Merge branch 'harmen' of https://git.wur.nl/wsg35306/marina-practical into harmen

Dockerfile

+FROM jupyter/datascience-notebook:2022-09-21
+
+RUN mamba install -y -c conda-forge ipysheet
+RUN mamba install -y -c conda-forge jupyter_contrib_nbextensions
+RUN jupyter nbextension enable toc2/main
+RUN jupyter nbextension enable hide_input/main
\ No newline at end of file

MARINA/MARINA_script_2050_GO.R

+#27-09-2022 - Lisanne Nauta: modified windows file paths to platform independent file paths 
 #18 April 2016 was the last update. The code was written by Maryna Strokal 
 
 #set directory
@@ -62,7 +63,7 @@ cal_par_o <- function(g5inputs) {
   
   combined <- cbind(Gdin,Gdon,Gp,ECDIP,ECDON,ECDOP,fRnatDIP,fRnatDON,fRnatDOP,FEwsDIN,FEwsDIP,FEwsDON,FEwsDOP,FErivDINo,FErivDIPo,FErivDONo,FErivDOPo)
   extra.col <- data.frame(code=rep(g5inputs$code), combined[,])
-  write.csv(extra.col, "calculated_parameters\\g5par_o.csv", row.names=F)
+  write.csv(extra.col, file.path("calculated_parameters","g5par_o.csv"), row.names=F)
   g5FEws_G<-extra.col # returns produced .csv with calculations 
 }
 
@@ -97,18 +98,18 @@ cal_par_m <- function(g5inputs_FErivm) {
   
   combined <- cbind(FErivDINm,FErivDIPm,FErivDONm,FErivDOPm)
   combined.code <- data.frame(code=rep(g5inputs$code), combined[,])
-  write.csv(combined.code,"calculated_parameters\\g5par_m.csv", row.names=F)
+  write.csv(combined.code, file.path("calculated_parameters","g5par_m.csv"), row.names=F)
   c0FErivm<-combined.code
 }
 
 #quantifying river export of DIN, DON, DIP, DOP
 
-g5inputs<-read.csv("inputs\\g5inputs.csv", header=T, sep=",") # read .csv inputs
+g5inputs<-read.csv(file.path("inputs","g5inputs.csv"), header=T, sep=",") # read .csv inputs
 
 for (i in 1:length(g5inputs)) {
   # i=1 for testing
   
-  g5inputs_FErivm<-read.csv("inputs\\g5inputs_FErivm.csv",header=T, sep=",")
+  g5inputs_FErivm<-read.csv(file.path("inputs","g5inputs_FErivm.csv"),header=T, sep=",")
   g5par_o<-cal_par_o(g5inputs) # call function that quantifies model parameters: FEws, EC, FEriv for outlets 
   g5par_m<-cal_par_m(g5inputs_FErivm) # call functions that quantifies FEriv for mouths
  
@@ -154,7 +155,7 @@ for (i in 1:length(g5inputs)) {
   
   combined2 <- cbind(DINdiffe,DINdifma,DINdifhum,DINdiffxag,DINdifdpag,DINdiffxna,DINdifdpna,DINpntma,DINpnthumuncon,DINpnthumcon,DONdiffe,DONdifma,DONdifhum,DONdiflchag,DONdiflchna,DONpntma,DONpnthumuncon,DONpnthumcon,DIPdiffe,DIPdifma,DIPdifhum,DIPdifwthag,DIPdifwthna,DIPpntma,DIPpnthumuncon,DIPpnthumcon,DIPpntdetcon,DOPdiffe,DOPdifma,DOPdifhum,DOPdiflchag,DOPdiflchna,DOPpntma,DOPpnthumuncon,DOPpnthumcon,DOPpntdetcon)
   extra.col2 <- data.frame(code=rep(g5inputs$code), combined2[,])
-  write.csv(extra.col2, "outputs\\g5outputs.csv", row.names=F)
+  write.csv(extra.col2, file.path("outputs","g5outputs.csv"), row.names=F)
   
 }
 

MARINA/inputs/g5inputs_original.csv

+code,areacell,frAgr,Nfe,Nma,Nhum,Nfxag,Ndpag,Nex,Nfxna,Ndpna,Npntma,Npnthumuncon,Npnthumcon,Pfe,Pma,Phum,Pex,Ppntma,Ppnthumuncon,Ppnthumcon,Ppntdetcon,FEpntDINhumcon,FEpntDONhumcon ,FEpntDIPhumcon ,FEpntDOPhumcon,Rnat,Ddin,Ddip,Ldin,Ldip,FQrem
+1,58641.80078,0.618381419,174142000,119342649.2,23601181.4,21823000,167787008,151638000,35712400,101299000,116268358.8,10242022.12,6020005.062,87410600,21617388.78,3933530.233,28405800,24457611.22,3488224.924,880804.6568,369248,0.610739095,0.14,1,0.01,0.501767157,0.009525247,0.031495742,0.619941784,0.5,0.107767432
+2,76653,0.258606969,73278000,68529981.5,35227328.43,12417900,76851696,79565800,90956600,222420992,52480018.5,15287331.21,8383747.061,37225300,12006069.35,5871221.405,14975700,11095730.65,5206554.831,1226650.705,514127,0.610739095,0.14,1,0.01,0.290225131,0.024439548,0.092805364,0.636146163,0.5,0.173173983
+3,193659,0.779168539,762457984,519373463.7,99865603.77,99800600,586536000,678387008,67530704,180048992,488376552.3,50503356.36,28938590.24,325807008,93247114.12,16702264.44,122752000,102679893.9,16273384.71,4234090.301,1774140,0.610739095,0.14,1,0.01,0.495553763,0.315661376,0.85,0.65,0.5,0.131430367
+4,30865.5,0.545975305,221471008,82650192.6,22817822.43,10624300,75112704,123155000,22430700,67356400,82431807.4,9902073.883,0,54313900,15802755.01,3802970.404,22025000,18891344.99,3372445.453,0,0,0.610739095,0.14,1,0.01,0.7347099,0.322883946,0.85,0.581112357,0.5,0.10385736
+5,33890,0.555066368,189620000,72762821.84,17585871.17,10880200,70917696,117308000,22605100,49615300,72302170.16,7631604.471,5272122.727,47443700,13806733.35,2930978.529,21237600,16606866.65,2599169.639,439343.5606,187603.0529,0.74,0.14,1,0.01,0.728964144,0.347889522,0.85,0.586767954,0.5,0.153919973
+6,48224.30078,0.561312449,351568992,110245072,20640641.6,20420300,109702000,228123008,31678600,87389296,108311920,8957259.564,70486682.77,79616496,21055584.55,3440106.934,40914300,24793715.45,3050660.866,10313113.99,4321860,0.610739095,0.14,1,0.01,0.708988966,0,0,0.608108909,0.5,0.250028407

README.md

+# Windows Laptop 
+
 ## PREREQUISITE
 
 ### Source Code
@@ -36,4 +38,24 @@ conda activate marina_pract
 jupyter notebook
 ```
 
+# Docker Setup
+
+## PREREQUISITE
+
+### Source Code
+Download the source code from [GitLab](https://git.wur.nl/wsg35306/marina-practical/).
 
+### Docker
+Download Docker or Docker Desktop
+
+## Setup
+1) Open powershell (windows) or macOS command prompt
+2) Change directory to the same level as the Dockerfile.
+3) **Make sure your working directory is on the same level as the Dockerfile.** 
+4) Run the following command: `docker build -t marinapractical:latest .`
+5) Run the following command: `docker create -v ${pwd}:/home/jovyan/marina_practical -it -e DOCKER_STACKS_JUPYTER_CMD=notebook -p 8888:8888 --name marinapractical marinapractical` 
+6) Open Docker Desktop.
+7) Go to containers/apps section.
+8) Start marinapractical container.
+9) Click on the container to see the logs.
+10) Copy the url and paste in a browser.

docker_build.bat

+docker build -t marinapractical:latest .
\ No newline at end of file

docker_create.bat

+docker create -v ${pwd}:/home/jovyan/marina_practical -it -e DOCKER_STACKS_JUPYTER_CMD=notebook -p 8888:8888 --name marinapractical marinapractical
\ No newline at end of file

docker_run.bat

+docker run -v ${pwd}:/home/jovyan/marina_practical -it -e DOCKER_STACKS_JUPYTER_CMD=notebook -p 8888:8888 --name marinapractical marinapractical
\ No newline at end of file