From fc2fb800f800ce9c1f99c301a53f81b64e202730 Mon Sep 17 00:00:00 2001
From: Anna Krystalli <annakrystalli@googlemail.com>
Date: Mon, 3 Jun 2024 14:42:52 -0400
Subject: [PATCH 1/3] Resolves #21 add note about dynamic validations only
 being perfomed if basic schema validation passes

---
 R/validate_config.R        | 12 +++++++++++-
 R/validate_hub_config.R    | 13 ++++++++++++-
 man/validate_config.Rd     | 15 +++++++++++++--
 man/validate_hub_config.Rd | 15 ++++++++++++++-
 4 files changed, 50 insertions(+), 5 deletions(-)

diff --git a/R/validate_config.R b/R/validate_config.R
index 576c33c..15a77aa 100644
--- a/R/validate_config.R
+++ b/R/validate_config.R
@@ -1,5 +1,15 @@
-#' Validate a hub config file against a Infectious Disease Modeling Hubs schema
+#' Validate a hub config file against a hubverse schema
 #'
+#' This function validates a single hub config file against it's corresponding
+#'  schema.
+#'  Note that, for `tasks.json` config files, validation is performed
+#'  in two stages:
+#'  1. Initial validation against the schema is performed using the [`jsonvalidate`]
+#'  package which uses the `"ajv"` (Another JSON Schema Validator) validation engine.
+#'  2. If the initial validation is successful, additional dynamic validations are
+#'  performed.
+#'  This means that only after the initial validation passes, will any dynamic
+#'  validation errors be detected.
 #' @param hub_path Path to a local hub directory.
 #' @param config Name of config file to validate. One of `"tasks"` or `"admin"`.
 #' @param config_path Defaults to `NULL` which assumes all config files are in
diff --git a/R/validate_hub_config.R b/R/validate_hub_config.R
index 4be2d01..e0f9dfb 100644
--- a/R/validate_hub_config.R
+++ b/R/validate_hub_config.R
@@ -1,6 +1,17 @@
 #' Validate Hub config files against Infectious Disease Modeling Hubs schema.
 #'
-#' Validate the `admin.json` and `tasks.json` Hub config files in a single call.
+#' Validate the `admin.json`, `tasks.json` and `model-metadata-schema.json` Hub
+#' config files in a single call.
+#'  Note that, for `tasks.json` and `model-metadata-schema.json` config files,
+#'  validation is performed in two stages:
+#'  1. Initial validation against the schema is performed using the [`jsonvalidate`]
+#'  package which uses the `"ajv"` (Another JSON Schema Validator) validation engine.
+#'  In the case of `model-metadata-schema.json`, `jsonvalidate` just checks that
+#'  the file is valid JSON and can be parsed correctly.
+#'  2. If the initial validation is successful, additional dynamic validations are
+#'  performed.
+#'  This means that only after the initial validation passes, will any dynamic
+#'  validation errors be detected.
 #' @inheritParams validate_config
 #'
 #' @return Returns a list of the results of validation, one for each `hub-config`
diff --git a/man/validate_config.Rd b/man/validate_config.Rd
index 7ace935..391a2ea 100644
--- a/man/validate_config.Rd
+++ b/man/validate_config.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/validate_config.R
 \name{validate_config}
 \alias{validate_config}
-\title{Validate a hub config file against a Infectious Disease Modeling Hubs schema}
+\title{Validate a hub config file against a hubverse schema}
 \usage{
 validate_config(
   hub_path = ".",
@@ -46,7 +46,18 @@ You can print a more concise and easier to view version of an errors table with
 \code{\link[=view_config_val_errors]{view_config_val_errors()}}.
 }
 \description{
-Validate a hub config file against a Infectious Disease Modeling Hubs schema
+This function validates a single hub config file against it's corresponding
+schema.
+Note that, for \code{tasks.json} config files, validation is performed
+in two stages:
+\enumerate{
+\item Initial validation against the schema is performed using the \code{\link{jsonvalidate}}
+package which uses the \code{"ajv"} (Another JSON Schema Validator) validation engine.
+\item If the initial validation is successful, additional dynamic validations are
+performed.
+This means that only after the initial validation passes, will any dynamic
+validation errors be detected.
+}
 }
 \examples{
 # Valid config file
diff --git a/man/validate_hub_config.Rd b/man/validate_hub_config.Rd
index cd0212c..b684fbb 100644
--- a/man/validate_hub_config.Rd
+++ b/man/validate_hub_config.Rd
@@ -38,7 +38,20 @@ You can print a more concise and easier to view version of an errors table with
 \code{\link[=view_config_val_errors]{view_config_val_errors()}}.
 }
 \description{
-Validate the \code{admin.json} and \code{tasks.json} Hub config files in a single call.
+Validate the \code{admin.json}, \code{tasks.json} and \code{model-metadata-schema.json} Hub
+config files in a single call.
+Note that, for \code{tasks.json} and \code{model-metadata-schema.json} config files,
+validation is performed in two stages:
+\enumerate{
+\item Initial validation against the schema is performed using the \code{\link{jsonvalidate}}
+package which uses the \code{"ajv"} (Another JSON Schema Validator) validation engine.
+In the case of \code{model-metadata-schema.json}, \code{jsonvalidate} just checks that
+the file is valid JSON and can be parsed correctly.
+\item If the initial validation is successful, additional dynamic validations are
+performed.
+This means that only after the initial validation passes, will any dynamic
+validation errors be detected.
+}
 }
 \examples{
 validate_hub_config(

From b5cae00121d73798db82df5ff631f19e552e1192 Mon Sep 17 00:00:00 2001
From: Anna Krystalli <annakrystalli@googlemail.com>
Date: Mon, 3 Jun 2024 15:02:37 -0400
Subject: [PATCH 2/3] Resolves #22. Remove hard-coded location datasets

---
 R/data.R                  |  30 ------------------------------
 data-raw/hub_locations.R  |  13 -------------
 data/hub_locations_eu.rda | Bin 473 -> 0 bytes
 data/hub_locations_us.rda | Bin 20542 -> 0 bytes
 man/hub_locations_eu.Rd   |  20 --------------------
 man/hub_locations_us.Rd   |  28 ----------------------------
 6 files changed, 91 deletions(-)
 delete mode 100644 R/data.R
 delete mode 100644 data-raw/hub_locations.R
 delete mode 100644 data/hub_locations_eu.rda
 delete mode 100644 data/hub_locations_us.rda
 delete mode 100644 man/hub_locations_eu.Rd
 delete mode 100644 man/hub_locations_us.Rd

diff --git a/R/data.R b/R/data.R
deleted file mode 100644
index fe7b0ae..0000000
--- a/R/data.R
+++ /dev/null
@@ -1,30 +0,0 @@
-#' Available US locations
-#'
-#' Data set with available locations for a US hub
-#'
-#' @format A data frame with 3202 rows and 5 columns:
-#' \describe{
-#'   \item{fips}{FIPS code}
-#'   \item{location_name}{Location name}
-#'   \item{geo_type}{Type of location for compatibility with
-#'      \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html
-#'          }{EpiData API geographic codings}
-#'      }
-#'   \item{geo_value}{Location abbreviation or FIPS code for compatibility with
-#'      \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html
-#'          }{EpiData API geographic codings}}
-#'   \item{abbreviation}{Corresponding state abbrevaition}
-#' }
-"hub_locations_us"
-
-
-#' Available European locations
-#'
-#' Data set with available European locations used in ECDC hubs
-#'
-#' @format A data frame with 32 rows and 2 columns:
-#' \describe{
-#'   \item{location_name}{Name of the location}
-#'   \item{location}{Location abbreviation}
-#' }
-"hub_locations_eu"
diff --git a/data-raw/hub_locations.R b/data-raw/hub_locations.R
deleted file mode 100644
index b1aed53..0000000
--- a/data-raw/hub_locations.R
+++ /dev/null
@@ -1,13 +0,0 @@
-## code to prepare `hub_locations` dataset goes here
-library(dplyr)
-hub_locations_us <- covidHubUtils::hub_locations |>
-  select(-population, -full_location_name) |>
-  tibble::as_tibble()
-
-hub_locations_eu <- covidHubUtils::hub_locations_ecdc |>
-  select(-population) |>
-  tibble::as_tibble()
-
-usethis::use_data(hub_locations_us, overwrite = TRUE)
-
-usethis::use_data(hub_locations_eu, overwrite = TRUE)
diff --git a/data/hub_locations_eu.rda b/data/hub_locations_eu.rda
deleted file mode 100644
index 1f8a168f13d2207d60d906c196b2b8417fb95460..0000000000000000000000000000000000000000
GIT binary patch
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HcmV?d00001

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diff --git a/data/hub_locations_us.rda b/data/hub_locations_us.rda
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diff --git a/man/hub_locations_eu.Rd b/man/hub_locations_eu.Rd
deleted file mode 100644
index 625cd37..0000000
--- a/man/hub_locations_eu.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{hub_locations_eu}
-\alias{hub_locations_eu}
-\title{Available European locations}
-\format{
-A data frame with 32 rows and 2 columns:
-\describe{
-\item{location_name}{Name of the location}
-\item{location}{Location abbreviation}
-}
-}
-\usage{
-hub_locations_eu
-}
-\description{
-Data set with available European locations used in ECDC hubs
-}
-\keyword{datasets}
diff --git a/man/hub_locations_us.Rd b/man/hub_locations_us.Rd
deleted file mode 100644
index c2a675c..0000000
--- a/man/hub_locations_us.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{hub_locations_us}
-\alias{hub_locations_us}
-\title{Available US locations}
-\format{
-A data frame with 3202 rows and 5 columns:
-\describe{
-\item{fips}{FIPS code}
-\item{location_name}{Location name}
-\item{geo_type}{Type of location for compatibility with
-\href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html
-}{EpiData API geographic codings}
-}
-\item{geo_value}{Location abbreviation or FIPS code for compatibility with
-\href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html
-}{EpiData API geographic codings}}
-\item{abbreviation}{Corresponding state abbrevaition}
-}
-}
-\usage{
-hub_locations_us
-}
-\description{
-Data set with available locations for a US hub
-}
-\keyword{datasets}

From e1ac013e8d0296c8e49305a638e65c71e08fa93b Mon Sep 17 00:00:00 2001
From: Anna Krystalli <annakrystalli@googlemail.com>
Date: Mon, 3 Jun 2024 15:32:54 -0400
Subject: [PATCH 3/3] add full URL to jsonvalidate

---
 R/validate_config.R        | 3 ++-
 R/validate_hub_config.R    | 5 +++--
 man/validate_config.Rd     | 3 ++-
 man/validate_hub_config.Rd | 5 +++--
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/validate_config.R b/R/validate_config.R
index 15a77aa..14e9ea5 100644
--- a/R/validate_config.R
+++ b/R/validate_config.R
@@ -4,7 +4,8 @@
 #'  schema.
 #'  Note that, for `tasks.json` config files, validation is performed
 #'  in two stages:
-#'  1. Initial validation against the schema is performed using the [`jsonvalidate`]
+#'  1. Initial validation against the schema is performed using the
+#'  [`jsonvalidate`](https://docs.ropensci.org/jsonvalidate/)
 #'  package which uses the `"ajv"` (Another JSON Schema Validator) validation engine.
 #'  2. If the initial validation is successful, additional dynamic validations are
 #'  performed.
diff --git a/R/validate_hub_config.R b/R/validate_hub_config.R
index e0f9dfb..9d85004 100644
--- a/R/validate_hub_config.R
+++ b/R/validate_hub_config.R
@@ -1,10 +1,11 @@
-#' Validate Hub config files against Infectious Disease Modeling Hubs schema.
+#' Validate Hub config files against hubverse schema.
 #'
 #' Validate the `admin.json`, `tasks.json` and `model-metadata-schema.json` Hub
 #' config files in a single call.
 #'  Note that, for `tasks.json` and `model-metadata-schema.json` config files,
 #'  validation is performed in two stages:
-#'  1. Initial validation against the schema is performed using the [`jsonvalidate`]
+#'  1. Initial validation against the schema is performed using the
+#'  [`jsonvalidate`](https://docs.ropensci.org/jsonvalidate/)
 #'  package which uses the `"ajv"` (Another JSON Schema Validator) validation engine.
 #'  In the case of `model-metadata-schema.json`, `jsonvalidate` just checks that
 #'  the file is valid JSON and can be parsed correctly.
diff --git a/man/validate_config.Rd b/man/validate_config.Rd
index 391a2ea..6b8f141 100644
--- a/man/validate_config.Rd
+++ b/man/validate_config.Rd
@@ -51,7 +51,8 @@ schema.
 Note that, for \code{tasks.json} config files, validation is performed
 in two stages:
 \enumerate{
-\item Initial validation against the schema is performed using the \code{\link{jsonvalidate}}
+\item Initial validation against the schema is performed using the
+\href{https://docs.ropensci.org/jsonvalidate/}{\code{jsonvalidate}}
 package which uses the \code{"ajv"} (Another JSON Schema Validator) validation engine.
 \item If the initial validation is successful, additional dynamic validations are
 performed.
diff --git a/man/validate_hub_config.Rd b/man/validate_hub_config.Rd
index b684fbb..1dcebea 100644
--- a/man/validate_hub_config.Rd
+++ b/man/validate_hub_config.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/validate_hub_config.R
 \name{validate_hub_config}
 \alias{validate_hub_config}
-\title{Validate Hub config files against Infectious Disease Modeling Hubs schema.}
+\title{Validate Hub config files against hubverse schema.}
 \usage{
 validate_hub_config(
   hub_path = ".",
@@ -43,7 +43,8 @@ config files in a single call.
 Note that, for \code{tasks.json} and \code{model-metadata-schema.json} config files,
 validation is performed in two stages:
 \enumerate{
-\item Initial validation against the schema is performed using the \code{\link{jsonvalidate}}
+\item Initial validation against the schema is performed using the
+\href{https://docs.ropensci.org/jsonvalidate/}{\code{jsonvalidate}}
 package which uses the \code{"ajv"} (Another JSON Schema Validator) validation engine.
 In the case of \code{model-metadata-schema.json}, \code{jsonvalidate} just checks that
 the file is valid JSON and can be parsed correctly.