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(manually merge conflicts)

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This commit is contained in:
carlfeberhard
2016-03-07 16:15:38 -05:00
parent 8078306d9a cff3eb8073
commit c15e5db2ec
73 changed files with 348 additions and 346 deletions
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client/galaxy/scripts/apps/analysis.js
+1 -1
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@@ -100,7 +100,7 @@ window.app = function app( options, bootstrapped ){
'(/)' : 'home',
// TODO: remove annoying 'root' from root urls
'(/)root*' : 'home',
'(/)tours(/:tour_id)' : 'show_tours',
'(/)tours(/)(:tour_id)' : 'show_tours',
},
show_tours : function( tour_id ){
client/galaxy/scripts/layout/menu.js
+4 -4
View File
@@ -144,15 +144,15 @@ var Collection = Backbone.Collection.extend({
target : '_blank'
},{
title : 'Interactive Tours',
url : 'tours',
onclick : function(){
if (Galaxy.app){
Galaxy.app.display(new Tours.ToursView());
} else {
// Redirect and use clientside routing to go to tour index
window.location = Galaxy.root + "#/tours";
window.location = Galaxy.root + "tours";
}
},
target : 'galaxy_main'
}
}]
};
options.terms_url && helpTab.menu.push({
@@ -383,4 +383,4 @@ return {
Tab : Tab
};
});
});
client/galaxy/scripts/mvc/tours.js
+3 -2
View File
@@ -101,14 +101,15 @@ define(['libs/bootstrap-tour'],function(BootstrapTour) {
"<ul>",
'<% _.each(tours, function(tour) { %>',
'<li>',
'<a href="#/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',
'<a href="/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',
'<%- tour.attributes.name || tour.id %>',
'</a>',
' - <%- tour.attributes.description || "No description given." %>',
'</li>',
'<% }); %>',
"</ul>"].join(''));
this.$el.html(tpl({tours: this.model.models})).on("click", ".tourItem", function(){
this.$el.html(tpl({tours: this.model.models})).on("click", ".tourItem", function(e){
e.preventDefault();
giveTour($(this).data("tour.id"));
});
}
config/tool_conf.xml.main
+4 -4
View File
@@ -28,18 +28,18 @@
</section>
<section id="textutil" name="Text Manipulation">
<tool file="filters/fixedValueColumn.xml" />
<tool file="filters/catWrapper.xml" />
<tool file="filters/catWrapper.xml" hidden="True" />
<tool file="filters/condense_characters.xml" />
<tool file="filters/convert_characters.xml" />
<tool file="filters/mergeCols.xml" />
<tool file="filters/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/cutWrapper.xml" hidden="True" />
<tool file="filters/changeCase.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/randomlines.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
<tool file="filters/headWrapper.xml" hidden="True" />
<tool file="filters/tailWrapper.xml" hidden="True" />
<tool file="filters/trimmer.xml" />
<tool file="filters/wc_gnu.xml" />
<tool file="filters/secure_hash_message_digest.xml" />
lib/galaxy/datatypes/registry.py
+71 -71
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@@ -647,81 +647,81 @@ class Registry( object ):
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'db3' : binary.SQlite(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'db3' : binary.SQlite(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'gemini.sqlite' : binary.GeminiSQLite(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'h5' : binary.H5(),
'idpdb' : binary.IdpDB(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'mz.sqlite' : binary.MzSQlite(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'csv' : tabular.CSV(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'h5' : binary.H5(),
'idpdb' : binary.IdpDB(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'mz.sqlite' : binary.MzSQlite(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'csv' : tabular.CSV(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
}
self.mimetypes_by_extension = {
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'db3' : 'application/octet-stream',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'db3' : 'application/octet-stream',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'gemini.sqlite' : 'application/octet-stream',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'h5' : 'application/octet-stream',
'idpdb' : 'application/octet-stream',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'mz.sqlite' : 'application/octet-stream',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'csv' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'h5' : 'application/octet-stream',
'idpdb' : 'application/octet-stream',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'mz.sqlite' : 'application/octet-stream',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'csv' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
}
# super supertype fix for input steps in workflows.
if 'data' not in self.datatypes_by_extension:
lib/galaxy/datatypes/tabular.py
+3 -4
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@@ -8,17 +8,16 @@ import gzip
import logging
import os
import re
import tempfile
import subprocess
import tempfile
from cgi import escape
from json import dumps
from galaxy import util
from galaxy.datatypes import data, metadata
from galaxy.util.checkers import is_gzip
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import get_headers
from galaxy.util.json import dumps
from galaxy.util.checkers import is_gzip
from . import dataproviders
lib/galaxy/external_services/result_handlers/basic.py
+1 -1
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@@ -1,5 +1,5 @@
from galaxy.util.json import loads
import logging
from json import loads
log = logging.getLogger( __name__ )
lib/galaxy/jobs/__init__.py
+9 -12
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@@ -1,13 +1,8 @@
"""
Support for running a tool in Galaxy via an internal job management system
"""
from abc import ABCMeta
from abc import abstractmethod
import time
import copy
import datetime
import galaxy
import logging
import os
import pwd
@@ -15,21 +10,23 @@ import random
import shutil
import subprocess
import sys
import time
import traceback
from abc import ABCMeta, abstractmethod
from json import loads
from xml.etree import ElementTree
import galaxy
from galaxy import model, util
from galaxy.util.xml_macros import load
from galaxy.datatypes import metadata
from galaxy.datatypes import metadata, sniff
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
from galaxy.jobs.actions.post import ActionBox
from galaxy.jobs.mapper import JobRunnerMapper
from galaxy.jobs.runners import BaseJobRunner, JobState
from galaxy.util import safe_makedirs, unicodify
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
from galaxy.util.json import loads
from galaxy.util import safe_makedirs
from galaxy.util import unicodify
from galaxy.datatypes import sniff
from galaxy.util.xml_macros import load
from .output_checker import check_output
from .datasets import TaskPathRewriter
@@ -1291,7 +1288,7 @@ class JobWrapper( object ):
dataset.extension = 'txt'
self.sa_session.add( dataset )
if job.states.ERROR == final_job_state:
log.debug( "setting dataset state to ERROR" )
log.debug( "(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id )
# TODO: This is where the state is being set to error. Change it!
dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
# Pause any dependent jobs (and those jobs' outputs)
lib/galaxy/jobs/actions/post.py
+4 -2
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@@ -6,10 +6,12 @@ immediate_actions listed below. Currently only used in workflows.
import datetime
import logging
import socket
from galaxy.util import send_mail
from galaxy.util.json import dumps
from json import dumps
from markupsafe import escape
from galaxy.util import send_mail
log = logging.getLogger( __name__ )
lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
+1 -1
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@@ -2,10 +2,10 @@
Module for managing jobs in Pacific Bioscience's SMRT Portal and automatically transferring files
produced by SMRT Portal.
"""
import json
import logging
import urllib2
from string import Template
from galaxy.util import json
from data_transfer import DataTransfer
lib/galaxy/jobs/transfer_manager.py
+6 -4
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@@ -2,13 +2,15 @@
Manage transfers from arbitrary URLs to temporary files. Socket interface for
IPC with multiple process configurations.
"""
import json
import logging
import os
import subprocess
import socket
import subprocess
import threading
from galaxy.util import listify, json, sleeper
from galaxy.util import listify, sleeper
from galaxy.util.json import jsonrpc_request, validate_jsonrpc_response
log = logging.getLogger( __name__ )
@@ -83,13 +85,13 @@ class TransferManager( object ):
for tj in transfer_jobs:
if via_socket and tj.state not in tj.terminal_states and tj.socket:
try:
request = json.jsonrpc_request( method='get_state', id=True )
request = jsonrpc_request( method='get_state', id=True )
sock = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
sock.settimeout( 5 )
sock.connect( ( 'localhost', tj.socket ) )
sock.send( json.dumps( request ) )
response = sock.recv( 8192 )
valid, response = json.validate_jsonrpc_response( response, id=request['id'] )
valid, response = validate_jsonrpc_response( response, id=request['id'] )
if not valid:
# No valid response received, make some pseudo-json-rpc
raise Exception( dict( code=128, message='Did not receive valid response from transfer daemon for state' ) )
lib/galaxy/managers/context.py
+1 -1
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@@ -3,8 +3,8 @@ Mixins for transaction-like objects.
"""
import os
from json import dumps
from galaxy.util.json import dumps
from galaxy.util import bunch
lib/galaxy/model/metadata.py
+4 -7
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@@ -6,28 +6,25 @@ Galaxy Metadata
import copy
import cPickle
import json
import logging
import os
import shutil
import sys
import tempfile
import weakref
from os.path import abspath
from six import string_types
from sqlalchemy.orm import object_session
import galaxy.model
from galaxy.util import listify
from galaxy.util.object_wrapper import sanitize_lists_to_string
from galaxy.util import stringify_dictionary_keys
from galaxy.util import string_as_bool
from galaxy.util import in_directory
from galaxy.util import (in_directory, listify, string_as_bool,
stringify_dictionary_keys)
from galaxy.util.json import safe_dumps
from galaxy.util.object_wrapper import sanitize_lists_to_string
from galaxy.util.odict import odict
from galaxy.web import form_builder
import logging
log = logging.getLogger(__name__)
STATEMENTS = "__galaxy_statements__" # this is the name of the property in a Datatype class where new metadata spec element Statements are stored
lib/galaxy/model/search.py
+3 -4
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@@ -26,8 +26,11 @@ select * from history where name='Unnamed history'
import logging
import re
from json import dumps
import parsley
from sqlalchemy import and_
from sqlalchemy.orm import aliased
from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation,
History, Library, LibraryFolder, LibraryDataset, StoredWorkflowTagAssociation,
@@ -37,10 +40,6 @@ from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssoci
Page, PageRevision)
from galaxy.model.tool_shed_install import ToolVersion
from galaxy.util.json import dumps
from sqlalchemy import and_
from sqlalchemy.orm import aliased
log = logging.getLogger( __name__ )
lib/galaxy/queue_worker.py
+1 -1
View File
@@ -90,7 +90,7 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
"""
def __init__(self, app, queue=None, task_mapping=control_message_to_task, connection=None):
super(GalaxyQueueWorker, self).__init__()
log.info("Initalizing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))
log.info("Initializing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))
self.daemon = True
if connection:
self.connection = connection
lib/galaxy/tools/actions/__init__.py
+3 -2
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@@ -1,15 +1,16 @@
import json
import re
from json import dumps
from six import string_types
from galaxy import model
from galaxy.exceptions import ObjectInvalid
from galaxy.model import LibraryDatasetDatasetAssociation
from galaxy import model
from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter
from galaxy.tools.parameters.wrapped import WrappedParameters
from galaxy.tools.parameters import update_param
from galaxy.util import ExecutionTimer
from galaxy.util.json import dumps
from galaxy.util.none_like import NoneDataset
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
lib/galaxy/tools/actions/metadata.py
+2 -2
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@@ -1,10 +1,10 @@
import logging
from json import dumps
from __init__ import ToolAction
from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
from galaxy.util.odict import odict
from galaxy.util.json import dumps
from galaxy.jobs.datasets import DatasetPath
from galaxy.util.odict import odict
log = logging.getLogger( __name__ )
lib/galaxy/tools/actions/upload_common.py
+4 -4
View File
@@ -1,18 +1,18 @@
import pwd
import logging
import os
import pwd
import StringIO
import subprocess
import tempfile
from cgi import FieldStorage
from json import dumps
from sqlalchemy.orm import eagerload_all
from galaxy import datatypes, util
from galaxy.util.odict import odict
from galaxy.util.json import dumps
from galaxy.exceptions import ObjectInvalid
from galaxy.util.odict import odict
import logging
log = logging.getLogger( __name__ )
lib/galaxy/tools/imp_exp/__init__.py
+2 -3
View File
@@ -4,17 +4,16 @@ import logging
import os
import shutil
import tempfile
from json import dumps, loads
from sqlalchemy.orm import eagerload, eagerload_all
from sqlalchemy.sql import expression
from galaxy import model
from galaxy.exceptions import MalformedContents
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.json import dumps, loads
from galaxy.web.framework.helpers import to_unicode
from sqlalchemy.sql import expression
log = logging.getLogger(__name__)
lib/galaxy/tools/imp_exp/export_history.py
+1 -2
View File
@@ -10,8 +10,7 @@ import optparse
import os
import sys
import tarfile
from galaxy.util.json import dumps, loads
from json import dumps, loads
def get_dataset_filename( name, ext, hid ):
lib/galaxy/tools/parameters/__init__.py
+33 -15
View File
@@ -2,10 +2,12 @@
Classes encapsulating Galaxy tool parameters.
"""
import re
from json import dumps, loads
from basic import RuntimeValue
from grouping import Conditional, Repeat, Section, UploadDataset
from galaxy.util.json import dumps, json_fix, loads
from galaxy.util.expressions import ExpressionContext
from galaxy.util.json import json_fix
REPLACE_ON_TRUTHY = object()
@@ -20,19 +22,35 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
If the callback returns a value, it will be replace the old value.
>>> from xml.etree.ElementTree import XML
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util.odict import odict
>>> from galaxy.tools.parameters.basic import TextToolParameter
>>> from galaxy.tools.parameters.grouping import Repeat
>>> a = TextToolParameter( None, XML( '<param name="a" type="text"/>' ) )
>>> a = TextToolParameter( None, XML( '<param name="a"/>' ) )
>>> b = Repeat()
>>> c = TextToolParameter( None, XML( '<param name="c" type="text"/>' ) )
>>> c = TextToolParameter( None, XML( '<param name="c"/>' ) )
>>> d = Repeat()
>>> e = TextToolParameter( None, XML( '<param name="e"/>' ) )
>>> f = Conditional()
>>> g = TextToolParameter( None, XML( '<param name="g"/>' ) )
>>> h = TextToolParameter( None, XML( '<param name="h"/>' ) )
>>> i = TextToolParameter( None, XML( '<param name="i"/>' ) )
>>> b.name = 'b'
>>> b.inputs = { 'c': c }
>>> def visitor( input, value, prefixed_name, **kwargs ):
... print '%s, %s, %s' % ( input.name, prefixed_name, value )
>>> visit_input_values( odict( [ ('a', a), ('b', b ) ] ), odict( [ ('a', 1), ('b', [ { 'c': 3 } ] ) ] ), visitor )
a, a, 1
c, b_0|c, 3
>>> b.inputs = odict([ ('c', c), ('d', d) ])
>>> d.name = 'd'
>>> d.inputs = odict([ ('e', e), ('f', f) ])
>>> f.test_param = g
>>> f.name = 'f'
>>> f.cases = [ Bunch( value='true', inputs= { 'h': h } ), Bunch( value='false', inputs= { 'i': i } ) ]
>>>
>>> def visitor( input, value, prefix, prefixed_name, **kwargs ):
... print 'name=%s, prefix=%s, prefixed_name=%s, value=%s' % ( input.name, prefix, prefixed_name, value )
>>> visit_input_values( odict([('a',a),('b',b)]), odict([ ('a', 1), ('b', [ odict([('c', 3), ( 'd', [odict([ ('e',5), ('f', odict([ ('g','true'), ('h',7) ])) ]) ])]) ]) ]), visitor )
name=a, prefix=, prefixed_name=a, value=1
name=c, prefix=b_0|, prefixed_name=b_0|c, value=3
name=e, prefix=b_0|d_0|, prefixed_name=b_0|d_0|e, value=5
name=g, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f|g, value=true
name=h, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f|h, value=7
"""
def callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None ):
args = {
@@ -56,7 +74,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
input_values[ input.name ] = new_value
context = ExpressionContext( input_values, context )
payload = { 'parent_prefix': name_prefix, 'context': context, 'no_replacement_value': no_replacement_value }
payload = { 'context': context, 'no_replacement_value': no_replacement_value }
for input in inputs.itervalues():
if isinstance( input, Repeat ) or isinstance( input, UploadDataset ):
values = input_values[ input.name ] = input_values.get( input.name, [] )
@@ -64,7 +82,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
d[ '__index__' ] = i
new_name_prefix = name_prefix + '%s_%d|' % ( input.name, i )
new_label_prefix = label_prefix + '%s %d > ' % ( input.title, i + 1 )
visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, **payload )
visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload )
elif isinstance( input, Conditional ):
values = input_values[ input.name ] = input_values.get( input.name, {} )
new_name_prefix = name_prefix + input.name + '|'
@@ -74,15 +92,15 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
except:
case_error = 'The selected case is unavailable/invalid.'
pass
callback_helper( input.test_param, values, new_name_prefix, label_prefix, parent_prefix, context=context, error=case_error )
callback_helper( input.test_param, values, new_name_prefix, label_prefix, parent_prefix=name_prefix, context=context, error=case_error )
values[ '__current_case__' ] = input.get_current_case( values[ input.test_param.name ] )
visit_input_values( input.cases[ values[ '__current_case__' ] ].inputs, values, callback, new_name_prefix, label_prefix, **payload )
visit_input_values( input.cases[ values[ '__current_case__' ] ].inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload )
elif isinstance( input, Section ):
values = input_values[ input.name ] = input_values.get( input.name, {} )
new_name_prefix = name_prefix + input.name + '|'
visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, **payload )
visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload )
else:
callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix, context=context )
callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context )
def check_param( trans, param, incoming_value, param_values ):
lib/galaxy/tools/parameters/basic.py
+8 -8
View File
@@ -1819,8 +1819,6 @@ class DataToolParameter( BaseDataToolParameter ):
return ''
def from_html( self, value, trans, other_values={} ):
# Can't look at history in workflow mode, skip validation and such,
# although, this should never be called in workflow mode right?
if trans.workflow_building_mode:
return None
if not value and not self.optional:
@@ -2035,12 +2033,14 @@ class DataToolParameter( BaseDataToolParameter ):
d['max'] = self.max
d['options'] = {'hda': [], 'hdca': []}
# return dictionary without options if context is unavailable
history = trans.history
if history is None or trans.workflow_building_mode:
return d
# prepare dataset/collection matching
dataset_matcher = DatasetMatcher( trans, self, None, other_values )
multiple = self.multiple
history = trans.history
if history is None:
return d
# build and append a new select option
def append( list, id, hid, name, src ):
@@ -2223,13 +2223,13 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
d['multiple'] = self.multiple
d['options'] = {'hda': [], 'hdca': []}
# return default content if context is not available
if other_values is None:
# return dictionary without options if context is unavailable
history = trans.history
if history is None or trans.workflow_building_mode or other_values is None:
return d
# prepare dataset/collection matching
dataset_matcher = DatasetMatcher( trans, self, None, other_values )
history = trans.history
# append directly matched collections
for hdca in self.match_collections( trans, history, dataset_matcher ):
lib/galaxy/tools/parameters/output_collect.py
+7
View File
@@ -131,6 +131,13 @@ class JobContext( object ):
filename=filename,
metadata_source_name=output_collection_def.metadata_source,
)
log.debug(
"(%s) Created dynamic collection dataset for path [%s] with element identifier [%s] for output [%s].",
self.job.id,
filename,
designation,
output_collection_def.name,
)
current_builder.add_dataset( element_identifiers[-1], dataset )
def create_dataset(
lib/galaxy/tools/parameters/validation.py
+1 -1
View File
@@ -58,7 +58,7 @@ class RegexValidator( Validator ):
self.expression = expression
def validate( self, value, trans=None ):
if re.match( self.expression, value ) is None:
if re.match( self.expression, value or '' ) is None:
raise ValueError( self.message )
lib/galaxy/tools/toolbox/base.py
+2 -2
View File
@@ -614,8 +614,8 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
log.exception( "Error reading tool from path: %s" % path )
def _get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ):
# Abstract class does't have a dependency on the database, for full tool shed
# support the actual Galaxy ToolBox implement this method and return a ToolShd repository.
# Abstract class doesn't have a dependency on the database, for full Tool Shed
# support the actual Galaxy ToolBox implements this method and returns a Tool Shed repository.
return None
def __add_tool( self, tool, load_panel_dict, panel_dict ):
lib/galaxy/util/__init__.py
+10 -18
View File
@@ -3,13 +3,13 @@
Utility functions used systemwide.
"""
from __future__ import absolute_import
import binascii
import collections
import errno
import grp
import json
import logging
import os
import random
@@ -19,25 +19,17 @@ import smtplib
import stat
import string
import sys
import time
import tempfile
import threading
from os.path import relpath, normpath
from hashlib import md5
from six import binary_type
from six import iteritems
from six import PY3
from six import string_types, text_type
from six.moves import email_mime_text
from six.moves.urllib import parse as urlparse
from six.moves import xrange
from six.moves import zip
from xml.etree import ElementTree, ElementInclude
from galaxy.util import json
import time
from datetime import datetime
from hashlib import md5
from os.path import normpath, relpath
from xml.etree import ElementInclude, ElementTree
from six import binary_type, iteritems, PY3, string_types, text_type
from six.moves import email_mime_text, xrange, zip
from six.moves.urllib import parse as urlparse
try:
import docutils.core as docutils_core
@@ -46,7 +38,7 @@ except ImportError:
docutils_core = None
docutils_html4css1 = None
from .inflection import Inflector, English
from .inflection import English, Inflector
inflector = Inflector(English)
if PY3:
lib/galaxy/util/dbkeys.py
+5 -3
View File
@@ -2,10 +2,12 @@
Functionality for dealing with dbkeys.
"""
# dbkeys read from disk using builds.txt
from galaxy.util import read_dbnames
from galaxy.util.json import loads
from galaxy.util.object_wrapper import sanitize_lists_to_string
from __future__ import absolute_import
import os.path
from json import loads
from galaxy.util import read_dbnames
from galaxy.util.object_wrapper import sanitize_lists_to_string
class GenomeBuilds( object ):
lib/galaxy/util/json.py
+5 -8
View File
@@ -1,6 +1,6 @@
from __future__ import absolute_import
__all__ = [ "dumps", "loads", "safe_dumps", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
__all__ = [ "safe_dumps", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
import copy
import collections
@@ -12,13 +12,10 @@ import string
from six import text_type, string_types, iteritems
dumps = json.dumps
loads = json.loads
log = logging.getLogger( __name__ )
to_json_string = dumps
from_json_string = loads
to_json_string = json.dumps
from_json_string = json.loads
def json_fix( val ):
@@ -77,7 +74,7 @@ def safe_dumps( *args, **kwargs ):
def validate_jsonrpc_request( request, regular_methods, notification_methods ):
try:
request = loads( request )
request = json.loads( request )
except Exception as e:
return False, request, jsonrpc_response( id=None,
error=dict( code=-32700,
@@ -114,7 +111,7 @@ def validate_jsonrpc_request( request, regular_methods, notification_methods ):
def validate_jsonrpc_response( response, id=None ):
try:
response = loads( response )
response = json.loads( response )
except Exception as e:
log.error( 'Response was not valid JSON: %s' % str( e ) )
log.debug( 'Response was: %s' % response )
lib/galaxy/visualization/data_providers/basic.py
+2 -1
View File
@@ -1,6 +1,7 @@
import sys
from json import loads
from galaxy.datatypes.tabular import Tabular
from galaxy.util.json import loads
class BaseDataProvider( object ):
lib/galaxy/visualization/data_providers/genome.py
+1 -2
View File
@@ -8,9 +8,9 @@ import os
import random
import re
import sys
from json import loads
import pysam
from bx.interval_index_file import Indexes
from bx.bbi.bigbed_file import BigBedFile
from bx.bbi.bigwig_file import BigWigFile
@@ -18,7 +18,6 @@ from pysam import ctabix
from galaxy.datatypes.interval import Bed, Gff, Gtf
from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes
from galaxy.util.json import loads
from galaxy.visualization.data_providers.basic import BaseDataProvider
from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
lib/galaxy/visualization/genomes.py
+3 -1
View File
@@ -2,9 +2,11 @@ import logging
import os
import re
import sys
from json import loads
from bx.seq.twobit import TwoBitFile
from galaxy.util.bunch import Bunch
from galaxy.util.json import loads
log = logging.getLogger( __name__ )
lib/galaxy/visualization/plugins/resource_parser.py
+3 -2
View File
@@ -2,6 +2,8 @@
Deserialize Galaxy resources (hdas, ldas, datasets, genomes, etc.) from
a dictionary of string data/ids (often from a query string).
"""
import json
import logging
import weakref
import galaxy.exceptions
@@ -10,7 +12,6 @@ from galaxy.util import bunch
from galaxy.managers import visualizations as visualization_manager
from galaxy.managers import hdas as hda_manager
import logging
log = logging.getLogger( __name__ )
@@ -31,7 +32,7 @@ class ResourceParser( object ):
'int' : int,
'float' : float,
# 'date' : lambda param: ,
'json' : ( lambda param: galaxy.util.json.loads(
'json' : ( lambda param: json.loads(
galaxy.util.sanitize_html.sanitize_html( param ) ) ),
}
lib/galaxy/web/framework/base.py
+8 -6
View File
@@ -7,6 +7,7 @@ import logging
import os.path
import socket
import tarfile
import tempfile
import types
import routes
@@ -93,6 +94,9 @@ class WebApplication( object ):
"""
self.mapper.connect( route, **kwargs )
def add_client_route( self, route ):
self.add_route(route, controller='root', action='index')
def set_transaction_factory( self, transaction_factory ):
"""
Use the callable `transaction_factory` to create the transaction
@@ -285,15 +289,13 @@ class DefaultWebTransaction( object ):
else:
return None
# For request.params, override cgi.FieldStorage.make_file to create persistent
# tempfiles. Necessary for externalizing the upload tool. It's a little hacky
# but for performance reasons it's way better to use Paste's tempfile than to
# create a new one and copy.
import tempfile
class FieldStorage( cgi.FieldStorage ):
def make_file(self, binary=None):
# For request.params, override cgi.FieldStorage.make_file to create persistent
# tempfiles. Necessary for externalizing the upload tool. It's a little hacky
# but for performance reasons it's way better to use Paste's tempfile than to
# create a new one and copy.
return tempfile.NamedTemporaryFile()
def read_lines(self):
lib/galaxy/web/framework/decorators.py
+13 -15
View File
@@ -1,21 +1,19 @@
import inspect
from traceback import format_exc
import logging
from functools import wraps
from six import string_types
from json import loads
from traceback import format_exc
import paste.httpexceptions
from six import string_types
from galaxy.web.framework import url_for
from galaxy import util
from galaxy.exceptions import error_codes
from galaxy.exceptions import MessageException
from galaxy.util.json import loads
from galaxy.util.json import safe_dumps as dumps
from galaxy.exceptions import error_codes, MessageException
from galaxy.util.json import safe_dumps
from galaxy.web.framework import url_for
import logging
log = logging.getLogger( __name__ )
JSON_CONTENT_TYPE = "application/json"
@@ -46,7 +44,7 @@ def json( func, **json_kwargs ):
@wraps(func)
def call_and_format( self, trans, *args, **kwargs ):
trans.response.set_content_type( JSON_CONTENT_TYPE )
return dumps( func( self, trans, *args, **kwargs ), **json_kwargs )
return safe_dumps( func( self, trans, *args, **kwargs ), **json_kwargs )
if not hasattr( func, '_orig' ):
call_and_format._orig = func
return expose( _save_orig_fn( call_and_format, func ) )
@@ -138,9 +136,9 @@ def expose_api( func, to_json=True, user_required=True ):
try:
rval = func( self, trans, *args, **kwargs)
if to_json and trans.debug:
rval = dumps( rval, indent=4, sort_keys=True )
rval = safe_dumps( rval, indent=4, sort_keys=True )
elif to_json:
rval = dumps( rval )
rval = safe_dumps( rval )
return rval
except paste.httpexceptions.HTTPException:
raise # handled
@@ -258,9 +256,9 @@ def _future_expose_api( func, to_json=True, user_required=True, user_or_session_
try:
rval = func( self, trans, *args, **kwargs)
if to_json and trans.debug:
rval = dumps( rval, indent=4, sort_keys=True )
rval = safe_dumps( rval, indent=4, sort_keys=True )
elif to_json:
rval = dumps( rval )
rval = safe_dumps( rval )
return rval
except MessageException as e:
traceback_string = format_exc()
@@ -334,7 +332,7 @@ def __api_error_response( trans, **kwds ):
# non-success (i.e. not 200 or 201) has been set, do not override
# underlying controller.
response.status = status_code
return dumps( error_dict )
return safe_dumps( error_dict )
def _future_expose_api_anonymous( func, to_json=True ):
lib/galaxy/web/framework/helpers/grids.py
+4 -6
View File
@@ -1,17 +1,15 @@
import logging
import math
from json import dumps, loads
from markupsafe import escape
from six import text_type
from six import string_types
from sqlalchemy.sql.expression import and_, func, or_, null, false, true
from six import string_types, text_type
from sqlalchemy.sql.expression import and_, false, func, null, or_, true
from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings
from galaxy.util import sanitize_text
from galaxy.util.json import loads, dumps
from galaxy.util.odict import odict
from galaxy.web.framework import decorators
from galaxy.web.framework import url_for
from galaxy.web.framework import decorators, url_for
from galaxy.web.framework.helpers import iff
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+4 -4
View File
@@ -2,12 +2,16 @@
API operations on the library datasets.
"""
import glob
import logging
import os
import os.path
import string
import sys
import tempfile
import zipfile
from json import dumps
from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
from galaxy import exceptions
from galaxy import util
@@ -15,15 +19,11 @@ from galaxy import web
from galaxy.exceptions import ObjectNotFound
from galaxy.managers import folders, roles
from galaxy.tools.actions import upload_common
from galaxy.util.json import dumps
from galaxy.util.streamball import StreamBall
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
import logging
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+4 -7
View File
@@ -1,27 +1,24 @@
import json
import logging
from paste.httpexceptions import HTTPBadRequest, HTTPForbidden
from time import strftime
from paste.httpexceptions import HTTPBadRequest, HTTPForbidden
import tool_shed.util.shed_util_common as suc
from galaxy import util
from galaxy import web
from galaxy import exceptions
from galaxy.web import _future_expose_api as expose_api
from galaxy.util import json
from galaxy.web.base.controller import BaseAPIController
from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
from tool_shed.util import workflow_util
from tool_shed.util import tool_util
import tool_shed.util.shed_util_common as suc
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/api/tools.py
+10 -14
View File
@@ -1,21 +1,17 @@
import logging
import urllib
from galaxy import exceptions
from galaxy import web, util
from galaxy import managers
from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesVisualizationMixin
from galaxy.visualization.genomes import GenomeRegion
from galaxy.util.json import dumps
from galaxy.managers.collections_util import dictify_dataset_collection_instance
from json import dumps
import galaxy.queue_worker
from galaxy import exceptions, managers, util, web
from galaxy.managers.collections_util import dictify_dataset_collection_instance
from galaxy.visualization.genomes import GenomeRegion
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesVisualizationMixin
import logging
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/buildapp.py
+9
View File
@@ -72,6 +72,15 @@ def paste_app_factory( global_conf, **kwargs ):
# Create the universe WSGI application
webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )
# CLIENTSIDE ROUTES
# The following are routes that are handled completely on the clientside.
# The following routes don't bootstrap any information, simply provide the
# base analysis interface at which point the application takes over.
webapp.add_client_route( '/tours' )
webapp.add_client_route( '/tours/{tour_id}' )
# STANDARD CONTROLLER ROUTES
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
# Force /history to go to view of current
webapp.add_route( '/history', controller='history', action='view' )
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+4 -5
View File
@@ -1,15 +1,15 @@
import json
import logging
import os
import shutil
from sqlalchemy import false, or_
from six import string_types
from sqlalchemy import false, or_
import tool_shed.repository_types.util as rt_util
from admin import AdminGalaxy
from galaxy import web
from galaxy import util
from galaxy.util import json
from galaxy import util, web
from galaxy.tools.deps import views
from galaxy.web.form_builder import CheckboxField
from tool_shed.galaxy_install import dependency_display
from tool_shed.galaxy_install import install_manager
@@ -31,7 +31,6 @@ from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
from tool_shed.util import workflow_util
from tool_shed.util.web_util import escape
from galaxy.tools.deps import views
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/controllers/data_manager.py
+4 -4
View File
@@ -1,14 +1,14 @@
import logging
from json import loads
import paste.httpexceptions
from markupsafe import escape
from six import string_types
import paste.httpexceptions
import galaxy.queue_worker
from galaxy import web
from galaxy.util.json import loads
from galaxy.web.base.controller import BaseUIController
# set up logger
import logging
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/controllers/dataset.py
-2
View File
@@ -21,8 +21,6 @@ log = logging.getLogger( __name__ )
comptypes = []
# TODO: not used in this file
from galaxy.util.json import loads # noqa
try:
import zlib # noqa
comptypes.append( 'zip' )
lib/galaxy/webapps/galaxy/controllers/library_common.py
+2 -3
View File
@@ -10,6 +10,7 @@ import tempfile
import urllib
import urllib2
import zipfile
from json import dumps, loads
from markupsafe import escape
from sqlalchemy import and_, false
@@ -18,9 +19,7 @@ from sqlalchemy.orm import eagerload_all
from galaxy import util, web
from galaxy.security import Action
from galaxy.tools.actions import upload_common
from galaxy.util import inflector
from galaxy.util import unicodify
from galaxy.util.json import dumps, loads
from galaxy.util import inflector, unicodify
from galaxy.util.streamball import StreamBall
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field
lib/galaxy/webapps/galaxy/controllers/page.py
+4 -3
View File
@@ -1,14 +1,15 @@
from json import loads
from markupsafe import escape
from sqlalchemy import and_, desc, false, true
from galaxy import managers, model, util, web
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.util import unicodify
from galaxy.util.json import loads
from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor
from galaxy.util.sanitize_html import _BaseHTMLProcessor, sanitize_html
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin
from galaxy.web.framework.helpers import time_ago, grids
from galaxy.web.framework.helpers import grids, time_ago
def format_bool( b ):
lib/galaxy/webapps/galaxy/controllers/root.py
+2 -1
View File
@@ -31,7 +31,8 @@ class RootController( controller.JSAppLauncher, UsesAnnotations ):
@web.expose
def default(self, trans, target1=None, target2=None, **kwd):
"""Called on any url that does not match a controller method.
"""
Called on any url that does not match a controller method.
"""
raise HTTPNotFound( 'This link may not be followed from within Galaxy.' )
lib/galaxy/webapps/galaxy/controllers/user.py
+2 -4
View File
@@ -8,8 +8,8 @@ import os
import random
import socket
import urllib
from datetime import datetime, timedelta
from json import dumps, loads
from markupsafe import escape
from sqlalchemy import and_, or_, true, func
@@ -17,12 +17,12 @@ from sqlalchemy import and_, or_, true, func
from galaxy import model
from galaxy import util
from galaxy import web
from galaxy.exceptions import ObjectInvalid
from galaxy.security.validate_user_input import (transform_publicname,
validate_email,
validate_password,
validate_publicname)
from galaxy.util import biostar, hash_util, docstring_trim, listify
from galaxy.util.json import dumps, loads
from galaxy.web import url_for
from galaxy.web.base.controller import (BaseUIController,
CreatesApiKeysMixin,
@@ -30,8 +30,6 @@ from galaxy.web.base.controller import (BaseUIController,
UsesFormDefinitionsMixin)
from galaxy.web.form_builder import build_select_field, CheckboxField
from galaxy.web.framework.helpers import grids, time_ago
from galaxy.exceptions import ObjectInvalid
log = logging.getLogger( __name__ )
lib/galaxy/webapps/galaxy/controllers/visualization.py
+4 -6
View File
@@ -1,24 +1,22 @@
from __future__ import absolute_import
import logging
from json import loads
from markupsafe import escape
from paste.httpexceptions import HTTPNotFound, HTTPBadRequest
from six import string_types
from sqlalchemy import and_, desc, false, or_, true
from galaxy import managers
from galaxy import model, web
from galaxy import util
from galaxy import managers, model, util, web
from galaxy.datatypes.interval import Bed
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.util.json import loads
from galaxy.util.sanitize_html import sanitize_html
from galaxy.visualization.plugins import registry
from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
from galaxy.visualization.data_providers.genome import RawBedDataProvider
from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
from galaxy.visualization.genomes import decode_dbkey
from galaxy.visualization.genomes import GenomeRegion
from galaxy.visualization.plugins import registry
from galaxy.web import error
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin
from galaxy.web.framework.helpers import grids, time_ago
lib/galaxy/webapps/tool_shed/controllers/repository.py
+1 -1
View File
@@ -1,3 +1,4 @@
import json
import logging
import os
import string
@@ -16,7 +17,6 @@ import tool_shed.repository_types.util as rt_util
from galaxy import util
from galaxy import web
from galaxy.util import json
from galaxy.web.base.controller import BaseUIController
from galaxy.web.form_builder import CheckboxField
from galaxy.web.framework.helpers import grids
lib/galaxy/workflow/modules.py
+6 -11
View File
@@ -1,20 +1,17 @@
"""
Modules used in building workflows
"""
import logging
import copy
import logging
from json import dumps, loads
from xml.etree.ElementTree import Element
import galaxy.tools
from galaxy import exceptions
from galaxy import model
from galaxy import web
from galaxy import exceptions, model, web
from galaxy.dataset_collections import matching
from galaxy.web.framework import formbuilder
from galaxy.jobs.actions.post import ActionBox
from galaxy.model import PostJobAction
from galaxy.tools.execute import execute
from galaxy.tools.parameters import check_param, visit_input_values
from galaxy.tools.parameters.basic import (
parameter_types,
@@ -23,11 +20,9 @@ from galaxy.tools.parameters.basic import (
RuntimeValue,
)
from galaxy.tools.parameters.wrapped import make_dict_copy
from galaxy.tools.execute import execute
from galaxy.util.bunch import Bunch
from galaxy.util import odict
from galaxy.util.json import loads
from galaxy.util.json import dumps
from galaxy.util.bunch import Bunch
from galaxy.web.framework import formbuilder
from tool_shed.util import common_util
log = logging.getLogger( __name__ )
lib/tool_shed/galaxy_install/repair_repository_manager.py
+7 -2
View File
@@ -56,7 +56,8 @@ class RepairRepositoryManager():
and attempt to make sure they are all properly installed as well as each repository's
tool dependencies. This method is called only from Galaxy when attempting to correct
issues with an installed repository that has installation problems somewhere in its
dependency hierarchy.
dependency hierarchy. Problems with dependencies that have never been installed
cannot be resolved with a repair.
"""
rdim = repository_dependency_manager.RepositoryDependencyInstallManager( self.app )
tsr_ids = []
@@ -150,8 +151,12 @@ class RepairRepositoryManager():
else:
repair_dict[ repository_name ] = [ error_message ]
return repair_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed )
metadata = repository.metadata
# The repository.metadata contains dependency information that corresponds to the current changeset revision,
# which may be different from what is stored in the database
# If any of these repository-repository dependency associations is obsolete, clean_dependency_relationships removes them.
suc.clean_dependency_relationships(self.app, metadata, repository, tool_shed_url)
repair_dict = {}
tpm = tool_panel_manager.ToolPanelManager( self.app )
if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
lib/tool_shed/galaxy_install/update_repository_manager.py
+2
View File
@@ -108,6 +108,8 @@ class UpdateRepositoryManager( object ):
Tool Shed. This happens when updating an installed repository to a new changeset revision.
"""
repository.metadata = updated_metadata_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed )
suc.clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url)
# Update the repository.changeset_revision column in the database.
repository.changeset_revision = updated_changeset_revision
repository.ctx_rev = updated_ctx_rev
lib/tool_shed/grids/repository_grids.py
+2 -1
View File
@@ -1,3 +1,4 @@
import json
import logging
from markupsafe import escape as escape_html
@@ -6,7 +7,7 @@ from sqlalchemy import and_, false, or_, true
import tool_shed.grids.util as grids_util
import tool_shed.repository_types.util as rt_util
import tool_shed.util.shed_util_common as suc
from galaxy.util import json, listify
from galaxy.util import listify
from galaxy.web.framework.helpers import grids
from galaxy.webapps.tool_shed import model
from tool_shed.util import hg_util, metadata_util
lib/tool_shed/util/readme_util.py
+2 -1
View File
@@ -1,3 +1,4 @@
import json
import logging
import os
import threading
@@ -6,7 +7,7 @@ from mako.template import Template
import tool_shed.util.shed_util_common as suc
from galaxy import web
from galaxy.util import json, rst_to_html, unicodify
from galaxy.util import rst_to_html, unicodify
from tool_shed.util import basic_util, common_util, hg_util
log = logging.getLogger( __name__ )
lib/tool_shed/util/shed_util_common.py
+6
View File
@@ -127,10 +127,16 @@ def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, t
rd = rrda.repository_dependency
r = rd.repository
if can_eliminate_repository_dependency(metadata_dict, tool_shed_url, r.name, r.owner):
message = "Repository dependency %s by owner %s is not required by repository %s, owner %s, "
message += "removing from list of repository dependencies."
log.debug(message % (r.name, r.owner, tool_shed_repository.name, tool_shed_repository.owner))
trans.install_model.context.delete(rrda)
trans.install_model.context.flush()
for td in tool_shed_repository.tool_dependencies:
if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version):
message = "Tool dependency %s, version %s is not required by repository %s, owner %s, "
message += "removing from list of tool dependencies."
log.debug(message % (td.name, td.version, tool_shed_repository.name, tool_shed_repository.owner))
trans.install_model.context.delete(td)
trans.install_model.context.flush()
lib/tool_shed/util/workflow_util.py
+3 -3
View File
@@ -1,18 +1,18 @@
""" Tool shed helper methods for dealing with workflows - only two methods are
utilized outside of this modules - generate_workflow_image and import_workflow.
"""
import json
import logging
import os
import galaxy.tools
import galaxy.tools.parameters
from galaxy.util import json
from galaxy.util.sanitize_html import sanitize_html
from galaxy.workflow.render import WorkflowCanvas
from galaxy.workflow.steps import attach_ordered_steps
from galaxy.workflow.modules import module_types
from galaxy.workflow.modules import ToolModule
from galaxy.workflow.modules import WorkflowModuleFactory
from galaxy.workflow.render import WorkflowCanvas
from galaxy.workflow.steps import attach_ordered_steps
from tool_shed.tools import tool_validator
manage_tools.sh
+5 -3
View File
@@ -1,9 +1,11 @@
#!/bin/sh
if [ -d .venv ];
: ${GALAXY_VIRTUAL_ENV:=.venv}
if [ -d "$GALAXY_VIRTUAL_ENV" ];
then
printf "Activating virtualenv at %s/.venv\n" $(pwd)
. .venv/bin/activate
printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
. "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
cd `dirname $0`
run_reports.sh
-13
View File
@@ -11,21 +11,8 @@
cd `dirname $0`
# If there is a .venv/ directory, assume it contains a virtualenv that we
# should run this instance in.
if [ -d .venv ];
then
. .venv/bin/activate
fi
./scripts/common_startup.sh --skip-samples
if [ -d .venv ];
then
printf "Activating virtualenv at %s/.venv\n" $(pwd)
. .venv/bin/activate
fi
if [ -z "$GALAXY_REPORTS_CONFIG" ]; then
if [ -f reports_wsgi.ini ]; then
GALAXY_REPORTS_CONFIG=reports_wsgi.ini
run_tool_shed.sh
-6
View File
@@ -4,12 +4,6 @@ cd `dirname $0`
./scripts/common_startup.sh
if [ -d .venv ];
then
printf "Activating virtualenv at %s/.venv\n" $(pwd)
. .venv/bin/activate
fi
tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
args=$@
scripts/check_python.py
+3 -3
View File
@@ -1,12 +1,12 @@
"""
If the current installed python version is not 2.6 to 2.7, prints an error
If the current installed python version is not 2.7, prints an error
message to stderr and returns 1
"""
import sys
msg = """ERROR: Your Python version is: %s
Galaxy is currently supported on Python 2.6 and 2.7. To run Galaxy,
Galaxy is currently supported on Python 2.7 only. To run Galaxy,
please download and install a supported version from python.org. If a
supported version is installed but is not your default, getgalaxy.org
contains instructions on how to force Galaxy to use a different version.""" % sys.version[:3]
@@ -14,7 +14,7 @@ contains instructions on how to force Galaxy to use a different version.""" % sy
def check_python():
try:
assert sys.version_info[:2] >= ( 2, 6 ) and sys.version_info[:2] <= ( 2, 7 )
assert sys.version_info[:2] == ( 2, 7 )
except AssertionError:
print >>sys.stderr, msg
raise
scripts/functional_tests.py
+1 -1
View File
@@ -13,6 +13,7 @@ import threading
import time
import urllib
from ConfigParser import SafeConfigParser
from json import dumps
import nose.core
import nose.config
@@ -31,7 +32,6 @@ from base.tool_shed_util import parse_tool_panel_config
from functional import database_contexts
from galaxy import tools
from galaxy.app import UniverseApplication
from galaxy.util.json import dumps
from galaxy.util.properties import load_app_properties
from galaxy.web import buildapp
scripts/transfer.py
+8 -7
View File
@@ -5,6 +5,7 @@ Manager (galaxy.jobs.transfer_manager) and should not normally be invoked by
hand.
"""
import ConfigParser
import json
import logging
import optparse
import os
@@ -16,9 +17,6 @@ import threading
import time
import urllib2
galaxy_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir ) )
sys.path.insert( 1, os.path.join( galaxy_root, 'lib' ) )
try:
import pexpect
except ImportError:
@@ -28,9 +26,12 @@ from daemon import DaemonContext
from sqlalchemy import create_engine, MetaData, Table
from sqlalchemy.orm import scoped_session, sessionmaker
import galaxy.model
from galaxy.util import json, bunch
galaxy_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir ) )
sys.path.insert( 1, os.path.join( galaxy_root, 'lib' ) )
import galaxy.model
from galaxy.util import bunch
from galaxy.util.json import jsonrpc_response, validate_jsonrpc_request
PEXPECT_IMPORT_MESSAGE = ('The Python pexpect package is required to use this '
'feature, please install it')
@@ -134,9 +135,9 @@ class ListenerRequestHandler( SocketServer.BaseRequestHandler ):
def handle( self ):
request = self.request.recv( 8192 )
response = {}
valid, request, response = json.validate_jsonrpc_request( request, ( 'get_state', ), () )
valid, request, response = validate_jsonrpc_request( request, ( 'get_state', ), () )
if valid:
self.request.send( json.dumps( json.jsonrpc_response( request=request, result=self.server.state_result.result ) ) )
self.request.send( json.dumps( jsonrpc_response( request=request, result=self.server.state_result.result ) ) )
else:
error_msg = 'Unable to serve request: %s' % response['error']['message']
if 'data' in response['error']:
static/maps/layout/menu.js.map
+1 -1
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static/maps/mvc/tours.js.map
+1 -1
View File
@@ -1 +1 @@
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{"version":3,"file":"tours.js","sources":["../../src/mvc/tours.js"],"names":["define","gxy_root","Galaxy","root","tour_opts","storage","window","sessionStorage","onEnd","removeItem","delay","orphan","hooked_tour_from_data","data","_","each","steps","step","preclick","onShow","$","click","postclick","onHide","textinsert","onShown","element","val","trigger","TourItem","Backbone","Model","extend","urlRoot","Tours","Collection","url","model","giveTour","tour_id","getJSON","tourdata","setItem","JSON","stringify","tour","Tour","init","goTo","restart","ToursView","View","initialize","self","this","setElement","fetch","success","render","error","console","tpl","template","join","$el","html","tours","models","on","e","preventDefault"],"mappings":"AAUAA,QAAQ,uBAAuB,WAE3B,GAAIC,GAA6B,mBAAXC,QAAyB,IAAMA,OAAOC,KAExDC,GAAcC,QAASC,OAAOC,eAChBC,MAAO,WACHD,eAAeE,WAAW,qBAE9BC,MAAO,IACPC,QAAO,GAGrBC,EAAwB,SAASC,GA2BjC,MA1BAC,GAAEC,KAAKF,EAAKG,MAAO,SAASC,GACpBA,EAAKC,WACLD,EAAKE,OAAQ,WACTL,EAAEC,KAAKE,EAAKC,SAAU,SAASA,GAE3BE,EAAEF,GAAUG,YAIpBJ,EAAKK,YACLL,EAAKM,OAAS,WACVT,EAAEC,KAAKE,EAAKK,UAAW,SAASA,GAE5BF,EAAEE,GAAWD,YAIrBJ,EAAKO,aAILP,EAAKQ,QAAS,WACVL,EAAEH,EAAKS,SAASC,IAAIV,EAAKO,YAAYI,QAAQ,cAIlDf,GAGPgB,EAAWC,SAASC,MAAMC,QAC5BC,QAAShC,EAAW,cAGlBiC,EAAQJ,SAASK,WAAWH,QAC9BI,IAAMnC,EAAW,YACjBoC,MAAOR,IAILS,EAAY,SAASC,GACrB,GAAIH,GAAMnC,EAAW,aAAesC,CACpCnB,GAAEoB,QAASJ,EAAK,SAAUvB,GAEtB,GAAI4B,GAAW7B,EAAsBC,EACrCN,gBAAemC,QAAQ,mBAAoBC,KAAKC,UAAU/B,GAE1D,IAAIgC,GAAO,GAAIC,MAAKhC,EAAEkB,QAClBhB,MAAOyB,EAASzB,OACjBZ,GAEHyC,GAAKE,OACLF,EAAKG,KAAK,GACVH,EAAKI,aAGTC,EAAYpB,SAASqB,KAAKnB,QAE1BoB,WAAY,WACR,GAAIC,GAAOC,IACXA,MAAKC,WAAW,UAChBD,KAAKjB,MAAQ,GAAIH,GACjBoB,KAAKjB,MAAMmB,OACTC,QAAS,WACPJ,EAAKK,UAEPC,MAAO,WAELC,QAAQD,MAAM,8BAKtBD,OAAQ,WACJ,GAAIG,GAAM/C,EAAEgD,UACR,wBACA,uFACA,2FACA,OACA,uCACI,OACI,gFACI,yCACJ,OACA,mEACJ,QACJ,YACA,SAASC,KAAK,IAClBT,MAAKU,IAAIC,KAAKJ,GAAKK,MAAOZ,KAAKjB,MAAM8B,UAAUC,GAAG,QAAS,YAAa,SAASC,GAC7EA,EAAEC,iBACFhC,EAASlB,EAAEkC,MAAMzC,KAAK,gBAKlC,QAAQqC,UAAWA,EACXtC,sBAAuBA,EACvBR,UAAWA,EACXkC,SAAUA"}
static/scripts/bundled/analysis.bundled.js
+1 -1
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static/scripts/bundled/analysis.bundled.js.map
+1 -1
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static/scripts/bundled/libs.bundled.js
+5 -5
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/layout/menu.js
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/mvc/tours.js
+1 -1
View File
@@ -1,2 +1,2 @@
define(["libs/bootstrap-tour"],function(){var a="undefined"==typeof Galaxy?"/":Galaxy.root,b={storage:window.sessionStorage,onEnd:function(){sessionStorage.removeItem("activeGalaxyTour")},delay:150,orphan:!0},c=function(a){return _.each(a.steps,function(a){a.preclick&&(a.onShow=function(){_.each(a.preclick,function(a){$(a).click()})}),a.postclick&&(a.onHide=function(){_.each(a.postclick,function(a){$(a).click()})}),a.textinsert&&(a.onShown=function(){$(a.element).val(a.textinsert).trigger("change")})}),a},d=Backbone.Model.extend({urlRoot:a+"api/tours"}),e=Backbone.Collection.extend({url:a+"api/tours",model:d}),f=function(d){var e=a+"api/tours/"+d;$.getJSON(e,function(a){var d=c(a);sessionStorage.setItem("activeGalaxyTour",JSON.stringify(a));var e=new Tour(_.extend({steps:d.steps},b));e.init(),e.goTo(0),e.restart()})},g=Backbone.View.extend({initialize:function(){var a=this;this.setElement("<div/>"),this.model=new e,this.model.fetch({success:function(){a.render()},error:function(){console.error("Failed to fetch tours.")}})},render:function(){var a=_.template(["<h2>Galaxy Tours</h2>","<p>This page presents a list of interactive tours available on this Galaxy server. ","Select any tour to get started (and remember, you can click 'End Tour' at any time).</p>","<ul>","<% _.each(tours, function(tour) { %>","<li>",'<a href="#/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',"<%- tour.attributes.name || tour.id %>","</a>",' - <%- tour.attributes.description || "No description given." %>',"</li>","<% }); %>","</ul>"].join(""));this.$el.html(a({tours:this.model.models})).on("click",".tourItem",function(){f($(this).data("tour.id"))})}});return{ToursView:g,hooked_tour_from_data:c,tour_opts:b,giveTour:f}});
define(["libs/bootstrap-tour"],function(){var a="undefined"==typeof Galaxy?"/":Galaxy.root,b={storage:window.sessionStorage,onEnd:function(){sessionStorage.removeItem("activeGalaxyTour")},delay:150,orphan:!0},c=function(a){return _.each(a.steps,function(a){a.preclick&&(a.onShow=function(){_.each(a.preclick,function(a){$(a).click()})}),a.postclick&&(a.onHide=function(){_.each(a.postclick,function(a){$(a).click()})}),a.textinsert&&(a.onShown=function(){$(a.element).val(a.textinsert).trigger("change")})}),a},d=Backbone.Model.extend({urlRoot:a+"api/tours"}),e=Backbone.Collection.extend({url:a+"api/tours",model:d}),f=function(d){var e=a+"api/tours/"+d;$.getJSON(e,function(a){var d=c(a);sessionStorage.setItem("activeGalaxyTour",JSON.stringify(a));var e=new Tour(_.extend({steps:d.steps},b));e.init(),e.goTo(0),e.restart()})},g=Backbone.View.extend({initialize:function(){var a=this;this.setElement("<div/>"),this.model=new e,this.model.fetch({success:function(){a.render()},error:function(){console.error("Failed to fetch tours.")}})},render:function(){var a=_.template(["<h2>Galaxy Tours</h2>","<p>This page presents a list of interactive tours available on this Galaxy server. ","Select any tour to get started (and remember, you can click 'End Tour' at any time).</p>","<ul>","<% _.each(tours, function(tour) { %>","<li>",'<a href="/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',"<%- tour.attributes.name || tour.id %>","</a>",' - <%- tour.attributes.description || "No description given." %>',"</li>","<% }); %>","</ul>"].join(""));this.$el.html(a({tours:this.model.models})).on("click",".tourItem",function(a){a.preventDefault(),f($(this).data("tour.id"))})}});return{ToursView:g,hooked_tour_from_data:c,tour_opts:b,giveTour:f}});
//# sourceMappingURL=../../maps/mvc/tours.js.map
templates/webapps/tool_shed/repository/view_repository.mako
+2 -3
View File
@@ -25,7 +25,7 @@
tip_str = ''
sharable_link_label = 'Link to this repository revision:'
sharable_link_changeset_revision = changeset_revision
if heads:
multiple_heads = len( heads ) > 1
else:
@@ -119,8 +119,7 @@
</div>
%if repository.long_description:
<div class="form-row">
<p>${repository.long_description|h}</p>
## ${render_long_description( to_html_string( repository.long_description ) )}
${render_long_description( to_html_string( repository.long_description ) )}
</div>
%endif
%if repository.homepage_url:
test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
+4 -4
View File
@@ -15,6 +15,10 @@ import sys
import tempfile
import threading
import time
from json import loads
import nose
from paste import httpserver
galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir))
sys.path[1:1] = [ os.path.join( galaxy_root, "scripts" ),
@@ -22,15 +26,11 @@ sys.path[1:1] = [ os.path.join( galaxy_root, "scripts" ),
os.path.join( galaxy_root, 'test' ),
os.path.join( galaxy_root, 'scripts', 'api' ) ]
import nose
from paste import httpserver
import install_and_test_tool_shed_repositories.base.util as install_and_test_base_util
from base.tool_shed_util import parse_tool_panel_config
from functional import database_contexts
from functional_tests import generate_config_file
from galaxy.app import UniverseApplication
from galaxy.util.json import loads
from galaxy.util import asbool
from galaxy.web import buildapp
test/tool_shed/base/twilltestcase.py
+1 -1
View File
@@ -7,6 +7,7 @@ import tarfile
import tempfile
import time
import urllib
from json import loads
import twill.commands as tc
from mercurial import commands, hg, ui
@@ -17,7 +18,6 @@ import galaxy.util
import galaxy.webapps.tool_shed.util.hgweb_config
from base.tool_shed_util import repository_installation_timeout
from base.twilltestcase import TwillTestCase
from galaxy.util.json import loads
from galaxy.web import security
from tool_shed.util import hg_util, xml_util
from tool_shed.util.encoding_util import tool_shed_encode
tools/data_source/upload.py
+1 -1
View File
@@ -12,13 +12,13 @@ import sys
import tempfile
import urllib
import zipfile
from json import dumps, loads
from galaxy import util
from galaxy.datatypes import sniff
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.registry import Registry
from galaxy.datatypes.util.image_util import get_image_ext
from galaxy.util.json import dumps, loads
from galaxy.util import multi_byte
from galaxy.util.checkers import check_binary, check_bz2, check_gzip, check_html, check_image, check_zip