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[hg] galaxy 3546: Eliminate the pop-up menus for folders and dat...
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/be396d94ca5a changeset: 3546:be396d94ca5a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Mar 18 16:02:09 2010 -0400 description: Eliminate the pop-up menus for folders and datasets if the library is deleted. diffstat: templates/library/common/browse_library.mako | 130 +++++++++++++------------- 1 files changed, 67 insertions(+), 63 deletions(-) diffs (187 lines): diff -r 2590120aed68 -r be396d94ca5a templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Thu Mar 18 12:57:29 2010 -0400 +++ b/templates/library/common/browse_library.mako Thu Mar 18 16:02:09 2010 -0400 @@ -208,38 +208,40 @@ %if ldda.library_dataset.deleted: </span> %endif - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> - %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: - %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> - %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %if not library.deleted: + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif - %endif - </div> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_manage ): + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif </td> <td id="libraryItemInfo">${render_library_item_info( ldda )}</td> <td>${uploaded_by}</td> @@ -252,7 +254,7 @@ %endif </%def> -<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"> +<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"> <% from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted @@ -300,40 +302,42 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a> + <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">${folder.name}</a> %if folder.description: <i>- ${folder.description}</i> %endif %if folder.deleted: </span> %endif - <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="folder_img-${folder.id}-popup"> - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_add ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> - %endif - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %endif - %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: - %if not library.deleted and not folder.deleted: - <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> - %elif not library.deleted and folder.deleted and not folder.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library_id, item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %if not library.deleted: + <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="folder_img-${folder.id}-popup"> + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_add ): + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif - %endif - </div> + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %endif + %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if not library.deleted and not folder.deleted: + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> + %elif not library.deleted and folder.deleted and not folder.purged: + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %endif + %endif + </div> + %endif </div> <td colspan="3"></td> </tr> @@ -345,7 +349,7 @@ %if cntrller == 'library': <% sub_folders = active_folders( trans, folder ) %> %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} %endfor %for library_dataset in folder.active_library_datasets: <% @@ -365,7 +369,7 @@ sub_folders, lddas = active_folders_and_lddas( trans, folder ) %> %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library_id, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} %endfor %for ldda in lddas: <% @@ -470,12 +474,12 @@ </tr> <% row_counter = RowCounter() %> %if cntrller in [ 'library', 'requests' ]: - ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted: ${render_actions_on_multiple_items()} %endif %elif cntrller in [ 'library_admin', 'requests_admin' ]: - ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted and not show_deleted: ${render_actions_on_multiple_items()} %endif

1 0

help with dynamic select parameters
by Lee, Joshua 24 Mar '10

24 Mar '10

Hi, I'm trying to create a tool where there are several select parameters whose choices are determine by the previous parameter(s). I have a toy example with three parameters: Category, Food, and Prep method. Depending on the chosen Category, only certain Foods are shown, which in turn determines which Prep methods are available. I'm trying to use the <options> tag with the "from_file" attribute. I have one column per parameter and one row per valid combination. My problem is that the front end can get into a state where a certain valid combinations will be unselectable. In the example below, I can never select "Fruit", "Kiwi", and "Raw". When I change the 1st select, the values for the 2nd select are loaded, but the values for the 3rd select cannot be updated. This is particularly problematic if there is only one choice for the 2nd select, because I cannot get it's "onchange" handler to fire (so the 3rd select is always empty). In my case, it would be nice if the first value of the 2nd select is chosen as a default, and the 3rd select is populated accordingly. Any help would be appreciated. Perhaps I'm not using these features as intended, but it seemed like a natural application. Thanks, Josh My data file looks like: Meat Chicken Fried Meat Chicken Grilled Meat Beef Grilled Meat Beef Stir-fried Veg Carrot Boiled Veg Fennel Raw Fruit Kiwi Raw And my tool's <inputs> section is: <inputs> <param name="paramA" type="select" label="Category"> <options from_file="test_select_options.txt"> <column name="value" index="0"/> <column name="name" index="0"/> <filter type="unique_value" name="unique" column="0"/> </options> </param> <param name="paramB" type="select" label="Food" > <options from_file="test_select_options.txt"> <column name="value" index="1"/> <column name="name" index="1"/> <filter type="unique_value" name="unique" column="1"/> <filter type="param_value" ref="paramA" name="A" column="0"/> </options> </param> <param name="paramC" type="select" label="How prepared"> <options from_file="test_select_options.txt"> <column name="value" index="2"/> <column name="name" index="2"/> <filter type="param_value" ref="paramA" name="A" column="0"/> <filter type="param_value" ref="paramB" name="B" column="1"/> </options> </param> </inputs>

2 1

Binary datatypes
by Pieter Neerincx 23 Mar '10

23 Mar '10

Hi Galaxy team, Some time ago I added a binary data type to my Galaxy development machine. I simply defined the input for a tool as the standard binary data type. Recently I upgraded my Galaxy instance and afterwards I could no longer upload binary data successfully :(. So, I looked at the docs to properly define a new binary data specific for that tool. I created a Python class, wrote a sniffer and listed the new stuff in the datatypes_conf.xml. To my surprise that did not work... After some digging I found that for a binary datatype I also had to hack the data upload tool in two places (see below). The word hack is maybe a bit too much for simply copying the lines for the already supported bam and Sff data types, but having to change code to support a new datatype sounds like a bad plan to me. Would it be possible to make sure support for a new binary data type is completely handled by config files and maybe a new python class, but without hacking code just like for non-binary data types? Cheers, Pi ------------------- def check_bam( temp_name ): return Bam().sniff( temp_name ) def check_sff( temp_name ): return Sff().sniff( temp_name ) # # Added mod for Thermo Finnigan RAW files START # def check_raw( temp_name ): return RAW().sniff( temp_name ) # # Added mod for Thermo Finnigan RAW files END # ..... # Is dataset content supported sniffable binary? elif check_bam( dataset.path ): ext = 'bam' data_type = 'bam' elif check_sff( dataset.path ): ext = 'sff' data_type = 'sff' # # Added mod for Thermo Finnigan RAW files START # elif check_raw( dataset.path ): ext = 'raw' data_type = 'raw' # # Added mod for Thermo Finnigan RAW files END #

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Feature Request: customize name of history item in a collected primary dataset
by Lee, Joshua 23 Mar '10

23 Mar '10

Hi, I have a tool that produces a variable number of outputs, which are written to the tmp database path with the specially formatted name "%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type ). In lib/galaxy/tools/__init__.py, the history item's "designation" is set to "name" and the item's "name" is set to output1.name. This potentially creates many items with the same name, which must be differentiated either through meta data or by examining the contents of the file. I would like to request a means to customize the name of the collected dataset. A simple but hack-y method would be to append another token to the name of the file. If this token exists, it would be used as the history item's name e.g. "primary_123_NAME123_visible_txt_dbkey_NEWNAME". This would also require that the optional DBKEY token would have to be validated for non-blank values. Josh

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format for csv file to import a sequencing request sample
by nsfox＠uwaterloo.ca 23 Mar '10

23 Mar '10

Hi, What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample? Thanks, Natalie

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Re: [galaxy-dev] Connect a local UCSC mirror to galaxy
by Greg Von Kuster 23 Mar '10

23 Mar '10

Hello Emeric, Please send your questions to the galaxy mailing lists ( galaxy-bugs(a)bx.psu.ed, galaxy-dev(a)bx.psu.edu, galaxy-user(a)bx.psu.edu ) instead of private email addresses as you will be much more likely to get answers in a timely fashion. Given the context of your question, I assume you want to point another UCSC-like "get data" tool to your mirror. If that is the case, simply copy the ~/tools/data_source/ucsc_tablebrowser.xml file to a different file name (e.g., my_mirror.xml) , and edit the following line in it to point to your mirror: <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> Next, add an entry for it in your tool_conf.xml file and restart your Galaxy instance. That's all you should need. On Mar 23, 2010, at 10:22 AM, Emeric Dubois wrote: > Hello Greg > > I have installed a partial mirror of UCSC and Galaxy on my server. > I want use my UCSC mirror to get data and display in my gallaxy installation. > Is it possible to do that ? How ? > Please, can you help me ? > > Thanks > > Emeric > > -- > ***************************************** > > Emeric Dubois > Plateforme MGX > Institut de Génomique Fonctionnelle > UMR 5203 CNRS – U 661 INSERM – Universite de Montpellier > 141 rue de la cardonille > 34094 Montpellier Cedex 05, France > Tel: 04 67 14 29 32 > > Emeric.Dubois(a)igf.cnrs.fr > > ***************************************** > > > -- > Ce message a été vérifié par MailScanner > pour des virus ou des polluriels et rien de > suspect n'a été trouvé. > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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transfer dataset failed because user could not login
by nsfox＠uwaterloo.ca 23 Mar '10

23 Mar '10

Hi, I know that I have had the data transfer functionality working in the past but it's currently failing ending with the following: 127.0.0.1 - - [23/Mar/2010:08:37:50 -0400] "GET /user/create?username=nsfox1%40example.org&confirm=testuser&messagetype=error&msg=User+with+that+email+already+exists&password=testuser&email=nsfox1%40example.org HTTP/1.1" 200 - "-" "Python-urllib/2.5" ERROR:root:Traceback (most recent call last): File "scripts/galaxy_messaging/server/data_transfer.py", line 166, in add_to_library raise DataTransferException("The "+self.datatx_email+" user could not login to Galaxy") DataTransferException: 'The nsfox1(a)example.org user could not login to Galaxy' ERROR:root:FATAL ERROR.The nsfox1(a)example.org user could not login to Galaxy DEBUG:root:[[u'data/ATC_AA', u'Error'], [u'data/ATC_AB', u'Error'], [u'data/CRA_AC', u'Error'], [u'data/CRA_AE', u'In progress']] DEBUG:root:###################### [u'data/CRA_AE', u'Error.The nsfox1(a)example.org user could not login to Galaxy'] I re-downloaded the Galaxy instance again but I'm still having this issue. The user I'm using here is an admin user with permission to add to the data library and when I go and login galaxy it works. Any suggestions as to what I might be wrong would be great. Thanks, Natalie

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addition to ".hgignore"
by Assaf Gordon 22 Mar '10

22 Mar '10

Hi, the following path: database/reports/compiled_templates can be added to ".hgignore" file to remove non-relevant compiled python files from "hg st". -gordon

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feature suggestion: XY-Plot with manually set axis range
by Assaf Gordon 21 Mar '10

21 Mar '10

Hello, A small feature requested by our users: The ability to set the axis ranges in the plotting tool (xy_plot.xml). The attached patch adds this ability as an optional parameter in the tool. Note1: if the input data goes beyond the user's suggest range, the range is extended. Note2: the patch contains CR/LF because it appears the 'xy_plot.xml' tool has windows-style newlines. -gordon

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Searching Sequencing Requests
by nsfox＠uwaterloo.ca 19 Mar '10

19 Mar '10

Hi, I'm getting an error "AttributeError: 'StateColumn' object has no attribute 'get_filter'" if I search anything on the sequencing request page. Searching specifically within the Name search or Description search does work though. Is this a known bug or did I possibly miss setting up something in my Galaxy Instance? Also, that search, which is currently not working for me, it only searches the information the sequencing requests page, right? I'd like to request being able to search the requests for something within the request or have some where of quickly determining the information of the sample with the requests without browsing to each one. Any information is appreciated. Thanks, Natalie

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