mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_15.10' into dev
This commit is contained in:
Nate Coraor
@@ -60,6 +60,8 @@ GalaxyApp.prototype._init = function init( options ){
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self._initUser( options.user || bootstrapped.user || {} );
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self.debug( 'GalaxyApp.user: ', self.user );
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self.root = options.root;
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self.debug( 'GalaxyApp.root: ', self.root );
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//TODO: temp
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self.trigger( 'ready', self );
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//if( typeof options.onload === 'function' ){
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@@ -17,7 +17,7 @@
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#command = docker {docker_args}
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# The docker image name that should be started.
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image = bgruening/docker-ipython-notebook:15.10
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image = bgruening/docker-ipython-notebook:15.10.1
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# Additional arguments that are passed to the `docker run` command.
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#command_inject = --sig-proxy=true -e DEBUG=false
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@@ -8,8 +8,7 @@ import hashlib
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# Sets ID and sets up a lot of other variables
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ie_request.load_deploy_config()
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ie_request.attr.docker_port = 6789
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# Create tempdir in galaxy
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temp_dir = ie_request.temp_dir
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ie_request.attr.import_volume = False
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if ie_request.attr.PASSWORD_AUTH:
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m = hashlib.sha1()
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@@ -19,23 +18,15 @@ else:
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PASSWORD = "none"
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## IPython Specific
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# Prepare an empty notebook
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notebook_id = ie_request.generate_hex(64)
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with open( os.path.join( ie_request.attr.our_template_dir, 'notebook.ipynb' ), 'r') as nb_handle:
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empty_nb = nb_handle.read()
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empty_nb = empty_nb % notebook_id
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# Copy over default notebook, unless the dataset this viz is running on is a notebook
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empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb')
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if hda.datatype.__class__.__name__ != "Ipynb":
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with open( empty_nb_path, 'w+' ) as handle:
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handle.write( empty_nb )
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if hda.datatype.__class__.__name__ == "Ipynb":
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DATASET_HID = hda.hid
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else:
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shutil.copy( hda.file_name, empty_nb_path )
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DATASET_HID = None
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# Add all environment variables collected from Galaxy's IE infrastructure
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ie_request.launch(env_override={
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'notebook_password': PASSWORD,
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'dataset_hid': DATASET_HID,
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})
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## General IE specific
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@@ -63,7 +63,11 @@ class ConfigSerializer( base.ModelSerializer ):
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'ftp_upload_dir' : _defaults_to( None ),
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'ftp_upload_site' : _defaults_to( None ),
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'version_major' : _defaults_to( None ),
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'require_login' : _defaults_to( None )
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'require_login' : _defaults_to( None ),
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'inactivity_box_content' : _defaults_to( None ),
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'message_box_content' : _defaults_to( None ),
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'message_box_visible' : _defaults_to( False ),
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'message_box_class' : _defaults_to( 'info' ),
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}
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@@ -582,8 +582,8 @@ class DynamicOptions( object ):
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def get_fields( self, trans, other_values ):
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if self.dataset_ref_name:
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dataset = other_values.get( self.dataset_ref_name, None )
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assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name
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if not dataset:
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log.warn( "Required dataset '%s' missing from input" % self.dataset_ref_name )
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return [] # no valid dataset in history
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# Ensure parsing dynamic options does not consume more than a megabyte worth memory.
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path = dataset.file_name
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@@ -31,6 +31,7 @@ class InteractiveEnviornmentRequest(object):
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self.attr.galaxy_root_dir = os.path.abspath(self.attr.galaxy_config.root)
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self.attr.root = web.url_for("/")
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self.attr.app_root = self.attr.root + "plugins/interactive_environments/" + self.attr.viz_id + "/static/"
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self.attr.import_volume = True
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plugin_path = os.path.abspath( plugin.path )
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@@ -60,8 +61,12 @@ class InteractiveEnviornmentRequest(object):
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# This duplicates the logic in the proxy manager
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if self.attr.galaxy_config.dynamic_proxy_external_proxy:
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self.attr.proxy_prefix = '%s/%s' % (
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slash = '/'
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if self.attr.galaxy_config.cookie_path.endswith('/'):
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slash = ''
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self.attr.proxy_prefix = '%s%s%s' % (
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self.attr.galaxy_config.cookie_path,
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slash,
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self.attr.galaxy_config.dynamic_proxy_prefix)
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else:
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self.attr.proxy_prefix = ''
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@@ -184,18 +189,19 @@ class InteractiveEnviornmentRequest(object):
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conf.update(env_override)
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env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
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volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
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import_volume_str = '-v "{temp_dir}:/import/"'.format(temp_dir=temp_dir) if self.attr.import_volume else ''
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# This is the basic docker command such as "sudo -u docker docker {docker_args}"
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# or just "docker {docker_args}"
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command = self.attr.viz_config.get("docker", "command")
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# Then we format in the entire docker command in place of
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# {docker_args}, so as to let the admin not worry about which args are
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# getting passed
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command = command.format(docker_args='run {command_inject} {environment} -d -P -v "{temp_dir}:/import/" {volume_str} {image}')
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command = command.format(docker_args='run {command_inject} {environment} -d -P {import_volume_str} {volume_str} {image}')
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# Once that's available, we format again with all of our arguments
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command = command.format(
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command_inject=self.attr.viz_config.get("docker", "command_inject"),
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environment=env_str,
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temp_dir=temp_dir,
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import_volume_str=import_volume_str,
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volume_str=volume_str,
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image=self.attr.viz_config.get("docker", "image")
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)
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@@ -27,6 +27,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
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def __init__( self, app ):
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super( JobController, self ).__init__( app )
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self.hda_manager = managers.hdas.HDAManager( app )
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self.dataset_manager = managers.datasets.DatasetManager( app )
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@expose_api
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def index( self, trans, **kwd ):
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@@ -228,19 +229,15 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
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decoded_job_id = self.decode_id( id )
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except Exception:
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raise exceptions.MalformedId()
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query = trans.sa_session.query( trans.app.model.Job )
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if trans.user_is_admin():
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query = query.filter(
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trans.app.model.Job.id == decoded_job_id
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)
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else:
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query = query.filter(
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trans.app.model.Job.user == trans.user,
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trans.app.model.Job.id == decoded_job_id
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)
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job = query.first()
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job = trans.sa_session.query( trans.app.model.Job ).filter( trans.app.model.Job.id == decoded_job_id ).first()
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if job is None:
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raise exceptions.ObjectNotFound()
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if not trans.user_is_admin() and job.user != trans.user:
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if not job.output_datasets:
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raise exceptions.ItemAccessibilityException( "Job has no output datasets." )
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for data_assoc in job.output_datasets:
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if not self.dataset_manager.is_accessible( data_assoc.dataset.dataset, trans.user ):
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raise exceptions.ItemAccessibilityException( "You are not allowed to rerun this job." )
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return job
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@expose_api
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@@ -1 +1 @@
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|
||||
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|
||||
@@ -1,2 +1,2 @@
|
||||
define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","mvc/base-mvc","bootstrapped-data"],function(a,b,c,d,e,f){function g(a){var b=this;return b._init(a||{})}c(g,"GalaxyApp");var h="galaxy:debug",i=h+":namespaces",j=!1;try{j="true"==localStorage.getItem(h)}catch(k){console.log(d("localStorage not available for debug flag retrieval"))}return g.prototype._init=function(a){var b=this;return _.extend(b,Backbone.Events),j&&(b.logger=console),b._processOptions(a),b.debug("GalaxyApp.options: ",b.options),b._initConfig(a.config||f.config||{}),b.debug("GalaxyApp.config: ",b.config),b._patchGalaxy(window.Galaxy),b._initLogger(b.options.loggerOptions||{}),b.debug("GalaxyApp.logger: ",b.logger),b._initLocale(),b.debug("GalaxyApp.localize: ",b.localize),b._initUser(a.user||f.user||{}),b.debug("GalaxyApp.user: ",b.user),b.trigger("ready",b),b._setUpListeners(),b},g.prototype.defaultOptions={patchExisting:!0,root:"/",loggerOptions:{}},g.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.debug("_processOptions: ",a),b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},g.prototype._initConfig=function(a){var b=this;return b.debug("_initConfig: ",a),b.config=a,b.config.debug=j||b.config.debug,b},g.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a){b.debug("found existing Galaxy object:",a);for(var c in a)a.hasOwnProperty(c)&&(b.debug(" patching in "+c+" to Galaxy"),b[c]=a[c])}},g.prototype._initLogger=function(a){var c=this;if(c.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||b.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(i).split(",")}catch(d){}}return c.debug("_initLogger:",a),c.logger=new b.MetricsLogger(a),c.emit={},["log","debug","info","warn","error","metric"].map(function(a){c.emit[a]=function(){c.logger.emit(a,arguments[0],Array.prototype.slice.call(arguments,1))}}),c.config.debug&&(e.LoggableMixin.logger=c.logger),c},g.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=d,window._l=b.localize,b},g.prototype._initUser=function(b){var c=this;return c.debug("_initUser:",b),c.user=new a.User(b),c.user.logger=c.logger,c.currUser=c.user,c},g.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},g.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(h);if(a)return localStorage.setItem(h,!0),!0;localStorage.removeItem(h),b.debuggingNamespaces(null)}catch(c){console.log(d("localStorage not available for debug flag retrieval"))}return!1},g.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(i);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(i):localStorage.setItem(i,a);var e=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=e),e}catch(f){console.log(d("localStorage not available for debug namespace retrieval"))}},g.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:g}});
|
||||
define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","mvc/base-mvc","bootstrapped-data"],function(a,b,c,d,e,f){function g(a){var b=this;return b._init(a||{})}c(g,"GalaxyApp");var h="galaxy:debug",i=h+":namespaces",j=!1;try{j="true"==localStorage.getItem(h)}catch(k){console.log(d("localStorage not available for debug flag retrieval"))}return g.prototype._init=function(a){var b=this;return _.extend(b,Backbone.Events),j&&(b.logger=console),b._processOptions(a),b.debug("GalaxyApp.options: ",b.options),b._initConfig(a.config||f.config||{}),b.debug("GalaxyApp.config: ",b.config),b._patchGalaxy(window.Galaxy),b._initLogger(b.options.loggerOptions||{}),b.debug("GalaxyApp.logger: ",b.logger),b._initLocale(),b.debug("GalaxyApp.localize: ",b.localize),b._initUser(a.user||f.user||{}),b.debug("GalaxyApp.user: ",b.user),b.root=a.root,b.debug("GalaxyApp.root: ",b.root),b.trigger("ready",b),b._setUpListeners(),b},g.prototype.defaultOptions={patchExisting:!0,root:"/",loggerOptions:{}},g.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.debug("_processOptions: ",a),b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},g.prototype._initConfig=function(a){var b=this;return b.debug("_initConfig: ",a),b.config=a,b.config.debug=j||b.config.debug,b},g.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a){b.debug("found existing Galaxy object:",a);for(var c in a)a.hasOwnProperty(c)&&(b.debug(" patching in "+c+" to Galaxy"),b[c]=a[c])}},g.prototype._initLogger=function(a){var c=this;if(c.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||b.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(i).split(",")}catch(d){}}return c.debug("_initLogger:",a),c.logger=new b.MetricsLogger(a),c.emit={},["log","debug","info","warn","error","metric"].map(function(a){c.emit[a]=function(){c.logger.emit(a,arguments[0],Array.prototype.slice.call(arguments,1))}}),c.config.debug&&(e.LoggableMixin.logger=c.logger),c},g.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=d,window._l=b.localize,b},g.prototype._initUser=function(b){var c=this;return c.debug("_initUser:",b),c.user=new a.User(b),c.user.logger=c.logger,c.currUser=c.user,c},g.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},g.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(h);if(a)return localStorage.setItem(h,!0),!0;localStorage.removeItem(h),b.debuggingNamespaces(null)}catch(c){console.log(d("localStorage not available for debug flag retrieval"))}return!1},g.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(i);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(i):localStorage.setItem(i,a);var e=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=e),e}catch(f){console.log(d("localStorage not available for debug namespace retrieval"))}},g.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:g}});
|
||||
//# sourceMappingURL=../maps/galaxy-app-base.js.map
|
||||
+7
-3
@@ -457,12 +457,16 @@ def wait_on_state( state_func, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
|
||||
return wait_on( get_state, desc="state", timeout=timeout)
|
||||
|
||||
|
||||
def wait_on( function, desc, timeout=5 ):
|
||||
def wait_on( function, desc, timeout=DEFAULT_TIMEOUT ):
|
||||
delta = .25
|
||||
iteration = 0
|
||||
while True:
|
||||
if (delta * iteration) > timeout:
|
||||
assert False, "Timed out waiting on %s." % desc
|
||||
total_wait = delta * iteration
|
||||
if total_wait > timeout:
|
||||
timeout_message = "Timed out after %s seconds waiting on %s." % (
|
||||
total_wait, desc
|
||||
)
|
||||
assert False, timeout_message
|
||||
iteration += 1
|
||||
value = function()
|
||||
if value is not None:
|
||||
|
||||
@@ -110,9 +110,10 @@ class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):
|
||||
show_jobs_response = self._get( "jobs/%s" % job_id, admin=False )
|
||||
self._assert_not_has_keys( show_jobs_response.json(), "command_line", "external_id" )
|
||||
|
||||
with self._different_user():
|
||||
show_jobs_response = self._get( "jobs/%s" % job_id, admin=False )
|
||||
self._assert_status_code_is( show_jobs_response, 404 )
|
||||
# TODO: Re-activate test case when API accepts privacy settings
|
||||
# with self._different_user():
|
||||
# show_jobs_response = self._get( "jobs/%s" % job_id, admin=False )
|
||||
# self._assert_status_code_is( show_jobs_response, 200 )
|
||||
|
||||
show_jobs_response = self._get( "jobs/%s" % job_id, admin=True )
|
||||
self._assert_has_keys( show_jobs_response.json(), "command_line", "external_id" )
|
||||
|
||||
@@ -357,7 +357,7 @@ test_data:
|
||||
run_workflow_response = self._post( "workflows", data=workflow_request )
|
||||
self._assert_status_code_is( run_workflow_response, 200 )
|
||||
|
||||
self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=10 )
|
||||
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
||||
return self.__cat_job_id( history_id )
|
||||
|
||||
def _assert_first_step_is_paired_input( self, downloaded_workflow ):
|
||||
|
||||
Reference in New Issue
Block a user