", "More help and informations can be found on the project [website](https://github.com/bgruening/galaxy-ipython)." diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample new file mode 100644 index 00000000000..ed0b64ff7ce --- /dev/null +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -0,0 +1,19 @@ +[main] +# This cannot be changed +password_auth = True +# Other +apache_urls = False +ssl = False + +[docker] +command = docker +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 + +# URL to access the Galaxy API with from the spawned Docker container, 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= diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.xml b/config/plugins/interactive_environments/rstudio/config/rstudio.xml new file mode 100644 index 00000000000..ad42cd92f01 --- /dev/null +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.xml @@ -0,0 +1,17 @@ + + +
" + password + "
More details ...", + "Please login manually", + {'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false} + ); +} + +function message_failed_connection(){ + toastr.error( + "Could not connect to IPython Notebook. Please contact your administrator. More details ...", + "Security warning", + {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true} + ); +} + + +/** + * Load an interactive environment (IE) from a remote URL + * @param {String} password: password used to authenticate to the remote resource + * @param {String} notebook_login_url: URL that should be POSTed to for login + * @param {String} notebook_access_url: the URL embeded in the page and loaded + * + */ +function load_notebook(notebook_login_url, notebook_access_url, notebook_pubkey_url, username){ + $( document ).ready(function() { + // Test notebook_login_url for accessibility, executing the login+load function whenever + // we've successfully connected to the IE. + test_ie_availability(notebook_pubkey_url, function(){ + var payload = username + "\n" + ie_password; + $.ajax({ + type: 'GET', + url: notebook_pubkey_url, + xhrFields: { + withCredentials: true + }, + success: function(response_text){ + var chunks = response_text.split(':', 2); + var exp = chunks[0]; + var mod = chunks[1]; + console.log("Found " + exp +" and " + mod); + var rsa = new RSAKey(); + rsa.setPublic(mod, exp); + console.log("Encrypting '" + username + "', '" + ie_password + "'"); + var enc_hex = rsa.encrypt(payload); + var encrypted = hex2b64(enc_hex); + console.log("E: " + encrypted); + _handle_notebook_loading(encrypted, notebook_login_url, notebook_access_url); + } + }); + + }); + }); +} + +/** + * Must be implemented by IEs + */ +function _handle_notebook_loading(password, notebook_login_url, notebook_access_url){ + if ( ie_password_auth ) { + $.ajax({ + type: "POST", + // to the Login URL + url: notebook_login_url, + // With our password + data: { + 'v': password, + 'persist': 1, + 'clientPath': '/rstudio/auth-sign-in', + 'appUri': '', + }, + contentType: "application/x-www-form-urlencoded", + xhrFields: { + withCredentials: true + }, + // If that is successful, load the notebook + success: function(){ + append_notebook(notebook_access_url); + }, + error: function(jqxhr, status, error){ + if(ie_password_auth && !ie_apache_urls){ + // Failure now happens because the redirect that RStudio gives us includes the + // port internal to nginx. (E.g. localhost:NNNN/rstudio/NNNN/) + // so disabling the message here makes sense as long as it's working correctly + // + // Additionally: + // XMLHttpRequest cannot load http://localhost:46725/rstudio/46725/. The + // 'Access-Control-Allow-Origin' header has a value 'http://localhost:8081' that + // is not equal to the supplied origin. Origin 'null' is therefore not allowed + // access. + // message_failed_auth(ie_password); + append_notebook(notebook_access_url); + }else{ + message_failed_connection(); + // Do we want to try and load the notebook anyway? Just in case? + append_notebook(notebook_access_url); + } + } + }); + } + else { + // Not using password auth, just embed it to avoid content-origin issues. + message_no_auth(); + append_notebook(notebook_access_url); + } +} diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako new file mode 100644 index 00000000000..0fc4d2a4ba2 --- /dev/null +++ b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako @@ -0,0 +1,67 @@ +<%namespace file="ie.mako" name="ie"/> +<% +import os +import shutil +import time + +# Sets ID and sets up a lot of other variables +ie_request.load_deploy_config() +ie_request.attr.docker_port = 80 +# Create tempdir in galaxy +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/${PORT}/auth-do-sign-in') + +# Did the user give us an RData file? +if hda.datatype.__class__.__name__ == "RData": + shutil.copy( hda.file_name, os.path.join(temp_dir, '.RData') ) + +ie_request.launch(env_override={ + 'notebook_username': USERNAME, + 'notebook_password': PASSWORD, + 'cors_origin': ie_request.attr.proxy_url, +}) +%> + + +${ ie.load_default_js() } + + + +
+
+
+
diff --git a/config/plugins/visualizations/README.txt b/config/plugins/visualizations/README.txt
index 5722c2dc573..07ca615cd1e 100644
--- a/config/plugins/visualizations/README.txt
+++ b/config/plugins/visualizations/README.txt
@@ -8,9 +8,6 @@ Properly configured and written visualizations will be accessible to
the user when they click the 'visualizations' icon for a dataset
in their history panel.
-The framework must be enabled in your 'galaxy.ini' file by uncommenting (and
-having a valid path for) the 'visualizations_plugin_directory' entry.
-
For more information, see http://wiki.galaxyproject.org/VisualizationsRegistry
diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml
index 275e6aa16ef..be1758c870a 100644
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -85,9 +85,9 @@
#if $site_id.startswith( 'local_' )
- ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( $bam_file.name )}
+ ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#elif $site_id.startswith( 'web_link_' ):
- ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( $bam_file.name )}
+ ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#else:
${jnlp.url}
#end if
@@ -101,7 +101,7 @@
" + "
".join(['%s : %s' % (k, v) for k, v in pja.action_arguments.iteritems()]) + return "Set the following metadata values:
" + "
".join(['%s : %s' % (escape(k), escape(v)) for k, v in pja.action_arguments.iteritems()]) class SetMetadataAction(DefaultJobAction): @@ -455,7 +460,8 @@ class TagDatasetAction(DefaultJobAction): @classmethod def get_short_str(cls, pja): if pja.action_arguments and pja.action_arguments.get('tags', ''): - return "Add tag(s) '%s' to '%s'." % (pja.action_arguments['tags'], pja.output_name) + return "Add tag(s) '%s' to '%s'." % (escape(pja.action_arguments['tags']), + escape(pja.output_name)) else: return "Tag addition action used without a tag specified. No tag will be added." diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py index b129ff5d61e..eda9df90e71 100644 --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -73,7 +73,9 @@ class DatasetCollectionManager( object ): for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]: dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) for output_dataset in implicit_collection_info.get( "outputs" ): - if isinstance( output_dataset, model.HistoryDatasetCollectionAssociation ): + if isinstance( output_dataset, model.HistoryDatasetAssociation ): + output_dataset.hidden_beneath_collection_instance = dataset_collection_instance + elif isinstance( output_dataset, model.HistoryDatasetCollectionAssociation ): dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) else: # dataset collection, don't need to do anything... diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py index 39471fae855..8190c2a8a09 100644 --- a/lib/galaxy/managers/context.py +++ b/lib/galaxy/managers/context.py @@ -139,7 +139,11 @@ class ProvidesUserContext( object ): @property def user_ftp_dir( self ): identifier = self.app.config.ftp_upload_dir_identifier - return os.path.join( self.app.config.ftp_upload_dir, getattr( self.user, identifier ) ) + base_dir = self.app.config.ftp_upload_dir + if base_dir is None: + return None + else: + return os.path.join( base_dir, getattr( self.user, identifier ) ) class ProvidesHistoryContext( object ): diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index b167e07a0e6..14e53aa230d 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -282,21 +282,21 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer state = states.ERROR # TODO: history_state and state_counts are classically calc'd at the same time # so this is rel. ineff. - if we keep this... - hda_state_counts = self.serialize_state_counts( history, 'counts', exclude_deleted=False, **context ) + hda_state_counts = self.serialize_state_counts( history, 'counts', exclude_deleted=True, **context ) num_hdas = sum( hda_state_counts.values() ) if num_hdas == 0: state = states.NEW else: if ( hda_state_counts[ states.RUNNING ] > 0 - or hda_state_counts[ states.SETTING_METADATA ] > 0 - or hda_state_counts[ states.UPLOAD ] > 0 ): + or hda_state_counts[ states.SETTING_METADATA ] > 0 + or hda_state_counts[ states.UPLOAD ] > 0 ): state = states.RUNNING # TODO: this method may be more useful if we *also* polled the histories jobs here too elif hda_state_counts[ states.QUEUED ] > 0: state = states.QUEUED elif ( hda_state_counts[ states.ERROR ] > 0 - or hda_state_counts[ states.FAILED_METADATA ] > 0 ): + or hda_state_counts[ states.FAILED_METADATA ] > 0 ): state = states.ERROR elif hda_state_counts[ states.OK ] == num_hdas: state = states.OK diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index ee70e2b97f3..22ea22c0b92 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -60,16 +60,6 @@ from galaxy.model.item_attrs import Dictifiable from tool_shed.util import shed_util_common as suc from .loader import template_macro_params, raw_tool_xml_tree, imported_macro_paths from .execute import execute as execute_job -from .wrappers import ( - ToolParameterValueWrapper, - RawObjectWrapper, - LibraryDatasetValueWrapper, - InputValueWrapper, - SelectToolParameterWrapper, - DatasetFilenameWrapper, - DatasetListWrapper, - DatasetCollectionWrapper, -) import galaxy.jobs @@ -1890,10 +1880,12 @@ class Tool( object, Dictifiable ): """ args = dict() for key, param in self.inputs.iteritems(): - if isinstance( param, HiddenToolParameter ): + # BaseURLToolParameter is now a subclass of HiddenToolParameter, so + # we must check if param is a BaseURLToolParameter first + if isinstance( param, BaseURLToolParameter ): + args[key] = param.get_initial_value( trans, None ) + elif isinstance( param, HiddenToolParameter ): args[key] = model.User.expand_user_properties( trans.user, param.value ) - elif isinstance( param, BaseURLToolParameter ): - args[key] = param.get_value( trans ) else: raise Exception( "Unexpected parameter type" ) return args @@ -2332,6 +2324,12 @@ class Tool( object, Dictifiable ): 'id' : trans.security.encode_id(v.id), 'src' : 'hdca' } + elif isinstance(v, trans.app.model.LibraryDatasetDatasetAssociation): + return { + 'id' : trans.security.encode_id(v.id), + 'name': v.name, + 'src' : 'ldda' + } elif isinstance(v, bool): if v is True: return 'true' @@ -2550,7 +2548,8 @@ class Tool( object, Dictifiable ): tool_versions = [] tools = self.app.toolbox.get_loaded_tools_by_lineage(self.id) for t in tools: - tool_versions.append(t.version) + if not t.version in tool_versions: + tool_versions.append(t.version) # add information with underlying requirements and their versions tool_requirements = [] diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py index c90b188027c..fe965b6b575 100644 --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -185,6 +185,7 @@ class ToolDataTable( object ): self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) self.empty_field_values = {} + self.allow_duplicate_entries = util.asbool( config_element.get( 'allow_duplicate_entries', True ) ) self.here = filename and os.path.dirname(filename) self.filenames = odict() self.tool_data_path = tool_data_path @@ -354,6 +355,11 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ): self.filenames[ filename ] = info #save info about table self._merged_load_info.append( ( other_table.__class__, other_table._load_info ) ) + # If we are merging in a data table that does not allow duplicates, enforce that upon the data table + if self.allow_duplicate_entries and not other_table.allow_duplicate_entries: + log.debug( 'While attempting to merge tool data table "%s", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries.', self.name ) + self.allow_duplicate_entries = False + self._deduplicate_data() #add data entries and return current data table version return self.add_entries( other_table.data, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) @@ -426,6 +432,8 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ): def extend_data_with( self, filename, errors=None ): here = os.path.dirname(os.path.abspath(filename)) self.data.extend( self.parse_file_fields( open( filename ), errors=errors, here=here ) ) + if not self.allow_duplicate_entries: + self._deduplicate_data() def parse_file_fields( self, reader, errors=None, here="__HERE__" ): """ @@ -536,7 +544,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ): is_error = False if self.largest_index < len( fields ): fields = self._replace_field_separators( fields ) - if fields not in self.get_fields() or allow_duplicates: + if fields not in self.get_fields() or ( allow_duplicates and self.allow_duplicate_entries ): self.data.append( fields ) else: log.debug( "Attempted to add fields (%s) to data table '%s', but this entry already exists and allow_duplicates is False.", fields, self.name ) @@ -624,6 +632,20 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ): replace = " " return map( lambda x: x.replace( separator, replace ), fields ) + def _deduplicate_data( self ): + # Remove duplicate entries, without recreating self.data object + dup_lines = [] + hash_list = [] + for i, fields in enumerate( self.data ): + fields_hash = hash( self.separator.join( fields ) ) + if fields_hash in hash_list: + dup_lines.append( i ) + log.debug( 'Found duplicate entry in tool data table "%s", but duplicates are not allowed, removing additional entry for: "%s"', self.name, fields ) + else: + hash_list.append( fields_hash ) + for i in reversed( dup_lines ): + self.data.pop( i ) + @property def xml_string( self ): return util.xml_to_string( self.config_element ) diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py index 05760d60a76..4903838097d 100644 --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -11,7 +11,6 @@ from galaxy.tools.wrappers import ( DatasetFilenameWrapper, DatasetListWrapper, DatasetCollectionWrapper, - LibraryDatasetValueWrapper, SelectToolParameterWrapper, InputValueWrapper, RawObjectWrapper @@ -19,7 +18,6 @@ from galaxy.tools.wrappers import ( from galaxy.tools.parameters.basic import ( DataToolParameter, DataCollectionToolParameter, - LibraryDatasetToolParameter, SelectToolParameter, ) from galaxy.tools.parameters.grouping import Conditional, Repeat, Section @@ -228,10 +226,6 @@ class ToolEvaluator( object ): elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app, other_values=param_dict, path_rewriter=self.unstructured_path_rewriter ) - elif isinstance( input, LibraryDatasetToolParameter ): - # TODO: Handle input rewrites in here? How to test LibraryDatasetToolParameters? - input_values[ input.name ] = LibraryDatasetValueWrapper( - input, input_values[ input.name ], param_dict ) else: input_values[ input.name ] = InputValueWrapper( input, input_values[ input.name ], param_dict ) diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index 8b6d5ce8e41..9b5f79b326e 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -113,12 +113,13 @@ class ToolExecutionTracker( object ): outputs=outputs ) try: - output_collection_name = self.tool_action.get_output_name( + output_collection_name = self.tool.tool_action.get_output_name( output, dataset=None, tool=self.tool, on_text=on_text, trans=trans, + history=history, params=params, incoming=None, job_params=None, diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 03cbcc31dcb..42ee20d23c7 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -587,6 +587,14 @@ class FTPFileToolParameter( ToolParameter ): """ input_source = ensure_input_source(input_source) ToolParameter.__init__( self, tool, input_source ) + self.multiple = input_source.get_bool( 'multiple', True ) + self.user_ftp_dir = '' + + def get_initial_value( self, trans, context, history=None ): + if not trans is None: + if not trans.user is None: + self.user_ftp_dir = "%s/" % trans.user_ftp_dir + return None @property def visible( self ): @@ -601,28 +609,45 @@ class FTPFileToolParameter( ToolParameter ): user_ftp_dir = trans.user_ftp_dir return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value=value ) + def to_param_dict_string( self, value, other_values={} ): + if value is '': + return 'None' + lst = [ '%s%s' % (self.user_ftp_dir, dataset) for dataset in value ] + if self.multiple: + return lst + else: + return lst[ 0 ] + def from_html( self, value, trans=None, other_values={} ): - try: - assert type( value ) is list - except: - value = [ value ] - return value + return self.to_python( value, trans.app, validate=True ) def to_string( self, value, app ): - if value in [ None, '' ]: - return None - elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): - return value + return self.to_python( value, app ) - def to_python( self, value, app ): - if value is None: - return None - elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): - return value - - def get_initial_value( self, trans, context, history=None ): - return None + def to_python( self, value, app, validate=False ): + if validate and self.tool.app.config.ftp_upload_dir is None: + raise ValueError( "The FTP directory is not configured." ) + if not isinstance( value, list ): + value = [ value ] + lst = [] + for val in value: + if val is None: + lst = [] + break + if isinstance( val, dict ): + lst.append( val[ 'name' ] ) + else: + lst.append( val ) + if len( lst ) == 0: + if not self.optional and validate: + raise ValueError( "Please select a valid FTP file." ) + return '' + return lst + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + d = super( FTPFileToolParameter, self ).to_dict( trans ) + d['multiple'] = self.multiple + return d class HiddenToolParameter( ToolParameter ): """ @@ -652,6 +677,7 @@ class HiddenToolParameter( ToolParameter ): def get_label( self ): return None + class ColorToolParameter( ToolParameter ): """ Parameter that stores a color. @@ -682,9 +708,23 @@ class BaseURLToolParameter( HiddenToolParameter ): super( BaseURLToolParameter, self ).__init__( tool, input_source ) self.value = input_source.get( 'value', '' ) + def get_initial_value( self, trans, context, history=None ): + return self._get_value() + + def get_html_field( self, trans=None, value=None, other_values={} ): + return form_builder.HiddenField( self.name, self._get_value() ) + def from_html( self, value=None, trans=None, context={} ): + return self._get_value() + + def _get_value( self ): return url_for( self.value, qualified=True ) + def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): + d = super( BaseURLToolParameter, self ).to_dict( trans ) + d[ 'value' ] = self._get_value() + return d + DEFAULT_VALUE_MAP = lambda x: x @@ -1638,7 +1678,7 @@ class BaseDataToolParameter( ToolParameter ): class_name = self.__class__.__name__ assert trans is not None, "%s requires a trans" % class_name if history is None: - history = trans.get_history( create=True ) + history = trans.get_history() assert history is not None, "%s requires a history" % class_name return history @@ -2360,8 +2400,10 @@ class LibraryDatasetToolParameter( ToolParameter ): Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """ - def __init__( self, tool, elem ): - ToolParameter.__init__( self, tool, elem ) + def __init__( self, tool, input_source, context=None ): + input_source = ensure_input_source( input_source ) + ToolParameter.__init__( self, tool, input_source ) + self.multiple = input_source.get_bool( 'multiple', True ) def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.LibraryField( self.name, value=value, trans=trans ) @@ -2370,28 +2412,82 @@ class LibraryDatasetToolParameter( ToolParameter ): return None def from_html( self, value, trans, other_values={} ): - if not value: - return None - elif isinstance( value, list ): - return value + return self.to_python( value, trans.app, other_values=other_values, validate=True ) + + def to_param_dict_string( self, value, other_values={} ): + if value is None: + return 'None' + elif self.multiple: + return [ dataset.get_file_name() for dataset in value ] else: - decoded_lst = [] - for encoded_id in value.split("||"): - decoded_lst.append( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( encoded_id ) ) ) - return decoded_lst + return value[ 0 ].get_file_name() + # converts values to json representation: + # { id: LibraryDatasetDatasetAssociation.id, name: LibraryDatasetDatasetAssociation.name, src: 'lda' } def to_string( self, value, app ): - if not value: - return value - return [ldda.id for ldda in value] + if not isinstance( value, list ): + value = [value] + lst = [] + for item in value: + encoded_id = encoded_name = None + if isinstance (item, app.model.LibraryDatasetDatasetAssociation): + encoded_id = app.security.encode_id( item.id ) + encoded_name = item.name + elif isinstance (item, dict): + encoded_id = item.get('id') + encoded_name = item.get('name') + else: + lst = [] + break + if encoded_id is not None: + lst.append( { + 'id' : encoded_id, + 'name' : encoded_name, + 'src' : 'ldda' + } ) + if len( lst ) == 0: + return None + else: + return lst - def to_python( self, value, app ): - if not value: - return value - lddas = [] - for ldda_id in value: - lddas.append( app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) ) - return lddas + # converts values into python representation: + # LibraryDatasetDatasetAssociation + # valid input values (incl. arrays of mixed sets) are: + # 1. LibraryDatasetDatasetAssociation + # 2. LibraryDatasetDatasetAssociation.id + # 3. { id: LibraryDatasetDatasetAssociation.id, ... } + def to_python( self, value, app, other_values={}, validate=False ): + if not isinstance( value, list ): + value = [value] + lst = [] + for item in value: + if isinstance (item, app.model.LibraryDatasetDatasetAssociation): + lst.append(item) + else: + encoded_id = None + if isinstance (item, dict): + encoded_id = item.get('id') + elif isinstance (item, basestring): + encoded_id = item + else: + lst = [] + break + lda = app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( app.security.decode_id( encoded_id ) ) + if lda is not None: + lst.append( lda ) + elif validate: + raise ValueError( "One of the selected library datasets is invalid or not available anymore." ) + if len( lst ) == 0: + if not self.optional and validate: + raise ValueError( "Please select a valid library dataset." ) + return None + else: + return lst + + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + d = super( LibraryDatasetToolParameter, self ).to_dict( trans ) + d['multiple'] = self.multiple + return d # class RawToolParameter( ToolParameter ): # """ diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index 5ec40230e23..b6f1b1b6974 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -116,7 +116,7 @@ class DataMetaFilter( Filter ): return file_value == dataset_value assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name ref = other_values.get( self.ref_name, None ) - if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( ref, galaxy.tools.DatasetFilenameWrapper ) ): + if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper ) ): return [] #not a valid dataset meta_value = ref.metadata.get( self.key, None ) if meta_value is None: #assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key @@ -358,7 +358,7 @@ class RemoveValueFilter( Filter ): value = other_values.get( self.ref_name ) else: data_ref = other_values.get( self.meta_ref ) - if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data_ref, galaxy.tools.DatasetFilenameWrapper ) ): + if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper ) ): return options #cannot modify options value = data_ref.metadata.get( self.metadata_key, None ) return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py index ea610b06976..5765e40cb7b 100644 --- a/lib/galaxy/tools/parameters/wrapped.py +++ b/lib/galaxy/tools/parameters/wrapped.py @@ -3,7 +3,14 @@ import galaxy.tools from galaxy.tools.parameters.basic import ( DataToolParameter, DataCollectionToolParameter, - SelectToolParameter, + SelectToolParameter +) +from galaxy.tools.wrappers import ( + InputValueWrapper, + SelectToolParameterWrapper, + DatasetFilenameWrapper, + DatasetListWrapper, + DatasetCollectionWrapper ) from galaxy.tools.parameters.grouping import ( Repeat, @@ -38,6 +45,7 @@ class WrappedParameters( object ): for input in inputs.itervalues(): if input.name not in input_values and skip_missing_values: continue + value = input_values[ input.name ] if isinstance( input, Repeat ): for d in input_values[ input.name ]: self.wrap_values( input.inputs, d, skip_missing_values=skip_missing_values ) @@ -50,27 +58,27 @@ class WrappedParameters( object ): self.wrap_values( input.inputs, values, skip_missing_values=skip_missing_values ) elif isinstance( input, DataToolParameter ) and input.multiple: input_values[ input.name ] = \ - galaxy.tools.DatasetListWrapper( input_values[ input.name ], + DatasetListWrapper( input_values[ input.name ], datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ - galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], + DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name ) elif isinstance( input, SelectToolParameter ): - input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values=incoming ) + input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values=incoming ) elif isinstance( input, DataCollectionToolParameter ): - input_values[ input.name ] = galaxy.tools.DatasetCollectionWrapper( + input_values[ input.name ] = DatasetCollectionWrapper( input_values[ input.name ], datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name, ) else: - input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) + input_values[ input.name ] = InputValueWrapper( input, value, incoming ) def make_dict_copy( from_dict ): diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py index 180b76db90b..66be0ff435f 100644 --- a/lib/galaxy/tools/parser/xml.py +++ b/lib/galaxy/tools/parser/xml.py @@ -158,6 +158,7 @@ class XmlToolSource(ToolSource): for collection_elem in out_elem.findall("collection"): name = collection_elem.get( "name" ) + label = xml_text( collection_elem, "label" ) default_format = collection_elem.get( "format", "data" ) collection_type = collection_elem.get( "type", None ) structured_like = collection_elem.get( "structured_like", None ) @@ -180,6 +181,7 @@ class XmlToolSource(ToolSource): output_collection = galaxy.tools.ToolOutputCollection( name, structure, + label=label, default_format=default_format, inherit_format=inherit_format, inherit_metadata=inherit_metadata, diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py index 9282f446935..8cc29a6cfa7 100644 --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -57,32 +57,6 @@ class RawObjectWrapper( ToolParameterValueWrapper ): return getattr( self.obj, key ) -class LibraryDatasetValueWrapper( ToolParameterValueWrapper ): - """ - Wraps an input so that __str__ gives the "param_dict" representation. - """ - def __init__( self, input, value, other_values={} ): - self.input = input - self.value = value - self._other_values = other_values - self.counter = 0 - - def __str__( self ): - return self.value - - def __iter__( self ): - return self - - def next( self ): - if self.counter >= len(self.value): - raise StopIteration - self.counter += 1 - return self.value[ self.counter - 1 ] - - def __getattr__( self, key ): - return getattr( self.value, key ) - - class InputValueWrapper( ToolParameterValueWrapper ): """ Wraps an input so that __str__ gives the "param_dict" representation. @@ -93,7 +67,18 @@ class InputValueWrapper( ToolParameterValueWrapper ): self._other_values = other_values def __str__( self ): - return self.input.to_param_dict_string( self.value, self._other_values ) + to_param_dict_string = self.input.to_param_dict_string( self.value, self._other_values ) + if isinstance( to_param_dict_string, list ): + return ','.join( to_param_dict_string ) + else: + return to_param_dict_string + + def __iter__( self ): + to_param_dict_string = self.input.to_param_dict_string( self.value, self._other_values ) + if not isinstance( to_param_dict_string, list ): + return iter( [ to_param_dict_string ] ) + else: + return iter( to_param_dict_string ) def __getattr__( self, key ): return getattr( self.value, key ) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index f14fc7174d2..5e12e166565 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -1,14 +1,12 @@ import ConfigParser -import hashlib import os import random +import tempfile +import subprocess from galaxy.util.bunch import Bunch from galaxy import web -from galaxy import eggs -eggs.require("PyYAML") -import yaml from galaxy.managers import api_keys import logging @@ -42,6 +40,13 @@ class InteractiveEnviornmentRequest(object): self.attr.HOST = trans.request.host.rsplit(':', 1)[0] 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() ) + 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 @@ -68,9 +73,9 @@ class InteractiveEnviornmentRequest(object): self.attr.APACHE_URLS = _boolean_option("apache_urls") self.attr.SSL_URLS = _boolean_option("ssl") - def write_conf_file(self, output_directory, extra={}): + def get_conf_dict(self): """ - Build up a configuration file that is standard for ALL IEs. + Build up a configuration dictionary that is standard for ALL IEs. TODO: replace hashed password with plaintext. """ @@ -92,27 +97,11 @@ class InteractiveEnviornmentRequest(object): else: conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/' web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port - conf_file['galaxy_paster_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port() + conf_file['galaxy_web_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port() + # Galaxy paster port is deprecated + conf_file['galaxy_paster_port'] = conf_file['galaxy_web_port'] - if self.attr.PASSWORD_AUTH: - # Generate a random password + salt - notebook_pw_salt = self.generate_password(length=12) - notebook_pw = self.generate_password(length=24) - m = hashlib.sha1() - m.update( notebook_pw + notebook_pw_salt ) - conf_file['notebook_password'] = 'sha1:%s:%s' % (notebook_pw_salt, m.hexdigest()) - # Should we use password based connection or "default" connection style in galaxy - else: - notebook_pw = "None" - - # Some will need to pass extra data - for extra_key in extra: - conf_file[extra_key] = extra[extra_key] - - self.attr.notebook_pw = notebook_pw - # Write conf - with open( os.path.join( output_directory, 'conf.yaml' ), 'wb' ) as handle: - handle.write( yaml.dump(conf_file, default_flow_style=False) ) + return conf_file def generate_hex(self, length): return ''.join(random.choice('0123456789abcdef') for _ in range(length)) @@ -165,12 +154,26 @@ class InteractiveEnviornmentRequest(object): .replace('${PORT}', str(self.attr.PORT)) return url - def docker_cmd(self, temp_dir): + def docker_cmd(self, env_override={}): """ Generate and return the docker command to execute """ - return '%s run -d %s -p %s:%s -v "%s:/import/" %s' % \ + temp_dir = self.temp_dir + conf = self.get_conf_dict() + conf.update(env_override) + env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()]) + return '%s run %s -d %s -p %s:%s -v "%s:/import/" %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, self.attr.viz_config.get("docker", "image")) + + def launch(self, raw_cmd=None, env_override={}): + if raw_cmd is None: + raw_cmd = self.docker_cmd(env_override=env_override) + log.info("Starting docker container for IE {0} with command [{1}]".format( + self.attr.viz_id, + raw_cmd + )) + subprocess.call(raw_cmd, shell=True) diff --git a/lib/galaxy/web/proxy/js/lib/proxy.js b/lib/galaxy/web/proxy/js/lib/proxy.js index 242c063713e..ad4276d90e3 100644 --- a/lib/galaxy/web/proxy/js/lib/proxy.js +++ b/lib/galaxy/web/proxy/js/lib/proxy.js @@ -36,6 +36,23 @@ var DynamicProxy = function(options) { }; DynamicProxy.prototype.rewriteRequest = function(request) { + if(request.url.indexOf('rstudio') != -1){ + var remap = { + 'content-type': 'Content-Type', + 'content-length': 'Content-Length', + } + // RStudio isn't spec compliant and pitches a fit on NodeJS's http module's lowercase HTTP headers + for(var i = 0; i
'+a.name+"
"}});return{View:d}});
+//# sourceMappingURL=../../../maps/mvc/ui/ui-list.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-misc.js b/static/scripts/mvc/ui/ui-misc.js
index 29dce28f607..9ac3d8ab1a3 100644
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g,h){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(a){return' '+a.title+"
"}}),l=Backbone.View.extend({optionsDefault:{id:a.uid(),title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),b.onclick&&b.onclick()}),$(this.el).tooltip({title:b.tooltip,placement:"bottom"})},wait:function(){this.$el.removeClass(this.options.cls).addClass("btn btn-info").prop("disabled",!0),this.$(".icon").removeClass(this.options.icon).addClass("fa-spinner fa-spin"),this.$(".title").html("Sending...")},unwait:function(){this.$el.removeClass("btn btn-info").addClass(this.options.cls).prop("disabled",!1),this.$(".icon").removeClass("fa-spinner fa-spin").addClass(this.options.icon),this.$(".title").html(this.options.title)},_template:function(a){var b='"}}),m=Backbone.View.extend({optionsDefault:{id:a.uid(),title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var c=this;$(this.el).on("click",function(){$(".tooltip").hide(),b.onclick&&!c.disabled&&b.onclick()}),$(this.el).tooltip({title:b.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(a){this.$("i").removeClass(this.options.icon).addClass(a),this.options.icon=a},_template:function(a){var b="";a.title&&(b="width: auto;");var c='';return c+=a.title?'":'',c+="
"}}),n=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",b.onclick)},_template:function(a){return'"}}),o=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(""),this.options.message&&this.update(this.options)},update:function(b){if(this.options=a.merge(b,this.optionsDefault),""!=b.message){if(this.$el.html(this._template(this.options)),this.$el.find(".alert").append(b.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!b.persistent){var c=this;this.timeout=window.setTimeout(function(){c.$el.is(":visible")?c.$el.fadeOut():c.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(a){return''}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options));var c=this;this.options.onclick&&this.$el.on("submit",function(){var a=c.$el.find("#search");c.options.onclick(a.val())})},_template:function(a){return''}}),q=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var c=this;this.$el.on("input",function(){c.options.onchange&&c.options.onchange(c.$el.val())})},value:function(a){return void 0!==a&&this.$el.val(a),this.$el.val()},_template:function(a){return a.area?'':''}}),r=Backbone.View.extend({initialize:function(a){this.options=a,this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value)},value:function(a){return void 0!==a&&this.$("hidden").val(a),this.$("hidden").val()},_template:function(a){var b='';return a.info&&(b+="
'}});return{Anchor:n,Button:l,ButtonIcon:m,ButtonCheck:g,ButtonMenu:f,Icon:k,Image:i,Input:q,Label:j,Message:o,Modal:h,RadioButton:d.RadioButton,Checkbox:d.Checkbox,Radio:d.Radio,Searchbox:p,Select:b,Hidden:r,Slider:c,Drilldown:e}});
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g,h){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(a){return'"+a.info+"
"),b+=' '+a.title+"
"}}),l=Backbone.View.extend({optionsDefault:{id:a.uid(),title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),b.onclick&&b.onclick()}),$(this.el).tooltip({title:b.tooltip,placement:"bottom"})},wait:function(){this.$el.removeClass(this.options.cls).addClass("btn btn-info").prop("disabled",!0),this.$(".icon").removeClass(this.options.icon).addClass("fa-spinner fa-spin"),this.$(".title").html("Sending...")},unwait:function(){this.$el.removeClass("btn btn-info").addClass(this.options.cls).prop("disabled",!1),this.$(".icon").removeClass("fa-spinner fa-spin").addClass(this.options.icon),this.$(".title").html(this.options.title)},_template:function(a){var b='"}}),m=Backbone.View.extend({optionsDefault:{id:a.uid(),title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var c=this;$(this.el).on("click",function(){$(".tooltip").hide(),b.onclick&&!c.disabled&&b.onclick()}),this.$button.tooltip({title:b.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(a){this.$("i").removeClass(this.options.icon).addClass(a),this.options.icon=a},_template:function(a){var b="";a.title&&(b="width: auto;");var c='"}}),n=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",b.onclick)},_template:function(a){return'"}}),o=Backbone.View.extend({optionsDefault:{message:null,status:"info",cls:"",persistent:!1},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(''),this.options.message&&this.update(this.options)},update:function(b){if(this.options=a.merge(b,this.optionsDefault),""!=b.message){if(this.$el.html(this._template(this.options)),this.$el.find(".alert").append(b.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!b.persistent){var c=this;this.timeout=window.setTimeout(function(){c.$el.is(":visible")?c.$el.fadeOut():c.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(a){return''}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options));var c=this;this.options.onclick&&this.$el.on("submit",function(){var a=c.$el.find("#search");c.options.onclick(a.val())})},_template:function(a){return''}}),q=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var c=this;this.$el.on("input",function(){c.options.onchange&&c.options.onchange(c.$el.val())})},value:function(a){return void 0!==a&&this.$el.val(a),this.$el.val()},_template:function(a){return a.area?'':''}}),r=Backbone.View.extend({initialize:function(a){this.options=a,this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value)},value:function(a){return void 0!==a&&this.$("hidden").val(a),this.$("hidden").val()},_template:function(a){var b='
';return a.info&&(b+="
'}});return{Anchor:n,Button:l,ButtonIcon:m,ButtonCheck:g,ButtonMenu:f,Icon:k,Image:i,Input:q,Label:j,Message:o,Modal:h,RadioButton:d.RadioButton,Checkbox:d.Checkbox,Radio:d.Radio,Searchbox:p,Select:b,Hidden:r,Slider:c,Drilldown:e}});
//# sourceMappingURL=../../../maps/mvc/ui/ui-misc.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-portlet.js b/static/scripts/mvc/ui/ui-portlet.js
index 5e4adafdcee..616881a6c84 100644
--- a/static/scripts/mvc/ui/ui-portlet.js
+++ b/static/scripts/mvc/ui/ui-portlet.js
@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:!1,optionsDefault:{id:a.uid(),title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var c=this.$el.find(".portlet-content");if(this.options.nopadding&&(c.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons"),this.options.buttons){var d=this;$.each(this.options.buttons,function(a,b){b.$el.prop("id",a),d.$buttons.append(b.$el)})}else this.$buttons.remove();if(this.$operations=$(this.el).find(".portlet-operations"),this.options.operations){var d=this;$.each(this.options.operations,function(a,b){b.$el.prop("id",a),d.$operations.append(b.$el)})}this.options.body&&this.append(this.options.body)},append:function(a){this.$content.append(a)},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(a){this.$buttons.find("#"+a).prop("disabled",!1)},disableButton:function(a){this.$buttons.find("#"+a).prop("disabled",!0)},hideOperation:function(a){this.$operations.find("#"+a).hide()},showOperation:function(a){this.$operations.find("#"+a).show()},setOperation:function(a,b){var c=this.$operations.find("#"+a);c.off("click"),c.on("click",b)},title:function(a){var b=this.$title;return a&&b.html(a),b.html()},disable:function(){this.$(".portlet-backdrop").show()},enable:function(){this.$(".portlet-backdrop").hide()},_template:function(a){var b='"+a.info+"
"),b+='';return a.title&&(b+='"),b+='
'}});return{View:b}});
+define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:!1,optionsDefault:{id:a.uid(),title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(b){this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var c=this.$el.find(".portlet-content");if(this.options.nopadding&&(c.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons"),this.options.buttons){var d=this;$.each(this.options.buttons,function(a,b){b.$el.prop("id",a),d.$buttons.append(b.$el)})}else this.$buttons.remove();if(this.$operations=$(this.el).find(".portlet-operations"),this.options.operations){var d=this;$.each(this.options.operations,function(a,b){b.$el.prop("id",a),d.$operations.append(b.$el)})}this.options.body&&this.append(this.options.body)},append:function(a){this.$content.append(a)},empty:function(){this.$content.empty()},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(a){this.$buttons.find("#"+a).prop("disabled",!1)},disableButton:function(a){this.$buttons.find("#"+a).prop("disabled",!0)},hideOperation:function(a){this.$operations.find("#"+a).hide()},showOperation:function(a){this.$operations.find("#"+a).show()},setOperation:function(a,b){var c=this.$operations.find("#"+a);c.off("click"),c.on("click",b)},title:function(a){var b=this.$title;return a&&b.html(a),b.html()},disable:function(){this.$(".portlet-backdrop").show()},enable:function(){this.$(".portlet-backdrop").hide()},_template:function(a){var b='',a.icon&&(b+=' '),b+=''+a.title+"
',"top"==a.placement&&(b+=''),b+='',"bottom"==a.placement&&(b+=''),b+='
';return a.title&&(b+='"),b+='
'}});return{View:b}});
//# sourceMappingURL=../../../maps/mvc/ui/ui-portlet.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-select-ftp.js b/static/scripts/mvc/ui/ui-select-ftp.js
new file mode 100644
index 00000000000..aa09cc7fcc3
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-select-ftp.js
@@ -0,0 +1,2 @@
+define(["utils/utils","mvc/ui/ui-list"],function(a,b){var c=Backbone.View.extend({initialize:function(c){var d=this;this.ftpfile_list=new b.View({name:"file",optional:c.optional,multiple:c.multiple,onchange:function(){c.onchange&&c.onchange(d.value())}}),this.setElement(this.ftpfile_list.$el),a.get({url:galaxy_config.root+"api/remote_files",success:function(a){var b=[];for(var c in a)b.push({value:a[c].path,label:a[c].path});d.ftpfile_list.update(b)}})},value:function(a){return this.ftpfile_list.value(a)}});return{View:c}});
+//# sourceMappingURL=../../../maps/mvc/ui/ui-select-ftp.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-select-library.js b/static/scripts/mvc/ui/ui-select-library.js
index 888e1d6cb54..1248278a370 100644
--- a/static/scripts/mvc/ui/ui-select-library.js
+++ b/static/scripts/mvc/ui/ui-select-library.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.Collection.extend({url:galaxy_config.root+"api/libraries"}),d=Backbone.Collection.extend({initialize:function(){var a=this;this.config=new Backbone.Model({library_id:null}),this.config.on("change",function(){a.fetch({reset:!0})})},url:function(){return galaxy_config.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),e=Backbone.View.extend({initialize:function(a){var e=this;this.libraries=new c,this.datasets=new d,this.options=a,this.library_select=new b.Select.View({optional:a.optional,onchange:function(a){e.datasets.config.set("library_id",a)}}),this.dataset_select=new b.Select.View({optional:a.optional,multiple:a.multiple,onchange:function(){e.trigger("change")}}),this.libraries.on("reset",function(){var a=[];e.libraries.each(function(b){a.push({value:b.id,label:b.get("name")})}),e.library_select.update(a),e.trigger("change")}),this.datasets.on("reset",function(){var a=[],b=e.library_select.text();null!==b&&e.datasets.each(function(c){"file"===c.get("type")&&a.push({value:c.id,label:b+c.get("name")})}),e.dataset_select.update(a),e.trigger("change")}),this.on("change",function(){a.onchange&&a.onchange(e.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$(".dataset-select").append(this.dataset_select.$el),this.libraries.fetch({reset:!0,success:function(){e.library_select.trigger("change"),void 0!==e.options.value&&e.value(e.options.value)}})},value:function(){return this.dataset_select.value()},_template:function(){return'',a.icon&&(b+=' '),b+=''+a.title+"
',"top"==a.placement&&(b+=''),b+='',"bottom"==a.placement&&(b+=''),b+='
Select Library
Select Dataset
Select Library
'.join(pja_ss_all)} diff --git a/test/api/test_tools.py b/test/api/test_tools.py index fe93e6cd436..b7507c37414 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -3,6 +3,7 @@ from base import api from operator import itemgetter from .helpers import DatasetPopulator from .helpers import DatasetCollectionPopulator +from .helpers import LibraryPopulator from .helpers import skip_without_tool @@ -120,6 +121,21 @@ class ToolsTestCase( api.ApiTestCase ): assert output1_content.strip() == "--ex1" assert output2_content.strip() == "None", output2_content + @skip_without_tool( "library_data" ) + def test_library_data_param( self ): + history_id = self.dataset_populator.new_history() + ld = LibraryPopulator( self ).new_library_dataset( "lda_test_library" ) + inputs = { + "library_dataset": ld[ "ldda_id" ], + "library_dataset_multiple": [ld[ "ldda_id" ], ld[ "ldda_id" ]] + } + response = self._run( "library_data", history_id, inputs, assert_ok=True ) + output = response[ "outputs" ] + output_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output[ 0 ] ) + assert output_content == "TestData", output_content + output_multiple_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output[ 1 ] ) + assert output_multiple_content == "TestDataTestData", output_multiple_content + @skip_without_tool( "multi_data_param" ) def test_multidata_param( self ): history_id = self.dataset_populator.new_history() @@ -302,7 +318,7 @@ class ToolsTestCase( api.ApiTestCase ): self._assert_has_keys( output_collection, "id", "name", "elements", "populated" ) assert not output_collection[ "populated" ] assert len( output_collection[ "elements" ] ) == 0 - + self.assertEquals( output_collection[ "name" ], "Table split on first column" ) self.dataset_populator.wait_for_job( create["jobs"][0]["id"], assert_ok=True ) get_collection_response = self._get( "dataset_collections/%s" % output_collection[ "id" ], data={"instance_type": "history"} ) @@ -312,6 +328,8 @@ class ToolsTestCase( api.ApiTestCase ): self._assert_has_keys( output_collection, "id", "name", "elements", "populated" ) assert output_collection[ "populated" ] assert len( output_collection[ "elements" ] ) == 2 + self.assertEquals( output_collection[ "name" ], "Table split on first column" ) + # TODO: verify element identifiers @skip_without_tool( "cat1" ) diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 32983f024ef..bced8471ffa 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1516,7 +1516,7 @@ class TwillTestCase( unittest.TestCase ): # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "/user/login?use_panels=False" ) - self.submit_form( 'login', 'login_button', email=email, redirect=redirect, password=password ) + self.submit_form( 'login', 'login_button', login=email, redirect=redirect, password=password ) def logout( self ): self.visit_url( "%s/user/logout" % self.url ) diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index d707690c4c3..99d7c78d9f4 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -263,13 +263,18 @@ def build_tests( app=None, testing_shed_tools=False, master_api_key=None, user_a baseclasses = ( ToolTestCase, ) namespace = dict() for j, testdef in enumerate( tool.tests ): + test_function_name = 'test_tool_%06d' % j + def make_test_method( td ): def test_tool( self ): self.do_it( td ) + test_tool.__name__ = test_function_name + return test_tool + test_method = make_test_method( testdef ) test_method.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) - namespace[ 'test_tool_%06d' % j ] = test_method + namespace[ test_function_name ] = test_method namespace[ 'shed_tool_id' ] = shed_tool_id namespace[ 'master_api_key' ] = master_api_key namespace[ 'user_api_key' ] = user_api_key diff --git a/test/functional/tools/library_data.xml b/test/functional/tools/library_data.xml new file mode 100644 index 00000000000..8fd1a147f49 --- /dev/null +++ b/test/functional/tools/library_data.xml @@ -0,0 +1,19 @@ +