get_data script and notebook have ipymd installed still need to figure out how it works.

.gitignore

@@ -2,3 +2,5 @@
 workspace/temp_data
 workspace/.ipynb_checkpoints
 workspace/data
+.Rproj.user
+*.Rhistory

Dockerfile

@@ -50,4 +50,13 @@ RUN apt-get -y install \
 		   $(lsb_release -cs) \
 		   stable" && \
 		apt-get -y install docker-ce docker-ce-cli containerd.io
-		
+		
\ No newline at end of file
+USER root
+
+RUN wget http://sslhelp.doi.net/docs/DOIRootCA2.cer -O /usr/local/share/ca-certificates/DOIRootCA2.crt && \
+    chmod 644 /usr/local/share/ca-certificates/DOIRootCA2.crt && update-ca-certificates
+
+RUN Rscript -e 'install.packages("sbtools",repos="https://owi.usgs.gov/R")'
+
+RUN pip --cert /usr/local/share/ca-certificates/DOIRootCA2.crt install ipymd && \
+    pip --cert /usr/local/share/ca-certificates/DOIRootCA2.crt install git+https://github.com/eea/odfpy

docker-compose.yml

@@ -2,7 +2,7 @@ version: '3'
 
 services:
   wbeep:
-    image: dblodgett/gfv2:v0.1
+    image: dblodgett/gfv2:v0.2
     # build: .
     container_name: gfv2
     user: root
@@ -12,5 +12,5 @@ services:
       - ./workspace:/jupyter
     command: >
       sh -c "usermod -a -G docker jovyan &&
-             start.sh jupyter lab --LabApp.token='' --ContentsManager.root_dir='/jupyter'"
+             start.sh jupyter lab --LabApp.token='' --ContentsManager.root_dir='/jupyter' --NotebookApp.notebook_dir='/jupyter' --NotebookApp.contents_manager_class='ipymd.IPymdContentsManager'"
              
\ No newline at end of file

workspace/get_data.R

+library(sbtools)
+library(nhdplusTools)
+data_dir <- "data"
+
+hu12_points_path <- file.path(data_dir, "hu_points.gpkg")
+
+if(!file.exists(hu12_points_path)) {
+  if(is.null(sbtools::current_session()))
+    sb <- authenticate_sb()
+  
+  sbtools::item_file_download("5dbc53d4e4b06957974eddae", names = "hu_points.gpkg", 
+                              destinations = hu12_points_path, session = sb)
+}
+
+gagesiii_points_path <- file.path(data_dir, "GAGESIII_gages")
+
+if(!file.exists(gagesiii_points_path)) {
+  dir.create(gagesiii_points_path, recursive = TRUE, showWarnings = FALSE)
+  
+  if(is.null(sbtools::current_session()))
+    authenticate_sb()
+  
+  g3z <- "GAGESIII_gages.zip"
+  
+  sbtools::item_file_download("5dbc53d4e4b06957974eddae", names = g3z, 
+                              destinations = file.path(gagesiii_points_path, g3z))
+  
+  unzip(file.path(gagesiii_points_path, g3z), exdir = gagesiii_points_path)
+  
+  rm(g3z)
+}
+
+nhdplus_dir <- file.path(data_dir, "NHDPlusNationalData")
+if(!file.exists(nhdplus_dir)) {
+  nhdplus_gdb <- download_nhdplusv2(data_dir)
+
+  nhdplus_path(nhdplus_gdb)
+
+  staged_nhdplus <- stage_national_data()
+}
+
+

workspace/get_data.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "USGS Support Package: https://owi.usgs.gov/R/packages.html#support\n"
+     ]
+    }
+   ],
+   "source": [
+    "source(\"get_data.R\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<ol class=list-inline>\n",
+       "\t<li>'data_dir'</li>\n",
+       "\t<li>'gagesiii_points_path'</li>\n",
+       "\t<li>'hu12_points_path'</li>\n",
+       "\t<li>'nhdplus_dir'</li>\n",
+       "</ol>\n"
+      ],
+      "text/latex": [
+       "\\begin{enumerate*}\n",
+       "\\item 'data\\_dir'\n",
+       "\\item 'gagesiii\\_points\\_path'\n",
+       "\\item 'hu12\\_points\\_path'\n",
+       "\\item 'nhdplus\\_dir'\n",
+       "\\end{enumerate*}\n"
+      ],
+      "text/markdown": [
+       "1. 'data_dir'\n",
+       "2. 'gagesiii_points_path'\n",
+       "3. 'hu12_points_path'\n",
+       "4. 'nhdplus_dir'\n",
+       "\n",
+       "\n"
+      ],
+      "text/plain": [
+       "[1] \"data_dir\"             \"gagesiii_points_path\" \"hu12_points_path\"    \n",
+       "[4] \"nhdplus_dir\"         "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "ls()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "'data'"
+      ],
+      "text/latex": [
+       "'data'"
+      ],
+      "text/markdown": [
+       "'data'"
+      ],
+      "text/plain": [
+       "[1] \"data\""
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "'data/GAGESIII_gages'"
+      ],
+      "text/latex": [
+       "'data/GAGESIII\\_gages'"
+      ],
+      "text/markdown": [
+       "'data/GAGESIII_gages'"
+      ],
+      "text/plain": [
+       "[1] \"data/GAGESIII_gages\""
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "'data/hu_points.gpkg'"
+      ],
+      "text/latex": [
+       "'data/hu\\_points.gpkg'"
+      ],
+      "text/markdown": [
+       "'data/hu_points.gpkg'"
+      ],
+      "text/plain": [
+       "[1] \"data/hu_points.gpkg\""
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "'data/NHDPlusNationalData'"
+      ],
+      "text/latex": [
+       "'data/NHDPlusNationalData'"
+      ],
+      "text/markdown": [
+       "'data/NHDPlusNationalData'"
+      ],
+      "text/plain": [
+       "[1] \"data/NHDPlusNationalData\""
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "data_dir\n",
+    "gagesiii_points_path\n",
+    "hu12_points_path\n",
+    "nhdplus_dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "3.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

workspace/workspace.Rproj

+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX