Merge pull request #18 from wilsontom/devel

Version 0.2.0

.Rbuildignore

@@ -7,3 +7,7 @@ README.md
 cran-comments.md
 NOTES.md
 cran_submission/
+_pkgdown.yml
+README_examples.R
+README.Rmd
+docs/

.gitignore

@@ -1,2 +1,3 @@
 .Rproj.user
 cran_submission/
+README_examples.R

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: classyfireR
 Type: Package
 Title: R Interface to the ClassyFire RESTful API
-Version: 0.1.2
-Date: 2018-12-06
+Version: 0.2.0
+Date: 2019-02-25
 Authors@R: c(
     person("Tom", "Wilson", , "tpw2@aber.ac.uk", c("aut", "cre")))
 Description: Access to the ClassyFire RESTful API <http://classyfire.wishartlab.com>. Retrieve existing entity classifications and submit new entities for classification. 
@@ -13,17 +13,18 @@ Imports:
     jsonlite,
     tibble,
     crayon, 
-    clisymbols
+    clisymbols,
+    purrr,
+    dplyr,
+    stringr
 Suggests: 
     testthat,
     covr,
-    dplyr,
-    purrr,
     tidyr
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/wilsontom/classyfireR
 BugReports: https://github.com/wilsontom/classyfireR/issues
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,8 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-export(entity_classification)
-export(get_status_code)
-export(retrieve_classification)
-export(submit_classification)
+export(get_classification)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
 importFrom(magrittr,"%>%")
+importFrom(purrr,map)
+importFrom(purrr,map_chr)
+importFrom(stringr,str_c)
+importFrom(tibble,tibble)
 importFrom(utils,globalVariables)

NEWS.md

@@ -1,16 +1,20 @@
-### NEWS
+# classyfireR 0.2.0
 
-#### v0.1.2
+* Remove POST submission functions. ClassyFire database is now extensive enough that new submission are rarely needed. This will prevent the intermitent failing of checks on CRAN aswell. 
+* Add `pkgdown` website for docs
+* `entity_classification` renamed to `get_classification`
+* All available classificatons now returned (@jasenfinch)
 
-- Fix unit test to catch when server is unresponsive. This will fix intermittent CRAN check fails
+# classyfireR 0.1.2
 
-#### v0.1.1
+* Fix unit test to catch when server is unresponsive. This will fix intermittent CRAN check fails
 
-- Add more detailed examples ready for CRAN submission
+# classyfireR 0.1.1
 
-#### V0.1.0
+* Add more detailed examples ready for CRAN submission
 
+# classyfireR 0.1.0
 
-- Low level access to the ClassyFire RESTful API
-- Retrieve existing classifications using InChI Keys
-- Submit new classifications to the server using InChI Codes and retrieve the results
+* Low level access to the ClassyFire RESTful API
+* Retrieve existing classifications using InChI Keys
+* Submit new classifications to the server using InChI Codes and retrieve the results

R/classyfireR.R

@@ -0,0 +1,2 @@
+
+globalVariables(c('Level','Classification'))

R/entity_classification.R → R/get_classification.R

@@ -1,4 +1,4 @@
-#' Entity Classification
+#' Get Entity Classification
 #'
 #' Retrieve entity classification from `http://classyfire.wishartlab.com/entities/'
 #'
@@ -12,13 +12,13 @@
 #' @examples
 #'
 #' # Valid InChI key where all four classification levels are available
-#' entity_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')
+#' get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')
 #'
 #' # Valid InChI key where only three classification levels are available
-#' entity_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-N')
+#' get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-N')
 #'
 #' # Invalid InChI key
-#' entity_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-B')
+#' get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-B')
 #'
 #'
 #' # Using `dplyr` a vector of InChI Keys can be submitted and easily parsed
@@ -34,7 +34,7 @@
 #' 'WHEUWNKSCXYKBU-QPWUGHHJSA-N',
 #' 'WHBMMWSBFZVSSR-GSVOUGTGSA-N')
 #'
-#'  classification_list <- map(keys, entity_classification)
+#'  classification_list <- map(keys, get_classification)
 #'
 #'  classification_list <- map(classification_list, ~{select(.,-CHEMONT)})
 #'
@@ -44,18 +44,23 @@
 #'
 #'  rownames(spread_tibble) <- keys
 #'
-#'  classification_df <-  data.frame(InChIKey = rownames(spread_tibble),
-#'                                Kingdom = spread_tibble$kingdom,
-#'                                 SuperClass = spread_tibble$superclass,
-#'                                 Class = spread_tibble$class,
-#'                                 SubClass = spread_tibble$subclass)
+#'  classification_tibble <-  tibble(
+#'      InChIKey = rownames(spread_tibble),
+#'      Kingdom = spread_tibble$kingdom,
+#'      SuperClass = spread_tibble$superclass,
+#'      Class = spread_tibble$class,
+#'      SubClass = spread_tibble$subclass,
+#'      Level5 = spread_tibble$level.5,
+#'      Level6 = spread_tibble$level.6,
+#'      Level7 = spread_tibble$level.7
+#'     )
 #'
-#'  print(classification_df)
+#'  print(classification_tibble)
 #'
 #'
 #'
 #' @export
-entity_classification <- function(inchi_key)
+get_classification <- function(inchi_key)
 {
   entity_url <- 'http://classyfire.wishartlab.com/entities/'
 

R/internals.R

@@ -8,6 +8,11 @@
 #' * __Classification__ The compound classification
 #' * __CHEMONT__ Chemical Ontology Identification code
 #' @keywords internal
+#' @importFrom dplyr bind_rows filter
+#' @importFrom purrr map map_chr
+#' @importFrom stringr str_c
+#' @importFrom tibble tibble
+#' @importFrom magrittr %>%
 
 parse_json_output <- function(json_res)
 {
@@ -16,27 +21,34 @@ parse_json_output <- function(json_res)
       kingdom = json_res[['kingdom']],
       superclass = json_res[['superclass']],
       class = json_res[['class']],
-      subclass = json_res[['subclass']]
+      subclass = json_res[['subclass']],
+      intermediate_nodes = json_res[['intermediate_nodes']],
+      direct_parent = json_res[['direct_parent']]
     )
 
-  len <- lapply(list_output, length) %>% unlist()
+  if (length(list_output$intermediate_nodes) == 0) {
+    list_output$intermediate_nodes <- NULL
+  }
 
-  class_tibble <-
-    tibble::tibble(Level = names(len),
-                   Classification = 'NA',
-                   CHEMONT = 'NA')
+  list_output <- list_output[!sapply(list_output,is.null)]
 
-  for (i in seq_along(len)) {
-    if (len[[i]] == 4) {
-      class_tibble[i, 'Classification'] <- list_output[[i]]$name
-      class_tibble[i, 'CHEMONT'] <- list_output[[i]]$chemont_id
-    } else{
-      class_tibble[i, 'Classification'] <- NA
-      class_tibble[i, 'CHEMONT'] <- NA
-    }
-  }
+  class_tibble <- map(1:length(list_output),~{
+    l <- list_output[[.]]
+    tibble(
+      Level = names(list_output)[.],
+      Classification = l$name,
+      CHEMONT = l$chemont_id
+    )
+  }) %>%
+    bind_rows() %>%
+    filter(!duplicated(Classification))
 
+  nIntermediate <- class_tibble %>%
+    filter(Level == 'intermediate_nodes') %>%
+    nrow()
 
-  return(class_tibble)
+  class_tibble$Level[class_tibble$Level == 'intermediate_nodes'] <- map_chr(5:(5 + (nIntermediate - 1)),~{str_c('level ',.)})
+  class_tibble$Level[class_tibble$Level == 'direct_parent'] <- str_c('level ',5 + nIntermediate)
 
+  return(class_tibble)
 }