Install packages using environment.yml

Former-commit-id: 76231559

AngularApp/prototype/src/app/cache.service.ts

@@ -18,7 +18,7 @@ export class CacheService {
   private _queryWindow;
 
   public windowSize = 120;
-  public nrOfTables = 50;
+  public nrOfTables = 20;
   public hashSize = 4;
   public stepSize = 200;
   public querySelectionMode = true;

AngularApp/prototype/src/app/table-overview/table-overview.component.ts

@@ -105,17 +105,17 @@ export class TableOverviewComponent implements OnInit {
         return this.distanceMetric(hash1) - this.distanceMetric(hash2);
       });
       if (this.service.queryWindow) {
-        const queryEntry = this.calculateSignature(table.hash, this.service.queryWindow);
-        listOfWindows.push(table.entries[queryEntry]);
-        opacity = orderedHashes.map((hash: string) => {
-            return hash === queryEntry ? 1.0 : 0.5;
-          }
-        );
-        rank = table.entries[queryEntry].length;
+        // const queryEntry = this.calculateSignature(table.hash, this.service.queryWindow);
+        // listOfWindows.push(table.entries[queryEntry]);
+        // opacity = orderedHashes.map((hash: string) => {
+        //     return hash === queryEntry ? 1.0 : 0.5;
+        //   }
+        // );
+        // rank = table.entries[queryEntry].length;
       }
       this.subplots.push(
         {
-          rank: rank,
+          // rank: rank,
           data: [{
             x: orderedHashes.map((hash: string, i) => {
               return i; // Number('0b' + hash);
@@ -149,7 +149,7 @@ export class TableOverviewComponent implements OnInit {
         }
       );
     }
-    this.subplots.sort((plot1, plot2) => plot1.rank - plot2.rank);
+    // this.subplots.sort((plot1, plot2) => plot1.rank - plot2.rank);
     if (this.service.queryWindow) {
       const temp = await this.service.getAverageTableWindows(listOfWindows);
       this.averages = temp.map(x => this.averagePlot(x));

Flaskserver/.idea/workspace.xml

@@ -21,12 +21,8 @@
   <component name="ChangeListManager">
     <list default="true" id="556080ba-825c-4b55-a92a-867a4df4fb32" name="Default Changelist" comment="">
       <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/cache.service.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/cache.service.ts" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/progress-view/progress-view.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/progress-view/progress-view.component.ts" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/main.py" beforeDir="false" afterPath="$PROJECT_DIR$/main.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/processed-data.npy" beforeDir="false" afterPath="$PROJECT_DIR$/processed-data.npy" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />

Flaskserver/main.py

@@ -40,14 +40,13 @@ def read_data():
 def create_windows():
     t0 = time()
     if reload:
-        size = bbi.chromsizes('test.bigWig')['chr1']
         raw_data = request.json
         window_size = int(raw_data['parameters']["windowsize"])
         data = bigwig.chunk(
             'test.bigWig',
             12000,
-            12000 / window_size,
-            12000 / 6,
+            int(12000 / window_size),
+            int(12000 / 6),
             ['chr1'],
             verbose=True,
         )
@@ -59,16 +58,12 @@ def create_windows():
 @app.route('/create-tables', methods=['POST'])
 def create_tables():
     t0 = time()
-    print("loading")
     data = np.load('processed-data.npy')
-    print('Number of tables: ' + str(data.shape))
-    print(time()-t0)
     raw_data = orjson.loads(request.data)
-    print(time()-t0)
     window_size = int(raw_data['parameters']["windowsize"])
     hash_size = int(raw_data['parameters']["hashsize"])
     table_size = int(raw_data['parameters']["tablesize"])
-    data = np.array(data)
+
     print('Starting: ' + str(time()-t0))
     tables_hash_function = [np.random.uniform(-100, 100, size=(window_size, hash_size)) for _ in range(table_size)]
     print('Init time: ' + str(time() - t0))

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/INSTALLER

-pip

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/LICENSE.rst

-Copyright 2010 Pallets
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-1.  Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-2.  Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
-
-3.  Neither the name of the copyright holder nor the names of its
-    contributors may be used to endorse or promote products derived from
-    this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/METADATA

-Metadata-Version: 2.1
-Name: Flask
-Version: 1.1.2
-Summary: A simple framework for building complex web applications.
-Home-page: https://palletsprojects.com/p/flask/
-Author: Armin Ronacher
-Author-email: armin.ronacher@active-4.com
-Maintainer: Pallets
-Maintainer-email: contact@palletsprojects.com
-License: BSD-3-Clause
-Project-URL: Documentation, https://flask.palletsprojects.com/
-Project-URL: Code, https://github.com/pallets/flask
-Project-URL: Issue tracker, https://github.com/pallets/flask/issues
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Web Environment
-Classifier: Framework :: Flask
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
-Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
-Classifier: Topic :: Internet :: WWW/HTTP :: WSGI :: Application
-Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*
-Requires-Dist: Werkzeug (>=0.15)
-Requires-Dist: Jinja2 (>=2.10.1)
-Requires-Dist: itsdangerous (>=0.24)
-Requires-Dist: click (>=5.1)
-Provides-Extra: dev
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: coverage ; extra == 'dev'
-Requires-Dist: tox ; extra == 'dev'
-Requires-Dist: sphinx ; extra == 'dev'
-Requires-Dist: pallets-sphinx-themes ; extra == 'dev'
-Requires-Dist: sphinxcontrib-log-cabinet ; extra == 'dev'
-Requires-Dist: sphinx-issues ; extra == 'dev'
-Provides-Extra: docs
-Requires-Dist: sphinx ; extra == 'docs'
-Requires-Dist: pallets-sphinx-themes ; extra == 'docs'
-Requires-Dist: sphinxcontrib-log-cabinet ; extra == 'docs'
-Requires-Dist: sphinx-issues ; extra == 'docs'
-Provides-Extra: dotenv
-Requires-Dist: python-dotenv ; extra == 'dotenv'
-
-Flask
-=====
-
-Flask is a lightweight `WSGI`_ web application framework. It is designed
-to make getting started quick and easy, with the ability to scale up to
-complex applications. It began as a simple wrapper around `Werkzeug`_
-and `Jinja`_ and has become one of the most popular Python web
-application frameworks.
-
-Flask offers suggestions, but doesn't enforce any dependencies or
-project layout. It is up to the developer to choose the tools and
-libraries they want to use. There are many extensions provided by the
-community that make adding new functionality easy.
-
-
-Installing
-----------
-
-Install and update using `pip`_:
-
-.. code-block:: text
-
-    pip install -U Flask
-
-
-A Simple Example
-----------------
-
-.. code-block:: python
-
-    from flask import Flask
-
-    app = Flask(__name__)
-
-    @app.route("/")
-    def hello():
-        return "Hello, World!"
-
-.. code-block:: text
-
-    $ env FLASK_APP=hello.py flask run
-     * Serving Flask app "hello"
-     * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
-
-
-Contributing
-------------
-
-For guidance on setting up a development environment and how to make a
-contribution to Flask, see the `contributing guidelines`_.
-
-.. _contributing guidelines: https://github.com/pallets/flask/blob/master/CONTRIBUTING.rst
-
-
-Donate
-------
-
-The Pallets organization develops and supports Flask and the libraries
-it uses. In order to grow the community of contributors and users, and
-allow the maintainers to devote more time to the projects, `please
-donate today`_.
-
-.. _please donate today: https://psfmember.org/civicrm/contribute/transact?reset=1&id=20
-
-
-Links
------
-
-* Website: https://palletsprojects.com/p/flask/
-* Documentation: https://flask.palletsprojects.com/
-* Releases: https://pypi.org/project/Flask/
-* Code: https://github.com/pallets/flask
-* Issue tracker: https://github.com/pallets/flask/issues
-* Test status: https://dev.azure.com/pallets/flask/_build
-* Official chat: https://discord.gg/t6rrQZH
-
-.. _WSGI: https://wsgi.readthedocs.io
-.. _Werkzeug: https://www.palletsprojects.com/p/werkzeug/
-.. _Jinja: https://www.palletsprojects.com/p/jinja/
-.. _pip: https://pip.pypa.io/en/stable/quickstart/
-
-

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/RECORD

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Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/WHEEL

-Wheel-Version: 1.0
-Generator: bdist_wheel (0.33.6)
-Root-Is-Purelib: true
-Tag: py2-none-any
-Tag: py3-none-any
-

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/entry_points.txt

-[console_scripts]
-flask = flask.cli:main
-

Flaskserver/venv/Lib/site-packages/Flask-1.1.2.dist-info/top_level.txt

-flask

Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/INSTALLER

-pip

Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/LICENSE.rst

-Copyright 2007 Pallets
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-1.  Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-2.  Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
-
-3.  Neither the name of the copyright holder nor the names of its
-    contributors may be used to endorse or promote products derived from
-    this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/METADATA

-Metadata-Version: 2.1
-Name: Jinja2
-Version: 2.11.2
-Summary: A very fast and expressive template engine.
-Home-page: https://palletsprojects.com/p/jinja/
-Author: Armin Ronacher
-Author-email: armin.ronacher@active-4.com
-Maintainer: Pallets
-Maintainer-email: contact@palletsprojects.com
-License: BSD-3-Clause
-Project-URL: Documentation, https://jinja.palletsprojects.com/
-Project-URL: Code, https://github.com/pallets/jinja
-Project-URL: Issue tracker, https://github.com/pallets/jinja/issues
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Web Environment
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
-Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Topic :: Text Processing :: Markup :: HTML
-Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*
-Description-Content-Type: text/x-rst
-Requires-Dist: MarkupSafe (>=0.23)
-Provides-Extra: i18n
-Requires-Dist: Babel (>=0.8) ; extra == 'i18n'
-
-Jinja
-=====
-
-Jinja is a fast, expressive, extensible templating engine. Special
-placeholders in the template allow writing code similar to Python
-syntax. Then the template is passed data to render the final document.
-
-It includes:
-
--   Template inheritance and inclusion.
--   Define and import macros within templates.
--   HTML templates can use autoescaping to prevent XSS from untrusted
-    user input.
--   A sandboxed environment can safely render untrusted templates.
--   AsyncIO support for generating templates and calling async
-    functions.
--   I18N support with Babel.
--   Templates are compiled to optimized Python code just-in-time and
-    cached, or can be compiled ahead-of-time.
--   Exceptions point to the correct line in templates to make debugging
-    easier.
--   Extensible filters, tests, functions, and even syntax.
-
-Jinja's philosophy is that while application logic belongs in Python if
-possible, it shouldn't make the template designer's job difficult by
-restricting functionality too much.
-
-
-Installing
-----------
-
-Install and update using `pip`_:
-
-.. code-block:: text
-
-    $ pip install -U Jinja2
-
-.. _pip: https://pip.pypa.io/en/stable/quickstart/
-
-
-In A Nutshell
--------------
-
-.. code-block:: jinja
-
-    {% extends "base.html" %}
-    {% block title %}Members{% endblock %}
-    {% block content %}
-      <ul>
-      {% for user in users %}
-        <li><a href="{{ user.url }}">{{ user.username }}</a></li>
-      {% endfor %}
-      </ul>
-    {% endblock %}
-
-
-Links
------
-
--   Website: https://palletsprojects.com/p/jinja/
--   Documentation: https://jinja.palletsprojects.com/
--   Releases: https://pypi.org/project/Jinja2/
--   Code: https://github.com/pallets/jinja
--   Issue tracker: https://github.com/pallets/jinja/issues
--   Test status: https://dev.azure.com/pallets/jinja/_build
--   Official chat: https://discord.gg/t6rrQZH
-
-

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Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/WHEEL

-Wheel-Version: 1.0
-Generator: bdist_wheel (0.34.2)
-Root-Is-Purelib: true
-Tag: py2-none-any
-Tag: py3-none-any
-

Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/entry_points.txt

-[babel.extractors]
-jinja2 = jinja2.ext:babel_extract [i18n]
-

Flaskserver/venv/Lib/site-packages/Jinja2-2.11.2.dist-info/top_level.txt

-jinja2

Flaskserver/venv/Lib/site-packages/MarkupSafe-1.1.1.dist-info/INSTALLER

-pip

Flaskserver/venv/Lib/site-packages/MarkupSafe-1.1.1.dist-info/LICENSE.rst

-Copyright 2010 Pallets
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-1.  Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-2.  Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
-
-3.  Neither the name of the copyright holder nor the names of its
-    contributors may be used to endorse or promote products derived from
-    this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT