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Use request context in handle inputs

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This commit is contained in:
guerler
2016-01-26 14:49:35 -05:00
parent a711757426
commit 0ca9c7027b
6 changed files with 26 additions and 52 deletions
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lib/galaxy/tools/__init__.py
+17 -40
View File
@@ -1049,17 +1049,17 @@ class Tool( object, Dictifiable ):
# outputs?
return True
def new_state( self, trans, history=None ):
def new_state( self, trans ):
"""
Create a new `DefaultToolState` for this tool. It will be initialized
with default values for inputs.
"""
state = DefaultToolState()
state.inputs = {}
self.fill_in_new_state( trans, self.inputs, state.inputs, history=history )
self.fill_in_new_state( trans, self.inputs, state.inputs )
return state
def fill_in_new_state( self, trans, inputs, state, context=None, history=None ):
def fill_in_new_state( self, trans, inputs, state, context=None ):
"""
Fill in a tool state dictionary with default values for all parameters
in the dictionary `inputs`. Grouping elements are filled in recursively.
@@ -1068,22 +1068,6 @@ class Tool( object, Dictifiable ):
for input in inputs.itervalues():
state[ input.name ] = input.get_initial_value( trans, context )
def get_param_html_map( self, trans, page=0, other_values={} ):
"""
Return a dictionary containing the HTML representation of each
parameter. This is used for rendering display elements. It is
currently not compatible with grouping constructs.
NOTE: This should be considered deprecated, it is only used for tools
with `display` elements. These should be eliminated.
"""
rval = dict()
for key, param in self.inputs_by_page[page].iteritems():
if not isinstance( param, ToolParameter ):
raise Exception( "'get_param_html_map' only supported for simple paramters" )
rval[key] = param.get_html( trans, other_values=other_values )
return rval
def get_param( self, key ):
"""
Returns the parameter named `key` or None if there is no such
@@ -1128,6 +1112,7 @@ class Tool( object, Dictifiable ):
to the form or execute the tool (only if 'execute' was clicked and
there were no errors).
"""
request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history or trans.history )
rerun_remap_job_id = None
if 'rerun_remap_job_id' in incoming:
try:
@@ -1152,7 +1137,7 @@ class Tool( object, Dictifiable ):
all_params = []
validate_input = self.get_hook( 'validate_input' )
for expanded_incoming in expanded_incomings:
expanded_state = self.new_state( trans, history=history )
expanded_state = self.new_state( request_context )
# Process incoming data
if not self.check_values:
# If `self.check_values` is false we don't do any checking or
@@ -1163,7 +1148,7 @@ class Tool( object, Dictifiable ):
else:
# Update state for all inputs on the current page taking new
# values from `incoming`.
errors = self.populate_state( trans, self.inputs, expanded_state.inputs, expanded_incoming, history, source=source )
errors = self.populate_state( request_context, self.inputs, expanded_state.inputs, expanded_incoming, source=source )
# If the tool provides a `validate_input` hook, call it.
if validate_input:
validate_input( trans, errors, expanded_state.inputs, self.inputs )
@@ -1176,7 +1161,7 @@ class Tool( object, Dictifiable ):
if any( all_errors ):
raise exceptions.MessageException( err_data=all_errors[ 0 ] )
else:
execution_tracker = execute_job( trans, self, all_params, history=history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info )
execution_tracker = execute_job( trans, self, all_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info )
if execution_tracker.successful_jobs:
return dict( out_data=execution_tracker.output_datasets,
num_jobs=len( execution_tracker.successful_jobs ),
@@ -1219,7 +1204,7 @@ class Tool( object, Dictifiable ):
elif isinstance(x, list):
[ self.find_fieldstorage( y ) for y in x ]
def populate_state( self, trans, inputs, state, incoming, history=None, source="html", prefix="", context=None ):
def populate_state( self, trans, inputs, state, incoming, source="html", prefix="", context=None ):
errors = dict()
# Push this level onto the context stack
context = ExpressionContext( state, context )
@@ -1239,14 +1224,13 @@ class Tool( object, Dictifiable ):
if rep_index < input.max:
new_state = {}
new_state['__index__'] = rep_index
self.fill_in_new_state( trans, input.inputs, new_state, context, history=history )
self.fill_in_new_state( trans, input.inputs, new_state, context )
group_state.append( new_state )
group_errors.append( {} )
rep_errors = self.populate_state( trans,
input.inputs,
new_state,
incoming,
history,
source,
prefix=rep_name + "|",
context=context )
@@ -1288,12 +1272,11 @@ class Tool( object, Dictifiable ):
# Current case has changed, throw away old state
group_state = state[input.name] = {}
# TODO: we should try to preserve values if we can
self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context, history=history )
self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context )
group_errors = self.populate_state( trans,
input.cases[current_case].inputs,
group_state,
incoming,
history,
source,
prefix=group_prefix,
context=context)
@@ -1306,12 +1289,11 @@ class Tool( object, Dictifiable ):
elif isinstance( input, Section ):
group_state = state[input.name]
group_prefix = "%s|" % ( key )
self.fill_in_new_state( trans, input.inputs, group_state, context, history=history )
self.fill_in_new_state( trans, input.inputs, group_state, context )
group_errors = self.populate_state( trans,
input.inputs,
group_state,
incoming,
history,
source,
prefix=group_prefix,
context=context )
@@ -1344,7 +1326,6 @@ class Tool( object, Dictifiable ):
input.inputs,
rep_state,
incoming,
history,
source,
prefix=rep_prefix,
context=context)
@@ -2065,12 +2046,7 @@ class Tool( object, Dictifiable ):
raise exceptions.MessageException( '[history_id=%s] Failed to retrieve history. %s.' % ( history_id, str( e ) ) )
# build request context
request_context = WorkRequestContext(
app = trans.app,
user = trans.user,
history = history,
workflow_building_mode = workflow_mode
)
request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history, workflow_building_mode=workflow_mode )
# load job parameters into incoming
tool_message = ''
@@ -2078,7 +2054,7 @@ class Tool( object, Dictifiable ):
try:
job_params = job.get_param_values( self.app, ignore_errors=True )
self.check_and_update_param_values( job_params, request_context, update_values=False )
self._map_source_to_history( request_context, self.inputs, job_params, history )
self._map_source_to_history( request_context, self.inputs, job_params )
tool_message = self._compare_tool_version( job )
params_to_incoming( kwd, self.inputs, job_params, self.app, to_html=False )
except Exception, e:
@@ -2298,14 +2274,14 @@ class Tool( object, Dictifiable ):
# initialize and populate tool state
state_inputs = {}
state_errors = {}
populate_state( request_context, self.inputs, state_inputs, state_errors, params.__dict__ )
populate_state( self.inputs, state_inputs, state_errors, params.__dict__ )
# create basic tool model
tool_model = self.to_dict( request_context )
tool_model['inputs'] = {}
# build tool model and tool state
iterate( request_context, tool_model['inputs'], self.inputs, state_inputs, '' )
iterate( tool_model['inputs'], self.inputs, state_inputs, '' )
# sanitize tool state
sanitize_state(state_inputs)
@@ -2375,10 +2351,11 @@ class Tool( object, Dictifiable ):
pass
return False
def _map_source_to_history(self, trans, tool_inputs, params, history):
def _map_source_to_history( self, trans, tool_inputs, params ):
# Need to remap dataset parameters. Job parameters point to original
# dataset used; parameter should be the analygous dataset in the
# current history.
history = trans.history
# Create index for hdas.
hda_source_dict = {}
lib/galaxy/tools/evaluation.py
+3 -6
View File
@@ -54,15 +54,12 @@ class ToolEvaluator( object ):
incoming = self.tool.params_from_strings( incoming, self.app )
# Full parameter validation
request_context = WorkRequestContext(
app = self.app,
user = job.history.user,
history = job.history
)
request_context = WorkRequestContext( app=self.app, user=job.history.user, history=job.history )
def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
value = input.from_html( value, request_context, context )
input.validate( value, request_context )
visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
visit_input_values( self.tool.inputs, incoming, validate_inputs, details=True )
# Restore input / output data lists
inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
lib/galaxy/tools/parameters/__init__.py
+1
View File
@@ -4,6 +4,7 @@ Classes encapsulating Galaxy tool parameters.
from basic import DataCollectionToolParameter, DataToolParameter, SelectToolParameter
from grouping import Conditional, Repeat, Section, UploadDataset
from galaxy.util import string_as_bool
from galaxy.util.json import dumps, json_fix, loads
from galaxy.util.expressions import ExpressionContext
lib/galaxy/tools/parameters/basic.py
+4 -2
View File
@@ -615,6 +615,7 @@ class FTPFileToolParameter( ToolParameter ):
input_source = ensure_input_source(input_source)
ToolParameter.__init__( self, tool, input_source )
self.multiple = input_source.get_bool( 'multiple', True )
self.optional = input_source.parse_optional( True )
self.user_ftp_dir = ''
def get_initial_value( self, trans, other_values ):
@@ -652,8 +653,6 @@ class FTPFileToolParameter( ToolParameter ):
return self.to_python( value, app )
def to_python( self, value, app, validate=False ):
if validate and self.tool.app.config.ftp_upload_dir is None:
raise ValueError( "The FTP directory is not configured." )
if not isinstance( value, list ):
value = [ value ]
lst = []
@@ -669,6 +668,8 @@ class FTPFileToolParameter( ToolParameter ):
if not self.optional and validate:
raise ValueError( "Please select a valid FTP file." )
return ''
if validate and self.tool.app.config.ftp_upload_dir is None:
raise ValueError( "The FTP directory is not configured." )
return lst
def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):
@@ -2576,6 +2577,7 @@ parameter_types = dict(
drill_down=DrillDownSelectToolParameter
)
class RuntimeValue( object ):
"""
Wrapper to note a value that is not yet set, but will be required at
lib/galaxy/tools/parameters/dynamic_options.py
-1
View File
@@ -5,7 +5,6 @@ on the values of other parameters or other aspects of the current state)
import logging
import os
import basic
import validation
from galaxy.util import string_as_bool
from galaxy.model import User
lib/galaxy/workflow/extract.py
+1 -3
View File
@@ -6,9 +6,7 @@ from galaxy import exceptions
from galaxy import model
from galaxy.tools.parameters.basic import (
DataToolParameter,
DataCollectionToolParameter,
DrillDownSelectToolParameter,
SelectToolParameter
DataCollectionToolParameter
)
from galaxy.tools.parser import ToolOutputCollectionPart
from galaxy.tools.parameters.grouping import (