get identifier for taxa

phenoscape · Oct 28, 2015 · fe7d29e · fe7d29e
1 parent bd13fb4
commit fe7d29e
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Showing 3 changed files with 17 additions and 10 deletions.
diff --git a/R/pk_ontotrace.R b/R/pk_ontotrace.R
@@ -68,21 +68,23 @@ pk_ontotrace <- function(taxon, entity, relation = "part of", get_metadata = FAL
 
   nex <- nexml_read(out)
 
+
   m <- get_characters(nex) # returned data.frame with taxon names as row index
   m[] <- lapply(m, function(x) as.numeric(as.character(x)))
-  ont_row_names <- row.names(m)
+  ont_row_names <- rownames(m)
   rownames(m) <- NULL
   m <- dplyr::mutate(m, taxon = ont_row_names)
-  m_re <- m[, c(ncol(m), 1:ncol(m)-1)]
+  m_re <- dplyr::as_data_frame(m[, c(ncol(m), 1:ncol(m)-1)])
 
   # TODO: add ordered taxonID and entityID to the list
   if (get_metadata == TRUE) {
-    id_taxa <- get_metadata(nex, level = "otu")
-    id_entity <- get_metadata(nex, level = "char")
+    id_taxa <- get_taxa(nex)
+    #id_entity <- get_metadata(nex, level = "char")
 
     m_re <- list(matrix = m_re,
-                 id_taxa = id_taxa[which(names(id_taxa) == meta_attr_taxon)],
-                 id_entity = id_entity[which(names(id_entity) == meta_attr_entitiy)]
+                 id_taxa = id_taxa
+                 #id_taxa = id_taxa[which(names(id_taxa) == meta_attr_taxon)]
+                 #id_entity = id_entity[which(names(id_entity) == meta_attr_entitiy)]
                  )
   }
   return(m_re)

diff --git a/man/pk_ontotrace.Rd b/man/pk_ontotrace.Rd
@@ -4,7 +4,7 @@
 \alias{pk_ontotrace}
 \title{Returns a NeXML-format evolutionary character matrix.}
 \usage{
-pk_ontotrace(taxon, entity, relation = "part of", get_metadata = TRUE,
+pk_ontotrace(taxon, entity, relation = "part of", get_metadata = FALSE,
   variable_only = TRUE)
 }
 \arguments{

diff --git a/tests/testthat/test-pk.R b/tests/testthat/test-pk.R
@@ -58,14 +58,19 @@ test_that("Test OnToTrace", {
   rel <- pk_ontotrace(taxon = c("Ictalurus", "Ameiurus"),
                       entity = c("fin", "spine"),
                       relation = "develops from")
+
+  single1 <- pk_ontotrace(taxon = "Ictalurus", entity = "fin", get_metadata = TRUE)
+
   err1 <- function() pk_ontotrace(taxon = "Ictalurus TT", entity = "fin", relation = "other relation")
   err2 <- function() pk_ontotrace(taxon = c("Ictalurus", "Ameiurus XXX"), entity = c("fin", "spine"))
   err3 <- function() pk_ontotrace("Ictalurus TT", "fin")
 
 
-  expect_output(str(single), "data.frame")
-  expect_output(str(multi), "data.frame")
-  expect_output(str(rel), "data.frame")
+  expect_output(str(single), "Classes ‘tbl_df’, ‘tbl’ and 'data.frame'")
+  expect_output(str(multi), "Classes ‘tbl_df’, ‘tbl’ and 'data.frame'")
+  expect_output(str(rel), "Classes ‘tbl_df’, ‘tbl’ and 'data.frame'")
+
+  expect_output(str(single1), "List of 2")
 
   expect_equal(all(apply(single[,-1], 2, is.numeric)), TRUE)
   expect_equal(all(apply(multi[,-1], 2, is.numeric)), TRUE)