Release/0.2.1

NEWS.md

@@ -1,3 +1,10 @@
+### CHANGES IN recogito VERSION 0.2.1
+
+- Allow multiple documents to be annotated with text in recogito to cleanly updated
+  - recogitoOutput gains the arguments refresh, annotationMode, tags, rtags
+  allowing text updates, annotationMode(RELATIONS,ANNOTATION), annotation tags, 
+  and relations tags to be updated through the reactive component.
+
 ### CHANGES IN recogito VERSION 0.2.0
 
 - read_annotorious now extracts from x$target$selector instead of x$target[[1]]$value

R/annotorious.R

@@ -235,7 +235,7 @@ renderOpenSeaDragonNoToolbar <- function(expr, env = parent.frame(), quoted = FA
 #' url <- paste("https://upload.wikimedia.org/",
 #'              "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
 #'              sep = "")
-#' url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
+#' url <- system.file(package = "recogito", "examples/annotorious", "Pamphlet_dutch_tulipomania_1637.jpg")
 #' x <- '[
 #' {
 #' "type":"Annotation",

R/recogito.R

@@ -48,16 +48,18 @@
 #'                 dependencies = tagsetcss)
 #' x
 recogito <- function(inputId = "annotations",
-                     text,
+                     text="",
                      type = c("relations", "tags"),
                      tags = c("Location", "Person", "Place", "Other"),
-                     mode = c("html", "pre"),
-                     annotations = "{}", width = NULL, height = NULL, elementId = NULL, dependencies = NULL) {
+                     rtags= c("isLinked"),
+                     refresh = FALSE,
+                     annotationMode="ANNOTATION",
+                     annotations="{}",
+                     mode = c("html", "pre"), width = NULL, height = NULL, elementId = NULL, dependencies = NULL) {
   type <- match.arg(type)
   mode <- match.arg(mode)
   x <- list(inputId = inputId, text = text, tags = tags, type = type,
-            #path = tempfile(pattern = "annotations_", fileext = ".json"),
-            mode = mode, annotations = annotations)
+            mode = mode, refresh = refresh, annotations = annotations, annotationMode = annotationMode)
   if(type == "relations"){
     htmlwidgets::createWidget(name = 'recogito', x,
                               width = width, height = height, package = 'recogito', elementId = elementId, dependencies = dependencies)
@@ -71,11 +73,9 @@ recogito <- function(inputId = "annotations",
 
 widget_html.recogito <- function(id, style, class, ...){
   el <- htmltools::tags$div(
-    id = sprintf("%s-outer-container", id), style = "position:relative;",
+    id = sprintf("%s-outer-container", id), style = "position:relative;", 
     htmltools::tags$div(
       id = sprintf("%s-content", id), class = "plaintext", style = "max-width:920px;font-family:'Lato', sans-serif;font-size:17px;line-height:27px;",
-      htmltools::tags$button(id = sprintf("%s-toggle", id), "MODE: ANNOTATION"),
-      #tags$button(id = "toggle-mode", "MODE: ANNOTATION"),
       htmltools::tags$hr(),
       htmltools::tags$div(id = id, class = class)
     )
@@ -170,8 +170,10 @@ widget_html.recogitotagsonly <- function(id, style, class, ...){
 #'
 #' recogitoOutput(outputId = "annotation_text")
 #' recogitotagsonlyOutput(outputId = "annotation_text")
-recogitoOutput <- function(outputId, width = '100%', height = '400px'){
+recogitoOutput <- function(outputId, width = '100%', height = '400px',mode="html",tags=c("PERSON","TIME"),rtags=c("isLinked"),annotationMode="ANNOTATION"){
+  htmltools::tags$div(id = paste0(outputId,"-data"), `init-data`=jsonlite::toJSON(list(mode=mode,tags=tags,rtags=rtags)),
   htmlwidgets::shinyWidgetOutput(outputId, name = 'recogito', width, height, package = 'recogito')
+  )
 }
 
 

README.md

@@ -145,6 +145,43 @@ Look to documentation of the functions
 help(package = "recogito")
 ```
 
+### Testing 
+Two example applications are provided for recogito
+
+-  inst/examples/recogito
+-  inst/examples/recogitotagsonly
+
+Before running the unit tests these two applications need to be running 
+on port 5447 and 5448 
+
+```
+library(shiny)
+library(devtools)
+devtools::load_all()
+appDir = system.file(package="recogito","examples/recogito")
+runApp(appDir,port=5447L)
+```
+
+In another R session 
+
+```
+library(shiny)
+library(devtools)
+devtools::load_all()
+appDir = system.file(package="recogito","examples/recogitotagsonly")
+runApp(appDir,port=5448L)
+```
+
+In a third R session with working directory in the recogito 
+package directory  you can run the selenium tests  
+
+```
+devtools::test()
+
+```
+
+See documentation from RSelenium for more details 
+
 
 ### DIGI
 

inst/examples/test-annotorious.R → inst/examples/annotorious/app.R

@@ -14,7 +14,6 @@ server <- function(input, output) {
     read_annotorious(input$annotations)
   })
 }
-shinyApp(ui, server)
 
 
 if(FALSE){
@@ -44,3 +43,5 @@ if(FALSE){
   image_crop(img, geometry_area(x = x$x, y = x$y, width = x$width, height = x$height))
   image_crop(img, geometry_area(x = x$x, y = x$y, width = x$width, height = x$height))
 }
+
+shinyApp(ui, server)

inst/examples/recogito/app.R

@@ -0,0 +1,128 @@
+txt       <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
+
+library(shiny)
+library(recogito)
+txt <- "Tell me, O muse, of that ingenious hero who travelled far and wide after he had sacked
+the famous town of Troy. Many cities did he visit, and many were the nations with whose manners and customs
+he was acquainted; moreover he suffered much by sea while trying to save his own life and bring his men safely
+home; but do what he might he could not save his men, for they perished through their own sheer folly in eating
+the cattle of the Sun-god Hyperion; so the god prevented them from ever reaching home. Tell me, too, about all
+these things, O daughter of Jove, from whatsoever source you may know them.\n
+So now all who escaped death in battle or by shipwreck had got safely home except Ulysses,
+and he, though he was longing to return to his wife and country, was detained by the goddess Calypso, who
+had got him into a large cave and wanted to marry him. But as years went by, there came a time when the gods
+settled that he should go back to Ithaca; even then, however, when he was among his own people, his troubles
+were not yet over; nevertheless all the gods had now begun to pity him except Neptune, who still persecuted
+him without ceasing and would not let him get home."
+
+## Example Annotation 
+annotation <- '[                          
+ {                                
+ "type":"Annotation",     
+ "body":[                 
+    {"type":"TextualBody","value":"sdfsd","purpose":"commenting"},
+    {"type":"TextualBody","value":"Person","purpose":"tagging"}],
+ "target":{"selector":[
+   {"type":"TextQuoteSelector","exact":"ngenious hero"},
+   {"type":"TextPositionSelector","start":42,"end":55}]},
+ "@context":"http://www.w3.org/ns/anno.jsonld",
+ "id":"#a4ea53d4-69f3-4392-a3dd-cbb7e9ad50cb"
+ },
+ {  
+ "type":"Annotation",
+ "body":[{"type":"TextualBody","value":"Person","purpose":"tagging"},
+   {"type":"TextualBody","value":"Location","purpose":"tagging"}],
+ "target":{"selector":[{"type":"TextQuoteSelector","exact":"far and"},
+   {"type":"TextPositionSelector","start":70,"end":77}]},
+ "@context":"http://www.w3.org/ns/anno.jsonld",
+ "id":"#d7050196-2537-42bf-9d1b-a3f9e4c9fbc6"
+ }      
+ ]' 
+
+
+## Function to generate new text for annotation 
+getText <- function(){
+  text = letters[floor(runif(2000)*25+1)]
+  text[sample(1:2000,500)]=" "
+  text=paste(text,collapse="")
+text
+}
+
+tagset    <- c("LOCATION", "TIME", "PERSON")
+rtagset    <- c("subject", "related", "isLinked")
+tagstyles <- "
+.tag-PERSON {
+color:red;
+}
+.tag-LOCATION {
+background-color:green;
+}
+.tag-TIME {
+font-weight: bold;
+}
+"
+
+ui <- fluidPage(tags$head(tags$style(HTML(tagstyles))),
+                actionButton("nexttext","Next"),
+                actionButton("loadannotation","Load Annotation"),
+                actionButton("annotationmode","MODE: ANNOTATION"),
+                tags$br(),
+                recogitoOutput(outputId = "annotation_text",
+                              mode="PRE",
+                              tags=tagset,
+                              rtags=rtagset,
+                              annotationMode='ANNOTATION'
+                              ),
+                tags$hr(),
+                tags$h3("Results"),
+                verbatimTextOutput(outputId = "annotation_result"))
+
+server <- function(input, output, session) {
+
+  mode <- reactiveValues(value = "ANNOTATION")
+
+  output$annotation_text <- renderRecogito({
+    recogito("annotations", text = txt, refresh=TRUE)
+  })
+
+  output$annotation_result <- renderPrint({
+    if(length(input$annotations) > 0){
+      x <- read_recogito(input$annotations)
+      x
+    }
+  })
+
+  ## Load annotations onto existing text 
+  observeEvent(input$loadannotation, {
+    output$annotation_text <- renderRecogito({
+      recogito("annotations", annotations = annotation,refresh=FALSE)
+    })
+  })
+
+  ## Load New Text into Interface
+  observeEvent(input$nexttext, {
+    newText = getText()
+    output$annotation_text <- renderRecogito({
+      recogito("annotations", annotations = "{}", text = newText,refresh=TRUE)
+    })
+  })
+
+  ## Change from annotation mode to relation mode  
+  observeEvent(input$annotationmode, {
+    if(mode$value=="ANNOTATION"){
+      output$annotation_text <- renderRecogito({
+        recogito("annotations", refresh=FALSE, annotationMode="RELATIONS")
+      })
+      updateActionButton(session,"annotationmode",label="MODE: RELATIONS")
+      mode$value <- "RELATIONS"
+    }else{
+      output$annotation_text <- renderRecogito({
+        recogito("annotations", refresh=FALSE,annotationMode="ANNOTATION")
+      })
+      updateActionButton(session,"annotationmode",label="MODE: ANNOTATION")
+      mode$value <- "ANNOTATION"
+    }
+  })
+
+}
+shinyApp(ui, server)

inst/examples/recogito/tests/shinytest.R

@@ -0,0 +1,3 @@
+library(shinytest)
+shinytest::testApp("../")
+

inst/examples/recogito/tests/shinytest/tagging-expected/001.json

@@ -0,0 +1,39 @@
+{
+  "input": {
+    "annotationmode": 0,
+    "loadannotation": 0,
+    "nexttext": 0
+  },
+  "output": {
+    "annotation_result": "",
+    "annotation_text": {
+      "x": {
+        "inputId": "annotations",
+        "text": "Tell me, O muse, of that ingenious hero who travelled far and wide after he had sacked\nthe famous town of Troy. Many cities did he visit, and many were the nations with whose manners and customs\nhe was acquainted; moreover he suffered much by sea while trying to save his own life and bring his men safely\nhome; but do what he might he could not save his men, for they perished through their own sheer folly in eating\nthe cattle of the Sun-god Hyperion; so the god prevented them from ever reaching home. Tell me, too, about all\nthese things, O daughter of Jove, from whatsoever source you may know them.\n\nSo now all who escaped death in battle or by shipwreck had got safely home except Ulysses,\nand he, though he was longing to return to his wife and country, was detained by the goddess Calypso, who\nhad got him into a large cave and wanted to marry him. But as years went by, there came a time when the gods\nsettled that he should go back to Ithaca; even then, however, when he was among his own people, his troubles\nwere not yet over; nevertheless all the gods had now begun to pity him except Neptune, who still persecuted\nhim without ceasing and would not let him get home.",
+        "tags": [
+          "Location",
+          "Person",
+          "Place",
+          "Other"
+        ],
+        "type": "relations",
+        "mode": "html",
+        "refresh": true,
+        "annotations": "{}",
+        "annotationMode": "ANNOTATION"
+      },
+      "evals": [
+
+      ],
+      "jsHooks": [
+
+      ],
+      "deps": [
+
+      ]
+    }
+  },
+  "export": {
+
+  }
+}

inst/examples/recogito/tests/shinytest/tagging.R

@@ -0,0 +1,4 @@
+app <- ShinyDriver$new("../../")
+app$snapshotInit("tagging")
+
+app$snapshot()

inst/examples/recogitotagsonly/tests/shinytest.R

@@ -0,0 +1,3 @@
+library(shinytest)
+shinytest::testApp("../")
+

inst/examples/recogitotagsonly/tests/shinytest/tagging-expected/001.json

@@ -0,0 +1,36 @@
+{
+  "input": {
+
+  },
+  "output": {
+    "annotation_result": "",
+    "annotation_text": {
+      "x": {
+        "inputId": "annotations",
+        "text": "Tell me, O muse, of that ingenious hero who travelled far and wide after he had sacked\nthe famous town of Troy. Many cities did he visit, and many were the nations with whose manners and customs\nhe was acquainted; moreover he suffered much by sea while trying to save his own life and bring his men safely\nhome; but do what he might he could not save his men, for they perished through their own sheer folly in eating\nthe cattle of the Sun-god Hyperion; so the god prevented them from ever reaching home. Tell me, too, about all\nthese things, O daughter of Jove, from whatsoever source you may know them.\n\nSo now all who escaped death in battle or by shipwreck had got safely home except Ulysses,\nand he, though he was longing to return to his wife and country, was detained by the goddess Calypso, who\nhad got him into a large cave and wanted to marry him. But as years went by, there came a time when the gods\nsettled that he should go back to Ithaca; even then, however, when he was among his own people, his troubles\nwere not yet over; nevertheless all the gods had now begun to pity him except Neptune, who still persecuted\nhim without ceasing and would not let him get home.",
+        "tags": [
+          "LOCATION",
+          "TIME",
+          "PERSON"
+        ],
+        "type": "relations",
+        "mode": "html",
+        "refresh": false,
+        "annotations": "{}",
+        "annotationMode": "ANNOTATION"
+      },
+      "evals": [
+
+      ],
+      "jsHooks": [
+
+      ],
+      "deps": [
+
+      ]
+    }
+  },
+  "export": {
+
+  }
+}

inst/examples/recogitotagsonly/tests/shinytest/tagging.R

@@ -0,0 +1,26 @@
+library("base")
+app <- ShinyDriver$new("../../")
+app$snapshotInit("tagging")
+
+app$executeScript(
+'
+move = $.Event(\'mousemove\');
+moveover = $.Event(\'mousemove\');
+down = $.Event(\'mousedown\');
+up = $.Event(\'mouseup\');
+
+// coordinates
+move.pageX = 100;
+move.pageY = 100; 
+moveover.pageX = 300;
+moveover.pageY = 100; 
+
+$(document).trigger(move);
+$(document).trigger(down);
+$(document).trigger(moveover);
+$(document).trigger(up);
+'
+)
+Sys.sleep(3)
+
+app$snapshot()