From 251f9d6cf40edda6ca1c6f954d045ecebc42f074 Mon Sep 17 00:00:00 2001
From: einarr <einarr@pvv.ntnu.no>
Date: Tue, 25 Apr 2006 12:19:25 +0000
Subject: [PATCH] Added command line options to create a new project based on a
 given workflow.

---
 fluents                     | 68 +++++++++++++++++++++++++++++++++++++
 fluent => system/fluents.py | 23 ++-----------
 system/workflow.py          |  1 +
 workflows/go_workflow.py    |  1 +
 workflows/pca_workflow.py   |  1 +
 5 files changed, 74 insertions(+), 20 deletions(-)
 create mode 100755 fluents
 rename fluent => system/fluents.py (84%)

diff --git a/fluents b/fluents
new file mode 100755
index 0000000..ac42eef
--- /dev/null
+++ b/fluents
@@ -0,0 +1,68 @@
+#!/usr/bin/python
+
+from getopt import getopt
+import sys
+from system import fluents, project, workflow
+import workflows
+
+PROGRAM_NAME = 'fluents'
+VERSION = '0.1.0'
+
+parameters = {'workflow': workflow.EmptyWorkflow}
+
+def show_help():
+    print 'fluent %s' % VERSION
+    print 'This software is released under the GNU General Public Licence'
+    print
+    print 'Usage: fluent [options]'
+    print 
+    print 'Description:'
+    print '    Fluent is a lightweight data analysis application for bilinear models.'
+    print
+    print 'Options:'
+    print '    -h --help              Show this help text'
+    print '    -l --list-workflows    Lists available workflows'
+    print '    -w --workflow=<wf>     Generates a new project based on workflow wf.'
+    print
+
+def list_workflows():
+    print 'fluent %s' % VERSION
+    print
+    print 'Workflows:'
+
+    wfs = workflow.workflow_list()
+    names = [wf.name for wf in wfs]
+    names.sort()
+
+    for n in names:
+        print '    %s (%s)' % (n.id, n.name)
+
+def parse_options():
+    short_opts = 'hlw:'
+    long_opts = ['help', 'list-workflows', 'workflow=']
+
+    options, params = getopt(sys.argv[1:], short_opts, long_opts)
+
+    for opt, val in options:
+        if opt in ['-h', '--help']:
+            show_help()
+        elif opt in ['-l', '--list-workflows']:
+            list_workflows()
+        elif opt in ['-w', '--workflow']:
+            wfs = workflow.workflow_list()
+            for wf in wfs:
+                if wf.ident == val:
+                    parameters['workflow'] = wf
+            parameters['workflow']
+
+if __name__ == '__main__':
+    parse_options()
+    
+    import gtk
+    import gnome
+    
+    gnome.program_init(PROGRAM_NAME, VERSION)
+    app = fluents.FluentApp(parameters['workflow'])
+    app.set_project(project.Project())
+    app.show()
+    gtk.main()
diff --git a/fluent b/system/fluents.py
similarity index 84%
rename from fluent
rename to system/fluents.py
index 1e47090..d96b361 100755
--- a/fluent
+++ b/system/fluents.py
@@ -20,14 +20,14 @@ GLADEFILENAME = 'system/fluent.glade'
 
 class FluentApp:
 
-    def __init__(self):
+    def __init__(self, wf):
         # Application variables
         self.project = None
         self.current_data = None
         
         gtk.glade.set_custom_handler(self.custom_object_factory)
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
-        self.workflow = workflow.EmptyWorkflow(self)
+        self.workflow = wf(self)
 
     def set_project(self, project):
         logger.log('notice', 'Creating a new project')
@@ -93,8 +93,7 @@ class FluentApp:
                    'on_zoom_out_button_clicked' : (self.on_multiple_view),
                    'on_new1_activate' : (self.on_create_project),
                    'on_button_new_clicked' : (self.on_create_project),
-                   'on_about1_activate' : (self.on_help_about),
-                   'on_workflow_refresh_clicked' : (self.on_workflow_refresh_clicked)}
+                   'on_about1_activate' : (self.on_help_about)}
         self.widget_tree.signal_autoconnect(signals)
 
         # Log that we've set up the app now
@@ -124,19 +123,3 @@ class FluentApp:
         about = widget_tree.get_widget('aboutdialog')
         about.run()
 
-    def on_workflow_refresh_clicked(self, *ignored):        
-        try:
-            reload(sys.modules[self.workflow.__class__.__module__])
-        except Exception, e:
-            logger.log('error', 'Relading workflow failed.')
-            logger.log('error', e)
-        else:
-            logger.log('notice', 'Successfully reloaded workflow.')
-        
-if __name__ == '__main__':
-    gnome.program_init(PROGRAM_NAME, VERSION)
-    app = FluentApp()
-    app.show()
-    gtk.main()
-
-
diff --git a/system/workflow.py b/system/workflow.py
index 970be89..d38198d 100644
--- a/system/workflow.py
+++ b/system/workflow.py
@@ -53,6 +53,7 @@ class Workflow:
     """
 
     name = "Workflow"
+    ident = None
     description = "Workflow Description"
 
     def __init__(self, app):
diff --git a/workflows/go_workflow.py b/workflows/go_workflow.py
index 411ca6e..5e38c94 100644
--- a/workflows/go_workflow.py
+++ b/workflows/go_workflow.py
@@ -9,6 +9,7 @@ import cPickle
 class EinarsWorkflow (workflow.Workflow):
 
     name = 'Test Workflow'
+    ident = 'go'
     description = 'Gene Ontology Workflow. This workflow currently serves as a general testing workflow.'
     def __init__(self, app):
         workflow.Workflow.__init__(self, app)
diff --git a/workflows/pca_workflow.py b/workflows/pca_workflow.py
index 91e562f..11558a6 100644
--- a/workflows/pca_workflow.py
+++ b/workflows/pca_workflow.py
@@ -8,6 +8,7 @@ from system import dataset, logger, plots
 
 class PCAWorkflow(wf.Workflow):
     name = 'PCA Workflow'
+    ident = 'pca'
     description = 'PCA workflow. Uses real microarray data from a study of diabetes (Mootha et al.).'
 
     def __init__(self, app):