5:14 p.m.
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker(a)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>";
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