From 0b6c36595948dffc982528b6036b2b1fc8d11fd8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Santanch=C3=A8?= <santanche@gmail.com>
Date: Wed, 20 Dec 2023 20:22:52 -0300
Subject: [PATCH 1/3] feat (report): new report offline

---
 .../public/editor/annotate/js/metrics.js      |  13 +-
 .../category/cases/play/index-offline.html    | 116 +++++++++++++
 .../cases/play/schemas/heart-robot-blocks.csv |   1 +
 ...rt-robot.csv => heart-robot-kolb-test.csv} |   0
 .../cases/play/schemas/heart-robot-test.csv   |   1 +
 .../public/report/js/report-offline.js        | 163 ++++++++++++++++++
 6 files changed, 285 insertions(+), 9 deletions(-)
 create mode 100644 src/adonisjs/public/report/category/cases/play/index-offline.html
 create mode 100644 src/adonisjs/public/report/category/cases/play/schemas/heart-robot-blocks.csv
 rename src/adonisjs/public/report/category/cases/play/schemas/{heart-robot.csv => heart-robot-kolb-test.csv} (100%)
 create mode 100644 src/adonisjs/public/report/category/cases/play/schemas/heart-robot-test.csv
 create mode 100644 src/adonisjs/public/report/js/report-offline.js
diff --git a/src/adonisjs/public/editor/annotate/js/metrics.js b/src/adonisjs/public/editor/annotate/js/metrics.js
index 6c7e69bd..9afb776e 100644
--- a/src/adonisjs/public/editor/annotate/js/metrics.js
+++ b/src/adonisjs/public/editor/annotate/js/metrics.js
@@ -4,7 +4,7 @@ class AnnotationMetrics {
     const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])
   
     // group by category (first element)
-    // group = [category, position, count]
+    // group = [category, position of the first group element, count]
     const grouped = []
     for (let cat = 1; cat <= 8; cat++) {
       let prev = -1
@@ -12,15 +12,17 @@ class AnnotationMetrics {
       let catG = null
       for (let i = 0; i < sortedL.length; i++) {
         if (sortedL[i][0] === cat) {
+          // if any element in the previous position is not in the same category
           if (prev == -1 || (sortedL[prev][0] !== cat &&
               (prevG == -1 || sortedL[prev][1] > sortedL[prevG][1]))) {
-            catG = [cat, sortedL[i][1], 1]
+            catG = [cat, sortedL[i][1], 1]  // new category grouping
             grouped.push(catG)
           } else {
             catG[2]++
           }
           prevG = i
         }
+        // last distinct position in the sequence
         if (i+1 == sortedL.length || sortedL[i+1][1] !== sortedL[i][1])
           prev = i
       }
@@ -42,13 +44,6 @@ class AnnotationMetrics {
             subs++
             sortedG[prev][2] += sortedG[i][2]
             sortedG.splice(i, 1)
-            // if (sortedG[prev][2] >= sortedG[i][2]) {
-            //   sortedG[prev][2] += sortedG[i][2]
-            //   sortedG.splice(i, 1)
-            // } else {
-            //   sortedG[i][2] += sortedG[prev][2]
-            //   sortedG.splice(prev, 1)
-            // }
           }
         }
       }
diff --git a/src/adonisjs/public/report/category/cases/play/index-offline.html b/src/adonisjs/public/report/category/cases/play/index-offline.html
new file mode 100644
index 00000000..3bf92892
--- /dev/null
+++ b/src/adonisjs/public/report/category/cases/play/index-offline.html
@@ -0,0 +1,116 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="utf-8">
+    <title>Report Play</title>
+
+    <meta content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no, shrink-to-fit=no" name="viewport">
+
+    <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png">
+    <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png">
+    <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png">
+    <link rel="shortcut icon" href="/icons/favicon.ico">
+    <link rel="manifest" href="/site.webmanifest">
+
+    <link rel="stylesheet" href="/lib/fontawesome-5-10-1/css/all.min.css">
+    <link rel="stylesheet" href="/lib/bootstrap-4.4.1/css/bootstrap.min.css">
+
+    <link rel="stylesheet" href="/dccs/css/dccs.css">
+    <link rel="stylesheet" href="/dccs/css/properties.css">
+    <link rel="stylesheet" href="/infra/css/common-player.css">
+    <link rel="stylesheet" href="/infra/css/common-author.css">
+
+    <script src="/lib/axios-0.21.0/axios.min.js"></script>
+
+    <script src="/lib/jquery-3-4-1/jquery-3.4.1.slim.min.js"></script>
+    <script src="/lib/popper-1-15-0/popper.min.js"></script>
+    <script src="/lib/bootstrap-4.4.1/js/bootstrap.min.js"></script>
+
+    <script src="/config/config.js"></script>
+    <script src="/dccs/infra/bus.js"></script>
+
+    <script src="/dccs/base/primitive-dcc.js"></script>
+    <script src="/dccs/base/scope-dcc.js"></script>
+    <script src="/dccs/base/dcc.js"></script>
+    <script src="/dccs/base/dcc-base.js "></script>
+    <script src="/dccs/base/dcc-visual.js "></script>
+
+    <script src="/infra/basic.js"></script>
+    <script src="/infra/dcc-common-server-proxy.js"></script>
+    <script src="/infra/dcc-common-server-address.js"></script>
+    <script src="/infra/conditional-layout.js"></script>
+
+    <script src="/dccs/base/dcc-block.js"></script>
+    <script src="/dccs/components/visual/dcc-button.js"></script>
+    <script src="/dccs/components/visual/dcc-notice-input.js"></script>
+
+    <script src="/dccs/components/web/dcc-rest.js"></script>
+    <script src="/dccs/components/web/dcc-include.js"></script>
+    <script src="/dccs/components/web/dcc-dhtml.js"></script>
+
+    <script src="/dccs/components/data/dcc-submit.js"></script>
+    <script src="/dccs/components/data/dcc-model.js"></script>
+    <script src="/dccs/components/data/dcc-record.js"></script>
+    <script src="/dccs/components/data/dcc-table-csv.js"></script>
+
+    <script src="/dccs/base/subscribe-dcc.js"></script>
+    <script src="/dccs/base/trigger-dcc.js"></script>
+    <script src="/dccs/base/property-dcc.js"></script>
+    <script src="/dccs/base/connect-dcc.js"></script>
+
+    <script src="/infra/dcc-rest-proxy.js"></script>
+    <script src="/infra/dcc-basic.js"></script>
+
+    <script src="/dccs/infra/bridge.js" type="module"></script>
+
+    <script src="/report/js/report-offline.js" type="module"></script>
+
+    <script>
+      Basic.service.rootPath = '../../../'
+    </script>
+  </head>
+
+  <body onload="reportManager.start()">
+    <oid-sphere assets="/player/case/images/heart/" stylesheet="/dccs/lib/oid/oiddefault.css" global></oid-sphere>
+
+    <div id="alert-feedback" class="alert alert-success ml-2 mt-5" role="alert" style="position:absolute; display:none;">
+    </div>
+
+    <main role="main">
+      <div class="home-author-padding align-items-center rounded row sticky-top" style="z-index:3;">
+         <div class="h-100 w-100 draft-content-padding scroll-y">
+            <div class="home-text" style="height: auto !important;">
+              <p>Report</p>
+            </div>
+
+            <hr>
+            <div class="mt-2">
+              Schema: list of fields to be retrieved
+              <dcc-table-csv separator="," view=""></dcc-table-csv>
+            </div>
+            <hr>
+
+            <p>Tracking file:</p>
+            <file-oid publish="loaded~json/loaded"></file-oid>
+
+            <br>
+
+            <div id="case-boxes" class="container-fluid draft-scroll-container">
+              <button-oid label="Add Report" publish="click~report/add"></button-oid>
+              <button-oid label="Download" publish="click~report/download"></button-oid>
+            </div>
+
+            <p>Status: <span id="report-status"></span></p>
+
+            <p>Id: <span id="report-id"></span></p>
+
+            <p>Track:</p>
+            <textarea id="report-track" lines="30" style="width:100%" readonly></textarea>
+
+            <p>State:</p>
+            <textarea id="report-state" lines="30" style="width:100%" readonly></textarea>
+         </div>
+      </div>
+    </main>
+  </body>
+</html>
diff --git a/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-blocks.csv b/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-blocks.csv
new file mode 100644
index 00000000..a9237265
--- /dev/null
+++ b/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-blocks.csv
@@ -0,0 +1 @@
+blocks
\ No newline at end of file
diff --git a/src/adonisjs/public/report/category/cases/play/schemas/heart-robot.csv b/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-kolb-test.csv
similarity index 100%
rename from src/adonisjs/public/report/category/cases/play/schemas/heart-robot.csv
rename to src/adonisjs/public/report/category/cases/play/schemas/heart-robot-kolb-test.csv
diff --git a/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-test.csv b/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-test.csv
new file mode 100644
index 00000000..956f6346
--- /dev/null
+++ b/src/adonisjs/public/report/category/cases/play/schemas/heart-robot-test.csv
@@ -0,0 +1 @@
+Teste1.ta1,Teste2.ta2,Teste3.ta3,Teste4.ta4,Teste5.ta5,PosTeste1.tp1,PosTeste2.tp2,PosTeste3.tp3,PosTeste4.tp4,PosTeste5.tp5
\ No newline at end of file
diff --git a/src/adonisjs/public/report/js/report-offline.js b/src/adonisjs/public/report/js/report-offline.js
new file mode 100644
index 00000000..5b875c6a
--- /dev/null
+++ b/src/adonisjs/public/report/js/report-offline.js
@@ -0,0 +1,163 @@
+import { Bus } from '/dccs/lib/oid/oid-full-dev.js'
+
+export class ReportManager {
+  start () {
+    MessageBus.i.subscribe('table/updated', this._updateCSV.bind(this))
+    Bus.i.subscribe('json/loaded', this._updateJSON.bind(this))
+    Bus.i.subscribe('report/add', this._addReport.bind(this))
+    Bus.i.subscribe('report/download', this._downloadReport.bind(this))
+
+    document.querySelector('#report-track').value = ''
+    document.querySelector('#report-state').value = ''
+  }
+
+  _updateCSV (topic, message) {
+    console.log('===== CSV received')
+    console.log(message.table.schema)
+    this._schema = message.table.schema
+    if (this._schema[0] == 'blocks')
+      this._table = '"user id","time","type","value"\n'
+    else {
+      this._table = '"user id","start","date"'
+      for (const s of this._schema)
+        this._table += ',"' + s + '","time","miliseconds"'
+      this._table += '\n'
+    }
+    document.querySelector('#report-status').innerHTML = 'Schema loaded'
+  }
+
+  _updateJSON(topic, message) {
+    console.log('===== JSON received')
+
+    this._id = '[empty]'
+    this._track = {}
+    this._state = {}
+    if (message.value != null) {
+      const idRest = message.value.split('[[TRACK]]')
+      this._id = idRest[0].trim()
+      if (idRest.length > 1) {
+        const trackState = idRest[1].split('[[STATE]]')
+        this._track = JSON.parse(trackState[0].trim())
+        if (trackState.length > 1)
+          this._state = JSON.parse(trackState[1].trim())
+      }
+    }
+
+    document.querySelector('#report-status').innerHTML = 'Tracking loaded'
+
+    document.querySelector('#report-id').innerHTML = this._id
+    document.querySelector('#report-track').value = JSON.stringify(this._track, null, 2)
+    document.querySelector('#report-state').value = JSON.stringify(this._state, null, 2)
+  }
+
+  _addReport () {
+    if (this._schema != null && this._table != null && this._track != null) {
+      if (this._schema[0] == 'blocks')
+        this._addBlocks()
+      else
+        this._addVariables()
+    }
+
+    document.querySelector('#report-status').innerHTML = 'Report added'
+
+    document.querySelector('#report-id').innerHTML = ''
+    document.querySelector('#report-track').value = ''
+    document.querySelector('#report-state').value = ''
+  }
+
+  _addBlocks () {
+    const zeroPad = (num) => String(num).padStart(2, '0')
+
+    let table = this._table
+    const track = this._prepareTrack(this._track.knotTrack, this._track.varTrack)
+    let lastTime = new Date(track.timeStart)
+    const head = '"' + this._id + '","'
+
+    for (const v of this._track.varTrack) {
+      if (v.blocks || v.talk) {
+        table += head + v.changed + '","'
+        if (v.blocks) {
+          if (v.blocks.value[0] != '{' && v.blocks.value[0] != '[')
+            table += 'a","' + v.blocks.value + '"\n'
+          else {
+            const vblock = v.blocks.value.split('\n')
+
+            let fblock = ''
+            for (const b of vblock)
+              fblock += JSON.stringify(JSON.parse(b), null, 2) + '\n'
+
+            table += 'b","' + fblock.replace(/"/g, '""') + '"\n'
+          }
+        } else if (v.talk) {
+          table += 't","' + v.talk.value.replace(/"/g, '""').replace(/<br>/g, '\n') + '"\n'
+        }
+      }
+    }
+
+    this._table = table
+  }
+
+  _addVariables () {
+    const zeroPad = (num) => String(num).padStart(2, '0')
+
+    let table = this._table
+    const track = this._prepareTrack(this._track.knotTrack, this._track.varTrack)
+    let lastTime = new Date(track.timeStart)
+    table += '"' + this._id + '","' +
+            track.timeStart + '","' +
+            zeroPad(lastTime.getDate()) + '/' +
+            zeroPad(lastTime.getMonth() + 1) + '/' +
+            zeroPad(lastTime.getFullYear()) + '"'
+    for (const s of this._schema) {
+      let time = -1
+      if (track[s] != null) {
+        const t = new Date(track[s])
+        time = new Date(t - lastTime)
+        lastTime = t
+      }
+
+      const variables = this._track.variables
+      console.log('=== variable ' + s)
+      console.log(variables[s])
+      table += ',"'  + 
+                (variables[s] == null
+                ? ''
+                : (typeof variables[s] === 'string' || variables[s] instanceof String)
+                  ? variables[s].replace(/"/g, '""')
+                  : variables[s]
+                ) +
+                '","' + (time == -1 ? ''
+                  : zeroPad(time.getMinutes()) + ':' +
+                    zeroPad(time.getSeconds())) + '","' +
+                ((time == -1) ? '' : time.getTime()) + '"'
+    }
+    this._table = table + '\n'
+  }
+
+  _prepareTrack (knotTrack, varTrack) {
+    const track = {timeStart: knotTrack[0].timeStart}
+    for (const v of varTrack) {
+      const changed = v.changed
+      for (const t in v)
+        if (t != 'changed' && !track[v[t]])
+          track[t] = changed
+    }
+    return track
+  }
+
+  _downloadReport () {
+    if (this._table != null) {
+      const element = document.createElement('a')
+      element.setAttribute('href',
+        'data:text/plain;charset=utf-8,' + encodeURIComponent(this._table))
+      element.setAttribute('download', 'log.csv')
+      element.style.display = 'none'
+      document.body.appendChild(element)
+      element.click()
+      document.body.removeChild(element)
+    }
+  }
+}
+
+ReportManager.i = new ReportManager()
+window.reportManager = ReportManager.i

From 64841f267643b3d0097409cd6a6579f1452601f5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Santanch=C3=A8?= <santanche@gmail.com>
Date: Wed, 20 Dec 2023 20:55:18 -0300
Subject: [PATCH 2/3] refactor (metrics): metrics file centralized

---
 .../public/editor/annotate/js/metrics.js      |  34 +++-
 .../public/editor/annotate/metrics/index.html |   5 +-
 .../public/editor/annotate/metrics/metrics.js | 187 ------------------
 .../editor/annotate/metrics/test-metrics.js   |  34 ++++
 4 files changed, 70 insertions(+), 190 deletions(-)
 delete mode 100644 src/adonisjs/public/editor/annotate/metrics/metrics.js
 create mode 100644 src/adonisjs/public/editor/annotate/metrics/test-metrics.js

diff --git a/src/adonisjs/public/editor/annotate/js/metrics.js b/src/adonisjs/public/editor/annotate/js/metrics.js
index 9afb776e..a8b430bd 100644
--- a/src/adonisjs/public/editor/annotate/js/metrics.js
+++ b/src/adonisjs/public/editor/annotate/js/metrics.js
@@ -1,5 +1,5 @@
 class AnnotationMetrics {
-  _selfOrderCount(categoriesOrder) {
+  _selfOrderCount(categoriesOrder, present) {
     // sort by text position (second element)
     const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])
   
@@ -48,6 +48,18 @@ class AnnotationMetrics {
         }
       }
     }
+
+    if (present != null) {
+      present('\n\n=== Self Order Count ===')
+      present('--- sorted by position')
+      present(sortedL)
+      present('--- grouped by category')
+      present(JSON.parse(JSON.stringify(grouped)))
+      present('--- group sorted by position')
+      present(JSON.parse(JSON.stringify(sortedG)))
+      present('--- final group after ordering')
+      present(sortedG)
+    }
   
     return {
       groups: groupsText,
@@ -60,7 +72,7 @@ class AnnotationMetrics {
   * Category clustering calculator for free recall
   * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665324/
   */
-  _clusteringFreeRecall (categoriesOrder) {
+  _clusteringFreeRecall (categoriesOrder, present) {
     const n = categoriesOrder.length  // number of recalled items
 
     // sort by text position (second element)
@@ -105,6 +117,24 @@ class AnnotationMetrics {
 
     const arc = (r - er) / (max - er)  // adjusted ratio of clustering
 
+    if (present != null) {
+      present('\n\n=== Clustering Free Recall ===')
+      present(JSON.stringify(categoriesOrder))
+      present('--- n = ' + n)
+      present('--- sorted by position')
+      present(JSON.stringify(sortedL))
+      present('--- c = ' + c)
+      present('--- ni')
+      present(nc)
+      present('--- r = ' + r)
+      present('--- max = ' + max)
+      present('--- E(r) = ' + Math.round(er * 100) / 100)
+      present('--- RR = ' + Math.round(rr * 100) / 100)
+      present('--- MRR = ' + Math.round(mrr * 100) / 100)
+      present('--- DS = ' + Math.round(ds * 100) / 100)
+      present('--- ARC = ' + Math.round(arc * 100) / 100)
+    }
+
     return arc
   }
 }
diff --git a/src/adonisjs/public/editor/annotate/metrics/index.html b/src/adonisjs/public/editor/annotate/metrics/index.html
index dfc93750..e46a4720 100644
--- a/src/adonisjs/public/editor/annotate/metrics/index.html
+++ b/src/adonisjs/public/editor/annotate/metrics/index.html
@@ -1,8 +1,11 @@
 <!DOCTYPE html>
 <html>
+  <head>
+    <script src="../js/metrics.js"></script>
+  </head>
   <body>
     <textarea id="console" rows="50" style="width:100%" readonly></textarea>
-    <script type="text/javascript" src="metrics.js">
+    <script type="text/javascript" src="test-metrics.js">
     </script>
   </body>
 </html>
diff --git a/src/adonisjs/public/editor/annotate/metrics/metrics.js b/src/adonisjs/public/editor/annotate/metrics/metrics.js
deleted file mode 100644
index 71f1e5b7..00000000
--- a/src/adonisjs/public/editor/annotate/metrics/metrics.js
+++ /dev/null
@@ -1,187 +0,0 @@
-function sortSubstitutionCount(numbersList) {
-  const sortedL = numbersList.slice().sort((a, b) => a - b)
-  present(numbersList)
-  present(sortedL)
-  let subs = 0
-  for (let i = 0; i < numbersList.length; i++) {
-    if (numbersList[i] !== sortedL[i]) {
-      subs++
-    }
-  }
-  return Math.ceil(subs/2)
-}
-
-// present(sortSubstitutionCount([1, 1, 1, 2, 3, 3, 4]))
-// present(sortSubstitutionCount([1, 1, 1, 3, 2, 3, 4]))
-// present(sortSubstitutionCount([1, 1, 1, 3, 3, 2, 4]))
-// present(sortSubstitutionCount([1, 1, 1, 4, 3, 2, 3]))
-// present(sortSubstitutionCount([1, 4, 1, 3, 3, 2, 1]))
-// present(sortSubstitutionCount([4, 3, 3, 2, 1, 1, 1]))
-
-function selfOrderCount(categoriesOrder) {
-  // sort by text position (second element)
-  const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])
-  present('Sorted by position')
-  present(sortedL)
-
-  // group by category (first element)
-  // group = [category, position, count]
-  const grouped = []
-  for (let cat = 1; cat <= 8; cat++) {
-    let prev = -1
-    let prevG = -1
-    let catG = null
-    for (let i = 0; i < sortedL.length; i++) {
-      if (sortedL[i][0] === cat) {
-        if (prev == -1 || (sortedL[prev][0] !== cat &&
-            (prevG == -1 || sortedL[prev][1] > sortedL[prevG][1]))) {
-          catG = [cat, sortedL[i][1], 1]
-          grouped.push(catG)
-        } else {
-          catG[2]++
-        }
-        prevG = i
-      }
-      if (i+1 == sortedL.length || sortedL[i+1][1] !== sortedL[i][1])
-        prev = i
-    }
-  }
-  present('Grouped by category')
-  present(JSON.parse(JSON.stringify(grouped)))
-
-  // sort groups by position (second element)
-  const sortedG = grouped.sort((a, b) => a[1] - b[1])
-  present('Group sorted by position')
-  present(JSON.parse(JSON.stringify(sortedG)))
-
-  // count order change to group together categories
-  let subs = 0
-  for (let cat = 1; cat <= 8; cat++) {
-    let prev = -1
-    for (let i = 0; i < sortedG.length; i++) {
-      if (sortedG[i][0] === cat) {
-        if (prev === -1)
-          prev = i
-        else {
-          subs++
-          if (sortedG[prev][2] >= sortedG[i][2]) {
-            sortedG[prev][2] += sortedG[i][2]
-            sortedG.splice(i, 1)
-          } else {
-            sortedG[i][2] += sortedG[prev][2]
-            sortedG.splice(prev, 1)
-          }
-        }
-      }
-    }
-  }
-  present('Final group after ordering')
-  present(sortedG)
-
-  return subs
-}
-
-// present(selfOrderCount(
-//   [[1, 10], [2, 20], [1, 20], [2, 30]]))
-// present(selfOrderCount(
-//   [[1, 10], [2, 20], [1, 25], [2, 30]]))
-// present(selfOrderCount(
-//   [[1, 10], [2, 20], [1, 20], [3, 20], [1, 30], [2, 30], [3, 30]]))
-// present(selfOrderCount(
-//   [[2, 71], [2, 96], [3, 98], [2, 100], [5, 120], [5, 130], [5, 135], [3, 140], [5, 180]]))
-// present(selfOrderCount(
-//   [[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]]))
-// present(selfOrderCount(
-//   [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]]))
-
-/*
- * Category clustering calculator for free recall
- * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665324/
- * tested here and traferred to /editor/annotate/js/metrics.js
-*/
-function clusteringFreeRecall(categoriesOrder, console) {
-
-  const n = categoriesOrder.length  // number of recalled items
-
-  // sort by text position (second element)
-  const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])
-
-  const nc = {}  // number of recalled items in each recalled category
-  let r = 0  // number of category repetition
-  for (let i = 0; i < sortedL.length; i++) {
-    const cat = sortedL[i][0]
-    if (!nc[cat])
-      nc[cat] = 1
-    else
-      nc[cat]++
-    let nextPos = i + 1
-    while (nextPos < sortedL.length && sortedL[nextPos][1] === sortedL[i][1])
-      nextPos++
-    if (nextPos < sortedL.length) {
-      let sp = nextPos
-      while (sp < sortedL.length && sortedL[sp][1] === sortedL[nextPos][1]) {
-        if (cat == sortedL[sp][0]) {
-          r++
-          break
-        }
-        sp++
-      }
-    }
-  }
-
-  const c = Object.keys(nc).length  // number of recalled categories
-  const max = n - c  // maximum possible number of category repetitions
-
-  let er = 0  // expected number of category repetitions
-  for (const cat in nc)
-    er += nc[cat] * nc[cat]
-  er = er / n - 1
-
-  const rr = r / (n - 1)  // ratio of repetition
-
-  const mrr = r / max  // modified ratio of repetition
-
-  const ds = r - er  // deviation score
-
-  const arc = (r - er) / (max - er)  // adjusted ratio of clustering
-
-  if (console) {
-    present('\n\n=== Clustering Free Recall ===')
-    present(JSON.stringify(categoriesOrder))
-    present('--- n = ' + n)
-    present('--- sorted by position')
-    present(JSON.stringify(sortedL))
-    present('--- c = ' + c)
-    present('--- ni')
-    present(nc)
-    present('--- r = ' + r)
-    present('--- max = ' + max)
-    present('--- E(r) = ' + Math.round(er * 100) / 100)
-    present('--- RR = ' + Math.round(rr * 100) / 100)
-    present('--- MRR = ' + Math.round(mrr * 100) / 100)
-    present('--- DS = ' + Math.round(ds * 100) / 100)
-    present('--- ARC = ' + Math.round(arc * 100) / 100)
-  }
-
-  return arc
-}
-
-function present (output) {
-  document.querySelector('#console').value += output + '\n'
-}
-
-present(clusteringFreeRecall(
-  [[2, 1], [4, 2], [4, 3], [3, 4], [2, 5], [3, 6], [1, 7], [4, 8], [4, 9]], true
-))
-present(clusteringFreeRecall(
-  [[3, 1], [4, 2], [4, 3], [3, 4], [1, 5], [1, 6], [3, 7], [1, 8], [1, 9], [2, 10], [2, 11], [2, 12], [4, 13], [4, 14], [3, 15]], true
-))
-present(clusteringFreeRecall(
-  [[2, 1], [2, 2], [3, 3], [1, 4], [1, 5], [1, 6], [1, 7], [2, 8], [3, 9], [3, 10], [2, 11], [1, 12], [4, 13], [4, 14], [4, 15], [4, 16], [2, 17], [2, 18], [3, 19], [1, 20]], true
-))
-present(clusteringFreeRecall(
-  [[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]], true))
-present(clusteringFreeRecall(
-  [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]], true))
-present(clusteringFreeRecall(
-  [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [7,98], [5, 130], [5, 135], [3, 140], [5, 180]], true))
\ No newline at end of file
diff --git a/src/adonisjs/public/editor/annotate/metrics/test-metrics.js b/src/adonisjs/public/editor/annotate/metrics/test-metrics.js
new file mode 100644
index 00000000..4d745ff4
--- /dev/null
+++ b/src/adonisjs/public/editor/annotate/metrics/test-metrics.js
@@ -0,0 +1,34 @@
+document.querySelector('#console').value = ''
+
+function present (output) {
+  document.querySelector('#console').value += output + '\n'
+}
+
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[1, 10], [2, 20], [1, 20], [2, 30]], present)))
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[1, 10], [2, 20], [1, 25], [2, 30]], present)))
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[1, 10], [2, 20], [1, 20], [3, 20], [1, 30], [2, 30], [3, 30]], present)))
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[2, 71], [2, 96], [3, 98], [2, 100], [5, 120], [5, 130], [5, 135], [3, 140], [5, 180]], present)))
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]], present)))
+present(JSON.stringify(AnnotationMetrics.i._selfOrderCount(
+  [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]], present)))
+
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[2, 1], [4, 2], [4, 3], [3, 4], [2, 5], [3, 6], [1, 7], [4, 8], [4, 9]], present
+))
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[3, 1], [4, 2], [4, 3], [3, 4], [1, 5], [1, 6], [3, 7], [1, 8], [1, 9], [2, 10], [2, 11], [2, 12], [4, 13], [4, 14], [3, 15]], present
+))
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[2, 1], [2, 2], [3, 3], [1, 4], [1, 5], [1, 6], [1, 7], [2, 8], [3, 9], [3, 10], [2, 11], [1, 12], [4, 13], [4, 14], [4, 15], [4, 16], [2, 17], [2, 18], [3, 19], [1, 20]], present
+))
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]], present))
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]], present))
+present(AnnotationMetrics.i._clusteringFreeRecall(
+  [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [7,98], [5, 130], [5, 135], [3, 140], [5, 180]], present))
\ No newline at end of file

From cd6641a261f83e20761ba352f61b12452029e25b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Santanch=C3=A8?= <santanche@gmail.com>
Date: Thu, 21 Dec 2023 21:20:24 -0300
Subject: [PATCH 3/3] feat (annotator): BILOU export

---
 .../public/report/annotations/index.html      |  10 +-
 .../public/report/js/report-annotations.js    | 183 ++++++++++++++++--
 2 files changed, 180 insertions(+), 13 deletions(-)

diff --git a/src/adonisjs/public/report/annotations/index.html b/src/adonisjs/public/report/annotations/index.html
index 868ac0e2..704f583e 100644
--- a/src/adonisjs/public/report/annotations/index.html
+++ b/src/adonisjs/public/report/annotations/index.html
@@ -23,6 +23,7 @@
     <link rel="stylesheet" href="/editor/css/editor.css">
 
     <script src="/lib/axios-0.21.0/axios.min.js"></script>
+    <script src="/lib/showdown/showdown.min.js"></script>
 
     <script src="/lib/jquery-3-4-1/jquery-3.4.1.slim.min.js"></script>
     <script src="/lib/popper-1-15-0/popper.min.js"></script>
@@ -61,7 +62,9 @@
     <script src="/dccs/base/property-dcc.js"></script>
     <script src="/dccs/base/connect-dcc.js"></script>
 
-
+    <script src="/translator/translator.js"></script>
+    <script src="/translator/item-templates.js"></script>
+ 
     <script src="/infra/dcc-rest-proxy.js"></script>
     <script src="/infra/dcc-basic.js"></script>
 
@@ -98,7 +101,10 @@
               <dcc-rest id="harena-room-cases" bind="harena-room-cases" subscribe="room/cases/get"></dcc-rest>
               <dcc-rest id="harena-room-case-annotations" bind="harena-room-case-annotations"
                         subscribe="case/annotations/get"></dcc-rest>
-              <dcc-button label="Export" xstyle="in" topic="report/download"></dcc-button>
+              <dcc-rest id="harena-room-load-case" bind="harena-room-load-case"
+                        subscribe="case/source/get"></dcc-rest>
+              <dcc-button label="Export Analysis" xstyle="in" topic="report/download"></dcc-button>
+              <dcc-button label="Export BILOU" xstyle="in" topic="report/bilou"></dcc-button>
             </div>
 
          </div>
diff --git a/src/adonisjs/public/report/js/report-annotations.js b/src/adonisjs/public/report/js/report-annotations.js
index f798548d..459e48cd 100644
--- a/src/adonisjs/public/report/js/report-annotations.js
+++ b/src/adonisjs/public/report/js/report-annotations.js
@@ -1,7 +1,7 @@
 class ReportManager {
   start () {
-    this._download = this._download.bind(this)
-    MessageBus.i.subscribe('report/download', this._download)
+    MessageBus.i.subscribe('report/download', this._downloadAnalysis.bind(this))
+    MessageBus.i.subscribe('report/bilou', this._downloadBILOU.bind(this))
     this._roomId = new URL(document.location).searchParams.get('roomid')
   }
 
@@ -78,6 +78,141 @@ class ReportManager {
     return result
   }
 
+  async _buildBILOU (caseId, annotations) {
+    const tt = await this._tokenize(caseId)
+    const tokens = tt.tokens
+
+    const ranges = []
+    for (const an of annotations) {
+      // find a proper category
+      let cat = null
+      for (const c of an.categories)
+        if (ReportManager.catList.includes(c)) {
+          cat = c
+          break
+        }
+
+      if (cat != null) {
+        if (!this._rangeConflict(ranges, an.fragments)) {
+          this._addRanges(ranges, an.fragments)
+          for (let f = 0; f < an.fragments.length; f++) {
+            let firstMatch = true
+            let firstToken = null
+            let prevLast = null
+            for (const tk of tokens) {
+              if (tk[1] >= an.fragments[f].start &&
+                  tk[1] <= an.fragments[f].start + an.fragments[f].size - 1) {
+                tk[3] =
+                  (an.fragments.length == 1 && firstMatch)
+                    ? 'U'
+                    : ((f == 0 && firstMatch)
+                      ? 'B'
+                      : ((f+1 < an.fragments.length) || (tk[2] < an.fragments[f].last))
+                        ? 'I'
+                        : 'L')
+                tk[4] = cat
+                if (firstMatch)
+                  firstToken = tk
+                else if (firstToken != -1) {
+                  firstToken[3] = 'B'
+                  firstToken = -1
+                }
+                firstMatch = false
+                if (prevLast != null) {
+                  prevLast[3] = 'I'
+                  prevLast = null
+                }
+                if (tk[3] == 'L')
+                  prevLast = tk
+              }
+            }
+          }
+        }
+      }
+    }
+
+    console.log('=== tokens NER')
+    console.log(tokens)
+
+    return {
+      doc_id: caseId,
+      text: tt.text,
+      labels: tokens
+    }
+  }
+
+  async _tokenize (caseId) {
+    
+    const tokens = []
+
+    let result = {}
+
+    const cs = await MessageBus.i.request('case/source/get',
+                                          {room_id: this._roomId, case_id: caseId})
+
+    if (cs != null && cs.message != null) {
+      const compiled =
+      await Translator.instance.compileMarkdown(
+        cs.message.id, cs.message.source)
+
+      let text = ''
+      for (const knot in compiled.knots) {
+        const mkHTML =
+          await Translator.instance.generateHTML(compiled.knots[knot])
+        text += mkHTML
+      }
+  
+      text = text.replace(/<[^>]+>/gm,'')
+                 .replace(/<\/[^>]+>/gm, '')
+                 .replace(/^[\r\n][\r\n]?/, '')
+  
+      let c = 0
+      let tk = ''
+      let tks = -1
+      while (c <= text.length) {
+        if (c == text.length || ReportManager.separators.includes(text[c])) {
+          if (tks != -1) {
+            tokens.push([tk, tks, c-1, 'O', null])
+            tk = ''
+            tks = -1
+          }
+        } else {
+          if (tks == -1)
+            tks = c
+          tk += text[c]
+        }
+        c++
+      }
+
+      result = {
+        text: text,
+        tokens: tokens
+      }
+    }
+  
+    return result
+  }
+
+  _rangeConflict (ranges, fragments) {
+    const start = fragments[0].start
+    const final = fragments[fragments.length-1].start + fragments[fragments.length-1].size - 1
+    let r = 0
+    while (r < ranges.length && start < ranges[r][1]) {
+      if ((start >= ranges[r][0] && start <= ranges[r][1]) ||
+          (final >= ranges[r][0] && final <= ranges[r][1]) ||
+          (ranges[r][0] >= start && ranges[r][0] <= final) ||
+          (ranges[r][1] >= start && ranges[r][1] <= final))
+        return true
+      r++
+    }
+    return false
+  }
+
+  _addRanges (ranges, fragments) {
+    for (const f of fragments)
+      ranges.push([f.start, f.start + f.size - 1])
+  }
+
   _calculateMetrics (annotations) {
     let ctideas = 0, ctright = 0, ctinfright = 0
     let ctwrong = 0, ctrightencap = 0, ctinfrightencap = 0, ctwrongencap = 0
@@ -141,7 +276,26 @@ class ReportManager {
            `${(ctideas == 0) ? 0 : selfOrder.score / ctideas},${clustering}${countCat},"${o1csv}","${o2csv}"`
   }
 
-  async _download () {
+  async _downloadBILOU () {
+    const tprefix = document.querySelector('#tprefix').value
+
+    const cases = await this._requestCases()
+
+    console.log(cases)
+    let table = ''
+
+    if (cases != null) {
+      for (const c of cases.message) {
+        const ant = await this._loadAnnotations(c.id)
+        const bilou = await this._buildBILOU(c.id, ant.annotations)
+        table += JSON.stringify(bilou) + '\n'
+      }
+
+      this._download(table)
+    }
+  }
+
+  async _downloadAnalysis () {
     const tprefix = document.querySelector('#tprefix').value
 
     const cases = await this._requestCases()
@@ -172,21 +326,28 @@ class ReportManager {
                  metrics + '\n'
       }
 
-      const element = document.createElement('a')
-      element.setAttribute('href',
-        'data:text/plain;charset=utf-8,' + encodeURIComponent(table))
-      element.setAttribute('download', 'annotations.csv')
-      element.style.display = 'none'
-      document.body.appendChild(element)
-      element.click()
-      document.body.removeChild(element)
+      this._download(table)
     }
   }
+
+  _download (table) {
+    const element = document.createElement('a')
+    element.setAttribute('href',
+      'data:text/plain;charset=utf-8,' + encodeURIComponent(table))
+    element.setAttribute('download', 'annotations.csv')
+    element.style.display = 'none'
+    document.body.appendChild(element)
+    element.click()
+    document.body.removeChild(element)
+  }
 }
 
 (function () {
   ReportManager.i = new ReportManager()
 
+  ReportManager.separators = [
+    ' ', '\n', '\r', '\t', '.', ',', ';', ':', '(', ')', '[', ']', '{', '}']
+
   // <TODO> Copy of the same constants in annotator.js
   // isc: Illness Script Components
   ReportManager.category = {
