add application class

bin/jflow_application.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import cherrypy
+import cgi
+import tempfile
+import json
+import sys
+import datetime
+from functools import wraps
+import time
+import os
+import argparse
+
+try:
+    import _preamble
+except ImportError:
+    sys.exc_clear()
+
+from jflowapp.server import ApplicationServer
+
+
+WEB_DIR = os.path.abspath(os.path.join(__file__, "../../docs"))
+
+class MyJflowApp( ApplicationServer ):
+    
+    pass
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--daemon", action="store_true", dest="daemon", default=False, help="Run the server as daemon")
+    args = vars(parser.parse_args())
+
+    app_conf = {
+        '/': 
+            {'tools.staticdir.root': WEB_DIR, 'tools.CORS.on': True},
+        os.path.join('/', 'css'): 
+            {'tools.staticdir.on'  : True, 'tools.staticdir.dir' : './css/'},
+        os.path.join('/', 'js'): 
+            {'tools.staticdir.on'  : True, 'tools.staticdir.dir' : './js/'},
+        os.path.join('/', 'img'): 
+            {'tools.staticdir.on'  : True, 'tools.staticdir.dir' : './img/'},
+        os.path.join('/', 'fonts'): 
+            {'tools.staticdir.on'  : True, 'tools.staticdir.dir' : './fonts/'},
+        os.path.join('/', 'app'): 
+            {'tools.staticdir.on'  : True, 'tools.staticdir.dir' : './'}
+    }
+    
+    ApplicationServer.quickstart(MyJflowApp, app_conf, daemon=args["daemon"])
+    
\ No newline at end of file

src/jflowapp/__init__.py

+#
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
\ No newline at end of file

src/jflowapp/application.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+import pickle
+
+from jflow.workflow import Workflow
+
+ 
+class Result (object):
+     
+    def __init__(self, name, type):
+        self.name = name
+        self.type = type
+        self.content = None
+     
+    def serialize(self, output):
+        dumpfh = open(os.path.join(output, "toto.dump"), "wb")
+        pickle.dump(self, dumpfh)
+        dumpfh.close()
+
+
+class Application (Workflow):
+    
+    def __init__(self, args={}, id=None, function= "process"):
+        Workflow.__init__(self, args, id, function)
+        self.__results = {}
+    
+    def add_result_table(self, name, content):
+        self.__results[name] = Result(name, "table")
+        self.__results[name].content = content
+        
+    def post_process(self):
+        self.define_results()
+        for result in self.__results:
+            self.__results[result].serialize(self.directory)
+            
+            
+            
+            
+            
\ No newline at end of file

src/jflowapp/applications_manager.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import pkgutil
+import workflows
+import inspect
+import jflowapp
+import sys
+
+from jflowapp.application import Application
+from jflow.workflows_manager import WorkflowsManager
+
+
+class ApplicationsManager(WorkflowsManager):
+
+    def __init__(self):
+        WorkflowsManager.__init__(self)
+
+    def get_available_applications(self, function="process", filter_groups = [], select = False ):
+        if function.__class__.__name__ == "str":
+            functions = [function]
+        else:
+            functions = set(function)
+        wf_instances, wf_methodes = [], []
+        
+        if isinstance(filter_groups, str): filter_groups = [filter_groups]
+        
+        # Load all modules within the workflow module
+        for importer, modname, ispkg in pkgutil.iter_modules(workflows.__path__, workflows.__name__ + "."):
+            __import__(modname)
+            # Search for Workflow classes
+            for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
+                if issubclass(obj, jflowapp.application.Application) and obj.__name__ != jflowapp.application.Application.__name__:
+                    for function in functions:
+                        # check if the application has the requested methode
+                        # inspect.ismethod has been changed for inspect.isfunction in Python3
+                        for ifunction in inspect.getmembers(obj, predicate=inspect.isfunction):    
+                            if ifunction[0] == function:
+                                # try to build the application
+                                try: 
+                                    select_application = True
+                                    inst = obj(function=function)
+                                    if filter_groups :
+                                        select_application = (inst.get_workflow_group() in filter_groups) == select
+                                    
+                                    if select_application: 
+                                        wf_instances.append(inst)
+                                        wf_methodes.append(function)
+                                except: pass
+        return [wf_instances, wf_methodes]
+    
\ No newline at end of file

src/jflowapp/server.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+import cherrypy
+from functools import wraps
+from jinja2 import Environment, FileSystemLoader
+
+from jflow.server import JFlowServer
+from jflowapp.applications_manager import ApplicationsManager
+
+
+class ApplicationServer( JFlowServer ):
+
+    TMPL_REP_PATH = "./views/"
+
+    def __init__(self):
+        JFlowServer.__init__(self)
+        self.wfmanager = ApplicationsManager()
+        workflows = self.wfmanager.get_available_applications()
+        print (workflows)
+        self.first_instance = workflows[0][0]
+        self.name = self.first_instance.get_name()
+        self.description = self.first_instance.get_description()
+
+    def get_template(self, template, func = None):
+        jinja_env = Environment(loader=FileSystemLoader(os.path.join(os.path.dirname(os.path.abspath(__file__)), self.TMPL_REP_PATH)))
+        if func != None:
+            jinja_env.filters[func.__name__] = func
+        return jinja_env.get_template( template )
+    
+    @cherrypy.expose
+    def index(self):        
+        return self.get_template('jflow_application_template.tmpl').render(application_name=self.name, page = "index", application_description=self.description)
+    
+    @cherrypy.expose
+    def process(self):
+        return self.get_template('jflow_process.tmpl').render(application_name = self.name, wf_class = self.first_instance.__class__.__name__, page = "process", application_description=self.description)
+    
+    @cherrypy.expose
+    def results(self, workflow_id):
+        try:
+            return self.get_template(self.name+'_results.tmpl').render(application_name=self.name, wf_id = "13", application_description=self.description)
+        except:
+            return self.get_template('jflow_results.tmpl').render(application_name=self.name, wf_id = workflow_id, application_description=self.description)
+

src/jflowapp/views/jflow_application_template.tmpl

+{#
+	# Copyright (C) 2015 INRA
+	#
+	# This program is free software: you can redistribute it and/or modify
+	# it under the terms of the GNU General Public License as published by
+	# the Free Software Foundation, either version 3 of the License, or
+	# (at your option) any later version.
+	#
+	# This program is distributed in the hope that it will be useful,
+	# but WITHOUT ANY WARRANTY; without even the implied warranty of
+	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	# GNU General Public License for more details.
+	#
+	# You should have received a copy of the GNU General Public License
+	# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#}
+
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <meta name="description" content="">
+
+    <title>{{application_name}}</title>
+
+    <!-- Bootstrap core CSS -->
+    <link href="css/bootstrap.min.css" rel="stylesheet">
+    <!-- Bootstrap theme -->
+    <link href="css/bootstrap-theme.min.css" rel="stylesheet">
+
+    <!-- Custom styles for this template -->
+    <link href="css/theme.css" rel="stylesheet">
+
+    <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+
+  <body role="document">
+
+    <!-- Fixed navbar -->
+    <div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
+      <div class="container">
+        <div class="navbar-header">
+          <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
+            <span class="sr-only">Toggle navigation</span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+          </button>
+          <a class="navbar-brand" href="./index">{{application_name}}</a>
+        </div>
+        <div class="navbar-collapse collapse">
+          <ul class="nav navbar-nav">
+            <li {% if page == "index" %} class="active" {% endif %}><a href="./index">About</a></li>
+            <li {% if page == "process" %} class="active" {% endif %}><a href="./process">Process</a></li>
+			<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
+          </ul>
+        </div><!--/.nav-collapse -->
+      </div>
+    </div>
+
+    <div class="container theme-showcase" role="main">
+
+      <!-- Jumbotron -->
+      <div class="jumbotron" style="margin-top:-25px;text-align:justify">
+        <h1>{{application_name}}</h1>
+        <p class="lead">{{application_description}}</p>
+      </div>
+
+ 
+	<div class="container theme-showcase" role="main">
+		{% block page_body_content %}
+		{% endblock page_body_content %}
+	</div>
+ 
+
+      <hr>
+      <footer>
+      	<div class="container" style="text-align: center;">
+		  <p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
+		</div>
+      </footer>
+      
+    </div> <!-- /container -->
+
+	<script src="js/jquery.min.js"></script>
+	<script src="js/bootstrap.min.js"></script>
+	<script src='js/jflow.min.js' type='text/javascript'></script>
+
+	{% block js_file %}
+	{% endblock js_file %}
+	
+	<script type='text/javascript'>
+		$(document).ready(function(){
+			{% block js_block %}
+			{% endblock js_block %}
+		}); 
+	</script>
+		 
+  </body>
+</html>

src/jflowapp/views/jflow_process.tmpl

+{#
+	# Copyright (C) 2015 INRA
+	#
+	# This program is free software: you can redistribute it and/or modify
+	# it under the terms of the GNU General Public License as published by
+	# the Free Software Foundation, either version 3 of the License, or
+	# (at your option) any later version.
+	#
+	# This program is distributed in the hope that it will be useful,
+	# but WITHOUT ANY WARRANTY; without even the implied warranty of
+	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	# GNU General Public License for more details.
+	#
+	# You should have received a copy of the GNU General Public License
+	# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#}
+
+{% extends "jflow_application_template.tmpl" %}
+
+{% block page_body_content %}
+	<div id="jflow-form"> </div>
+{% endblock page_body_content %}
+
+{% block js_block %}
+	$('#jflow-form').wfform({
+		workflowClass: "{{wf_class}}"
+    });
+    
+	$('#jflow-form').on('run.wfform', function(event, running_wf) {
+		window.location = "/results?workflow_id="+running_wf.id;
+    });
+        
+{% endblock js_block %}
\ No newline at end of file

src/jflowapp/views/jflow_results.tmpl

+{#
+	# Copyright (C) 2015 INRA
+	#
+	# This program is free software: you can redistribute it and/or modify
+	# it under the terms of the GNU General Public License as published by
+	# the Free Software Foundation, either version 3 of the License, or
+	# (at your option) any later version.
+	#
+	# This program is distributed in the hope that it will be useful,
+	# but WITHOUT ANY WARRANTY; without even the implied warranty of
+	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	# GNU General Public License for more details.
+	#
+	# You should have received a copy of the GNU General Public License
+	# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#}
+
+{% extends "jflow_application_template.tmpl" %}
+
+{% block page_body_content %}
+	<div id="results"> </div>
+{% endblock page_body_content %}
+
+{% block js_block %}
+	$('#results').wfoutputs({
+		workflowID: {{wf_id}}
+	})	;
+{% endblock js_block %}

src/jflowapp/views/rrbsstatistics_results.tmpl

+{#
+	# Copyright (C) 2015 INRA
+	#
+	# This program is free software: you can redistribute it and/or modify
+	# it under the terms of the GNU General Public License as published by
+	# the Free Software Foundation, either version 3 of the License, or
+	# (at your option) any later version.
+	#
+	# This program is distributed in the hope that it will be useful,
+	# but WITHOUT ANY WARRANTY; without even the implied warranty of
+	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	# GNU General Public License for more details.
+	#
+	# You should have received a copy of the GNU General Public License
+	# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#}
+
+{% extends "jflow_application_template.tmpl" %}
+
+{% block page_body_content %}
+	<div id="results"> </div>
+{% endblock page_body_content %}
+
+{% block js_block %}
+	$('#results').wfoutputs({
+		workflowID: {{wf_id}}
+	})	;
+{% endblock js_block %}