def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
"""Build a temp file with errors in it"""
errors = []
for name, data in inp_data.items():
validation_errors = data.validation_errors
for error in validation_errors:
# build dummy class
try:
temp = eval(error.err_type)()
except:
temp = object()
# stuff attributes
temp.__dict__ = util.string_to_object( error.attributes )
errors.append(temp)
# There *should* only be 1 input, so we assume there is and continue
# base64 pickel
errors_str = util.object_to_string( errors )
# write
database_tmp = "./database/tmp" # globaly visible path
error_file = tempfile.NamedTemporaryFile(mode="w", dir=database_tmp, suffix=".b64")
error_file_name = error_file.name
error_file.close()
error_file = open(error_file_name, "w")
error_file.write(errors_str)
error_file.close()
param_dict["errorsfile"] = error_file_name
def main():
options, args = doc_optparse.parse( __doc__ )
try:
extension = options.ext
except:
doc_optparse.exception()
# create datatype
data = model.Dataset( extension=extension, id=int( args[0] ) )
data.file_path = "/home/ian/trunk/database/files/"
if options.metadata:
data.metadata = util.string_to_object( options.metadata )
errors = data.datatype.validate( data )
print util.object_to_string(errors)
class UCSCProxy( BaseUIController ):
def create_display(self, store):
"""Creates a more meaningulf display name"""
track = store.get('hgta_track','no track')
table = store.get('hgta_table','no table')
region = store.get('hgta_regionType','')
if region not in [ 'genome', 'encode']:
region = store.get('position','')
if track == table:
display = 'UCSC: %s (%s)' % (track, region)
else:
display = 'UCSC: %s, %s (%s)' % (track, table, region)
return display
@web.expose
def index(self, trans, init=False, **kwd):
base_url = None
params = dict(kwd)
try:
store = params.get("__GALAXY__", None)
if store:
store = util.string_to_object(store)
else:
store = {}
UCSC_URL = 'UCSC_URL'
base_url = store.get(UCSC_URL, "http://genome.ucsc.edu/cgi-bin/hgTables?")
params = dict(kwd)
params['init'] = init
if not init:
for key, value in kwd.items():
store[key] = value
try: del store["__GALAXY__"]
except: pass
else:
store = {}
if init == "1":
base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "2":
base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "3":
base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?"
store[UCSC_URL] = base_url
try: del params["__GALAXY__"]
except: pass
url = base_url + urllib.urlencode(params)
page = urllib.urlopen(url)
content = page.info().get('Content-type', '')
except Exception, exc:
trans.log_event( "Proxy Error -> %s" % str(exc) )
msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc)
return msg
if content.startswith('text/plain'):
params['display'] = self.create_display(store)
params['dbkey'] = store.get('db', '*')
params['tool_id'] = 'ucsc_proxy'
params['proxy_url'] = base_url
params['runtool_btn'] = 'T'
#url = "/echo?" + urllib.urlencode(params)
url = "/tool_runner/index?" + urllib.urlencode(params)
trans.response.send_redirect(url)
else:
try:
text = page.read()
# Serialize store into a form element
store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \
+ util.object_to_string(store) + "\" \>"
# Remove text regions that should not be exposed
for key,value in altered_regions.items():
text = text.replace(key,value)
# Capture only the forms
newtext = beginning
for form in re.finditer("(?s)(<FORM.*?)(</FORM>)",text):
newtext = newtext + form.group(1) + store_text + form.group(2)
if 'hgta_doLookupPosition' in params:
lookup = re.search("(?s).*?(<H2>.*</PRE>)",text)
if lookup:
newtext = newtext + lookup.group(1)
# if these keys are in the params, then pass the content through
passthruContent = ['hgta_doSummaryStats', 'hgta_doSchema', 'hgta_doSchemaDb']
for k in passthruContent:
if k in params:
content = re.search("(?s)CONTENT TABLES.*?-->(.*/TABLE>)",text)
if content:
newtext = newtext + "<TABLE>" + content.group(1)
newtext = newtext + ending
return newtext
except KeyError, exc:
log.error(str(exc))
trans.log_event( "Proxy Error -> %s" % str(exc) )
msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc)
return msg
def __state_to_string(self, tool_state):
return object_to_string(tool_state.encode(self.tool, self.app))
def render_body(context,**pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
_import_ns = {}
_mako_get_namespace(context, '__anon_0x2302d290')._populate(_import_ns, [u'overlay'])
_mako_get_namespace(context, '__anon_0x2302d150')._populate(_import_ns, [u'render_msg'])
add_frame = _import_ns.get('add_frame', context.get('add_frame', UNDEFINED))
errors = _import_ns.get('errors', context.get('errors', UNDEFINED))
render_msg = _import_ns.get('render_msg', context.get('render_msg', UNDEFINED))
unicode = _import_ns.get('unicode', context.get('unicode', UNDEFINED))
overlay = _import_ns.get('overlay', context.get('overlay', UNDEFINED))
h = _import_ns.get('h', context.get('h', UNDEFINED))
app = _import_ns.get('app', context.get('app', UNDEFINED))
def do_inputs(inputs,tool_state,errors,prefix,other_values=None):
return render_do_inputs(context.locals_(__M_locals),inputs,tool_state,errors,prefix,other_values)
len = _import_ns.get('len', context.get('len', UNDEFINED))
util = _import_ns.get('util', context.get('util', UNDEFINED))
tool_id_version_message = _import_ns.get('tool_id_version_message', context.get('tool_id_version_message', UNDEFINED))
def row_for_rerun():
return render_row_for_rerun(context.locals_(__M_locals))
type = _import_ns.get('type', context.get('type', UNDEFINED))
tool_state = _import_ns.get('tool_state', context.get('tool_state', UNDEFINED))
trans = _import_ns.get('trans', context.get('trans', UNDEFINED))
AttributeError = _import_ns.get('AttributeError', context.get('AttributeError', UNDEFINED))
tool = _import_ns.get('tool', context.get('tool', UNDEFINED))
tool_version_select_field = _import_ns.get('tool_version_select_field', context.get('tool_version_select_field', UNDEFINED))
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n')
# SOURCE LINE 2
__M_writer(u'\n')
# SOURCE LINE 3
__M_writer(u'\n\n')
# SOURCE LINE 5
import galaxy.util
__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 ['galaxy'] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n')
# SOURCE LINE 14
__M_writer(u'\n\n')
# SOURCE LINE 110
__M_writer(u'\n\n')
# SOURCE LINE 203
__M_writer(u'\n\n')
# SOURCE LINE 231
__M_writer(u'\n\n')
# SOURCE LINE 235
__M_writer(u'\n\n')
# SOURCE LINE 242
__M_writer(u'\n\n')
# SOURCE LINE 250
__M_writer(u'\n\n')
# SOURCE LINE 258
__M_writer(u'\n\n')
# SOURCE LINE 270
__M_writer(u'\n\n')
# SOURCE LINE 272
overlay(visible=False)
__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 [] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n')
# SOURCE LINE 274
if add_frame.from_noframe:
# SOURCE LINE 275
__M_writer(u' <div class="warningmessage">\n <strong>Welcome to Galaxy</strong>\n <hr/>\n It appears that you found this tool from a link outside of Galaxy.\n If you\'re not familiar with Galaxy, please consider visiting the\n <a href="')
# SOURCE LINE 280
__M_writer(unicode(h.url_for( controller='root' )))
__M_writer(u'" target="_top">welcome page</a>.\n To learn more about what Galaxy is and what it can do for you, please visit\n the <a href="')
# SOURCE LINE 282
__M_writer(unicode(add_frame.wiki_url))
__M_writer(u'" target="_top">Galaxy wiki</a>.\n </div>\n <br/>\n')
pass
# SOURCE LINE 286
__M_writer(u'\n')
# SOURCE LINE 287
# Render an error message if a dynamically generated select list is missing a required
# index file or entry in the tool_data_table_conf.xml file.
message = ""
params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry
params_with_missing_index_file = tool.params_with_missing_index_file
if params_with_missing_data_table_entry:
param = params_with_missing_data_table_entry[0]
message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name
if tool.params_with_missing_index_file:
param = params_with_missing_index_file[0]
message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file
# Handle calculating the redirect url for the special case where we have nginx proxy
# upload and need to do url_for on the redirect portion of the tool action.
try:
tool_url = h.url_for(tool.action)
except AttributeError:
assert len(tool.action) == 2
tool_url = tool.action[0] + h.url_for(tool.action[1])
__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_url','message','params_with_missing_data_table_entry','params_with_missing_index_file','param'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 307
__M_writer(u'\n\n')
# SOURCE LINE 309
# Name of the tool in lower case
low_tool_name = tool.name.lower()
__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 ['low_tool_name'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 312
__M_writer(u'\n\n')
# SOURCE LINE 314
if tool_id_version_message:
# SOURCE LINE 315
__M_writer(u' ')
__M_writer(unicode(render_msg( tool_id_version_message, 'warning' )))
__M_writer(u'\n')
pass
# SOURCE LINE 317
__M_writer(u'\n<div class="toolForm" id="')
# SOURCE LINE 318
__M_writer(unicode(tool.id))
__M_writer(u'">\n <form id="tool_form" name="tool_form" action="')
# SOURCE LINE 319
__M_writer(unicode(tool_url))
__M_writer(u'" enctype="')
__M_writer(unicode(tool.enctype))
__M_writer(u'" target="')
__M_writer(unicode(tool.target))
__M_writer(u'" method="')
__M_writer(unicode(tool.method))
__M_writer(u'">\n')
# SOURCE LINE 320
if tool.has_multiple_pages:
# SOURCE LINE 321
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (step ')
__M_writer(unicode(tool_state.page+1))
__M_writer(u' of ')
__M_writer(unicode(tool.npages))
__M_writer(u')\n')
# SOURCE LINE 322
elif not tool_version_select_field:
# SOURCE LINE 323
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (version ')
__M_writer(unicode(tool.version))
__M_writer(u')\n')
# SOURCE LINE 324
else:
# SOURCE LINE 325
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' ')
__M_writer(unicode(tool_version_select_field.get_html()))
__M_writer(u'\n')
pass
# SOURCE LINE 327
__M_writer(u'\n <span class="pull-right">\n')
# SOURCE LINE 329
if trans.app.config.biostar_url:
# SOURCE LINE 331
__M_writer(u' Help from Biostar\n <div class="icon-btn-group">\n <a href="')
# SOURCE LINE 333
__M_writer(unicode(h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )))
__M_writer(u'"\n target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a>\n <a href="')
# SOURCE LINE 335
__M_writer(unicode(h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )))
__M_writer(u'"\n target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a>\n </div>\n')
pass
# SOURCE LINE 339
__M_writer(u' <div class="icon-btn-group">\n <a href="#" data-link="')
# SOURCE LINE 340
__M_writer(unicode(h.url_for( controller='root', action='index', tool_id=tool.id )))
__M_writer(u'"\n class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a>\n </div>\n </span>\n </div>\n <div class="toolFormBody">\n <input type="hidden" name="refresh" value="refresh">\n <input type="hidden" name="tool_id" value="')
# SOURCE LINE 347
__M_writer(unicode(tool.id))
__M_writer(u'">\n <input type="hidden" name="tool_state" value="')
# SOURCE LINE 348
__M_writer(unicode(util.object_to_string( tool_state.encode( tool, app ) )))
__M_writer(u'">\n')
# SOURCE LINE 349
if tool.display_by_page[tool_state.page]:
# SOURCE LINE 350
__M_writer(u' ')
__M_writer(unicode(trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )))
__M_writer(u'\n ')
# SOURCE LINE 351
__M_writer(unicode(row_for_rerun()))
__M_writer(u'\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n')
# SOURCE LINE 353
else:
# SOURCE LINE 354
__M_writer(u' ')
__M_writer(unicode(do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )))
__M_writer(u'\n')
# SOURCE LINE 355
if tool_state.page == tool.last_page:
# SOURCE LINE 356
__M_writer(u' ')
__M_writer(unicode(row_for_rerun()))
__M_writer(u'\n')
pass
# SOURCE LINE 358
__M_writer(u' <div class="form-row form-actions">\n')
# SOURCE LINE 359
if tool_state.page == tool.last_page:
# SOURCE LINE 360
__M_writer(u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n')
# SOURCE LINE 361
else:
# SOURCE LINE 362
__M_writer(u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step">\n')
pass
# SOURCE LINE 364
__M_writer(u' </div>\n')
pass
# SOURCE LINE 366
__M_writer(u' </div>\n </form>\n</div>\n')
# SOURCE LINE 369
if tool.help:
# SOURCE LINE 370
__M_writer(u' <div class="toolHelp">\n <div class="toolHelpBody">\n ')
# SOURCE LINE 372
if tool.has_multiple_pages:
tool_help = tool.help_by_page[tool_state.page]
else:
tool_help = tool.help
# Help is Mako template, so render using current static path.
tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) )
# Convert to unicode to display non-ascii characters.
if type( tool_help ) is not unicode:
tool_help = unicode( tool_help, 'utf-8')
__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_help'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 384
__M_writer(u'\n ')
# SOURCE LINE 385
__M_writer(unicode(tool_help))
__M_writer(u'\n </div>\n </div>\n')
pass
# SOURCE LINE 389
if tool.tool_shed_repository:
# SOURCE LINE 390
__M_writer(u' ')
tool_url = tool.tool_shed_repository.get_sharable_url( tool.app )
__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_url'] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n')
# SOURCE LINE 391
if tool_url:
# SOURCE LINE 392
__M_writer(u' <br/>\n ')
# SOURCE LINE 393
__M_writer(unicode( render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) ))
__M_writer(u'\n')
pass
pass
# SOURCE LINE 396
if tool.citations:
# SOURCE LINE 397
__M_writer(u' <script>\n require(["mvc/citation/citation-model", "mvc/citation/citation-view"\n ], function( citationModel, citationView ){\n $(function() {\n var citations = new citationModel.ToolCitationCollection();\n citations.tool_id = "')
# SOURCE LINE 402
__M_writer(unicode(tool.id))
__M_writer(u'";\n var citation_list_view = new citationView.CitationListView({ collection: citations } );\n citation_list_view.render();\n citations.fetch();\n } );\n } );\n </script>\n <div id="citations">\n </div>\n')
pass
# SOURCE LINE 412
__M_writer(u'\n')
return ''
finally:
context.caller_stack._pop_frame()
def __state_to_string( self, tool_state ):
return object_to_string( tool_state.encode( self.tool, self.app ) )
def render_body(context, **pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
_import_ns = {}
_mako_get_namespace(context, '__anon_0x2302d290')._populate(
_import_ns, [u'overlay'])
_mako_get_namespace(context, '__anon_0x2302d150')._populate(
_import_ns, [u'render_msg'])
add_frame = _import_ns.get('add_frame',
context.get('add_frame', UNDEFINED))
errors = _import_ns.get('errors', context.get('errors', UNDEFINED))
render_msg = _import_ns.get('render_msg',
context.get('render_msg', UNDEFINED))
unicode = _import_ns.get('unicode', context.get('unicode', UNDEFINED))
overlay = _import_ns.get('overlay', context.get('overlay', UNDEFINED))
h = _import_ns.get('h', context.get('h', UNDEFINED))
app = _import_ns.get('app', context.get('app', UNDEFINED))
def do_inputs(inputs, tool_state, errors, prefix, other_values=None):
return render_do_inputs(context.locals_(__M_locals), inputs,
tool_state, errors, prefix, other_values)
len = _import_ns.get('len', context.get('len', UNDEFINED))
util = _import_ns.get('util', context.get('util', UNDEFINED))
tool_id_version_message = _import_ns.get(
'tool_id_version_message',
context.get('tool_id_version_message', UNDEFINED))
def row_for_rerun():
return render_row_for_rerun(context.locals_(__M_locals))
type = _import_ns.get('type', context.get('type', UNDEFINED))
tool_state = _import_ns.get('tool_state',
context.get('tool_state', UNDEFINED))
trans = _import_ns.get('trans', context.get('trans', UNDEFINED))
AttributeError = _import_ns.get(
'AttributeError', context.get('AttributeError', UNDEFINED))
tool = _import_ns.get('tool', context.get('tool', UNDEFINED))
tool_version_select_field = _import_ns.get(
'tool_version_select_field',
context.get('tool_version_select_field', UNDEFINED))
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n')
# SOURCE LINE 2
__M_writer(u'\n')
# SOURCE LINE 3
__M_writer(u'\n\n')
# SOURCE LINE 5
import galaxy.util
__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 ['galaxy']
if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n')
# SOURCE LINE 14
__M_writer(u'\n\n')
# SOURCE LINE 110
__M_writer(u'\n\n')
# SOURCE LINE 203
__M_writer(u'\n\n')
# SOURCE LINE 231
__M_writer(u'\n\n')
# SOURCE LINE 235
__M_writer(u'\n\n')
# SOURCE LINE 242
__M_writer(u'\n\n')
# SOURCE LINE 250
__M_writer(u'\n\n')
# SOURCE LINE 258
__M_writer(u'\n\n')
# SOURCE LINE 270
__M_writer(u'\n\n')
# SOURCE LINE 272
overlay(visible=False)
__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 []
if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n')
# SOURCE LINE 274
if add_frame.from_noframe:
# SOURCE LINE 275
__M_writer(
u' <div class="warningmessage">\n <strong>Welcome to Galaxy</strong>\n <hr/>\n It appears that you found this tool from a link outside of Galaxy.\n If you\'re not familiar with Galaxy, please consider visiting the\n <a href="'
)
# SOURCE LINE 280
__M_writer(unicode(h.url_for(controller='root')))
__M_writer(
u'" target="_top">welcome page</a>.\n To learn more about what Galaxy is and what it can do for you, please visit\n the <a href="'
)
# SOURCE LINE 282
__M_writer(unicode(add_frame.wiki_url))
__M_writer(
u'" target="_top">Galaxy wiki</a>.\n </div>\n <br/>\n')
pass
# SOURCE LINE 286
__M_writer(u'\n')
# SOURCE LINE 287
# Render an error message if a dynamically generated select list is missing a required
# index file or entry in the tool_data_table_conf.xml file.
message = ""
params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry
params_with_missing_index_file = tool.params_with_missing_index_file
if params_with_missing_data_table_entry:
param = params_with_missing_data_table_entry[0]
message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name
if tool.params_with_missing_index_file:
param = params_with_missing_index_file[0]
message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file
# Handle calculating the redirect url for the special case where we have nginx proxy
# upload and need to do url_for on the redirect portion of the tool action.
try:
tool_url = h.url_for(tool.action)
except AttributeError:
assert len(tool.action) == 2
tool_url = tool.action[0] + h.url_for(tool.action[1])
__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_url', 'message',
'params_with_missing_data_table_entry',
'params_with_missing_index_file', 'param'
] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 307
__M_writer(u'\n\n')
# SOURCE LINE 309
# Name of the tool in lower case
low_tool_name = tool.name.lower()
__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 ['low_tool_name']
if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 312
__M_writer(u'\n\n')
# SOURCE LINE 314
if tool_id_version_message:
# SOURCE LINE 315
__M_writer(u' ')
__M_writer(unicode(render_msg(tool_id_version_message, 'warning')))
__M_writer(u'\n')
pass
# SOURCE LINE 317
__M_writer(u'\n<div class="toolForm" id="')
# SOURCE LINE 318
__M_writer(unicode(tool.id))
__M_writer(u'">\n <form id="tool_form" name="tool_form" action="')
# SOURCE LINE 319
__M_writer(unicode(tool_url))
__M_writer(u'" enctype="')
__M_writer(unicode(tool.enctype))
__M_writer(u'" target="')
__M_writer(unicode(tool.target))
__M_writer(u'" method="')
__M_writer(unicode(tool.method))
__M_writer(u'">\n')
# SOURCE LINE 320
if tool.has_multiple_pages:
# SOURCE LINE 321
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (step ')
__M_writer(unicode(tool_state.page + 1))
__M_writer(u' of ')
__M_writer(unicode(tool.npages))
__M_writer(u')\n')
# SOURCE LINE 322
elif not tool_version_select_field:
# SOURCE LINE 323
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (version ')
__M_writer(unicode(tool.version))
__M_writer(u')\n')
# SOURCE LINE 324
else:
# SOURCE LINE 325
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' ')
__M_writer(unicode(tool_version_select_field.get_html()))
__M_writer(u'\n')
pass
# SOURCE LINE 327
__M_writer(u'\n <span class="pull-right">\n')
# SOURCE LINE 329
if trans.app.config.biostar_url:
# SOURCE LINE 331
__M_writer(
u' Help from Biostar\n <div class="icon-btn-group">\n <a href="'
)
# SOURCE LINE 333
__M_writer(
unicode(
h.url_for(controller='biostar',
action='biostar_tool_tag_redirect',
tool_id=tool.id)))
__M_writer(
u'"\n target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a>\n <a href="'
)
# SOURCE LINE 335
__M_writer(
unicode(
h.url_for(controller='biostar',
action='biostar_tool_question_redirect',
tool_id=tool.id)))
__M_writer(
u'"\n target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a>\n </div>\n'
)
pass
# SOURCE LINE 339
__M_writer(
u' <div class="icon-btn-group">\n <a href="#" data-link="'
)
# SOURCE LINE 340
__M_writer(
unicode(
h.url_for(controller='root', action='index', tool_id=tool.id)))
__M_writer(
u'"\n class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a>\n </div>\n </span>\n </div>\n <div class="toolFormBody">\n <input type="hidden" name="refresh" value="refresh">\n <input type="hidden" name="tool_id" value="'
)
# SOURCE LINE 347
__M_writer(unicode(tool.id))
__M_writer(
u'">\n <input type="hidden" name="tool_state" value="')
# SOURCE LINE 348
__M_writer(unicode(util.object_to_string(tool_state.encode(tool,
app))))
__M_writer(u'">\n')
# SOURCE LINE 349
if tool.display_by_page[tool_state.page]:
# SOURCE LINE 350
__M_writer(u' ')
__M_writer(
unicode(
trans.fill_template_string(
tool.display_by_page[tool_state.page],
context=tool.get_param_html_map(
trans, tool_state.page, tool_state.inputs))))
__M_writer(u'\n ')
# SOURCE LINE 351
__M_writer(unicode(row_for_rerun()))
__M_writer(
u'\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n'
)
# SOURCE LINE 353
else:
# SOURCE LINE 354
__M_writer(u' ')
__M_writer(
unicode(
do_inputs(tool.inputs_by_page[tool_state.page],
tool_state.inputs, errors, "")))
__M_writer(u'\n')
# SOURCE LINE 355
if tool_state.page == tool.last_page:
# SOURCE LINE 356
__M_writer(u' ')
__M_writer(unicode(row_for_rerun()))
__M_writer(u'\n')
pass
# SOURCE LINE 358
__M_writer(
u' <div class="form-row form-actions">\n')
# SOURCE LINE 359
if tool_state.page == tool.last_page:
# SOURCE LINE 360
__M_writer(
u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n'
)
# SOURCE LINE 361
else:
# SOURCE LINE 362
__M_writer(
u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step">\n'
)
pass
# SOURCE LINE 364
__M_writer(u' </div>\n')
pass
# SOURCE LINE 366
__M_writer(u' </div>\n </form>\n</div>\n')
# SOURCE LINE 369
if tool.help:
# SOURCE LINE 370
__M_writer(
u' <div class="toolHelp">\n <div class="toolHelpBody">\n '
)
# SOURCE LINE 372
if tool.has_multiple_pages:
tool_help = tool.help_by_page[tool_state.page]
else:
tool_help = tool.help
# Help is Mako template, so render using current static path.
tool_help = tool_help.render(static_path=h.url_for('/static'),
host_url=h.url_for('/',
qualified=True))
# Convert to unicode to display non-ascii characters.
if type(tool_help) is not unicode:
tool_help = unicode(tool_help, 'utf-8')
__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_help']
if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 384
__M_writer(u'\n ')
# SOURCE LINE 385
__M_writer(unicode(tool_help))
__M_writer(u'\n </div>\n </div>\n')
pass
# SOURCE LINE 389
if tool.tool_shed_repository:
# SOURCE LINE 390
__M_writer(u' ')
tool_url = tool.tool_shed_repository.get_sharable_url(tool.app)
__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_url']
if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n')
# SOURCE LINE 391
if tool_url:
# SOURCE LINE 392
__M_writer(u' <br/>\n ')
# SOURCE LINE 393
__M_writer(
unicode(
render_msg(
'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>'
% (tool_url, tool_url), 'info')))
__M_writer(u'\n')
pass
pass
# SOURCE LINE 396
if tool.citations:
# SOURCE LINE 397
__M_writer(
u' <script>\n require(["mvc/citation/citation-model", "mvc/citation/citation-view"\n ], function( citationModel, citationView ){\n $(function() {\n var citations = new citationModel.ToolCitationCollection();\n citations.tool_id = "'
)
# SOURCE LINE 402
__M_writer(unicode(tool.id))
__M_writer(
u'";\n var citation_list_view = new citationView.CitationListView({ collection: citations } );\n citation_list_view.render();\n citations.fetch();\n } );\n } );\n </script>\n <div id="citations">\n </div>\n'
)
pass
# SOURCE LINE 412
__M_writer(u'\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)
_import_ns = {}
_mako_get_namespace(context, '__anon_0x11b84b190')._populate(_import_ns, [u'render_msg'])
_mako_get_namespace(context, '__anon_0x1120963d0')._populate(_import_ns, [u'overlay'])
render_msg = _import_ns.get('render_msg', context.get('render_msg', UNDEFINED))
app = _import_ns.get('app', context.get('app', UNDEFINED))
unicode = _import_ns.get('unicode', context.get('unicode', UNDEFINED))
enumerate = _import_ns.get('enumerate', context.get('enumerate', UNDEFINED))
errors = _import_ns.get('errors', context.get('errors', UNDEFINED))
overlay = _import_ns.get('overlay', context.get('overlay', UNDEFINED))
self = _import_ns.get('self', context.get('self', UNDEFINED))
dict = _import_ns.get('dict', context.get('dict', UNDEFINED))
tool_id_version_message = _import_ns.get('tool_id_version_message', context.get('tool_id_version_message', UNDEFINED))
tool_version_select_field = _import_ns.get('tool_version_select_field', context.get('tool_version_select_field', UNDEFINED))
type = _import_ns.get('type', context.get('type', UNDEFINED))
tool = _import_ns.get('tool', context.get('tool', UNDEFINED))
len = _import_ns.get('len', context.get('len', UNDEFINED))
util = _import_ns.get('util', context.get('util', UNDEFINED))
job = _import_ns.get('job', context.get('job', UNDEFINED))
tool_state = _import_ns.get('tool_state', context.get('tool_state', UNDEFINED))
add_frame = _import_ns.get('add_frame', context.get('add_frame', UNDEFINED))
h = _import_ns.get('h', context.get('h', UNDEFINED))
def do_inputs(inputs,tool_state,errors,prefix,other_values=None):
return render_do_inputs(context.locals_(__M_locals),inputs,tool_state,errors,prefix,other_values)
def row_for_rerun():
return render_row_for_rerun(context.locals_(__M_locals))
trans = _import_ns.get('trans', context.get('trans', UNDEFINED))
AttributeError = _import_ns.get('AttributeError', context.get('AttributeError', UNDEFINED))
__M_writer = context.writer()
# SOURCE LINE 1
__M_writer(u'\n\n')
# SOURCE LINE 3
__M_writer(unicode(h.js("libs/bibtex", "libs/jquery/jquery-ui")))
__M_writer(u'\n')
# SOURCE LINE 4
__M_writer(unicode(h.css('base', 'jquery-ui/smoothness/jquery-ui')))
__M_writer(u'\n\n')
# SOURCE LINE 7
if util.string_as_bool(trans.app.config.get('toolform_upgrade', True)):
# SOURCE LINE 8
__M_writer(u' ')
## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
## This avoids making two separate requests since the classic form requires the mako anyway.
params = dict(trans.request.params)
params['__dataset_id__'] = params.get('id', None)
params['__job_id__'] = params.get('job_id', None)
self.form_config = tool.to_json(trans, params)
self.form_config.update({
'id' : tool.id,
'job_id' : trans.security.encode_id( job.id ) if job else None,
'history_id' : trans.security.encode_id( trans.history.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 ['params'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 20
__M_writer(u"\n <script>\n require(['mvc/tools/tools-form'], function(ToolsForm){\n $(function(){\n var form = new ToolsForm.View(")
# SOURCE LINE 24
__M_writer(unicode( h.dumps(self.form_config) ))
__M_writer(u');\n $(\'body\').append(form.$el);\n });\n });\n </script>\n <div id="tool-form-classic" style="display: none;">\n')
# SOURCE LINE 30
else:
# SOURCE LINE 31
__M_writer(u' <div id="tool-form-classic">\n')
pass
# SOURCE LINE 33
__M_writer(u'\n ')
# SOURCE LINE 34
__M_writer(u'\n ')
# SOURCE LINE 35
__M_writer(u'\n\n ')
# SOURCE LINE 37
import galaxy.util
__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 ['galaxy'] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n ')
# SOURCE LINE 46
__M_writer(u'\n\n ')
# SOURCE LINE 142
__M_writer(u'\n\n ')
# SOURCE LINE 235
__M_writer(u'\n\n ')
# SOURCE LINE 263
__M_writer(u'\n\n ')
# SOURCE LINE 267
__M_writer(u'\n\n ')
# SOURCE LINE 274
__M_writer(u'\n\n ')
# SOURCE LINE 282
__M_writer(u'\n\n ')
# SOURCE LINE 290
__M_writer(u'\n\n ')
# SOURCE LINE 302
__M_writer(u'\n\n ')
# SOURCE LINE 304
overlay(visible=False)
__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 [] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n\n')
# SOURCE LINE 306
if add_frame.from_noframe:
# SOURCE LINE 307
__M_writer(u' <div class="warningmessage">\n <strong>Welcome to Galaxy</strong>\n <hr/>\n It appears that you found this tool from a link outside of Galaxy.\n If you\'re not familiar with Galaxy, please consider visiting the\n <a href="')
# SOURCE LINE 312
__M_writer(unicode(h.url_for( controller='root' )))
__M_writer(u'" target="_top">welcome page</a>.\n To learn more about what Galaxy is and what it can do for you, please visit\n the <a href="')
# SOURCE LINE 314
__M_writer(unicode(add_frame.wiki_url))
__M_writer(u'" target="_top">Galaxy wiki</a>.\n </div>\n <br/>\n')
pass
# SOURCE LINE 318
__M_writer(u'\n ')
# SOURCE LINE 319
# Render an error message if a dynamically generated select list is missing a required
# index file or entry in the tool_data_table_conf.xml file.
message = ""
params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry
params_with_missing_index_file = tool.params_with_missing_index_file
if params_with_missing_data_table_entry:
param = params_with_missing_data_table_entry[0]
message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name
if tool.params_with_missing_index_file:
param = params_with_missing_index_file[0]
message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file
# Handle calculating the redirect url for the special case where we have nginx proxy
# upload and need to do url_for on the redirect portion of the tool action.
try:
tool_url = h.url_for(tool.action)
except AttributeError:
assert len(tool.action) == 2
tool_url = tool.action[0] + h.url_for(tool.action[1])
__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_url','message','params_with_missing_data_table_entry','params_with_missing_index_file','param'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 339
__M_writer(u'\n\n ')
# SOURCE LINE 341
# Name of the tool in lower case
low_tool_name = tool.name.lower()
__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 ['low_tool_name'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 344
__M_writer(u'\n\n')
# SOURCE LINE 346
if tool_id_version_message:
# SOURCE LINE 347
__M_writer(u' ')
__M_writer(unicode(render_msg( tool_id_version_message, 'warning' )))
__M_writer(u'\n')
pass
# SOURCE LINE 349
__M_writer(u'\n <div class="toolForm" id="')
# SOURCE LINE 350
__M_writer(unicode(tool.id))
__M_writer(u'">\n <form id="tool_form" name="tool_form" action="')
# SOURCE LINE 351
__M_writer(unicode(tool_url))
__M_writer(u'" enctype="')
__M_writer(unicode(tool.enctype))
__M_writer(u'" target="')
__M_writer(unicode(tool.target))
__M_writer(u'" method="')
__M_writer(unicode(tool.method))
__M_writer(u'">\n')
# SOURCE LINE 352
if tool.has_multiple_pages:
# SOURCE LINE 353
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (step ')
__M_writer(unicode(tool_state.page+1))
__M_writer(u' of ')
__M_writer(unicode(tool.npages))
__M_writer(u')\n')
# SOURCE LINE 354
elif not tool_version_select_field:
# SOURCE LINE 355
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' (Galaxy tool version ')
__M_writer(unicode(tool.version))
__M_writer(u')\n')
# SOURCE LINE 356
else:
# SOURCE LINE 357
__M_writer(u' <div class="toolFormTitle">')
__M_writer(unicode(tool.name))
__M_writer(u' ')
__M_writer(unicode(tool_version_select_field.get_html()))
__M_writer(u'\n')
pass
# SOURCE LINE 360
if tool.requirements:
# SOURCE LINE 361
__M_writer(u' <a href="#" class="icon-btn" title="Underlying versions" tabindex="0" data-toggle="popover" data-placement="bottom" data-content=\n "\n')
# SOURCE LINE 363
for i, requirement in enumerate( tool.requirements ):
# SOURCE LINE 364
__M_writer(u' ')
__M_writer(unicode( requirement.name ))
__M_writer(u' ')
__M_writer(unicode( ('v ' + requirement.version ) if requirement.version else ' ' ))
__M_writer(u' ')
__M_writer(unicode( '' if i + 1 == len( tool.requirements ) else ' | ' ))
__M_writer(u' \n')
pass
# SOURCE LINE 366
__M_writer(u' "\n onclick="$(function () {\n $( \'[ data-toggle=\\\'popover\\\' ]\' ).popover();\n $( this ).popover( \'show\' );\n })">\n <span class="fa fa-info-circle"></span>\n </a>\n')
pass
# SOURCE LINE 374
__M_writer(u'\n <span class="pull-right">\n')
# SOURCE LINE 376
if trans.app.config.biostar_url:
# SOURCE LINE 378
__M_writer(u' Help from Biostar\n <div class="icon-btn-group">\n <a href="')
# SOURCE LINE 380
__M_writer(unicode(h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )))
__M_writer(u'"\n target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a>\n <a href="')
# SOURCE LINE 382
__M_writer(unicode(h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )))
__M_writer(u'"\n target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a>\n </div>\n')
pass
# SOURCE LINE 386
__M_writer(u' <div class="icon-btn-group">\n <a href="#" data-link="')
# SOURCE LINE 387
__M_writer(unicode(h.url_for( controller='root', action='index', tool_id=tool.id, qualified=True )))
__M_writer(u'"\n class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a>\n </div>\n </span>\n </div>\n <div class="toolFormBody">\n <input type="hidden" name="refresh" value="refresh">\n <input type="hidden" name="tool_id" value="')
# SOURCE LINE 394
__M_writer(unicode(tool.id))
__M_writer(u'">\n <input type="hidden" name="tool_state" value="')
# SOURCE LINE 395
__M_writer(unicode(util.object_to_string( tool_state.encode( tool, app ) )))
__M_writer(u'">\n')
# SOURCE LINE 396
if tool.display_by_page[tool_state.page]:
# SOURCE LINE 397
__M_writer(u' ')
__M_writer(unicode(trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )))
__M_writer(u'\n ')
# SOURCE LINE 398
__M_writer(unicode(row_for_rerun()))
__M_writer(u'\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n')
# SOURCE LINE 400
else:
# SOURCE LINE 401
__M_writer(u' ')
__M_writer(unicode(do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )))
__M_writer(u'\n')
# SOURCE LINE 402
if tool_state.page == tool.last_page:
# SOURCE LINE 403
__M_writer(u' ')
__M_writer(unicode(row_for_rerun()))
__M_writer(u'\n')
pass
# SOURCE LINE 405
__M_writer(u' <div class="form-row form-actions">\n')
# SOURCE LINE 406
if tool_state.page == tool.last_page:
# SOURCE LINE 407
__M_writer(u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n')
# SOURCE LINE 408
else:
# SOURCE LINE 409
__M_writer(u' <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step">\n')
pass
# SOURCE LINE 411
__M_writer(u' </div>\n')
pass
# SOURCE LINE 413
__M_writer(u' </div>\n </form>\n </div>\n')
# SOURCE LINE 416
if tool.help:
# SOURCE LINE 417
__M_writer(u' <div class="toolHelp">\n <div class="toolHelpBody">\n ')
# SOURCE LINE 419
if tool.has_multiple_pages:
tool_help = tool.help_by_page[tool_state.page]
else:
tool_help = tool.help
# Help is Mako template, so render using current static path.
tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) )
# Convert to unicode to display non-ascii characters.
if type( tool_help ) is not unicode:
tool_help = unicode( tool_help, 'utf-8')
__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_help'] if __M_key in __M_locals_builtin_stored]))
# SOURCE LINE 431
__M_writer(u'\n ')
# SOURCE LINE 432
__M_writer(unicode(tool_help))
__M_writer(u'\n </div>\n </div>\n')
pass
# SOURCE LINE 436
if tool.tool_shed_repository:
# SOURCE LINE 437
__M_writer(u' ')
tool_url = tool.tool_shed_repository.get_sharable_url( tool.app )
__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_url'] if __M_key in __M_locals_builtin_stored]))
__M_writer(u'\n')
# SOURCE LINE 438
if tool_url:
# SOURCE LINE 439
__M_writer(u' <br/>\n ')
# SOURCE LINE 440
__M_writer(unicode( render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) ))
__M_writer(u'\n')
pass
pass
# SOURCE LINE 443
if tool.citations:
# SOURCE LINE 444
__M_writer(u' <script>\n require(["mvc/citation/citation-model", "mvc/citation/citation-view"\n ], function( citationModel, citationView ){\n $(function() {\n var citations = new citationModel.ToolCitationCollection();\n citations.tool_id = "')
# SOURCE LINE 449
__M_writer(unicode(tool.id))
__M_writer(u'";\n var citation_list_view = new citationView.CitationListView({ collection: citations } );\n citation_list_view.render();\n citations.fetch();\n } );\n } );\n </script>\n <div id="citations">\n </div>\n')
pass
# SOURCE LINE 459
__M_writer(u'</div>\n')
return ''
finally:
context.caller_stack._pop_frame()