R/fill_module.R
In earnaud/MetaShARK-v2: metashark
Defines functions
fill
fillUI
#' @import shiny
#'
#' @noRd
fillUI <- function(id) {
tabsetPanel(
id = NS(id, "tabs"),
tabPanel(
tags$h4("EML Assembly Line"),
fluidPage(
style = "padding-top:2.5%; background-color: #ffffff57",
## Top row ----
tags$table(
style = "width: 100%",
HTML(
'<svg style="height: 50px; width: 100%; float: left;
position: absolute; overflow: initial;">
<line y1="0" y2="0" x1="-1000" x2="300px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
<line y1="0" y2="50" x1="300px" x2="350px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
<line y1="50" y2="50" x1="350px" x2="2000px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
</svg>'
),
tags$tr(
tags$td(
style = "
width: 350px; min-width: 350px; max-width: 500px;
white-space: nowrap; overflow: hidden; text-overflow: ellipsis;
",
h3(
textOutput(NS(id, "current_step"))
)
),
tags$td(
style = "width: 300px; min-width: 300px",
h3(
class = "help-block", # helpText merged to h3
textOutput(NS(id, "current_DP"))
)
),
tags$td(
div(
id = NS(id, "top_buttons"),
style = "float: right; min-width: 200px",
shinyWidgets::actionBttn(
NS(id, "help"),
"Help",
icon("question-circle"),
style = "simple",
color = "primary"
),
shinyWidgets::actionBttn(
NS(id, "save"),
"Save",
icon("save"),
style = "simple",
color = "success"
),
shinyWidgets::actionBttn(
NS(id, "quit"),
"Quit",
icon("times-circle"),
style = "simple",
color = "danger"
)
)
)
)
),
## Pages ----
pagesUI(
NS(id, "wizard"),
parent_id = id
)
) # end fluidPage
),
# MetaFIN ====
tabPanel(
tags$h4("MetaFIN"),
tags$div(
style = "background-color: #ffffff57",
MetaFINUI(
NS(id, "metafin"),
wip = base::get("metashark_args", envir = .GlobalEnv)$wip
)
)
)
)
}
#' @import shiny
#' @importFrom shinyjs onclick show hide
#'
#' @noRd
fill <- function(id, main_env) {
moduleServer(id, function(input, output, session) {
if (main_env$dev)
shinyjs::onclick("dev", {
if (main_env$current_tab() == "fill" &&
main_env$EAL$page != 3) {
browser()
}
},
asis = TRUE
)
# Variable initialization ====
steps <- isolate(main_env$VALUES$steps)
# Wizard ====
# pages change
pagesServer("wizard", main_env)
# Display data package title
output$current_DP <- renderText({
req(main_env$EAL$page > 1)
main_env$save_variable$SelectDP$dp.title
})
# modules content
sapply(seq_along(isolate(main_env$VALUES$steps)), function(i) {
.id <- isolate(main_env$VALUES$steps)[i]
.to_call <- switch(i,
"SelectDP",
"DataFiles",
"Attributes",
"CatVars",
"GeoCov",
"TaxCov",
"Personnel",
"Misc",
"MakeEML"
)
do.call(
what = .to_call,
args = list(
id = .id,
main_env = main_env
)
)
})
## Quit ----
# show modal.state 'quit' button clicked
observeEvent(input$quit, {
req(input$quit)
showModal(
modalDialog(
title = "You are leaving data description.",
"Are you sure to leave? Some of your metadata have maybe not been
saved.",
easyClose = FALSE,
footer = tagList(
modalButton("Cancel"),
actionButton(
NS(id, "save_quit"),
"Save & Quit"
),
actionButton(
NS(id, "simple_quit"),
"Quit",
icon("times-circle"),
class = "redButton"
)
)
) # end of modalDialog
)
},
label = "EAL quit?"
)
# calls save method and quits
observeEvent(input$save_quit, {
req(input$save_quit)
# Save work at this state
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
# Clean & reset variables
removeModal()
main_env <- cleanModules(main_env)
},
label = "EAL save+quit",
ignoreInit = TRUE
)
# quits simply
observeEvent(input$simple_quit, {
req(input$quit)
# Clean & reset variables
removeModal()
main_env <- cleanModules(main_env)
},
label = "EAL quit",
ignoreInit = TRUE
)
# quit management
## Save ----
observeEvent(input$save, {
devmsg("%s", main_env$EAL$page, tag = "fill_module.R")
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
})
## Autosave ----
observeEvent(main_env$EAL$page, {
req(main_env$EAL$page != 1)
devmsg("step: %s", tag = "fill_module.R/autosave", main_env$EAL$page)
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
},
priority = -2,
label = "EAL: autosave"
) # important priority
## Current step ----
output$current_step <- renderText({
req(main_env$EAL$current)
gsub(
"_",
" ",
switch(main_env$EAL$current,
SelectDP = "Select Data Package",
main_env$EAL$current
)
)
})
# Navigation ====
observeEvent(main_env$EAL$page, {
req(main_env$EAL$page != main_env$EAL$old_page)
withProgress({
## Save & Template ----
devmsg(tag = "fill_module.R/navigation", "save & template")
if (main_env$EAL$old_page > 1) {
saveReactive(
main_env,
main_env$EAL$old_page,
# do not template on 'previous'
do_template = main_env$EAL$old_page < main_env$EAL$page
)
}
incProgress(1 / 8)
## set EAL variables ----
devmsg(tag = "fill_module.R/navigation", "set EAL variables")
# left Data Files
if (main_env$EAL$old_page == 2) {
unlink(main_env$PATHS$eal_tmp)
}
# reached Data Files
if (main_env$EAL$page == 2) {
main_env$PATHS$eal_tmp <- tempdir()
}
# Properly change page
main_env$EAL$current <- main_env$VALUES$steps[main_env$EAL$page]
main_env$EAL$tag_list <- tagList()
incProgress(1 / 8)
## Reset local_rv ----
devmsg(tag = "fill_module.R/navigation", "set local_rv")
main_env <- setLocalRV(main_env)
incProgress(1 / 8)
## Set UI for new page ----
## TODO
updatePageUI(main_env, session)
incProgress(1 / 8)
## Change page ----
devmsg(tag = "fill_module.R/navigation", "change pane")
updateTabsetPanel(
session,
"wizard-wizard",
selected = steps[main_env$EAL$page]
)
incProgress(1 / 8)
## Update history ----
if (!main_env$EAL$current %in% main_env$EAL$history) {
main_env$EAL$history <- c(
main_env$EAL$history,
main_env$EAL$current
)
}
devmsg(tag = "fill_module.R/navigation", "update history")
incProgress(1 / 8)
## Savevar changes ----
devmsg(tag = "fill_module.R/navigation", "save_variables change")
main_env$save_variable$step <- main_env$EAL$page
main_env$save_variable$history <- main_env$EAL$history
## Accessory UI elements ----
devmsg(tag = "fill_module.R/navigation", "display UI")
if (main_env$EAL$page > 1) {
shinyjs::show("top_row")
shinyjs::show("current_DP")
shinyjs::show("help")
shinyjs::show("save")
shinyjs::show("quit")
} else {
shinyjs::hide("top_row")
shinyjs::hide("current_DP")
shinyjs::hide("help")
shinyjs::hide("save")
shinyjs::hide("quit")
}
incProgress(1 / 8)
devmsg(tag = "fill_module.R/navigation", "ended")
## Helps ====
main_env$EAL$help <- modalDialog(
title = paste0(main_env$EAL$current, " - Help"),
switch(main_env$EAL$page,
### SelectDP ====
tagList(
tags$p("This module allows you to manage your", tags$strong("data packages"), ".
A data package (aka DP) is a collection of a dataset and its associated metadata
and resources (scripts, literature, ...). You can:"),
tags$ul(
tags$li("Load an existing data package among local ones (left). You
will resume its edition at the last saved encountered step."),
tags$li(
"Create a new data package. You must fill in", tags$strong("three fields"),
tags$i("Data package name"), "will be used for identifying the DP,",
tags$i("Data package title"), "will be displayed when consulting the DP
page once formatted (explained in last step),",
tags$i("Data package license"), "is the license assigned to this production for
intellectual rights properties"
)
)
# , tags$p("Also, notice the", tags$strong("quick"), "check box above DP name.
# Checking this box enables \"quick mode\" which will pre-fill most of the
# fields in further steps. You still will be able to edit them at your
# convenience.")
),
### Data Files ====
tagList(
tags$p("This module allows you to load data files from the dataset you want to
describe. Once uploaded, you can set:"),
tags$ul(
tags$li(tags$i("Content name:"), "A name for the data contained in the file (e.g. table name)."),
tags$li(tags$i("URL:"), "If the file is accessible remotely, here is a way to reference it."),
tags$li(tags$i("Description:"), "A short text provided to describe the file, its content,
relevant information about the data in the entity.")
),
tags$p("To edit your selection, select files among the list
with the check boxes on their left, then click the \"Remove\"
button."),
tags$p("Recommended size per file is around 1 Gb. Such files
and heavier ones might slow down the
app.")
),
### Attributes ====
tagList(
tags$p("This module allows you to describe precisely each
attribute of each file. Some of these metadata are guessed
from the data files. Such fields are annoted with a star (*).
For each attribute, you can set:"),
tags$ul(
tags$li(tags$i("Attribute Name*:"), "the name of the
attribute."),
tags$li(tags$i("Attribute Description:"), "a description of
the attribute."),
tags$li(tags$i("Attribute Class*:"), "the type of content in
the attributes among \"numeric\", \"character\",
\"categorical\" and \"Date\". Categorical means a character
string with encoded values (e.g. Male/Female)."),
tags$li(tags$i("Date format (only for Date class): how the
dates of the attributes are written (e.g. DD-MM-YYYY).")),
tags$li(tags$i("Unit (only for Numeric class):"), "which is
the unit used for the numeric data of the attributes. The
list is huge and refers to", tags$a("STMML units",
href = "http://www.ch.ic.ac.uk/rzepa/codata2/"
), ". You can
also define you own unit (see Custom Units thereafter)."),
tags$li(tags$i("Missing Value Code:"), "a one-word code used
instead of a missing value among the data of the attribute
currently described."),
tags$li(tags$i("Missing Value Code Explanation:"), "a short
definition of the meaning(s) given for the missing value
code.")
),
tags$h3("Custom units creation"),
tags$p("EML allows the user to define its own units, but this
require to fulfill some more fields. However, the custom units
you will have defined will be saved into the Custom Unit table
at the bottom of this page. You will find the written custom
units in the units selection once they are written. To define
a custom unit, chose the unit to be \"custom\". A custom unit
is defined with:"),
tags$ul(
tags$li(tags$i("Unit id:"), "the id of the unit (e.g.
gramsPerOneThirdMeter)."),
tags$li(tags$i("Unit type:"), "the physical property
measured by the custom unit (e.g. mass)."),
tags$li(tags$i("Parent unit in SI:"), "from which unit among
the most common one is custom unit derived (e.g. gram)."),
tags$li(tags$i("Multiplier to SI:"), "by how many has the
custom unit to be multiplied to be equal to its parent
unit."),
tags$li(tags$i("Unit description:"), "some additional notes
about the unit, how to compute it.")
)
),
### Catvars ====
tagList(
tags$p("This module allows you to detail the categorical
variables (class \"categorical\" in Attributes). For each
variable, you will be able to detail each of its value by a
short description.")
),
### Geocov ====
tagList(
tags$p("This module allows you to define the geographic area
in which the data have been produced. You have the choice
between two methods to define geographic coverage:"),
tags$ul(
tags$li(
tags$h4("Variable selection (recommended)"),
tags$p("This method allows you to fetch interesting
attributes for geographic coverage. Prefer storing all of
your locations into a single table or equally dimensioned
tables, under 3 to 5 columns: one for the site description
and one or two others for latitude and longitude. For
latitude and longitude, chosing a single column will be
interpreted as points, while chosing two will result in an
area. Southern latitude and western longitude shall be
noted with negative values.")
),
tags$li(
tags$h4("Manual geographic coverage"),
tags$p("Chose this method if your dataset does not include
data sites description and/or coordinates. You will be
able to provide as many sites as you wish, as single
points or rectangle areas.You can detail a more precise
number by using the left/right (or down/up) arrows of your
keyboard. Precision can be given at 0.01°.")
)
)
),
### Taxcov ====
tagList(
tags$p("This module allows you to define the taxonomical
coverage of the study. You will be asked to select columns
among your files containing the species name. Also, let the
app know if the taxonomic coverage shall be written with
scientific, common or both names. At last, select at least one
taxonomic authority among the ones suggested."),
),
### Personnel ====
tagList(
tags$p(
"This module allows you to get a full list of people
who contributed to the creation of this dataset. The
recommended best practice is to", tags$b("use the ORCID"),
"of a person. With this and the help of {rorcid}, the app will
be able to fetch all available and interesting data. You will
be able to correct this afterwards. Also, note that you must
fill in the fields for two roles: creator and contact."
),
tags$p("Suggested roles are the following:"),
tags$ul(
tags$li("Creator: person who contributed to produce the
data."),
tags$li("Contact: persone to contact for any question about
the data."),
tags$li("Principal investigator: person who led the creation
of the dataset. Selecting this will allow you to
fill in additional information about the project and
its funding."),
tags$li("Custom: as the roles list is not exhaustive, feel
free to add any role you consider important.")
)
),
### Misc ====
tagList(
tags$p("This module allows you to define the last details of
your data package. Note that you can write some of these
metadata using the markdown syntax. Here are brief
descriptions of the fields:"),
tags$ul(
tags$li("Abstract: the abstract of the publication linked to
those data."),
tags$li("Methods: the methods used in the production of this
dataset."),
tags$li(
"Keywords: you can type a list of keywords for
your dataset. For each keyword, you can add a keyword
thesaurus, like",
tags$a("the LTER controlled vocabulary",
href =
"http://vocab.lternet.edu/vocab/vocab/index.php"
),
", which are controlled vocabulary your exact keyword
originates from. Keywords thesaurus are not required."
),
tags$li("Temporal coverage: this lets you define the
duration of the study during which the data have
been produced."),
tags$li("Additional information: if any information has
been omitted, you can provide it here (e.g. collection
metadata from GBIF-EML).")
)
),
### Make EML ====
tagList(
tags$p("Here we are (well done) ! This is the final step to
write EML. Just click the button and let the magic happen.
If an error occurs, this will be displayed to the screen. In
this case, do not hesitate to get in touch with the dev
team."),
tags$p("You can also use the {emldown} package to get a
human-readable version of the generated EML. The button
below it will let you download the result of this step.")
)
),
footer = modalButton("Close"),
easyClose = TRUE, fade = TRUE
)
incProgress(1 / 8)
},
message = sprintf("loading %s", main_env$VALUES$steps[main_env$EAL$page])
)
},
label = "EAL0: change page"
)
observeEvent(input$help, {
showModal(main_env$EAL$help)
})
# (End) ====
})
}
earnaud/MetaShARK-v2 documentation built on Sept. 21, 2022, 10:52 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions fill fillUI
#' @import shiny
#'
#' @noRd
fillUI <- function(id) {
tabsetPanel(
id = NS(id, "tabs"),
tabPanel(
tags$h4("EML Assembly Line"),
fluidPage(
style = "padding-top:2.5%; background-color: #ffffff57",
## Top row ----
tags$table(
style = "width: 100%",
HTML(
'<svg style="height: 50px; width: 100%; float: left;
position: absolute; overflow: initial;">
<line y1="0" y2="0" x1="-1000" x2="300px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
<line y1="0" y2="50" x1="300px" x2="350px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
<line y1="50" y2="50" x1="350px" x2="2000px"
style="stroke:rgb(149, 149, 149);stroke-width:3"></line>
</svg>'
),
tags$tr(
tags$td(
style = "
width: 350px; min-width: 350px; max-width: 500px;
white-space: nowrap; overflow: hidden; text-overflow: ellipsis;
",
h3(
textOutput(NS(id, "current_step"))
)
),
tags$td(
style = "width: 300px; min-width: 300px",
h3(
class = "help-block", # helpText merged to h3
textOutput(NS(id, "current_DP"))
)
),
tags$td(
div(
id = NS(id, "top_buttons"),
style = "float: right; min-width: 200px",
shinyWidgets::actionBttn(
NS(id, "help"),
"Help",
icon("question-circle"),
style = "simple",
color = "primary"
),
shinyWidgets::actionBttn(
NS(id, "save"),
"Save",
icon("save"),
style = "simple",
color = "success"
),
shinyWidgets::actionBttn(
NS(id, "quit"),
"Quit",
icon("times-circle"),
style = "simple",
color = "danger"
)
)
)
)
),
## Pages ----
pagesUI(
NS(id, "wizard"),
parent_id = id
)
) # end fluidPage
),
# MetaFIN ====
tabPanel(
tags$h4("MetaFIN"),
tags$div(
style = "background-color: #ffffff57",
MetaFINUI(
NS(id, "metafin"),
wip = base::get("metashark_args", envir = .GlobalEnv)$wip
)
)
)
)
}
#' @import shiny
#' @importFrom shinyjs onclick show hide
#'
#' @noRd
fill <- function(id, main_env) {
moduleServer(id, function(input, output, session) {
if (main_env$dev)
shinyjs::onclick("dev", {
if (main_env$current_tab() == "fill" &&
main_env$EAL$page != 3) {
browser()
}
},
asis = TRUE
)
# Variable initialization ====
steps <- isolate(main_env$VALUES$steps)
# Wizard ====
# pages change
pagesServer("wizard", main_env)
# Display data package title
output$current_DP <- renderText({
req(main_env$EAL$page > 1)
main_env$save_variable$SelectDP$dp.title
})
# modules content
sapply(seq_along(isolate(main_env$VALUES$steps)), function(i) {
.id <- isolate(main_env$VALUES$steps)[i]
.to_call <- switch(i,
"SelectDP",
"DataFiles",
"Attributes",
"CatVars",
"GeoCov",
"TaxCov",
"Personnel",
"Misc",
"MakeEML"
)
do.call(
what = .to_call,
args = list(
id = .id,
main_env = main_env
)
)
})
## Quit ----
# show modal.state 'quit' button clicked
observeEvent(input$quit, {
req(input$quit)
showModal(
modalDialog(
title = "You are leaving data description.",
"Are you sure to leave? Some of your metadata have maybe not been
saved.",
easyClose = FALSE,
footer = tagList(
modalButton("Cancel"),
actionButton(
NS(id, "save_quit"),
"Save & Quit"
),
actionButton(
NS(id, "simple_quit"),
"Quit",
icon("times-circle"),
class = "redButton"
)
)
) # end of modalDialog
)
},
label = "EAL quit?"
)
# calls save method and quits
observeEvent(input$save_quit, {
req(input$save_quit)
# Save work at this state
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
# Clean & reset variables
removeModal()
main_env <- cleanModules(main_env)
},
label = "EAL save+quit",
ignoreInit = TRUE
)
# quits simply
observeEvent(input$simple_quit, {
req(input$quit)
# Clean & reset variables
removeModal()
main_env <- cleanModules(main_env)
},
label = "EAL quit",
ignoreInit = TRUE
)
# quit management
## Save ----
observeEvent(input$save, {
devmsg("%s", main_env$EAL$page, tag = "fill_module.R")
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
})
## Autosave ----
observeEvent(main_env$EAL$page, {
req(main_env$EAL$page != 1)
devmsg("step: %s", tag = "fill_module.R/autosave", main_env$EAL$page)
saveReactive(main_env, main_env$EAL$page, do_template = FALSE)
},
priority = -2,
label = "EAL: autosave"
) # important priority
## Current step ----
output$current_step <- renderText({
req(main_env$EAL$current)
gsub(
"_",
" ",
switch(main_env$EAL$current,
SelectDP = "Select Data Package",
main_env$EAL$current
)
)
})
# Navigation ====
observeEvent(main_env$EAL$page, {
req(main_env$EAL$page != main_env$EAL$old_page)
withProgress({
## Save & Template ----
devmsg(tag = "fill_module.R/navigation", "save & template")
if (main_env$EAL$old_page > 1) {
saveReactive(
main_env,
main_env$EAL$old_page,
# do not template on 'previous'
do_template = main_env$EAL$old_page < main_env$EAL$page
)
}
incProgress(1 / 8)
## set EAL variables ----
devmsg(tag = "fill_module.R/navigation", "set EAL variables")
# left Data Files
if (main_env$EAL$old_page == 2) {
unlink(main_env$PATHS$eal_tmp)
}
# reached Data Files
if (main_env$EAL$page == 2) {
main_env$PATHS$eal_tmp <- tempdir()
}
# Properly change page
main_env$EAL$current <- main_env$VALUES$steps[main_env$EAL$page]
main_env$EAL$tag_list <- tagList()
incProgress(1 / 8)
## Reset local_rv ----
devmsg(tag = "fill_module.R/navigation", "set local_rv")
main_env <- setLocalRV(main_env)
incProgress(1 / 8)
## Set UI for new page ----
## TODO
updatePageUI(main_env, session)
incProgress(1 / 8)
## Change page ----
devmsg(tag = "fill_module.R/navigation", "change pane")
updateTabsetPanel(
session,
"wizard-wizard",
selected = steps[main_env$EAL$page]
)
incProgress(1 / 8)
## Update history ----
if (!main_env$EAL$current %in% main_env$EAL$history) {
main_env$EAL$history <- c(
main_env$EAL$history,
main_env$EAL$current
)
}
devmsg(tag = "fill_module.R/navigation", "update history")
incProgress(1 / 8)
## Savevar changes ----
devmsg(tag = "fill_module.R/navigation", "save_variables change")
main_env$save_variable$step <- main_env$EAL$page
main_env$save_variable$history <- main_env$EAL$history
## Accessory UI elements ----
devmsg(tag = "fill_module.R/navigation", "display UI")
if (main_env$EAL$page > 1) {
shinyjs::show("top_row")
shinyjs::show("current_DP")
shinyjs::show("help")
shinyjs::show("save")
shinyjs::show("quit")
} else {
shinyjs::hide("top_row")
shinyjs::hide("current_DP")
shinyjs::hide("help")
shinyjs::hide("save")
shinyjs::hide("quit")
}
incProgress(1 / 8)
devmsg(tag = "fill_module.R/navigation", "ended")
## Helps ====
main_env$EAL$help <- modalDialog(
title = paste0(main_env$EAL$current, " - Help"),
switch(main_env$EAL$page,
### SelectDP ====
tagList(
tags$p("This module allows you to manage your", tags$strong("data packages"), ".
A data package (aka DP) is a collection of a dataset and its associated metadata
and resources (scripts, literature, ...). You can:"),
tags$ul(
tags$li("Load an existing data package among local ones (left). You
will resume its edition at the last saved encountered step."),
tags$li(
"Create a new data package. You must fill in", tags$strong("three fields"),
tags$i("Data package name"), "will be used for identifying the DP,",
tags$i("Data package title"), "will be displayed when consulting the DP
page once formatted (explained in last step),",
tags$i("Data package license"), "is the license assigned to this production for
intellectual rights properties"
)
)
# , tags$p("Also, notice the", tags$strong("quick"), "check box above DP name.
# Checking this box enables \"quick mode\" which will pre-fill most of the
# fields in further steps. You still will be able to edit them at your
# convenience.")
),
### Data Files ====
tagList(
tags$p("This module allows you to load data files from the dataset you want to
describe. Once uploaded, you can set:"),
tags$ul(
tags$li(tags$i("Content name:"), "A name for the data contained in the file (e.g. table name)."),
tags$li(tags$i("URL:"), "If the file is accessible remotely, here is a way to reference it."),
tags$li(tags$i("Description:"), "A short text provided to describe the file, its content,
relevant information about the data in the entity.")
),
tags$p("To edit your selection, select files among the list
with the check boxes on their left, then click the \"Remove\"
button."),
tags$p("Recommended size per file is around 1 Gb. Such files
and heavier ones might slow down the
app.")
),
### Attributes ====
tagList(
tags$p("This module allows you to describe precisely each
attribute of each file. Some of these metadata are guessed
from the data files. Such fields are annoted with a star (*).
For each attribute, you can set:"),
tags$ul(
tags$li(tags$i("Attribute Name*:"), "the name of the
attribute."),
tags$li(tags$i("Attribute Description:"), "a description of
the attribute."),
tags$li(tags$i("Attribute Class*:"), "the type of content in
the attributes among \"numeric\", \"character\",
\"categorical\" and \"Date\". Categorical means a character
string with encoded values (e.g. Male/Female)."),
tags$li(tags$i("Date format (only for Date class): how the
dates of the attributes are written (e.g. DD-MM-YYYY).")),
tags$li(tags$i("Unit (only for Numeric class):"), "which is
the unit used for the numeric data of the attributes. The
list is huge and refers to", tags$a("STMML units",
href = "http://www.ch.ic.ac.uk/rzepa/codata2/"
), ". You can
also define you own unit (see Custom Units thereafter)."),
tags$li(tags$i("Missing Value Code:"), "a one-word code used
instead of a missing value among the data of the attribute
currently described."),
tags$li(tags$i("Missing Value Code Explanation:"), "a short
definition of the meaning(s) given for the missing value
code.")
),
tags$h3("Custom units creation"),
tags$p("EML allows the user to define its own units, but this
require to fulfill some more fields. However, the custom units
you will have defined will be saved into the Custom Unit table
at the bottom of this page. You will find the written custom
units in the units selection once they are written. To define
a custom unit, chose the unit to be \"custom\". A custom unit
is defined with:"),
tags$ul(
tags$li(tags$i("Unit id:"), "the id of the unit (e.g.
gramsPerOneThirdMeter)."),
tags$li(tags$i("Unit type:"), "the physical property
measured by the custom unit (e.g. mass)."),
tags$li(tags$i("Parent unit in SI:"), "from which unit among
the most common one is custom unit derived (e.g. gram)."),
tags$li(tags$i("Multiplier to SI:"), "by how many has the
custom unit to be multiplied to be equal to its parent
unit."),
tags$li(tags$i("Unit description:"), "some additional notes
about the unit, how to compute it.")
)
),
### Catvars ====
tagList(
tags$p("This module allows you to detail the categorical
variables (class \"categorical\" in Attributes). For each
variable, you will be able to detail each of its value by a
short description.")
),
### Geocov ====
tagList(
tags$p("This module allows you to define the geographic area
in which the data have been produced. You have the choice
between two methods to define geographic coverage:"),
tags$ul(
tags$li(
tags$h4("Variable selection (recommended)"),
tags$p("This method allows you to fetch interesting
attributes for geographic coverage. Prefer storing all of
your locations into a single table or equally dimensioned
tables, under 3 to 5 columns: one for the site description
and one or two others for latitude and longitude. For
latitude and longitude, chosing a single column will be
interpreted as points, while chosing two will result in an
area. Southern latitude and western longitude shall be
noted with negative values.")
),
tags$li(
tags$h4("Manual geographic coverage"),
tags$p("Chose this method if your dataset does not include
data sites description and/or coordinates. You will be
able to provide as many sites as you wish, as single
points or rectangle areas.You can detail a more precise
number by using the left/right (or down/up) arrows of your
keyboard. Precision can be given at 0.01°.")
)
)
),
### Taxcov ====
tagList(
tags$p("This module allows you to define the taxonomical
coverage of the study. You will be asked to select columns
among your files containing the species name. Also, let the
app know if the taxonomic coverage shall be written with
scientific, common or both names. At last, select at least one
taxonomic authority among the ones suggested."),
),
### Personnel ====
tagList(
tags$p(
"This module allows you to get a full list of people
who contributed to the creation of this dataset. The
recommended best practice is to", tags$b("use the ORCID"),
"of a person. With this and the help of {rorcid}, the app will
be able to fetch all available and interesting data. You will
be able to correct this afterwards. Also, note that you must
fill in the fields for two roles: creator and contact."
),
tags$p("Suggested roles are the following:"),
tags$ul(
tags$li("Creator: person who contributed to produce the
data."),
tags$li("Contact: persone to contact for any question about
the data."),
tags$li("Principal investigator: person who led the creation
of the dataset. Selecting this will allow you to
fill in additional information about the project and
its funding."),
tags$li("Custom: as the roles list is not exhaustive, feel
free to add any role you consider important.")
)
),
### Misc ====
tagList(
tags$p("This module allows you to define the last details of
your data package. Note that you can write some of these
metadata using the markdown syntax. Here are brief
descriptions of the fields:"),
tags$ul(
tags$li("Abstract: the abstract of the publication linked to
those data."),
tags$li("Methods: the methods used in the production of this
dataset."),
tags$li(
"Keywords: you can type a list of keywords for
your dataset. For each keyword, you can add a keyword
thesaurus, like",
tags$a("the LTER controlled vocabulary",
href =
"http://vocab.lternet.edu/vocab/vocab/index.php"
),
", which are controlled vocabulary your exact keyword
originates from. Keywords thesaurus are not required."
),
tags$li("Temporal coverage: this lets you define the
duration of the study during which the data have
been produced."),
tags$li("Additional information: if any information has
been omitted, you can provide it here (e.g. collection
metadata from GBIF-EML).")
)
),
### Make EML ====
tagList(
tags$p("Here we are (well done) ! This is the final step to
write EML. Just click the button and let the magic happen.
If an error occurs, this will be displayed to the screen. In
this case, do not hesitate to get in touch with the dev
team."),
tags$p("You can also use the {emldown} package to get a
human-readable version of the generated EML. The button
below it will let you download the result of this step.")
)
),
footer = modalButton("Close"),
easyClose = TRUE, fade = TRUE
)
incProgress(1 / 8)
},
message = sprintf("loading %s", main_env$VALUES$steps[main_env$EAL$page])
)
},
label = "EAL0: change page"
)
observeEvent(input$help, {
showModal(main_env$EAL$help)
})
# (End) ====
})
}
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