Merge pull request #127 from nuest/master

Release fixes after manual inspection

DESCRIPTION

@@ -1,19 +1,31 @@
 Package: sos4R
 Type: Package
-Title: An R Client for the OGC Sensor Observation Service
+Title: Client for OGC Sensor Observation Services
 Version: 0.3.0
-Authors@R: c(person(given = "Daniel", family = "Nuest", role = c("cre", "aut"),
-	email = "daniel.nuest@uni-muenster.de", comment = c(ORCID = "0000-0002-0024-5046")),
-	person("Edzer", "Pebesma", role = "ctb", comment = c(ORCID = "0000-0001-8049-7069")),
-	person("Ben", "Graeler", role = "ctb", comment = c(ORCID = "0000-0001-5443-4304")),
-	person("Benjamin", "Pross", role = "ctb"),
-	person("Eike Hinderk", "Juerrens", role = "ctb"))
-Author: Daniel Nuest [cre, aut] (<https://orcid.org/0000-0002-0024-5046>),
-  Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>),
-  Ben Graeler [ctb] (<https://orcid.org/0000-0001-5443-4304>),
-  Benjamin Pross [ctb],
-  Eike Hinderk Juerrens [ctb]
-Maintainer: Daniel Nuest <daniel.nuest@uni-muenster.de>
+Date: 2019-04-13
+Authors@R:
+  c(person(given = "Daniel",
+           family = "Nuest",
+           role = c("cre", "aut"),
+           email = "daniel.nuest@uni-muenster.de",
+           comment = c(ORCID = "0000-0002-0024-5046")),
+	  person(given = "Edzer",
+	         family = "Pebesma",
+	         role = "ctb",
+	         comment = c(ORCID = "0000-0001-8049-7069")),
+	  person(given = "Ben",
+	         family = "Graeler",
+	         role = "ctb",
+	         comment = c(ORCID = "0000-0001-5443-4304")),
+	  person(given = "Benjamin",
+	         family = "Pross",
+	         role = "ctb"),
+	  person(given = "Eike Hinderk",
+	         family = "Juerrens",
+	         role = "ctb"),
+	  person(given = "52°North Initiative for Geospatial Open Source Software GmbH",
+	         email = "info@52north.org",
+	         role = "cph"))
 Depends: R (>= 3.4.0)
 Imports:
     httr,
@@ -22,6 +34,7 @@ Imports:
     stringr,
     xml2,
 Suggests:
+    readr,
     spacetime,
     gstat,
     maps,
@@ -34,10 +47,11 @@ Suggests:
     rgdal,
     knitr,
     rmarkdown
-Description: A client for Sensor Observation Services (SOS) as
-        specified by the Open Geospatial Consortium (OGC). The package allows
-        users to retrieve metadata from SOS web services and to
-        interactively create requests for near real-time observation
+Description: A client for Sensor Observation Services (SOS, see 
+        <https://www.opengeospatial.org/standards/sos>) as specified by the 
+        Open Geospatial Consortium (OGC). With the package users can
+        retrieve (meta)data from SOS instances and interactively 
+        create requests for near real-time observation
         data based on the available sensors, phenomena, observations etc.
         using thematic, temporal, and spatial filtering.
 License: GPL-2

DEV-README.md

@@ -237,9 +237,11 @@ Add tests.
 
 A new release shall be uploaded to CRAN after testing and under the following procedure:
 
+- Install the current version of the package from source
 - Run the [tests](#tests) locally and resolve all problems
 - Run a check locally, e.g. `devtools::check(document = FALSE)` and fix errors, warnings, and notes
-- Update NEWS file based on latest commits
+- Update NEWS file based on latest commits, add missing changes/updates/notable things
+- Update the `Date` field in the `DESCRIPTION` file to match the release date
 - Create a PR from `dev` to `master` and check the CI status, fix all problems
   - https://travis-ci.org/52North/sos4R
   - https://ci.appveyor.com/project/52North/sos4r
@@ -253,9 +255,19 @@ A new release shall be uploaded to CRAN after testing and under the following pr
   - (optional) `rhub::check(email = <...>)` for running checks on different operating systems
 - Regenerate the website with `pkgdown::build_site()` and re-knit `README.Rmd`, commit changes
 - Push changes to `dev` branch
-- Create a git tag with the version number using the letter `v` followed by the version number (see above, must match `DESCRIPTION`), e.g. `v1.2.3`, and push it to the main repository
 - Read and follow http://cran.r-project.org/web/packages/policies.html and http://r-pkgs.had.co.nz/release.html#release-check again, make necessary changes
 - Merge the PR
+- Update your local `master` to upstream's `master` branch
+-_ Do the actual release_ with `devtools::release()` (which will ask you again if you did many of the steps before)
+- Wait for the good news, check where the package is in the queue with `foghorn::cran_incoming(pkg = "sos4R")`
+- When available on CRAN:
+  - Create a git tag with the version number using the letter `v` followed by the version number (see above, must match `DESCRIPTION`), e.g. `v1.2.3`, and push it to the main repository
+  - Create a release on GitHub based on the new tag, named just as the version tag
+  - Checkout the `dev` branch
+  - Merge `upstream/master`
+  - Update the version in `DESCRIPTION` to a new development version, e.g. from `0.3.0` to `0.4.0.9000`
+  - Email on 52N mailing list(s) (coordinate with 52N staff)
+  - Tweet
 
 You can then do the actual release with
 

R/SOS-methods-parsing.R

@@ -485,11 +485,13 @@ setMethod(f = "parseFile",
           }
 )
 
-#
-# parse commma seperated values ----
-#
 parseCSV <- function(obj, verbose = FALSE) {
-  if (verbose) cat("[parseCSV] Processing CSV...\n")
+  if (verbose) cat("[parseCSV] Parsing CSV...\n")
+
+  if (inherits(x = obj, what = "data.frame")) {
+    if (verbose) cat("[parseCSV] Already a data.frame, returning object\n")
+    return(obj)
+  }
 
   .lines <- strsplit(x = obj, split = "\n")[[1]]
   .data <- do.call(what = "strsplit", args = list(.lines, split = ","))
@@ -506,11 +508,6 @@ parseCSV <- function(obj, verbose = FALSE) {
   .rows <- length(.data)
   if (verbose) cat("[parseCSV] Got", .rows, "lines of data.\n")
 
-  if (.rows == 1) {
-    warnings(paste("Received just one line of data: ", .data, "\n"))
-    return(.data[[1]])
-  }
-
   .df <- NULL
   for (.r in seq(2,.rows)) {
     if (verbose) cat("[parseCSV] Processing row in CSV:", .data[[.r]], "\n")
@@ -524,8 +521,6 @@ parseCSV <- function(obj, verbose = FALSE) {
       names(.df) <- .names[[i]]
       .row.df <- cbind(.row.df, .df)
     }
-    #		print(paste("row", .r))
-    #		print(.row.df)
 
     if (is.null(.df))
       .df <- .row.df

R/SOS-methods-util.R

@@ -380,15 +380,24 @@ setMethod(f = "sosGetCRS",
           definition = function(obj, verbose = FALSE) {
             if (verbose) cat("[sosGetCRS] from '", obj, "'\n", sep = "")
 
-            # get the position of EPSG code
-            .split <- strsplit(as.character(obj), split = ":")
-            .idx <- which(toupper(.split[[1]]) == "EPSG")
-            if (length(.idx) == 0) {
-              # possibly versioned, try one index higher?
-              warning(paste("Could not create CRS from the given object:", obj))
-              return(NULL)
+            .epsg <- NA
+            # URN
+            if (grepl(pattern = "urn:ogc", x = obj)) {
+              .epsg <- sub(pattern = "(.*)epsg:[0-9]*(:?)",
+                           replacement = "",
+                           x = tolower(obj))[[1]]
+            }
+            # URL
+            if (grepl(pattern = "opengis.net", x = obj)) {
+              .epsg <- sub(pattern = "(.*)epsg/[0-9]*(/?)",
+                           replacement = "",
+                           x = tolower(obj))[[1]]
+            }
+
+            if (is.na(.epsg)) {
+              warning("Could not create CRS from string ", obj)
+              return(NA)
             }
-            .epsg <- .split[[1]][[length(.split[[1]])]]
 
             .initString <- paste("+init=epsg", .epsg, sep = ":")
 

R/SOS-methods.R

@@ -1514,10 +1514,17 @@ setMethod(f = "checkRequest",
     xml <- xml2::read_xml(text)
     return(xml)
   }
-  else if (contentType == "application/xml") {
+  else if (contentType == "application/xml" || contentType == "text/xml") {
     xml <- httr::content(x = response, encoding = sosDefaultCharacterEncoding)
     return(xml)
   }
+  else if (contentType == "text/csv") {
+    if (!requireNamespace("readr", quietly = TRUE))
+      stop("package readr required to handle text/csv format, please install")
+
+    tibble <- httr::content(x = response, encoding = sosDefaultCharacterEncoding)
+    return(tibble)
+  }
 
   stop("Unsupported content type in response")
 }

cran-comments.md

@@ -8,10 +8,29 @@
 
 ## R CMD check results
 
-No notes.
+No errors.
 No warnings.
 
+1 NOTE:
+
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: 'Daniel Nuest <daniel.nuest@uni-muenster.de>'
+
+New submission
+
+Package was archived on CRAN
+
+Possibly mis-spelled words in DESCRIPTION:
+  Geospatial (36:31)
+  OGC (3:67, 36:54)
+
+CRAN repository db overrides:
+  X-CRAN-Comment: Archived on 2018-06-17 as check problems were not
+    corrected despite reminders.
+
 ## Other
 
 The package was "archived on 2018-06-17 as check problems were not corrected despite reminders."
 Issues could now finally be resolved with a complete overhaul of implementation (switching from XML to xml2) and we kindly request re-publication on CRAN.
+
+Comments during manual inspection were handled with this resubmission.

demo/00Index

@@ -1,11 +1,3 @@
-ades			demo script for SOS with French groundwater level data
-airquality		spatial analysis demo for air quality SOS by ifgi and EEA
-austria			demo script for SOSs by Research Studios Austria
-coastlab		demo script for SOSs by Helmholtz-Zentrum Geesthacht
-co-ops			[under construction] demo script for SOSs by the NOAA Center for Operational Oceanographic Products and Services focussing on non-O&M response formats and filtering
-ioos			demo script for SOS by Integrated Ocean Observing System
-marinemeta		demo script for SOS by Marine Metadata Interoperability Initiative
-oceanwatch		demo script for SOS by NOAA/SWFSC/ERD
-pegel			demo script for water gauge data in Germany by Pegelonline
-southesk		plotting and data consilidation demo for SOSs from South Esk Testbed by CSIRO
-eo2heaven		health-related and air quality SOS for the state of Saxony, Germany, and Durban, South Africa by TU Dresden
+co-ops			SOSs by the NOAA Center for Operational Oceanographic Products and Services focussing on non-O&M response formats and filtering
+ioos			  SOS by Integrated Ocean Observing System
+pegel			  Water gauge data in Germany by Pegelonline