From 21074c6e93b7a415c813f6e88f9840d0aa01a542 Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:46:24 +0100
Subject: [PATCH 1/8] Update journalStructure.md

---
 docs/journalStructure.md | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index 12da8218..3a953a75 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -23,6 +23,8 @@ This document contains the structure of Journals having Impact Factor greater th
 * ProteomeXchange Consortium - PeptideAtlas: stores datasets focusing on peptide identifications and their associated spectral evidence
 * ImmPort (Immunology Database and Analysis Portal)
 * Zenodo
+* China National GeneBank DataBase (CNGBdb)
+* BioProject
 
 
 _________________________________________________________________
@@ -53,3 +55,25 @@ _________________________________________________________________
   * not provided
   * available from authors upon request
   * no new code, used existing code
+
+## Science Immunology: IF 17.6
+* unable to access without institute registration
+
+## Other Nature journals:
+* Nature Biotechnology: 68.2
+* Nature Medicine: 87.5
+* Nature Genetics: 31.7
+* Nature: 50.5
+* Nature Cell Biology: 17.3
+* Nature Neuroscience: 29.9
+* Nature Cancer: 38.7
+* Nature Methods: 36.1
+* Nature Metabolism: 25.5
+* Nature Protocols: 17.1
+* Nature Biomedical Engineering: 28.9
+
+## Other Cell journals:
+* Cancer Cell: 48.8
+* Immunity: 43.47
+
+

From 2fafe364973dceb9db1dc4fcaa04a7498a33f2bb Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:51:34 +0100
Subject: [PATCH 2/8] Update journalStructure.md

---
 docs/journalStructure.md | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index 3a953a75..7ae65dd1 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -56,9 +56,6 @@ _________________________________________________________________
   * available from authors upon request
   * no new code, used existing code
 
-## Science Immunology: IF 17.6
-* unable to access without institute registration
-
 ## Other Nature journals:
 * Nature Biotechnology: 68.2
 * Nature Medicine: 87.5
@@ -76,4 +73,4 @@ _________________________________________________________________
 * Cancer Cell: 48.8
 * Immunity: 43.47
 
-
+Note: Science journals cannot be accessed without Institution registration.

From c328eba200e61aeaf5c43aa3c39cea9a94e1234d Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:53:29 +0100
Subject: [PATCH 3/8] Update journalStructure.md

---
 docs/journalStructure.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index 7ae65dd1..bb0dc88b 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -73,4 +73,4 @@ _________________________________________________________________
 * Cancer Cell: 48.8
 * Immunity: 43.47
 
-Note: Science journals cannot be accessed without Institution registration.
+Note: Most of the Science journals cannot be accessed without Institution registration.

From c3a37ba40e7dc997d5ed420b7a1ccca2add34d75 Mon Sep 17 00:00:00 2001
From: TripZz <nico.greiner9@gmail.com>
Date: Thu, 31 Oct 2024 00:31:20 +0100
Subject: [PATCH 4/8] NN-595 Implement document export window

---
 frontend/package.json                         |   3 +
 frontend/src/App.vue                          |   3 +
 frontend/src/assets/toolbar/word.png          | Bin 0 -> 10686 bytes
 frontend/src/components/DocumentWindow.vue    | 394 ++++++++++++++++++
 frontend/src/components/PersistentWindow.vue  |  33 +-
 .../components/toolbar/CitationToolBar.vue    |   6 +
 .../src/components/toolbar/MainToolBar.vue    |   8 +-
 .../src/components/toolbar/TermToolBar.vue    |   6 +
 .../components/visualization/CitationVis.vue  |  18 +
 .../src/components/visualization/MainVis.vue  |  21 +-
 .../src/components/visualization/TermVis.vue  |  16 +
 frontend/src/store/index.js                   |   5 +
 package-lock.json                             |  69 +++
 package.json                                  |   5 +
 14 files changed, 583 insertions(+), 4 deletions(-)
 create mode 100644 frontend/src/assets/toolbar/word.png
 create mode 100644 frontend/src/components/DocumentWindow.vue
 create mode 100644 package-lock.json
 create mode 100644 package.json

diff --git a/frontend/package.json b/frontend/package.json
index 6c62e747..d120f190 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -15,9 +15,12 @@
     "axios": "^1.7.4",
     "d3": "^7.9.0",
     "d3-scale": "^4.0.2",
+    "file-saver": "^2.0.5",
     "mitt": "^3.0.1",
     "ml-hclust": "^3.1.0",
     "nouislider": "^15.8.1",
+    "quill": "^2.0.2",
+    "quill-to-word": "^1.3.0",
     "random-color-rgb": "^1.1.1",
     "smallest-enclosing-circle": "^1.0.2",
     "validator": "^13.12.0",
diff --git a/frontend/src/App.vue b/frontend/src/App.vue
index b4f54788..3df487ba 100644
--- a/frontend/src/App.vue
+++ b/frontend/src/App.vue
@@ -1,6 +1,7 @@
 <template>
   <div class="container" id="container">
     <PersistentWindow />
+    <DocumentWindow />
     <router-view v-slot="{ Component }">
       <keep-alive exclude="HomeView">
         <component :is="Component" />
@@ -15,6 +16,7 @@ import CitationView from "@/views/CitationView.vue";
 import ProteinView from "@/views/ProteinView.vue";
 import HomeView from "@/views/HomeView.vue";
 import PersistentWindow from "@/components/PersistentWindow.vue";
+import DocumentWindow from "@/components/DocumentWindow.vue";
 
 export default {
   name: "App",
@@ -24,6 +26,7 @@ export default {
     HomeView,
     CitationView,
     PersistentWindow,
+    DocumentWindow,
   },
 };
 </script>
diff --git a/frontend/src/assets/toolbar/word.png b/frontend/src/assets/toolbar/word.png
new file mode 100644
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diff --git a/frontend/src/components/DocumentWindow.vue b/frontend/src/components/DocumentWindow.vue
new file mode 100644
index 00000000..2b934dbb
--- /dev/null
+++ b/frontend/src/components/DocumentWindow.vue
@@ -0,0 +1,394 @@
+<template>
+  <div
+    id="expdocument"
+    class="persistent-window"
+    v-show="showPersistentComponent"
+  >
+    <div id="expdocument_header" class="header">
+      <h3>AxoWord</h3>
+      <span class="close-btn" @click="closeWindow">×</span>
+    </div>
+    <div class="content-wrapper">
+      <!-- Bullet Section -->
+      <div class="bullet-section">
+        <br />
+        <h4>Protein history</h4>
+        <ul>
+          <li
+            v-for="(bullet, index) in proteins"
+            :key="index"
+            @click="addBullet(bullet.label)"
+          >
+            {{ bullet.label }}
+          </li>
+        </ul>
+        <br /><br />
+        <h4>Abstract history</h4>
+        <ul>
+          <li
+            v-for="(bullet, index) in abstracts"
+            :key="index"
+            @click="addBullet(bullet.label)"
+          >
+            {{ bullet.label }}
+          </li>
+        </ul>
+        <br /><br />
+        <h4>Favourite terms</h4>
+        <ul>
+          <li
+            v-for="(bullet, index) in pathways"
+            :key="index"
+            @click="addBullet(bullet.name)"
+          >
+            {{ bullet.name }}
+          </li>
+        </ul>
+        <br /><br />
+        <h4>Current graphs</h4>
+        <ul>
+          <li @click="addScreen('black', 'png')">add current graph</li>
+        </ul>
+        <br /><br />
+        <h4>Chatbot tag history</h4>
+        <ul>
+          <li
+            v-for="(bullet, index) in tags"
+            :key="index"
+            @click="addBullet(bullet)"
+          >
+            {{ bullet.id }}
+          </li>
+        </ul>
+      </div>
+      <!-- Quill Editor Section -->
+      <div class="editor-section">
+        <div ref="editor"></div>
+        <!-- Editor container -->
+      </div>
+    </div>
+    <div class="export-bar">
+      <button @click="exportdocX">Export Document</button>
+    </div>
+  </div>
+</template>
+
+<script>
+import Quill from "quill";
+import "quill/dist/quill.snow.css";
+import { saveAs } from "file-saver";
+import * as quillToWord from "quill-to-word";
+let quill = null;
+
+export default {
+  name: "DocumentWindow",
+  data() {
+    return {
+      windowCheck: false,
+      abstracts: [],
+      pathways: [],
+      proteins: [],
+      tags: [],
+    };
+  },
+  computed: {
+    showPersistentComponent() {
+      let route = this.$route.name;
+      return (
+        this.windowCheck &&
+        route !== "home" &&
+        route !== "input" &&
+        route !== "file" &&
+        route !== "import"
+      );
+    },
+    quillEditor() {
+      return new Quill(this.$refs.editor, {
+        theme: "snow",
+        placeholder: "Start with your journey...",
+        modules: {
+          toolbar: [
+            [{ header: [1, 2, false] }],
+            ["bold", "italic", "underline"],
+            ["link", "image"],
+          ],
+        },
+      });
+    },
+  },
+  mounted() {
+    let com = this;
+    com.dragElement(document.getElementById("expdocument"));
+
+    com.emitter.on("openWord", () => {
+      com.windowCheck = !com.windowCheck;
+    });
+
+    com.emitter.on("addToWord", (text) => {
+      if (!com.windowCheck) {
+        com.windowCheck = true;
+      }
+      com.addBullet(text);
+    });
+
+    com.emitter.on("addImageToWord", (img) => {
+      if (!com.windowCheck) {
+        com.windowCheck = true;
+      }
+      com.addImage(img);
+    });
+
+    this.emitter.on("updateFavouriteList", (value) => {
+      this.pathways = value;
+    });
+
+    this.emitter.on("updateHistory", (value) => {
+      if (value.type == "protein") com.proteins.unshift(value.data);
+      if (value.type == "abstracts") com.abstracts.unshift(value.data);
+      if (value.type == "tags")
+        com.tags = [...new Set([...com.tags, ...value.data])].reverse();
+    });
+
+    com.pathways = com.$store.state.favourite_enrichments;
+
+    quill = this.quillEditor;
+  },
+  methods: {
+    addBullet(bullet) {
+      // Get the current selection or place the bullet at the end
+      if (typeof bullet === "object") this.addTag(bullet);
+      else {
+        var selection = quill.getSelection(true);
+        if (selection) {
+          quill.insertText(selection.index, `${bullet}\n`);
+        } else {
+          // If there is no selection, insert at the end of the document
+          quill.insertText(0, `${bullet}`);
+        }
+      }
+    },
+    addTag(bullet) {
+      console.log(bullet.data);
+      if (bullet.type == "protein") this.addBullet(bullet.data.label);
+      if (bullet.type == "subset")
+        this.addBullet(
+          `${bullet.id} (${bullet.data.map((node) => node.label).join(", ")})`
+        );
+      if (bullet.type == "term") this.addBullet(bullet.data.name);
+      console.log(bullet);
+    },
+    addImage(imgURL) {
+      var selection = quill.getSelection(true);
+      if (selection) {
+        console.log(selection.index);
+        quill.insertEmbed(selection.index, "image", imgURL);
+      } else {
+        // If there is no selection, insert at the end of the document
+        quill.insertEmbed(0, "image", imgURL);
+      }
+    },
+    addScreen(mode, format) {
+      let path = this.$route.name;
+      if (
+        path == "protein-graph" ||
+        path == "terms-graph" ||
+        path == "citation-graph"
+      ) {
+        this.emitter.emit("exportGraphWord", {
+          params: { mode, format },
+          mode: path,
+        });
+      }
+    },
+    async exportdocX() {
+      const delta = quill.getContents();
+      const quillToWordConfig = {
+        exportAs: "blob",
+      };
+      const docAsBlob = await quillToWord.generateWord(
+        delta,
+        quillToWordConfig
+      );
+      saveAs(docAsBlob, "word-export.docx");
+    },
+    dragElement(elmnt) {
+      var pos1 = 0,
+        pos2 = 0,
+        pos3 = 0,
+        pos4 = 0;
+      if (document.getElementById(elmnt.id + "_header")) {
+        document.getElementById(elmnt.id + "_header").onmousedown =
+          dragMouseDown;
+      } else {
+        elmnt.onmousedown = dragMouseDown;
+      }
+
+      function dragMouseDown(e) {
+        e = e || window.event;
+        e.preventDefault();
+        pos3 = e.clientX;
+        pos4 = e.clientY;
+        document.onmouseup = closeDragElement;
+        document.onmousemove = elementDrag;
+      }
+
+      function elementDrag(e) {
+        e = e || window.event;
+        e.preventDefault();
+        var parentWidth = window.innerWidth;
+        var parentHeight = window.innerHeight;
+        var elementWidth = elmnt.offsetWidth;
+        var elementHeight = elmnt.offsetHeight;
+
+        pos1 = pos3 - e.clientX;
+        pos2 = pos4 - e.clientY;
+        pos3 = e.clientX;
+        pos4 = e.clientY;
+
+        var newTop = elmnt.offsetTop - pos2;
+        var newLeft = elmnt.offsetLeft - pos1;
+
+        if (newTop < 0) newTop = 0;
+        if (newLeft < 0) newLeft = 0;
+        if (newTop + elementHeight > parentHeight)
+          newTop = parentHeight - elementHeight;
+        if (newLeft + elementWidth > parentWidth)
+          newLeft = parentWidth - elementWidth;
+
+        elmnt.style.top = newTop + "px";
+        elmnt.style.left = newLeft + "px";
+      }
+
+      function closeDragElement() {
+        document.onmouseup = null;
+        document.onmousemove = null;
+      }
+    },
+    closeWindow() {
+      this.windowCheck = false;
+    },
+  },
+};
+</script>
+
+<style scoped>
+.persistent-window {
+  position: absolute;
+  right: 1%;
+  top: 1.5%;
+  height: 97%;
+  width: 50%;
+  -webkit-backdrop-filter: blur(7.5px);
+  border: 1px solid #e0e0e0;
+  background-color: rgb(57, 57, 57);
+  box-shadow: 0px 4px 16px rgba(0, 0, 0, 0.1);
+  overflow: auto;
+  display: flex;
+  flex-direction: column;
+  font-family: "Segoe UI", Tahoma, Geneva, Verdana, sans-serif;
+  z-index: 99999;
+  resize: horizontal;
+}
+
+/* Header styles remain the same */
+.header {
+  background-color: rgb(57, 57, 57);
+  color: white;
+  padding: 15px;
+  cursor: move;
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  font-size: 16px;
+  font-weight: bold;
+  position: relative;
+}
+
+.close-btn {
+  font-size: 20px;
+  cursor: pointer;
+  padding: 0 5px;
+}
+
+/* Flexbox layout for bullet section and editor */
+.content-wrapper {
+  display: flex;
+  height: 100%;
+}
+
+/* Bullet section styles */
+.bullet-section {
+  width: 30%;
+  height: 45vw;
+  overflow-y: scroll;
+  background-color: rgb(57, 57, 57);
+  padding: 10px;
+  color: white;
+}
+
+.bullet-section ul {
+  list-style: none;
+  padding: 0;
+  overflow-y: scroll;
+  height: 15%;
+}
+
+.bullet-section li {
+  padding: 5px 0;
+  font-size: 0.7vw;
+  margin-left: 5px;
+  cursor: pointer;
+  color: white;
+}
+
+.bullet-section li:hover {
+  color: #00aaff;
+}
+
+/* Editor styles */
+#editor {
+  width: 100%;
+  padding: 10px;
+  overflow-y: auto;
+  z-index: 999999999;
+}
+
+.editor-section {
+  display: flex;
+  flex-direction: column;
+  width: 100%;
+  height: 45vw;
+}
+
+.export-bar {
+  color: white;
+  padding: 15px;
+  width: 99%;
+  display: flex;
+  justify-content: end;
+  cursor: move;
+  display: flex;
+  font-size: 16px;
+  font-weight: bold;
+  position: relative;
+}
+
+.export-bar button {
+  padding: 8px 16px;
+  background-color: #007bff;
+  color: white;
+  border: none;
+  cursor: pointer;
+  border-radius: 4px;
+}
+
+.export-bar button:hover {
+  background-color: #0056b3;
+}
+</style>
+
+<style>
+.ql-snow {
+  background-color: rgba(255, 255, 255, 0.4);
+}
+</style>
diff --git a/frontend/src/components/PersistentWindow.vue b/frontend/src/components/PersistentWindow.vue
index 14bab52a..e67f3eb5 100644
--- a/frontend/src/components/PersistentWindow.vue
+++ b/frontend/src/components/PersistentWindow.vue
@@ -28,12 +28,17 @@
             {{ element.id }}
           </span>
         </div>
-        <div v-if="msg.ref !== null">
+        <div v-if="msg.ref">
           <span class="small-tag blue" @click="searchRef(msg.ref)">
             reference
           </span>
         </div>
         <p>{{ msg.text }}</p>
+        <img
+          src="@/assets/pane/copy.png"
+          v-on:click="copyToClipboard(msg.text)"
+        />
+        <img src="@/assets/toolbar/word.png" v-on:click="addToWord(msg.text)" />
       </div>
     </div>
 
@@ -102,6 +107,19 @@ export default {
     });
   },
   methods: {
+    copyToClipboard(text) {
+      navigator.clipboard
+        .writeText(text)
+        .then(() => {
+          alert("Message copied to clipboard");
+        })
+        .catch((err) => {
+          console.error("Could not copy text: ", err);
+        });
+    },
+    addToWord(text) {
+      this.emitter.emit("addToWord", text);
+    },
     addLink(tag) {
       if (!this.windowCheck) this.windowCheck = true;
       if (tag && !this.tags.includes(tag)) {
@@ -238,6 +256,11 @@ export default {
         this.abort_chatbot();
       }
 
+      this.emitter.emit("updateHistory", {
+        type: "tags",
+        data: [...this.tags],
+      });
+
       this.messages.push({
         sender: "Bot",
         text: "Waiting for response...",
@@ -396,4 +419,12 @@ export default {
   color: rgb(175, 175, 175); /* Slightly darker red for remove button */
   font-size: 12px; /* Smaller "x" size */
 }
+
+.chat-history img {
+  filter: invert(50%);
+  position: relative;
+  width: 0.7vw;
+  margin-top: 0.5vw;
+  bottom: 0;
+}
 </style>
diff --git a/frontend/src/components/toolbar/CitationToolBar.vue b/frontend/src/components/toolbar/CitationToolBar.vue
index 8308d434..06e41b68 100644
--- a/frontend/src/components/toolbar/CitationToolBar.vue
+++ b/frontend/src/components/toolbar/CitationToolBar.vue
@@ -22,6 +22,9 @@
       <li v-on:click="chatbot()">
         <img src="@/assets/toolbar/bote.png" alt="bot Icon" />
       </li>
+      <li v-on:click="word()">
+        <img src="@/assets/toolbar/word.png" alt="word Icon" />
+      </li>
       <li
         v-on:click="hide_labels(label_check)"
         :class="{ crossed: label_check }"
@@ -99,6 +102,9 @@ export default {
     chatbot() {
       this.emitter.emit("openChatbot");
     },
+    word() {
+      this.emitter.emit("openWord");
+    },
     hide_labels(check) {
       this.label_check = !check;
       this.emitter.emit("hideLabels", {
diff --git a/frontend/src/components/toolbar/MainToolBar.vue b/frontend/src/components/toolbar/MainToolBar.vue
index 7f83332b..7baea74e 100644
--- a/frontend/src/components/toolbar/MainToolBar.vue
+++ b/frontend/src/components/toolbar/MainToolBar.vue
@@ -25,6 +25,9 @@
       <li v-on:click="chatbot()">
         <img src="@/assets/toolbar/bote.png" alt="bot Icon" />
       </li>
+      <li v-on:click="word()">
+        <img src="@/assets/toolbar/word.png" alt="word Icon" />
+      </li>
       <li
         v-on:click="hide_labels(label_check)"
         :class="{ crossed: label_check }"
@@ -108,6 +111,9 @@ export default {
     chatbot() {
       this.emitter.emit("openChatbot");
     },
+    word() {
+      this.emitter.emit("openWord");
+    },
     hide_labels(check) {
       this.label_check = !check;
       this.emitter.emit("hideLabels", {
@@ -130,7 +136,7 @@ export default {
   align-items: center;
   padding: 5% 0;
   z-index: 99;
-  margin: 0.5vw 0 0 0;
+  margin: 0.5vw 0 0 0.5vw;
 }
 
 .menu-bar li {
diff --git a/frontend/src/components/toolbar/TermToolBar.vue b/frontend/src/components/toolbar/TermToolBar.vue
index feab34f9..d885d724 100644
--- a/frontend/src/components/toolbar/TermToolBar.vue
+++ b/frontend/src/components/toolbar/TermToolBar.vue
@@ -22,6 +22,9 @@
       <li v-on:click="chatbot()">
         <img src="@/assets/toolbar/bote.png" alt="bot Icon" />
       </li>
+      <li v-on:click="word()">
+        <img src="@/assets/toolbar/word.png" alt="word Icon" />
+      </li>
       <li
         v-on:click="hide_labels(label_check)"
         :class="{ crossed: label_check }"
@@ -99,6 +102,9 @@ export default {
     chatbot() {
       this.emitter.emit("openChatbot");
     },
+    word() {
+      this.emitter.emit("openWord");
+    },
     hide_labels(check) {
       this.label_check = !check;
       this.emitter.emit("hideLabels", {
diff --git a/frontend/src/components/visualization/CitationVis.vue b/frontend/src/components/visualization/CitationVis.vue
index 84af3247..97580c61 100644
--- a/frontend/src/components/visualization/CitationVis.vue
+++ b/frontend/src/components/visualization/CitationVis.vue
@@ -131,6 +131,8 @@ export default {
         return;
       }
 
+      this.emitter.emit("updateHistory", { type: "abstracts", data: node });
+
       var sigma_node = sigma_instance.graph.getNodeFromIndex(
         node.attributes["Ensembl ID"]
       );
@@ -484,6 +486,15 @@ export default {
         saveAsSVG(sigma_instance, { download: true }, params.mode);
       else saveAsPNG(sigma_instance, { download: true }, params.mode);
     },
+    exportGraphAsURL(params) {
+      let exportURL = null;
+      if (params.format == "svg")
+        exportURL = saveAsSVG(sigma_instance, { download: false }, params.mode);
+      else
+        exportURL = saveAsPNG(sigma_instance, { download: false }, params.mode);
+
+      this.emitter.emit("addImageToWord", exportURL);
+    },
     hide_labels(state) {
       if (state) {
         sigma_instance.graph.nodes().forEach(function (n) {
@@ -756,6 +767,8 @@ export default {
     sigma_instance.graph.clear();
     sigma_instance.graph.read(com.citation_data);
 
+    this.$store.commit("assign_sigma_instance", sigma_instance);
+
     this.get_module_circles();
 
     com.edit_opacity("full");
@@ -853,6 +866,10 @@ export default {
       if (state.mode == "citation") this.exportGraphAsImage(state.params);
     });
 
+    this.emitter.on("exportGraphWord", (state) => {
+      if (state.mode == "citation-graph") this.exportGraphAsURL(state.params);
+    });
+
     this.emitter.on("resetSelect", (state) => {
       if (state.mode == "citation") this.reset_label_select();
     });
@@ -884,6 +901,7 @@ export default {
   },
   activated() {
     sigma_instance.refresh();
+    this.$store.commit("assign_sigma_instance", sigma_instance);
   },
 };
 </script>
diff --git a/frontend/src/components/visualization/MainVis.vue b/frontend/src/components/visualization/MainVis.vue
index db25f2a7..7e662450 100644
--- a/frontend/src/components/visualization/MainVis.vue
+++ b/frontend/src/components/visualization/MainVis.vue
@@ -180,6 +180,7 @@ export default {
         com.resetFocus(sigma_instance.cameras[0]);
         return;
       }
+      this.emitter.emit("updateHistory", { type: "protein", data: node });
 
       if (com.three_view)
         var sigma_node = sigma_instance.graph.getNodeFromIndex(node.id);
@@ -264,8 +265,6 @@ export default {
     active_term(term) {
       const com = this;
 
-      console.log(term);
-
       this.$store.commit("assign_active_subset", term ? term.symbols : null);
 
       if (term == null) {
@@ -777,6 +776,15 @@ export default {
         saveAsSVG(sigma_instance, { download: true }, params.mode);
       else saveAsPNG(sigma_instance, { download: true }, params.mode);
     },
+    exportGraphAsURL(params) {
+      let exportURL = null;
+      if (params.format == "svg")
+        exportURL = saveAsSVG(sigma_instance, { download: false }, params.mode);
+      else
+        exportURL = saveAsPNG(sigma_instance, { download: false }, params.mode);
+
+      this.emitter.emit("addImageToWord", exportURL);
+    },
     show_unconnectedGraph(state) {
       var com = this;
 
@@ -1219,6 +1227,8 @@ export default {
       sigma_instance.graph.clear();
       sigma_instance.graph.read(com.gephi_data);
 
+      this.$store.commit("assign_sigma_instance", sigma_instance);
+
       com.edit_opacity("full");
 
       com.hide_labels(true);
@@ -1334,6 +1344,10 @@ export default {
         if (state.mode == "protein") this.exportGraphAsImage(state.params);
       });
 
+      this.emitter.on("exportGraphWord", (state) => {
+        if (state.mode == "protein-graph") this.exportGraphAsURL(state.params);
+      });
+
       this.emitter.on("resetSelect", (state) => {
         if (state.mode == "protein") this.reset_label_select();
       });
@@ -1375,6 +1389,9 @@ export default {
       sigma_instance.refresh();
     });
   },
+  activated() {
+    this.$store.commit("assign_sigma_instance", sigma_instance);
+  },
 };
 </script>
 
diff --git a/frontend/src/components/visualization/TermVis.vue b/frontend/src/components/visualization/TermVis.vue
index e31b7411..45ba3c92 100644
--- a/frontend/src/components/visualization/TermVis.vue
+++ b/frontend/src/components/visualization/TermVis.vue
@@ -479,6 +479,15 @@ export default {
         saveAsSVG(sigma_instance, { download: true }, params.mode);
       else saveAsPNG(sigma_instance, { download: true }, params.mode);
     },
+    exportGraphAsURL(params) {
+      let exportURL = null;
+      if (params.format == "svg")
+        exportURL = saveAsSVG(sigma_instance, { download: false }, params.mode);
+      else
+        exportURL = saveAsPNG(sigma_instance, { download: false }, params.mode);
+
+      this.emitter.emit("addImageToWord", exportURL);
+    },
     hide_labels(state) {
       if (state) {
         sigma_instance.graph.nodes().forEach(function (n) {
@@ -751,6 +760,8 @@ export default {
     sigma_instance.graph.clear();
     sigma_instance.graph.read(com.term_data);
 
+    this.$store.commit("assign_sigma_instance", sigma_instance);
+
     this.get_module_circles();
 
     com.edit_opacity("full");
@@ -852,6 +863,10 @@ export default {
       if (state.mode == "term") this.exportGraphAsImage(state.params);
     });
 
+    this.emitter.on("exportGraphWord", (state) => {
+      if (state.mode == "terms-graph") this.exportGraphAsURL(state.params);
+    });
+
     this.emitter.on("resetSelect", (state) => {
       if (state.mode == "term") this.reset_label_select();
     });
@@ -882,6 +897,7 @@ export default {
   },
   activated() {
     sigma_instance.refresh();
+    this.$store.commit("assign_sigma_instance", sigma_instance);
   },
 };
 </script>
diff --git a/frontend/src/store/index.js b/frontend/src/store/index.js
index d82156ac..eb3792da 100644
--- a/frontend/src/store/index.js
+++ b/frontend/src/store/index.js
@@ -2,6 +2,7 @@ import { createStore } from "vuex";
 
 export const store = createStore({
   state: {
+    sigma_instance: null,
     gephi_json: null,
     term_graph_data: null,
     term_graph_dict: [],
@@ -37,6 +38,10 @@ export const store = createStore({
     favourite_subsets: new Set(),
   },
   mutations: {
+    assign_sigma_instance(state, value) {
+      console.log(value);
+      state.sigma_instance = value;
+    },
     assign(state, value) {
       state.gephi_json = value;
     },
diff --git a/package-lock.json b/package-lock.json
new file mode 100644
index 00000000..9d269a93
--- /dev/null
+++ b/package-lock.json
@@ -0,0 +1,69 @@
+{
+  "name": "protein-graph-database",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "dependencies": {
+        "quill": "^2.0.2"
+      }
+    },
+    "node_modules/eventemitter3": {
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/eventemitter3/-/eventemitter3-5.0.1.tgz",
+      "integrity": "sha512-GWkBvjiSZK87ELrYOSESUYeVIc9mvLLf/nXalMOS5dYrgZq9o5OVkbZAVM06CVxYsCwH9BDZFPlQTlPA1j4ahA=="
+    },
+    "node_modules/fast-diff": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/fast-diff/-/fast-diff-1.3.0.tgz",
+      "integrity": "sha512-VxPP4NqbUjj6MaAOafWeUn2cXWLcCtljklUtZf0Ind4XQ+QPtmA0b18zZy0jIQx+ExRVCR/ZQpBmik5lXshNsw=="
+    },
+    "node_modules/lodash-es": {
+      "version": "4.17.21",
+      "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.17.21.tgz",
+      "integrity": "sha512-mKnC+QJ9pWVzv+C4/U3rRsHapFfHvQFoFB92e52xeyGMcX6/OlIl78je1u8vePzYZSkkogMPJ2yjxxsb89cxyw=="
+    },
+    "node_modules/lodash.clonedeep": {
+      "version": "4.5.0",
+      "resolved": "https://registry.npmjs.org/lodash.clonedeep/-/lodash.clonedeep-4.5.0.tgz",
+      "integrity": "sha512-H5ZhCF25riFd9uB5UCkVKo61m3S/xZk1x4wA6yp/L3RFP6Z/eHH1ymQcGLo7J3GMPfm0V/7m1tryHuGVxpqEBQ=="
+    },
+    "node_modules/lodash.isequal": {
+      "version": "4.5.0",
+      "resolved": "https://registry.npmjs.org/lodash.isequal/-/lodash.isequal-4.5.0.tgz",
+      "integrity": "sha512-pDo3lu8Jhfjqls6GkMgpahsF9kCyayhgykjyLMNFTKWrpVdAQtYyB4muAMWozBB4ig/dtWAmsMxLEI8wuz+DYQ=="
+    },
+    "node_modules/parchment": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/parchment/-/parchment-3.0.0.tgz",
+      "integrity": "sha512-HUrJFQ/StvgmXRcQ1ftY6VEZUq3jA2t9ncFN4F84J/vN0/FPpQF+8FKXb3l6fLces6q0uOHj6NJn+2xvZnxO6A=="
+    },
+    "node_modules/quill": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/quill/-/quill-2.0.2.tgz",
+      "integrity": "sha512-QfazNrhMakEdRG57IoYFwffUIr04LWJxbS/ZkidRFXYCQt63c1gK6Z7IHUXMx/Vh25WgPBU42oBaNzQ0K1R/xw==",
+      "dependencies": {
+        "eventemitter3": "^5.0.1",
+        "lodash-es": "^4.17.21",
+        "parchment": "^3.0.0",
+        "quill-delta": "^5.1.0"
+      },
+      "engines": {
+        "npm": ">=8.2.3"
+      }
+    },
+    "node_modules/quill-delta": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/quill-delta/-/quill-delta-5.1.0.tgz",
+      "integrity": "sha512-X74oCeRI4/p0ucjb5Ma8adTXd9Scumz367kkMK5V/IatcX6A0vlgLgKbzXWy5nZmCGeNJm2oQX0d2Eqj+ZIlCA==",
+      "dependencies": {
+        "fast-diff": "^1.3.0",
+        "lodash.clonedeep": "^4.5.0",
+        "lodash.isequal": "^4.5.0"
+      },
+      "engines": {
+        "node": ">= 12.0.0"
+      }
+    }
+  }
+}
diff --git a/package.json b/package.json
new file mode 100644
index 00000000..10c06b54
--- /dev/null
+++ b/package.json
@@ -0,0 +1,5 @@
+{
+  "dependencies": {
+    "quill": "^2.0.2"
+  }
+}

From 1247c27fad5daa7c713bc8ece0bbb479840f2bcf Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:22:57 +0100
Subject: [PATCH 5/8] Update journalStructure.md

---
 docs/journalStructure.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index bb0dc88b..b087d883 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -68,6 +68,7 @@ _________________________________________________________________
 * Nature Metabolism: 25.5
 * Nature Protocols: 17.1
 * Nature Biomedical Engineering: 28.9
+* Nature Microbiology: 20.5
 
 ## Other Cell journals:
 * Cancer Cell: 48.8

From 5d405a3fc5b8631c3ab8b7223faa3198b54cbb64 Mon Sep 17 00:00:00 2001
From: TripZz <nico.greiner9@gmail.com>
Date: Thu, 31 Oct 2024 20:20:14 +0100
Subject: [PATCH 6/8] NN-605 Adding AI enrich button to document window -bridge
 frontend/backend with enriched data

---
 backend/src/main.py                        | 10 ++++++++++
 frontend/src/components/DocumentWindow.vue | 20 +++++++++++++++++---
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/backend/src/main.py b/backend/src/main.py
index 0d6e4102..e77a889f 100644
--- a/backend/src/main.py
+++ b/backend/src/main.py
@@ -186,6 +186,16 @@ def chatbot_response():
     return Response(response, mimetype="application/json")
 
 
+# ====================== AI enrich text ======================
+# TODO Refactor this
+# Request comes from ContextSection.vue
+@app.route("/api/subgraph/textenrich", methods=["POST"])
+def enrich_text():
+    content = request.form.get("content")
+
+    return Response(json.dumps(content), mimetype="application/json")
+
+
 # ====================== Subgraph API ======================
 # request comes from home.js
 # TODO Refactor this
diff --git a/frontend/src/components/DocumentWindow.vue b/frontend/src/components/DocumentWindow.vue
index 2b934dbb..98889506 100644
--- a/frontend/src/components/DocumentWindow.vue
+++ b/frontend/src/components/DocumentWindow.vue
@@ -68,6 +68,7 @@
       </div>
     </div>
     <div class="export-bar">
+      <button @click="textImprove">AI improve</button>
       <button @click="exportdocX">Export Document</button>
     </div>
   </div>
@@ -89,6 +90,9 @@ export default {
       pathways: [],
       proteins: [],
       tags: [],
+      api: {
+        textenrich: "api/subgraph/textenrich",
+      },
     };
   },
   computed: {
@@ -168,14 +172,12 @@ export default {
       }
     },
     addTag(bullet) {
-      console.log(bullet.data);
       if (bullet.type == "protein") this.addBullet(bullet.data.label);
       if (bullet.type == "subset")
         this.addBullet(
           `${bullet.id} (${bullet.data.map((node) => node.label).join(", ")})`
         );
       if (bullet.type == "term") this.addBullet(bullet.data.name);
-      console.log(bullet);
     },
     addImage(imgURL) {
       var selection = quill.getSelection(true);
@@ -211,6 +213,17 @@ export default {
       );
       saveAs(docAsBlob, "word-export.docx");
     },
+    async textImprove() {
+      const delta = quill.getContents();
+      var com = this;
+
+      var formData = new FormData();
+      formData.append("content", JSON.stringify(delta.ops));
+
+      com.axios.post(com.api.textenrich, formData).then((response) => {
+        console.log(response);
+      });
+    },
     dragElement(elmnt) {
       var pos1 = 0,
         pos2 = 0,
@@ -362,7 +375,7 @@ export default {
 
 .export-bar {
   color: white;
-  padding: 15px;
+  padding: 1%;
   width: 99%;
   display: flex;
   justify-content: end;
@@ -375,6 +388,7 @@ export default {
 
 .export-bar button {
   padding: 8px 16px;
+  margin-left: 2%;
   background-color: #007bff;
   color: white;
   border: none;

From 4b3a43d6e44ab96b608090918b63398d0ae8fe9e Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Fri, 1 Nov 2024 15:33:42 +0100
Subject: [PATCH 7/8] Update journalStructure.md

---
 docs/journalStructure.md | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index b087d883..15cf096e 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -30,15 +30,33 @@ This document contains the structure of Journals having Impact Factor greater th
 _________________________________________________________________
 
 ## Cell: IF 45.5
-### Resource availability
-* materials availability
-* **Data and Code/Software Availability**
+_Structure 01:_
+### Resource availability:
+#### Materials availability
+#### Data and Code/Software Availability
+  * contains info regarding sequencing data and source code
   * if code unavailable > “This paper does not report original code” (MUST BE ADDED but not always added)
   * code available upon request from authors
   * already-existing SWs and Algorithms used but no unique code generated - found in Key Resources Table
   * ‘original code’
   * ‘unique code’
   * ‘custom code’
+ 
+_Structure 02:_
+### Data and Code/Software Availability:
+  * contains info regarding sequencing data and source code
+
+## Cell Stem Cell: IF 19.8
+### Resource availability:
+#### Lead contact
+#### Materials availability 
+  * contains information regarding code in some publications where 'Data and SW Availability' is missing
+#### Data and Code/Software Availability
+  * sometimes this section is skipped
+
+## Other Cell journals:
+* Cancer Cell: 48.8
+* Immunity: 43.47
 
 ## Nature Immunology: IF 27.7
 ### Data availability
@@ -70,8 +88,5 @@ _________________________________________________________________
 * Nature Biomedical Engineering: 28.9
 * Nature Microbiology: 20.5
 
-## Other Cell journals:
-* Cancer Cell: 48.8
-* Immunity: 43.47
 
 Note: Most of the Science journals cannot be accessed without Institution registration.

From 7c150b9716fe066c8da8806f51d2c5a28412467a Mon Sep 17 00:00:00 2001
From: Momina Atif Dar <51847536+mominaadar@users.noreply.github.com>
Date: Fri, 1 Nov 2024 21:19:55 +0100
Subject: [PATCH 8/8] Update journalStructure.md

---
 docs/journalStructure.md | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/docs/journalStructure.md b/docs/journalStructure.md
index 15cf096e..2e89c356 100644
--- a/docs/journalStructure.md
+++ b/docs/journalStructure.md
@@ -41,18 +41,25 @@ _Structure 01:_
   * ‘original code’
   * ‘unique code’
   * ‘custom code’
+  * github link for original source code or custom code generated by using already-existing SW
  
 _Structure 02:_
 ### Data and Code/Software Availability:
   * contains info regarding sequencing data and source code
 
-## Cell Stem Cell: IF 19.8
+## Cell Stem Cell: IF 19.8 
+(some publications are not publicly accessible)
 ### Resource availability:
 #### Lead contact
+  * requests for resources and reagents
 #### Materials availability 
-  * contains information regarding code in some publications where 'Data and SW Availability' is missing
 #### Data and Code/Software Availability
-  * sometimes this section is skipped
+  * section not found in several publications
+  * sequencing data listed but not source code
+  * 'original code'
+  * 'novel code'
+  * accession numbers of sequencing data & source code URL (Github/Zenodo) listed in Key Resources Table
+  * accession number stated in plain text instead of a URL
 
 ## Other Cell journals:
 * Cancer Cell: 48.8