From 5888fcde232a5a48212403face4bcb43ee65abfc Mon Sep 17 00:00:00 2001 From: LTLA Date: Tue, 27 Aug 2024 20:33:54 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Artifact?= =?UTF-8?q?DB/alabaster.base@484111131748dcabb00d4bb1b636559964dff50d=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- LICENSE-text.html | 23 +------ articles/index.html | 2 +- articles/userguide.html | 10 +-- authors.html | 6 +- index.html | 2 +- pkgdown.yml | 2 +- reference/Rfc3339.html | 56 ++++++++-------- reference/acquireFile.html | 4 +- reference/altReadObject.html | 2 +- reference/altSaveObject.html | 2 +- reference/anyMissing.html | 2 +- .../chooseMissingPlaceholderForHdf5.html | 2 +- reference/createRedirection.html | 2 +- reference/hdf5.html | 2 +- reference/index.html | 4 +- reference/listObjects.html | 2 +- reference/loadDirectory.html | 2 +- reference/moveObject.html | 2 +- reference/quickLoadObject.html | 2 +- reference/quickReadCsv.html | 2 +- reference/readAtomicVector.html | 2 +- reference/readBaseFactor.html | 2 +- reference/readBaseList.html | 2 +- reference/readDataFrame.html | 2 +- reference/readDataFrameFactor.html | 2 +- reference/readMetadata.html | 2 +- reference/readObject.html | 2 +- reference/readObjectFile.html | 2 +- reference/removeObject.html | 2 +- reference/saveAtomicVector.html | 2 +- reference/saveBaseFactor.html | 2 +- reference/saveBaseList.html | 2 +- reference/saveDataFrameFactor.html | 2 +- reference/saveFormats.html | 2 +- reference/saveMetadata.html | 2 +- reference/saveObject.html | 2 +- reference/stageDataFrame.html | 2 +- reference/transformVectorForHdf5.html | 2 +- reference/validateDirectory.html | 64 +++++++------------ reference/validateObject.html | 2 +- reference/writeMetadata.html | 2 +- 42 files changed, 101 insertions(+), 136 deletions(-) diff --git a/404.html b/404.html index 5d7be46..7f45126 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/LICENSE-text.html b/LICENSE-text.html index 8586183..b5d2e06 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -53,25 +53,8 @@

License

-
Copyright 2022 Genentech Inc.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
-of the Software, and to permit persons to whom the Software is furnished to do
-so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+
COPYRIGHT HOLDER: Genentech Inc.
+YEAR: 2022
 

 
   
diff --git a/articles/index.html b/articles/index.html
index 90f6c31..1f2a945 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         alabaster.base
-        1.5.5
+        1.5.6
       
     
 
diff --git a/articles/userguide.html b/articles/userguide.html
index e5adb24..225709a 100644
--- a/articles/userguide.html
+++ b/articles/userguide.html
@@ -32,7 +32,7 @@
       
       
         alabaster.base
-        1.5.5
+        1.5.6
       
     
 
@@ -527,20 +527,20 @@ 
Session information## [8] base     
 ## 
 ## other attached packages:
-## [1] Matrix_1.7-0         alabaster.base_1.5.5 S4Vectors_0.43.2    
+## [1] Matrix_1.7-0         alabaster.base_1.5.6 S4Vectors_0.43.2    
 ## [4] BiocGenerics_0.51.0  BiocStyle_2.33.1    
 ## 
 ## loaded via a namespace (and not attached):
 ##  [1] cli_3.6.3               knitr_1.48              rlang_1.1.4            
-##  [4] xfun_0.46               textshaping_0.4.0       jsonlite_1.8.8         
+##  [4] xfun_0.47               textshaping_0.4.0       jsonlite_1.8.8         
 ##  [7] htmltools_0.5.8.1       ragg_1.3.2              sass_0.4.9             
 ## [10] rmarkdown_2.28          grid_4.4.1              evaluate_0.24.0        
 ## [13] jquerylib_0.1.4         fastmap_1.2.0           Rhdf5lib_1.27.0        
 ## [16] alabaster.schemas_1.5.0 yaml_2.3.10             lifecycle_1.0.4        
-## [19] bookdown_0.40           BiocManager_1.30.23     compiler_4.4.1         
+## [19] bookdown_0.40           BiocManager_1.30.24     compiler_4.4.1         
 ## [22] fs_1.6.4                Rcpp_1.0.13             rhdf5filters_1.17.0    
 ## [25] htmlwidgets_1.6.4       lattice_0.22-6          rhdf5_2.49.0           
-## [28] systemfonts_1.1.0       digest_0.6.36           R6_2.5.1               
+## [28] systemfonts_1.1.0       digest_0.6.37           R6_2.5.1               
 ## [31] bslib_0.8.0             tools_4.4.1             pkgdown_2.1.0          
 ## [34] cachem_1.1.0            desc_1.4.3
diff --git a/authors.html b/authors.html index cee829f..dcbc448 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -70,13 +70,13 @@

Citation

Lun A (2024). alabaster.base: Save Bioconductor Objects To File. -R package version 1.5.5, https://github.com/ArtifactDB/alabaster.base. +R package version 1.5.6, https://github.com/ArtifactDB/alabaster.base. 

@Manual{,
   title = {alabaster.base: Save Bioconductor Objects To File},
   author = {Aaron Lun},
   year = {2024},
-  note = {R package version 1.5.5},
+  note = {R package version 1.5.6},
   url = {https://github.com/ArtifactDB/alabaster.base},
 }
diff --git a/index.html b/index.html index 13d6ed8..3fc9b81 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/pkgdown.yml b/pkgdown.yml index 805b2de..2f906c9 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.0 pkgdown_sha: ~ articles: userguide: userguide.html -last_built: 2024-08-19T17:41Z +last_built: 2024-08-27T20:33Z diff --git a/reference/Rfc3339.html b/reference/Rfc3339.html index d9435d0..d3d7b74 100644 --- a/reference/Rfc3339.html +++ b/reference/Rfc3339.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -163,46 +163,46 @@

Author

Examples

out <- as.Rfc3339(Sys.time() + 1:10)
 out
-#>  [1] "2024-08-19T17:41:20+00:00" "2024-08-19T17:41:21+00:00"
-#>  [3] "2024-08-19T17:41:22+00:00" "2024-08-19T17:41:23+00:00"
-#>  [5] "2024-08-19T17:41:24+00:00" "2024-08-19T17:41:25+00:00"
-#>  [7] "2024-08-19T17:41:26+00:00" "2024-08-19T17:41:27+00:00"
-#>  [9] "2024-08-19T17:41:28+00:00" "2024-08-19T17:41:29+00:00"
+#>  [1] "2024-08-27T20:33:39+00:00" "2024-08-27T20:33:40+00:00"
+#>  [3] "2024-08-27T20:33:41+00:00" "2024-08-27T20:33:42+00:00"
+#>  [5] "2024-08-27T20:33:43+00:00" "2024-08-27T20:33:44+00:00"
+#>  [7] "2024-08-27T20:33:45+00:00" "2024-08-27T20:33:46+00:00"
+#>  [9] "2024-08-27T20:33:47+00:00" "2024-08-27T20:33:48+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 
 out[2:5]
-#> [1] "2024-08-19T17:41:21+00:00" "2024-08-19T17:41:22+00:00"
-#> [3] "2024-08-19T17:41:23+00:00" "2024-08-19T17:41:24+00:00"
+#> [1] "2024-08-27T20:33:40+00:00" "2024-08-27T20:33:41+00:00"
+#> [3] "2024-08-27T20:33:42+00:00" "2024-08-27T20:33:43+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 out[2] <- "2"
 c(out, out)
-#>  [1] "2024-08-19T17:41:20+00:00" NA                         
-#>  [3] "2024-08-19T17:41:22+00:00" "2024-08-19T17:41:23+00:00"
-#>  [5] "2024-08-19T17:41:24+00:00" "2024-08-19T17:41:25+00:00"
-#>  [7] "2024-08-19T17:41:26+00:00" "2024-08-19T17:41:27+00:00"
-#>  [9] "2024-08-19T17:41:28+00:00" "2024-08-19T17:41:29+00:00"
-#> [11] "2024-08-19T17:41:20+00:00" NA                         
-#> [13] "2024-08-19T17:41:22+00:00" "2024-08-19T17:41:23+00:00"
-#> [15] "2024-08-19T17:41:24+00:00" "2024-08-19T17:41:25+00:00"
-#> [17] "2024-08-19T17:41:26+00:00" "2024-08-19T17:41:27+00:00"
-#> [19] "2024-08-19T17:41:28+00:00" "2024-08-19T17:41:29+00:00"
+#>  [1] "2024-08-27T20:33:39+00:00" NA                         
+#>  [3] "2024-08-27T20:33:41+00:00" "2024-08-27T20:33:42+00:00"
+#>  [5] "2024-08-27T20:33:43+00:00" "2024-08-27T20:33:44+00:00"
+#>  [7] "2024-08-27T20:33:45+00:00" "2024-08-27T20:33:46+00:00"
+#>  [9] "2024-08-27T20:33:47+00:00" "2024-08-27T20:33:48+00:00"
+#> [11] "2024-08-27T20:33:39+00:00" NA                         
+#> [13] "2024-08-27T20:33:41+00:00" "2024-08-27T20:33:42+00:00"
+#> [15] "2024-08-27T20:33:43+00:00" "2024-08-27T20:33:44+00:00"
+#> [17] "2024-08-27T20:33:45+00:00" "2024-08-27T20:33:46+00:00"
+#> [19] "2024-08-27T20:33:47+00:00" "2024-08-27T20:33:48+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 
 as.character(out)
-#>  [1] "2024-08-19T17:41:20+00:00" NA                         
-#>  [3] "2024-08-19T17:41:22+00:00" "2024-08-19T17:41:23+00:00"
-#>  [5] "2024-08-19T17:41:24+00:00" "2024-08-19T17:41:25+00:00"
-#>  [7] "2024-08-19T17:41:26+00:00" "2024-08-19T17:41:27+00:00"
-#>  [9] "2024-08-19T17:41:28+00:00" "2024-08-19T17:41:29+00:00"
+#>  [1] "2024-08-27T20:33:39+00:00" NA                         
+#>  [3] "2024-08-27T20:33:41+00:00" "2024-08-27T20:33:42+00:00"
+#>  [5] "2024-08-27T20:33:43+00:00" "2024-08-27T20:33:44+00:00"
+#>  [7] "2024-08-27T20:33:45+00:00" "2024-08-27T20:33:46+00:00"
+#>  [9] "2024-08-27T20:33:47+00:00" "2024-08-27T20:33:48+00:00"
 as.POSIXct(out)
-#>  [1] "2024-08-19 17:41:20 UTC" NA                       
-#>  [3] "2024-08-19 17:41:22 UTC" "2024-08-19 17:41:23 UTC"
-#>  [5] "2024-08-19 17:41:24 UTC" "2024-08-19 17:41:25 UTC"
-#>  [7] "2024-08-19 17:41:26 UTC" "2024-08-19 17:41:27 UTC"
-#>  [9] "2024-08-19 17:41:28 UTC" "2024-08-19 17:41:29 UTC"
+#>  [1] "2024-08-27 20:33:39 UTC" NA                       
+#>  [3] "2024-08-27 20:33:41 UTC" "2024-08-27 20:33:42 UTC"
+#>  [5] "2024-08-27 20:33:43 UTC" "2024-08-27 20:33:44 UTC"
+#>  [7] "2024-08-27 20:33:45 UTC" "2024-08-27 20:33:46 UTC"
+#>  [9] "2024-08-27 20:33:47 UTC" "2024-08-27 20:33:48 UTC"
diff --git a/reference/acquireFile.html b/reference/acquireFile.html index f8d6f80..04a6b90 100644 --- a/reference/acquireFile.html +++ b/reference/acquireFile.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -184,7 +184,7 @@

Examples

# Retrieving the file: acquireFile(tmp, "coldata/simple.csv.gz") -#> [1] "/tmp/RtmpAd9Zg6/file3b5525f9832/coldata/simple.csv.gz" +#> [1] "/tmp/RtmpvBCzJU/file3a156969cbc/coldata/simple.csv.gz" diff --git a/reference/altReadObject.html b/reference/altReadObject.html index bd0f29b..57b1eb3 100644 --- a/reference/altReadObject.html +++ b/reference/altReadObject.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/altSaveObject.html b/reference/altSaveObject.html index 49d61de..306afc7 100644 --- a/reference/altSaveObject.html +++ b/reference/altSaveObject.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/anyMissing.html b/reference/anyMissing.html index c711bc4..721db84 100644 --- a/reference/anyMissing.html +++ b/reference/anyMissing.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/chooseMissingPlaceholderForHdf5.html b/reference/chooseMissingPlaceholderForHdf5.html index ee231ff..d536fe6 100644 --- a/reference/chooseMissingPlaceholderForHdf5.html +++ b/reference/chooseMissingPlaceholderForHdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/createRedirection.html b/reference/createRedirection.html index 91b0e47..4a9c072 100644 --- a/reference/createRedirection.html +++ b/reference/createRedirection.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/hdf5.html b/reference/hdf5.html index eb5fba5..0246910 100644 --- a/reference/hdf5.html +++ b/reference/hdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/index.html b/reference/index.html index 55b4f27..8676afa 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -184,7 +184,7 @@

All functions

validateDirectory()

-

Check if a staging directory is valid

+

Validate a directory of objects

validateObject() registerValidateObjectFunction() registerValidateObjectHeightFunction() registerValidateObjectDimensionsFunction() registerValidateObjectSatisfiesInterface() registerValidateObjectDerivedFrom()

diff --git a/reference/listObjects.html b/reference/listObjects.html index d3b0d20..ad665d2 100644 --- a/reference/listObjects.html +++ b/reference/listObjects.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/loadDirectory.html b/reference/loadDirectory.html index a17009b..409910d 100644 --- a/reference/loadDirectory.html +++ b/reference/loadDirectory.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/moveObject.html b/reference/moveObject.html index ad9ddbd..849746d 100644 --- a/reference/moveObject.html +++ b/reference/moveObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/quickLoadObject.html b/reference/quickLoadObject.html index dd8734d..e6ac7bb 100644 --- a/reference/quickLoadObject.html +++ b/reference/quickLoadObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/quickReadCsv.html b/reference/quickReadCsv.html index 3406a29..cefcdf9 100644 --- a/reference/quickReadCsv.html +++ b/reference/quickReadCsv.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readAtomicVector.html b/reference/readAtomicVector.html index 9c1caea..84ebd14 100644 --- a/reference/readAtomicVector.html +++ b/reference/readAtomicVector.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readBaseFactor.html b/reference/readBaseFactor.html index 177cd8d..16455a7 100644 --- a/reference/readBaseFactor.html +++ b/reference/readBaseFactor.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readBaseList.html b/reference/readBaseList.html index 83a7a98..0efa1fa 100644 --- a/reference/readBaseList.html +++ b/reference/readBaseList.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readDataFrame.html b/reference/readDataFrame.html index 144abe3..1daba59 100644 --- a/reference/readDataFrame.html +++ b/reference/readDataFrame.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readDataFrameFactor.html b/reference/readDataFrameFactor.html index 49fc4d6..0c3abef 100644 --- a/reference/readDataFrameFactor.html +++ b/reference/readDataFrameFactor.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readMetadata.html b/reference/readMetadata.html index 6517f4f..b116908 100644 --- a/reference/readMetadata.html +++ b/reference/readMetadata.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readObject.html b/reference/readObject.html index 837e1db..6d710cc 100644 --- a/reference/readObject.html +++ b/reference/readObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/readObjectFile.html b/reference/readObjectFile.html index 9a13c27..c4603c0 100644 --- a/reference/readObjectFile.html +++ b/reference/readObjectFile.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/removeObject.html b/reference/removeObject.html index af27fd9..1576c23 100644 --- a/reference/removeObject.html +++ b/reference/removeObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveAtomicVector.html b/reference/saveAtomicVector.html index 0080683..9649e9a 100644 --- a/reference/saveAtomicVector.html +++ b/reference/saveAtomicVector.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveBaseFactor.html b/reference/saveBaseFactor.html index 22c1e2e..9956901 100644 --- a/reference/saveBaseFactor.html +++ b/reference/saveBaseFactor.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveBaseList.html b/reference/saveBaseList.html index 5d8698b..27b7d8d 100644 --- a/reference/saveBaseList.html +++ b/reference/saveBaseList.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveDataFrameFactor.html b/reference/saveDataFrameFactor.html index 60d8923..400f34c 100644 --- a/reference/saveDataFrameFactor.html +++ b/reference/saveDataFrameFactor.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveFormats.html b/reference/saveFormats.html index 2a191ac..a4e3284 100644 --- a/reference/saveFormats.html +++ b/reference/saveFormats.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveMetadata.html b/reference/saveMetadata.html index b12f7f6..0474790 100644 --- a/reference/saveMetadata.html +++ b/reference/saveMetadata.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/saveObject.html b/reference/saveObject.html index a12c02f..c431e43 100644 --- a/reference/saveObject.html +++ b/reference/saveObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/stageDataFrame.html b/reference/stageDataFrame.html index c5481eb..d6be30a 100644 --- a/reference/stageDataFrame.html +++ b/reference/stageDataFrame.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/transformVectorForHdf5.html b/reference/transformVectorForHdf5.html index 93add1a..0fe28ca 100644 --- a/reference/transformVectorForHdf5.html +++ b/reference/transformVectorForHdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/validateDirectory.html b/reference/validateDirectory.html index 6fbc232..95ae3b8 100644 --- a/reference/validateDirectory.html +++ b/reference/validateDirectory.html @@ -1,5 +1,5 @@ -Check if a staging directory is valid — validateDirectory • alabaster.baseValidate a directory of objects — validateDirectory • alabaster.base @@ -17,7 +17,7 @@ alabaster.base - 1.5.5 + 1.5.6 @@ -50,22 +50,17 @@
-

Check if a staging directory is valid

+

Validate a directory of objects

Source: R/validateDirectory.R
-

Check whether a staging directory is valid in terms of its structure and metadata.

+

Check whether each object in a directory is valid by calling validateObject on each non-nested object.

- 
validateDirectory(
-  dir,
-  validate.metadata = TRUE,
-  schema.locations = NULL,
-  attempt.load = FALSE
-)
+ 
validateDirectory(dir, legacy = NULL, ...)
@@ -73,41 +68,27 @@

Arguments

dir
-

String containing the path to a staging directory.

+

String containing the path to a directory with subdirectories populated by saveObject.

-
validate.metadata
-

Whether to validate each metadata JSON file against the schema.

+
legacy
+

Logical scalar indicating whether to validate a directory with legacy objects (created by the old stageObject). +If NULL, this is auto-detected from the contents of dir.

-
schema.locations
-

Character vector containing the name of the package containing the JSON schemas. -Only used if validate.metadata=TRUE; if NULL, defaults to the locations described in ?loadObject.

- - -
attempt.load
-

Whether to validate each object by attempting to load it into memory.

+
...
+

Further arguments to use when legacy=TRUE, for back-compatibility only.

Value

-

NULL invisibly on success, otherwise an error is raised.

+

Character vector of the paths inside dir that were validated, invisibly. +If any validation failed, an error is raised.

Details

-

This function verifies that the restrictions described in stageObject are respected, namely:

  • Each object is represented by subdirectory with a single JSON document.

    • -

  • Each JSON metadata document's path property exists and is consistent with the path of the document itself.

    • -

  • Child objects are nested in subdirectories of the parent object's directory.

    • -

  • Child objects have the is_child property set to true in their metadata.

    • -

  • Each child object is referenced exactly once in its parent object's metadata.

    • -

This function will also check that redirections are valid:

  • The path property of the redirection does not exist and is consistent with the path of the redirection document.

    • -

  • The redirection target location exists in the directory.

    • -

If validate.metadata=TRUE, this function will validate each metadata file against its specified JSON schema. -Applications may set schema.locations to point to an appropriate set of schemas other than the defaults in alabaster.base.

-

If attempt.load=TRUE, this function will attempt to load each non-child object into memory. -This serves as an additional validation step to check that the contents of each file are valid (at least, according to the current altLoadObject function). -However, it may be time-consuming and so defaults to FALSE. -Child objects are assumed to be loaded as part of their parents and are not explicitly checked.

+

We assume that the process of validating an object will call validateObject on any nested objects. +This allows us to skip explicit calls to validateObject on each component of a complex object.

Author

@@ -128,17 +109,18 @@

Examples

# Mocking up the directory: tmp <- tempfile() dir.create(tmp, recursive=TRUE) -writeMetadata(stageObject(df, tmp, "foo"), tmp) -#> $type -#> [1] "local" -#> -#> $path -#> [1] "foo/simple.csv.gz" -#> +saveObject(df, file.path(tmp, "foo")) # Checking that it's valid: validateDirectory(tmp) +# Adding an invalid object: +dir.create(file.path(tmp, "bar")) +write(file=file.path(tmp, "bar", "OBJECT"), '[ "WHEEE" ]') +try(validateDirectory(tmp)) +#> Error in value[[3L]](cond) : +#> failed to validate 'bar'; failed to read the OBJECT file at '/tmp/RtmpvBCzJU/file3a1372da62/bar'; metadata should be a JSON object +
diff --git a/reference/validateObject.html b/reference/validateObject.html index b75daaf..32323a8 100644 --- a/reference/validateObject.html +++ b/reference/validateObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.5 + 1.5.6 diff --git a/reference/writeMetadata.html b/reference/writeMetadata.html index ebec05e..82911c4 100644 --- a/reference/writeMetadata.html +++ b/reference/writeMetadata.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.5 + 1.5.6