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robinzixuan · Feb 2, 2021 · 7b81748 · 7b81748
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diff --git a/.htaccess b/.htaccess
@@ -9,7 +9,7 @@
 # [...]
 # </Directory>
 #
-# (See also https://nlp.dlwlrat.org/troubleshooting.html)
+# (See also https://nlp.SciAnnotate.org/troubleshooting.html)
 <FilesMatch "^(\.htaccess|config\.py)$">
  Require all granted
 </FilesMatch>

diff --git a/Dockerfile b/Dockerfile
@@ -1,5 +1,5 @@
 FROM python:3.7.9
 WORKDIR /
-RUN git clone https://github.com/leonard-thong/dlwlrat.git /dlwlrat && cd dlwlrat && git checkout lmy-dev && bash ./docker_install.sh
-WORKDIR /dlwlrat
+RUN git clone https://github.com/leonard-thong/SciAnnotate.git /SciAnnotate && cd SciAnnotate && git checkout lmy-dev && bash ./docker_install.sh
+WORKDIR /SciAnnotate
 CMD ["python3", "standalone.py"]
diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
-# Deep Learning Model Annotation Tool (dlwlrat) #
+# Deep Learning Model Annotation Tool (SciAnnotate) #
 
 ## Quick start installation: standalone server ##
 
 First, please note the following:
 
-- The dlwlrat standalone server only is available in dlwlrat v1.0 and above.
+- The SciAnnotate standalone server only is available in SciAnnotate v1.0 and above.
 - The standalone server is experimental and should not be used for sensitive data or systems accessible from the internet.
 
 
@@ -17,7 +17,7 @@ Start the standalone server
  python standalone.py
 
 
-You should then be able to access the dlwlrat server from the address printed out by standalone.py.
+You should then be able to access the SciAnnotate server from the address printed out by standalone.py.
 
 ## Add New Labeling Functions
 

diff --git a/ajax.cgi b/ajax.cgi
@@ -2,8 +2,8 @@
 # -*- Mode: Python; tab-width: 4; indent-tabs-mode: nil; -*-
 # vim:set ft=python ts=4 sw=4 sts=4 autoindent:
 
-"""Entry for CGI calls to dlwlrat. A simple wrapper around the CGI handling that
-then delegates the work to the CGI-agnostic dlwlrat server.
+"""Entry for CGI calls to SciAnnotate. A simple wrapper around the CGI handling that
+then delegates the work to the CGI-agnostic SciAnnotate server.
 
 Author: Pontus Stenetorp <pontus is s u-tokyo ac jp>
 Version: 2011-02-07

diff --git a/ajax.fcgi b/ajax.fcgi
@@ -3,8 +3,8 @@
 # vim:set ft=python ts=4 sw=4 sts=4 autoindent:
 
 '''
-Entry for FastCGI calls to dlwlrat. This is a simple wrapper around a persistent
-WSGI server that delegates the processing to the FastCGI-agnostic dlwlrat server.
+Entry for FastCGI calls to SciAnnotate. This is a simple wrapper around a persistent
+WSGI server that delegates the processing to the FastCGI-agnostic SciAnnotate server.
 
 Depends on flup:
 
@@ -37,7 +37,7 @@ sys_path.append(path_join(dirname(__file__), 'server/src'))
 
 from server import serve
 
-def dlwlrat_app(environ, start_response):
+def SciAnnotate_app(environ, start_response):
  # Get the data required by the server
  try:
  remote_addr = environ['REMOTE_ADDR']
@@ -73,5 +73,5 @@ def dlwlrat_app(environ, start_response):
 
 if __name__ == '__main__':
  from sys import exit
- WSGIServer(dlwlrat_app).run()
+ WSGIServer(SciAnnotate_app).run()
  exit(0)
diff --git a/config_template.py b/config_template.py
@@ -3,12 +3,12 @@
 # This configuration file specifies the global setup of the brat
 # server. It is recommended that you use the installation script
 # instead of editing this file directly. To do this, run the following
-# command in the dlwlrat directory:
+# command in the SciAnnotate directory:
 #
 # ./install.sh
 #
 # if you wish to configure the server manually, you will first need to
-# make sure that this file appears as config.py in the dlwlrat server
+# make sure that this file appears as config.py in the SciAnnotate server
 # root directory. If this file is currently named config_template.py,
 # you can do this as follows:
 #
@@ -24,7 +24,7 @@
 # Contact email for users to use if the software encounters errors
 ADMIN_CONTACT_EMAIL = CHANGE_ME
 
-# Directories required by the dlwlrat server:
+# Directories required by the SciAnnotate server:
 #
 # BASE_DIR: directory in which the server is installed
 # DATA_DIR: directory containing texts and annotations

diff --git a/diff.xhtml b/diff.xhtml
@@ -7,7 +7,7 @@
 
 <html lang="en-US" xml:lang="en-US" xmlns="https://www.w3.org/1999/xhtml">
  <head>
- <title>dlwlrat</title>
+ <title>SciAnnotate</title>
  <meta http-equiv="Content-Type" content="application/xhtml+xml; charset=utf-8"/>
  <meta name="google" value="notranslate"/>
  <link href="static/jquery-theme/jquery-ui.css" rel="stylesheet" type="text/css"/>
@@ -139,7 +139,7 @@
  <p class="unselectable">Your browser has JavaScript
  disabled, or does not support it.</p>
  <p class="unselectable">
- <span class="logo">dlwlrat</span>
+ <span class="logo">SciAnnotate</span>
  needs JavaScript in order to run.
  </p>
  <p class="unselectable">Please enable JavaScript or try
@@ -160,7 +160,7 @@
  <div id="commentpopup"/>
  <div id="header" class="ui-widget">
  <div id="mainHeader" class="ui-widget-header">
- <div id="mainlogo" class="logo unselectable">dlwlrat</div>
+ <div id="mainlogo" class="logo unselectable">SciAnnotate</div>
  <span id="navbuttons">
  <img id="prev" alt="Previous document (Cursor Left)" title="Previous document (Cursor Left)" src="static/img/arrow-180.png"/><img id="next" alt="Next document (Cursor Right)" title="Next document (Cursor Right)" src="static/img/arrow.png"/>
  </span>
@@ -788,44 +788,44 @@
  <img src="static/img/spinner.gif"/>
  </div>
  <!-- "About" dialog -->
- <div id="about" class="dialog unselectable" title="About dlwlrat">
- <div id="aboutlogo" class="logo">dlwlrat</div>
+ <div id="about" class="dialog unselectable" title="About SciAnnotate">
+ <div id="aboutlogo" class="logo">SciAnnotate</div>
  <!--This software is distributed under the <a target="licence" href="https://www.opensource.org/licenses/isc-license">ISC Licence</a>.-->
- <div align="center">dlwlrat rapid annotation tool</div>
+ <div align="center">SciAnnotate rapid annotation tool</div>
  <div style="font-size:60%" align="center">v1.0 "Lame Pony"</div>
- <div id="copyright">&copy; 2020-2021 The dlwlrat contributors</div>
+ <div id="copyright">&copy; 2020-2021 The SciAnnotate contributors</div>
  </div>
  <!-- Welcome/tutorial dialog -->
  <div id="tutorial" class="dialog unselectable" title="Tutorial">
- <h2>Welcome to the dlwlrat annotation tool!</h2>
+ <h2>Welcome to the SciAnnotate annotation tool!</h2>
  <div id="browserwarning">
  <p>
  Please be aware that
- <span class="logo">dlwlrat</span>
+ <span class="logo">SciAnnotate</span>
  is currently only fully supported on
  <a href="https://www.google.com/chrome">Google Chrome</a>
  and
  <a href="https://www.apple.com/safari/">Safari</a>.
  In other browsers, it may exhibit various degrees of problems,
  from minor annoyances to severe ones that make
- <span class="logo">dlwlrat</span>
+ <span class="logo">SciAnnotate</span>
  unusable. For more information, see the page on
  <a href="https://brat.nlplab.org/supported-browsers.html" target="manual">browser support</a>.
  </p>
  <p>
- Please consider using <span class="logo">dlwlrat</span> in
+ Please consider using <span class="logo">SciAnnotate</span> in
  a fully supported browser for a better user experience.
  </p>
  </div>
  <p>Below is a mini-tutorial for basic usage. For detailed
  instructions, please see
- the <a href="https://brat.nlplab.org/manual.html" target="manual">dlwlrat
+ the <a href="https://brat.nlplab.org/manual.html" target="manual">SciAnnotate
  user manual</a>.</p>
  <h3>Selecting a document</h3>
  <p>After closing this tutorial, you will see the collection
  browser, which allows you to access the different text
  collections and individual documents in those collections on
- your dlwlrat installation. Simply double-click on a collection
+ your SciAnnotate installation. Simply double-click on a collection
  name to show its contents or on a document name to open it.
  </p>
  <p>You can later return to the collection browser by pressing the
@@ -873,7 +873,7 @@
  configuration of each collection.)
  </p>
  <h3>Advanced usage</h3>
- <p>Please see the <a href="https://brat.nlplab.org/manual.html">dlwlrat user
+ <p>Please see the <a href="https://brat.nlplab.org/manual.html">SciAnnotate user
  manual</a> for more!
  </p>
  </div>

diff --git a/dlwlrat.tar.gz b/dlwlrat.tar.gz
diff --git a/docker_install.sh b/docker_install.sh
@@ -67,7 +67,7 @@ else
  fi
  done
  echo "Please enter the administrator contact email:"
- admin_email="admin@dlwlrat.org"
+ admin_email="admin@SciAnnotate.org"
 fi
 
 # Put a configuration in place.

diff --git a/index.xhtml b/index.xhtml
@@ -5,7 +5,7 @@
 <html lang="en-US" xml:lang="en-US" xmlns="https://www.w3.org/1999/xhtml">
 
 <head>
- <title>dlwlrat</title>
+ <title>SciAnnotate</title>
  <meta http-equiv="Content-Type" content="application/xhtml+xml; charset=utf-8" />
  <meta http-equiv="Access-Control-Allow-Origin" content="*" />
  <meta name="google" value="notranslate" />
@@ -125,7 +125,7 @@
  <h1 class="unselectable">No JavaScript</h1>
  <p class="unselectable">Your browser has JavaScript disabled, or does not support it.</p>
  <p class="unselectable">
- <span class="logo">dlwlrat</span> needs JavaScript in order to run.
+ <span class="logo">SciAnnotate</span> needs JavaScript in order to run.
  </p>
  <p class="unselectable">Please enable JavaScript or try a <a
  href="https://brat.nlplab.org/supported-browsers.html">supported browser</a>
@@ -190,7 +190,7 @@
  <div id="commentpopup" />
  <div id="header" class="ui-widget">
  <div id="mainHeader" class="ui-widget-header">
- <div id="mainlogo" class="logo unselectable">dlwlrat</div>
+ <div id="mainlogo" class="logo unselectable">SciAnnotate</div>
  <span id="navbuttons">
  <img id="prev" alt="Previous document (Cursor Left)" title="Previous document (Cursor Left)"
  src="static/img/arrow-180.png" /><img id="next" alt="Next document (Cursor Right)"
@@ -1046,33 +1046,33 @@
  <img src="static/img/spinner.gif" />
  </div>
  <!-- "About" dialog -->
- <div id="about" class="dialog unselectable" title="About dlwlrat">
- <div id="aboutlogo" class="logo">dlwlrat</div>
+ <div id="about" class="dialog unselectable" title="About SciAnnotate">
+ <div id="aboutlogo" class="logo">SciAnnotate</div>
  <!--This software is distributed under the <a target="licence" href="https://www.opensource.org/licenses/isc-license">ISC Licence</a>.-->
- <div align="center">dlwlrat rapid annotation tool</div>
+ <div align="center">SciAnnotate rapid annotation tool</div>
  <div style="font-size:60%" align="center">v1.0 "Lame Pony"</div>
- <div id="copyright">&copy; 2020-2021 The dlwlrat contributors</div>
+ <div id="copyright">&copy; 2020-2021 The SciAnnotate contributors</div>
  </div>
  <!-- Welcome/tutorial dialog -->
  <div id="tutorial" class="dialog unselectable" title="Tutorial">
- <h2>Welcome to the dlwlrat annotation tool!</h2>
+ <h2>Welcome to the SciAnnotate annotation tool!</h2>
  <div id="browserwarning">
  <p>
  Please be aware that
- <span class="logo">dlwlrat</span> is currently only fully supported on
+ <span class="logo">SciAnnotate</span> is currently only fully supported on
  <a href="https://www.google.com/chrome">Google Chrome</a> and
  <a href="https://www.apple.com/safari/">Safari</a>. In other browsers, it may exhibit various degrees of problems, from minor annoyances to severe ones that make
- <span class="logo">dlwlrat</span> unusable. For more information, see the page on
+ <span class="logo">SciAnnotate</span> unusable. For more information, see the page on
  <a href="https://brat.nlplab.org/supported-browsers.html" target="manual">browser support</a>.
  </p>
  <p>
- Please consider using <span class="logo">dlwlrat</span> in a fully supported browser for a better user experience.
+ Please consider using <span class="logo">SciAnnotate</span> in a fully supported browser for a better user experience.
  </p>
  </div>
- <p>Below is a mini-tutorial for basic usage. For detailed instructions, please see the <a href="https://brat.nlplab.org/manual.html" target="manual">dlwlrat
+ <p>Below is a mini-tutorial for basic usage. For detailed instructions, please see the <a href="https://brat.nlplab.org/manual.html" target="manual">SciAnnotate
  user manual</a>.</p>
  <h3>Selecting a document</h3>
- <p>After closing this tutorial, you will see the collection browser, which allows you to access the different text collections and individual documents in those collections on your dlwlrat installation. Simply double-click on a collection name to show
+ <p>After closing this tutorial, you will see the collection browser, which allows you to access the different text collections and individual documents in those collections on your SciAnnotate installation. Simply double-click on a collection name to show
  its contents or on a document name to open it.
  </p>
  <p>You can later return to the collection browser by pressing the TAB key or by clicking on &quot;Collection&quot; in the menu.
@@ -1105,7 +1105,7 @@
  <p>(The available annotation types and other aspects depend on the configuration of each collection.)
  </p>
  <h3>Advanced usage</h3>
- <p>Please see the <a href="https://brat.nlplab.org/manual.html">dlwlrat user
+ <p>Please see the <a href="https://brat.nlplab.org/manual.html">SciAnnotate user
  manual</a> for more!
  </p>
  </div>

diff --git a/offline.xhtml b/offline.xhtml
@@ -85,11 +85,11 @@
  <div id="waiter" class="dialog" title="Please wait">
  <img src="static/img/spinner.gif"/>
  </div>
- <div id="about" class="dialog unselectable" title="About dlwlrat">
- <div id="aboutlogo" class="logo">dlwlrat</div>
+ <div id="about" class="dialog unselectable" title="About SciAnnotate">
+ <div id="aboutlogo" class="logo">SciAnnotate</div>
  <!--This software is distributed under the <a target="licence" href="https://www.opensource.org/licenses/isc-license">ISC Licence</a>.-->
- <div align="center">dlwlrat rapid annotation tool</div>
- <div id="copyright">&copy; 2020-2021 The dlwlrat contributors</div>
+ <div align="center">SciAnnotate rapid annotation tool</div>
+ <div id="copyright">&copy; 2020-2021 The SciAnnotate contributors</div>
  </div>
  </body>
 </html>
diff --git a/server/src/utils.py b/server/src/utils.py
@@ -217,7 +217,7 @@ def cache_model_results(**kwargs):
  real_dir = real_directory(collection)
  document = path_join(real_dir, document)
  model_results = json.loads(kwargs['data'])
- with open('/tmp/DLWLRAT-Model-{}.json'.format(get_md5_hash(document)), 'w') as f:
+ with open('/tmp/SciAnnotate-Model-{}.json'.format(get_md5_hash(document)), 'w') as f:
  json.dump(model_results, f)
 
  model_resutls_entities = model_results['entities']
@@ -239,7 +239,7 @@ def get_cached_model_results(**kwargs):
  real_dir = real_directory(collection)
  document = path_join(real_dir, document)
  cached_model_results = None
- with open('/tmp/DLWLRAT-Model-{}.json'.format(get_md5_hash(document)), 'w') as f:
+ with open('/tmp/SciAnnotate-Model-{}.json'.format(get_md5_hash(document)), 'w') as f:
  cached_model_results = json.load(f)
  res['data'] = cached_model_results
  return res

diff --git a/static/style-ui.css b/static/style-ui.css
@@ -317,7 +317,7 @@ div.scroll_wrapper_upper div.scroller {
  margin-right: 100px;
 }
 #document_name input {
- width: 95%;
+ width: 90%;
  border: none;
  font-family: 'denmark'
 }

diff --git a/tools/servlet/README.md b/tools/servlet/README.md
@@ -1,30 +1,30 @@
-# dlwlrat servlet #
+# SciAnnotate servlet #
 
-This is a full-fledged dlwlrat CGI servlet to deploy dlwlrat on Tomcat. While this
+This is a full-fledged SciAnnotate CGI servlet to deploy SciAnnotate on Tomcat. While this
 is a bit of an exotic usecase, it is an existing one and this README along
 with the XML provided should keep you from crying your eyes out while solving
 this exercise.
 
 # Building #
 
 First, some words on how this works. You will attempt to create a WAR (Web
-application ARchive) containing a working dlwlrat installation. This means you
-will first have to install dlwlrat as usual and deploy your data. Create the dlwlrat
-folder structure as shown (`dlwlrat/WEB-INF`, `dlwlrat/META-INF`) with the given
-`web.xml` and `context.xml`. Copy your previously installed dlwlrat installation
-to `dlwlrat/`, then, proving that you don't need ant to build something Java-ish,
-simply go to the parent folder of `dlwlrat`, where the `GNUmakefile` is, and run:
+application ARchive) containing a working SciAnnotate installation. This means you
+will first have to install SciAnnotate as usual and deploy your data. Create the SciAnnotate
+folder structure as shown (`SciAnnotate/WEB-INF`, `SciAnnotate/META-INF`) with the given
+`web.xml` and `context.xml`. Copy your previously installed SciAnnotate installation
+to `SciAnnotate/`, then, proving that you don't need ant to build something Java-ish,
+simply go to the parent folder of `SciAnnotate`, where the `GNUmakefile` is, and run:
 
  make
 
-This will produce an archive `dlwlrat.war` that you can deploy on Tomcat.
+This will produce an archive `SciAnnotate.war` that you can deploy on Tomcat.
 
 # Installation #
 
-Drop the `dlwlrat.war` into the Tomcat `webapps` directory and you should be able
+Drop the `SciAnnotate.war` into the Tomcat `webapps` directory and you should be able
 to access your installation using:
 
- https://${HOSTNAME}:${PORT}/dlwlrat/
+ https://${HOSTNAME}:${PORT}/SciAnnotate/
 
-From now on, dlwlrat should work as usual with the exception that it is Tomcat
+From now on, SciAnnotate should work as usual with the exception that it is Tomcat
 serving your requests.