Enhancement/handle null taskids

.github/workflows/R-CMD-check.yaml

@@ -5,6 +5,8 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  schedule:
+    - cron:  '0 0 * * *'
 
 name: R-CMD-check
 

DESCRIPTION

@@ -37,8 +37,8 @@ Imports:
     dplyr,
     fs,
     gh,
-    hubAdmin,
-    hubData,
+    hubAdmin (>= 0.1.0),
+    hubData (>= 0.1.0),
     hubUtils (>= 0.0.1),
     jsonlite,
     jsonvalidate,
@@ -63,7 +63,8 @@ Remotes:
     Infectious-Disease-Modeling-Hubs/hubUtils,
     Infectious-Disease-Modeling-Hubs/hubData,
     Infectious-Disease-Modeling-Hubs/hubAdmin,
-    assignUser/octolog
+    assignUser/octolog,
+    apache/arrow/[email protected]
 Config/testthat/edition: 3
 Config/Needs/website: pkgdown, Infectious-Disease-Modeling-Hubs/hubStyle
 Encoding: UTF-8

NEWS.md

@@ -1,3 +1,10 @@
+# hubValidations 0.0.1
+
+* Release stable 0.0.1 version
+* Enforce minimum dependence on latest `hubData` (0.1.0) & `hubAdmin` (0.1.0). This allows for successful validation of submissions to hubs with multiple model tasks, where a given model task might contain non relevant task IDs and both `required` and `optional` properties have been set to `null` in `tasks.json` (#75). See the [relevant section in `hubDocs` documentation](https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html#required-and-optional-elements) for more details.
+* Improve formatting of current time print in `validate_submission_time()` message by removing decimal seconds and including local time zone.
+
+
 # hubValidations 0.0.0.9008
 
 * Added new articles on:

R/check_submission_time.R

@@ -24,7 +24,9 @@ check_submission_time <- function(hub_path, file_path, ref_date_from = c(
     details <- NULL
   } else {
     details <- cli::format_inline(
-      "Current time {.val {Sys.time()}} is outside window {.val {submission_window}}."
+      "Current time {.val {format(Sys.time(),
+      format = '%Y-%m-%d %H:%M:%S',
+      usetz = TRUE)}} is outside window {.val {submission_window}}."
     )
   }
 

README.Rmd

@@ -31,6 +31,15 @@ You can install the development version of hubValidations like so:
 remotes::install_github("Infectious-Disease-Modeling-Hubs/hubValidations")
 ```
 
+> ##### 💡 TIP 
+> `hubValidations` has a dependency on the `arrow` package. For troubleshooting `arrow` installation problems, please consult the [`arrow` package documentation](https://arrow.apache.org/docs/r/#installation).
+>
+> You could also try installing the package from the [Apache R Universe repository](https://apache.r-universe.dev) with:
+>
+> ```r
+> install.packages("arrow", repos = c("https://apache.r-universe.dev", "https://cran.r-project.org"))
+> ```
+
 *** 
 
 ## Code of Conduct

README.md

@@ -23,6 +23,20 @@ You can install the development version of hubValidations like so:
 remotes::install_github("Infectious-Disease-Modeling-Hubs/hubValidations")
 ```
 
+> ##### 💡 TIP
+>
+> `hubValidations` has a dependency on the `arrow` package. For
+> troubleshooting `arrow` installation problems, please consult the
+> [`arrow` package
+> documentation](https://arrow.apache.org/docs/r/#installation).
+>
+> You could also try installing the package from the [Apache R Universe
+> repository](https://apache.r-universe.dev) with:
+>
+> ``` r
+> install.packages("arrow", repos = c("https://apache.r-universe.dev", "https://cran.r-project.org"))
+> ```
+
 ------------------------------------------------------------------------
 
 ## Code of Conduct

hubValidations.Rproj

@@ -6,7 +6,7 @@ AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
-NumSpacesForTab: 4
+NumSpacesForTab: 2
 Encoding: UTF-8
 
 RnwWeave: Sweave

tests/testthat/test-validate_submission.R

@@ -158,3 +158,46 @@ test_that("validate_submission fails when csv cannot be parsed according to sche
     c("check_error", "hub_check", "rlang_error", "error", "condition")
   )
 })
+
+test_that("File containing task ID with all null properties validate correctly", {
+  expect_snapshot(
+    str(
+      validate_submission(
+        hub_path = test_path("testdata/hub-null"),
+        file_path = "team-model/2023-11-26-team-model.parquet",
+        skip_submit_window_check = TRUE
+      )
+    )
+  )
+  expect_true(
+    suppressMessages(
+      check_for_errors(
+        validate_submission(
+          hub_path = test_path("testdata/hub-null"),
+          file_path = "team-model/2023-11-26-team-model.parquet",
+          skip_submit_window_check = TRUE
+        )
+      )
+    )
+  )
+  expect_snapshot(
+    str(
+      validate_submission(
+        hub_path = test_path("testdata/hub-null"),
+        file_path = "team-model/2023-11-19-team-model.parquet",
+        skip_submit_window_check = TRUE
+      )
+    )
+  )
+  expect_true(
+    suppressMessages(
+      check_for_errors(
+        validate_submission(
+          hub_path = test_path("testdata/hub-null"),
+          file_path = "team-model/2023-11-19-team-model.parquet",
+          skip_submit_window_check = TRUE
+        )
+      )
+    )
+  )
+})

tests/testthat/testdata/hub-null/hub-config/admin.json

@@ -0,0 +1,13 @@
+{
+    "schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/admin-schema.json",
+    "name": "US CDC FluSight",
+    "maintainer": "US CDC",
+    "contact": {
+        "name": "Joe Bloggs",
+        "email": "[email protected]"
+    },
+    "repository_host": "GitHub",
+    "repository_url": "https://github.com/cdcepi/Flusight-forecast-data",
+    "file_format": ["csv", "parquet", "arrow"],
+    "timezone": "US/Eastern"
+}

tests/testthat/testdata/hub-null/hub-config/model-metadata-schema.json

@@ -0,0 +1,128 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "title": "Schema for Modeling Hub model metadata",
+    "description": "This is the schema for model metadata files, please refer to https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe/wiki/Metadata for more information.",
+    "type": "object",
+    "properties": {
+        "team_name": {
+            "description": "The name of the team submitting the model",
+            "type": "string"
+        },
+        "team_abbr": {
+            "description": "Abbreviated name of the team submitting the model",
+            "type": "string",
+            "pattern": "^[a-zA-Z0-9_+]+$",
+            "maxLength": 16
+        },
+        "model_name": {
+            "description": "The name of the model",
+            "type": "string"
+        },
+        "model_abbr": {
+            "description": "Abbreviated name of the model",
+            "type": "string",
+            "pattern": "^[a-zA-Z0-9_+]+$",
+            "maxLength": 16
+        },
+        "model_version": {
+            "description": "Identifier of the version of the model",
+            "type": "string"
+        },
+        "model_contributors": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "name": {
+                        "type": "string"
+                    },
+                    "affiliation": {
+                        "type": "string"
+                    },
+                    "email": {
+                        "type": "string",
+                        "format": "email"
+                    },
+                    "orcid": {
+                        "type": "string",
+                        "pattern": "^\\d{4}\\-\\d{4}\\-\\d{4}\\-[\\dX]{4}$"
+                    }
+                },
+                "additionalProperties": false,
+                "required": ["name", "affiliation", "email"]
+            }
+        },
+        "website_url": {
+            "description": "Public facing website for the model",
+            "type": "string",
+            "format": "uri"
+        },
+        "repo_url": {
+            "description": "Repository containing code for the model",
+            "type": "string",
+            "format": "uri"
+        },
+        "license": {
+            "description": "License for use of model output data",
+            "type": "string",
+            "enum": [
+                "CC0-1.0",
+                "CC-BY-4.0",
+                "CC-BY_SA-4.0",
+                "PPDL",
+                "ODC-by",
+                "ODbL",
+                "OGL-3.0"
+            ]
+        },
+        "designated_model": {
+            "description": "Team-specified indicator for whether the model should be eligible for inclusion in a Hub ensemble and public visualization. A team may designate up to two models.",
+            "type": "boolean"
+        },
+        "citation": {
+            "description": "One or more citations for this model",
+            "type": "string",
+            "examples": ["Gibson GC , Reich NG , Sheldon D. Real-time mechanistic bayesian forecasts of Covid-19 mortality. medRxiv. 2020. https://doi.org/10.1101/2020.12.22.20248736"]
+        },
+        "team_funding": {
+            "description": "Any information about funding source for the team or members of the team.",
+            "type": "string",
+            "examples": ["National Institutes of General Medical Sciences (R01GM123456). The content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS."]
+        },
+        "data_inputs": {
+            "description": "List or description of data inputs used by the model",
+            "type": "string"
+        },
+        "methods": {
+            "description": "A brief (200 char.) description of the methods used by this model",
+            "type": "string",
+            "maxLength": 200
+        },
+        "methods_long": {
+            "description": "A full description of the methods used by this model. Among other details, this should include whether spatial correlation is considered and how the model accounts for uncertainty.",
+            "type": "string"
+        },
+        "ensemble_of_models": {
+            "description": "Indicator for whether this model is an ensemble of any separate component models",
+            "type": "boolean"
+        },
+        "ensemble_of_hub_models": {
+            "description": "Indicator for whether this model is an ensemble specifically of other models submitted to this Hub",
+            "type": "boolean"
+        }
+    },
+    "additionalProperties": true,
+    "required": [
+        "team_name",
+        "team_abbr",
+        "model_name",
+        "model_abbr",
+        "model_contributors",
+        "license",
+        "data_inputs",
+        "methods",
+        "methods_long",
+        "ensemble_of_models",
+        "ensemble_of_hub_models"
+    ]
+}