add startup message, vignette section advertising 'discover' API change

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cellxgenedp
 Title: Discover and Access Single Cell Data Sets in the cellxgene Data Portal
-Version: 1.4.0
+Version: 1.4.1
 Authors@R: 
     c(person(
         given = "Martin",
@@ -32,6 +32,8 @@ Suggests:
     testthat (>= 3.0.0),
     mockery
 biocViews: SingleCell, DataImport, ThirdPartyClient
+URL: https://mtmorgan.github.io/cellxgenedp/
+BugReports: https://github.com/mtmorgan/cellxgenedp/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr

NEWS.md

@@ -4,6 +4,10 @@ SIGNIFICANT USER-VISIBLE CHANGES
 
 * (v 1.3.3) add publisher_metadata(), authors(), and links() to make access
   to nested 'collections()' data more straight-forward
+
+* (v 1.4.1) use CELLxGENE 'Discover' API, changing column names of
+  some return values. See 'API changes' of the 'Discover and download
+  datasets...' vignette.
 
 # cellxgenedp 1.2
 

R/utilities.R

@@ -45,3 +45,22 @@
         }
     }
 }
+
+.wrap <-
+    function(...)
+{
+    x <- paste0(...)
+    paste(strwrap(x), collapse = "\n")
+}
+
+.onAttach <-
+    function(libname, pkgname)
+{
+    packageStartupMessage(.wrap(
+        "The interface to CELLxGENE has changed; versions of ",
+        "cellxgenedp prior to 1.4.1 / 1.5.2 will cease to work when ",
+        "CELLxGENE removes the previous interface. See the section ",
+        "'API changes' of the 'Discover and download datasets...' ",
+        "vignette for important details."
+    ))
+}

vignettes/using_cellxgenedp.Rmd

@@ -19,6 +19,11 @@ vignette: |
     %\VignetteEncoding{UTF-8}
 ---
 
+NOTE: The interface to CELLxGENE has changed; versions of
+[cellxgenedp][] prior to 1.4.1 / 1.5.2 will cease to work when
+CELLxGENE removes the previous interface. See the vignette section
+'API changes' for additional details.
+
 # Installation and use
 
 This package is available in _Bioconductor_ version 3.15 and
@@ -345,6 +350,38 @@ as derived single-cell data files.
 [hca]: https://bioconductor.org/packages/hca
 [HCAportal]: https://data.humancellatlas.org/explore
 
+# API changes
+
+Data access provided by CELLxGENE has changed to a new 'Discover'
+[API][]. The main functionality of the [cellxgenedp][] package has not
+changed, but specific columns have been removed, replaced or added, as
+follows:
+
+`collections()`
+
+- Removed: `access_type`, `data_submission_policy_version`
+- Replaced: `updated_at` replaced with `revised_at`
+- Added: `collection_version_id`, `collection_url`, `doi`,
+  `revising_in`, `revision_of`
+
+`datasets()`
+
+- Removed: `is_valid`, `processing_status`, `published`, `revision`,
+  `created_at`
+- Replaced: `dataset_deployments` replaced with `explorer_url`, `name`
+  replaced with `title`, `updated_at` replaced with `revised_at`
+- Added: `dataset_version_id`, `batch_condition`,
+  `x_approximate_distribution`
+
+`files()`
+
+- Removed: `file_id`, `filename`, `s3_uri`, `user_submitted`,
+  `created_at`, `updated_at`
+- Added: `filesize`, `url`
+
+
+[API]: https://api.cellxgene.cziscience.com/curation/ui/
+
 # Session info {.unnumbered}
 
 ```{r sessionInfo, echo=FALSE}