Integrate Heng's provenance vis to ReproUnzip 🎉

reprounzip-qt/reprounzip_qt/gui/unpack.py

@@ -259,6 +259,9 @@ def __init__(self, package='', **kwargs):
 
         buttons = QtGui.QHBoxLayout()
         buttons.addStretch(1)
+        vis = QtGui.QPushButton("Show provenance")
+        vis.clicked.connect(self._show_vis)
+        buttons.addWidget(vis)
         self.unpack_widget = QtGui.QPushButton("Unpack experiment",
                                                enabled=False)
         self.unpack_widget.clicked.connect(self._unpack)
@@ -318,3 +321,6 @@ def _unpack(self):
                                    options.get('root'))
         else:
             error_msg(self, "No unpacker selected", 'warning')
+
+    def _show_vis(self):
+        handle_error(self, reprounzip.show_vis(self.package_widget.text()))

reprounzip-qt/reprounzip_qt/reprounzip_interface.py

@@ -301,6 +301,17 @@ def download(directory, name, path, unpacker=None, root=None):
         return code == 0
 
 
+def show_vis(package):
+    reprounzip = find_command('reprounzip')
+    if reprounzip is None:
+        return ("Couldn't find reprounzip command -- is reprounzip installed?",
+                'critical')
+
+    run_in_builtin_terminal([reprounzip, 'vis', package], {},
+                            text="Running provenance visualization")
+    return True
+
+
 def run_in_builtin_terminal_maybe(cmd, root, env={}, **kwargs):
     if root is None:
         code = run_in_builtin_terminal(cmd, env, **kwargs)

reprounzip-vis/LICENSE.txt

@@ -0,0 +1,27 @@
+Copyright (C) 2014-2017, New York University
+All rights reserved.
+
+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.

reprounzip-vis/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.rst
+include LICENSE.txt

reprounzip-vis/README.rst

@@ -0,0 +1,26 @@
+ReproZip
+========
+
+`ReproZip <https://www.reprozip.org/>`__ is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science. It tracks operating system calls and creates a package that contains all the binaries, files and dependencies required to run a given command on the author's computational environment (packing step).  A reviewer can then extract the experiment in his environment to reproduce the results (unpacking step).
+
+reprounzip
+----------
+
+This is the component responsible for the unpacking step on Linux distributions.
+
+Please refer to `reprozip <https://pypi.python.org/pypi/reprozip>`__, `reprounzip-vagrant <https://pypi.python.org/pypi/reprounzip-vagrant>`_, and `reprounzip-docker <https://pypi.python.org/pypi/reprounzip-docker>`_ for other components and plugins.
+
+A GUI is available at `reprounzip-qt <https://pypi.python.org/pypi/reprounzip-qt>`_.
+
+Additional Information
+----------------------
+
+For more detailed information, please refer to our `website <https://www.reprozip.org/>`_, as well as to our `documentation <https://reprozip.readthedocs.io/>`_.
+
+ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. The team includes:
+
+* `Fernando Chirigati <https://vgc.poly.edu/~fchirigati/>`_
+* `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
+* `Remi Rampin <https://remirampin.com/>`_
+* `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
+* `Vicky Steeves <https://vickysteeves.com/>`_

reprounzip-vis/reprounzip_vis/__init__.py

@@ -0,0 +1,88 @@
+import argparse
+import BaseHTTPServer
+import SocketServer
+import mimetypes
+import os
+import pkg_resources
+from rpaths import Path
+import shutil
+import tempfile
+import webbrowser
+
+from reprounzip.common import RPZPack
+from reprounzip.unpackers.common import COMPAT_OK
+from reprounzip.unpackers.graph import generate
+
+__version__ = '0.1'
+
+
+class VisHTTPHandler(BaseHTTPServer.BaseHTTPRequestHandler):
+    server_version = 'ReproUnzip/' + __version__
+
+    def do_GET(self):
+        print("Serving %s" % self.path)
+        if self.path == '/provenance.json':
+            self.send_response(200)
+            self.send_header('Content-Type', 'application/json')
+            self.end_headers()
+            with open(self.provenance_json, 'rb') as f:
+                shutil.copyfileobj(f, self.wfile)
+        else:
+            try:
+                f = pkg_resources.resource_stream('reprounzip_vis',
+                                                  'static/' + self.path)
+            except IOError:
+                self.send_response(404)
+            else:
+                self.send_response(200)
+                if self.path == '/':
+                    ctype = 'text/html'
+                else:
+                    ctype = mimetypes.guess_type(self.path)[0]
+                self.send_header('Content-Type', ctype)
+                self.end_headers()
+                shutil.copyfileobj(f, self.wfile)
+                f.close()
+
+
+def show_vis(args):
+    # Extract JSON from package
+    fd, json_file = tempfile.mkstemp(prefix='reprounzip_vis_', suffix='.json')
+    try:
+        rpz_pack = RPZPack(args.pack)
+        with rpz_pack.with_config() as config:
+            with rpz_pack.with_trace() as trace:
+                generate(Path(json_file), config, trace, graph_format='json')
+        os.close(fd)
+
+        VisHTTPHandler.provenance_json = json_file
+
+        # Serve static files and JSON document to browser
+        port = 8002
+
+        httpd = SocketServer.TCPServer(('', port), VisHTTPHandler)
+        print("serving at port %d" % port)
+
+        # Open web browser
+        webbrowser.open('http://localhost:%d/index.html' % port)
+
+        # Serve until killed
+        try:
+            httpd.serve_forever()
+        except KeyboardInterrupt:
+            pass
+        finally:
+            httpd.server_close()
+    finally:
+        os.remove(json_file)
+
+
+def setup_vis(parser, **kwargs):
+    """Visualizes the provenance of a package as a D3 graph in the browser.
+    """
+    parser.add_argument(
+        'pack', nargs=argparse.OPTIONAL,
+        help="Pack to visualize")
+    parser.set_defaults(func=show_vis)
+
+    return {'test_compatibility': COMPAT_OK}