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galaxy-dist commit 5e75bad5a780: Merge.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannon.baker(a)emory.edu> # Date 1277239092 14400 # Node ID 5e75bad5a780acb7c2975bcc375216c1abb5d148 # Parent f2f31fe4cf08f9500a886184b5c5f15fa4184e4d # Parent 464734ed09ad4b36afc3409b5d975732b1c6eb21 Merge.

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galaxy-dist commit f2f31fe4cf08: New: Send Email Action, Delete Action.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannon.baker(a)emory.edu> # Date 1277238844 14400 # Node ID f2f31fe4cf08f9500a886184b5c5f15fa4184e4d # Parent 1f8035729ccd73f31522e816cf5467409e841b91 New: Send Email Action, Delete Action. Note that delete action is dangerous and will break a workflow if you delete datasets that are required in later steps. Partial refactoring to make addition of actions simpler. --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -5,18 +5,50 @@ from galaxy.util.json import from_json_s from galaxy.web.form_builder import * + +# For email notification PJA +from email.MIMEText import MIMEText +import smtplib + log = logging.getLogger( __name__ ) # DBTODO This still needs refactoring and general cleanup. +def get_form_template(action_type, title, content, help, on_output = True ): + if on_output: + form = """ + if (pja.action_type == "%s"){ + p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ + <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>"; + %s + p_str += "</div><div class='toolParamHelp'>%s</div></div>"; + }""" % (action_type, title, content, help) + else: + form = """ + if (pja.action_type == "%s"){ + p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ + <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>"; + %s + p_str += "</div><div class='toolParamHelp'>%s</div></div>"; + }""" % (action_type, title, content, help) + return form + +# def get_field(action, argument, i_type, label = None): +# fstr = '' +# fname = """pja__"+pja.output_name+"__%s__%s""" % (action, argument) +# if label: +# fstr += """<label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>""" +# fstr += """<input type='text' value=" + chromCol + " name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>""" + class DefaultJobAction(object): name = "DefaultJobAction" + verbose_name = "Default Job" @classmethod def execute(cls, job): pass - @classmethod + @classmethod def get_config_form(cls, trans): return "<p>Default Job Action Config Form</p>" @@ -26,11 +58,42 @@ class DefaultJobAction(object): return "%s -> %s" % (pja.action_type, pja.action_arguments) else: return "%s" % pja.action_type - + + +class EmailAction(DefaultJobAction): + name = "EmailAction" + verbose_name = "Email Notification" + @classmethod + def execute(cls, trans, action, job): + smtp_server = trans.app.config.smtp_server + if smtp_server is None: + return trans.show_error_message( "Mail is not configured for this galaxy instance, workflow action aborted." ) + # Build the email message + msg = MIMEText( "Your job '%s' at Galaxy instance %s is complete as of %s." % (job.history.name, trans.request.host, job.update_time)) + msg[ 'To' ] = job.user.email + msg[ 'From' ] = job.user.email + msg[ 'Subject' ] = "Galaxy workflow step notification '%s'" + try: + s = smtplib.SMTP() + s.connect( smtp_server ) + s.sendmail( frm, [ to ], msg.as_string() ) + s.close() + return trans.show_ok_message( "Your error report has been sent" ) + except Exception, e: + return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) + + @classmethod + def get_config_form(cls, trans): + form = """ + p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action. You will be emailed upon job completion.</label>\ + <input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; + """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output = False) + class ChangeDatatypeAction(DefaultJobAction): name = "ChangeDatatypeAction" - + verbose_name = "Change Datatype" @classmethod def execute(cls, trans, action, job): for dataset_assoc in job.output_datasets: @@ -45,24 +108,21 @@ class ChangeDatatypeAction(DefaultJobAct for dt_name in dtnames: dt_list += """<option id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype__%s' value='%s'>%s</option>""" % (dt_name, dt_name, dt_name) ps = """ - if (pja.action_type == "ChangeDatatypeAction"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>" + pja.action_type + " <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\ - <div class='toolFormBody'><label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label><select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\ + p_str += "<label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label>\ + <select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\ %s\ </select>"; - if (pja.action_arguments != undefined && pja.action_arguments.newtype != undefined){ - p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>" - } - p_str += "</div><div class='toolParamHelp'>This action will change the datatype of the output to the indicated value.</div></div>"; - } + if (pja.action_arguments != undefined && pja.action_arguments.newtype != undefined){ + p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"; + } """ % dt_list # Note the scrip + t hack above. Is there a better way? - return ps + return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.') class RenameDatasetAction(DefaultJobAction): name = "RenameDatasetAction" - + verbose_name = "Rename Dataset" + @classmethod def execute(cls, trans, action, job): for dataset_assoc in job.output_datasets: @@ -71,23 +131,22 @@ class RenameDatasetAction(DefaultJobActi @classmethod def get_config_form(cls, trans): - return """ - if (pja.action_type == "RenameDatasetAction"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>"; - if ((pja.action_arguments != undefined) && (pja.action_arguments.newname != undefined)){ - p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>"; - } - else{ - p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='New Name'/>"; - } - p_str += "</div><div class='toolParamHelp'>This action will rename the result dataset.</div></div>"; - } + form = """ + if ((pja.action_arguments != undefined) && (pja.action_arguments.newname != undefined)){ + p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ + <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>"; + } + else{ + p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ + <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>"; + } """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") class HideDatasetAction(DefaultJobAction): name = "HideDatasetAction" - + verbose_name = "Hide Dataset" + @classmethod def execute(cls, trans, action, job): for dataset_assoc in job.output_datasets: @@ -96,14 +155,79 @@ class HideDatasetAction(DefaultJobAction @classmethod def get_config_form(cls, trans): - return """ - if (pja.action_type == "HideDatasetAction"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>"; - p_str += "<label for='pja__"+pja.output_name+"__HideDatasetAction'>There are no additional options for this action.</label><input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; - p_str += "</div><div class='toolParamHelp'>This action will *hide* the result dataset from your history.</div></div>"; + form = """ + p_str += "<label for='pja__"+pja.output_name+"__HideDatasetAction'>There are no additional options for this action.</label>\ + <input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; + """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") + +class DeleteDatasetAction(DefaultJobAction): + # This is disabled for right now. Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data. + name = "DeleteDatasetAction" + verbose_name = "Delete Dataset" + + @classmethod + def execute(cls, trans, action, job): + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + dataset_assoc.dataset.deleted=True + + @classmethod + def get_config_form(cls, trans): + form = """ + p_str += "<label for='pja__"+pja.output_name+"__DeleteDatasetAction'>There are no additional options for this action. This dataset will be marked deleted.</label>\ + <input type='hidden' name='pja__"+pja.output_name+"__DeleteDatasetAction'/>"; + """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") + + +class ColumnSetAction(DefaultJobAction): + name = "ColumnSetAction" + verbose_name = "Assign Columns" + @classmethod + def execute(cls, trans, action, job): + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + for k, v in action.action_arguments.items(): + if v != '': + # Try to use both pure integer and 'cX' format. + if v[0] == 'c': + v = v[1:] + v = int(v) + if v != 0: + setattr(dataset_assoc.dataset.metadata, k, v) + + @classmethod + def get_config_form(cls, trans): + form = """ + var chrom_col = '' + if (pja.action_arguments != undefined){ + (pja.action_arguments.chromCol == undefined) ? chromCol = "" : chromCol=pja.action_arguments.chromCol; + (pja.action_arguments.startCol == undefined) ? startCol = "" : startCol=pja.action_arguments.startCol; + (pja.action_arguments.endCol == undefined) ? endCol = "" : endCol=pja.action_arguments.endCol; + (pja.action_arguments.strandCol == undefined) ? strandCol = "" : strandCol=pja.action_arguments.strandCol; + (pja.action_arguments.nameCol == undefined) ? nameCol = "" : nameCol=pja.action_arguments.nameCol; + }else{ + chromCol = ''; + startCol = ''; + endCol = ''; + strandCol = ''; + nameCol = ''; } + p_str += "<p>Leave any of these fields blank if they do not need to be set.</p>\ + <label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>\ + <input type='text' value='" + chromCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>\ + <label for='pja__"+pja.output_name+"__ColumnSetAction__startCol'>Start Column</label>\ + <input type='text' value='" + startCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__startCol'/>\ + <label for='pja__"+pja.output_name+"__ColumnSetAction__endCol'>End Column</label>\ + <input type='text' value='" + endCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__endCol'/>\ + <label for='pja__"+pja.output_name+"__ColumnSetAction__strandCol'>Strand Column</label>\ + <input type='text' value='" + strandCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__strandCol'/>\ + <label for='pja__"+pja.output_name+"__ColumnSetAction__nameCol'>Name Column</label>\ + <input type='text' value='" + nameCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__nameCol'/>\"; """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will set column assignments in the output dataset. Blank fields are ignored.") + class SetMetadataAction(DefaultJobAction): name = "SetMetadataAction" @@ -116,28 +240,38 @@ class SetMetadataAction(DefaultJobAction @classmethod def get_config_form(cls, trans): - dt_list = "" - mdict = {} - for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): - for mn, mt in dtype_value.metadata_spec.items(): - if mt.visible: - mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','') - for k, v in mdict.items(): - dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>" - return """ - if (pja.action_type == "SetMetadataAction"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\ - <div class='toolFormBody'>\ - %s\ - </div><div class='toolParamHelp'>This tool sets metadata in output.</div></div>"; - } - """ % dt_list + # dt_list = "" + # mdict = {} + # for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): + # for mn, mt in dtype_value.metadata_spec.items(): + # if mt.visible: + # mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','') + # for k, v in mdict.items(): + # dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>" + # form = """ + # p_str += "%s"; + # """ % dt_list + # return get_form_template('SetMetadataAction', 'Set Metadata', form, "This action will change metadata for the dataset.") + form = """ + p_str += "<p>Leave any of these fields blank if they do not need to be set.</p><label for='pja__"+pja.output_name+"__SetMetadataAction__chromCol'>Chrom Column</label>\ + <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__chromCol'/>\ + <label for='pja__"+pja.output_name+"__SetMetadataAction__startCol'>Start Column</label>\ + <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__startCol'/>\ + <label for='pja__"+pja.output_name+"__SetMetadataAction__endCol'>End Column</label>\ + <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__endCol'/>\ + <label for='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'>Comment Lines</label>\ + <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'/>\ + "; + """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will set metadata in the output dataset.") ACTIONS = { "RenameDatasetAction" : RenameDatasetAction, "HideDatasetAction" : HideDatasetAction, "ChangeDatatypeAction": ChangeDatatypeAction, - # "SetMetadataAction" : SetMetadataAction, + "ColumnSetAction" : ColumnSetAction, + "EmailAction" : EmailAction, + # "SetMetadataAction" : SetMetadataAction, + # "DeleteDatasetAction" : DeleteDatasetAction, } class ActionBox(object): @@ -147,13 +281,13 @@ class ActionBox(object): ACTIONS[action.action_type].execute(action, job, trans) else: return False - + @classmethod def get_short_str(cls, action): if action.action_type in ACTIONS: return ACTIONS[action.action_type].get_short_str(action) else: - return "Unknown PostJobAction" + return "Unknown Action" @classmethod def handle_incoming(cls, incoming): @@ -180,7 +314,7 @@ class ActionBox(object): def get_add_list(cls): addlist = "<select id='new_pja_list' name='new_pja_list'>" for action in ACTIONS: - addlist += "<option value='%s'>%s</option>" % (ACTIONS[action].name, ACTIONS[action].name) + addlist += "<option value='%s'>%s</option>" % (ACTIONS[action].name, ACTIONS[action].verbose_name) addlist += "</select>" return addlist @@ -193,4 +327,5 @@ class ActionBox(object): @classmethod def execute(cls, trans, pja, job): - ACTIONS[pja.action_type].execute(trans, pja, job) + if ACTIONS.has_key(pja.action_type): + ACTIONS[pja.action_type].execute(trans, pja, job) --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -313,9 +313,9 @@ // DBTODO Refactor to the post module. // This function preloads how to display known pja's. function display_pja(pja, node){ - // DBTODO SANITIZE INPUTS. Way too easy to break the page right now with a change dataset name action. + // DBTODO SANITIZE INPUTS. p_str = ''; - ${ActionBox.get_forms(trans)}; + ${ActionBox.get_forms(trans)} $("#pja_container").append(p_str); $("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){ action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text(); @@ -376,7 +376,7 @@ // Add step actions. if (node && node.type=='tool'){ pjastr = "<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> \ - <label>New Actions:</label><br/>" + display_pja_list() + display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\ + " + display_pja_list() + " <br/> "+ display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\ </div><div class='form-row'>\ <div style='margin-right: 10px;'><span id='pja_container'></span>"; pjastr += "<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";

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galaxy-dist commit b4237641ca4d: Make the PSU BX browser a UCSC browser instead of being a different display type.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1277829642 14400 # Node ID b4237641ca4d28631c9e65c726693057d4b8dab3 # Parent eea2c040ccb7bd0d2a7c6e5eab8e65f98a163009 Make the PSU BX browser a UCSC browser instead of being a different display type. --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -105,8 +105,7 @@ mailing_join_addr = galaxy-user-join@bx. # Use the new iframe / javascript based layout use_new_layout = true -# Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing -bx_display_sites = main +# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing ucsc_display_sites = main,test,archaea,ucla gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly # Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -278,12 +278,6 @@ def object_to_string( obj ): def string_to_object( s ): return pickle.loads( binascii.unhexlify( s ) ) -def get_bx_by_build(build): - sites = [] - for site in bx_build_sites: - if build in site['builds']: - sites.append((site['name'],site['url'])) - return sites def get_ucsc_by_build(build): sites = [] for site in ucsc_build_sites: @@ -484,7 +478,6 @@ def umask_fix_perms( path, umask, unmask galaxy_root_path = os.path.join(__path__[0], "..","..","..") # The dbnames list is used in edit attributes and the upload tool dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) -bx_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "bx", "bx_build_sites.txt" ) ) ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False ) --- a/tool-data/shared/bx/bx_build_sites.txt +++ /dev/null @@ -1,1 +0,0 @@ -main http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 bx-main --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -54,7 +54,6 @@ class Interval( Tabular ): """Initialize interval datatype, by adding UCSC display apps""" Tabular.__init__(self, **kwd) self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - self.add_display_app ( 'main', 'BX', 'as_ucsc_display_file', 'bx_links' ) def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) @@ -247,29 +246,6 @@ class Interval( Tabular ): link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val - def bx_links( self, dataset, type, app, base_url ): - # TODO: abstract these methods to eliminate duplicate code. - ret_val = [] - if dataset.has_data: - viewport_tuple = self.get_estimated_display_viewport(dataset) - if viewport_tuple: - chrom = viewport_tuple[0] - start = viewport_tuple[1] - stop = viewport_tuple[2] - for site_name, site_url in util.get_bx_by_build(dataset.dbkey): - if site_name in app.config.bx_display_sites: - # HACK: UCSC doesn't support https, so force http even - # if our URL scheme is https. Making this work - # requires additional hackery in your upstream proxy. - # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='bx_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) - redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) - return ret_val def validate( self, dataset ): """Validate an interval file using the bx GenomicIntervalReader""" --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt @@ -5,3 +5,4 @@ archaea http://archaea.ucsc.edu/cgi-bin/ #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVu ln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 +psu bx main http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -83,7 +83,6 @@ class Configuration( object ): self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) - self.bx_display_sites = kwargs.get( 'bx_display_sites', "main" ).lower().split(",") self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",")

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galaxy-dist commit 7d3a9212b15e: Enable recently used tools menu to show only tools that are currently in the toolbox.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1277147965 14400 # Node ID 7d3a9212b15e82327c2af7c3222995f358532d60 # Parent 91d047183110888b3bbcbfc99a0b5f2c38c2d6bf Enable recently used tools menu to show only tools that are currently in the toolbox. --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -6,7 +6,6 @@ from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html -from galaxy.util.odict import odict from galaxy.model.orm import * log = logging.getLogger( __name__ ) @@ -33,20 +32,18 @@ class RootController( BaseController, Us else: ## Get most recently used tools. toolbox = self.get_toolbox() - recent_tool_ids = odict() + recent_tools = [] if trans.user: for row in trans.sa_session.query( self.app.model.Job.tool_id ). \ filter( self.app.model.Job.user==trans.user ). \ order_by( self.app.model.Job.create_time.desc() ): tool_id = row[0] - recent_tool_ids[tool_id] = tool_id - ## TODO: make number of recently used tools a user preference. - if len ( recent_tool_ids ) == 5: - break - - # Create list of recently used tools. - recent_tools = [ toolbox.tools_by_id[ tool_id ] for tool_id in recent_tool_ids.keys() ] - + if tool_id in toolbox.tools_by_id: + recent_tools.append( toolbox.tools_by_id[tool_id] ) + ## TODO: make number of recently used tools a user preference. + if len ( recent_tools ) == 5: + break + return trans.fill_template('/root/tool_menu.mako', toolbox=toolbox, recent_tools=recent_tools ) @web.json

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galaxy-dist commit 072d5f7ba872: Remove the rest of the memory_usage debugging module since all of its calls were removed from controller methods.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1277831187 14400 # Node ID 072d5f7ba872c828fc21f6ddd9e8485deded89d3 # Parent b4237641ca4d28631c9e65c726693057d4b8dab3 Remove the rest of the memory_usage debugging module since all of its calls were removed from controller methods. --- a/lib/galaxy/util/memory_usage.py +++ /dev/null @@ -1,44 +0,0 @@ -import os, platform, logging -from galaxy.datatypes.data import nice_size - -log = logging.getLogger( __name__ ) - -_proc_status = '/proc/%d/status' % os.getpid() - -_scale = { 'kB': 1024.0, 'mB': 1024.0*1024.0, 'KB': 1024.0, 'MB': 1024.0*1024.0 } - -def _VmB( VmKey ): - '''Private. - ''' - global _proc_status, _scale - # get pseudo file /proc/<pid>/status - try: - t = open( _proc_status ) - v = t.read() - t.close() - except: - log.debug("memory_usage is currently supported only on Linux, your platform is %s %s" % ( platform.system(), platform.release() ) ) - return 0.0 # non-Linux? - # get VmKey line e.g. 'VmRSS: 9999 kB\n ...' - i = v.index( VmKey ) - v = v[ i: ].split( None, 3 ) # whitespace - if len( v ) < 3: - return 0.0 # invalid format? - # convert Vm value to bytes - return float( v[ 1 ] ) * _scale[ v[ 2 ] ] -def memory( since=0.0, pretty=False ): - '''Return memory usage in bytes. - ''' - size = _VmB( 'VmSize:' ) - since - if pretty: - return nice_size( size ) - else: - return size -def resident( since=0.0 ): - '''Return resident memory usage in bytes. - ''' - return _VmB( 'VmRSS:' ) - since -def stacksize( since=0.0 ): - '''Return stack size in bytes. - ''' - return _VmB( 'VmStk:' ) - since --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,10 +64,6 @@ class UniverseApplication( object ): from galaxy.util import memdump if memdump.Memdump: self.memdump = memdump.Memdump() - # Enable memory_usage logging if configured - if self.config.log_memory_usage: - from galaxy.util import memory_usage - self.memory_usage = memory_usage # Start the job queue self.job_manager = jobs.JobManager( self ) # FIXME: These are exposed directly for backward compatibility --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -80,7 +80,6 @@ class Configuration( object ): self.pbs_stage_path = kwargs.get('pbs_stage_path', "" ) self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) - self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")

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galaxy-dist commit 91d047183110: Fix bug that prevented correct toggling of recently used menu.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1277147258 14400 # Node ID 91d047183110888b3bbcbfc99a0b5f2c38c2d6bf # Parent 4cdf4cca0f313c5c3a6045db287a32a3d1e4d30b Fix bug that prevented correct toggling of recently used menu. --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -124,10 +124,7 @@ else { // "Show" menu. - var tool_search_query = $('#galaxy_tools').contents().find('#tool-search-query'); - var tool_search_active = tool_search_query.is(":visible") && tool_search_query.val().length > 3; - - if (!tool_search_active) + if (!$('#galaxy_tools').contents().find('#tool-search-query').hasClass("search_active")) // Default. ru_menu.slideDown(); else --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -113,6 +113,8 @@ if ( this.value.length < 3 ) { reset_tool_search(false); } else if ( this.value != this.lastValue ) { + // Add class to denote that searching is active. + $(this).addClass("search_active"); // input.addClass(config.loadingClass); // Add '*' to facilitate partial matching. var q = this.value + '*'; --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -478,7 +478,8 @@ function reset_tool_search( initValue ) if (tool_menu_frame.length == 0) tool_menu_frame = $(document); - // Remove matching class. + // Remove classes that indicate searching is active. + $(this).removeClass("search_active"); tool_menu_frame.find(".toolTitle").removeClass("search_match"); // Reset visibility of tools and labels. --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function 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galaxy-dist commit 980a38b7f874: Bugfix: Allow administrators to create users when use_remote_user is enabled.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1277738970 14400 # Node ID 980a38b7f8748e5a852ff06d9cdf59be810f97f7 # Parent 89fbba1fc87e5dc59e449bab7a38addd24493337 Bugfix: Allow administrators to create users when use_remote_user is enabled. --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -50,11 +50,12 @@ UCSC_ARCHAEA_SERVERS = ( ) class RemoteUser( object ): - def __init__( self, app, maildomain=None, ucsc_display_sites=[] ): + def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app self.maildomain = maildomain self.allow_ucsc_main = False self.allow_ucsc_archaea = False + self.admin_users = admin_users if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: @@ -76,14 +77,7 @@ class RemoteUser( object ): # un-authenticated. Any other possible values need to go here as well. if environ.has_key( 'HTTP_REMOTE_USER' ) and environ[ 'HTTP_REMOTE_USER' ] != '(null)': path_info = environ.get('PATH_INFO', '') - if path_info.startswith( '/user' ): - title = "Access to Galaxy user controls is disabled" - message = """ - User controls are disabled when Galaxy is configured - for external authentication. - """ - return self.error( start_response, title, message ) - elif not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): + if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): if self.maildomain is not None: environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain else: @@ -99,6 +93,15 @@ class RemoteUser( object ): before you may access Galaxy. """ return self.error( start_response, title, message ) + if path_info.startswith( '/user/create' ) and environ[ 'HTTP_REMOTE_USER' ] in self.admin_users: + pass # admins can create users + elif path_info.startswith( '/user' ): + title = "Access to Galaxy user controls is disabled" + message = """ + User controls are disabled when Galaxy is configured + for external authentication. + """ + return self.error( start_response, title, message ) return self.app( environ, start_response ) else: title = "Access to Galaxy is denied" --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -139,7 +139,9 @@ def wrap_in_middleware( app, global_conf # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.web.framework.middleware.remoteuser import RemoteUser - app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), ucsc_display_sites=conf.get( 'ucsc_display_sites', [] ) ) + app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), + ucsc_display_sites=conf.get( 'ucsc_display_sites', [] ), + admin_users=conf.get( 'admin_users', '' ).split( ',' ) ) log.debug( "Enabling 'remote user' middleware" ) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side.

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galaxy-dist commit 89fbba1fc87e: Include annotations and tags when exporting histories to and importing histories from file.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1277733095 14400 # Node ID 89fbba1fc87e5dc59e449bab7a38addd24493337 # Parent 71b1a5920fc12514a9e151770eaf250d6fc6da46 Include annotations and tags when exporting histories to and importing histories from file. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -476,12 +476,24 @@ class HistoryController( BaseController, history_attrs = from_json_string( history_attr_str ) # Create history. - # TODO: set tags, annotations. - new_history = model.History( name='imported: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) trans.sa_session.add( new_history ) - trans.sa_session.flush() - # TODO: Ignore hid_counter for now since it just artificially increases the hid for all the history's HDAs. - #new_history.hid_counter = history_attrs['hid_counter'] + + # Builds a tag string for a tag, value pair. + def get_tag_str( tag, value ): + if not value: + return tag + else: + return tag + ":" + value + + # Add annotation, tags. + if trans.user: + self.add_item_annotation( trans, new_history, history_attrs[ 'annotation' ] ) + for tag, value in history_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) + + # Ignore hid_counter since it artificially increases the hid for all HDAs? + # new_history.hid_counter = history_attrs['hid_counter'] new_history.genome_build = history_attrs['genome_build'] trans.sa_session.flush() @@ -515,7 +527,7 @@ class HistoryController( BaseController, metadata = metadata, history = new_history, create_dataset = True, - sa_session = trans.sa_session ) + sa_session = trans.sa_session ) hda.state = hda.states.OK trans.sa_session.add( hda ) trans.sa_session.flush() @@ -528,7 +540,12 @@ class HistoryController( BaseController, temp_dataset_name = '%s/datasets/%s' % ( temp_output_dir, dataset_attrs['file_name'] ) shutil.copyfile( temp_dataset_name, hda.file_name ) - # TODO: set tags, annotations. + # Set tags, annotations. + if trans.user: + self.add_item_annotation( trans, hda, dataset_attrs[ 'annotation' ] ) + for tag, value in dataset_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) + trans.sa_session.flush() # Cleanup. if os.path.exists( temp_output_dir ): @@ -537,7 +554,7 @@ class HistoryController( BaseController, return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) except Exception, e: return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) - + return trans.show_form( web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) @@ -567,7 +584,7 @@ class HistoryController( BaseController, # Create archive and stream back to client. - # Simple method to convert strings to unicode in utf-8 format. Method should be used for all user input. + # Convert strings to unicode in utf-8 format. Method should be used for all user input. def unicode_wrangler( a_string ): a_string_type = type ( a_string ) if a_string_type is str: @@ -575,18 +592,28 @@ class HistoryController( BaseController, elif a_string_type is unicode: return a_string.encode( 'utf-8' ) + # Create dictionary of an item's tags. + def get_item_tag_dict( item ): + tags = {} + for tag in item.tags: + tag_user_tname = unicode_wrangler( tag.user_tname ) + tag_user_value = unicode_wrangler( tag.user_value ) + tags[ tag_user_tname ] = tag_user_value + return tags + try: # Use temporary directory for temp output files. temp_output_dir = tempfile.mkdtemp() # Write history attributes to file. - # TODO: include tags, annotations. history_attrs = { "create_time" : history.create_time.__str__(), "update_time" : history.update_time.__str__(), "name" : unicode_wrangler( history.name ), "hid_counter" : history.hid_counter, - "genome_build" : history.genome_build + "genome_build" : history.genome_build, + "annotation" : unicode_wrangler( self.get_item_annotation_str( trans, history.user, history ) ), + "tags" : get_item_tag_dict( history ) } history_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name history_attrs_out = open( history_attrs_file_name, 'w' ) @@ -597,7 +624,6 @@ class HistoryController( BaseController, history_attrs_file_name = new_name # Write datasets' attributes to file. - # TODO: include tags, annotations. datasets = self.get_history_datasets( trans, history ) datasets_attrs = [] for dataset in datasets: @@ -615,7 +641,9 @@ class HistoryController( BaseController, "designation" : dataset.designation, "deleted" : dataset.deleted, "visible" : dataset.visible, - "file_name" : dataset.file_name.split('/')[-1] + "file_name" : dataset.file_name.split('/')[-1], + "annotation" : unicode_wrangler( self.get_item_annotation_str( trans, history.user, dataset ) ), + "tags" : get_item_tag_dict( dataset ) } datasets_attrs.append( attribute_dict ) datasets_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name

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galaxy-dist commit eea2c040ccb7: Bugfix: If a LibraryDataset does not have an associated LDDA (this should not be possible but apparently has happened), supress an exception in the library browser that prevents viewing the library at all.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1277740771 14400 # Node ID eea2c040ccb7bd0d2a7c6e5eab8e65f98a163009 # Parent c37eed98f8c974d7591db0b845a515c731d00787 Bugfix: If a LibraryDataset does not have an associated LDDA (this should not be possible but apparently has happened), supress an exception in the library browser that prevents viewing the library at all. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -959,16 +959,16 @@ class LibraryFolder( object ): intermed.sort() return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) # This needs to be a list - active_library_datasets = [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] + active_library_datasets = [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ] return sort_by_attr( [ ld for ld in active_library_datasets ], 'name' ) @property def activatable_library_datasets( self ): # This needs to be a list - return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ] + return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ] @property def active_datasets( self ): # This needs to be a list - return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] + return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ] def get_display_name( self ): # Library folder name can be either a string or a unicode object. If string, # convert to unicode object assuming 'utf-8' format.

1 0

galaxy-dist commit c37eed98f8c9: Update UCSC table browser datasource tools to treat data marked as 'gff' as 'gtf'.
by commits-noreply＠bitbucket.org 29 Jun '10

29 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1277740225 14400 # Node ID c37eed98f8c974d7591db0b845a515c731d00787 # Parent 980a38b7f8748e5a852ff06d9cdf59be810f97f7 Update UCSC table browser datasource tools to treat data marked as 'gff' as 'gtf'. --- a/tools/data_source/ucsc_tablebrowser_archaea.xml +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml @@ -30,6 +30,7 @@ <value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /><value galaxy_value="fasta" remote_value="sequence" /> + <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param></request_param_translation> --- a/tools/data_source/ucsc_tablebrowser.xml +++ b/tools/data_source/ucsc_tablebrowser.xml @@ -30,6 +30,7 @@ <value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /><value galaxy_value="fasta" remote_value="sequence" /> + <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param></request_param_translation> --- a/tools/data_source/ucsc_tablebrowser_test.xml +++ b/tools/data_source/ucsc_tablebrowser_test.xml @@ -30,6 +30,7 @@ <value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /><value galaxy_value="fasta" remote_value="sequence" /> + <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param></request_param_translation>

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