[galaxy-commits] galaxy-dist commit f2f31fe4cf08: New: Send Email Action, Delete Action.

29 Jun 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker@emory.edu>
# Date 1277238844 14400
# Node ID f2f31fe4cf08f9500a886184b5c5f15fa4184e4d
# Parent  1f8035729ccd73f31522e816cf5467409e841b91
New: Send Email Action, Delete Action.
Note that delete action is dangerous and will break a workflow if you delete datasets that are required in later steps.

Partial refactoring to make addition of actions simpler.

--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -5,18 +5,50 @@ from galaxy.util.json import from_json_s
 
 from galaxy.web.form_builder import *
 
+
+#  For email notification PJA
+from email.MIMEText import MIMEText
+import smtplib
+
 log = logging.getLogger( __name__ )
 
 # DBTODO This still needs refactoring and general cleanup.
 
+def get_form_template(action_type, title, content, help, on_output = True ):
+    if on_output:
+        form = """
+            if (pja.action_type == "%s"){
+            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\
+            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
+                %s
+                p_str += "</div><div class='toolParamHelp'>%s</div></div>";
+            }""" % (action_type, title, content, help)
+    else:
+    	form =  """
+            if (pja.action_type == "%s"){
+            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \
+            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
+                %s
+                p_str += "</div><div class='toolParamHelp'>%s</div></div>";
+            }""" % (action_type, title, content, help)
+    return form
+
+# def get_field(action, argument, i_type, label = None):
+#     fstr = ''
+#     fname = """pja__"+pja.output_name+"__%s__%s""" % (action, argument)
+#     if label:
+#         fstr += """<label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>"""
+#     fstr += """<input type='text' value=" + chromCol + " name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>"""
+
 class DefaultJobAction(object):
     name = "DefaultJobAction"
+    verbose_name = "Default Job"
 
     @classmethod
     def execute(cls, job):
         pass
 
-    @classmethod        
+    @classmethod
     def get_config_form(cls, trans):
         return "<p>Default Job Action Config Form</p>"
 
@@ -26,11 +58,42 @@ class DefaultJobAction(object):
             return "%s -> %s" % (pja.action_type, pja.action_arguments)
         else:
             return "%s" % pja.action_type
-        
+
+
+class EmailAction(DefaultJobAction):
+    name = "EmailAction"
+    verbose_name = "Email Notification"
+    @classmethod
+    def execute(cls, trans, action, job):
+        smtp_server = trans.app.config.smtp_server
+        if smtp_server is None:
+            return trans.show_error_message( "Mail is not configured for this galaxy instance, workflow action aborted." )
+        # Build the email message
+        msg = MIMEText( "Your job '%s' at Galaxy instance %s is complete as of %s." % (job.history.name, trans.request.host, job.update_time))
+        msg[ 'To' ] = job.user.email
+        msg[ 'From' ] = job.user.email
+        msg[ 'Subject' ] = "Galaxy workflow step notification '%s'"
+        try:
+            s = smtplib.SMTP()
+            s.connect( smtp_server )
+            s.sendmail( frm, [ to ], msg.as_string() )
+            s.close()
+            return trans.show_ok_message( "Your error report has been sent" )
+        except Exception, e:
+            return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) )
+
+    @classmethod
+    def get_config_form(cls, trans):
+        form = """
+        	p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action.  You will be emailed upon job completion.</label>\
+        	            <input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>";
+            """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output = False)
+
 
 class ChangeDatatypeAction(DefaultJobAction):
     name = "ChangeDatatypeAction"
-
+    verbose_name = "Change Datatype"
     @classmethod
     def execute(cls, trans, action, job):
         for dataset_assoc in job.output_datasets:
@@ -45,24 +108,21 @@ class ChangeDatatypeAction(DefaultJobAct
         for dt_name in dtnames:
             dt_list += """<option id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype__%s' value='%s'>%s</option>""" % (dt_name, dt_name, dt_name)
         ps = """
-            if (pja.action_type == "ChangeDatatypeAction"){
-                p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>" + pja.action_type + " <br/> on " + pja.output_name + "\
-    			<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\
-    			<div class='toolFormBody'><label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label><select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\
+			p_str += "<label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label>\
+			    <select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\
 		        %s\
 		        </select>";
-		        if (pja.action_arguments != undefined && pja.action_arguments.newtype != undefined){
-                     p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"
-		        }
-		        p_str += "</div><div class='toolParamHelp'>This action will change the datatype of the output to the indicated value.</div></div>";
-    		}
+	        if (pja.action_arguments != undefined && pja.action_arguments.newtype != undefined){
+                 p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>";
+	        }
 		    """ % dt_list
             # Note the scrip + t hack above.  Is there a better way?
-        return ps
+        return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.')
 
 class RenameDatasetAction(DefaultJobAction):
     name = "RenameDatasetAction"
-
+    verbose_name = "Rename Dataset"
+    
     @classmethod
     def execute(cls, trans, action, job):
         for dataset_assoc in job.output_datasets:
@@ -71,23 +131,22 @@ class RenameDatasetAction(DefaultJobActi
 
     @classmethod
     def get_config_form(cls, trans):
-        return """
-            if (pja.action_type == "RenameDatasetAction"){
-    			p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
-    			<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
-    			if ((pja.action_arguments != undefined) && (pja.action_arguments.newname != undefined)){
-    				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>";
-    			}
-    			else{
-    				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='New Name'/>";
-    			}
-    			p_str += "</div><div class='toolParamHelp'>This action will rename the result dataset.</div></div>";
-    		}
+        form = """
+			if ((pja.action_arguments != undefined) && (pja.action_arguments.newname != undefined)){
+				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
+				          <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>";
+			}
+			else{
+				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
+				          <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>";
+			}
 		    """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
 
 class HideDatasetAction(DefaultJobAction):
     name = "HideDatasetAction"
-
+    verbose_name = "Hide Dataset"
+    
     @classmethod
     def execute(cls, trans, action, job):
         for dataset_assoc in job.output_datasets:
@@ -96,14 +155,79 @@ class HideDatasetAction(DefaultJobAction
 
     @classmethod
     def get_config_form(cls, trans):
-        return """
-            if (pja.action_type == "HideDatasetAction"){
-            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
-            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
-            	p_str += "<label for='pja__"+pja.output_name+"__HideDatasetAction'>There are no additional options for this action.</label><input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>";
-            	p_str += "</div><div class='toolParamHelp'>This action will *hide* the result dataset from your history.</div></div>";
+        form = """
+        	p_str += "<label for='pja__"+pja.output_name+"__HideDatasetAction'>There are no additional options for this action.</label>\
+        	            <input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>";
+            """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
+
+class DeleteDatasetAction(DefaultJobAction):
+    # This is disabled for right now.  Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data.
+    name = "DeleteDatasetAction"
+    verbose_name = "Delete Dataset"
+
+    @classmethod
+    def execute(cls, trans, action, job):
+        for dataset_assoc in job.output_datasets:
+            if action.output_name == '' or dataset_assoc.name == action.output_name:
+                dataset_assoc.dataset.deleted=True
+
+    @classmethod
+    def get_config_form(cls, trans):
+        form = """
+        	p_str += "<label for='pja__"+pja.output_name+"__DeleteDatasetAction'>There are no additional options for this action.  This dataset will be marked deleted.</label>\
+        	            <input type='hidden' name='pja__"+pja.output_name+"__DeleteDatasetAction'/>";
+            """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
+
+
+class ColumnSetAction(DefaultJobAction):
+    name = "ColumnSetAction"
+    verbose_name = "Assign Columns"
+    @classmethod
+    def execute(cls, trans, action, job):
+        for dataset_assoc in job.output_datasets:
+            if action.output_name == '' or dataset_assoc.name == action.output_name:
+                for k, v in action.action_arguments.items():
+                    if v != '':
+                        # Try to use both pure integer and 'cX' format.
+                        if v[0] == 'c':
+                            v = v[1:]
+                        v = int(v)
+                        if v != 0:
+                            setattr(dataset_assoc.dataset.metadata, k, v)
+
+    @classmethod
+    def get_config_form(cls, trans):
+        form = """
+            var chrom_col = ''
+            if (pja.action_arguments != undefined){
+                (pja.action_arguments.chromCol == undefined) ? chromCol = "" : chromCol=pja.action_arguments.chromCol;
+                (pja.action_arguments.startCol == undefined) ? startCol = "" : startCol=pja.action_arguments.startCol;
+                (pja.action_arguments.endCol == undefined) ? endCol = "" : endCol=pja.action_arguments.endCol;
+                (pja.action_arguments.strandCol == undefined) ? strandCol = "" : strandCol=pja.action_arguments.strandCol;
+                (pja.action_arguments.nameCol == undefined) ? nameCol = "" : nameCol=pja.action_arguments.nameCol;
+            }else{
+                chromCol = '';
+                startCol = '';
+                endCol = '';
+                strandCol = '';
+                nameCol = '';
             }
+            p_str += "<p>Leave any of these fields blank if they do not need to be set.</p>\
+                    <label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>\
+                        <input type='text' value='" + chromCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>\
+                    <label for='pja__"+pja.output_name+"__ColumnSetAction__startCol'>Start Column</label>\
+                        <input type='text' value='" + startCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__startCol'/>\
+                    <label for='pja__"+pja.output_name+"__ColumnSetAction__endCol'>End Column</label>\
+                        <input type='text' value='" + endCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__endCol'/>\
+                    <label for='pja__"+pja.output_name+"__ColumnSetAction__strandCol'>Strand Column</label>\
+                        <input type='text' value='" + strandCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__strandCol'/>\
+                    <label for='pja__"+pja.output_name+"__ColumnSetAction__nameCol'>Name Column</label>\
+                        <input type='text' value='" + nameCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__nameCol'/>\";
             """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will set column assignments in the output dataset.  Blank fields are ignored.")
+
 
 class SetMetadataAction(DefaultJobAction):
     name = "SetMetadataAction"
@@ -116,28 +240,38 @@ class SetMetadataAction(DefaultJobAction
             
     @classmethod
     def get_config_form(cls, trans):
-        dt_list = ""
-        mdict = {}
-        for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems():
-            for mn, mt in dtype_value.metadata_spec.items():
-                if mt.visible:
-                    mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','')
-        for k, v in mdict.items():
-            dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>"
-        return """
-            if (pja.action_type == "SetMetadataAction"){
-            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
-            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\
-            	<div class='toolFormBody'>\
-            	%s\
-            	</div><div class='toolParamHelp'>This tool sets metadata in output.</div></div>";
-            }
-    		""" % dt_list
+        #         dt_list = ""
+        #         mdict = {}
+        #         for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems():
+        #             for mn, mt in dtype_value.metadata_spec.items():
+        #                 if mt.visible:
+        #                     mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','')
+        #         for k, v in mdict.items():
+        #             dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>"
+        #         form = """
+        #           p_str += "%s";
+        #   """ % dt_list
+        # return get_form_template('SetMetadataAction', 'Set Metadata', form, "This action will change metadata for the dataset.")
+        form = """
+          p_str += "<p>Leave any of these fields blank if they do not need to be set.</p><label for='pja__"+pja.output_name+"__SetMetadataAction__chromCol'>Chrom Column</label>\
+                        <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__chromCol'/>\
+                    <label for='pja__"+pja.output_name+"__SetMetadataAction__startCol'>Start Column</label>\
+                        <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__startCol'/>\
+                    <label for='pja__"+pja.output_name+"__SetMetadataAction__endCol'>End Column</label>\
+                        <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__endCol'/>\
+                    <label for='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'>Comment Lines</label>\
+                        <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'/>\
+                      ";
+            """
+        return get_form_template(cls.name, cls.verbose_name, form, "This action will set metadata in the output dataset.")
 
 ACTIONS = { "RenameDatasetAction" : RenameDatasetAction,
             "HideDatasetAction" : HideDatasetAction,
             "ChangeDatatypeAction": ChangeDatatypeAction, 
-            # "SetMetadataAction" : SetMetadataAction, 
+            "ColumnSetAction" : ColumnSetAction,
+            "EmailAction" : EmailAction,
+            # "SetMetadataAction" : SetMetadataAction,
+            # "DeleteDatasetAction" : DeleteDatasetAction,
              }
             
 class ActionBox(object):
@@ -147,13 +281,13 @@ class ActionBox(object):
             ACTIONS[action.action_type].execute(action, job, trans)
         else:
             return False
-
+    
     @classmethod
     def get_short_str(cls, action):
         if action.action_type in ACTIONS:
             return ACTIONS[action.action_type].get_short_str(action)
         else:
-            return "Unknown PostJobAction"
+            return "Unknown Action"
 
     @classmethod
     def handle_incoming(cls, incoming):
@@ -180,7 +314,7 @@ class ActionBox(object):
     def get_add_list(cls):
         addlist = "<select id='new_pja_list' name='new_pja_list'>"
         for action in ACTIONS:
-            addlist += "<option value='%s'>%s</option>" % (ACTIONS[action].name, ACTIONS[action].name)
+            addlist += "<option value='%s'>%s</option>" % (ACTIONS[action].name, ACTIONS[action].verbose_name)
         addlist += "</select>"
         return addlist
         
@@ -193,4 +327,5 @@ class ActionBox(object):
     
     @classmethod
     def execute(cls, trans, pja, job):
-        ACTIONS[pja.action_type].execute(trans, pja, job)
+        if ACTIONS.has_key(pja.action_type):
+            ACTIONS[pja.action_type].execute(trans, pja, job)

--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -313,9 +313,9 @@
 	// DBTODO Refactor to the post module.
 	// This function preloads how to display known pja's.
 	function display_pja(pja, node){
-		// DBTODO SANITIZE INPUTS.  Way too easy to break the page right now with a change dataset name action.
+		// DBTODO SANITIZE INPUTS.
 		p_str = '';
-		${ActionBox.get_forms(trans)};
+		${ActionBox.get_forms(trans)}
 		$("#pja_container").append(p_str);
 		$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
 			action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
@@ -376,7 +376,7 @@
 		// Add step actions.
 		if (node && node.type=='tool'){
 			pjastr = "<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> \
-                <label>New Actions:</label><br/>" + display_pja_list() + display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\
+                " + display_pja_list() + " <br/> "+ display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\
                 </div><div class='form-row'>\
 				<div style='margin-right: 10px;'><span id='pja_container'></span>";
 			pjastr += "<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";

    

[galaxy-commits] galaxy-dist commit f2f31fe4cf08: New: Send Email Action, Delete Action.

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