From 6bc61bfae612c9593718dd55f6927f5c44fd06bf Mon Sep 17 00:00:00 2001
From: Yuta Yamate <11874627+yutayamate@users.noreply.github.com>
Date: Sat, 1 Jun 2019 14:43:12 +0900
Subject: [PATCH 1/3] Update author information

---
 functree/templates/about.html | 22 +++++++++++-----------
 package.json                  |  5 ++---
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/functree/templates/about.html b/functree/templates/about.html
index f91ba99..3727372 100644
--- a/functree/templates/about.html
+++ b/functree/templates/about.html
@@ -6,8 +6,8 @@
     <div class="page-header">
         <h2>{{title}}</h2>
 	    <p>This is FuncTree 2 - version {{version}}</p>
-	    <p>FuncTree 2 is actively developed at the <a href="http://comp.bio.titech.ac.jp" target="_blank">Yamada Lab</a>, Tokyo Institute of Technology, 
-	    by Youssef Darzi (<a href="https://github.com/omixer" target="_blank">@omixer</a>), Yuta Yamate (<a href="https://github.com/yyuuta88" target="_blank">@yyuuta88</a>),
+	    <p>FuncTree 2 is actively developed at the <a href="http://comp.bio.titech.ac.jp" target="_blank">Yamada Lab</a>, Tokyo Institute of Technology,
+	    by Youssef Darzi (<a href="https://github.com/omixer" target="_blank">@omixer</a>), Yuta Yamate (<a href="https://github.com/yutayamate" target="_blank">@yutayamate</a>),
 	    and Takuji Yamada.
 	    </p>
 	    <p>Source code is available on <a href="https://github.com/yamada-lab/functree-ng" target="_blank">github.com/yamada-lab/functree-ng</a></p>
@@ -18,18 +18,18 @@ <h3>Publications</h3>
     	<i><a href="https://doi.org/10.1093/bioinformatics/btz245" target="_blank">FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization</a></i>
 		<br />
 		Darzi Y, Yamate Y, Yamada T.
-		<br /> 
+		<br />
 		Bioinformatics, btz245. 20 April 2019; <a href="https://doi.org/10.1093/bioinformatics/btz245" target="_blank">https://doi.org/10.1093/bioinformatics/btz245</a>
 		</p>
-		
+
 		<p>
     	<i><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126967" target="_blank">FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data</a></i>
 		<br />
 		Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T.
-		<br /> 
+		<br />
 		PLoS ONE 10(5): e0126967. 2015 May 14; <a href="https://doi.org/10.1371/journal.pone.0126967" target="_blank">https://doi.org/10.1371/journal.pone.0126967</a>
 		</p>
-		
+
     </div>
     <hr />
     <h3>Change log</h3>
@@ -68,7 +68,7 @@ <h5>Version 0.8.0.0 (2019-02-28)</h5>
 				<li>Streamlining of the controls layout and the UI.
 				<li>Bug fix: selection of leaf nodes with value > 0 only.
 			</ul>
-		<li>Addition of bar plots to "Module undefined" nodes to highlight the amount of pathway KO not assigned to a module.  
+		<li>Addition of bar plots to "Module undefined" nodes to highlight the amount of pathway KO not assigned to a module.
 	</ul>
 	<h5>Version 0.7.6.3 (2019-02-25)</h5>
 	<ul>
@@ -79,7 +79,7 @@ <h5>Version 0.7.6.2 (2019-02-15)</h5>
 		<li>Addition of a toggle action to show/hide node labels.
 		<li>Addition of a description to the database selection.
 		<li>Upgrade of Flask.
-	</ul>    
+	</ul>
     <h5>Version 0.7.6.1 (2019-01-18)</h5>
 	<ul>
 		<li>Addition of a help section on the Functree explorer page, and improvement of the main documentation.
@@ -87,7 +87,7 @@ <h5>Version 0.7.6.1 (2019-01-18)</h5>
     <h5>Version 0.7.6 (2019-01-15)</h5>
 	<ul>
 		<li>Addition of a zoom control widget.
-		<li>Replacement of D3 categorical20 color palette by the color blind friendly palette tableau10. 
+		<li>Replacement of D3 categorical20 color palette by the color blind friendly palette tableau10.
 	</ul>
     <h5>Version 0.7.5 (2018-08-10)</h5>
 	<ul>
@@ -95,11 +95,11 @@ <h5>Version 0.7.5 (2018-08-10)</h5>
 	</ul>
     <h5>Version 0.7.4 (2018-06-20)</h5>
 	<ul>
-		<li>Performance improvement: mapping time is reduced to around 15 seconds on dev machine using the example profile.tsv. 
+		<li>Performance improvement: mapping time is reduced to around 15 seconds on dev machine using the example profile.tsv.
 	</ul>
 	<h5>Version 0.7.3 (2018-06-19)</h5>
 	<ul>
-		<li>Performance improvement: mapping time is reduced from 3 minutes to 1 minute and 20 seconds. Module coverage computation time is lowered from 80 seconds to 5 seconds. 
+		<li>Performance improvement: mapping time is reduced from 3 minutes to 1 minute and 20 seconds. Module coverage computation time is lowered from 80 seconds to 5 seconds.
 	</ul>
 </div>
 {% endblock %}
diff --git a/package.json b/package.json
index 19d2c8b..ca1d096 100644
--- a/package.json
+++ b/package.json
@@ -1,10 +1,9 @@
 {
   "name": "functree-ng",
-  "description": "Visualization and analysis tool for omics data based on biological functional tree",
+  "description": "FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization",
   "author": {
     "name": "Yuta Yamate",
-    "email": "yyamate@bio.titech.ac.jp",
-    "url": "https://yyuuta88.github.io"
+    "url": "https://github.com/yutayamate"
   },
   "repository": {
     "type": "git",

From 0830ffffff96778be3a932d94f5e5d5167f7bf3a Mon Sep 17 00:00:00 2001
From: omixer <youssef.darzi@gmail.com>
Date: Mon, 17 Jun 2019 23:27:02 +0900
Subject: [PATCH 2/3] Fix layer mapping of custom tree upload

---
 functree/tree.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/functree/tree.py b/functree/tree.py
index b387331..dcdc34e 100755
--- a/functree/tree.py
+++ b/functree/tree.py
@@ -136,7 +136,7 @@ def from_tsv(path, name):
     '''
     root = Node(entry=name, name=name, layer='root')
 
-    # process annoatation if available 
+    # process annotation if available 
     entry_label = {}
     line = path.readline()
     
@@ -149,8 +149,14 @@ def from_tsv(path, name):
                 entry, label = line.split('\t')
                 entry_label[entry] = label
                 line = path.readline()
+    # set header to current line
+    header = line
+    # if file has annotation
+    if len(entry_label) > 0 :
+        # read header from next line
+        header = path.readline()
     
-    levels = path.readline().strip().decode().split('\t')
+    levels = header.strip().decode().split('\t')
     levels.insert(0, 'root')
     nodes_layer = {key: {} for key in levels}
     nodes_layer['root'] = {'root': root}

From 5d3ef4e2b9edfe433565a17e9154f6c751070491 Mon Sep 17 00:00:00 2001
From: omixer <youssef.darzi@gmail.com>
Date: Thu, 18 Mar 2021 13:23:56 +0900
Subject: [PATCH 3/3] Upgrade dependencies

---
 functree/analysis/__init__.py |  47 +++++++++++++++++-----------------
 functree/favicon.ico          | Bin 0 -> 1150 bytes
 functree/templates/about.html |   6 +++++
 package.json                  |   4 +--
 requirements.txt              |   8 +++---
 5 files changed, 35 insertions(+), 30 deletions(-)
 create mode 100644 functree/favicon.ico

diff --git a/functree/analysis/__init__.py b/functree/analysis/__init__.py
index 61bcad8..cb695dc 100644
--- a/functree/analysis/__init__.py
+++ b/functree/analysis/__init__.py
@@ -64,30 +64,29 @@ def calc_abundances(df, nodes, method, results):
     df_dict =  {}
     for node in nodes:
         entry_profile = None
-        # Skip nodes which was already in df_out
-        if node['entry'] in df_dict:
-            continue
-
-        if 'children' not in node:
-            try:
-                # If node in abundace matrix, input as is
-                entry_profile = df.loc[node['entry']]
-            except KeyError:
-                pass
-        else:
-            # get leaf ids of the current node 
-            targets = [child_node['entry'] for child_node in tree.get_nodes(node) if 'children' not in child_node]
-            try:
-                # loc is row names of data frame
-                loc = df.loc[targets]
-                # sample abundance for a biological entry
-                # Calculated for children of nodes that are not in the input abundance matrix
-                entry_profile = eval('loc.{}()'.format(method))
-            except KeyError:
-                pass
-        # the entry on the tree is not in the submitted profile
-        if entry_profile is not None:
-            df_dict[node['entry']] = entry_profile.to_dict().values()
+        # Compute value for nodes not in df_out
+        if node['entry'] not in df_dict:
+            # if leaf is reached
+            if 'children' not in node:
+                try:
+                    # If node in abundance matrix, input as is
+                    entry_profile = df.loc[node['entry']]
+                except KeyError:
+                    pass
+            else:
+                # get leaf ids of the current node 
+                targets = [child_node['entry'] for child_node in tree.get_nodes(node) if 'children' not in child_node]
+                try:
+                    # loc is row names of data frame
+                    loc = df.loc[targets]
+                    # sample abundance for a biological entry
+                    # Calculated for children of nodes that are not in the input abundance matrix
+                    entry_profile = eval('loc.{}()'.format(method))
+                except KeyError:
+                    pass
+            # the entry on the tree is not in the submitted profile
+            if entry_profile is not None:
+                df_dict[node['entry']] = entry_profile.to_dict().values()
 
     df_out = pd.DataFrame.from_dict(df_dict, "index")
     if not df_out.empty:
diff --git a/functree/favicon.ico b/functree/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..a001af111e26677e771e16fe44e98ccb667ab052
GIT binary patch
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diff --git a/functree/templates/about.html b/functree/templates/about.html
index 3727372..05d3412 100644
--- a/functree/templates/about.html
+++ b/functree/templates/about.html
@@ -34,6 +34,12 @@ <h3>Publications</h3>
     <hr />
     <h3>Change log</h3>
     <br />
+    <h5>Version 0.8.4.0 (2021-03-18)</h5>
+    <ul>
+    	<li>Fix layer mapping of custom tree upload.
+    	<li>Fix potential security vulnerabilities.
+    	<li>Update author info.
+    </ul>
     <h5>Version 0.8.3.0 (2019-05-08)</h5>
     <ul>
     	<li>Update citation.
diff --git a/package.json b/package.json
index ca1d096..3d3508a 100644
--- a/package.json
+++ b/package.json
@@ -14,7 +14,7 @@
   },
   "license": "MIT",
   "dependencies": {
-    "axios": "^0.17.1",
+    "axios": "^0.21.1",
     "bootstrap": "^3.3.7",
     "bootstrap-menu": "^1.0.14",
     "corejs-typeahead": "^1.2.1",
@@ -23,7 +23,7 @@
     "datatables.net-bs": "^1.10.19",
     "datatables.net-buttons": "^1.3.1",
     "font-awesome": "^4.7.0",
-    "highcharts": "^6.0.4",
+    "highcharts": "^9.0.1",
     "jquery": "^3.2.1",
     "particles.js": "^2.0.0",
     "vue": "^2.4.2",
diff --git a/requirements.txt b/requirements.txt
index de4bcf5..2eac6da 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 blinker==1.4
 cairocffi==0.8.0
-CairoSVG==2.0.3
+CairoSVG==2.5.1
 cffi==1.10.0
 click==6.7
 cssselect==1.0.1
@@ -12,14 +12,14 @@ flask-mongoengine==0.9.3
 Flask-WTF==0.14.2
 itsdangerous==0.24
 Jinja2==2.10.1
-lxml==3.8.0
+lxml==4.6.2
 MarkupSafe==1.0
 mongoengine==0.13.0
 networkx==2.1
 numpy==1.13.1
 olefile==0.44
 pandas==0.20.3
-Pillow==4.2.1
+Pillow==7.1.0
 pycparser==2.18
 pymongo==3.4.0
 python-dateutil==2.6.1
@@ -30,5 +30,5 @@ setuptools-scm==1.15.6
 six==1.10.0
 tinycss==0.4
 uWSGI==2.0.15
-Werkzeug==0.12.2
+Werkzeug==0.15.3
 WTForms==2.1