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Merge branch 'dev' of github.com:galaxyproject/galaxy into dev

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This commit is contained in:
Eric Rasche
2015-09-25 16:59:55 -05:00
parent b6105acd2b bd3e86c046
commit f7a68ec295
51 changed files with 385 additions and 142 deletions
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.gitignore
+1
View File
@@ -76,6 +76,7 @@ tool-data/shared/igv/igv_build_sites.txt
tool-data/shared/rviewer/rviewer_build_sites.txt
tool-data/shared/ncbi/builds.txt
tool-data/shared/ucsc/builds.txt
tool-data/shared/ucsc/manual_builds.txt
tool-data/shared/ensembl/builds.txt
tool-data/shared/ucsc/publicbuilds.txt
tool-data/shared/ucsc/ucsc_build_sites.txt
client/galaxy/scripts/mvc/collection/collection-model.js
+5 -3
View File
@@ -241,10 +241,12 @@ var DatasetCollection = Backbone.Model
return json;
},
/** is the collection done with updates and ready to be used? (finished running, etc.) */
/** Is this collection in a 'ready' state no processing (for the collection) is left
* to do on the server.
*/
inReadyState : function(){
//TODO: state currenly unimplemented for collections
return true;
var populated = this.get( 'populated' );
return ( this.isDeletedOrPurged() || populated );
},
//TODO:?? the following are the same interface as DatasetAssociation - can we combine?
client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+16 -14
View File
@@ -159,20 +159,22 @@ var DatasetListItemEdit = _super.extend(
/** Render icon-button to re-run the job that created this dataset. */
_renderRerunButton : function(){
var creating_job = this.model.get('creating_job');
return faIconButton({
title : _l( 'Run this job again' ),
href : this.model.urls.rerun,
classes : 'rerun-btn',
target : this.linkTarget,
faIcon : 'fa-refresh',
onclick : function(ev) {
ev.preventDefault();
var form = new ToolsForm.View({'job_id' : creating_job});
form.deferred.execute(function(){
Galaxy.app.display(form.$el);
});
}
});
if (this.model.get('rerunnable')){
return faIconButton({
title : _l( 'Run this job again' ),
href : this.model.urls.rerun,
classes : 'rerun-btn',
target : this.linkTarget,
faIcon : 'fa-refresh',
onclick : function(ev) {
ev.preventDefault();
var form = new ToolsForm.View({'job_id' : creating_job});
form.deferred.execute(function(){
Galaxy.app.display(form.$el);
});
}
});
}
},
/** Render an icon-button or popupmenu of links based on the applicable visualizations */
client/galaxy/scripts/mvc/dataset/dataset-li.js
+9 -3
View File
@@ -37,8 +37,6 @@ var DatasetListItemView = _super.extend(
/** where should pages from links be displayed? (default to new tab/window) */
this.linkTarget = attributes.linkTarget || '_blank';
this._setUpListeners();
},
/** event listeners */
@@ -60,13 +58,21 @@ var DatasetListItemView = _super.extend(
},
// ......................................................................... expandable
/** In this override, only get details if in the ready state.
/** In this override, only get details if in the ready state, get rerunnable if in other states.
* Note: fetch with no 'change' event triggering to prevent automatic rendering.
*/
_fetchModelDetails : function(){
var view = this;
if( view.model.inReadyState() && !view.model.hasDetails() ){
return view.model.fetch({ silent: true });
// special case the need for the rerunnable and creating_job attributes
// needed for rendering re-run button on queued, running datasets
} else if( !view.model.has( 'rerunnable' ) ){
return view.model.fetch({ silent: true, data: {
// only fetch rerunnable and creating_job to keep overhead down
keys: [ 'rerunnable', 'creating_job' ].join(',')
}});
}
return jQuery.when();
},
client/galaxy/scripts/mvc/history/hdca-li.js
+3 -5
View File
@@ -21,11 +21,9 @@ var HDCAListItemView = _super.extend(
/** event listeners */
_setUpListeners : function(){
_super.prototype._setUpListeners.call( this );
// re-rendering on deletion
this.model.on( 'change', function( model, options ){
if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){
this.render();
}
this.render();
}, this );
},
@@ -46,7 +44,7 @@ var HDCAListItemView = _super.extend(
_swapNewRender : function( $newRender ){
_super.prototype._swapNewRender.call( this, $newRender );
//TODO: model currently has no state
var state = this.model.get( 'state' ) || STATES.OK;
var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK;
//if( this.model.has( 'state' ) ){
this.$el.addClass( 'state-' + state );
//}
client/galaxy/scripts/mvc/tools/tools-form-base.js
+2 -2
View File
@@ -120,12 +120,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
if (self.form == undefined){
self.form = new Form();
}
self.form.modal.show({
Galaxy.modal.show({
title : 'Tool cannot be executed',
body : error_message,
buttons : {
'Close' : function() {
self.form.modal.hide();
Galaxy.modal.hide();
}
}
});
client/galaxy/scripts/mvc/tools/tools-jobs.js
+4 -3
View File
@@ -35,6 +35,7 @@ return {
success : function(response) {
callback && callback();
form.reciept(ToolTemplate.success(response));
// begin checking the history for updates
self._refreshHdas();
},
error : function(response, response_full) {
@@ -135,11 +136,11 @@ return {
/** Refreshes the history panel
*/
_refreshHdas: function() {
_refreshHdas: function(detailIds, options) {
if (parent.Galaxy && parent.Galaxy.currHistoryPanel) {
parent.Galaxy.currHistoryPanel.refreshContents();
parent.Galaxy.currHistoryPanel.refreshContents(detailIds, options);
}
}
};
});
});
config/galaxy.ini.sample
+14
View File
@@ -574,6 +574,12 @@ nglims_config_file = tool-data/nglims.yaml
# nodejs to wrap connections in SSL).
#dynamic_proxy_external_proxy=False
# Additionally, when the dynamic proxy is proxied by an upstream server, you'll
# want to specify a prefixed URL so both Galaxy and the proxy reside under the
# same path that your cookies are under. This will result in a url like
# https://FQDN/galaxy-prefix/gie_proxy for proxying
#dynamic_proxy_prefix=gie_proxy
# -- Logging and Debugging
# If True, Galaxy will attempt to configure a simple root logger if a
@@ -648,6 +654,14 @@ use_interactive = True
# lot of CPU.
#use_heartbeat = False
# Log to Sentry
# Sentry is an open source logging and error aggregation platform. Setting
# sentry_dsn will enable the Sentry middleware and errors will be sent to the
# indicated sentry instance. This connection string is available in your
# sentry instance under <project_name> -> Settings -> API Keys.
#sentry_dsn = None
# -- Data Libraries
# These library upload options are described in much more detail in the wiki:
config/job_conf.xml.sample_advanced
+1 -1
View File
@@ -263,7 +263,7 @@
options should be reserved for defining cluster
specific options.
-->
<env id="_JAVA_OPTIONS">-Xmx=6GB</env>
<env id="_JAVA_OPTIONS">-Xmx6G</env>
<env id="ANOTHER_OPTION" raw="true">'5'</env> <!-- raw disables auto quoting -->
<env file="/mnt/java_cluster/environment_setup.sh" /> <!-- will be sourced -->
<env exec="module load javastuff/2.10" /> <!-- will be sourced -->
config/plugins/interactive_environments/ipython/config/ipython.ini.sample
+20 -14
View File
@@ -1,5 +1,4 @@
[main]
# Following options are ignored if using the Galaxy dynamic proxy but
# are useful if mapping a range of ports for environment consumption.
#apache_urls = False
@@ -7,32 +6,39 @@
#ssl = False
[docker]
# Command to execute docker. For example `sudo docker` or `docker-lxc`.
command = docker
# Command to launch docker container. For example `sudo docker` or `docker-lxc`.
# If you need to use a command like `sg` you can do that here, just be sure to
# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
#
# It is recommended that you use command_inject if you need to inject
# additional parameters. This command string is re-used for a `docker inspect`
# command and will likely cause errors if it is extensively modified, past the
# usual group/sudo changes.
#command = docker {docker_args}
# The docker image name that should be started.
image = bgruening/docker-ipython-notebook:dev
# Additional arguments that are passed to the `docker run` command.
command_inject = --sig-proxy=true -e DEBUG=false
# Command to wrap around the full docker command.
# For example, `sg 'docker' '{cmd}'` where {cmd} will be replaced by the full
# docker command. Make sure to surround the {cmd} with single quotes(').
# Default: empty
#command_wrapper =
#command_inject = --sig-proxy=true -e DEBUG=false
# URL to access the Galaxy API with from the spawn Docker containter, if empty
# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
# Docker host of the spawned container if that is also not set.
#galaxy_url =
#galaxy_url =
# The Docker hostname. It can be useful to run the Docker daemon on a different
# host than Galaxy.
#docker_hostname = localhost
# Try to set the tempdirectory to world execute - this can fix the issue
# where 'sudo docker' is not able to mount the folder otherwise.
# where 'sudo docker' is not able to mount the folder otherwise.
# "finalize namespace chdir to /import permission denied"
wx_tempdir = False
#wx_tempdir = False
# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
# located on an NFS share, which does not work well as Docker volume. In this case
# you can have a shared sshfs share which you can use as temporary directory to
# share data between the IE and Galaxy.
#docker_galaxy_temp_dir = None
config/plugins/interactive_environments/ipython/templates/ipython.mako
+5 -7
View File
@@ -33,18 +33,16 @@ if hda.datatype.__class__.__name__ != "Ipynb":
else:
shutil.copy( hda.file_name, empty_nb_path )
## General IE specific
# Access URLs for the notebook from within galaxy.
notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb')
notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree')
# Add all environment variables collected from Galaxy's IE infrastructure
ie_request.launch(env_override={
'notebook_password': PASSWORD,
})
## General IE specific
# Access URLs for the notebook from within galaxy.
notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/notebooks/ipython_galaxy_notebook.ipynb')
notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/login?next=${PROXY_PREFIX}%2Fipython%2Ftree')
%>
<html>
<head>
config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
+36 -11
View File
@@ -1,19 +1,44 @@
[main]
# This cannot be changed
# This CANNOT be changed. Eventually will be deprecated
password_auth = True
# Other
apache_urls = False
ssl = False
# Following options are ignored if using the Galaxy dynamic proxy but
# are useful if mapping a range of ports for environment consumption.
#apache_urls = False
#ssl = False
[docker]
command = docker
# Command to launch docker container. For example `sudo docker` or `docker-lxc`.
# If you need to use a command like `sg` you can do that here, just be sure to
# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
#
# It is recommended that you use command_inject if you need to inject
# additional parameters. This command string is re-used for a `docker inspect`
# command and will likely cause errors if it is extensively modified, past the
# usual group/sudo changes.
#command = docker {docker_args}
# The docker image name that should be started.
image = erasche/docker-rstudio-notebook:dev
# Additional arguments that are passed to the `docker run` command. `-u`
# settings are completely ignored.
command_inject = --sig-proxy=true -e DEBUG=false
# Additional arguments that are passed to the `docker run` command.
#command_inject = --sig-proxy=true -e DEBUG=false
# URL to access the Galaxy API with from the spawned Docker container, if empty
# URL to access the Galaxy API with from the spawn Docker containter, if empty
# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
# Docker host of the spawned container, if that is also not set.
#galaxy_url=
# Docker host of the spawned container if that is also not set.
#galaxy_url =
# The Docker hostname. It can be useful to run the Docker daemon on a different
# host than Galaxy.
#docker_hostname = localhost
# Try to set the tempdirectory to world execute - this can fix the issue
# where 'sudo docker' is not able to mount the folder otherwise.
# "finalize namespace chdir to /import permission denied"
#wx_tempdir = False
# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
# located on an NFS share, which does not work well as Docker volume. In this case
# you can have a shared sshfs share which you can use as temporary directory to
# share data between the IE and Galaxy.
#docker_galaxy_temp_dir = None
config/plugins/interactive_environments/rstudio/templates/rstudio.mako
+9 -9
View File
@@ -12,14 +12,6 @@ temp_dir = ie_request.temp_dir
PASSWORD = ie_request.notebook_pw
USERNAME = "galaxy"
## General IE specific
# Access URLs for the notebook from within galaxy.
# TODO: Make this work without pointing directly to IE. Currently does not work
# through proxy.
notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-public-key')
notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/')
notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-do-sign-in')
# Did the user give us an RData file?
if hda.datatype.__class__.__name__ == "RData":
shutil.copy( hda.file_name, os.path.join(temp_dir, '.RData') )
@@ -27,8 +19,16 @@ if hda.datatype.__class__.__name__ == "RData":
ie_request.launch(env_override={
'notebook_username': USERNAME,
'notebook_password': PASSWORD,
'cors_origin': ie_request.attr.proxy_url,
})
## General IE specific
# Access URLs for the notebook from within galaxy.
# TODO: Make this work without pointing directly to IE. Currently does not work
# through proxy.
notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-public-key')
notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/')
notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-do-sign-in')
%>
<html>
<head>
lib/galaxy/config.py
+1
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@@ -443,6 +443,7 @@ class Configuration( object ):
self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) )
self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" )
self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) )
self.dynamic_proxy_prefix = kwargs.get( "dynamic_proxy_prefix", "gie_proxy" )
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
lib/galaxy/datatypes/binary.py
+2 -2
View File
@@ -39,11 +39,11 @@ class Binary( data.Data ):
@staticmethod
def register_sniffable_binary_format(data_type, ext, type_class):
Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class})
Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class})
@staticmethod
def register_unsniffable_binary_ext(ext):
Binary.unsniffable_binary_formats.append(ext)
Binary.unsniffable_binary_formats.append(ext.lower())
@staticmethod
def is_sniffable_binary( filename ):
lib/galaxy/jobs/__init__.py
+1 -1
View File
@@ -1402,7 +1402,7 @@ class JobWrapper( object ):
job = has_metrics.get_job()
per_plugin_properties = self.app.job_metrics.collect_properties( job.destination_id, self.job_id, self.working_directory )
if per_plugin_properties:
log.info( "Collecting job metrics for %s: %s" % ( has_metrics, getattr( has_metrics, 'id', None ) ) )
log.info( "Collecting metrics for %s %s" % ( type(has_metrics).__name__, getattr( has_metrics, 'id', None ) ) )
for plugin, properties in per_plugin_properties.iteritems():
for metric_name, metric_value in properties.iteritems():
if metric_value is not None:
lib/galaxy/managers/hdas.py
+9
View File
@@ -280,6 +280,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
'peek',
'creating_job',
'rerunnable',
'uuid',
'permissions',
@@ -328,6 +329,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
'resubmitted' : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ),
'creating_job' : self.serialize_creating_job,
'rerunnable' : self.rerunnable,
'display_apps' : self.serialize_display_apps,
'display_types' : self.serialize_old_display_applications,
@@ -439,6 +441,13 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
else:
return None
def rerunnable( self, hda, key, **context ):
if hda.creating_job:
tool = self.app.toolbox.get_tool(hda.creating_job.tool_id, hda.creating_job.tool_version)
if tool and tool.is_workflow_compatible:
return True
return False
class HDADeserializer( datasets.DatasetAssociationDeserializer,
taggable.TaggableDeserializerMixin,
lib/galaxy/model/__init__.py
+3
View File
@@ -3047,6 +3047,9 @@ class DatasetCollectionInstance( object, HasName ):
id=self.id,
name=self.name,
collection_type=self.collection.collection_type,
populated=self.collection.populated,
populated_state=self.collection.populated_state,
populated_state_message=self.collection.populated_state_message,
type="collection", # contents type (distinguished from file or folder (in case of library))
)
lib/galaxy/tools/__init__.py
+2
View File
@@ -1538,6 +1538,8 @@ class Tool( object, Dictifiable ):
group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max }
any_group_errors = True
rep_index += 1
if any_group_errors:
errors[ input.name ] = group_errors
elif isinstance( input, Conditional ):
group_state = state[input.name]
group_prefix = "%s|" % ( key )
lib/galaxy/tools/parser/yaml.py
+1 -1
View File
@@ -75,7 +75,7 @@ class YamlToolSource(ToolSource):
for output in output_defs:
outputs[output.name] = output
# TODO: parse outputs collections
return output_defs, odict()
return outputs, odict()
def _parse_output(self, tool, name, output_dict):
# TODO: handle filters, actions, change_format
lib/galaxy/web/base/interactive_environments.py
+121 -39
View File
@@ -1,6 +1,7 @@
import ConfigParser
import os
import json
import stat
import random
import tempfile
@@ -40,18 +41,15 @@ class InteractiveEnviornmentRequest(object):
self.load_deploy_config()
self.attr.docker_hostname = self.attr.viz_config.get("docker", "docker_hostname")
self.attr.proxy_request = trans.app.proxy_manager.setup_proxy(
trans, host=self.attr.docker_hostname
)
self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ]
self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ]
# Generate per-request passwords the IE plugin can use to configure
# the destination container.
self.notebook_pw_salt = self.generate_password(length=12)
self.notebook_pw = self.generate_password(length=24)
self.temp_dir = os.path.abspath( tempfile.mkdtemp() )
ie_parent_temp_dir = self.attr.viz_config.get("docker", "docker_galaxy_temp_dir") or None
self.temp_dir = os.path.abspath( tempfile.mkdtemp( dir=ie_parent_temp_dir ) )
if self.attr.viz_config.getboolean("docker", "wx_tempdir"):
# Ensure permissions are set
try:
@@ -60,15 +58,26 @@ class InteractiveEnviornmentRequest(object):
log.error( "Could not change permissions of tmpdir %s" % self.temp_dir )
# continue anyway
# This duplicates the logic in the proxy manager
if self.attr.galaxy_config.dynamic_proxy_external_proxy:
self.attr.proxy_prefix = '%s/%s' % (
self.attr.galaxy_config.cookie_path,
self.attr.galaxy_config.dynamic_proxy_prefix)
else:
self.attr.proxy_prefix = ''
def load_deploy_config(self, default_dict={}):
# For backwards compat, any new variables added to the base .ini file
# will need to be recorded here. The ConfigParser doesn't provide a
# .get() that will ignore missing sections, so we must make use of
# their defaults dictionary instead.
default_dict['command_inject'] = '--sig-proxy=true'
default_dict['docker_hostname'] = 'localhost'
default_dict['wx_tempdir'] = 'False'
default_dict['command_wrapper'] = ''
default_dict = {
'command': 'docker {docker_args}',
'command_inject': '--sig-proxy=true -e DEBUG=false',
'docker_hostname': 'localhost',
'wx_tempdir': 'False',
'docker_galaxy_temp_dir': None
}
viz_config = ConfigParser.SafeConfigParser(default_dict)
conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
if not os.path.exists( conf_path ):
@@ -102,8 +111,10 @@ class InteractiveEnviornmentRequest(object):
'history_id': self.attr.history_id,
'api_key': api_key,
'remote_host': request.remote_addr,
'docker_port': self.attr.PORT,
# DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update.
'cors_origin': request.host_url,
'user_email': self.trans.user.email,
'proxy_prefix': self.attr.proxy_prefix,
}
if self.attr.viz_config.has_option("docker", "galaxy_url"):
@@ -138,36 +149,27 @@ class InteractiveEnviornmentRequest(object):
return "false"
def url_template(self, url_template):
"""Process a URL template
There are several variables accessible to the user:
- ${PROXY_URL} will be replaced with the dynamically create proxy's url
- ${PROXY_PREFIX} will be replaced with the prefix that may occur
"""
Process a URL template
There are several variables accessible to the user:
- ${PROXY_URL} will be replaced with dynamically create proxy
- ${PORT} will be replaced with the port the docker image is attached to
"""
# Figure out our substitutions
# Next several lines for older style replacements (not used with Galaxy dynamic
# proxy)
if self.attr.SSL_URLS:
protocol = 'https'
else:
protocol = 'http'
if not self.attr.APACHE_URLS:
# If they are not using apache URLs, that implies there's a port attached to the host
# string, thus we replace just the first instance of host that we see.
url_template = url_template.replace('${HOST}', '${HOST}:${PORT}', 1)
url_template = url_template.replace('${PROTO}', protocol) \
.replace('${HOST}', self.attr.HOST)
# Only the following replacements are used with Galaxy dynamic proxy
# URLs
url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \
.replace('${PORT}', str(self.attr.PORT))
.replace('${PROXY_PREFIX}', str(self.attr.proxy_prefix.replace('/', '%2F')))
return url
def volume(self, host_path, container_path, **kwds):
@@ -182,18 +184,22 @@ class InteractiveEnviornmentRequest(object):
conf.update(env_override)
env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
cmd = '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \
(self.attr.viz_config.get("docker", "command"),
env_str,
self.attr.viz_config.get("docker", "command_inject"),
self.attr.PORT, self.attr.docker_port,
temp_dir,
volume_str,
self.attr.viz_config.get("docker", "image"))
cmd_wrapper = self.attr.viz_config.get("docker", "command_wrapper")
if cmd_wrapper != '' and '{cmd}' in cmd_wrapper:
cmd = cmd_wrapper.format( cmd=cmd )
return cmd
# This is the basic docker command such as "sudo -u docker docker {docker_args}"
# or just "docker {docker_args}"
command = self.attr.viz_config.get("docker", "command")
# Then we format in the entire docker command in place of
# {docker_args}, so as to let the admin not worry about which args are
# getting passed
command = command.format(docker_args='run {command_inject} {environment} -d -P -v "{temp_dir}:/import/" {volume_str} {image}')
# Once that's available, we format again with all of our arguments
command = command.format(
command_inject=self.attr.viz_config.get("docker", "command_inject"),
environment=env_str,
temp_dir=temp_dir,
volume_str=volume_str,
image=self.attr.viz_config.get("docker", "image")
)
return command
def launch(self, raw_cmd=None, env_override={}, volumes=[]):
if raw_cmd is None:
@@ -206,5 +212,81 @@ class InteractiveEnviornmentRequest(object):
stdout, stderr = p.communicate()
if p.returncode != 0 or len(stderr):
log.error( "%s\n%s" % (stdout, stderr) )
return None
else:
log.debug( "Container id: %s" % stdout)
port_mappings = self.get_proxied_ports(stdout)
if len(port_mappings) > 1:
log.warning("Don't know how to handle proxies to containers with multiple exposed ports. Arbitrarily choosing first")
elif len(port_mappings) == 0:
log.warning("No exposed ports to map! Images MUST EXPOSE")
return None
# Fetch the first port_mapping
(service, host_ip, host_port) = port_mappings[0]
# Now we configure our proxy_requst object and we manually specify
# the port to map to and ensure the proxy is available.
self.attr.proxy_request = self.trans.app.proxy_manager.setup_proxy(
self.trans,
host=self.attr.docker_hostname,
port=host_port,
proxy_prefix=self.attr.proxy_prefix,
)
# These variables then become available for use in templating URLs
self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ]
# Commented out because it needs to be documented and visible that
# this variable was moved here. Usually would remove commented
# code, but again, needs to be clear where this went. Remove at a
# later time.
#
# PORT is no longer exposed internally. All requests are forced to
# go through the proxy we ship.
# self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ]
def get_proxied_ports(self, container_id):
"""Run docker inspect on a container to figure out which ports were
mapped where.
:type container_id: str
:param container_id: a docker container ID
:returns: a list of triples containing (internal_port, external_ip,
external_port), of which the ports are probably the only
useful information.
Someday code that calls this should be refactored whenever we get
containers with multiple ports working.
"""
command = self.attr.viz_config.get("docker", "command")
command = command.format(docker_args="inspect %s" % container_id)
log.info("Inspecting docker container {0} with command [{1}]".format(
container_id,
command
))
p = Popen(command, stdout=PIPE, stderr=PIPE, close_fds=True, shell=True)
stdout, stderr = p.communicate()
if p.returncode != 0 or len(stderr):
log.error( "%s\n%s" % (stdout, stderr) )
return None
inspect_data = json.loads(stdout)
# [{
# "NetworkSettings" : {
# "Ports" : {
# "3306/tcp" : [
# {
# "HostIp" : "127.0.0.1",
# "HostPort" : "3306"
# }
# ]
mappings = []
port_mappings = inspect_data[0]['NetworkSettings']['Ports']
for port_name in port_mappings:
for binding in port_mappings[port_name]:
mappings.append((
port_name.replace('/tcp', '').replace('/udp', ''),
binding['HostIp'],
binding['HostPort']
))
return mappings
lib/galaxy/web/proxy/__init__.py
+5 -3
View File
@@ -17,7 +17,9 @@ SECURE_COOKIE = "galaxysession"
class ProxyManager(object):
def __init__( self, config ):
for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]:
for option in ["manage_dynamic_proxy", "dynamic_proxy_bind_port",
"dynamic_proxy_bind_ip", "dynamic_proxy_debug",
"dynamic_proxy_external_proxy", "dynamic_proxy_prefix"]:
setattr( self, option, getattr( config, option ) )
self.launch_by = "node" # TODO: Support docker
if self.manage_dynamic_proxy:
@@ -29,7 +31,7 @@ class ProxyManager(object):
def shutdown( self ):
self.lazy_process.shutdown()
def setup_proxy( self, trans, host=DEFAULT_PROXY_TO_HOST, port=None ):
def setup_proxy( self, trans, host=DEFAULT_PROXY_TO_HOST, port=None, proxy_prefix="" ):
if self.manage_dynamic_proxy:
log.info("Attempting to start dynamic proxy process")
self.lazy_process.start_process()
@@ -46,7 +48,7 @@ class ProxyManager(object):
if not self.dynamic_proxy_external_proxy:
proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port)
else:
proxy_url = '%s://%s' % (scheme, host)
proxy_url = '%s://%s%s' % (scheme, host, proxy_prefix)
return {
'proxy_url': proxy_url,
'proxied_port': proxy_requests.port,
lib/galaxy/workflow/run.py
+4 -1
View File
@@ -285,7 +285,10 @@ class WorkflowProgress( object ):
raise modules.DelayedWorkflowEvaluation()
return replacement
def set_outputs_for_input( self, step, outputs={} ):
def set_outputs_for_input( self, step, outputs=None ):
if outputs is None:
outputs = {}
if self.inputs_by_step_id:
outputs[ 'output' ] = self.inputs_by_step_id[ step.id ]
scripts/common_startup.sh
+1
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@@ -16,6 +16,7 @@ SAMPLES="
config/shed_data_manager_conf.xml.sample
lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
tool-data/shared/ucsc/builds.txt.sample
tool-data/shared/ucsc/manual_builds.txt.sample
tool-data/shared/ucsc/ucsc_build_sites.txt.sample
tool-data/shared/igv/igv_build_sites.txt.sample
tool-data/shared/rviewer/rviewer_build_sites.txt.sample
static/maps/mvc/collection/collection-model.js.map
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static/maps/mvc/dataset/dataset-li-edit.js.map
+1 -1
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static/maps/mvc/dataset/dataset-li.js.map
+1 -1
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static/maps/mvc/history/hdca-li.js.map
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@@ -1 +1 @@
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static/maps/mvc/tools/tools-form-base.js.map
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static/maps/mvc/tools/tools-jobs.js.map
+1 -1
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@@ -1 +1 @@
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static/maps/mvc/upload/upload-row.js.map
+1
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static/scripts/mvc/collection/collection-model.js
+1 -1
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@@ -1,2 +1,2 @@
define(["mvc/dataset/dataset-model","mvc/base-mvc","utils/localization"],function(a,b){var c={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(a){return _.extend(a,a.object,{element_id:a.id}),delete a.object,a},constructor:function(a){a=this._mergeObject(a),this.idAttribute="element_id",Backbone.Model.apply(this,arguments)},parse:function(a){var b=a;return b=this._mergeObject(b)}},d=Backbone.Model.extend(b.LoggableMixin).extend(c),e=Backbone.Collection.extend(b.LoggableMixin).extend({model:d,initialize:function(a,b){this.debug(this+"(DCECollection).initialize:",a,b),b=b||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),f=a.DatasetAssociation.extend(b.mixin(c,{defaults:_.extend({},a.DatasetAssociation.prototype.defaults,c.defaults),constructor:function(a,b){this.debug(" DatasetDCE.constructor:",a,b),c.constructor.call(this,a,b)},initialize:function(b,c){this.debug(this+"(DatasetDCE).initialize:",b,c),a.DatasetAssociation.prototype.initialize.call(this,b,c)},toString:function(){var a=this.get("element_identifier");return["DatasetDCE(",a,")"].join("")}})),g=e.extend({model:f,initialize:function(a,b){this.debug(this+"(DatasetDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=Backbone.Model.extend(b.LoggableMixin).extend(b.SearchableModelMixin).extend({defaults:{collection_type:null,deleted:!1},collectionClass:e,initialize:function(a,b){this.debug(this+"(DatasetCollection).initialize:",a,b,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var a=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(a),this.elements},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return this.elements&&(a.elements=this.elements.toJSON()),a},inReadyState:function(){return!0},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(){return this.elements},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}});
define(["mvc/dataset/dataset-model","mvc/base-mvc","utils/localization"],function(a,b){var c={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(a){return _.extend(a,a.object,{element_id:a.id}),delete a.object,a},constructor:function(a){a=this._mergeObject(a),this.idAttribute="element_id",Backbone.Model.apply(this,arguments)},parse:function(a){var b=a;return b=this._mergeObject(b)}},d=Backbone.Model.extend(b.LoggableMixin).extend(c),e=Backbone.Collection.extend(b.LoggableMixin).extend({model:d,initialize:function(a,b){this.debug(this+"(DCECollection).initialize:",a,b),b=b||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),f=a.DatasetAssociation.extend(b.mixin(c,{defaults:_.extend({},a.DatasetAssociation.prototype.defaults,c.defaults),constructor:function(a,b){this.debug(" DatasetDCE.constructor:",a,b),c.constructor.call(this,a,b)},initialize:function(b,c){this.debug(this+"(DatasetDCE).initialize:",b,c),a.DatasetAssociation.prototype.initialize.call(this,b,c)},toString:function(){var a=this.get("element_identifier");return["DatasetDCE(",a,")"].join("")}})),g=e.extend({model:f,initialize:function(a,b){this.debug(this+"(DatasetDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=Backbone.Model.extend(b.LoggableMixin).extend(b.SearchableModelMixin).extend({defaults:{collection_type:null,deleted:!1},collectionClass:e,initialize:function(a,b){this.debug(this+"(DatasetCollection).initialize:",a,b,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var a=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(a),this.elements},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return this.elements&&(a.elements=this.elements.toJSON()),a},inReadyState:function(){var a=this.get("populated");return this.isDeletedOrPurged()||a},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(){return this.elements},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}});
//# sourceMappingURL=../../../maps/mvc/collection/collection-model.js.map
static/scripts/mvc/dataset/dataset-li-edit.js
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static/scripts/mvc/dataset/dataset-li.js
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static/scripts/mvc/history/hdca-li.js
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define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',e("This collection has been hidden"),"</div>","<% } %>"],"collection")}),b=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- collection.hid %></span> ','<span class="name"><%- collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}});
define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',e("This collection has been hidden"),"</div>","<% } %>"],"collection")}),b=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- collection.hid %></span> ','<span class="name"><%- collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}});
//# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map
static/scripts/mvc/tools/tools-form-base.js
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define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),e.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){e.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),Galaxy.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map
static/scripts/mvc/tools/tools-jobs.js
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@@ -1,2 +1,2 @@
define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}});
define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(a,b){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a,b)}}});
//# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map
static/scripts/mvc/upload/upload-row.js
+2
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test-data/1.RData
BIN
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test/api/helpers.py
+15 -3
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@@ -100,10 +100,14 @@ class BaseDatasetPopulator( object ):
file_type = kwds.get( "file_type", 'txt' )
upload_params = {
'files_0|NAME': name,
'files_0|url_paste': content,
'dbkey': dbkey,
'file_type': file_type,
}
if isinstance( content, file ):
upload_params[ "files_0|file_data"] = content
else:
upload_params[ 'files_0|url_paste' ] = content
if "to_posix_lines" in kwds:
upload_params[ "files_0|to_posix_lines"] = kwds[ "to_posix_lines" ]
if "space_to_tab" in kwds:
@@ -116,6 +120,10 @@ class BaseDatasetPopulator( object ):
)
def run_tool_payload( self, tool_id, inputs, history_id, **kwds ):
if "files_0|file_data" in inputs:
kwds[ "__files" ] = { "files_0|file_data": inputs[ "files_0|file_data" ] }
del inputs[ "files_0|file_data" ]
return dict(
tool_id=tool_id,
inputs=json.dumps(inputs),
@@ -174,8 +182,12 @@ class DatasetPopulator( BaseDatasetPopulator ):
def __init__( self, galaxy_interactor ):
self.galaxy_interactor = galaxy_interactor
def _post( self, route, data={} ):
return self.galaxy_interactor.post( route, data )
def _post( self, route, data={}, files=None ):
files = data.get( "__files", None )
if files is not None:
del data[ "__files" ]
return self.galaxy_interactor.post( route, data, files=files )
def _get( self, route ):
return self.galaxy_interactor.get( route )
test/api/test_dataset_collections.py
+1
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@@ -87,6 +87,7 @@ class DatasetCollectionApiTestCase( api.ApiTestCase ):
pair_1_object = pair_1_element[ "object" ]
self._assert_has_keys( pair_1_object, "collection_type", "elements" )
self.assertEquals( pair_1_object[ "collection_type" ], "paired" )
self.assertEquals( pair_1_object[ "populated" ], True )
pair_elements = pair_1_object[ "elements" ]
assert len( pair_elements ) == 2
pair_1_element_1 = pair_elements[ 0 ]
test/api/test_tools.py
+28 -1
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@@ -5,6 +5,7 @@ from .helpers import DatasetPopulator
from .helpers import DatasetCollectionPopulator
from .helpers import LibraryPopulator
from .helpers import skip_without_tool
from base.test_data import TestDataResolver
class ToolsTestCase( api.ApiTestCase ):
@@ -109,6 +110,12 @@ class ToolsTestCase( api.ApiTestCase ):
result_content = self._upload_and_get_content( table )
self.assertEquals( result_content, table )
def test_rdata_not_decompressed( self ):
# Prevent regression of https://github.com/galaxyproject/galaxy/issues/753
rdata_path = TestDataResolver().get_filename("1.RData")
rdata_metadata = self._upload_and_get_details( open(rdata_path, "rb"), file_type="auto" )
self.assertEquals( rdata_metadata[ "file_ext" ], "rdata" )
@skip_without_tool( "multi_select" )
def test_multi_select_as_list( self ):
history_id = self.dataset_populator.new_history()
@@ -230,6 +237,18 @@ class ToolsTestCase( api.ApiTestCase ):
response = self._run( "validation_default", history_id, inputs )
self._assert_status_code_is( response, 400 )
@skip_without_tool( "validation_repeat" )
def test_validation_in_repeat( self ):
history_id = self.dataset_populator.new_history()
inputs = {
'r1_0|text': "123",
'r2_0|text': "",
}
response = self._run( "validation_repeat", history_id, inputs )
import time
time.sleep(10)
self._assert_status_code_is( response, 400 )
@skip_without_tool( "multi_select" )
def test_select_legal_values( self ):
history_id = self.dataset_populator.new_history()
@@ -1042,12 +1061,20 @@ class ToolsTestCase( api.ApiTestCase ):
else:
return create_response
def _upload_and_get_content( self, content, **upload_kwds ):
def _upload( self, content, **upload_kwds ):
history_id = self.dataset_populator.new_history()
new_dataset = self.dataset_populator.new_dataset( history_id, content=content, **upload_kwds )
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
return history_id, new_dataset
def _upload_and_get_content( self, content, **upload_kwds ):
history_id, new_dataset = self._upload( content, **upload_kwds )
return self.dataset_populator.get_history_dataset_content( history_id, dataset=new_dataset )
def _upload_and_get_details( self, content, **upload_kwds ):
history_id, new_dataset = self._upload( content, **upload_kwds )
return self.dataset_populator.get_history_dataset_details( history_id, dataset=new_dataset )
def __tool_ids( self ):
index = self._get( "tools" )
tools_index = index.json()
test/api/test_workflows.py
+42
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@@ -575,6 +575,48 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
content = self.dataset_populator.get_history_dataset_content( history_id, hid=0 )
self.assertEquals("10.0\n30.0\n20.0\n40.0\n", content )
@skip_without_tool( "collection_split_on_column" )
@skip_without_tool( "min_repeat" )
def test_workflow_run_dynamic_output_collections_2( self ):
# A more advanced output collection workflow, testing regression of
# https://github.com/galaxyproject/galaxy/issues/776
history_id = self.dataset_populator.new_history()
workflow_id = self._upload_yaml_workflow("""
- label: test_input_1
type: input
- label: test_input_2
type: input
- label: test_input_3
type: input
- label: split_up
tool_id: collection_split_on_column
state:
input1:
$link: test_input_2
- label: min_repeat
tool_id: min_repeat
state:
queries:
- input:
$link: test_input_1
queries2:
- input2:
$link: split_up#split_output
""")
hda1 = self.dataset_populator.new_dataset( history_id, content="samp1\t10.0\nsamp2\t20.0\n" )
hda2 = self.dataset_populator.new_dataset( history_id, content="samp1\t20.0\nsamp2\t40.0\n" )
hda3 = self.dataset_populator.new_dataset( history_id, content="samp1\t30.0\nsamp2\t60.0\n" )
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
inputs = {
'0': self._ds_entry(hda1),
'1': self._ds_entry(hda2),
'2': self._ds_entry(hda3),
}
invocation_id = self.__invoke_workflow( history_id, workflow_id, inputs )
self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
content = self.dataset_populator.get_history_dataset_content( history_id, hid=7 )
self.assertEquals(content.strip(), "samp1\t10.0\nsamp2\t20.0")
def test_workflow_request( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
workflow_request, history_id = self._setup_workflow_run( workflow )
test/base/test_data.py
+1 -1
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@@ -23,7 +23,7 @@ LIST_SEP = re.compile("\s*,\s*")
class TestDataResolver(object):
def __init__(self, env_var, environ=os.environ):
def __init__(self, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ):
file_dirs = environ.get(env_var, None)
if file_dirs:
self.resolvers = map(lambda u: build_resolver(u, environ), LIST_SEP.split(file_dirs))
test/base/twilltestcase.py
+1 -1
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@@ -50,7 +50,7 @@ class TwillTestCase( unittest.TestCase ):
self.host = os.environ.get( 'GALAXY_TEST_HOST' )
self.port = os.environ.get( 'GALAXY_TEST_PORT' )
self.url = "http://%s:%s" % ( self.host, self.port )
self.test_data_resolver = TestDataResolver( 'GALAXY_TEST_FILE_DIR' )
self.test_data_resolver = TestDataResolver( )
self.tool_shed_test_file = os.environ.get( 'GALAXY_TOOL_SHED_TEST_FILE', None )
if self.tool_shed_test_file:
f = open( self.tool_shed_test_file, 'r' )
test/functional/tools/disambiguate_cond.xml
+2
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@@ -38,8 +38,10 @@
<when value="true">
<param type="data" name="file" />
</when>
<when value="false" />
</conditional>
</when>
<when value="false" />
</conditional>
</inputs>
<outputs>
test/functional/tools/min_repeat.xml
+3 -3
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@@ -1,4 +1,4 @@
<tool id="min_repeat" name="min_repeat">
<tool id="min_repeat" name="min_repeat" version="0.1.0">
<command>
cat #for $q in $queries# ${q.input} #end for# > $out_file1 ;
cat #for $q in $queries2# ${q.input2} #end for# > $out_file2
@@ -12,8 +12,8 @@
</repeat>
</inputs>
<outputs>
<data name="out_file1" format="txt" />
<data name="out_file2" format="txt" />
<data name="out_file1" format="txt" label="Repeat 1 Datasets on ${on_string}" />
<data name="out_file2" format="txt" label="Repeat 2 Datasets on ${on_string}" />
</outputs>
<tests>
<test>
test/functional/tools/samples_tool_conf.xml
-1
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@@ -6,7 +6,6 @@
<tool file="boolean_conditional.xml" />
<tool file="composite.xml" />
<tool file="environment_variables.xml" />
<tool file="compare_bam_as_sam.xml" />
<tool file="code_file.xml" />
<tool file="disambiguate_cond.xml" />
<tool file="multi_repeats.xml"/>
test/functional/tools/validation_repeat.xml
+1
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@@ -13,6 +13,7 @@
</repeat>
<repeat name="r2" label="Repeat 2">
<param name="text" type="text" label="text input">
<validator type="empty_field" />
<sanitizer>
<valid initial="none">
<add value="a"/>
test/unit/jobs/test_job_configuration.py
+1 -1
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@@ -119,7 +119,7 @@ class JobConfXmlParserTestCase( unittest.TestCase ):
env_dest = self.job_config.destinations[ "java_cluster" ][ 0 ]
assert len( env_dest.env ) == 4, len( env_dest.env )
assert env_dest.env[ 0 ][ "name" ] == "_JAVA_OPTIONS"
assert env_dest.env[ 0 ][ "value" ] == '-Xmx=6GB'
assert env_dest.env[ 0 ][ "value" ] == '-Xmx6G'
assert env_dest.env[ 1 ][ "name" ] == "ANOTHER_OPTION"
assert env_dest.env[ 1 ][ "raw" ] is True
tool-data/shared/ucsc/manual_builds.txt → tool-data/shared/ucsc/manual_builds.txt.sample
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