1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a90c63fe697/ Changeset: 6a90c63fe697 User: dannon Date: 2014-06-06 22:44:47 Summary: Cleanup, pep8 for postjobactions. Affected #: 1 file diff -r f23dd6b6b6a54c09b0a6f6b890170869ded5723b -r 6a90c63fe697c60350129d6c245d7516fc649bc4 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -9,7 +9,8 @@ log = logging.getLogger( __name__ ) -def get_form_template(action_type, title, content, help, on_output = True ): + +def get_form_template(action_type, title, content, help, on_output=True ): if on_output: form = """ if (pja.action_type == "%s"){ @@ -19,7 +20,7 @@ p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) else: - form = """ + 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='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; @@ -37,7 +38,7 @@ verbose_name = "Default Job" @classmethod - def execute(cls, app, sa_session, action, job, replacement_dict = None): + def execute(cls, app, sa_session, action, job, replacement_dict=None): pass @classmethod @@ -61,12 +62,12 @@ @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): - if action.action_arguments and action.action_arguments.has_key('host'): + if action.action_arguments and 'host' in action.action_arguments: host = action.action_arguments['host'] else: host = 'usegalaxy.org' frm = 'galaxy-noreply@%s' % host - to = job.user.email + to = job.user.email subject = "Galaxy workflow step notification '%s'" % (job.history.name) outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets) body = "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" )) @@ -81,11 +82,11 @@ 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' value='%s' name='pja__"+pja.output_name+"__EmailAction__host'/><input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; """ % trans.request.host - 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) + 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) @classmethod def get_short_str(cls, pja): - if pja.action_arguments and pja.action_arguments.has_key('host'): + if pja.action_arguments and 'host' in pja.action_arguments: return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] else: return "Email the current user when this job is complete." @@ -94,6 +95,7 @@ class ChangeDatatypeAction(DefaultJobAction): name = "ChangeDatatypeAction" verbose_name = "Change Datatype" + @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: @@ -116,7 +118,7 @@ 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? + # Note the scrip + t hack above. Is there a better way? return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.') @classmethod @@ -131,7 +133,7 @@ @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): # Prevent renaming a dataset to the empty string. - if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': + if action.action_arguments and action.action_arguments.get('newname', ''): new_name = action.action_arguments['newname'] # TODO: Unify and simplify replacement options. @@ -165,10 +167,9 @@ tokens = to_be_replaced.split("|") operations = [] if len(tokens) > 1: - input_file_var = tokens[0].strip() - for i in range(1, len(tokens)): - operations.append(tokens[i].strip()) - + input_file_var = tokens[0].strip() + for i in range(1, len(tokens)): + operations.append(tokens[i].strip()) replacement = "" # Lookp through inputs find one with "to_be_replaced" input # variable name, and get the replacement name @@ -220,7 +221,7 @@ @classmethod def get_short_str(cls, pja): # Prevent renaming a dataset to the empty string. - if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': + if pja.action_arguments and pja.action_arguments.get('newname', ''): return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) else: return "Rename action used without a new name specified. Output name will be unchanged." @@ -234,19 +235,21 @@ def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: if dataset_assoc.dataset.state != dataset_assoc.dataset.states.ERROR and ( action.output_name == '' or dataset_assoc.name == action.output_name ): - dataset_assoc.dataset.visible=False + dataset_assoc.dataset.visible = False @classmethod def get_config_form(cls, trans): - return """ - if (pja.action_type == "HideDatasetAction"){ - p_str += "<input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; - } - """ + return """ + if (pja.action_type == "HideDatasetAction"){ + p_str += "<input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; + } + """ + @classmethod def get_short_str(cls, pja): return "Hide output '%s'." % pja.output_name + 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" @@ -256,7 +259,7 @@ def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: if action.output_name == '' or dataset_assoc.name == action.output_name: - dataset_assoc.dataset.deleted=True + dataset_assoc.dataset.deleted = True @classmethod def get_config_form(cls, trans): @@ -271,10 +274,10 @@ return "Delete this dataset after creation." - class ColumnSetAction(DefaultJobAction): name = "ColumnSetAction" verbose_name = "Assign Columns" + @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: @@ -401,22 +404,21 @@ p_str += "<label for='pja__"+pja.output_name+"__DeleteIntermediatesAction'>There are no additional options for this action.</label>\ <input type='hidden' name='pja__"+pja.output_name+"__DeleteIntermediatesAction'/>"; """ - return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.This action will delete non-output datasets of parent steps in this workflow.", on_output = False) + return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.", on_output=False) @classmethod def get_short_str(cls, pja): return "Delete parent datasets of this step created in this workflow that aren't flagged as outputs." - class ActionBox(object): - actions = { "RenameDatasetAction" : RenameDatasetAction, - "HideDatasetAction" : HideDatasetAction, + actions = { "RenameDatasetAction": RenameDatasetAction, + "HideDatasetAction": HideDatasetAction, "ChangeDatatypeAction": ChangeDatatypeAction, - "ColumnSetAction" : ColumnSetAction, - "EmailAction" : EmailAction, - "DeleteIntermediatesAction" : DeleteIntermediatesAction, + "ColumnSetAction": ColumnSetAction, + "EmailAction": EmailAction, + "DeleteIntermediatesAction": DeleteIntermediatesAction, } public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction', @@ -438,10 +440,10 @@ sp = key.split('__') ao_key = sp[2] + sp[1] # flag / output_name / pjatype / desc - if not ao_key in npd: - npd[ao_key] = {'action_type' : sp[2], - 'output_name' : sp[1], - 'action_arguments' : {}} + if ao_key not in npd: + npd[ao_key] = {'action_type': sp[2], + 'output_name': sp[1], + 'action_arguments': {}} if len(sp) > 3: if sp[3] == 'output_name': npd[ao_key]['output_name'] = val @@ -468,6 +470,6 @@ return forms @classmethod - def execute(cls, app, sa_session, pja, job, replacement_dict = None): - if ActionBox.actions.has_key(pja.action_type): + def execute(cls, app, sa_session, pja, job, replacement_dict=None): + if pja.action_type in ActionBox.actions: ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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