First RStudio commit.

Known bug:
- in EMLAL-module: triggers error: `Error in FUN: 'options' must be a fully named list, or have no names (NULL)`

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

MetaShARK.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

contributing.md

@@ -7,7 +7,7 @@ As the project grows in size and code lines, it appears its design is not clean,
 The naming convention is inspired by the [Python naming convention](https://www.python.org/dev/peps/pep-0008/#package-and-module-names)
 
 **variables**
-*local.var*	variables are named in lowercase letters, and might be separated by single dots for legibility purposes
+*localVar*	variables are named in lowercase letters 'camelCase'.  
 *GLOBAL.VAR*	global variables (defined outside any function) are named with capital letters, and separated with dots.
 *Class*		class are named as variables, but their names begin with a capital letter
 
@@ -28,6 +28,19 @@ The naming convention is inspired by the [Python naming convention](https://www.
 *element-type*	element are named (through their 'id' argument) in lowercase separated with "-". They shall be built as follow `id-type[-misc]` with type the structure of the element.
 *\*put.ids*	in/output elements ids in the server are named in lowercase separated with dots. They shall be built as follow `what.info` with *what* the informative element and *info* the action/information contained about *what*.
 
+##
+For the **Fill/EMLAL** module, a specific variable is built: *fill*. It is of type `list` and contains `reactiveValues` in its leaves. Intermediate levels are sub-lists. The variable is built as follow:  
+. fill  
+├- emlal  
+|  ├- selectDP  
+|  ├- createDP  
+└- metafin  
+The building logic is:  
+* *root* is a list with elements corresponding to each metadata filling module (EML Assembly Line, MetaFIN).
+* 1st level nodes match filling module and contain sublist for each step of the filling process.
+* 2nd level nodes' elements are `reactiveValues` object containing the filled metadata.  
+Each of the modules node are returned at the end of their respective module. While reading a module, beware of the way their input is written.  
+
 ## Git files organization
 + _old
 + shinyApp

shinyApp/dataPackagesOutput/emlAssemblyLine/example_files/decomp.csv

@@ -0,0 +1 @@
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asperaVascular,2015-01-01,2,0,2015,43.49,Vascular,2015-01-01,2,0,2015,40.85,Vascular,2015-01-01,2,0,2015,39.25,Vascular,2015-01-01,2,0,2015,44.05,MossesVascular,2015-01-01,3,0,2015,48.35,Unsorted biomassVascular,2015-01-01,3,0,2015,53.93,Achillea millefoliumVascular,2015-01-01,3,0,2015,57.65,Achillea millefoliumVascular,2015-01-01,3,0,2015,46.64,Achillea millefoliumVascular,2015-01-01,1,5,2015,47.12,Crepis tectorumVascular,2015-01-01,1,5,2015,49.55,Cyperus sp.Vascular,2015-01-01,1,5,2015,42.38,Euphorbia glyptospermaVascular,2015-01-01,1,5,2015,49.61,Lespedeza capitataVascular,2015-01-01,2,5,2015,36.88,Achillea millefoliumVascular,2015-01-01,2,5,2015,49.98,Achillea millefoliumVascular,2015-01-01,2,5,2015,27.11,Achillea millefoliumVascular,2015-01-01,2,5,2015,56.04,Achillea millefoliumVascular,2015-01-01,3,5,2015,36.83,Cyperus sp.Vascular,2015-01-01,3,5,2015,50.84,Lepidium densiflorumVascular,2015-01-01,3,5,2015,48.14,Lespedeza capitataVascular,2015-01-01,3,5,2015,50.09,Poa pratensisVascular,2015-01-01,1,10,2015,-99999,Rumex acetosellaVascular,2015-01-01,1,10,2015,48.83,Schizachyrium scopariumVascular,2015-01-01,1,10,2015,47.8,Unsorted biomassVascular,2015-01-01,1,10,2015,44.35,Bouteloua gracilisVascular,2015-01-01,2,10,2015,36.41,Cyperus sp.Vascular,2015-01-01,2,10,2015,45.09,Koeleria cristataVascular,2015-01-01,2,10,2015,39.27,Lespedeza capitataVascular,2015-01-01,2,10,2015,27.94,Liatris asperaVascular,2015-01-01,3,10,2015,51.17,MossesVascular,2015-01-01,3,10,2015,48.98,Unsorted biomassVascular,2015-01-01,3,10,2015,45.69,Achillea millefoliumVascular,2015-01-01,3,10,2015,56.33,Achillea millefoliumVascular,2015-01-01,1,15,2015,45.13,Achillea millefoliumVascular,2015-01-01,1,15,2015,41.27,Crepis tectorumVascular,2015-01-01,1,15,2015,44.5,Cyperus sp.Vascular,2015-01-01,1,15,2015,45.79,Euphorbia glyptospermaVascular,2015-01-01,2,15,2015,24.64,Lespedeza capitataVascular,2015-01-01,2,15,2015,31.82,Achillea millefoliumVascular,2015-01-01,2,15,2015,40.5,Achillea millefoliumVascular,2015-01-01,2,15,2015,35.23,Achillea millefoliumVascular,2015-01-01,3,15,2015,20.77,Achillea millefoliumVascular,2015-01-01,3,15,2015,38.1,Cyperus sp.Vascular,2015-01-01,3,15,2015,33.44,Lepidium densiflorumVascular,2015-01-01,3,15,2015,38.4,Lespedeza capitataVascular,2015-01-01,1,20,2015,30.45,Poa pratensisVascular,2015-01-01,1,20,2015,-99999,Rumex acetosellaVascular,2015-01-01,1,20,2015,33.12,Schizachyrium scopariumVascular,2015-01-01,1,20,2015,32.19,Unsorted biomassVascular,2015-01-01,2,20,2015,24.09,Bouteloua gracilisVascular,2015-01-01,2,20,2015,37.39,Cyperus sp.Vascular,2015-01-01,2,20,2015,29.52,Koeleria cristataVascular,2015-01-01,2,20,2015,30.02,Lespedeza capitataVascular,2015-01-01,3,20,2015,41.79,Liatris asperaVascular,2015-01-01,3,20,2015,41.24,MossesVascular,2015-01-01,3,20,2015,45.6,Unsorted biomassVascular,2015-01-01,3,20,2015,35.72,Achillea millefoliumVascular,2015-01-01,1,25,2015,40.97,Achillea millefoliumVascular,2015-01-01,1,25,2015,41.92,Achillea millefoliumVascular,2015-01-01,1,25,2015,36.92,Crepis tectorumVascular,2015-01-01,1,25,2015,47.19,Cyperus sp.Vascular,2015-01-01,2,25,2015,27.13,Euphorbia glyptospermaVascular,2015-01-01,2,25,2015,33.67,Lespedeza capitataVascular,2015-01-01,2,25,2015,40.77,Achillea millefoliumVascular,2015-01-01,2,25,2015,45.95,Achillea millefoliumVascular,2015-01-01,3,25,2015,40.8,Achillea millefoliumVascular,2015-01-01,3,25,2015,27.64,Achillea millefoliumVascular,2015-01-01,3,25,2015,30.73,Cyperus sp.Vascular,2015-01-01,3,25,2015,41.32,Lepidium densiflorum