def _workflow_to_dict_run(self, trans, stored):
"""
Builds workflow dictionary used by run workflow form
"""
workflow = stored.latest_workflow
if len(workflow.steps) == 0:
raise exceptions.MessageException(
'Workflow cannot be run because it does not have any steps.')
if attach_ordered_steps(workflow, workflow.steps):
raise exceptions.MessageException(
'Workflow cannot be run because it contains cycles.')
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
has_upgrade_messages = False
step_version_changes = []
missing_tools = []
errors = {}
for step in workflow.steps:
try:
module_injector.inject(step,
steps=workflow.steps,
exact_tools=False)
except exceptions.ToolMissingException:
if step.tool_id not in missing_tools:
missing_tools.append(step.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is None:
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
if step_errors:
errors[step.id] = step_errors
if missing_tools:
workflow.annotation = self.get_item_annotation_str(
trans.sa_session, trans.user, workflow)
raise exceptions.MessageException('Following tools missing: %s' %
', '.join(missing_tools))
workflow.annotation = self.get_item_annotation_str(
trans.sa_session, trans.user, workflow)
step_order_indices = {}
for step in workflow.steps:
step_order_indices[step.id] = step.order_index
step_models = []
for i, step in enumerate(workflow.steps):
step_model = None
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool(
step.tool_id, tool_version=step.tool_version)
params_to_incoming(incoming, tool.inputs, step.state.inputs,
trans.app)
step_model = tool.to_json(
trans,
incoming,
workflow_building_mode=workflow_building_modes.USE_HISTORY)
step_model['post_job_actions'] = [{
'short_str':
ActionBox.get_short_str(pja),
'action_type':
pja.action_type,
'output_name':
pja.output_name,
'action_arguments':
pja.action_arguments
} for pja in step.post_job_actions]
else:
inputs = step.module.get_runtime_inputs(
connections=step.output_connections)
step_model = {
'inputs':
[input.to_dict(trans) for input in inputs.values()]
}
step_model['step_type'] = step.type
step_model['step_label'] = step.label
step_model['step_name'] = step.module.get_name()
step_model['step_version'] = step.module.get_version()
step_model['step_index'] = step.order_index
step_model['output_connections'] = [{
'input_step_index':
step_order_indices.get(oc.input_step_id),
'output_step_index':
step_order_indices.get(oc.output_step_id),
'input_name':
oc.input_name,
'output_name':
oc.output_name
} for oc in step.output_connections]
if step.annotations:
step_model['annotation'] = step.annotations[0].annotation
if step.upgrade_messages:
step_model['messages'] = step.upgrade_messages
step_models.append(step_model)
return {
'id':
trans.app.security.encode_id(stored.id),
'history_id':
trans.app.security.encode_id(trans.history.id)
if trans.history else None,
'name':
stored.name,
'steps':
step_models,
'step_version_changes':
step_version_changes,
'has_upgrade_messages':
has_upgrade_messages,
'workflow_resource_parameters':
self._workflow_resource_parameters(trans, stored, workflow),
}
def render_body(context, **pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
basestring = context.get('basestring', UNDEFINED)
errors = context.get('errors', UNDEFINED)
tuple = context.get('tuple', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
app = context.get('app', UNDEFINED)
workflow = context.get('workflow', UNDEFINED)
def do_inputs(inputs, values, errors, prefix, step, other_values=None):
return render_do_inputs(context.locals_(__M_locals), inputs,
values, errors, prefix, step, other_values)
len = context.get('len', UNDEFINED)
dict = context.get('dict', UNDEFINED)
t = context.get('t', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
has_upgrade_messages = context.get('has_upgrade_messages', UNDEFINED)
steps = context.get('steps', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n\n')
# SOURCE LINE 13
__M_writer(u'\n\n')
# SOURCE LINE 32
__M_writer(u'\n\n')
# SOURCE LINE 34
from galaxy.tools.parameters import DataToolParameter, RuntimeValue
from galaxy.jobs.actions.post import ActionBox
import re
import colorsys
import random
wf_parms = {}
for step in steps:
for v in step.state.inputs.itervalues():
if isinstance(v, basestring):
for rematch in re.findall('\$\{.+?\}', v):
if rematch[2:-1] not in wf_parms:
wf_parms[rematch[2:-1]] = ""
if wf_parms:
hue_offset = 1.0 / len(wf_parms)
hue = 0.0
for k in wf_parms.iterkeys():
wf_parms[k] = "#%X%X%X" % tuple(
[int(x * 255) for x in colorsys.hsv_to_rgb(hue, .1, .9)])
hue += hue_offset
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin()[__M_key]) for __M_key in [
'hue', 'hue_offset', 'wf_parms', 'ActionBox',
'DataToolParameter', 'rematch', 'k', 'random', 're',
'step', 'RuntimeValue', 'colorsys', 'v', 'x'
] if __M_key in __M_locals_builtin()
]))
# SOURCE LINE 54
__M_writer(u'\n\n')
# SOURCE LINE 91
__M_writer(u'\n\n')
# SOURCE LINE 163
__M_writer(u'\n\n<h2>Running workflow "')
# SOURCE LINE 165
__M_writer(unicode(h.to_unicode(workflow.name)))
__M_writer(u'"</h2>\n\n')
# SOURCE LINE 167
if has_upgrade_messages:
# SOURCE LINE 168
__M_writer(
u'<div class="warningmessage">\n Problems were encountered when loading this workflow, likely due to tool\n version changes. Missing parameter values have been replaced with default.\n Please review the parameter values below.\n</div>\n'
)
# SOURCE LINE 174
__M_writer(u'\n')
# SOURCE LINE 175
if workflow.annotation:
# SOURCE LINE 176
__M_writer(u' <div class="workflow-annotation">Annotation: ')
__M_writer(unicode(workflow.annotation))
__M_writer(u'</div>\n <hr/>\n')
# SOURCE LINE 179
__M_writer(u'\n<form id="tool_form" name="tool_form" method="POST">\n')
# SOURCE LINE 182
__M_writer(u'\n\n')
# SOURCE LINE 184
if wf_parms:
# SOURCE LINE 185
__M_writer(
u'<div class="metadataForm">\n <div class="metadataFormTitle">Workflow Parameters</div>\n <div class="metadataFormBody">\n'
)
# SOURCE LINE 188
for parm in wf_parms:
# SOURCE LINE 189
__M_writer(
u" <div class='form-row'><label style='width:100px;'>"
)
__M_writer(unicode(parm))
__M_writer(u'<input style="border:2px solid ')
__M_writer(unicode(wf_parms[parm]))
__M_writer(
u';border-left-width:8px;" type="text" class=\'wf_parm_input ptag_'
)
__M_writer(unicode(parm))
__M_writer(u'\' name="wf_parm|')
__M_writer(unicode(parm))
__M_writer(u'" value=""/></label></div>\n')
# SOURCE LINE 191
__M_writer(
u' </div>\n</div>\n <script type="text/javascript">\n // Set the change hooks for workflow parameters.\n $(document).ready(function () {\n $(\'.wf_parm_input\').bind(\'change keypress keyup\', function(event){\n // DBTODO This is probably not reliable. Ensure we have the right class.\n var new_text = $(this).val();\n if (new_text === \'\'){\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(tag_id);\n }else{\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(new_text);\n // Now set the hidden input to the generated text.\n $(\'.wfpspan.wf_parm__\'+tag_id).not(\'.pja_wfp\').each(function(){\n // var new_text = $(this).parent().text();\n $(this).parent().siblings().children().val(new_text);\n });\n }\n });\n });\n </script>\n'
)
# SOURCE LINE 217
__M_writer(u'\n')
# SOURCE LINE 218
for i, step in enumerate(steps):
# SOURCE LINE 219
if step.type == 'tool' or step.type is None:
# SOURCE LINE 220
__M_writer(u' ')
tool = app.toolbox.tools_by_id[step.tool_id]
__M_locals.update(
__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key])
for __M_key in ['tool']
if __M_key in __M_locals_builtin()]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 221
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(step.state.encode(tool, app)))
__M_writer(
u'">\n <div class="toolForm">\n <div class="toolFormTitle">\n Step '
)
# SOURCE LINE 224
__M_writer(unicode(int(step.order_index) + 1))
__M_writer(u': ')
__M_writer(unicode(tool.name))
__M_writer(u'\n')
# SOURCE LINE 225
if step.annotations:
# SOURCE LINE 226
__M_writer(
u' <div class="step-annotation">Annotation: '
)
__M_writer(
unicode(h.to_unicode(step.annotations[0].annotation)))
__M_writer(u'</div>\n')
# SOURCE LINE 228
__M_writer(
u' </div>\n <div class="toolFormBody">\n '
)
# SOURCE LINE 230
__M_writer(
unicode(
do_inputs(tool.inputs, step.state.inputs,
errors.get(step.id, dict()), "", step)))
__M_writer(u'\n')
# SOURCE LINE 231
if step.post_job_actions:
# SOURCE LINE 232
__M_writer(
u" <hr/>\n <div class='form-row'>\n"
)
# SOURCE LINE 234
if len(step.post_job_actions) > 1:
# SOURCE LINE 235
__M_writer(
u' <label>Actions:</label>\n')
# SOURCE LINE 236
else:
# SOURCE LINE 237
__M_writer(
u' <label>Action:</label>\n')
# SOURCE LINE 239
pja_ss_all = []
for pja_ss in [
ActionBox.get_short_str(pja)
for pja in step.post_job_actions
]:
for rematch in re.findall('\$\{.+?\}', pja_ss):
pja_ss = pja_ss.replace(
rematch,
'<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>'
% (wf_parms[rematch[2:-1]], rematch[2:-1],
rematch[2:-1]))
pja_ss_all.append(pja_ss)
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin()[__M_key])
for __M_key in
['rematch', 'pja_ss_all', 'pja', 'pja_ss']
if __M_key in __M_locals_builtin()
]))
# SOURCE LINE 245
__M_writer(u'\n ')
# SOURCE LINE 246
__M_writer(unicode('<br/>'.join(pja_ss_all)))
__M_writer(u'\n </div>\n')
# SOURCE LINE 249
__M_writer(u' </div>\n </div>\n')
# SOURCE LINE 251
else:
# SOURCE LINE 252
__M_writer(u' ')
module = step.module
__M_locals.update(
__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key])
for __M_key in ['module']
if __M_key in __M_locals_builtin()]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 253
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(module.encode_runtime_state(t, step.state)))
__M_writer(
u'">\n <div class="toolForm">\n <div class="toolFormTitle">\n Step '
)
# SOURCE LINE 256
__M_writer(unicode(int(step.order_index) + 1))
__M_writer(u': ')
__M_writer(unicode(module.name))
__M_writer(u'\n')
# SOURCE LINE 257
if step.annotations:
# SOURCE LINE 258
__M_writer(
u' <div class="step-annotation">Annotation: '
)
__M_writer(unicode(step.annotations[0].annotation))
__M_writer(u'</div>\n')
# SOURCE LINE 260
__M_writer(
u' </div>\n <div class="toolFormBody">\n '
)
# SOURCE LINE 262
__M_writer(
unicode(
do_inputs(module.get_runtime_inputs(),
step.state.inputs,
errors.get(step.id, dict()), "", step)))
__M_writer(u'\n </div>\n </div>\n')
# SOURCE LINE 267
__M_writer(
u'<input type="submit" name="run_workflow" value="Run workflow" />\n</form>'
)
return ''
finally:
context.caller_stack._pop_frame()
def render_body(context, **pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
isinstance = context.get('isinstance', UNDEFINED)
basestring = context.get('basestring', UNDEFINED)
errors = context.get('errors', UNDEFINED)
tuple = context.get('tuple', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
history_id = context.get('history_id', UNDEFINED)
workflow = context.get('workflow', UNDEFINED)
def do_inputs(inputs,
values,
errors,
prefix,
step,
other_values=None,
already_used=None):
return render_do_inputs(context.locals_(__M_locals), inputs,
values, errors, prefix, step, other_values,
already_used)
len = context.get('len', UNDEFINED)
step_version_changes = context.get('step_version_changes', UNDEFINED)
dict = context.get('dict', UNDEFINED)
t = context.get('t', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
has_upgrade_messages = context.get('has_upgrade_messages', UNDEFINED)
steps = context.get('steps', UNDEFINED)
trans = context.get('trans', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n\n')
# SOURCE LINE 243
__M_writer(u'\n\n')
# SOURCE LINE 298
__M_writer(u'\n\n')
# SOURCE LINE 300
from galaxy.tools.parameters import DataToolParameter, RuntimeValue
from galaxy.tools.parameters import DataCollectionToolParameter
from galaxy.jobs.actions.post import ActionBox
import re
import colorsys
import random
used_accumulator = []
wf_parms = {}
for step in steps:
for v in [
ActionBox.get_short_str(pja)
for pja in step.post_job_actions
] + step.state.inputs.values():
if isinstance(v, basestring):
for rematch in re.findall('\$\{.+?\}', v):
if rematch[2:-1] not in wf_parms:
wf_parms[rematch[2:-1]] = ""
if wf_parms:
hue_offset = 1.0 / len(wf_parms)
hue = 0.0
for k in wf_parms.iterkeys():
wf_parms[k] = "#%X%X%X" % tuple(
[int(x * 255) for x in colorsys.hsv_to_rgb(hue, .1, .9)])
hue += hue_offset
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in [
'hue', 'hue_offset', 'wf_parms', 'ActionBox',
'DataToolParameter', 'rematch', 'used_accumulator', 'k',
'random', 'pja', 're', 'step', 'RuntimeValue', 'colorsys',
'v', 'DataCollectionToolParameter', 'x'
] if __M_key in __M_locals_builtin_stored
]))
# SOURCE LINE 323
__M_writer(u'\n\n')
# SOURCE LINE 365
__M_writer(u'\n\n')
# SOURCE LINE 470
__M_writer(
u'\n\n<div id=\'ec_button_container\'>\n <span class="action-button" id="show_all_tool_body">Expand All</span>\n <span class="action-button" id="hide_all_tool_body">Collapse</span>\n</div>\n\n<h2>Running workflow "'
)
# SOURCE LINE 477
__M_writer(unicode(h.to_unicode(workflow.name)))
__M_writer(u'"</h2>\n\n')
# SOURCE LINE 479
if has_upgrade_messages:
# SOURCE LINE 480
__M_writer(
u'<div class="warningmessage">\n Problems were encountered when loading this workflow, likely due to tool\n version changes. Missing parameter values have been replaced with default.\n Please review the parameter values below.\n</div>\n'
)
pass
# SOURCE LINE 486
__M_writer(u'\n')
# SOURCE LINE 487
if step_version_changes:
# SOURCE LINE 488
__M_writer(
u' <div class="infomessage">\n The following tools are beinge executed with a different version from\n what was available when this workflow was last saved because the\n previous version is no longer available for use on this galaxy\n instance.\n To upgrade your workflow and dismiss this message simply edit the\n workflow and re-save it to update the stored tool version.\n <ul>\n'
)
# SOURCE LINE 496
for vc in step_version_changes:
# SOURCE LINE 497
__M_writer(u' <li>')
__M_writer(unicode(vc))
__M_writer(u'</li>\n')
pass
# SOURCE LINE 499
__M_writer(u' </ul>\n </div>\n')
pass
# SOURCE LINE 502
__M_writer(u'\n')
# SOURCE LINE 503
if workflow.annotation:
# SOURCE LINE 504
__M_writer(u' <div class="workflow-annotation">')
__M_writer(unicode(workflow.annotation))
__M_writer(u'</div>\n <hr/>\n')
pass
# SOURCE LINE 507
__M_writer(u'\n<form id="tool_form" name="tool_form" method="POST">\n')
# SOURCE LINE 510
__M_writer(u'\n')
# SOURCE LINE 511
if wf_parms:
# SOURCE LINE 512
__M_writer(
u'<div class="metadataForm">\n <div class="metadataFormTitle">Workflow Parameters</div>\n <div class="metadataFormBody">\n'
)
# SOURCE LINE 515
for parm in wf_parms:
# SOURCE LINE 516
__M_writer(
u" <div class='form-row'><label style='width:100px;'>"
)
__M_writer(unicode(parm))
__M_writer(u'<input style="border:2px solid ')
__M_writer(unicode(wf_parms[parm]))
__M_writer(
u';border-left-width:8px;" type="text" class=\'wf_parm_input ptag_'
)
__M_writer(unicode(parm))
__M_writer(u'\' name="wf_parm|')
__M_writer(unicode(parm))
__M_writer(u'" value=""/></label></div>\n')
pass
# SOURCE LINE 518
__M_writer(
u' </div>\n</div>\n <script type="text/javascript">\n // Set the change hooks for workflow parameters.\n $(document).ready(function () {\n $(\'.wf_parm_input\').bind(\'change keypress keyup\', function(event){\n // DBTODO This is probably not reliable. Ensure we have the right class.\n var new_text = $(this).val();\n if (new_text === \'\'){\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(tag_id);\n }else{\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(new_text);\n // Now set the hidden input to the generated text.\n $(\'.wfpspan.wf_parm__\'+tag_id).not(\'.pja_wfp\').each(function(){\n var new_text = $(this).parent().text();\n $(this).parent().siblings().children().val(new_text);\n });\n }\n });\n });\n </script>\n'
)
pass
# SOURCE LINE 544
for i, step in enumerate(steps):
# SOURCE LINE 545
__M_writer(
u' <!-- Only way module would be missing is if tool is missing, but\n that would cause missing_tools.mako to render instead of this\n template. -->\n '
)
# SOURCE LINE 548
module = step.module
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key])
for __M_key in ['module']
if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 549
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(module.encode_runtime_state(t, step.state)))
__M_writer(u'">\n')
# SOURCE LINE 550
if step.type == 'tool' or step.type is None:
# SOURCE LINE 551
__M_writer(u' ')
tool = trans.app.toolbox.get_tool(step.tool_id)
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin_stored[__M_key])
for __M_key in ['tool']
if __M_key in __M_locals_builtin_stored
]))
# SOURCE LINE 553
__M_writer(
u'\n <div class="toolForm">\n <div class="toolFormTitle">\n <span class=\'title_ul_text\'>Step '
)
# SOURCE LINE 556
__M_writer(unicode(int(step.order_index) + 1))
__M_writer(u': ')
__M_writer(unicode(tool.name))
__M_writer(u'</span>\n')
# SOURCE LINE 557
if tool.version:
# SOURCE LINE 558
__M_writer(u' (version ')
__M_writer(unicode(tool.version))
__M_writer(u')\n')
pass
# SOURCE LINE 560
if step.annotations:
# SOURCE LINE 561
__M_writer(
u' <div class="step-annotation">')
__M_writer(
unicode(h.to_unicode(step.annotations[0].annotation)))
__M_writer(u'</div>\n')
pass
# SOURCE LINE 563
__M_writer(
u' </div>\n <div class="toolFormBody">\n '
)
# SOURCE LINE 565
__M_writer(
unicode(
do_inputs(tool.inputs, step.state.inputs,
errors.get(step.id, dict()), "", step, None,
used_accumulator)))
__M_writer(u'\n')
# SOURCE LINE 566
if step.post_job_actions:
# SOURCE LINE 567
__M_writer(
u" <hr/>\n <div class='form-row'>\n"
)
# SOURCE LINE 569
if len(step.post_job_actions) > 1:
# SOURCE LINE 570
__M_writer(
u' <label>Actions:</label>\n'
)
# SOURCE LINE 571
else:
# SOURCE LINE 572
__M_writer(
u' <label>Action:</label>\n'
)
pass
# SOURCE LINE 574
__M_writer(u' ')
pja_ss_all = []
for pja_ss in [
ActionBox.get_short_str(pja)
for pja in step.post_job_actions
]:
for rematch in re.findall('\$\{.+?\}', pja_ss):
pja_ss = pja_ss.replace(
rematch,
'<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>'
% (wf_parms[rematch[2:-1]], rematch[2:-1],
rematch[2:-1]))
pja_ss_all.append(pja_ss)
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin_stored[__M_key])
for __M_key in
['rematch', 'pja_ss_all', 'pja', 'pja_ss']
if __M_key in __M_locals_builtin_stored
]))
# SOURCE LINE 580
__M_writer(u'\n ')
# SOURCE LINE 581
__M_writer(unicode('<br/>'.join(pja_ss_all)))
__M_writer(u'\n </div>\n')
pass
# SOURCE LINE 584
__M_writer(u' </div>\n </div>\n')
# SOURCE LINE 586
else:
# SOURCE LINE 587
__M_writer(
u' <div class="toolForm">\n <div class="toolFormTitle">\n <span class=\'title_ul_text\'>Step '
)
# SOURCE LINE 589
__M_writer(unicode(int(step.order_index) + 1))
__M_writer(u': ')
__M_writer(unicode(module.name))
__M_writer(u'</span>\n')
# SOURCE LINE 590
if step.annotations:
# SOURCE LINE 591
__M_writer(
u' <div class="step-annotation">')
__M_writer(unicode(step.annotations[0].annotation))
__M_writer(u'</div>\n')
pass
# SOURCE LINE 593
__M_writer(
u' </div>\n <div class="toolFormBody">\n '
)
# SOURCE LINE 595
# Filter possible inputs to data types that are valid for subsequent steps
type_filter = []
for oc in step.output_connections:
for ic in oc.input_step.module.get_data_inputs():
if 'extensions' in ic and ic['name'] == oc.input_name:
type_filter += ic['extensions']
if not type_filter:
type_filter = ['data']
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin([
(__M_key, __M_locals_builtin_stored[__M_key])
for __M_key in ['ic', 'oc', 'type_filter']
if __M_key in __M_locals_builtin_stored
]))
# SOURCE LINE 604
__M_writer(u'\n ')
# SOURCE LINE 605
__M_writer(
unicode(
do_inputs(module.get_runtime_inputs(type_filter),
step.state.inputs,
errors.get(step.id, dict()), "", step, None,
used_accumulator)))
__M_writer(u'\n </div>\n </div>\n')
pass
pass
# SOURCE LINE 610
if history_id is None:
# SOURCE LINE 611
__M_writer(
u' <p id=\'new_history_p\'>\n <input type="checkbox" name=\'new_history\' value="true" id=\'new_history_cbx\'/><label for=\'new_history_cbx\'>Send results to a new history </label>\n <span id="new_history_input">named: <input type=\'text\' name=\'new_history_name\' value=\''
)
# SOURCE LINE 613
__M_writer(
filters.html_escape(unicode(h.to_unicode(workflow.name))))
__M_writer(u"'/></span>\n </p>\n")
pass
# SOURCE LINE 616
__M_writer(
u'<input type="submit" class="btn btn-primary" name="run_workflow" value="Run workflow" />\n</form>\n'
)
return ''
finally:
context.caller_stack._pop_frame()
def render_body(context,**pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
isinstance = context.get('isinstance', UNDEFINED)
basestring = context.get('basestring', UNDEFINED)
errors = context.get('errors', UNDEFINED)
tuple = context.get('tuple', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
history_id = context.get('history_id', UNDEFINED)
workflow = context.get('workflow', UNDEFINED)
def do_inputs(inputs,values,errors,prefix,step,other_values=None,already_used=None):
return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used)
len = context.get('len', UNDEFINED)
step_version_changes = context.get('step_version_changes', UNDEFINED)
dict = context.get('dict', UNDEFINED)
t = context.get('t', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
has_upgrade_messages = context.get('has_upgrade_messages', UNDEFINED)
steps = context.get('steps', UNDEFINED)
trans = context.get('trans', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n\n')
# SOURCE LINE 243
__M_writer(u'\n\n')
# SOURCE LINE 298
__M_writer(u'\n\n')
# SOURCE LINE 300
from galaxy.tools.parameters import DataToolParameter, RuntimeValue
from galaxy.tools.parameters import DataCollectionToolParameter
from galaxy.jobs.actions.post import ActionBox
import re
import colorsys
import random
used_accumulator = []
wf_parms = {}
for step in steps:
for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
if isinstance(v, basestring):
for rematch in re.findall('\$\{.+?\}', v):
if rematch[2:-1] not in wf_parms:
wf_parms[rematch[2:-1]] = ""
if wf_parms:
hue_offset = 1.0 / len(wf_parms)
hue = 0.0
for k in wf_parms.iterkeys():
wf_parms[k] = "#%X%X%X" % tuple([int(x * 255) for x in colorsys.hsv_to_rgb(hue, .1, .9)])
hue += hue_offset
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['hue','hue_offset','wf_parms','ActionBox','DataToolParameter','rematch','used_accumulator','k','random','pja','re','step','RuntimeValue','colorsys','v','DataCollectionToolParameter','x'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 323
__M_writer(u'\n\n')
# SOURCE LINE 365
__M_writer(u'\n\n')
# SOURCE LINE 470
__M_writer(u'\n\n<div id=\'ec_button_container\'>\n <span class="action-button" id="show_all_tool_body">Expand All</span>\n <span class="action-button" id="hide_all_tool_body">Collapse</span>\n</div>\n\n<h2>Running workflow "')
# SOURCE LINE 477
__M_writer(unicode(h.to_unicode( workflow.name )))
__M_writer(u'"</h2>\n\n')
# SOURCE LINE 479
if has_upgrade_messages:
# SOURCE LINE 480
__M_writer(u'<div class="warningmessage">\n Problems were encountered when loading this workflow, likely due to tool\n version changes. Missing parameter values have been replaced with default.\n Please review the parameter values below.\n</div>\n')
pass
# SOURCE LINE 486
__M_writer(u'\n')
# SOURCE LINE 487
if step_version_changes:
# SOURCE LINE 488
__M_writer(u' <div class="infomessage">\n The following tools are beinge executed with a different version from\n what was available when this workflow was last saved because the\n previous version is no longer available for use on this galaxy\n instance.\n To upgrade your workflow and dismiss this message simply edit the\n workflow and re-save it to update the stored tool version.\n <ul>\n')
# SOURCE LINE 496
for vc in step_version_changes:
# SOURCE LINE 497
__M_writer(u' <li>')
__M_writer(unicode(vc))
__M_writer(u'</li>\n')
pass
# SOURCE LINE 499
__M_writer(u' </ul>\n </div>\n')
pass
# SOURCE LINE 502
__M_writer(u'\n')
# SOURCE LINE 503
if workflow.annotation:
# SOURCE LINE 504
__M_writer(u' <div class="workflow-annotation">')
__M_writer(unicode(workflow.annotation))
__M_writer(u'</div>\n <hr/>\n')
pass
# SOURCE LINE 507
__M_writer(u'\n<form id="tool_form" name="tool_form" method="POST">\n')
# SOURCE LINE 510
__M_writer(u'\n')
# SOURCE LINE 511
if wf_parms:
# SOURCE LINE 512
__M_writer(u'<div class="metadataForm">\n <div class="metadataFormTitle">Workflow Parameters</div>\n <div class="metadataFormBody">\n')
# SOURCE LINE 515
for parm in wf_parms:
# SOURCE LINE 516
__M_writer(u" <div class='form-row'><label style='width:100px;'>")
__M_writer(unicode(parm))
__M_writer(u'<input style="border:2px solid ')
__M_writer(unicode(wf_parms[parm]))
__M_writer(u';border-left-width:8px;" type="text" class=\'wf_parm_input ptag_')
__M_writer(unicode(parm))
__M_writer(u'\' name="wf_parm|')
__M_writer(unicode(parm))
__M_writer(u'" value=""/></label></div>\n')
pass
# SOURCE LINE 518
__M_writer(u' </div>\n</div>\n <script type="text/javascript">\n // Set the change hooks for workflow parameters.\n $(document).ready(function () {\n $(\'.wf_parm_input\').bind(\'change keypress keyup\', function(event){\n // DBTODO This is probably not reliable. Ensure we have the right class.\n var new_text = $(this).val();\n if (new_text === \'\'){\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(tag_id);\n }else{\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(new_text);\n // Now set the hidden input to the generated text.\n $(\'.wfpspan.wf_parm__\'+tag_id).not(\'.pja_wfp\').each(function(){\n var new_text = $(this).parent().text();\n $(this).parent().siblings().children().val(new_text);\n });\n }\n });\n });\n </script>\n')
pass
# SOURCE LINE 544
for i, step in enumerate( steps ):
# SOURCE LINE 545
__M_writer(u' <!-- Only way module would be missing is if tool is missing, but\n that would cause missing_tools.mako to render instead of this\n template. -->\n ')
# SOURCE LINE 548
module = step.module
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['module'] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 549
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(module.encode_runtime_state( t, step.state )))
__M_writer(u'">\n')
# SOURCE LINE 550
if step.type == 'tool' or step.type is None:
# SOURCE LINE 551
__M_writer(u' ')
tool = trans.app.toolbox.get_tool( step.tool_id )
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['tool'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 553
__M_writer(u'\n <div class="toolForm">\n <div class="toolFormTitle">\n <span class=\'title_ul_text\'>Step ')
# SOURCE LINE 556
__M_writer(unicode(int(step.order_index)+1))
__M_writer(u': ')
__M_writer(unicode(tool.name))
__M_writer(u'</span>\n')
# SOURCE LINE 557
if tool.version:
# SOURCE LINE 558
__M_writer(u' (version ')
__M_writer(unicode(tool.version))
__M_writer(u')\n')
pass
# SOURCE LINE 560
if step.annotations:
# SOURCE LINE 561
__M_writer(u' <div class="step-annotation">')
__M_writer(unicode(h.to_unicode( step.annotations[0].annotation )))
__M_writer(u'</div>\n')
pass
# SOURCE LINE 563
__M_writer(u' </div>\n <div class="toolFormBody">\n ')
# SOURCE LINE 565
__M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )))
__M_writer(u'\n')
# SOURCE LINE 566
if step.post_job_actions:
# SOURCE LINE 567
__M_writer(u" <hr/>\n <div class='form-row'>\n")
# SOURCE LINE 569
if len(step.post_job_actions) > 1:
# SOURCE LINE 570
__M_writer(u' <label>Actions:</label>\n')
# SOURCE LINE 571
else:
# SOURCE LINE 572
__M_writer(u' <label>Action:</label>\n')
pass
# SOURCE LINE 574
__M_writer(u' ')
pja_ss_all = []
for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
for rematch in re.findall('\$\{.+?\}', pja_ss):
pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
pja_ss_all.append(pja_ss)
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['rematch','pja_ss_all','pja','pja_ss'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 580
__M_writer(u'\n ')
# SOURCE LINE 581
__M_writer(unicode('<br/>'.join(pja_ss_all)))
__M_writer(u'\n </div>\n')
pass
# SOURCE LINE 584
__M_writer(u' </div>\n </div>\n')
# SOURCE LINE 586
else:
# SOURCE LINE 587
__M_writer(u' <div class="toolForm">\n <div class="toolFormTitle">\n <span class=\'title_ul_text\'>Step ')
# SOURCE LINE 589
__M_writer(unicode(int(step.order_index)+1))
__M_writer(u': ')
__M_writer(unicode(module.name))
__M_writer(u'</span>\n')
# SOURCE LINE 590
if step.annotations:
# SOURCE LINE 591
__M_writer(u' <div class="step-annotation">')
__M_writer(unicode(step.annotations[0].annotation))
__M_writer(u'</div>\n')
pass
# SOURCE LINE 593
__M_writer(u' </div>\n <div class="toolFormBody">\n ')
# SOURCE LINE 595
# Filter possible inputs to data types that are valid for subsequent steps
type_filter = []
for oc in step.output_connections:
for ic in oc.input_step.module.get_data_inputs():
if 'extensions' in ic and ic['name'] == oc.input_name:
type_filter += ic['extensions']
if not type_filter:
type_filter = ['data']
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['ic','oc','type_filter'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 604
__M_writer(u'\n ')
# SOURCE LINE 605
__M_writer(unicode(do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )))
__M_writer(u'\n </div>\n </div>\n')
pass
pass
# SOURCE LINE 610
if history_id is None:
# SOURCE LINE 611
__M_writer(u' <p id=\'new_history_p\'>\n <input type="checkbox" name=\'new_history\' value="true" id=\'new_history_cbx\'/><label for=\'new_history_cbx\'>Send results to a new history </label>\n <span id="new_history_input">named: <input type=\'text\' name=\'new_history_name\' value=\'')
# SOURCE LINE 613
__M_writer(filters.html_escape(unicode( h.to_unicode( workflow.name ) )))
__M_writer(u"'/></span>\n </p>\n")
pass
# SOURCE LINE 616
__M_writer(u'<input type="submit" class="btn btn-primary" name="run_workflow" value="Run workflow" />\n</form>\n')
return ''
finally:
context.caller_stack._pop_frame()
def _workflow_to_dict_run(self, trans, stored):
"""
Builds workflow dictionary used by run workflow form
"""
workflow = stored.latest_workflow
if len(workflow.steps) == 0:
raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
if attach_ordered_steps(workflow, workflow.steps):
raise exceptions.MessageException('Workflow cannot be run because it contains cycles.')
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
has_upgrade_messages = False
step_version_changes = []
missing_tools = []
errors = {}
for step in workflow.steps:
try:
module_injector.inject(step, steps=workflow.steps, exact_tools=False)
except exceptions.ToolMissingException:
if step.tool_id not in missing_tools:
missing_tools.append(step.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is None:
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
if step_errors:
errors[step.id] = step_errors
if missing_tools:
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
raise exceptions.MessageException('Following tools missing: %s' % missing_tools)
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
step_order_indices = {}
for step in workflow.steps:
step_order_indices[step.id] = step.order_index
step_models = []
for i, step in enumerate(workflow.steps):
step_model = None
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version)
params_to_incoming(incoming, tool.inputs, step.state.inputs, trans.app)
step_model = tool.to_json(trans, incoming, workflow_building_mode=workflow_building_modes.USE_HISTORY)
step_model['post_job_actions'] = [{
'short_str' : ActionBox.get_short_str(pja),
'action_type' : pja.action_type,
'output_name' : pja.output_name,
'action_arguments' : pja.action_arguments
} for pja in step.post_job_actions]
else:
inputs = step.module.get_runtime_inputs(connections=step.output_connections)
step_model = {
'inputs' : [input.to_dict(trans) for input in inputs.values()]
}
step_model['step_type'] = step.type
step_model['step_label'] = step.label
step_model['step_name'] = step.module.get_name()
step_model['step_version'] = step.module.get_version()
step_model['step_index'] = step.order_index
step_model['output_connections'] = [{
'input_step_index' : step_order_indices.get(oc.input_step_id),
'output_step_index' : step_order_indices.get(oc.output_step_id),
'input_name' : oc.input_name,
'output_name' : oc.output_name
} for oc in step.output_connections]
if step.annotations:
step_model['annotation'] = step.annotations[0].annotation
if step.upgrade_messages:
step_model['messages'] = step.upgrade_messages
step_models.append(step_model)
return {
'id': trans.app.security.encode_id(stored.id),
'history_id': trans.app.security.encode_id(trans.history.id) if trans.history else None,
'name': stored.name,
'steps': step_models,
'step_version_changes': step_version_changes,
'has_upgrade_messages': has_upgrade_messages,
'workflow_resource_parameters': self._workflow_resource_parameters(trans, stored, workflow),
}
def render_body(context,**pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
basestring = context.get('basestring', UNDEFINED)
errors = context.get('errors', UNDEFINED)
tuple = context.get('tuple', UNDEFINED)
int = context.get('int', UNDEFINED)
h = context.get('h', UNDEFINED)
app = context.get('app', UNDEFINED)
workflow = context.get('workflow', UNDEFINED)
def do_inputs(inputs,values,errors,prefix,step,other_values=None):
return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values)
len = context.get('len', UNDEFINED)
dict = context.get('dict', UNDEFINED)
t = context.get('t', UNDEFINED)
enumerate = context.get('enumerate', UNDEFINED)
has_upgrade_messages = context.get('has_upgrade_messages', UNDEFINED)
steps = context.get('steps', UNDEFINED)
isinstance = context.get('isinstance', UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n\n')
# SOURCE LINE 13
__M_writer(u'\n\n')
# SOURCE LINE 32
__M_writer(u'\n\n')
# SOURCE LINE 34
from galaxy.tools.parameters import DataToolParameter, RuntimeValue
from galaxy.jobs.actions.post import ActionBox
import re
import colorsys
import random
wf_parms = {}
for step in steps:
for v in step.state.inputs.itervalues():
if isinstance(v, basestring):
for rematch in re.findall('\$\{.+?\}', v):
if rematch[2:-1] not in wf_parms:
wf_parms[rematch[2:-1]] = ""
if wf_parms:
hue_offset = 1.0 / len(wf_parms)
hue = 0.0
for k in wf_parms.iterkeys():
wf_parms[k] = "#%X%X%X" % tuple([int(x * 255) for x in colorsys.hsv_to_rgb(hue, .1, .9)])
hue += hue_offset
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key]) for __M_key in ['hue','hue_offset','wf_parms','ActionBox','DataToolParameter','rematch','k','random','re','step','RuntimeValue','colorsys','v','x'] if __M_key in __M_locals_builtin()]))
# SOURCE LINE 54
__M_writer(u'\n\n')
# SOURCE LINE 91
__M_writer(u'\n\n')
# SOURCE LINE 163
__M_writer(u'\n\n<h2>Running workflow "')
# SOURCE LINE 165
__M_writer(unicode(h.to_unicode( workflow.name )))
__M_writer(u'"</h2>\n\n')
# SOURCE LINE 167
if has_upgrade_messages:
# SOURCE LINE 168
__M_writer(u'<div class="warningmessage">\n Problems were encountered when loading this workflow, likely due to tool\n version changes. Missing parameter values have been replaced with default.\n Please review the parameter values below.\n</div>\n')
# SOURCE LINE 174
__M_writer(u'\n')
# SOURCE LINE 175
if workflow.annotation:
# SOURCE LINE 176
__M_writer(u' <div class="workflow-annotation">Annotation: ')
__M_writer(unicode(workflow.annotation))
__M_writer(u'</div>\n <hr/>\n')
# SOURCE LINE 179
__M_writer(u'\n<form id="tool_form" name="tool_form" method="POST">\n')
# SOURCE LINE 182
__M_writer(u'\n\n')
# SOURCE LINE 184
if wf_parms:
# SOURCE LINE 185
__M_writer(u'<div class="metadataForm">\n <div class="metadataFormTitle">Workflow Parameters</div>\n <div class="metadataFormBody">\n')
# SOURCE LINE 188
for parm in wf_parms:
# SOURCE LINE 189
__M_writer(u" <div class='form-row'><label style='width:100px;'>")
__M_writer(unicode(parm))
__M_writer(u'<input style="border:2px solid ')
__M_writer(unicode(wf_parms[parm]))
__M_writer(u';border-left-width:8px;" type="text" class=\'wf_parm_input ptag_')
__M_writer(unicode(parm))
__M_writer(u'\' name="wf_parm|')
__M_writer(unicode(parm))
__M_writer(u'" value=""/></label></div>\n')
# SOURCE LINE 191
__M_writer(u' </div>\n</div>\n <script type="text/javascript">\n // Set the change hooks for workflow parameters.\n $(document).ready(function () {\n $(\'.wf_parm_input\').bind(\'change keypress keyup\', function(event){\n // DBTODO This is probably not reliable. Ensure we have the right class.\n var new_text = $(this).val();\n if (new_text === \'\'){\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(tag_id);\n }else{\n var tag_id = $(this).attr("class").split(\' \')[1].substring(5);\n // Set text properly.\n $(\'.wfpspan.wf_parm__\'+tag_id).text(new_text);\n // Now set the hidden input to the generated text.\n $(\'.wfpspan.wf_parm__\'+tag_id).not(\'.pja_wfp\').each(function(){\n // var new_text = $(this).parent().text();\n $(this).parent().siblings().children().val(new_text);\n });\n }\n });\n });\n </script>\n')
# SOURCE LINE 217
__M_writer(u'\n')
# SOURCE LINE 218
for i, step in enumerate( steps ):
# SOURCE LINE 219
if step.type == 'tool' or step.type is None:
# SOURCE LINE 220
__M_writer(u' ')
tool = app.toolbox.tools_by_id[step.tool_id]
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key]) for __M_key in ['tool'] if __M_key in __M_locals_builtin()]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 221
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(step.state.encode( tool, app )))
__M_writer(u'">\n <div class="toolForm">\n <div class="toolFormTitle">\n Step ')
# SOURCE LINE 224
__M_writer(unicode(int(step.order_index)+1))
__M_writer(u': ')
__M_writer(unicode(tool.name))
__M_writer(u'\n')
# SOURCE LINE 225
if step.annotations:
# SOURCE LINE 226
__M_writer(u' <div class="step-annotation">Annotation: ')
__M_writer(unicode(h.to_unicode( step.annotations[0].annotation )))
__M_writer(u'</div>\n')
# SOURCE LINE 228
__M_writer(u' </div>\n <div class="toolFormBody">\n ')
# SOURCE LINE 230
__M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step )))
__M_writer(u'\n')
# SOURCE LINE 231
if step.post_job_actions:
# SOURCE LINE 232
__M_writer(u" <hr/>\n <div class='form-row'>\n")
# SOURCE LINE 234
if len(step.post_job_actions) > 1:
# SOURCE LINE 235
__M_writer(u' <label>Actions:</label>\n')
# SOURCE LINE 236
else:
# SOURCE LINE 237
__M_writer(u' <label>Action:</label>\n')
# SOURCE LINE 239
pja_ss_all = []
for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
for rematch in re.findall('\$\{.+?\}', pja_ss):
pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
pja_ss_all.append(pja_ss)
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key]) for __M_key in ['rematch','pja_ss_all','pja','pja_ss'] if __M_key in __M_locals_builtin()]))
# SOURCE LINE 245
__M_writer(u'\n ')
# SOURCE LINE 246
__M_writer(unicode('<br/>'.join(pja_ss_all)))
__M_writer(u'\n </div>\n')
# SOURCE LINE 249
__M_writer(u' </div>\n </div>\n')
# SOURCE LINE 251
else:
# SOURCE LINE 252
__M_writer(u' ')
module = step.module
__M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin()[__M_key]) for __M_key in ['module'] if __M_key in __M_locals_builtin()]))
__M_writer(u'\n <input type="hidden" name="')
# SOURCE LINE 253
__M_writer(unicode(step.id))
__M_writer(u'|tool_state" value="')
__M_writer(unicode(module.encode_runtime_state( t, step.state )))
__M_writer(u'">\n <div class="toolForm">\n <div class="toolFormTitle">\n Step ')
# SOURCE LINE 256
__M_writer(unicode(int(step.order_index)+1))
__M_writer(u': ')
__M_writer(unicode(module.name))
__M_writer(u'\n')
# SOURCE LINE 257
if step.annotations:
# SOURCE LINE 258
__M_writer(u' <div class="step-annotation">Annotation: ')
__M_writer(unicode(step.annotations[0].annotation))
__M_writer(u'</div>\n')
# SOURCE LINE 260
__M_writer(u' </div>\n <div class="toolFormBody">\n ')
# SOURCE LINE 262
__M_writer(unicode(do_inputs( module.get_runtime_inputs(), step.state.inputs, errors.get( step.id, dict() ), "", step )))
__M_writer(u'\n </div>\n </div>\n')
# SOURCE LINE 267
__M_writer(u'<input type="submit" name="run_workflow" value="Run workflow" />\n</form>')
return ''
finally:
context.caller_stack._pop_frame()
