Merge pull request #34 from aberHRML/devel

0.3.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: classyfireR
 Type: Package
 Title: R Interface to the ClassyFire RESTful API
-Version: 0.3.1
-Date: 2019-11-22
+Version: 0.3.2
+Date: 2019-12-16
 Authors@R: c(
     person("Tom", "Wilson", , "tpw2@aber.ac.uk", c("aut", "cre"),  comment = c(ORCID = "0000-0003-3112-4682")),
     person("Jasen", "Finch", , "jsf9@aber.ac.uk", "aut"))
@@ -28,7 +28,7 @@ Encoding: UTF-8
 LazyData: true
 URL: https://github.com/aberHRML/classyfireR
 BugReports: https://github.com/aberHRML/classyfireR/issues
-RoxygenNote: 7.0.0
+RoxygenNote: 7.0.2
 Roxygen: list(markdown = TRUE)
 Collate: 
     'allGenerics.R'

NAMESPACE

@@ -11,4 +11,6 @@ exportMethods(direct_parent)
 exportMethods(meta)
 exportMethods(show)
 importFrom(magrittr,"%>%")
+importFrom(methods,show)
+importFrom(tibble,tibble)
 importFrom(utils,globalVariables)

NEWS.md

@@ -1,3 +1,9 @@
+# classyfireR 0.3.2
+
+* Add check to `get_classification` for when a valid http status code (200) is returned but the content of the return is `{}`. This appears to be an error during InChIKey validation. 
+
+* Add further length checks in `get_classification` for when there are no `alternative_parents` returned. 
+
 # classyfireR 0.3.1
 
 * Add length checks in `get_classification` for when elements of the `json` output is missing (ie, no external descriptors present)

R/get_classification.R

@@ -36,9 +36,16 @@ get_classification <- function(inchi_key)
   }
 
   if (response$status_code == 200) {
-    message(crayon::green(clisymbols::symbol$tick, inchi_key))
     text_content <- httr::content(response, 'text')
 
+    if (text_content == '{}') {
+      message(crayon::red(clisymbols::symbol$cross, inchi_key))
+      return(invisible(NULL))
+    } else{
+      message(crayon::green(clisymbols::symbol$tick, inchi_key))
+    }
+
+
     json_res <- jsonlite::fromJSON(text_content)
 
     classification <- parse_json_output(json_res)
@@ -58,24 +65,28 @@ get_classification <- function(inchi_key)
 
     object@direct_parent <- json_res$direct_parent
 
-    object@alternative_parents <-
-      tibble::tibble(
-        name = json_res$alternative_parents$name,
-        description = json_res$alternative_parents$description,
-        chemont_id = json_res$alternative_parents$chemont_id,
-        url = json_res$alternative_parents$url
-      )
+    if (length(json_res$alternative_parents) > 0) {
+      object@alternative_parents <-
+        tibble::tibble(
+          name = json_res$alternative_parents$name,
+          description = json_res$alternative_parents$description,
+          chemont_id = json_res$alternative_parents$chemont_id,
+          url = json_res$alternative_parents$url
+        )
+    } else{
+      object@alternative_parents <- tibble::tibble()
+    }
 
-    if(length(json_res$predicted_chebi_terms) > 0) {
+    if (length(json_res$predicted_chebi_terms) > 0) {
       object@predicted_chebi <- json_res$predicted_chebi_terms
-    }else{
+    } else{
       object@predicted_chebi <- vector(mode = 'character')
     }
 
 
-    if(length(json_res$external_descriptors) > 0) {
+    if (length(json_res$external_descriptors) > 0) {
       object@external_descriptors <- parse_external_desc(json_res)
-    }else{
+    } else{
       object@external_descriptors <- tibble::tibble()
     }
 

R/internals.R

@@ -59,7 +59,6 @@ parse_json_output <- function(json_res)
 
 
 
-
 #' Parse External Descriptors
 #'
 #' Parse the list output of returned External Descriptors
@@ -69,23 +68,24 @@ parse_json_output <- function(json_res)
 #' * __source__ External source name
 #' * __source_id__ External source ID
 #' * __annotations__ External source annotation
+#' @importFrom tibble tibble
 #' @keywords internal
 
 parse_external_desc <- function(x)
 {
-  external_ann <- list()
-  for (i in seq_along(x$external_descriptors$annotations)) {
-    external_ann[[i]] <-
-      paste(x$external_descriptors$annotations[[i]], collapse = ' // ')
-  }
 
-  external_desc <-
-    tibble::tibble(
-      source = x$external_descriptors$source,
-      source_id = x$external_descriptors$source_id,
-      annotations = unlist(external_ann)
-    )
+    external_ann <- list()
+    for (i in seq_along(x$external_descriptors$annotations)) {
+      external_ann[[i]] <-
+        paste(x$external_descriptors$annotations[[i]], collapse = ' // ')
+    }
 
-  return(external_desc)
+    external_desc <-
+      tibble(
+        source = x$external_descriptors$source,
+        source_id = x$external_descriptors$source_id,
+        annotations = unlist(external_ann)
+      )
 
+  return(external_desc)
 }

R/show-method.R

@@ -1,6 +1,7 @@
 #' show-ClassyFire
 #' @rdname show
 #' @param object a `ClassyFire` S4 object
+#' @importFrom methods show
 #' @export
 
 setMethod('show', signature = 'ClassyFire',

README.md

@@ -3,7 +3,7 @@
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![Build Status](https://travis-ci.org/aberHRML/classyfireR.svg?branch=master)](https://travis-ci.org/aberHRML/classyfireR) [![Build status](https://ci.appveyor.com/api/projects/status/ua94fiotdmc0ssq5/branch/master?svg=true)](https://ci.appveyor.com/project/wilsontom/classyfirer/branch/master) [![codecov](https://codecov.io/gh/aberHRML/classyfireR/branch/master/graph/badge.svg)](https://codecov.io/gh/aberHRML/classyfireR) ![License](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg "GNU GPL v3.0") [![DOI](https://zenodo.org/badge/118162964.svg)](https://zenodo.org/badge/latestdoi/118162964)
 
-[![CRAN](https://www.r-pkg.org/badges/version/classyfireR)](https://cran.r-project.org/web/packages/classyfireR/index.html) ![total downloads](https://cranlogs.r-pkg.org/badges/grand-total/classyfireR?color=red)
+[![CRAN](https://www.r-pkg.org/badges/version/classyfireR)](https://cran.r-project.org/web/packages/classyfireR/index.html) ![total downloads](https://cranlogs.r-pkg.org/badges/grand-total/classyfireR?color=red) [![GitHub](https://img.shields.io/github/v/release/aberHRML/classyfireR?color=brightgreen&label=GitHub%20Version)](https://github.com/aberHRML/classyfireR/releases)
 > __R Interface to the [ClassyFire REST API](http://classyfire.wishartlab.com)__