Merge pull request #22 from Sweetdevil144/master

Update server URLs in code
PecanProject · Apr 1, 2024 · 8c000c4 · 8c000c4
2 parents 362f289 + 7bee1a5
commit 8c000c4
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Showing 58 changed files with 151 additions and 118 deletions.
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -14,9 +14,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         shell: Rscript {0}
@@ -62,4 +62,4 @@ jobs:
         shell: Rscript {0}
         run: |
           pkgdown::deploy_to_branch(new_process = FALSE)
-          
+          
diff --git a/R/connect.R b/R/connect.R
@@ -12,7 +12,7 @@
 ##' @return A server object that can be passed into other functions for making requests to the PEcAn API
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 
 connect <- function(url, username=NULL, password=NULL){
   res <- list(url=sub('^/|/$','',url), username=username, password=password)

diff --git a/R/download.input.R b/R/download.input.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Download the 'niwot.clim' file (id = 99000000003)
 ##' download.input(server, input_id='99000000003', save_as='local.niwot.clim')

diff --git a/R/download.run.input.R b/R/download.run.input.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Download the 'sipnet.clim' input for the run with id = '99000000282'
 ##' download.run.input(server, run_id=99000000282, filename='sipnet.clim', save_as='test.sipnet.clim')

diff --git a/R/download.run.output.R b/R/download.run.output.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Download the 'README.txt' output for the run with id = '99000000282'
 ##' download.run.output(server, run_id=99000000282, filename='README.txt', save_as='test.README.txt')

diff --git a/R/download.workflow.file.R b/R/download.workflow.file.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Download the 'ensemble.ts.99000000017.NPP.2002.2002.Rdata' output file for the workflow with id = 99000000031
 ##' download.workflow.file(server, workflow_id=99000000031, filename='ensemble.ts.99000000017.NPP.2002.2002.Rdata')

diff --git a/R/get.format.R b/R/get.format.R
@@ -8,7 +8,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of the Ameriflux.level4.h format (id = 19)
 ##' res <- get.format(server, format_id=19)

diff --git a/R/get.model.R b/R/get.model.R
@@ -8,7 +8,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of the SIPNET ssr model (id = 1000000022)
 ##' res <- get.model(server, model_id=1000000022)

diff --git a/R/get.pft.R b/R/get.pft.R
@@ -8,7 +8,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of the temperate.deciduous PFT (id = 41)
 ##' res <- get.pft(server, pft_id=41)

diff --git a/R/get.run.R b/R/get.run.R
@@ -9,7 +9,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of run with id = '1002042201'
 ##' res <- get.run(server, 1002042201)

diff --git a/R/get.runs.R b/R/get.runs.R
@@ -10,7 +10,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all runs for the workflow with ID '1000009172'
 ##' res <- get.runs(server, workflow_id=1000009172)

diff --git a/R/get.site.R b/R/get.site.R
@@ -2,52 +2,47 @@
 ##' Hits the `/api/sites/{site_id}` API endpoint.
 ##' @name get.site
 ##' @title Get details of PEcAn Site from the database using site id
-##' @param server Server object obtained using the connect() function 
+##' @param server Server object obtained using the connect() function
 ##' @param site_id ID of the model to retrieve
 ##' @return Response obtained from the `/api/sites/{site_id}` endpoint
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
-##' 
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
+##'
 ##' # Get details of the WillowCreek(US-WCr) site (id = 676)
 ##' res <- get.site(server, site_id=676)
 
-get.site <- function(server, site_id){
+get.site <- function(server, site_id) {
   res <- NULL
   tryCatch(
     expr = {
       url <- paste0(server$url, "/api/sites/", site_id)
-      
-      if(! is.null(server$username) && ! is.null(server$password)){
+
+      if (!is.null(server$username) && !is.null(server$password)) {
         res <- httr::GET(
           url,
           httr::authenticate(server$username, server$password)
         )
-      }
-      else{
+      } else {
         res <- httr::GET(url)
       }
     },
     error = function(e) {
       message("Sorry! Server not responding.")
     }
   )
-  
-  if(! is.null(res)) {
-    if(res$status_code == 200){
+
+  if (!is.null(res)) {
+    if (res$status_code == 200) {
       return(jsonlite::fromJSON(rawToChar(res$content)))
-    }
-    else if(res$status_code == 401){
+    } else if (res$status_code == 401) {
       stop("Invalid credentials")
-    }
-    else if(res$status_code == 404){
+    } else if (res$status_code == 404) {
       stop("Site not found")
-    }
-    else if(res$status_code == 500){
+    } else if (res$status_code == 500) {
       stop("Internal server error")
-    }
-    else{
+    } else {
       stop("Unidentified error")
     }
   }

diff --git a/R/get.status.R b/R/get.status.R
@@ -8,7 +8,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' res <- get.status(server)
 
 get.status <- function(server){

diff --git a/R/get.workflow.R b/R/get.workflow.R
@@ -9,7 +9,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of workflow with id = '1000009172'
 ##' res <- get.workflow(server, workflow_id=1000009172)

diff --git a/R/get.workflow.status.R b/R/get.workflow.status.R
@@ -9,7 +9,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of workflow with id = '1000009172'
 ##' res <- get.workflow.status(server, workflow_id=1000009172)

diff --git a/R/get.workflows.R b/R/get.workflows.R
@@ -13,7 +13,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get list of all workflows
 ##' res1 <- get.workflows(server)

diff --git a/R/ping.R b/R/ping.R
@@ -8,7 +8,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' res <- ping(server)
 
 ping <- function(server){

diff --git a/R/plot_run_vars.R b/R/plot_run_vars.R
@@ -14,7 +14,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Plot the Gross Primary Productivity vs Time for the run with ID '99000000282' for the year 2002
 ##' plot_run_vars(server, run_id=99000000282, year=2002, y_var="GPP")

diff --git a/R/search.formats.R b/R/search.formats.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all formats
 ##' res1 <- search.formats(server)

diff --git a/R/search.inputs.R b/R/search.inputs.R
@@ -14,7 +14,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all inputs
 ##' res1 <- search.inputs(server)

diff --git a/R/search.models.R b/R/search.models.R
@@ -11,7 +11,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all models
 ##' res1 <- search.models(server)

diff --git a/R/search.pfts.R b/R/search.pfts.R
@@ -13,7 +13,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all PFTs
 ##' res1 <- search.pfts(server)

diff --git a/R/search.sites.R b/R/search.sites.R
@@ -10,7 +10,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Get details of all sites
 ##' res1 <- search.sites(server)

diff --git a/R/submit.workflow.R b/R/submit.workflow.R
@@ -20,7 +20,7 @@
 ##' @author Tezan Sahu, Alexey Shiklomanov
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' 
 ##' # Submit a workflow with the SIPNET r136 model (id = 1000000014) for Niwot Ridge site (id = 772) with 
 ##' # PFT as 'temperate.coniferous' starting from 01-01-2002 to 31-12-2003 using the input met data with

diff --git a/R/submit.workflow.json.R b/R/submit.workflow.json.R
@@ -9,7 +9,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' res <- submit.workflow.json(server, "api.sipnet.json")
 
 submit.workflow.json <- function(server, jsonFile){

diff --git a/R/submit.workflow.xml.R b/R/submit.workflow.xml.R
@@ -9,7 +9,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' res <- submit.workflow.xml(server, "api.sipnet.xml")
 
 submit.workflow.xml <- function(server, xmlFile){

diff --git a/R/submit.workflows.csv.R b/R/submit.workflows.csv.R
@@ -10,7 +10,7 @@
 ##' @author Tezan Sahu
 ##' @export
 ##' @examples
-##' server <- connect(url="http://localhost:8000", username="carya", password="illinois")
+##' server <- connect(url="http://pecan.localhost:80", username="carya", password="illinois")
 ##' res <- submit.workflows.csv(server, "default_tests.csv")
 
 submit.workflows.csv <- function(server, csvFile) {