Merge branch 'multi_platform_imp_runserver' into dev

.gitignore

@@ -7,5 +7,5 @@ venv/
 arborist-settings.json
 *.pyc
 dist/
-*.egg-info/
+*.egg*
 build/

arborist/__init__.py

@@ -1,10 +1,12 @@
 
 import os
+import sys
 from collections import OrderedDict
 
 from flask import Flask, flash, request, redirect, url_for, render_template, \
                   json, Response, send_from_directory
 from werkzeug import secure_filename
+from werkzeug.routing import BaseConverter, ValidationError
 
 import urllib
 from markupsafe import Markup
@@ -20,14 +22,57 @@
 STUDIES_FOLDER = 'studies'
 ALLOWED_EXTENSIONS = set(['txt', 'tsv'])
 
-app = Flask(__name__)
+path = os.path.dirname(os.path.realpath(__file__))
+# See if the application is run from windows executable.
+if path.find('library.zip') >= 0:
+    pos = path.find('library.zip')
+    path = path[:pos]
+    app = Flask(__name__,
+                static_folder=path+'static',
+                template_folder=path+'templates')
+
+# See if the application is run from inside a .app (MacOSX)
+elif path.find('.app/Contents/Resources/') >= 0:
+    pos = path.rfind('lib/')
+    path = path[:pos]
+    app = Flask(__name__,
+                static_folder=path + 'static',
+                template_folder=path + 'templates')
+else:
+    app = Flask(__name__)
+
 app.secret_key = 'not_so_secret'
 
 app.jinja_env.add_extension("jinja2.ext.do")
 app.jinja_env.trim_blocks = True
 app.jinja_env.lstrip_blocks = True
 app.jinja_env.filters['path_join'] = lambda paths: os.path.join(*paths)
 
+
+def add_slash_if_not_windows(url_path):
+    if sys.platform != 'win32':
+        url_path = '/' + url_path
+        print "not windows: "+url_path
+    else:
+        print "windows: "+url_path
+    return url_path
+
+
+class FolderPathConverter(BaseConverter):
+    def __init__(self, url_map):
+        print "init!"
+        super(FolderPathConverter, self).__init__(url_map)
+        self.regex = '.*'
+
+    def to_python(self, value):
+        print "FolderPathConverter: "+value
+        return add_slash_if_not_windows(value)
+
+    def to_url(self, value):
+        return value
+
+app.url_map.converters['folderpath'] = FolderPathConverter
+
 if not os.path.isdir(STUDIES_FOLDER):
     os.mkdir(STUDIES_FOLDER)
 
@@ -57,9 +102,8 @@ def index():
 
 
 @app.route('/folder/create/', defaults={'studiesfolder': ''}, methods=['POST'])
-@app.route('/folder/<path:studiesfolder>/create/', methods=['POST'])
+@app.route('/folder/<folderpath:studiesfolder>/create/', methods=['POST'])
 def create_folder(studiesfolder):
-    studiesfolder = '/'+studiesfolder
     if 'foldername' in request.form:
         foldername = os.path.join(studiesfolder,
                                   request.form['foldername'])
@@ -72,9 +116,8 @@ def create_folder(studiesfolder):
 
 
 @app.route('/folder/', defaults={'studiesfolder': ''})
-@app.route('/folder/<path:studiesfolder>/')
+@app.route('/folder/<folderpath:studiesfolder>/')
 def studies_overview(studiesfolder):
-    studiesfolder = '/'+studiesfolder
     parentfolder = os.path.abspath(os.path.join(studiesfolder, os.pardir))
     studies = {}
 
@@ -98,10 +141,8 @@ def studies_overview(studiesfolder):
 
 
 @app.route('/folder/s/<study>/', defaults={'studiesfolder': ''})
-@app.route('/folder/<path:studiesfolder>/s/<study>/')
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/')
 def study_page(studiesfolder, study):
-    studiesfolder = '/'+studiesfolder
-
     paramsdict = {}
 
     for datatype in possible_datatypes:
@@ -148,9 +189,8 @@ def study_page(studiesfolder, study):
                            possible_datatypes=possible_datatypes)
 
 
-@app.route(('/folder/<path:studiesfolder>/s/<study>/clinical/create/'))
+@app.route(('/folder/<folderpath:studiesfolder>/s/<study>/clinical/create/'))
 def create_mapping_file(studiesfolder, study):
-    studiesfolder = '/'+studiesfolder
     columnmappingfile = 'COLUMN_MAP_FILE'
     wordmappingfile = 'WORD_MAP_FILE'
 
@@ -179,9 +219,8 @@ def create_mapping_file(studiesfolder, study):
     return json.jsonify(mappingfilename=mappingfilename)
 
 
-@app.route('/folder/<path:studiesfolder>/s/<study>/params/<datatype>/create/')
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/params/<datatype>/create/')
 def create_params(studiesfolder, study, datatype):
-    studiesfolder = '/'+studiesfolder
     feedback = get_feedback_dict()
     paramsfile = os.path.join(studiesfolder, study, datatype+'.params')
 
@@ -201,10 +240,9 @@ def create_params(studiesfolder, study, datatype):
                             datatype=datatype))
 
 
-@app.route('/folder/<path:studiesfolder>/s/<study>/params/<datatype>/',
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/params/<datatype>/',
            methods=['GET', 'POST'])
 def edit_params(studiesfolder, study, datatype):
-    studiesfolder = '/'+studiesfolder
     feedback = get_feedback_dict()
     paramsfile = os.path.join(studiesfolder, study, datatype+'.params')
 
@@ -275,11 +313,8 @@ def edit_params(studiesfolder, study, datatype):
                            feedback=feedback)
 
 
-@app.route('/folder/<path:studiesfolder>/s/<study>/tree/')
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/tree/')
 def edit_tree(studiesfolder, study):
-    studiesfolder = '/'+studiesfolder
-
-    # Get column mapping file and paths in there
     columnsfile = get_column_map_file(studiesfolder, study)
     if columnsfile is not None:
         tree_array = columns_to_tree(columnsfile)
@@ -306,10 +341,9 @@ def edit_tree(studiesfolder, study):
                            json=treejson)
 
 
-@app.route('/folder/<path:studiesfolder>/s/<study>/tree/add/',
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/tree/add/',
            methods=['POST'])
 def add_datafile(studiesfolder, study):
-    studiesfolder = '/'+studiesfolder
     file = request.files['file']
 
     if file and allowed_file(file.filename):
@@ -336,10 +370,9 @@ def add_datafile(studiesfolder, study):
                             study=study))
 
 
-@app.route('/folder/<path:studiesfolder>/s/<study>/tree/save_columnsfile/',
+@app.route('/folder/<folderpath:studiesfolder>/s/<study>/tree/save_columnsfile/',
            methods=['POST'])
 def save_columnsfile(studiesfolder, study):
-    studiesfolder = '/'+studiesfolder
     feedback = get_feedback_dict()
 
     tree = request.get_json()

runserver.py

@@ -1,9 +1,31 @@
 #!/usr/bin/env python
 from arborist import app
+import socket
 import argparse
+import webbrowser
 
 parser = argparse.ArgumentParser(description='Launch the Arborist')
 parser.add_argument('--debug', action="store_true", default=False, help="Run in debug mode")
+parser.add_argument('--port', type=int,
+                    help="Set port to try to listen to. By default the OS is asked what port to use.")
 args = parser.parse_args()
 
-app.run(debug=args.debug)
+
+def get_open_port():
+    s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    s.bind(('', 0))
+    s.listen(1)
+    port = s.getsockname()[1]
+    s.close()
+    return port
+
+if not args.port:
+    port = get_open_port()
+else:
+    port = args.port
+
+if not args.debug:
+    running_on = 'http://localhost:{}'.format(port)
+    webbrowser.open(running_on, new=0, autoraise=True)
+
+app.run(debug=args.debug, port=port)

setup.py

@@ -1,16 +1,141 @@
+"""
+Setuptools and py2app/py2exe build script for transmart-arborist.
+
+To install dependencies for your machine:
+    Usage:
+        python setup.py install
+
+To build a packaged executable:
+    Usage (Mac OS X):
+        python setup.py py2app
+
+        Usage (Windows):
+        python setup.py py2exe
+"""
+
+import sys
+import os
+import glob
 from setuptools import setup, find_packages
 
+mainscript = 'runserver.py'
+extra_options = {}
+# Which directories to take all normal files from, these have to be specified explicitely.
+patterns = [
+          'static/*',
+          'templates/*',
+          'static/img/*',
+          'static/img/message/*',
+          'static/img/tree/*',
+          'static/jstree/*',
+          'static/jstree/dist/*',
+          'static/jstree/dist/themes/*',
+          'static/jstree/dist/themes/default/*',
+          'static/jstree/dist/themes/default-dark/*',
+           ]
+
+
+def find_data_files(source, target, patterns):
+    """Locates the specified data-files and returns the matches
+    in a data_files compatible format.
+
+    source is the root of the source data tree.
+        Use '' or '.' for current directory.
+    target is the root of the target data tree.
+        Use '' or '.' for the distribution directory.
+    patterns is a sequence of glob-patterns for the
+        files you want to copy.
+    """
+    if glob.has_magic(source) or glob.has_magic(target):
+        raise ValueError("Magic not allowed in src, target")
+    ret = {}
+    for pattern in patterns:
+        pattern = os.path.join(source, pattern)
+        for filename in glob.glob(pattern):
+            if os.path.isfile(filename):
+                targetpath = os.path.join(target, os.path.relpath(filename, source))
+                path = os.path.dirname(targetpath)
+                ret.setdefault(path, []).append(filename)
+    return sorted(ret.items())
+
+
+def osx_app_build_options():
+    """
+    Collects additional requirements for building a MacOSX packaged executable. Only works on
+    OS X and must have py2app manually installed.
+    """
+    data_files = find_data_files(source=os.getcwd() + '/arborist',
+                                 target='',
+                                 patterns=patterns)
+    py2app_options = {'argv_emulation': True,
+                      'packages': ['jinja2',
+                                   'flask',
+                                   'email',
+                                   ],
+                      'includes': ['os',
+                                   'flask',
+                                   'sys',
+                                   ],
+                      'excludes': ['mime'],
+                      }
+
+    extra_options = dict(setup_requires=['py2app'],
+                         app=[mainscript],
+                         options={'py2app': py2app_options},
+                         data_files=data_files,
+                         )
+    return extra_options
+
+
+def win32_exe_build_options():
+    """
+    This collects additional requirements for building a Windows executable.
+    only works when running from Windows and having manually
+    installed the py2exe package.
+    """
+    import py2exe
+    data_files = find_data_files(source=os.getcwd() + r'/arborist',
+                                 target='',
+                                 patterns=patterns)
+    py2exe_options = {'packages': ['werkzeug',
+                                   'email.mime',
+                                   'jinja2',
+                                   ],
+                      'includes': ['os',
+                                   'flask',
+                                   'sys',
+                                   'jinja2.ext',
+                                   ],
+                      }
+
+    extra_options = dict(setup_requires=['py2exe'],
+                         console=[mainscript],
+                         options={'py2exe': py2exe_options},
+                         data_files=data_files,
+                         )
+    return extra_options
+
+
+if sys.platform == 'darwin' and 'py2app' in sys.argv:
+    extra_options = osx_app_build_options()
+
+
+elif sys.platform == 'win32' and 'py2exe' in sys.argv:
+    extra_options = win32_exe_build_options()
+
+
 setup(
     name='tranSMART Arborist',
     version='1.3',
     description='Graphical tool to help you prepare your data for loading into the tranSMART data warehouse',
     url='https://github.com/thehyve/transmart-arborist',
-    author='Ward Weistra',
+    author='Ward Weistra and Jochem Bijlard',
     author_email='[email protected]',
     license='GNU General Public License V3',
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,
     install_requires=['Flask'],
-    scripts=['runserver.py']
+    scripts=[mainscript],
+    **extra_options
 )