| ... | ... |
@@ -19,10 +19,13 @@ get_classes = function(owlfile) {
|
| 19 | 19 |
#' the entity.) |
| 20 | 20 |
#' @examples |
| 21 | 21 |
#' pa = get_ordo_owl_path() |
| 22 |
-#' orde = setup_entities(pa) |
|
| 23 |
-#' orde |
|
| 24 |
-#' ancestors(orde[1000:1001]) |
|
| 25 |
-#' labels(orde[1000:1001]) |
|
| 22 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 23 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 24 |
+#' orde = setup_entities(pa) |
|
| 25 |
+#' orde |
|
| 26 |
+#' ancestors(orde[1000:1001]) |
|
| 27 |
+#' labels(orde[1000:1001]) |
|
| 28 |
+#' } |
|
| 26 | 29 |
#' @export |
| 27 | 30 |
setup_entities = function(owlfn) {
|
| 28 | 31 |
thecall = match.call() |
| ... | ... |
@@ -71,13 +74,17 @@ print.owlents = function(x, ...) {
|
| 71 | 74 |
#' @return a list of sets |
| 72 | 75 |
#' @examples |
| 73 | 76 |
#' pa = get_ordo_owl_path() |
| 74 |
-#' orde = setup_entities(pa) |
|
| 75 |
-#' orde |
|
| 76 |
-#' ancestors(orde[1:5]) |
|
| 77 |
-#' labels(orde[1:5]) |
|
| 77 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 78 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 79 |
+#' orde = setup_entities(pa) |
|
| 80 |
+#' orde |
|
| 81 |
+#' ancestors(orde[1:5]) |
|
| 82 |
+#' labels(orde[1:5]) |
|
| 83 |
+#' } |
|
| 78 | 84 |
#' @export |
| 79 | 85 |
ancestors = function(oe) {
|
| 80 |
- o2 = reticulate::import("owlready2")
|
|
| 86 |
+ o2 = try(reticulate::import("owlready2"))
|
|
| 87 |
+ if (inherits(o2, "try-error")) stop("ensure that reticulate can find owlready2")
|
|
| 81 | 88 |
ans = lapply(oe$allents, o2$EntityClass$ancestors) |
| 82 | 89 |
names(ans) = oe$clnames |
| 83 | 90 |
ans |
| ... | ... |
@@ -89,9 +96,12 @@ ancestors = function(oe) {
|
| 89 | 96 |
#' @return list of vectors of character() |
| 90 | 97 |
#' @examples |
| 91 | 98 |
#' pa = get_ordo_owl_path() |
| 92 |
-#' orde = setup_entities(pa) |
|
| 93 |
-#' al = ancestors(orde[1001:1002]) |
|
| 94 |
-#' ancestors_names(al) |
|
| 99 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 100 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 101 |
+#' orde = setup_entities(pa) |
|
| 102 |
+#' al = ancestors(orde[1001:1002]) |
|
| 103 |
+#' ancestors_names(al) |
|
| 104 |
+#' } |
|
| 95 | 105 |
#' @export |
| 96 | 106 |
ancestors_names = function(anclist) {
|
| 97 | 107 |
lapply(anclist, .ancestor_element_names) |
| ... | ... |
@@ -103,9 +113,12 @@ ancestors_names = function(anclist) {
|
| 103 | 113 |
#' @return list of vectors of character() |
| 104 | 114 |
#' @examples |
| 105 | 115 |
#' pa = get_ordo_owl_path() |
| 106 |
-#' orde = setup_entities(pa) |
|
| 107 |
-#' al = subclasses(orde[100:120]) |
|
| 108 |
-#' children_names(al) |
|
| 116 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 117 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 118 |
+#' orde = setup_entities(pa) |
|
| 119 |
+#' al = subclasses(orde[100:120]) |
|
| 120 |
+#' children_names(al) |
|
| 121 |
+#' } |
|
| 109 | 122 |
#' @export |
| 110 | 123 |
children_names = function(sclist) {
|
| 111 | 124 |
lapply(sclist, .subclass_element_names) |
| ... | ... |
@@ -131,10 +144,13 @@ children_names = function(sclist) {
|
| 131 | 144 |
#' @return list of vectors of tags of parents |
| 132 | 145 |
#' @examples |
| 133 | 146 |
#' pa = get_ordo_owl_path() |
| 134 |
-#' orde = setup_entities(pa) |
|
| 135 |
-#' orde |
|
| 136 |
-#' parents(orde[1000:1001]) |
|
| 137 |
-#' labels(orde[1000:1001]) |
|
| 147 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 148 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 149 |
+#' orde = setup_entities(pa) |
|
| 150 |
+#' orde |
|
| 151 |
+#' parents(orde[1000:1001]) |
|
| 152 |
+#' labels(orde[1000:1001]) |
|
| 153 |
+#' } |
|
| 138 | 154 |
#' @export |
| 139 | 155 |
parents = function(oe) {
|
| 140 | 156 |
pts = lapply(oe$allents, function(x) x$is_a) |
| ... | ... |
@@ -154,14 +170,17 @@ parents = function(oe) {
|
| 154 | 170 |
#' @param oe owlents instance |
| 155 | 171 |
#' @examples |
| 156 | 172 |
#' pa = get_ordo_owl_path() |
| 157 |
-#' orde = setup_entities(pa) |
|
| 158 |
-#' orde |
|
| 159 |
-#' sc <- subclasses(orde[1:5]) |
|
| 160 |
-#' labels(orde[3]) |
|
| 161 |
-#' o3 = reticulate::iterate(sc[[3]]) |
|
| 162 |
-#' print(length(o3)) |
|
| 163 |
-#' o3[[2]] |
|
| 164 |
-#' labels(orde["Orphanet_100011"]) |
|
| 173 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 174 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 175 |
+#' orde = setup_entities(pa) |
|
| 176 |
+#' orde |
|
| 177 |
+#' sc <- subclasses(orde[1:5]) |
|
| 178 |
+#' labels(orde[3]) |
|
| 179 |
+#' o3 = reticulate::iterate(sc[[3]]) |
|
| 180 |
+#' print(length(o3)) |
|
| 181 |
+#' o3[[2]] |
|
| 182 |
+#' labels(orde["Orphanet_100011"]) |
|
| 183 |
+#' } |
|
| 165 | 184 |
#' @export |
| 166 | 185 |
subclasses = function(oe) {
|
| 167 | 186 |
o2 = reticulate::import("owlready2")
|
| ... | ... |
@@ -181,9 +200,12 @@ subclasses = function(oe) {
|
| 181 | 200 |
#' The previous functionality which failed is available, not exported, as labelsOLD.owlents. |
| 182 | 201 |
#' @examples |
| 183 | 202 |
#' clont_path = owl2cache(url="http://purl.obolibrary.org/obo/cl.owl") |
| 184 |
-#' clont = setup_entities(clont_path) |
|
| 185 |
-#' labels(clont[1:5]) |
|
| 186 |
-#' labels(clont[51:55]) |
|
| 203 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 204 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 205 |
+#' clont = setup_entities(clont_path) |
|
| 206 |
+#' labels(clont[1:5]) |
|
| 207 |
+#' labels(clont[51:55]) |
|
| 208 |
+#' } |
|
| 187 | 209 |
#' @export |
| 188 | 210 |
labels.owlents = function (object, ...) |
| 189 | 211 |
{
|
| ... | ... |
@@ -205,32 +227,33 @@ labelsOLD.owlents = function(object, ...) {
|
| 205 | 227 |
|
| 206 | 228 |
|
| 207 | 229 |
#' use owlready2 ontology search facility on term labels |
| 208 |
-#' @param oents owlents instance |
|
| 230 |
+#' @param ontopath character(1) path to owl file |
|
| 209 | 231 |
#' @param regexp character(1) simple regular expression |
| 210 | 232 |
#' @param case_sensitive logical(1) should case be respected in search? |
| 211 | 233 |
#' @return A named list: term labels are elements, tags are names of elements. |
| 212 | 234 |
#' Will return NULL if nothing is found. |
| 213 | 235 |
#' @examples |
| 214 | 236 |
#' pa = get_ordo_owl_path() |
| 215 |
-#' orde = setup_entities(pa) |
|
| 216 |
-#' ol = search_labels(orde, "*Immunog*") |
|
| 217 |
-#' plot(orde, names(ol)) |
|
| 237 |
+#' ol = search_labels(pa, "*Immunog*") |
|
| 238 |
+#' orde = setup_entities2(pa) |
|
| 239 |
+#' onto_plot2(orde, names(ol)) |
|
| 218 | 240 |
#' @export |
| 219 |
-search_labels = function (oents, regexp, case_sensitive=TRUE) |
|
| 241 |
+search_labels = function (ontopath, regexp, case_sensitive=TRUE) |
|
| 220 | 242 |
{
|
| 221 |
-# |
|
| 222 |
-#search(_use_str_as_loc_str=True, _case_sensitive=True, _bm25=False, **kargs) |
|
| 223 |
-# |
|
| 224 |
- stopifnot(inherits(oents, "owlents")) |
|
| 243 |
+ stopifnot(inherits(ontopath, "character")) |
|
| 225 | 244 |
thecall = match.call() |
| 226 |
- o2 = reticulate::import("owlready2")
|
|
| 227 |
- ont = o2$get_ontology(oents$owlfn)$load() |
|
| 228 |
- ans = ont$search(`_case_sensitive`=case_sensitive, label = regexp) |
|
| 229 |
- lans = reticulate::iterate(ans, force) |
|
| 230 |
- if (length(lans)<=0) return(NULL) |
|
| 231 |
- allv = lapply(lans, function(x) x$label[0]) |
|
| 232 |
- alln = lapply(lans, function(x) x$name) |
|
| 233 |
- names(allv) = unlist(alln) |
|
| 234 |
- allv |
|
| 245 |
+ proc = basilisk::basiliskStart(bsklenv, testload="owlready2") # avoid package-specific import |
|
| 246 |
+ on.exit(basilisk::basiliskStop(proc)) |
|
| 247 |
+ basilisk::basiliskRun(proc, function(owlfn, thecall) {
|
|
| 248 |
+ o2 = reticulate::import("owlready2")
|
|
| 249 |
+ ont = o2$get_ontology(owlfn)$load() |
|
| 250 |
+ ans = ont$search(`_case_sensitive`=case_sensitive, label = regexp) |
|
| 251 |
+ lans = reticulate::iterate(ans, force) |
|
| 252 |
+ if (length(lans)<=0) return(NULL) |
|
| 253 |
+ allv = lapply(lans, function(x) x$label[0]) |
|
| 254 |
+ alln = lapply(lans, function(x) x$name) |
|
| 255 |
+ names(allv) = unlist(alln) |
|
| 256 |
+ allv |
|
| 257 |
+ }, ontopath, thecall) |
|
| 235 | 258 |
} |
| 236 | 259 |
|
| ... | ... |
@@ -11,8 +11,11 @@ |
| 11 | 11 |
#' "CL:0000623", "CL:0000451", "CL:0000556") |
| 12 | 12 |
#' cl3k = gsub(":", "_", cl3k)
|
| 13 | 13 |
#' clont_path = owl2cache(url="http://purl.obolibrary.org/obo/cl.owl") |
| 14 |
-#' clont = setup_entities(clont_path) |
|
| 15 |
-#' plot(clont,cl3k) |
|
| 14 |
+#' o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 15 |
+#' if (!inherits(o2, "try-error")) {
|
|
| 16 |
+#' clont = setup_entities(clont_path) |
|
| 17 |
+#' plot(clont,cl3k) |
|
| 18 |
+#' } |
|
| 16 | 19 |
#' @export |
| 17 | 20 |
plot.owlents = function(x, y, ..., dropThing=TRUE) {
|
| 18 | 21 |
if (missing(y)) stop("must provide classes for plotting as 'y'")
|
| ... | ... |
@@ -17,8 +17,11 @@ retrieve ancestor 'sets' |
| 17 | 17 |
} |
| 18 | 18 |
\examples{
|
| 19 | 19 |
pa = get_ordo_owl_path() |
| 20 |
-orde = setup_entities(pa) |
|
| 21 |
-orde |
|
| 22 |
-ancestors(orde[1:5]) |
|
| 23 |
-labels(orde[1:5]) |
|
| 20 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 21 |
+if (!inherits(o2, "try-error")) {
|
|
| 22 |
+ orde = setup_entities(pa) |
|
| 23 |
+ orde |
|
| 24 |
+ ancestors(orde[1:5]) |
|
| 25 |
+ labels(orde[1:5]) |
|
| 26 |
+} |
|
| 24 | 27 |
} |
| ... | ... |
@@ -20,7 +20,10 @@ non-entities are removed and names are extracted |
| 20 | 20 |
} |
| 21 | 21 |
\examples{
|
| 22 | 22 |
pa = get_ordo_owl_path() |
| 23 |
-orde = setup_entities(pa) |
|
| 24 |
-al = ancestors(orde[1001:1002]) |
|
| 25 |
-ancestors_names(al) |
|
| 23 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 24 |
+if (!inherits(o2, "try-error")) {
|
|
| 25 |
+ orde = setup_entities(pa) |
|
| 26 |
+ al = ancestors(orde[1001:1002]) |
|
| 27 |
+ ancestors_names(al) |
|
| 28 |
+} |
|
| 26 | 29 |
} |
| ... | ... |
@@ -20,7 +20,10 @@ non-entities are removed and names are extracted |
| 20 | 20 |
} |
| 21 | 21 |
\examples{
|
| 22 | 22 |
pa = get_ordo_owl_path() |
| 23 |
-orde = setup_entities(pa) |
|
| 24 |
-al = subclasses(orde[100:120]) |
|
| 25 |
-children_names(al) |
|
| 23 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 24 |
+if (!inherits(o2, "try-error")) {
|
|
| 25 |
+ orde = setup_entities(pa) |
|
| 26 |
+ al = subclasses(orde[100:120]) |
|
| 27 |
+ children_names(al) |
|
| 28 |
+} |
|
| 26 | 29 |
} |
| ... | ... |
@@ -24,7 +24,10 @@ The previous functionality which failed is available, not exported, as labelsOLD |
| 24 | 24 |
} |
| 25 | 25 |
\examples{
|
| 26 | 26 |
clont_path = owl2cache(url="http://purl.obolibrary.org/obo/cl.owl") |
| 27 |
-clont = setup_entities(clont_path) |
|
| 28 |
-labels(clont[1:5]) |
|
| 29 |
-labels(clont[51:55]) |
|
| 27 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 28 |
+if (!inherits(o2, "try-error")) {
|
|
| 29 |
+ clont = setup_entities(clont_path) |
|
| 30 |
+ labels(clont[1:5]) |
|
| 31 |
+ labels(clont[51:55]) |
|
| 32 |
+} |
|
| 30 | 33 |
} |
| ... | ... |
@@ -17,8 +17,11 @@ retrieve is_a |
| 17 | 17 |
} |
| 18 | 18 |
\examples{
|
| 19 | 19 |
pa = get_ordo_owl_path() |
| 20 |
-orde = setup_entities(pa) |
|
| 21 |
-orde |
|
| 22 |
-parents(orde[1000:1001]) |
|
| 23 |
-labels(orde[1000:1001]) |
|
| 20 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 21 |
+if (!inherits(o2, "try-error")) {
|
|
| 22 |
+ orde = setup_entities(pa) |
|
| 23 |
+ orde |
|
| 24 |
+ parents(orde[1000:1001]) |
|
| 25 |
+ labels(orde[1000:1001]) |
|
| 26 |
+} |
|
| 24 | 27 |
} |
| ... | ... |
@@ -25,6 +25,9 @@ cl3k = c("CL:0000492", "CL:0001054", "CL:0000236",
|
| 25 | 25 |
"CL:0000623", "CL:0000451", "CL:0000556") |
| 26 | 26 |
cl3k = gsub(":", "_", cl3k)
|
| 27 | 27 |
clont_path = owl2cache(url="http://purl.obolibrary.org/obo/cl.owl") |
| 28 |
-clont = setup_entities(clont_path) |
|
| 29 |
-plot(clont,cl3k) |
|
| 28 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 29 |
+if (!inherits(o2, "try-error")) {
|
|
| 30 |
+ clont = setup_entities(clont_path) |
|
| 31 |
+ plot(clont,cl3k) |
|
| 32 |
+} |
|
| 30 | 33 |
} |
| ... | ... |
@@ -4,10 +4,10 @@ |
| 4 | 4 |
\alias{search_labels}
|
| 5 | 5 |
\title{use owlready2 ontology search facility on term labels}
|
| 6 | 6 |
\usage{
|
| 7 |
-search_labels(oents, regexp, case_sensitive = TRUE) |
|
| 7 |
+search_labels(ontopath, regexp, case_sensitive = TRUE) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{oents}{owlents instance}
|
|
| 10 |
+\item{ontopath}{character(1) path to owl file}
|
|
| 11 | 11 |
|
| 12 | 12 |
\item{regexp}{character(1) simple regular expression}
|
| 13 | 13 |
|
| ... | ... |
@@ -22,7 +22,7 @@ use owlready2 ontology search facility on term labels |
| 22 | 22 |
} |
| 23 | 23 |
\examples{
|
| 24 | 24 |
pa = get_ordo_owl_path() |
| 25 |
-orde = setup_entities(pa) |
|
| 26 |
-ol = search_labels(orde, "*Immunog*") |
|
| 27 |
-plot(orde, names(ol)) |
|
| 25 |
+ol = search_labels(pa, "*Immunog*") |
|
| 26 |
+orde = setup_entities2(pa) |
|
| 27 |
+onto_plot2(orde, names(ol)) |
|
| 28 | 28 |
} |
| ... | ... |
@@ -22,8 +22,11 @@ construct owlents instance from an owl file |
| 22 | 22 |
} |
| 23 | 23 |
\examples{
|
| 24 | 24 |
pa = get_ordo_owl_path() |
| 25 |
-orde = setup_entities(pa) |
|
| 26 |
-orde |
|
| 27 |
-ancestors(orde[1000:1001]) |
|
| 28 |
-labels(orde[1000:1001]) |
|
| 25 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 26 |
+if (!inherits(o2, "try-error")) {
|
|
| 27 |
+ orde = setup_entities(pa) |
|
| 28 |
+ orde |
|
| 29 |
+ ancestors(orde[1000:1001]) |
|
| 30 |
+ labels(orde[1000:1001]) |
|
| 31 |
+} |
|
| 29 | 32 |
} |
| ... | ... |
@@ -14,12 +14,15 @@ retrieve subclass entities |
| 14 | 14 |
} |
| 15 | 15 |
\examples{
|
| 16 | 16 |
pa = get_ordo_owl_path() |
| 17 |
-orde = setup_entities(pa) |
|
| 18 |
-orde |
|
| 19 |
-sc <- subclasses(orde[1:5]) |
|
| 20 |
-labels(orde[3]) |
|
| 21 |
-o3 = reticulate::iterate(sc[[3]]) |
|
| 22 |
-print(length(o3)) |
|
| 23 |
-o3[[2]] |
|
| 24 |
-labels(orde["Orphanet_100011"]) |
|
| 17 |
+o2 = try(reticulate::import("owlready2"), silent=TRUE)
|
|
| 18 |
+if (!inherits(o2, "try-error")) {
|
|
| 19 |
+ orde = setup_entities(pa) |
|
| 20 |
+ orde |
|
| 21 |
+ sc <- subclasses(orde[1:5]) |
|
| 22 |
+ labels(orde[3]) |
|
| 23 |
+ o3 = reticulate::iterate(sc[[3]]) |
|
| 24 |
+ print(length(o3)) |
|
| 25 |
+ o3[[2]] |
|
| 26 |
+ labels(orde["Orphanet_100011"]) |
|
| 27 |
+} |
|
| 25 | 28 |
} |
