Merge pull request #187 from earnaud/dev

Winter production 2022 (1.7.0)

.github/workflows/docker-build.yml

@@ -0,0 +1,21 @@
+name: Docker Image CI
+
+on:
+  push:
+    branches:
+    - dev
+  pull_request:
+    branches:
+    - dev
+
+jobs:
+
+  build:
+    name: build latest
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag eliearnaud/metashark:latest-dev
+    - name: Push the Docker image
+      run: docker push eliearnaud/metashark:latest-dev

.gitignore

@@ -17,4 +17,6 @@ debug.txt
 .~lock.todo.ods#
 todo.ods
 test-enc.R
+.RDataTmp
 ~profvis_metashark.html
+roadmap_annotations.odt

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MetaShARK
 Title: metashark
-Version: 1.6.0
+Version: 1.7.0
 Authors@R: 
     person(given = "Elie",
            family = "ARNAUD",
@@ -18,6 +18,7 @@ Depends:
     R (>= 2.10)
 Imports: 
     config,
+    colourpicker,
     data.table,
     dataone,
     datapack,
@@ -31,6 +32,7 @@ Imports:
     htmltools,
     httr,
     jsonlite,
+    leaflet,
     methods,
     mime,
     profvis,
@@ -70,7 +72,7 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Collate: 
     'DataFiles_helpers2.R'
     'about_module.R'
@@ -132,6 +134,7 @@ Collate:
     'template_functions.R'
     'settings_rightSideBar.R'
     'runMetashark.R'
-    'utils-colorPickerInput.R'
-    'utils-coordinateInput.R'
-    'utils-customLocationInput.R'
+    'utils_colorPickerInput.R'
+    'utils_coordinateInput.R'
+    'utils_customLocationInput.R'
+    'utils_geospatial.R'

Dockerfile

@@ -1,6 +1,6 @@
 FROM rocker/shiny:4.1.0
 
-LABEL version="1.6.0"
+LABEL version="1.7.0"
 
 RUN apt update --fix-missing -y \
     && apt upgrade -y \
@@ -29,6 +29,8 @@ RUN aptitude install -y -f -o APT::Get::Fix-Missing=true \
 	libharfbuzz-dev \
 	libfribidi-dev \
 	mesa-common-dev \
+	libudunits2-dev \
+	libgdal-dev \
   && apt-get clean \ 
   && rm -rf /var/lib/apt/lists/*
 
@@ -40,8 +42,9 @@ RUN dpkg -S /usr/include/GL/gl.h \
 && echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
 && R -e 'install.packages("devtools")' \
 && R -e 'devtools::install_version("remotes", version = "2.3.0")'
+RUN R -e 'remotes::install_github("EDIorg/EMLassemblyline@d3d2eb90a67370c1138e234c09dd96c529408f90")' 
+RUN Rscript -e 'remotes::install_github("earnaud/SummeRnote")'
 
-RUN R -e 'remotes::install_github("EDIorg/EMLassemblyline@ad838f970ee259eda7f96d6a0bbe7f9fa509c66e")' 
 
 RUN  R -e 'remotes::install_version("RCurl",upgrade="never", version = "1.98-1.3")'\
 && R -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")' \
@@ -65,7 +68,12 @@ RUN  R -e 'remotes::install_version("RCurl",upgrade="never", version = "1.98-1.3
 && R -e 'remotes::install_version("golem",upgrade="never", version = "0.3.1")' \
 && R -e 'remotes::install_version("textutils",upgrade="never", version = "0.2-1")' \
 && R -e 'remotes::install_version("tippy",upgrade="never", version = "0.1.0")' \
-&& R -e 'remotes::install_version("shinybusy",upgrade="never", version = "0.2.2")'
+&& R -e 'remotes::install_version("shinybusy",upgrade="never", version = "0.2.2")' \
+&& R -e 'remotes::install_version("units",upgrade="never", version = "0.7-2")'\
+&& R -e 'remotes::install_version("sf",upgrade="never", version = "1.0-5")' \
+&& R -e 'remotes::install_version("leaflet",upgrade="never", version = "2.0.4.1")' \
+&& R -e 'remotes::install_version("leaflet.extras",upgrade="never", version = "1.0.0")' \
+&& R -e 'remotes::install_version("colourpicker",upgrade="never", version = "1.1.1")' 
 
 
 RUN R -e 'remotes::install_local(dir(".", pattern = "MetaShARK_.*\\.tar.gz"), upgrade="never")'

NAMESPACE

@@ -12,6 +12,7 @@ export(isHTMLTruthy)
 export(listReactiveValues)
 export(makeReactiveTrigger)
 export(optional)
+export(reactiveDirReader)
 export(readHTMLfromMD)
 export(remove_shiny_inputs)
 export(renderBibliography)
@@ -38,6 +39,7 @@ importFrom(SummeRnote,summernoteInput)
 importFrom(XML,compareXMLDocs)
 importFrom(XML,newXMLNode)
 importFrom(XML,xmlValue)
+importFrom(colourpicker,colourInput)
 importFrom(config,get)
 importFrom(data.table,fread)
 importFrom(data.table,fwrite)
@@ -66,12 +68,22 @@ importFrom(jsonlite,read_json)
 importFrom(jsonlite,serializeJSON)
 importFrom(jsonlite,unserializeJSON)
 importFrom(jsonlite,write_json)
+importFrom(leaflet,addAwesomeMarkers)
+importFrom(leaflet,addPolygons)
+importFrom(leaflet,addRectangles)
+importFrom(leaflet,addTiles)
+importFrom(leaflet,leaflet)
+importFrom(leaflet,leafletOutput)
+importFrom(leaflet,makeAwesomeIcon)
+importFrom(leaflet,renderLeaflet)
+importFrom(lubridate,guess_formats)
 importFrom(mime,guess_type)
 importFrom(readtext,readtext)
 importFrom(readxl,read_excel)
 importFrom(rmarkdown,pandoc_convert)
 importFrom(scales,brewer_pal)
-importFrom(shiny,in_devmode)
+importFrom(sf,st_as_text)
+importFrom(sf,st_polygon)
 importFrom(shiny,tags)
 importFrom(shinyBS,bsCollapse)
 importFrom(shinyBS,bsCollapsePanel)

NEWS.md

@@ -1,3 +1,27 @@
+# V1.7.0 (pre-release)
+
+## Features 
+
+* Style enhanced
+
+* Personnel step reworked
+
+* Navigation issues fixed
+
+* Geospatial data support
+
+## Work in progress
+
+* Bugs: test and stabilize this version
+
+* MetaFIN: continue `dev-metafin` branch
+
+* Annotations: add annotations module
+
+* Docker: optimize docker image
+
+* Tests: continue writing tests
+
 # V1.6.1
 
 ## Features 
@@ -6,12 +30,26 @@
 
 * Added a counter for the number of users, outputting in the logs.
 
+* New styles and display for enhanced graphic UI.
+
+* Custom geographic coverage now includes drawing tool.
+
+* Geographic coverage now supports .shp files.
+
+* Fixed EAL 8
+
+* Updated Docker (thanks to https://github.com/charlycou)
+
 ## Work in progress
 
-* Tests: write a complete set of tests. 
+* Tests: write a complete set of tests.
+
+* Bugs: many were spotted, many more to fix.
 
 * Annotations: continue `dev-metafin` branch.
 
+* Geospatial data: integration of EAL progress.
+
 # v1.6.0
 
 ## Features

R/DataFiles_helpers2.R

@@ -54,7 +54,7 @@ DataFileInputUI2 <- function(id, main.env) {
     shinyjs::hidden(
       tags$div(
         id = NS(id, "content"),
-        class = "contentRow",
+        # class = "contentRow",
         tagList(
           fluidRow(
             column(

R/about_module.R

@@ -6,33 +6,34 @@
 #' @noRd
 aboutUI <- function(id) {
   fluidPage(
+    # PNDB presentation
     tags$h1("About MetaShARK dev team"),
     HTML("MetaShARK is developped within the french Museum National 
           d'Histoire Naturelle / UMS Patrimoine Naturel / Pole 
           National de Biodiversite. Its development team is currently
           composed of <a href='https://fr.linkedin.com/in/elie-arnaud-440132151?trk=people-guest_profile-result-card_result-card_full-click'>Elie Arnaud</a>
           (lead developer) and <a href ='https://fr.linkedin.com/in/yvan-le-bras-aa2b3738?trk=people-guest_profile-result-card_result-card_full-click'>Yvan Le Bras</a> (team director)."),
-
+    # Thanks
     tags$h1("Thanks"),
     HTML("MetaShARK could not be built without the help of those people: </br>
         <ul>
           <li>Colin Smith (EDI, US)</li> who collaborates with us since March 
           2019, and currently provides us the <a href='https://github.com/EDIorg/EMLassemblyline'>EML Assembly Line</a> tool.
         </ul>"),
-
+    # References
     tags$h1("References"),
-    # Parties
+    ## Parties
     tags$h2("LTER and EML Actors"),
     tags$p("The following people and parties have worked upstream of
       MetaShARK dev team to provide the fundamentals united in
       the present tool."),
     uiOutput(NS(id, "actors")),
-    # Informatics
+    ## Informatics
     tags$h2("Computer material"),
     tags$p("The following references will lead the user to the source
       of tools and methods reused in MetaShARK."),
     uiOutput(NS(id, "informatics")),
-    # Science litterature
+    ## Science litterature
     tags$h2("Literature"),
     tags$p("MetaShARK is based on the following papers and articles
       concerning mainly ecological metadata."),

R/about_module_functions.R

@@ -11,29 +11,34 @@
 #' 
 #' @export
 renderBibliography <- function(bib) {
+  # read bibliography content
   .bib <- RefManageR::ReadBib(bib)
+  # avoid getting numbers: just render a list
   RefManageR::NoCite(.bib, "*")
 
+  # make the UI, once and for all  
   renderUI(
     withProgress(message = "Loading bibliography entry ...", value = 0, {
       HTML(
         paste(
-          utils::capture.output(
-            invisible(
+          utils::capture.output( # get output from i/o string
+            invisible( # do not print in logs
+              # for each elements of bibliography ...
               sapply(
                 .bib,
+                # ... render proper bibliography
                 function(b) {
                   incProgress(1 / length(.bib))
                   RefManageR::PrintBibliography(b,
                     .opts = list(style = "html")
                   )
                 }
               )
-            )
+            ) # end of invisible
           ),
           collapse = ""
-        )
+        ) # end of paste
       )
-    })
-  )
+    }) # end of withProgress
+  ) # end of renderUI
 }