From 8e6fe3faa435e3ee3e5fc14bb51a66c24205c898 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 10:55:06 -0600 Subject: [PATCH 01/12] initial commit: add ds and ds_secure apis as global variables; helper functions to access them. --- R/utils.R | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 R/utils.R diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 0000000..d2b2741 --- /dev/null +++ b/R/utils.R @@ -0,0 +1,18 @@ +## assign global package variables + +#initiate new environment accessible from within package: +.pkgglobalenv <- new.env(parent=emptyenv()) + +#data_store API base URL: +assign("ds_api", "https://irmadevservices.nps.gov/datastore/v6/rest/", envir=.pkgglobalenv) + +#data_store secure API base URL: +assign("ds_secure_api", "https://irmadevservices.nps.gov/datastore-secure/v6/rest/", envir=.pkgglobalenv) + +.ds_api <- function(x){ + get("ds_api", envir = .pkgglobalenv) +} + +.ds_secure_api <- function(x){ + get("ds_secure_api", envir = .pkgglobalenv) +} \ No newline at end of file From a62a9238db92ae75549d3dcbe1269af6ab47cafc Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 10:56:02 -0600 Subject: [PATCH 02/12] update to global variables for ds apis; update to v6 --- R/get_data_packages.R | 41 +++++++++++++++++++++-------------------- 1 file changed, 21 insertions(+), 20 deletions(-) diff --git a/R/get_data_packages.R b/R/get_data_packages.R index eae9e2f..6ab6761 100644 --- a/R/get_data_packages.R +++ b/R/get_data_packages.R @@ -52,9 +52,7 @@ get_data_packages <- function(reference_id, #check for newer version: if(force == FALSE){ cat("Working on: ", crayon::bold$green(reference_id[i]), ".\n", sep="") - url <- paste0( - "https://irmaservices.nps.gov/datastore-secure/v5/rest/ReferenceCodeSearch?q=", - reference_id[i]) + url <- paste0(.ds_secure_api(), "ReferenceCodeSearch?q=", reference_id[i]) #api call to see if ref exists test_req <- httr::GET(url, httr::authenticate(":", ":", "ntlm")) status_code <- httr::stop_for_status(test_req)$status_code @@ -89,8 +87,9 @@ get_data_packages <- function(reference_id, #check for a newer version: version <-ref_data$mostRecentVersion if(!is.na(version)){ - newest_url <- paste0( - "https://irmaservices.nps.gov/datastore-secure/v5/rest/ReferenceCodeSearch?q=", version) + newest_url <- paste0(.ds_secure_api(), + "ReferenceCodeSearch?q=", + version) new_req <- httr::GET(newest_url, httr::authenticate(":", ":", "ntlm")) new_status <- httr::stop_for_status(new_req)$status_code if(!new_status == 200){ @@ -142,9 +141,10 @@ get_data_packages <- function(reference_id, } #get HoldingID from the ReferenceID - defaults to the first holding - rest_holding_info_url <- paste0( - "https://irmaservices.nps.gov/datastore-secure/v4/rest/reference/", - reference_id[i], "/DigitalFiles") + rest_holding_info_url <- paste0(.ds_secure_api(), + "reference/", + reference_id[i], + "/DigitalFiles") xml <- suppressMessages(httr::content(httr::GET(rest_holding_info_url, httr::authenticate(":", ":", "ntlm")))) @@ -156,9 +156,9 @@ get_data_packages <- function(reference_id, for(j in seq_along(xml)){ #get file URL tryCatch( - {rest_download_url <- paste0( - "https://irmaservices.nps.gov/datastore-secure", - "/v4/rest/DownloadFile/",xml[[j]]$resourceId)}, + {rest_download_url <- paste0(.ds_secure_api(), + "DownloadFile/", + xml[[j]]$resourceId)}, error = function(e){ cat(crayon::red$bold( "ERROR: You do not have permissions to access ", @@ -234,9 +234,9 @@ get_data_packages <- function(reference_id, #check for newer version: if(force == FALSE){ cat("Working on: ", crayon::bold$green(reference_id[i]), ".\n", sep="") - url <- paste0( - "https://irmaservices.nps.gov/datastore/v5/rest/ReferenceCodeSearch?q=", - reference_id[i]) + url <- paste0(.ds_api(), + "ReferenceCodeSearch?q=", + reference_id[i]) #api call to see if ref exists test_req <- httr::GET(url, httr::authenticate(":", ":", "ntlm")) status_code <- httr::stop_for_status(test_req)$status_code @@ -279,9 +279,9 @@ get_data_packages <- function(reference_id, #Look for a newer version: version <-ref_data$mostRecentVersion if(!is.na(version)){ - newest_url <- paste0( - "https://irmaservices.nps.gov/datastore/v5/rest/ReferenceCodeSearch?q=", - version) + newest_url <- paste0(.ds_api(), + "ReferenceCodeSearch?q=", + version) new_req <- httr::GET(newest_url, httr::authenticate(":", ":", "ntlm")) new_status <- httr::stop_for_status(new_req)$status_code if(!new_status == 200){ @@ -333,9 +333,10 @@ get_data_packages <- function(reference_id, dir.create(destination_dir) } # get the HoldingID from the ReferenceID - rest_holding_info_url <- paste0( - "https://irmaservices.nps.gov/datastore/v4/rest/reference/", - reference_id[i], "/DigitalFiles") + rest_holding_info_url <- paste0(.ds_api(), + "reference/", + reference_id[i], + "/DigitalFiles") xml <- httr::content(httr::GET(rest_holding_info_url)) #test whether requires secure=TRUE & VPN; alert user: From bfa767eaf4f4f6251b69f207ed5e63b2c567e5f5 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:03:28 -0600 Subject: [PATCH 03/12] update DataStore api to v6 --- R/getReferenceInfo.R | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/R/getReferenceInfo.R b/R/getReferenceInfo.R index 6f8ecca..4855ec5 100644 --- a/R/getReferenceInfo.R +++ b/R/getReferenceInfo.R @@ -18,11 +18,11 @@ #' get_park_taxon_refs("APIS", 126749) #' } get_park_taxon_refs <- function(park_code, taxon_code) { - url <- paste( - "https://irmaservices.nps.gov/datastore-secure/v5/rest/UnitSpeciesSearch/", - park_code, "/", taxon_code, - sep = "" - ) + url <- paste0(.ds_secure_api(), + "UnitSpeciesSearch/", + park_code, + "/", + taxon_code) DSReference <- httr::content(httr::GET( url, httr::authenticate(":", ":", "ntlm") )) %>% @@ -97,10 +97,9 @@ get_park_taxon_url <- function(park_code, taxon_code) { #' get_ref_info(2266196, "Title") #' } get_ref_info <- function(holding_id, field) { - url <- paste0( - "https://irmaservices.nps.gov/datastore/v4/rest/Profile/", - holding_id - ) + url <- paste0(.ds_api(), + "Profile/", + holding_id) DSReference <- httr::content(httr::GET( url, httr::authenticate(":", ":", "ntlm") )) From ba5db61e82e90c73aa2501ddfb4e011a09d59653 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:16:00 -0600 Subject: [PATCH 04/12] update version; update links to issues etc --- DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d9ef764..6e95913 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: NPSutils Type: Package Title: Collection of Functions to read/write information from the NPS Data Store -Version: 0.2.0.3 +Version: 0.2.1 Authors@R: c( person(given = "Robert", family = "Baker", email = "robert_baker@nps.gov", role = c("aut", "cre"), @@ -36,5 +36,5 @@ Suggests: knitr, rmarkdown VignetteBuilder: knitr -URL: https://github.com/RobLBaker/NPSutils -BugReports: https://github.com/RobLBaker/NPSutils/issues +URL: https://github.com/nationalparkservice/NPSutils +BugReports: https://github.com/nationalparkservice/NPSutils/issues From d22f289a1fa08a38ff890efb35cd905834bc2d5f Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:16:13 -0600 Subject: [PATCH 05/12] update version to 0.3.0 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6e95913..8761db8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: NPSutils Type: Package Title: Collection of Functions to read/write information from the NPS Data Store -Version: 0.2.1 +Version: 0.3.0 Authors@R: c( person(given = "Robert", family = "Baker", email = "robert_baker@nps.gov", role = c("aut", "cre"), From 9715e60d9478211e756cdb2396281119b6c3f837 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:16:32 -0600 Subject: [PATCH 06/12] Add info about lots of updates including datastore api v6 --- NEWS.md | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/NEWS.md b/NEWS.md index 12a57e5..9bfa8b6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,16 +1,20 @@ -* added new functionality to `get_data_packages()`: it will now check to see if a DataStore reference ID is invalid or not. It will also check whether the reference is a data package or not. Substantial feedback is reported to the user if the flag force is set to FALSE. -* added a new function `rm_local_packages()` which can delete one or more (or all) packages within a folder called "data" (where your packages should be if you downloaded them with `get_data_packages()`). This only deletes local copies and does not delete any data from DataStore. -* changed function name `load_metadata()` is now `load_pkg_metadata()` so as not to conflict with `DPchecker::load_metadata()` -* updated all function names to be snake_case -* updated all file names to match function names -* updated `get_data_packages()` to (when `force = FALSE`) check for newer versions of requested data packages and prompt the user to download the newest version if they so choose. -* updated `get_data_packages()` to: +# NPSutils 0.3.0 + + * updated all datastore api requests from v4/v5 to v6 (units service remains at v2) + * add global variables for base datastore api urls and helper functions to access them in utils.R + * added new functionality to `get_data_packages()`: it will now check to see if a DataStore reference ID is invalid or not. It will also check whether the reference is a data package or not. Substantial feedback is reported to the user if the flag force is set to FALSE. + * added a new function `rm_local_packages()` which can delete one or more (or all) packages within a folder called "data" (where your packages should be if you downloaded them with `get_data_packages()`). This only deletes local copies and does not delete any data from DataStore. + * changed function name `load_metadata()` is now `load_pkg_metadata()` so as not to conflict with `DPchecker::load_metadata()` + * updated all function names to be snake_case + * updated all file names to match function names + * updated `get_data_packages()` to (when `force = FALSE`) check for newer versions of requested data packages and prompt the user to download the newest version if they so choose. + * updated `get_data_packages()` to: * include a force option. Force defaults to false for a verbose & interactive function. Setting force = TRUE removes the interactive portions and eliminates all informative messages except critical errors. * `get_data_packages()` now inspects the location the data packages are being written to. If a folder with the data package reference id already exists, the function will prompt the user asking if they want to re-download and overwrite the existing data package (when force = FALSE) * `get_data_packages()` now returns the full path to the data package folders, including the "/data" directory they are all in. -* update `get_park_taxon_refs()` to hit v5/rest services -* update documentation: make it clear that the taxon_code parameter in `get_park_taxon_refs()` is the IRMA taxon code, not the ITIS TSN. -* update documentation: make it explicit when `get_park_taxon_refs()` and `get_park_taxon_citations()` are hitting secure servers and warn users that the results may also need to be restricted. + * update `get_park_taxon_refs()` to hit v5/rest services + * update documentation: make it clear that the taxon_code parameter in `get_park_taxon_refs()` is the IRMA taxon code, not the ITIS TSN. + * update documentation: make it explicit when `get_park_taxon_refs()` and `get_park_taxon_citations()` are hitting secure servers and warn users that the results may also need to be restricted. # NPSutils 0.2.0.3 * added `map_wkt()` function to map points, polygons, or both from Well Known Text coordinates (WKT). WKT is used in place to GPS coordinates when sensitive species locations have been "fuzzed". In this case, providing a polygon rather than the an exact (albeit fuzzed) is preferable as it is clear that the location is not exact. WKT is an efficient way to store geographic shapes such as polygons in flat files such as .csv. From 7debf63c55a9375c8a37a9ae9d12f7f14d5ad58e Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:16:46 -0600 Subject: [PATCH 07/12] update to version 0.3.0 --- README.Rmd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.Rmd b/README.Rmd index 92eac8f..7395ff7 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,7 +18,8 @@ knitr::opts_chunk$set( [![CodeFactor](https://www.codefactor.io/repository/github/roblbaker/npsutils/badge)](https://www.codefactor.io/repository/github/roblbaker/npsutils) -# NPS Data Store Utilities - NPSutils +# NPS Data Store Utilities - NPSutils +##v0.3.0 This package is a collection of functions to acquire metadata and data from the [National Park Service Data Store](https://irma.nps.gov/DataStore/). This is an early version of this package and many features will be added in 2023. Please request enhancements and bug fixes through [Issues](https://github.com/nationalparkservice/NPSutils/issues). From 902681a53e3793e458b66d1f4b3d7a1b74c54b45 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:17:15 -0600 Subject: [PATCH 08/12] fix typo in documentation --- R/get_data_packages.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/get_data_packages.R b/R/get_data_packages.R index 6ab6761..023385a 100644 --- a/R/get_data_packages.R +++ b/R/get_data_packages.R @@ -2,7 +2,7 @@ #' #' @description `get_data_packages()` creates a directory called "data" in the current working directory (or user-specified location, see the `path` option). For each data package, it writes a new sub-directory within the "data" directory named with the corresponding data package reference ID. All the data package files are then copied to the directory specific to the data package. #' -#' @detail In the default mode (force = FALSE), `get_data_packages()` will inform a user if the directory for that data package already exists and give the user the option to overwrite it (or skip downloading). In the default mode (force = FALSE), `get_data_packages()` will also check to see if there are newer versions of the requested data package and if there are newer versions, `get_data_packages()` will inform the user of when the requested data package was issued, when the newest data package was issued, and will then ask the user if they would like to download the newest version instead of the requested version. In the default mode (force = FALSE), `get_data_packages()` will warn a user if the reference ID supplied was not found (does not exist or requires VPN) and if a reference ID refers to a product that is not a data package, `get_data_packages()` will ask if the user wants to attempt to download it anyway. +#' @details In the default mode (force = FALSE), `get_data_packages()` will inform a user if the directory for that data package already exists and give the user the option to overwrite it (or skip downloading). In the default mode (force = FALSE), `get_data_packages()` will also check to see if there are newer versions of the requested data package and if there are newer versions, `get_data_packages()` will inform the user of when the requested data package was issued, when the newest data package was issued, and will then ask the user if they would like to download the newest version instead of the requested version. In the default mode (force = FALSE), `get_data_packages()` will warn a user if the reference ID supplied was not found (does not exist or requires VPN) and if a reference ID refers to a product that is not a data package, `get_data_packages()` will ask if the user wants to attempt to download it anyway. #' #' Although `get_data_packages()` is designed to handle the data package reference type on DataStore, it should in theory work on any reference type and download all files associated with a reference (it ignores web links/web resources associated with a reference). If the reference includes a .zip file, the file will be downloaded and the contents extracted. The original .zip archive file will then be deleted. If the .zip contains files with the same name as files in the parent directory, the parent directory files will be over-written by the contents of the .zip archive. #' From 19f3c1b2688be48e6525d40fdf3830e2734f0063 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:17:42 -0600 Subject: [PATCH 09/12] autoupdate via devtools::document & pkgdown --- docs/404.html | 4 +-- docs/LICENSE-text.html | 4 +-- docs/LICENSE.html | 4 +-- docs/articles/NPSutils.html | 8 +++--- docs/articles/index.html | 4 +-- docs/authors.html | 12 ++++----- docs/index.html | 8 +++--- docs/news/index.html | 27 +++++++++++++++++--- docs/pkgdown.yml | 2 +- docs/reference/get_data_packages.html | 11 +++++--- docs/reference/get_park_code.html | 6 ++--- docs/reference/get_park_taxon_citations.html | 6 ++--- docs/reference/get_park_taxon_refs.html | 6 ++--- docs/reference/get_park_taxon_url.html | 6 ++--- docs/reference/get_ref_info.html | 6 ++--- docs/reference/get_unit_code.html | 6 ++--- docs/reference/get_unit_code_info.html | 6 ++--- docs/reference/get_unit_info.html | 6 ++--- docs/reference/index.html | 4 +-- docs/reference/load_data_package.html | 6 ++--- docs/reference/load_data_packages.html | 6 ++--- docs/reference/load_domains.html | 6 ++--- docs/reference/load_pkg_metadata.html | 6 ++--- docs/reference/map_wkt.html | 6 ++--- docs/reference/rm_local_packages.html | 6 ++--- docs/reference/validate_data_package.html | 6 ++--- 26 files changed, 102 insertions(+), 76 deletions(-) diff --git a/docs/404.html b/docs/404.html index 4819c4e..174853b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -50,7 +50,7 @@
  • - + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6640d43..5f153b5 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -32,7 +32,7 @@ Changelog
  • - + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 7461d4a..0fbbc87 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -32,7 +32,7 @@ Changelog
  • - + diff --git a/docs/articles/NPSutils.html b/docs/articles/NPSutils.html index be1e7e3..4478556 100644 --- a/docs/articles/NPSutils.html +++ b/docs/articles/NPSutils.html @@ -33,7 +33,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -51,7 +51,7 @@
  • - + diff --git a/docs/authors.html b/docs/authors.html index 15058ad..15af761 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -32,7 +32,7 @@ Changelog
  • - + @@ -67,21 +67,21 @@

    Authors

    Citation

    - Source: DESCRIPTION + Source: DESCRIPTION

    Baker R, DeVivo J, Patterson J (2023). NPSutils: Collection of Functions to read/write information from the NPS Data Store. -R package version 0.2.0.3, https://github.com/RobLBaker/NPSutils. +R package version 0.3.0, https://github.com/nationalparkservice/NPSutils. 

    @Manual{,
   title = {NPSutils: Collection of Functions to read/write information from the NPS Data Store},
   author = {Robert Baker and Joe DeVivo and Judd Patterson},
   year = {2023},
-  note = {R package version 0.2.0.3},
-  url = {https://github.com/RobLBaker/NPSutils},
+  note = {R package version 0.3.0},
+  url = {https://github.com/nationalparkservice/NPSutils},
 }
    diff --git a/docs/index.html b/docs/index.html index 2b8179c..1e1a10b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -51,7 +51,7 @@
  • - + @@ -47,9 +47,30 @@

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    +
    +

    NPSutils 0.3.0

    +
    • updated all datastore api requests from v4/v5 to v6 (units service remains at v2)
      • +
    • add global variables for base datastore api urls and helper functions to access them in utils.R
      • +
    • added new functionality to get_data_packages(): it will now check to see if a DataStore reference ID is invalid or not. It will also check whether the reference is a data package or not. Substantial feedback is reported to the user if the flag force is set to FALSE.
      • +
    • added a new function rm_local_packages() which can delete one or more (or all) packages within a folder called “data” (where your packages should be if you downloaded them with get_data_packages()). This only deletes local copies and does not delete any data from DataStore.
      • +
    • changed function name load_metadata() is now load_pkg_metadata() so as not to conflict with DPchecker::load_metadata() +
      • +
    • updated all function names to be snake_case
      • +
    • updated all file names to match function names
      • +
    • updated get_data_packages() to (when force = FALSE) check for newer versions of requested data packages and prompt the user to download the newest version if they so choose.
      • +
    • updated get_data_packages() to:
      • +
    • include a force option. Force defaults to false for a verbose & interactive function. Setting force = TRUE removes the interactive portions and eliminates all informative messages except critical errors.
      • +
    • +get_data_packages() now inspects the location the data packages are being written to. If a folder with the data package reference id already exists, the function will prompt the user asking if they want to re-download and overwrite the existing data package (when force = FALSE)
      • +
    • +get_data_packages() now returns the full path to the data package folders, including the “/data” directory they are all in.
      • +
    • update get_park_taxon_refs() to hit v5/rest services
      • +
    • update documentation: make it clear that the taxon_code parameter in get_park_taxon_refs() is the IRMA taxon code, not the ITIS TSN.
      • +
    • update documentation: make it explicit when get_park_taxon_refs() and get_park_taxon_citations() are hitting secure servers and warn users that the results may also need to be restricted.
      • +

    NPSutils 0.2.0.3

    • added map_wkt() function to map points, polygons, or both from Well Known Text coordinates (WKT). WKT is used in place to GPS coordinates when sensitive species locations have been “fuzzed”. In this case, providing a polygon rather than the an exact (albeit fuzzed) is preferable as it is clear that the location is not exact. WKT is an efficient way to store geographic shapes such as polygons in flat files such as .csv.
      • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5c77e15..c1a2f0b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.6.9000 pkgdown_sha: 5bb671b1a8bac8e926479868681936f7c9ee41b3 articles: NPSutils: NPSutils.html -last_built: 2023-08-30T14:19Z +last_built: 2023-08-30T17:14Z diff --git a/docs/reference/get_data_packages.html b/docs/reference/get_data_packages.html index e09fa91..0730bb3 100644 --- a/docs/reference/get_data_packages.html +++ b/docs/reference/get_data_packages.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Retrieve digital data package holding(s) from DataStore.

    - Source: R/get_data_packages.R + Source: R/get_data_packages.R
    @@ -89,6 +89,11 @@

    Value

    String. The path (including the /data folder) where all data package sub-directories and data files are contained.

    +
    +

    Details

    +

    In the default mode (force = FALSE), `get_data_packages()` will inform a user if the directory for that data package already exists and give the user the option to overwrite it (or skip downloading). In the default mode (force = FALSE), `get_data_packages()` will also check to see if there are newer versions of the requested data package and if there are newer versions, `get_data_packages()` will inform the user of when the requested data package was issued, when the newest data package was issued, and will then ask the user if they would like to download the newest version instead of the requested version. In the default mode (force = FALSE), `get_data_packages()` will warn a user if the reference ID supplied was not found (does not exist or requires VPN) and if a reference ID refers to a product that is not a data package, `get_data_packages()` will ask if the user wants to attempt to download it anyway.

    +

    Although `get_data_packages()` is designed to handle the data package reference type on DataStore, it should in theory work on any reference type and download all files associated with a reference (it ignores web links/web resources associated with a reference). If the reference includes a .zip file, the file will be downloaded and the contents extracted. The original .zip archive file will then be deleted. If the .zip contains files with the same name as files in the parent directory, the parent directory files will be over-written by the contents of the .zip archive.

    +

    Examples

    diff --git a/docs/reference/get_park_code.html b/docs/reference/get_park_code.html index 4cee1ac..9bc2cc2 100644 --- a/docs/reference/get_park_code.html +++ b/docs/reference/get_park_code.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Restricts get_unit_code to just National Parks

    - Source: R/getParkUnitInfo.R + Source: R/getParkUnitInfo.R
    diff --git a/docs/reference/get_park_taxon_citations.html b/docs/reference/get_park_taxon_citations.html index 9e251dc..accac33 100644 --- a/docs/reference/get_park_taxon_citations.html +++ b/docs/reference/get_park_taxon_citations.html @@ -19,7 +19,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -34,7 +34,7 @@ Changelog
  • - + @@ -49,7 +49,7 @@

    Get DataStore Citations for a park-species combination

    - Source: R/getReferenceInfo.R + Source: R/getReferenceInfo.R
    diff --git a/docs/reference/get_park_taxon_refs.html b/docs/reference/get_park_taxon_refs.html index 11d9815..7cf8664 100644 --- a/docs/reference/get_park_taxon_refs.html +++ b/docs/reference/get_park_taxon_refs.html @@ -21,7 +21,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -36,7 +36,7 @@ Changelog
  • - + @@ -51,7 +51,7 @@

    Get DS References for a park-species combination

    - Source: R/getReferenceInfo.R + Source: R/getReferenceInfo.R
    diff --git a/docs/reference/get_park_taxon_url.html b/docs/reference/get_park_taxon_url.html index 6de3c49..785d833 100644 --- a/docs/reference/get_park_taxon_url.html +++ b/docs/reference/get_park_taxon_url.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Get URL for references for a park-species combination

    - Source: R/getReferenceInfo.R + Source: R/getReferenceInfo.R
    diff --git a/docs/reference/get_ref_info.html b/docs/reference/get_ref_info.html index 1e06a6c..6c669ae 100644 --- a/docs/reference/get_ref_info.html +++ b/docs/reference/get_ref_info.html @@ -18,7 +18,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -33,7 +33,7 @@ Changelog
  • - + @@ -48,7 +48,7 @@

    Get citation for Data Store holding info by HoldingID

    - Source: R/getReferenceInfo.R + Source: R/getReferenceInfo.R
    diff --git a/docs/reference/get_unit_code.html b/docs/reference/get_unit_code.html index 51af620..b79eaf5 100644 --- a/docs/reference/get_unit_code.html +++ b/docs/reference/get_unit_code.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Dynamically access NPS park unit code data

    - Source: R/getParkUnitInfo.R + Source: R/getParkUnitInfo.R
    diff --git a/docs/reference/get_unit_code_info.html b/docs/reference/get_unit_code_info.html index 6b70279..ed09819 100644 --- a/docs/reference/get_unit_code_info.html +++ b/docs/reference/get_unit_code_info.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Gets information about a park Unit Code

    - Source: R/getParkUnitInfo.R + Source: R/getParkUnitInfo.R
    diff --git a/docs/reference/get_unit_info.html b/docs/reference/get_unit_info.html index fe6ae1d..8b01ce5 100644 --- a/docs/reference/get_unit_info.html +++ b/docs/reference/get_unit_info.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Search irmaservices.nps using any piece of information.

    - Source: R/getParkUnitInfo.R + Source: R/getParkUnitInfo.R
    diff --git a/docs/reference/index.html b/docs/reference/index.html index dffe48e..ec2b427 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + diff --git a/docs/reference/load_data_package.html b/docs/reference/load_data_package.html index b8f95fd..7808ca9 100644 --- a/docs/reference/load_data_package.html +++ b/docs/reference/load_data_package.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Read contents of data package file and constructs a list of tibbles based on the data file(s)

    - Source: R/load_data_package.R + Source: R/load_data_package.R
    diff --git a/docs/reference/load_data_packages.html b/docs/reference/load_data_packages.html index b50f121..13ca28e 100644 --- a/docs/reference/load_data_packages.html +++ b/docs/reference/load_data_packages.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Read contents of data package(s) and return a tibble with dataframe for each data file.

    - Source: R/load_data_packages.R + Source: R/load_data_packages.R
    diff --git a/docs/reference/load_domains.html b/docs/reference/load_domains.html index 915f84f..dfe6026 100644 --- a/docs/reference/load_domains.html +++ b/docs/reference/load_domains.html @@ -19,7 +19,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -34,7 +34,7 @@ Changelog
  • - + @@ -50,7 +50,7 @@

    Read contents of data package file and construct a data frame based on the metadata file summarizing the enumerated domains for categorical fields and their types/definitions.

    - Source: R/load_domains.R + Source: R/load_domains.R
    diff --git a/docs/reference/load_pkg_metadata.html b/docs/reference/load_pkg_metadata.html index 1710b56..55dbcf9 100644 --- a/docs/reference/load_pkg_metadata.html +++ b/docs/reference/load_pkg_metadata.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0 @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Read contents of data package file and construct a data frame based on the metadata file summarizing the fields and their types/definitions.

    - Source: R/load_pgk_metadata.R + Source: R/load_pgk_metadata.R
    diff --git a/docs/reference/map_wkt.html b/docs/reference/map_wkt.html index edb4f53..51c733a 100644 --- a/docs/reference/map_wkt.html +++ b/docs/reference/map_wkt.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Map WKT geometry (points and polygons)

    - Source: R/map_wkt.R + Source: R/map_wkt.R
    diff --git a/docs/reference/rm_local_packages.html b/docs/reference/rm_local_packages.html index 9e0c39d..1b2aac5 100644 --- a/docs/reference/rm_local_packages.html +++ b/docs/reference/rm_local_packages.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Delete data packages from your local machine

    - Source: R/rm_local_packages.R + Source: R/rm_local_packages.R
    diff --git a/docs/reference/validate_data_package.html b/docs/reference/validate_data_package.html index af19de6..eab42ad 100644 --- a/docs/reference/validate_data_package.html +++ b/docs/reference/validate_data_package.html @@ -17,7 +17,7 @@ NPSutils - 0.2.0.3 + 0.3.0
    @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Validate a Tabular Data Package

    - Source: R/validateDataPackage.R + Source: R/validateDataPackage.R
    From 85a7f4db723219d0806331e4f5aad53056752e34 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 30 Aug 2023 11:18:15 -0600 Subject: [PATCH 10/12] autoupdate via devtools::document & pkgdown --- man/get_data_packages.Rd | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/man/get_data_packages.Rd b/man/get_data_packages.Rd index 7900438..dd0bdf9 100644 --- a/man/get_data_packages.Rd +++ b/man/get_data_packages.Rd @@ -28,6 +28,11 @@ String. The path (including the /data folder) where all data package sub-directo \description{ `get_data_packages()` creates a directory called "data" in the current working directory (or user-specified location, see the `path` option). For each data package, it writes a new sub-directory within the "data" directory named with the corresponding data package reference ID. All the data package files are then copied to the directory specific to the data package. } +\details{ +In the default mode (force = FALSE), `get_data_packages()` will inform a user if the directory for that data package already exists and give the user the option to overwrite it (or skip downloading). In the default mode (force = FALSE), `get_data_packages()` will also check to see if there are newer versions of the requested data package and if there are newer versions, `get_data_packages()` will inform the user of when the requested data package was issued, when the newest data package was issued, and will then ask the user if they would like to download the newest version instead of the requested version. In the default mode (force = FALSE), `get_data_packages()` will warn a user if the reference ID supplied was not found (does not exist or requires VPN) and if a reference ID refers to a product that is not a data package, `get_data_packages()` will ask if the user wants to attempt to download it anyway. + +Although `get_data_packages()` is designed to handle the data package reference type on DataStore, it should in theory work on any reference type and download all files associated with a reference (it ignores web links/web resources associated with a reference). If the reference includes a .zip file, the file will be downloaded and the contents extracted. The original .zip archive file will then be deleted. If the .zip contains files with the same name as files in the parent directory, the parent directory files will be over-written by the contents of the .zip archive. +} \examples{ \dontrun{ #get a public data package From 88a7cc75139c89d245ea1e1aecd9d71c0a5c7151 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 5 Sep 2023 13:58:23 -0600 Subject: [PATCH 11/12] auto update via devtools::document and pkgdown --- docs/articles/NPSutils.html | 4 ++-- docs/index.html | 4 ++-- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/get_data_packages.html | 2 +- docs/reference/load_data_packages.html | 2 +- docs/reference/rm_local_packages.html | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/articles/NPSutils.html b/docs/articles/NPSutils.html index 4478556..00426a6 100644 --- a/docs/articles/NPSutils.html +++ b/docs/articles/NPSutils.html @@ -97,11 +97,11 @@

    Install from GitHub
     # install.packages("devtools")
-devtools::install_github("nationalparkservice/NPSutils")

    +devtools::install_github("nationalparkservice/NPSutils")

    NPSutils is also available as part of the NPSdataverse

     # install.packages("devtools")
-devtools::install_github("nationalparkservice/NPSdataverse")
    +devtools::install_github("nationalparkservice/NPSdataverse") diff --git a/docs/index.html b/docs/index.html index 1e1a10b..d388245 100644 --- a/docs/index.html +++ b/docs/index.html @@ -81,11 +81,11 @@

    Install from GitHub
     # install.packages("devtools")
-devtools::install_github("nationalparkservice/NPSutils")
    +devtools::install_github("nationalparkservice/NPSutils")

    NPSutils is also available as part of the NPSdataverse

     # install.packages("devtools")
-devtools::install_github("nationalparkservice/NPSdataverse")
    +devtools::install_github("nationalparkservice/NPSdataverse") diff --git a/docs/news/index.html b/docs/news/index.html index ebaa79b..4a7937b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -56,7 +56,7 @@

    NPSutils 0.3.0add global variables for base datastore api urls and helper functions to access them in utils.R

  • added new functionality to get_data_packages(): it will now check to see if a DataStore reference ID is invalid or not. It will also check whether the reference is a data package or not. Substantial feedback is reported to the user if the flag force is set to FALSE.
  • added a new function rm_local_packages() which can delete one or more (or all) packages within a folder called “data” (where your packages should be if you downloaded them with get_data_packages()). This only deletes local copies and does not delete any data from DataStore.
    • -
  • changed function name load_metadata() is now load_pkg_metadata() so as not to conflict with DPchecker::load_metadata() +
  • changed function name load_metadata() is now load_pkg_metadata() so as not to conflict with DPchecker::load_metadata()
  • updated all function names to be snake_case
  • updated all file names to match function names
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c1a2f0b..8e3fb26 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.6.9000 pkgdown_sha: 5bb671b1a8bac8e926479868681936f7c9ee41b3 articles: NPSutils: NPSutils.html -last_built: 2023-08-30T17:14Z +last_built: 2023-09-05T19:57Z diff --git a/docs/reference/get_data_packages.html b/docs/reference/get_data_packages.html index 0730bb3..fbe006c 100644 --- a/docs/reference/get_data_packages.html +++ b/docs/reference/get_data_packages.html @@ -59,7 +59,7 @@

    Retrieve digital data package holding(s) from DataStore.

    get_data_packages(
   reference_id,
   secure = FALSE,
-  path = here::here(),
+  path = here::here(),
   force = FALSE
 )
    diff --git a/docs/reference/load_data_packages.html b/docs/reference/load_data_packages.html index 13ca28e..6979787 100644 --- a/docs/reference/load_data_packages.html +++ b/docs/reference/load_data_packages.html @@ -58,7 +58,7 @@

    Read contents of data package(s) and return a tibble with dataframe for each 
    load_data_packages(
   datastore_reference,
-  path = here::here(),
+  path = here::here(),
   dataFormat = "*.csv",
   metadataFormat = "EML",
   simplify = TRUE
diff --git a/docs/reference/rm_local_packages.html b/docs/reference/rm_local_packages.html
index 1b2aac5..8ebf779 100644
--- a/docs/reference/rm_local_packages.html
+++ b/docs/reference/rm_local_packages.html
@@ -59,7 +59,7 @@ 
    Delete data packages from your local machine
    
     
    rm_local_packages(
   reference_id,
   all = FALSE,
-  path = here::here(),
+  path = here::here(),
   force = FALSE
 )
    From 78ea4763c78b73d7990b25a69ac829bffc72d992 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 5 Sep 2023 13:58:30 -0600 Subject: [PATCH 12/12] update DataStore API from v4/5 to v6 --- R/utils.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/utils.R b/R/utils.R index d2b2741..b365c4b 100644 --- a/R/utils.R +++ b/R/utils.R @@ -4,10 +4,10 @@ .pkgglobalenv <- new.env(parent=emptyenv()) #data_store API base URL: -assign("ds_api", "https://irmadevservices.nps.gov/datastore/v6/rest/", envir=.pkgglobalenv) +assign("ds_api", "https://irmaservices.nps.gov/datastore/v6/rest/", envir=.pkgglobalenv) #data_store secure API base URL: -assign("ds_secure_api", "https://irmadevservices.nps.gov/datastore-secure/v6/rest/", envir=.pkgglobalenv) +assign("ds_secure_api", "https://irmaservices.nps.gov/datastore-secure/v6/rest/", envir=.pkgglobalenv) .ds_api <- function(x){ get("ds_api", envir = .pkgglobalenv)