From a938752b0df3e39b25917f2274214d041043e330 Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 12:08:48 -0700
Subject: [PATCH 01/14] Add EML object as an alternative option for
 metadata_path in publish_update

---
 R/editing.R | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/R/editing.R b/R/editing.R
index e3a1b77..40bf436 100644
--- a/R/editing.R
+++ b/R/editing.R
@@ -233,7 +233,7 @@ update_object <- function(mn, pid, path, format_id=NULL, new_pid=NULL, sid=NULL)
 #' @param parent_data_pids (character)  Optional. Identifier for the data objects of the parent package. Not optional if the parent package contains data objects.
 #' @param parent_child_pids (character) Optional. Resource map identifier(s) of child packages in the parent package.  \code{resource_map_pid} should not be included. Not optional if the parent package contains other child packages.
 #' @param child_pids (character) Optional. Child packages resource map PIDs.
-#' @param metadata_path (character) Optional. Path to a metadata file to update with. If this is not set, the existing metadata document will be used.
+#' @param metadata_path (character or eml) Optional. An eml class object or a path to a metadata file to update with. If this is not set, the existing metadata document will be used.
 #' @param public (logical) Optional. Make the update public. If FALSE, will set the metadata and resource map to private (but not the data objects).
 #' This applies to the new metadata PID and its resource map and data object.
 #' access policies are not affected.
@@ -367,6 +367,15 @@ publish_update <- function(mn,
     # Get the metadata doc
     message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
+
+  } if(class(metadata_path) == "eml") {
+    # If an eml object is provided, use it directly after validating
+    if(!eml_validate(metadata_path)){
+      stop("The EML object is not valid.")
+    }
+
+    eml <- metadata_path
+
   } else {
     # Alternatively, read an edited metadata file from disk if provided
     if (!file.exists(metadata_path)) {

From c8287fbd8e2a4c2d3e933996a2047a50c9cc6d12 Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 13:32:21 -0700
Subject: [PATCH 02/14] fixed ifelse

---
 R/editing.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/editing.R b/R/editing.R
index 40bf436..c1edeb1 100644
--- a/R/editing.R
+++ b/R/editing.R
@@ -368,13 +368,13 @@ publish_update <- function(mn,
     message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
 
-  } if(class(metadata_path) == "eml") {
-    # If an eml object is provided, use it directly after validating
-    if(!eml_validate(metadata_path)){
-      stop("The EML object is not valid.")
-    }
+  } else if(class(metadata_path) == "eml") {
+      # If an eml object is provided, use it directly after validating
+      if(!eml_validate(metadata_path)){
+        stop("The EML object is not valid.")
+      }
 
-    eml <- metadata_path
+      eml <- metadata_path
 
   } else {
     # Alternatively, read an edited metadata file from disk if provided

From 57812840c29fe6c429432c89f0499626ae0e2ed0 Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 13:32:28 -0700
Subject: [PATCH 03/14] updated man

---
 man/publish_update.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/publish_update.Rd b/man/publish_update.Rd
index 3aaf5ba..76f4508 100644
--- a/man/publish_update.Rd
+++ b/man/publish_update.Rd
@@ -21,7 +21,7 @@ publish_update(mn, metadata_pid, resource_map_pid, data_pids = NULL,
 
 \item{child_pids}{(character) Optional. Child packages resource map PIDs.}
 
-\item{metadata_path}{(character) Optional. Path to a metadata file to update with. If this is not set, the existing metadata document will be used.}
+\item{metadata_path}{(character or eml) Optional. An eml class object or a path to a metadata file to update with. If this is not set, the existing metadata document will be used.}
 
 \item{identifier}{(character) Manually specify the identifier for the new metadata object.}
 

From 2710025b1079ccb95d295de58098ab8a7d16fcfb Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 14:06:18 -0700
Subject: [PATCH 04/14] Try uncaching packages to see if devel/new release will
 work

https://stat.ethz.ch/pipermail/r-sig-debian/2018-April/002829.html
https://github.com/r-spatial/sf/issues/729
https://github.com/Rdatatable/data.table/issues/2801
---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a4c91ba..da0bf51 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,6 @@ r:
   - release
   - devel
 sudo: false
-cache: packages
 addons:
   apt:
     packages:

From ac32bf34c536aa33eaa221d8b46211165f564330 Mon Sep 17 00:00:00 2001
From: isteves <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 15:27:58 -0700
Subject: [PATCH 05/14] Try `update: true`

Added `cache: packages` back in
---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index da0bf51..03dd703 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,8 +6,10 @@ r:
   - release
   - devel
 sudo: false
+cache: packages
 addons:
   apt:
+    update: true
     packages:
       - librdf0-dev
       - libnetcdf-dev

From ccdfa2082d240ed892cb398c2a9e0f112be6a060 Mon Sep 17 00:00:00 2001
From: Bryce Mecum <petridish@gmail.com>
Date: Thu, 10 May 2018 15:02:48 -0700
Subject: [PATCH 06/14] Reduce dependencies on ncdf4 and yaml

@isteves helpfully noted that the Travis CI builds started failing a while ago in https://github.com/NCEAS/arcticdatautils/issues/86. The failures indicate issues with Ubuntu PPAs and nothing to do with our tools. Though this happened around the time R 3.5.0 was released, which is a backwards incompatible R release indue to the introduction of ALTREP. This is:

1. My attempt to fix that so all the Travis builds pass
2. Reduce the deps arcticdatautils requires to install. ncdf4 and yaml are not packages that _need_ to be installed to get started using it so they should be in Suggests
---
 .travis.yml     | 2 --
 DESCRIPTION     | 4 ++--
 R/attributes.R  | 6 ++++++
 R/environment.R | 6 ++++++
 R/util.R        | 6 ++++++
 5 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a4c91ba..835edf6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,5 +11,3 @@ addons:
   apt:
     packages:
       - librdf0-dev
-      - libnetcdf-dev
-      - r-cran-ncdf4
diff --git a/DESCRIPTION b/DESCRIPTION
index 67fdc2e..ac8d1f5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,12 +21,10 @@ Imports:
     EML,
     httr,
     methods,
-    ncdf4,
     stringr,
     stringi,
     tools,
     uuid,
-    yaml,
     xml2,
     XML
 License: MIT + file LICENSE
@@ -35,7 +33,9 @@ Suggests:
     testthat,
     humaniformat,
     knitr,
+    ncdf4,
     rmarkdown,
+    yaml,
     xslt
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr
diff --git a/R/attributes.R b/R/attributes.R
index 8042a40..fed08e6 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -12,6 +12,12 @@
 get_ncdf4_attributes <- function(nc) {
   stopifnot(is(nc, "ncdf4") || file.exists(nc))
 
+  if (!requireNamespace("ncdf4")) {
+    stop(call. = FALSE, 
+         "The package 'ncdf4' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+  
   # Read the file in if `nc` is a character vector
   if (is.character(nc)) {
     nc <- ncdf4::nc_open(nc)
diff --git a/R/environment.R b/R/environment.R
index 8ff1c12..66c32aa 100644
--- a/R/environment.R
+++ b/R/environment.R
@@ -38,6 +38,12 @@ env_get <- function() {
 #'
 #'
 env_load <- function(name=NULL, path=NULL, skip_mn=FALSE) {
+  if (!requireNamespace("yaml")) {
+    stop(call. = FALSE, 
+         "The package 'yaml' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+
   # Determine the environment to load
   if (is.null(name)) {
     name <- env_get()
diff --git a/R/util.R b/R/util.R
index eaa5001..2ef7984 100644
--- a/R/util.R
+++ b/R/util.R
@@ -109,6 +109,12 @@ get_netcdf_format_id <- function(path) {
             nchar(path) > 0,
             file.exists(path))
 
+  if (!requireNamespace("ncdf4")) {
+    stop(call. = FALSE, 
+         "The package 'ncdf4' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+
   # Try to open the file, capturing errors
   cdf_file <- try({
     ncdf4::nc_open(path)

From 431593e088e234919e4bf88300d501f62227a62f Mon Sep 17 00:00:00 2001
From: Bryce Mecum <petridish@gmail.com>
Date: Thu, 10 May 2018 15:26:04 -0700
Subject: [PATCH 07/14] Turn off forcing suggests in travis build

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 835edf6..fcd9c84 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,6 +6,8 @@ r:
   - release
   - devel
 sudo: false
+env:
+  - _R_CHECK_FORCE_SUGGESTS_=0
 cache: packages
 addons:
   apt:

From 9e0ea67708deccee4c3dd635e0b843b72cbedef6 Mon Sep 17 00:00:00 2001
From: Bryce Mecum <petridish@gmail.com>
Date: Thu, 10 May 2018 15:42:41 -0700
Subject: [PATCH 08/14] Move dplyr to Suggests

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ac8d1f5..1cddca5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,6 @@ Depends:
     R (>= 3.2.3)
 Imports:
     digest,
-    dplyr,
     dataone,
     datapack,
     EML,
@@ -30,6 +29,7 @@ Imports:
 License: MIT + file LICENSE
 LazyData: true
 Suggests:
+    dplyr,
     testthat,
     humaniformat,
     knitr,

From 77ef74f042374cc334efe1d60f8a745ac71f1a3c Mon Sep 17 00:00:00 2001
From: Bryce Mecum <petridish@gmail.com>
Date: Thu, 10 May 2018 15:52:10 -0700
Subject: [PATCH 09/14] Incorporate carl's great ideas

https://github.com/NCEAS/arcticdatautils/pull/88#issuecomment-388208858
---
 .travis.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index fcd9c84..aee4c81 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,11 +5,13 @@ r:
   - oldrel
   - release
   - devel
+r_packages: ncdf4
 sudo: false
-env:
-  - _R_CHECK_FORCE_SUGGESTS_=0
 cache: packages
 addons:
   apt:
+    update: true
     packages:
       - librdf0-dev
+      - libnetcdf-dev
+      - netcdf-bin

From 0554abe993ee1e09a0449d5bb26a8ee3aa5d9412 Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 12:08:48 -0700
Subject: [PATCH 10/14] Add EML object as an alternative option for
 metadata_path in publish_update

---
 R/editing.R | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/R/editing.R b/R/editing.R
index e3a1b77..40bf436 100644
--- a/R/editing.R
+++ b/R/editing.R
@@ -233,7 +233,7 @@ update_object <- function(mn, pid, path, format_id=NULL, new_pid=NULL, sid=NULL)
 #' @param parent_data_pids (character)  Optional. Identifier for the data objects of the parent package. Not optional if the parent package contains data objects.
 #' @param parent_child_pids (character) Optional. Resource map identifier(s) of child packages in the parent package.  \code{resource_map_pid} should not be included. Not optional if the parent package contains other child packages.
 #' @param child_pids (character) Optional. Child packages resource map PIDs.
-#' @param metadata_path (character) Optional. Path to a metadata file to update with. If this is not set, the existing metadata document will be used.
+#' @param metadata_path (character or eml) Optional. An eml class object or a path to a metadata file to update with. If this is not set, the existing metadata document will be used.
 #' @param public (logical) Optional. Make the update public. If FALSE, will set the metadata and resource map to private (but not the data objects).
 #' This applies to the new metadata PID and its resource map and data object.
 #' access policies are not affected.
@@ -367,6 +367,15 @@ publish_update <- function(mn,
     # Get the metadata doc
     message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
+
+  } if(class(metadata_path) == "eml") {
+    # If an eml object is provided, use it directly after validating
+    if(!eml_validate(metadata_path)){
+      stop("The EML object is not valid.")
+    }
+
+    eml <- metadata_path
+
   } else {
     # Alternatively, read an edited metadata file from disk if provided
     if (!file.exists(metadata_path)) {

From 24b3c201e83d8389bce8b53fff1ea8a3893d04aa Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 13:32:21 -0700
Subject: [PATCH 11/14] fixed ifelse

---
 R/editing.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/editing.R b/R/editing.R
index 40bf436..c1edeb1 100644
--- a/R/editing.R
+++ b/R/editing.R
@@ -368,13 +368,13 @@ publish_update <- function(mn,
     message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
 
-  } if(class(metadata_path) == "eml") {
-    # If an eml object is provided, use it directly after validating
-    if(!eml_validate(metadata_path)){
-      stop("The EML object is not valid.")
-    }
+  } else if(class(metadata_path) == "eml") {
+      # If an eml object is provided, use it directly after validating
+      if(!eml_validate(metadata_path)){
+        stop("The EML object is not valid.")
+      }
 
-    eml <- metadata_path
+      eml <- metadata_path
 
   } else {
     # Alternatively, read an edited metadata file from disk if provided

From f33cf75787730e660306d481a3adaf45be4e4f25 Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 13:32:28 -0700
Subject: [PATCH 12/14] updated man

---
 man/publish_update.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/publish_update.Rd b/man/publish_update.Rd
index 3aaf5ba..76f4508 100644
--- a/man/publish_update.Rd
+++ b/man/publish_update.Rd
@@ -21,7 +21,7 @@ publish_update(mn, metadata_pid, resource_map_pid, data_pids = NULL,
 
 \item{child_pids}{(character) Optional. Child packages resource map PIDs.}
 
-\item{metadata_path}{(character) Optional. Path to a metadata file to update with. If this is not set, the existing metadata document will be used.}
+\item{metadata_path}{(character or eml) Optional. An eml class object or a path to a metadata file to update with. If this is not set, the existing metadata document will be used.}
 
 \item{identifier}{(character) Manually specify the identifier for the new metadata object.}
 

From 8346ada8973ba78508dbb28b0ca77a8b06c59b4c Mon Sep 17 00:00:00 2001
From: Irene <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 14:06:18 -0700
Subject: [PATCH 13/14] Try uncaching packages to see if devel/new release will
 work

https://stat.ethz.ch/pipermail/r-sig-debian/2018-April/002829.html
https://github.com/r-spatial/sf/issues/729
https://github.com/Rdatatable/data.table/issues/2801
---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index aee4c81..ee18f4c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,6 @@ r:
   - devel
 r_packages: ncdf4
 sudo: false
-cache: packages
 addons:
   apt:
     update: true

From 96ae41fce845f5262c418431c78cc49f0f4c6d4a Mon Sep 17 00:00:00 2001
From: isteves <25118334+isteves@users.noreply.github.com>
Date: Wed, 9 May 2018 15:27:58 -0700
Subject: [PATCH 14/14] Try `update: true`

Added `cache: packages` back in
---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index ee18f4c..aee4c81 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,6 +7,7 @@ r:
   - devel
 r_packages: ncdf4
 sudo: false
+cache: packages
 addons:
   apt:
     update: true