ResponsibleParty) and to be easily updated.
the second allows the user to enter data and metadata to generate an EML file. This part will suggest the user to access the saved files' content to reuse them (instead of re-writing everything).

Idea: as I see the EML files' structure, I have thought about developping a recursive way to fill it, but this would require a file to be "followed" which would sum up how an EML file is filled.

Weekly goals:

have the app interprete metadata template files (shinyApp/metadataTemplateInfo in my rep) to fill input UI fields
parse a full EML hierarchy to have a guideline file. This file will show, for each xmlElement (e.g. eml:eml) what are its children and what choices have to be done and which children are required/optional (e.g. for eml:eml, 'access', '(dataset or citation or protocol or software)' are required, and 'additionalMetadata' is optional) (from KNB ecoinformatics: https://knb.ecoinformatics.org/external//emlparser/docs/eml-2.1.1/eml.html#access). I'll also figure out how to manage xmlAttributes for a field.

(NB: it's quite special for me to communicate with you only during your nighttime)

earnaud commented 5 years ago

And I forgot: I prefer the stevan's solution to upload my shinyApp on a different git to furtherly join them. In fact, the app depends on EML AL and will adapt to it, not the inverse. I'm not completely used to work with GitHub, so is there a way to have an independent portion of the git dedicated to the app? or shall we just upload a folder among the others that is not meant to work with others? anyway I just dropped my shinyApp scripts in this git: https://github.com/earnaud/R-EMD

clnsmth commented 5 years ago

@vanderbi, I like the idea of auto-completing fields that are linked to resources like the standard units, controlled vocabularies, etc. This makes navigation of the related resource quick and efficient. I also like @earnaud's suggestion to have the information categorized by type. Is there a way to support both?

@earnaud, if R-EMD will be apart of EMLassemblyline then add these to the R directory. Otherwise I think the current directory structrue of R-EMD is appropriate. I just created a development branch for EMLassemblyline at EDIorg. Probably best to develop off this than my fork (sorry for not getting this set up sooner).

earnaud commented 5 years ago

@clnsmth :

for the units: I will work on the different types of inputs (and amongst them units), the fact is I have to manage quite few things, like EML file structures and how to efficiently set for each element the required type (e.g. single letter for middleName of Person).
for your dev branch, I can upload my R-EMD into it. I'll open issues on my R-EMD to let you know how I see the thing and how I want to structure it. I'll also edit the README to keep the viewers up to date.

earnaud commented 5 years ago

Could I get assigned to this task? just for other potential contributors to know. And by the way: EML Assembly Line front-end is currently being built in MetaShARK: https://github.com/earnaud/MetaShARK

earnaud commented 4 years ago

Some update notes:

MetaShARK has migrated into a new repo: https://github.com/earnaud/MetaShARK-v2
I encounter a problem from EMLassemblyline: is it possible for template_* functions to overwrite existing files? This happen to be needed if the user wants to remove files from its current dataset. Tell me if I shall prefereably use a shiny-based solution to remove existing files and replace them with the new ones

clnsmth commented 4 years ago

Thanks for this update @earnaud. Yes, I'll add an overwrite option to the templating functions.

earnaud commented 4 years ago

Thanks a lot, this will be really helpful for a complete development of the shiny app :+1: but this is not really critical by now

EDIorg / EMLassemblyline

New front end: Shiny #9