Remove shiny/BrownDog

Removed other instances of Browndog from `*.Rmd` and addSecrets.R

Signed-off-by: Abhinav Pandey <[email protected]>

base/settings/R/addSecrets.R

@@ -52,19 +52,6 @@ addSecrets <- function(settings, force = FALSE) {
     }
   }
 
-  # only copy these sections if tag exists
-  for (key in c("browndog")) {
-    if (! key %in% names(settings)) next
-
-    for (section in names(pecan[[key]])) {
-      if (section %in% names(settings[section])) {
-        PEcAn.logger::logger.info("Already have a section for", section)
-      } else {
-        PEcAn.logger::logger.info("Imported section for", section)
-        settings[[key]][section] <- pecan[[key]][section]
-      }
-    }
-  }
 
   return(invisible(settings))
 }

base/settings/tests/testthat/test.addSecrets.R

@@ -35,32 +35,3 @@ test_that("`addSecrets` adds secret settings when force is TRUE and secrets have
   expect_equal(updated_settings$database$section$name, "pecan")
   expect_equal(updated_settings$database$section$password, "pecan")  
 })
-
-test_that("`addSecrets` adds secret settings when force is FALSE and secrets have not been added", {
-  settings <- list(
-    settings.info = list(
-      secrets.added = FALSE
-    ),
-    browndog = list()
-  )
-
-  mocked_xmlToList_result <- list(
-    database = list(
-      section = list(
-        name = "pecan",
-        password = "pecan"
-      )
-    ),
-    browndog = list(
-      section = list(
-        name = "pecan"
-      )
-    )
-  )
-  mockery::stub(addSecrets, 'file.exists', TRUE)
-  mockery::stub(addSecrets, 'xmlToList', mocked_xmlToList_result)
-  updated_settings <- addSecrets(settings, force = FALSE)
-  expect_equal(updated_settings$database$section$name, "pecan")
-  expect_equal(updated_settings$database$section$password, "pecan")
-  expect_equal(updated_settings$browndog$section$name, "pecan")
-})

book_source/02_demos_tutorials_workflows/02_user_demos/05_advanced_user_guide/93_workflow_curl.Rmd

@@ -33,8 +33,6 @@ sensitivity=-1,1
 pecan_edit=on
 # redirect to edit the model configuration files
 model_edit=on
-# use browndog
-browndog=on
 ```
 
 For example the following will run the above workflow. Using -v in curl will show verbose output (needed) and the grep will make sure it only shows the redirect. This will show the actual workflowid:

book_source/02_demos_tutorials_workflows/04_more_web_interface/00_intermediate_users_guide.Rmd

@@ -3,7 +3,6 @@
 This section will provide information to those wanting to take advantage of PEcAn's customizations from the web interface.
 
 * [Additional web configuration] - Advanced options available from the web interface
-    - [Brown Dog](#browndog)
     - [Sensitivity and ensemble analyses][Advanced Setup][TODO: Under construction...]
     - [Editing model configurations][TODO: Under construction...]
 * [Settings-configured analyses] - Analyses only available by manually editing `pecan.xml`

book_source/02_demos_tutorials_workflows/04_more_web_interface/01_additional_web_config.Rmd

@@ -3,7 +3,6 @@
 Additional settings for web configuration:
 
 - [Web interface setup]{#intermediate-web-setup}
-- [Brown Dog]{#browndog}
 - [Advanced setup]{#intermediate-advanced-setup}
     - [Sensitivity analysis] (TODO)
     - [Uncertainty analysis] (TODO)
@@ -19,26 +18,16 @@ The list of configuration available
 
 1. **Database configuration** : BETYdb(Biofuel Ecophysiological Traits and Yields database) configuration details, can be edited according to need.
 
-2. **Browndog configuration** : Browndog configuration details, Used to connect browndog. Its included by default in VM.
+2. **FIA Database** : FIA(Forest Inventory and Analysis) Database configuration details, Can be used to add additional data to models.
 
-3. **FIA Database** : FIA(Forest Inventory and Analysis) Database configuration details, Can be used to add additional data to models.
+3. **Google MapKey** : Google Map key, used to access the google map by PEcAn.
 
-4. **Google MapKey** : Google Map key, used to access the google map by PEcAn.
+4. **Change Password** : A small infomation to change the VM user password. (if using Docker image it won't work)
 
-5. **Change Password** : A small infomation to change the VM user password. (if using Docker image it won't work)
-
-6. **Automatic Sync** : If ON then it will sync the database between local machine and the remote servers. **Still unders testing part might be buggy**.
+5. **Automatic Sync** : If ON then it will sync the database between local machine and the remote servers. **Still unders testing part might be buggy**.
 
 Still work on the adding other editing feature going on, this page will be updated as new configuration will be available. 
 
-### Brown Dog {#browndog}
-
-The Browndog service provides PEcAn with access to large and diverse sets of data at the click of a button in the format that PEcAn needs. By clicking the checkbox you will be using the Browndog Service to process data.
-
-For more information regarding meteorological data check out [Available Meteorological Drivers](#met-drivers).
-
-More information can be found at the [Browndog website](http://browndog.ncsa.illinois.edu/).
-
 ### Advanced Setup {#intermediate-advanced-setup}
 
 (TODO: Under construction...)

book_source/03_topical_pages/03_pecan_xml.Rmd

@@ -19,7 +19,6 @@ It contains the following major sections ("nodes"):
 	- [`parameter.data.assimilation`](#xml-parameter-data-assimilation) -- Parameter data assimilation
 	- [`multi.settings`](#xml-multi-settings) -- Multi Site Settings
 	- (experimental) [`state.data.assimilation`](#xml-state-data-assimilation) -- State data assimilation
-	- (experimental) [`browndog`](#xml-browndog) -- Brown Dog configuration
 	- (experimental) [`benchmarking`](#xml-benchmarking) -- Benchmarking
 	- [`remote_process`](#xml-remote_process) -- Remote data module 
 
@@ -972,27 +971,6 @@ For the MODIS LAI and SMAP soil moisture observations, the `search_window` speci
 * **run_parallel** : [optional] This tag defines if you want to proceed the MODIS LAI function parallely, the default value is FALSE.
 
 
-### (experimental) Brown Dog {#xml-browndog}
-
-This section describes how to connect to [Brown Dog](http://browndog.ncsa.illinois.edu). This facilitates processing and conversions of data.
-
-```xml
-  <browndog>
-	<url>...</url>
-	<username>...</username>
-	<password>...</password>
-  </browndog>
-```
-
-* `url`: (required) endpoint for Brown Dog to be used.
-* `username`: (optional) username to be used with the endpoint for Brown Dog.
-* `password`: (optional) password to be used with the endpoint for Brown Dog.
-
-This information is currently used by the following R functions:
-
-- `PEcAn.data.atmosphere::met.process` -- Generic function for processing meteorological input data.
-- `PEcAn.benchmark::load_data` -- Generic, versatile function for loading data in various formats.
-
 ### (experimental) Benchmarking {#xml-benchmarking}
 
 Coming soon...

book_source/03_topical_pages/11_adding_to_pecan.Rmd

@@ -697,9 +697,7 @@ This information is stored in a Format record in the bety database. Make sure to
 If the Format you are looking for is not available, you will need to create a new record. Before entering information into the database, you need to be able to answer the following questions about your data:
 
 - What is the file MIME type? 
-     - We have a suit of functions for loading in data in open formats such as CSV, txt, netCDF, etc. 
-     - PEcAn has partnered with the [NCSA BrownDog project](http://browndog.ncsa.illinois.edu/) to create a service that can read and convert as many data formats as possible. If your file type is less common or a proprietary type, you can use the [BrownDog DAP](http://dap.ncsa.illinois.edu/) to convert it to a format that can be used with PEcAn. 
-     - If BrownDog cannot convert your data, you will need to contact us about writing a data specific load function.
+     - We have a suit of functions for loading in data in open formats such as CSV, txt, netCDF, etc.
 
 - What variables does the file contain?
      - What are the variables named?

modules/benchmark/R/load_data.R

@@ -43,20 +43,6 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
     fcn <- match.fun(fcn1)
   } else if (exists(fcn2)) {
     fcn <- match.fun(fcn2)
-  } else if (!exists(fcn1) & !exists(fcn2) & requireNamespace("BrownDog", quietly = TRUE)) { 
-    #To Do: call to DAP to see if conversion to csv is possible
-    #Brown Dog API call through BDFiddle, requires username and password
-    key   <- BrownDog::get_key("https://bd-api.ncsa.illinois.edu",username,password)
-    token <- BrownDog::get_token("https://bd-api.ncsa.illinois.edu",key)
-    #output_path = where are we putting converted file?
-    converted.data.path <- BrownDog::convert_file(url = "https://bd-api.ncsa.illinois.edu", input_filename = data.path, 
-                                        output = "csv", output_path = output_path, token = token)
-    if (is.na(converted.data.path)){
-      PEcAn.logger::logger.error("Converted file was not returned from Brown Dog")
-    }
-    #not doing anything about mimetypes not convertible by BD right now
-    fcn <- match.fun("load_csv")
-    data.path <- converted.data.path
   } else {
     PEcAn.logger::logger.warn("Brown Dog is currently unable to perform conversion from ",mimetype," to a PEcAn usable format")
   }