mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_17.01' into dev
Conflicts:
client/galaxy/scripts/mvc/tool/tool-form-composite.js
preserved the dev version
static/maps/mvc/tool/tool-form-composite.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/tool/tool-form-composite.js
This commit is contained in:
Martin Cech
@@ -177,7 +177,7 @@ var History = Backbone.Model
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// if we don't flip this, then a fully-fetched list will not be re-checked via fetch
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this.contents.allFetched = false;
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var fetchFn = self.contents.currentPage !== 0
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? function(){ return self.contents.fetchPage( 0 ); }
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? function(){ return self.contents.fetchPage( self.contents.currentPage ); }
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: function(){ return self.contents.fetchUpdated( lastUpdateTime ); };
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// note: if there was no previous update time, all summary contents will be fetched
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return fetchFn()
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@@ -369,14 +369,17 @@ var HistoryView = _super.extend(
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}),
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_clickPrevPage : function( ev ){
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this.model.clearUpdateTimeout();
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this.model.contents.fetchPrevPage();
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},
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_clickNextPage : function( ev ){
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this.model.clearUpdateTimeout();
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this.model.contents.fetchNextPage();
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},
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_changePageSelect : function( ev ){
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this.model.clearUpdateTimeout();
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var page = $( ev.currentTarget ).val();
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this.model.contents.fetchPage( page );
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},
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@@ -110,17 +110,11 @@ var menu = [
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html : _l( 'Unhide Hidden Datasets' ),
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anon : true,
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func : function() {
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// TODO: Deprecate this functionality and replace with group dataset selector and action combination
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if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really unhide all hidden datasets?' ) ) ){
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var filtered = Galaxy.currHistoryPanel.model.contents.hidden();
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//TODO: batch
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filtered.ajaxQueue( Backbone.Model.prototype.save, { visible : true })
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.done( function(){
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Galaxy.currHistoryPanel.renderItems();
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})
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.fail( function(){
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alert( 'There was an error unhiding the datasets' );
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console.error( arguments );
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});
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$.post(Galaxy.root + "history/adjust_hidden",
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{ 'user_action' : 'unhide' },
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function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
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}
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},
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},
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@@ -128,18 +122,11 @@ var menu = [
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html : _l( 'Delete Hidden Datasets' ),
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anon : true,
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func : function() {
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// TODO: Deprecate this functionality and replace with group dataset selector and action combination
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if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really delete all hidden datasets?' ) ) ){
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var filtered = Galaxy.currHistoryPanel.model.contents.hidden();
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//TODO: batch
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// both delete *and* unhide them
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filtered.ajaxQueue( Backbone.Model.prototype.save, { deleted : true, visible: true })
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.done( function(){
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Galaxy.currHistoryPanel.renderItems();
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})
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.fail( function(){
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alert( 'There was an error deleting the datasets' );
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console.error( arguments );
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});
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$.post(Galaxy.root + "history/adjust_hidden",
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{ 'user_action' : 'delete' },
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function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
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}
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},
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},
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@@ -306,6 +306,10 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
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var is_simple_input = ([ 'data_input', 'data_collection_input' ]).indexOf( step.step_type ) != -1;
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_.each( step.inputs, function( input ) { input.flavor = 'module'; input.hide_label = is_simple_input; } );
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form = new Form( Utils.merge({
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<<<<<<< HEAD
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=======
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title : '<b>' + step.name + '</b>' + step.description,
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>>>>>>> release_17.01
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onchange : function() { _.each( self.links[ step.index ], function( link ) { self._refreshStep( link ) } ) },
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inputs : step.inputs && step.inputs.length > 0 ? step.inputs : [ { type: 'hidden', name: 'No options available.', ignore: null } ]
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}, step ) );
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@@ -450,7 +454,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
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Galaxy.emit.debug( 'tool-form-composite::submit', 'Submission successful.', response );
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self.$el.children().hide();
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self.$el.append( self._templateSuccess( response ) );
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// Show Webhook if job is running
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if ($.isArray( response ) && response.length > 0) {
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self.$el.append( $( '<div/>', { id: 'webhook-view' } ) );
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@@ -29,7 +29,7 @@ if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \
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-a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
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. "$GALAXY_VIRTUAL_ENV/bin/activate"
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fi
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GALAXY_PYTHON=`which python`
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GALAXY_PYTHON=`command -v python`
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"""
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@@ -11,6 +11,7 @@ import tempfile
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import threading
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from cgi import FieldStorage
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from datetime import datetime
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from distutils.version import LooseVersion
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from xml.etree import ElementTree
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from mako.template import Template
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@@ -100,7 +101,7 @@ log = logging.getLogger( __name__ )
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HELP_UNINITIALIZED = threading.Lock()
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MODEL_TOOLS_PATH = os.path.abspath(os.path.dirname(__file__))
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# Tools that require Galaxy's Python environment to be preserved.
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GALAXY_LIB_TOOLS = [
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GALAXY_LIB_TOOLS_UNVERSIONED = [
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"upload1",
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# Legacy tools bundled with Galaxy.
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"vcf_to_maf_customtrack1",
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@@ -136,10 +137,14 @@ GALAXY_LIB_TOOLS = [
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"sam_pileup",
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"find_diag_hits",
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"cufflinks",
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"sam_to_bam", # This was fixed with version 1.1.3 of the tool - TODO add Galaxy to PYTHONPATH only for older versions
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# Tools improperly migrated to the tool shed (iuc)
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"tabular_to_dbnsfp",
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]
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# Tools that needed galaxy on the PATH in the past but no longer do along
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# with the version at which they were fixed.
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GALAXY_LIB_TOOLS_VERSIONED = {
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"sam_to_bam": LooseVersion("1.1.3"),
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}
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class ToolErrorLog:
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@@ -414,6 +419,10 @@ class Tool( object, Dictifiable ):
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self.history_manager = histories.HistoryManager( app )
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self._view = views.DependencyResolversView(app)
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@property
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def version_object(self):
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return LooseVersion(self.version)
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@property
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def sa_session( self ):
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"""Returns a SQLAlchemy session"""
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@@ -486,7 +495,11 @@ class Tool( object, Dictifiable ):
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elif preserve_python_environment == "legacy_and_local" and self.repository_id is None:
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return True
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else:
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return self.old_id in GALAXY_LIB_TOOLS
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unversioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_UNVERSIONED
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versioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_VERSIONED
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legacy_tool = unversioned_legacy_tool or \
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(versioned_legacy_tool and self.version_object < GALAXY_LIB_TOOLS_VERSIONED[self.old_id])
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return legacy_tool
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def __get_job_tool_configuration(self, job_params=None):
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"""Generalized method for getting this tool's job configuration.
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@@ -149,6 +149,7 @@ class DependencyManager( object ):
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if dependencies:
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assert len(dependencies) == len(resolvable_requirements)
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for requirement, dependency in zip(resolvable_requirements, dependencies):
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log.debug(dependency.resolver_msg)
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requirement_to_dependency[requirement] = dependency
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# Shortcut - resolution complete.
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@@ -82,6 +82,41 @@ class CondaContext(installable.InstallableContext):
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ensure_channels = None
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self.ensure_channels = ensure_channels
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self.ensured_channels = False
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self._conda_version = None
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self._miniconda_version = None
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@property
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def conda_version(self):
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if self._conda_version is None:
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self._guess_conda_version()
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return self._conda_version
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def _guess_conda_version(self):
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conda_meta_path = self._conda_meta_path
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# Perhaps we should call "conda info --json" and parse it but for now we are going
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# to assume the default.
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conda_version = LooseVersion(CONDA_VERSION)
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miniconda_version = "3"
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if os.path.exists(conda_meta_path):
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for package in os.listdir(conda_meta_path):
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package_parts = package.split("-")
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if len(package_parts) < 3:
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continue
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package = '-'.join(package_parts[:-2])
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version = package_parts[-2]
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# build = package_parts[-1]
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if package == "conda":
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conda_version = LooseVersion(version)
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if package == "python" and version.startswith("2"):
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miniconda_version = "2"
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self._conda_version = conda_version
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self._miniconda_version = miniconda_version
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@property
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def _conda_meta_path(self):
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return os.path.join(self.conda_prefix, "conda-meta")
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def ensure_channels_configured(self):
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if not self.ensured_channels:
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@@ -495,7 +530,16 @@ def build_isolated_environment(
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export_path
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)
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export_paths.append(export_path)
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create_args = ["--unknown", "--offline"]
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create_args = ["--unknown"]
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# Works in 3.19, 4.0 - 4.2 - not in 4.3.
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# Adjust fix if they fix Conda - xref
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# - https://github.com/galaxyproject/galaxy/issues/3635
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# - https://github.com/conda/conda/issues/2035
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offline_works = conda_context.conda_version < LooseVersion("4.3")
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if offline_works:
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create_args.extend(["--offline"])
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else:
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create_args.extend(["--use-index-cache"])
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if path is None:
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create_args.extend(["--name", tempdir_name])
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else:
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@@ -147,6 +147,7 @@ class RemoteUser( object ):
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"""
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return self.error( start_response, title, message )
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user_accessible_paths = (
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'/users',
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'/user/api_keys',
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'/user/edit_username',
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'/user/dbkeys',
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@@ -78,6 +78,11 @@ def paste_app_factory( global_conf, **kwargs ):
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# Force /history to go to view of current
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webapp.add_route( '/history', controller='history', action='view' )
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webapp.add_route( '/history/view/{id}', controller='history', action='view' )
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# THIS IS A TEMPORARY ROUTE FOR THE 17.01 RELEASE
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# This route supports the previous hide/delete-all-hidden functionality in a history.
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# It will be removed after 17.01.
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webapp.add_route( '/history/adjust_hidden', controller='history', action='adjust_hidden')
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# Force /activate to go to the controller
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webapp.add_route( '/activate', controller='user', action='activate' )
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webapp.add_route( '/login', controller='root', action='login' )
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@@ -826,6 +826,20 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
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email=email,
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send_to_err=send_to_err )
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@web.expose
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def adjust_hidden( self, trans, id=None, **kwd ):
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""" THIS METHOD IS A TEMPORARY ADDITION. It'll allow us to fix the
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regression in history-wide actions, and will be removed in the first
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release after 17.01 """
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action = kwd.get('user_action', None)
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if action == 'delete':
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for hda in trans.history.datasets:
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if not hda.visible:
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hda.mark_deleted()
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elif action == 'unhide':
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trans.history.unhide_datasets()
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trans.sa_session.flush()
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@web.expose
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@web.require_login( "share restricted histories with other users" )
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def share_restricted( self, trans, id=None, email="", **kwd ):
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
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|
||||
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|
||||
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@@ -1,2 +1,2 @@
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map
|
||||
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@@ -0,0 +1,22 @@
|
||||
<tool id="mulled_example_multi_incomplete" name="mulled_example_multi_incomplete" version="0.1.0">
|
||||
<command><![CDATA[
|
||||
bedtools --version > $out_file1 ;
|
||||
echo "Moo" >> $out_file1 ;
|
||||
samtools >> $out_file1 2>&1 ;
|
||||
echo "Cow" >> $out_file1 ;
|
||||
]]></command>
|
||||
<requirements>
|
||||
<requirement type="package" version="1.3.1">samtools</requirement>
|
||||
<requirement type="package" version="2.26.0">bedtools</requirement>
|
||||
<!-- Because the Conda resolver will fail to install all three of these together
|
||||
it will need to build a per-job environment out of just the first two.
|
||||
-->
|
||||
<requirement type="package" version="4.5">notarealpackage</requirement>
|
||||
</requirements>
|
||||
<inputs>
|
||||
<param name="input1" type="data" optional="true" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="out_file1" format="txt" />
|
||||
</outputs>
|
||||
</tool>
|
||||
@@ -130,6 +130,7 @@
|
||||
<!-- Tools for dependency and container testing. -->
|
||||
<tool file="legacy_r.xml" />
|
||||
<tool file="mulled_example_multi_1.xml" />
|
||||
<tool file="mulled_example_multi_incomplete.xml" />
|
||||
<tool file="mulled_example_conflict.xml" />
|
||||
|
||||
<tool file="simple_constructs.yml" />
|
||||
|
||||
Reference in New Issue
Block a user