Carry prov forward in certain scenarios

.Rbuildignore

@@ -2,3 +2,8 @@
 ^\.Rproj\.user$
 ^etc$
 ^docs$
+^\_pkgdown\.yml$
+^index\.md$
+^\.travis\.yml$
+^LICENSE$
+^MAINTENANCE\.md$

.travis.yml

@@ -0,0 +1,25 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: r
+r:
+  - oldrel
+  - release
+  - devel
+r_packages:
+  - ncdf4
+  - sf
+sudo: false
+cache: packages
+addons:
+  apt:
+    update: true
+    packages:
+      - librdf0-dev
+      - libnetcdf-dev
+      - netcdf-bin
+      - libudunits2-dev # for udunits2
+      - libgeos-dev # for sf
+      - libproj-dev # for sf
+      - libgdal-dev # for sf
+      - libjq-dev
+      - libv8-dev

DESCRIPTION

@@ -1,37 +1,55 @@
 Package: arcticdatautils
-Title: Arctic Data Utilities
-Version: 0.6.2
+Title: Utilities for the Arctic Data Center
+Version: 0.7.0
 Authors@R: c(
   person("Bryce", "Mecum", email = "mecum@nceas.ucsb.edu", role = c("aut", "cre")),
   person("Matt", "Jones", email = "jones@nceas.ucsb.edu", role = "ctb"),
-  person("Jeanette", "Clark", email = "jclark@nceas.ucsb.edu", role = "ctb")
+  person("Jesse", "Goldstein", email = "jgoldstein@nceas.ucsb.edu", role = "ctb", comment = "Maintainer"),
+  person("Jeanette", "Clark", email = "jclark@nceas.ucsb.edu", role = "ctb", comment = "Maintainer"),
+  person("Dominic", "Mullen", email = "dmullen17@gmail.com", role = "ctb"),
+  person("Emily", "O'Dean", email = "eodean10@gmail.com", role = "ctb"),
+  person("Robyn", "Thiessen-Bock", email = "robyn.thiessenbock@gmail.com", role = "ctb"),
+  person("Derek", "Strong", email = "dstrong@nceas.ucsb.edu", role = "ctb"),
+  person("Rachel", "Sun", email = "rachelsun@ucsb.edu", role = "ctb")
   )
-Description: This package provides a set of utility methods for uploading
-  and  editing data on the Arctic Data Catalog.
+Description: A set of utilities for working with the Arctic Data Center 
+  (https://arcticdata.io).
+License: Apache License (== 2.0)
+URL: https://nceas.github.io/arcticdatautils/
+BugReports: https://github.com/NCEAS/arcticdatautils/issues
+Encoding: UTF-8
+LazyData: true
 Depends:
     R (>= 3.2.3)
 Imports:
-    digest,
-    dplyr,
     dataone,
     datapack,
-    EML,
+    dplyr,
+    digest,
+    EML (>= 2.0),
     httr,
+    jsonlite,
+    magrittr,
     methods,
-    ncdf4,
     stringr,
     stringi,
     tools,
     uuid,
-    yaml,
     xml2,
     XML
-License: MIT + file LICENSE
-LazyData: true
 Suggests:
-    testthat,
+    emld,
+    humaniformat,
     knitr,
+    lubridate,
+    ncdf4,
+    RCurl,
+    purrr,
     rmarkdown,
-    xslt
-RoxygenNote: 6.0.1
+    sf,
+    testthat,
+    xslt,
+    yaml
+RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

MAINTENANCE.md

@@ -0,0 +1,85 @@
+# Maintenance
+
+This document serves as a guide for new maintainers of and contributors to the arcticdatautils package.
+
+*Note: This is a work-in-progress, so expect it to change and improve over time.*
+
+
+## Releases
+
+### Why release
+
+So users can use new features. Ideally, no one is installing from source, i.e., `remotes::install_github("nceas/arcticdatautils")`.
+
+### When to release
+
+Whenever, really.
+Since this package isn't on CRAN, you can release it as much as you like or need to.
+You might want to release either when:
+
+- You accrue enough changes to write an interest release announcement ("Hey, look at his cool new release that fixes annoying bug X!")
+- You accrue at least one change and users of the package need the fix immediately
+
+### How to release
+
+There are a few steps in releasing a new version of the package:
+
+1. Increment the `Version` tag in the `DESCRIPTION` file to the appropriate next version.
+
+  What this is set to specifies what the user sees from R when they run `sessionInfo()` or `devtools::session_info()` and tell you what version they have installed.
+
+  This package tries to use [Semantic Versioning](https://semver.org/) (semver) which can be summarized in three bullets:
+
+  > Given a version number MAJOR.MINOR.PATCH, increment the:
+  >
+  > - MAJOR version when you make incompatible API changes,
+  > - MINOR version when you add functionality in a backwards-compatible manner, and
+  > - PATCH version when you make backwards-compatible bug fixes.
+
+  Note: A common mistake people make is thinking that the next version after 0.9 is 1.0, but it could be 0.10, then 0.11, and so on.
+
+  `git` and GitHub helps us a lot with determining _what_ has changed so we can determine what the next release version number should be. We can compare a previous release to `master` to get a list of all commits what were made between that release and now:
+
+  > https://github.com/NCEAS/arcticdatautils/compare/v0.6.3...master
+
+
+- Make and push a commit with just that diff,
+
+  ```sh
+  git add DESCRIPTION
+  git commit -m "vx.y.z"
+  git push
+  ```
+
+  [Example here](https://github.com/NCEAS/arcticdatautils/commit/87f91179f4820ecdb283672e2179984d4f6cd334).
+
+2. Go to [the releases tab](https://github.com/NCEAS/arcticdatautils/releases) and click "Draft a new release"
+
+  - Tag version and Release title should match v{MAJOR}.{MINOR}.{PATCH}, e.g., v6.4.5
+  - The release description should include:
+    - A brief, 1-2 sentence description of what's changed since the last release
+    - Sections for ADDED/FIXED/REMOVED (omit section if not applicable), each with a bulleted list of changes in human-readable prose
+
+      Example: https://github.com/NCEAS/arcticdatautils/releases/tag/v0.6.2
+
+  - Make liberal use of GitHub's Compare feature: [Example](https://github.com/NCEAS/arcticdatautils/compare/v0.6.3...master) comparing `v0.6.3` to `master`.
+
+You're done, now go tell people to upgrade!
+
+```r
+remotes::install_github("nceas/arcticdatautils@*release")
+```
+
+Note: `@*release` specifies that the latest release should be installed.
+
+
+## Pull Requests
+
+- Follow the [tidyverse style conventions](http://style.tidyverse.org/), with the following specific style preferences: 
+    - use underscore for all variable names unless referring to an EML object (e.g., otherEntity, publicationDate, etc.)
+    - include argument checks in the form of `stopifnot()` statements for all functions
+- Before submitting a pull request, please update documentation, check package, and run tests:
+    - use `devtools::check()`
+    - fix any ERRORs and test failures to ensure the Travis CI build passes
+- Commit messages should follow these [guidelines](https://chris.beams.io/posts/git-commit/)
+- If fixing an issue, pull requests should reference that issue (e.g., "This update closes #93.")

NAMESPACE

@@ -1,108 +1,88 @@
 # Generated by roxygen2: do not edit by hand
 
-export(add_access_rules)
-export(add_additional_identifiers)
-export(add_admin_group_access)
-export(add_methods_step)
-export(add_string_to_title)
-export(change_eml_name)
-export(clear_methods)
-export(clear_replication_policy)
 export(convert_iso_to_eml)
+export(create_dummy_attributes_dataframe)
+export(create_dummy_enumeratedDomain_dataframe)
 export(create_dummy_metadata)
 export(create_dummy_object)
 export(create_dummy_package)
+export(create_dummy_package_full)
 export(create_dummy_parent_package)
-export(create_from_folder)
-export(create_object)
 export(create_resource_map)
-export(create_sysmeta)
-export(determine_child_pids)
-export(eml_add_entities)
-export(eml_address)
 export(eml_associated_party)
 export(eml_contact)
 export(eml_creator)
-export(eml_individual_name)
+export(eml_get_simple)
 export(eml_metadata_provider)
+export(eml_nsf_to_project)
+export(eml_otherEntity_to_dataTable)
 export(eml_party)
+export(eml_personnel)
 export(eml_project)
+export(eml_set_reference)
+export(eml_set_shared_attributes)
 export(eml_validate_attributes)
 export(env_get)
-export(env_load)
-export(filter_obsolete_pids)
-export(filter_packaging_statements)
 export(find_newest_object)
-export(find_newest_resource_map)
 export(format_eml)
 export(format_iso)
 export(generate_resource_map)
-export(generate_resource_map_pid)
+export(get_all_sysmeta)
 export(get_all_versions)
-export(get_current_version)
-export(get_doc_id)
-export(get_identifier)
-export(get_latest_release)
 export(get_mn_base_url)
 export(get_ncdf4_attributes)
-export(get_netcdf_format_id)
-export(get_or_create_pid)
+export(get_orcid_email)
+export(get_orcid_name)
 export(get_package)
 export(get_token)
-export(get_token_subject)
 export(guess_format_id)
-export(insert_file)
-export(insert_package)
-export(inv_add_extra_columns)
-export(inv_add_parent_package_column)
-export(inv_init)
-export(inv_load_checksums)
-export(inv_load_dois)
-export(inv_load_files)
-export(inv_load_identifiers)
-export(inv_load_sizes)
-export(inv_update)
 export(is_authorized)
-export(is_format_id)
 export(is_obsolete)
-export(is_resource_map)
+export(is_public_read)
 export(is_token_expired)
 export(is_token_set)
-export(log_message)
+export(list_submissions)
 export(mdq_run)
 export(new_uuid)
 export(object_exists)
 export(parse_resource_map)
-export(path_join)
-export(pid_to_eml_other_entity)
+export(pid_to_eml_entity)
 export(pid_to_eml_physical)
 export(publish_object)
 export(publish_update)
+export(read_zip_shapefile)
+export(recover_failed_submission)
+export(recover_prov)
+export(remove_access)
 export(remove_public_read)
-export(replace_package_id)
-export(replace_subject)
-export(set_abstract)
+export(reorder_pids)
 export(set_access)
 export(set_file_name)
-export(set_other_entities)
 export(set_public_read)
+export(set_public_read_all_versions)
 export(set_rights_and_access)
 export(set_rights_holder)
 export(show_indexing_status)
-export(show_random_dataset)
-export(substitute_eml_party)
-export(sysmeta_to_eml_other_entity)
 export(sysmeta_to_eml_physical)
-export(sysmeta_to_other_entity)
-export(theme_packages)
 export(update_object)
-export(update_package)
 export(update_resource_map)
-export(validate_environment)
-export(validate_inventory)
 export(view_profile)
-export(warn_current_version)
+export(which_in_eml)
 import(EML)
 import(XML)
 import(dataone)
 import(datapack)
+importFrom(httr,content)
+importFrom(magrittr,'%>%')
+importFrom(methods,"slot<-")
+importFrom(methods,as)
+importFrom(methods,is)
+importFrom(methods,new)
+importFrom(methods,slot)
+importFrom(stats,na.omit)
+importFrom(utils,URLencode)
+importFrom(utils,head)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)