mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
More ibrary work - highlights:
1) For datasets in the library browser, display message, uploaded by, date instead of format, db, info 2) Replace "Manage this dataset's versions" with "Upload a new version of this dataset" 3) When a library dataset is clicked in the library browser, display it's information rahter than it's peek.
This commit is contained in:
Greg Von Kuster
@@ -886,7 +886,7 @@ class Admin( BaseController ):
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return trans.response.send_redirect( web.url_for( controller='admin',
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action='library',
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id=id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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return trans.fill_template( '/admin/library/library_info.mako',
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@@ -1090,7 +1090,7 @@ class Admin( BaseController ):
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action='folder',
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id=id,
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library_id=library_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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return trans.fill_template( '/admin/library/folder_info.mako',
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@@ -1147,10 +1147,7 @@ class Admin( BaseController ):
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messagetype = params.get( 'messagetype', 'done' )
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if params.get( 'permissions', False ):
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action = 'permissions'
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elif params.get( 'versions', False ):
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action = 'versions'
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else:
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# 'information' will be the default
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action = 'information'
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library_dataset = trans.app.model.LibraryDataset.get( id )
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if not library_dataset:
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@@ -1181,17 +1178,6 @@ class Admin( BaseController ):
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render_templates=params.get( 'render_templates', False ),
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msg=msg,
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messagetype=messagetype )
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elif action == 'versions':
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if params.get( 'change_version_button', False ):
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target_lda = trans.app.model.LibraryDatasetDatasetAssociation.get( kwd.get( 'set_lda_id' ) )
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library_dataset.library_dataset_dataset_association = target_lda
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trans.app.model.flush()
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msg = 'The current version of this library dataset has been updated to be %s' % target_lda.name
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return trans.fill_template( '/admin/library/library_dataset_versions.mako',
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library_dataset=library_dataset,
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'permissions':
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if params.get( 'update_roles_button', False ):
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# The user clicked the Save button on the 'Edit permissions and role associations' form
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@@ -1296,9 +1282,10 @@ class Admin( BaseController ):
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else:
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if params.get( 'permissions', False ):
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action = 'permissions'
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elif params.get( 'edit_info', False ):
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action = 'edit_info'
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else:
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# 'information' will be the default
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action = 'information'
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action = 'info'
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if id.count( ',' ):
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ids = id.split( ',' )
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id = None
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@@ -1341,13 +1328,19 @@ class Admin( BaseController ):
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'information':
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elif action == 'info':
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return trans.fill_template( '/admin/library/ldda_info.mako',
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ldda=ldda,
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'edit_info':
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if params.get( 'change', False ):
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# The user clicked the Save button on the 'Change data type' form
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trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
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trans.app.model.flush()
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msg = "Data type changed for library dataset '%s'" % ldda.name
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return trans.fill_template( "/admin/library/ldda_info.mako",
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return trans.fill_template( "/admin/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1383,7 +1376,7 @@ class Admin( BaseController ):
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trans.app.model.flush()
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msg = 'Attributes updated for library dataset %s' % ldda.name
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messagetype = 'done'
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return trans.fill_template( "/admin/library/ldda_info.mako",
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return trans.fill_template( "/admin/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1402,7 +1395,7 @@ class Admin( BaseController ):
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ldda.datatype.after_edit( ldda )
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trans.app.model.flush()
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msg = 'Attributes updated for library dataset %s' % ldda.name
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return trans.fill_template( "/admin/library/ldda_info.mako",
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return trans.fill_template( "/admin/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1416,7 +1409,7 @@ class Admin( BaseController ):
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ldda.deleted = True
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ldda.flush()
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msg = 'Dataset %s has been removed from this library' % ldda.name
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return trans.fill_template( "/admin/library/ldda_info.mako",
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return trans.fill_template( "/admin/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1432,7 +1425,7 @@ class Admin( BaseController ):
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# case it resorts to the old dbkey. Setting the dbkey
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# sets it properly in the metadata
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ldda.metadata.dbkey = ldda.dbkey
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return trans.fill_template( "/admin/library/ldda_info.mako",
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return trans.fill_template( "/admin/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1851,7 +1844,7 @@ class Admin( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='error' ) )
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user = trans.get_user()
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@@ -1883,7 +1876,7 @@ class Admin( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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return trans.fill_template( "/admin/library/new_info.mako",
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@@ -1906,7 +1899,7 @@ class Admin( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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elif params.get( 'permissions', False ):
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@@ -118,7 +118,7 @@ class Library( BaseController ):
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return trans.response.send_redirect( web.url_for( controller='library',
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action='library',
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id=id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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return trans.fill_template( '/library/library_info.mako',
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@@ -327,10 +327,7 @@ class Library( BaseController ):
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messagetype = params.get( 'messagetype', 'done' )
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if params.get( 'permissions', False ):
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action = 'permissions'
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elif params.get( 'versions', False ):
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action = 'versions'
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else:
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# 'information' will be the default
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action = 'information'
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library_dataset = trans.app.model.LibraryDataset.get( id )
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if not library_dataset:
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@@ -368,24 +365,6 @@ class Library( BaseController ):
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render_templates=params.get( 'render_templates', False ),
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msg=msg,
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messagetype=messagetype )
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elif action == 'versions':
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if params.get( 'change_version_button', False ):
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if trans.app.security_agent.allow_action( trans.user,
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trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
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library_item=library_dataset ):
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target_lda = trans.app.model.LibraryDatasetDatasetAssociation.get( kwd.get( 'set_lda_id' ) )
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library_dataset.library_dataset_dataset_association = target_lda
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trans.app.model.flush()
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msg = 'The current version of this library dataset has been updated to be %s' % target_lda.name
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messagetype = 'done'
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else:
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msg = "You are not authorized to change the versions of this dataset"
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messagetype = "error"
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return trans.fill_template( '/library/library_dataset_versions.mako',
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library_dataset=library_dataset,
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'permissions':
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if params.get( 'update_roles_button', False ):
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if trans.app.security_agent.allow_action( trans.user,
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@@ -443,9 +422,10 @@ class Library( BaseController ):
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if id:
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if params.get( 'permissions', False ):
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action = 'permissions'
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elif params.get( 'edit_info', False ):
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action = 'edit_info'
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else:
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# 'information' will be the default
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action = 'information'
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action = 'info'
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if id.count( ',' ):
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ids = id.split( ',' )
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id = None
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@@ -500,7 +480,13 @@ class Library( BaseController ):
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'information':
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elif action == 'info':
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return trans.fill_template( '/library/ldda_info.mako',
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ldda=ldda,
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library_id=library_id,
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msg=msg,
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messagetype=messagetype )
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elif action == 'edit_info':
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if params.get( 'change', False ):
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# The user clicked the Save button on the 'Change data type' form
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if trans.app.security_agent.allow_action( trans.user,
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@@ -513,7 +499,7 @@ class Library( BaseController ):
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else:
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msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name
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messagetype = 'error'
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return trans.fill_template( "/library/ldda_info.mako",
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return trans.fill_template( "/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -555,7 +541,7 @@ class Library( BaseController ):
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else:
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msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name
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messagetype = 'error'
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return trans.fill_template( "/library/ldda_info.mako",
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return trans.fill_template( "/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -581,7 +567,7 @@ class Library( BaseController ):
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else:
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msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name
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messagetype = 'error'
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return trans.fill_template( "/library/ldda_info.mako",
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return trans.fill_template( "/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -602,7 +588,7 @@ class Library( BaseController ):
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else:
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msg = "you are not authorized to delete dataset '%s'" % ldda.name
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messagetype = 'error'
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return trans.fill_template( "/library/ldda_info.mako",
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return trans.fill_template( "/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -621,7 +607,7 @@ class Library( BaseController ):
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# case it resorts to the old dbkey. Setting the dbkey
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# sets it properly in the metadata
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ldda.metadata.dbkey = ldda.dbkey
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return trans.fill_template( "/library/ldda_info.mako",
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return trans.fill_template( "/library/ldda_edit_info.mako",
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ldda=ldda,
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library_id=library_id,
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datatypes=ldatatypes,
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@@ -1282,7 +1268,7 @@ class Library( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='error' ) )
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user = trans.get_user()
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@@ -1314,7 +1300,7 @@ class Library( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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return trans.fill_template( "/library/new_info.mako",
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@@ -1337,7 +1323,7 @@ class Library( BaseController ):
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id=library_item.id,
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library_id=library_id,
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folder_id=folder_id,
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information=True,
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edit_info=True,
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msg=util.sanitize_text( msg ),
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messagetype='done' ) )
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elif params.get( 'permissions', False ):
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@@ -74,7 +74,11 @@ def name_sorted( l ):
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<%def name="render_folder( parent, parent_pad, deleted, created_ldda_ids, library_id )">
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<%
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pad = parent_pad + 20
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root_folder = not parent.parent
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if root_folder:
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pad = parent_pad
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else:
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pad = parent_pad + 20
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if parent_pad == 0:
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expander = "/static/images/silk/resultset_bottom.png"
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folder = "/static/images/silk/folder_page.png"
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@@ -83,7 +87,6 @@ def name_sorted( l ):
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expander = "/static/images/silk/resultset_next.png"
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folder = "/static/images/silk/folder.png"
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subfolder = True
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root_folder = not parent.parent
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created_ldda_id_list = util.listify( created_ldda_ids )
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if created_ldda_id_list:
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created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ]
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@@ -208,9 +211,9 @@ def name_sorted( l ):
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## </div>
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%endif
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</th>
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<th width="100">Format</th>
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<th width="50">Db</th>
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<th width="200">Info</th>
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<th width="300">Information</th>
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<th width="150">Uploaded By</th>
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<th width="60">Date</th>
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</table>
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</div>
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</li>
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@@ -1,3 +1,5 @@
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<% from time import strftime %>
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<%def name="render_dataset( library_dataset, selected, library )">
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<%
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## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu
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@@ -5,6 +7,14 @@
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## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes
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## from the ldda.
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ldda = library_dataset.library_dataset_dataset_association
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if ldda.user:
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uploaded_by = ldda.user.email
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else:
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uploaded_by = 'anonymous'
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if ldda == ldda.library_dataset.library_dataset_dataset_association:
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current_version = True
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else:
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current_version = False
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%>
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<div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}">
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## Header row for library items (name, state, action buttons)
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@@ -17,7 +27,7 @@
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%else:
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<input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
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%endif
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<span class="historyItemTitle"><b>${ldda.name}</b></span>
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<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:50]}</b></a>
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%if not library.deleted:
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<%
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library_item_ids = {}
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@@ -25,11 +35,13 @@
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%>
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<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
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<div popupmenu="dataset-${ldda.id}-popup">
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<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">Edit this dataset's information</a>
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<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
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## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
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##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
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<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
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<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset', id=library_dataset.id, library_id=library.id, versions=True )}">Manage this dataset's versions</a>
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%if current_version:
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<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
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%endif
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%if ldda.has_data:
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<a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a>
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%endif
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@@ -38,46 +50,16 @@
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</div>
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%endif
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</td>
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<td width="100">${ldda.ext}</td>
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<td width="50"><span class="${ldda.dbkey}">${ldda.dbkey}</span></td>
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<td width="200">${ldda.info}</td>
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<td width="300">${ldda.message}</td>
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<td width="150">${uploaded_by}</td>
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<td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
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</tr>
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</table>
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</div>
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## Body for library items, extra info and actions, data "peek"
|
||||
<div id="info${ldda.id}" class="historyItemBody">
|
||||
<div>${ldda.blurb}</div>
|
||||
<div>
|
||||
%if ldda.has_data:
|
||||
%for display_app in ldda.datatype.get_display_types():
|
||||
<% display_links = ldda.datatype.get_display_links( ldda, display_app, app, request.base ) %>
|
||||
%if len( display_links ) > 0:
|
||||
${ldda.datatype.get_display_label(display_app)}
|
||||
%for ldda.name, display_link in display_links:
|
||||
<a target="_blank" href="${display_link}">${ldda.name}</a>
|
||||
%endfor
|
||||
%endif
|
||||
%endfor
|
||||
%endif
|
||||
</div>
|
||||
%if ldda.peek != "no peek":
|
||||
<div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
|
||||
%endif
|
||||
## Recurse for child datasets
|
||||
%if len( ldda.visible_children ) > 0:
|
||||
<div>
|
||||
There are ${len( ldda.visible_children )} secondary datasets.
|
||||
%for idx, child in enumerate( ldda.visible_children ):
|
||||
${ render_dataset( child, selected, library.deleted ) }
|
||||
%endfor
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<%def name="render_existing_library_item_info( library_item, library_id )">
|
||||
<%def name="render_library_item_info_for_edit( library_item, library_id )">
|
||||
<%
|
||||
library_item_type = 'unknown type'
|
||||
library_item_desc = ''
|
||||
@@ -123,7 +105,7 @@
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_item_info', library_id=library_id, id=element.id, library_item_type='library_item_info_elememt', permissions=True )}">Edit this information's permissions</a>
|
||||
</div>
|
||||
</label>
|
||||
<input type="text" name="info_element_${element.id}" value="${element.contents}" size="40"/>
|
||||
<textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
@@ -138,6 +120,55 @@
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_library_item_info( library_item, library_id )">
|
||||
<%
|
||||
library_item_type = 'unknown type'
|
||||
library_item_desc = ''
|
||||
library_item_info_associations = []
|
||||
if isinstance( library_item, trans.app.model.Library ):
|
||||
library_item_type = 'library'
|
||||
library_item_desc = 'library'
|
||||
library_item_info_associations = library_item.library_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryFolder ):
|
||||
library_item_type = 'folder'
|
||||
library_item_desc = 'folder'
|
||||
library_item_info_associations = library_item.library_folder_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryDataset ):
|
||||
library_item_type = 'library_dataset'
|
||||
library_item_desc = 'dataset'
|
||||
library_item_info_associations = library_item.library_dataset_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
|
||||
library_item_type = 'library_dataset_dataset_association'
|
||||
library_item_desc = 'library dataset'
|
||||
library_item_info_associations = library_item.library_dataset_dataset_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
|
||||
library_item_type = 'library_item_info'
|
||||
library_item_desc = 'information'
|
||||
library_item_info_associations = None
|
||||
%>
|
||||
%if library_item_info_associations:
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
|
||||
<div class="toolFormBody">
|
||||
%for library_item_info_association in library_item_info_associations:
|
||||
%for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
|
||||
<% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
|
||||
<div class="form-row">
|
||||
<label>${template_element.name}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${element.contents}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_available_templates( library_item, library_id, restrict=False, upload=False )">
|
||||
<%
|
||||
available_templates = library_item.get_library_item_info_templates( template_list=[], restrict=restrict )
|
||||
@@ -168,7 +199,7 @@
|
||||
<div class="toolFormBody">
|
||||
%for available_template in available_templates:
|
||||
%if upload in [ False, 'False' ]:
|
||||
# Only render a form if we're not within the upload form
|
||||
## Only render a form if we're not within the upload form
|
||||
<form name="add_template_info" action="${h.url_for( controller='admin', action='library_item_info', library_id=library_id, new_info=True )}" method="post">
|
||||
%endif
|
||||
<input type="hidden" name="library_item_id" value="${library_item.id}"/>
|
||||
@@ -178,7 +209,7 @@
|
||||
%for info_elem in available_template.elements:
|
||||
<div class="form-row">
|
||||
<label>${info_elem.name}</label>
|
||||
<input type="text" name="info_element_${available_template.id}_${info_elem.id}" value="" size="40"/>
|
||||
<textarea name="info_element_${available_template.id}_${info_elem.id}" rows="3" cols="35"></textarea>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${info_elem.description}
|
||||
</div>
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
@@ -39,7 +39,7 @@
|
||||
|
||||
<% folder.refresh() %>
|
||||
%if folder.library_folder_info_associations:
|
||||
${render_existing_library_item_info( folder, library_id )}
|
||||
${render_library_item_info_for_edit( folder, library_id )}
|
||||
%elif folder.library_folder_info_template_associations:
|
||||
${render_available_templates( folder, library_id, restrict=True )}
|
||||
%else:
|
||||
|
||||
@@ -0,0 +1,126 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
<% from galaxy import util %>
|
||||
|
||||
%if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
%endif
|
||||
<p/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if msg:
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<%def name="datatype( ldda, datatypes )">
|
||||
<select name="datatype">
|
||||
%for ext in datatypes:
|
||||
%if ldda.ext == ext:
|
||||
<option value="${ext}" selected="yes">${ext}</option>
|
||||
%else:
|
||||
<option value="${ext}">${ext}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_attributes" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<br/>
|
||||
<div class="form-row">
|
||||
<label>Name:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="name" value="${ldda.name}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Info:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="info" value="${ldda.info}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<div class="form-row">
|
||||
<label>${spec.desc}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.metadata.get_html_by_name( name )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
<form name="auto_detect" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="submit" name="detect" value="Auto-detect"/>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will inspect the dataset and attempt to correct the above column values if they are not accurate.
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change data type of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="change_datatype" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>New Type:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${datatype( ldda, datatypes )}
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will change the datatype of the existing dataset
|
||||
but <i>not</i> modify its contents. Use this if Galaxy
|
||||
has incorrectly guessed the type of your dataset.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<% ldda.refresh() %>
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_library_item_info_for_edit( ldda, library_id )}
|
||||
%elif ldda.library_dataset_dataset_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict=True )}
|
||||
%elif ldda.library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict='folder' )}
|
||||
%else:
|
||||
${render_available_templates( ldda, library_id, restrict=False )}
|
||||
%endif
|
||||
@@ -1,10 +1,17 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_library_item_info" />
|
||||
<% from galaxy import util %>
|
||||
|
||||
%if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
<%
|
||||
if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
current_version = True
|
||||
else:
|
||||
current_version = False
|
||||
%>
|
||||
|
||||
%if current_version:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
@@ -21,106 +28,101 @@
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<%def name="datatype( ldda, datatypes )">
|
||||
<select name="datatype">
|
||||
%for ext in datatypes:
|
||||
%if ldda.ext == ext:
|
||||
<option value="${ext}" selected="yes">${ext}</option>
|
||||
%else:
|
||||
<option value="${ext}">${ext}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
</%def>
|
||||
<%
|
||||
if ldda.user:
|
||||
uploaded_by = ldda.user.email
|
||||
else:
|
||||
uploaded_by = 'anonymous'
|
||||
%>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
|
||||
<div class="toolFormTitle">
|
||||
Information about ${ldda.name}
|
||||
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="dataset-${ldda.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
|
||||
## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
|
||||
##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
%if current_version:
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
%endif
|
||||
##TODO: need to revamp the way we remove datasets from disk.
|
||||
##<a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Remove this dataset from the library</a>
|
||||
</div>
|
||||
</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_attributes" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<br/>
|
||||
<div class="form-row">
|
||||
<label>Name:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="name" value="${ldda.name}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.message}
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Info:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="info" value="${ldda.info}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Uploaded by:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${uploaded_by}
|
||||
</div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<div class="form-row">
|
||||
<label>${spec.desc}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.metadata.get_html_by_name( name )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Date uploaded:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.create_time.strftime( "%Y-%m-%d" )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Build:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.dbkey}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Miscellaneous information:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.info}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div>${ldda.blurb}</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div id="info${ldda.id}" class="historyItemBody">
|
||||
%if ldda.peek != "no peek":
|
||||
<label>Peek:</lable>
|
||||
<div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
|
||||
%endif
|
||||
## Recurse for child datasets
|
||||
%if len( ldda.visible_children ) > 0:
|
||||
<div>
|
||||
There are ${len( ldda.visible_children )} secondary datasets.
|
||||
%for idx, child in enumerate( ldda.visible_children ):
|
||||
${ render_dataset( child, selected, library.deleted ) }
|
||||
%endfor
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_library_item_info( ldda, library_id )}
|
||||
%endif
|
||||
%if current_version:
|
||||
<% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
|
||||
%if expired_lddas:
|
||||
<div class="toolFormTitle">Expired versions of ${ldda.name}</div>
|
||||
%for expired_ldda in expired_lddas:
|
||||
<div class="form-row">
|
||||
<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a>
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
<form name="auto_detect" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="submit" name="detect" value="Auto-detect"/>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will inspect the dataset and attempt to correct the above column values if they are not accurate.
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change data type of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="change_datatype" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>New Type:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${datatype( ldda, datatypes )}
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will change the datatype of the existing dataset
|
||||
but <i>not</i> modify its contents. Use this if Galaxy
|
||||
has incorrectly guessed the type of your dataset.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<% ldda.refresh() %>
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_existing_library_item_info( ldda, library_id )}
|
||||
%elif ldda.library_dataset_dataset_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict=True )}
|
||||
%elif ldda.library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict='folder' )}
|
||||
%else:
|
||||
${render_available_templates( ldda, library_id, restrict=False )}
|
||||
%endif
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
%if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
@@ -48,7 +48,7 @@
|
||||
|
||||
<% library_dataset.refresh() %>
|
||||
%if library_dataset.library_dataset_info_associations:
|
||||
${render_existing_library_item_info( library_dataset, library_id )}
|
||||
${render_library_item_info_for_edit( library_dataset, library_id )}
|
||||
%elif library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( library_dataset, library_id, restrict='folder' )}
|
||||
%else:
|
||||
|
||||
@@ -1,55 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
%endif
|
||||
<p/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if msg:
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Set version of ${library_dataset.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="library_dataset_version" action="${h.url_for( controller='admin', action='library_dataset', id=library_dataset.id, library_id=library_id, versions=True )}" method="post">
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<div class="form-row">
|
||||
<input type="radio" name="set_lda_id" value="${library_dataset.library_dataset_dataset_association.id}" checked>${library_dataset.name} (current)
|
||||
<a id="dataset-${library_dataset.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="dataset-${library_dataset.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=library_dataset.library_dataset_dataset_association.id, information=True )}">Edit this dataset's information</a>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=library_dataset.library_dataset_dataset_association.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Replace this dataset with a new version</a>
|
||||
</div>
|
||||
%for ldda in library_dataset.expired_datasets:
|
||||
<br/>
|
||||
<input type="radio" name="set_lda_id" value="${ldda.id}" >${ldda.name}
|
||||
<a id="ldda-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="ldda-${ldda.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">Edit this dataset's information</a>
|
||||
<a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
</div>
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%if library_dataset.expired_datasets:
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change_version_button" value="Save"/>
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/admin/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
@@ -44,7 +44,7 @@
|
||||
|
||||
<% library.refresh() %>
|
||||
%if library.library_info_associations:
|
||||
${render_existing_library_item_info( library, library.id )}
|
||||
${render_library_item_info_for_edit( library, library.id )}
|
||||
%else:
|
||||
${render_available_templates( library, library.id, restrict=False )}
|
||||
%endif
|
||||
|
||||
@@ -125,7 +125,7 @@
|
||||
<textarea name="message" rows="3" cols="35"></textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
This information will be displayed in the "Information" column for this dataset in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
|
||||
@@ -113,7 +113,11 @@ def name_sorted( l ):
|
||||
return False
|
||||
if not show_folder:
|
||||
return ""
|
||||
pad = parent_pad + 20
|
||||
root_folder = not parent.parent
|
||||
if root_folder:
|
||||
pad = parent_pad
|
||||
else:
|
||||
pad = parent_pad + 20
|
||||
if parent_pad == 0:
|
||||
expander = "/static/images/silk/resultset_bottom.png"
|
||||
folder = "/static/images/silk/folder_page.png"
|
||||
@@ -122,7 +126,6 @@ def name_sorted( l ):
|
||||
expander = "/static/images/silk/resultset_next.png"
|
||||
folder = "/static/images/silk/folder.png"
|
||||
subfolder = True
|
||||
root_folder = not parent.parent
|
||||
created_ldda_id_list = util.listify( created_ldda_ids )
|
||||
if created_ldda_id_list:
|
||||
created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ]
|
||||
@@ -242,9 +245,9 @@ def name_sorted( l ):
|
||||
</div>
|
||||
</span>
|
||||
</th>
|
||||
<th width="100">Format</th>
|
||||
<th width="50">Db</th>
|
||||
<th width="200">Info</th>
|
||||
<th width="500">Information</th>
|
||||
<th width="150">Uploaded By</th>
|
||||
<th width="60">Date</th>
|
||||
</tr>
|
||||
</table>
|
||||
</div>
|
||||
|
||||
@@ -1,3 +1,5 @@
|
||||
<% from time import strftime %>
|
||||
|
||||
<%def name="render_dataset( library_dataset, selected, library )">
|
||||
<%
|
||||
## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu
|
||||
@@ -5,6 +7,14 @@
|
||||
## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes
|
||||
## from the ldda.
|
||||
ldda = library_dataset.library_dataset_dataset_association
|
||||
if ldda.user:
|
||||
uploaded_by = ldda.user.email
|
||||
else:
|
||||
uploaded_by = 'anonymous'
|
||||
if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
current_version = True
|
||||
else:
|
||||
current_version = False
|
||||
%>
|
||||
<div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}">
|
||||
## Header row for library items (name, state, action buttons)
|
||||
@@ -17,11 +27,11 @@
|
||||
%else:
|
||||
<input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
|
||||
%endif
|
||||
<span class="historyItemTitle"><b>${ldda.name}</b></span>
|
||||
<a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a>
|
||||
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="dataset-${ldda.id}-popup">
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">Edit this dataset's information</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
|
||||
%else:
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
|
||||
%endif
|
||||
@@ -31,8 +41,8 @@
|
||||
##%endif
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset', id=library_dataset.id, library_id=library.id, versions=True )}">Manage this dataset's versions</a>
|
||||
%if current_version and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
|
||||
%endif
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
@@ -41,48 +51,19 @@
|
||||
%endif
|
||||
</div>
|
||||
</td>
|
||||
<td width="100">${ldda.ext}</td>
|
||||
<td width="50"><span class="${ldda.dbkey}">${ldda.dbkey}</span></td>
|
||||
<td width="200">${ldda.info}</td>
|
||||
<td width="500">${ldda.message}</td>
|
||||
<td width="150">${uploaded_by}</td>
|
||||
<td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
|
||||
</tr>
|
||||
</table>
|
||||
</div>
|
||||
|
||||
## Body for library items, extra info and actions, data "peek"
|
||||
<div id="info${ldda.id}" class="historyItemBody">
|
||||
<div>${ldda.blurb}</div>
|
||||
<div>
|
||||
%if ldda.has_data:
|
||||
%for display_app in ldda.datatype.get_display_types():
|
||||
<% display_links = ldda.datatype.get_display_links( ldda, display_app, app, request.base ) %>
|
||||
%if len( display_links ) > 0:
|
||||
${ldda.datatype.get_display_label( display_app )}
|
||||
%for ldda.name, display_link in display_links:
|
||||
<a target="_blank" href="${display_link}">${ldda.name}</a>
|
||||
%endfor
|
||||
%endif
|
||||
%endfor
|
||||
%endif
|
||||
</div>
|
||||
%if ldda.peek != "no peek":
|
||||
<div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
|
||||
%endif
|
||||
## Recurse for child datasets
|
||||
%if len( ldda.visible_children ) > 0:
|
||||
<div>
|
||||
There are ${len( ldda.visible_children )} secondary datasets.
|
||||
%for idx, child in enumerate( ldda.visible_children ):
|
||||
${render_dataset( child, selected, library )}
|
||||
%endfor
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<%def name="render_existing_library_item_info( library_item, library_id )">
|
||||
<%def name="render_library_item_info_for_edit( library_item, library_id )">
|
||||
<%
|
||||
library_item_type = None
|
||||
library_item_type = 'unknown type'
|
||||
library_item_desc = ''
|
||||
library_item_info_associations = []
|
||||
if isinstance( library_item, trans.app.model.Library ):
|
||||
library_item_type = 'library'
|
||||
@@ -100,6 +81,10 @@
|
||||
library_item_type = 'library_dataset_dataset_association'
|
||||
library_item_desc = 'library dataset'
|
||||
library_item_info_associations = library_item.library_dataset_dataset_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
|
||||
library_item_type = 'library_item_info'
|
||||
library_item_desc = 'information'
|
||||
library_item_info_associations = None
|
||||
%>
|
||||
%if library_item_info_associations:
|
||||
<p/>
|
||||
@@ -132,7 +117,7 @@
|
||||
<label>${template_element.name}:</label>
|
||||
%endif
|
||||
%if can_modify:
|
||||
<input type="text" name="info_element_${element.id}" value="${element.contents}" size="40"/>
|
||||
<textarea name="info_element_${element.id}" rows="3" cols="35">${element.contents}</textarea>
|
||||
<% render_submit_button = True %>
|
||||
%else:
|
||||
${element.contents}
|
||||
@@ -153,6 +138,55 @@
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_library_item_info( library_item, library_id )">
|
||||
<%
|
||||
library_item_type = 'unknown type'
|
||||
library_item_desc = ''
|
||||
library_item_info_associations = []
|
||||
if isinstance( library_item, trans.app.model.Library ):
|
||||
library_item_type = 'library'
|
||||
library_item_desc = 'library'
|
||||
library_item_info_associations = library_item.library_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryFolder ):
|
||||
library_item_type = 'folder'
|
||||
library_item_desc = 'folder'
|
||||
library_item_info_associations = library_item.library_folder_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryDataset ):
|
||||
library_item_type = 'library_dataset'
|
||||
library_item_desc = 'dataset'
|
||||
library_item_info_associations = library_item.library_dataset_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryDatasetDatasetAssociation ):
|
||||
library_item_type = 'library_dataset_dataset_association'
|
||||
library_item_desc = 'library dataset'
|
||||
library_item_info_associations = library_item.library_dataset_dataset_info_associations
|
||||
elif isinstance( library_item, trans.app.model.LibraryItemInfoElement ):
|
||||
library_item_type = 'library_item_info'
|
||||
library_item_desc = 'information'
|
||||
library_item_info_associations = None
|
||||
%>
|
||||
%if library_item_info_associations:
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
|
||||
<div class="toolFormBody">
|
||||
%for library_item_info_association in library_item_info_associations:
|
||||
%for template_element in library_item_info_association.library_item_info.library_item_info_template.elements:
|
||||
<% element = library_item_info_association.library_item_info.get_element_by_template_element( template_element ) %>
|
||||
<div class="form-row">
|
||||
<label>${template_element.name}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${element.contents}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_available_templates( library_item, library_id, restrict=False, upload=False )">
|
||||
<%
|
||||
available_templates = library_item.get_library_item_info_templates( template_list=[], restrict=restrict )
|
||||
@@ -177,15 +211,14 @@
|
||||
library_item_ids[ 'library_id' ] = library_id
|
||||
%>
|
||||
%if available_templates:
|
||||
## There should only be 1 template here
|
||||
%for available_template in available_templates:
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=available_template ):
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
|
||||
<div class="toolFormBody">
|
||||
%for available_template in available_templates:
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=available_template ):
|
||||
%if upload in [ False, 'False' ]:
|
||||
# Only render a form if we're not within the upload form
|
||||
## Only render a form if we're not within the upload form
|
||||
<form name="add_template_info" action="${h.url_for( controller='library', action='library_item_info', library_id=library_id, new_info=True )}" method="post">
|
||||
%endif
|
||||
<input type="hidden" name="library_item_id" value="${library_item.id}"/>
|
||||
@@ -208,9 +241,9 @@
|
||||
</div>
|
||||
</form>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
%endfor
|
||||
%endif
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
@@ -57,7 +57,7 @@
|
||||
|
||||
<% folder.refresh() %>
|
||||
%if folder.library_folder_info_associations:
|
||||
${render_existing_library_item_info( folder, library_id )}
|
||||
${render_library_item_info_for_edit( folder, library_id )}
|
||||
%elif folder.library_folder_info_template_associations:
|
||||
${render_available_templates( folder, library_id, restrict=True )}
|
||||
%else:
|
||||
|
||||
@@ -0,0 +1,149 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
<% from galaxy import util %>
|
||||
|
||||
%if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
%endif
|
||||
<p/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if msg:
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<%def name="datatype( ldda, datatypes )">
|
||||
<select name="datatype">
|
||||
%for ext in datatypes:
|
||||
%if ldda.ext == ext:
|
||||
<option value="${ext}" selected="yes">${ext}</option>
|
||||
%else:
|
||||
<option value="${ext}">${ext}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
</%def>
|
||||
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_attributes" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>Name:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="name" value="${ldda.name}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Info:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="info" value="${ldda.info}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<div class="form-row">
|
||||
<label>${spec.desc}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.metadata.get_html_by_name( name )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
<form name="auto_detect" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="submit" name="detect" value="Auto-detect"/>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will inspect the dataset and attempt to correct the above column values if they are not accurate.
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change data type</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="change_datatype" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>New Type:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${datatype( ldda, datatypes )}
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will change the datatype of the existing dataset
|
||||
but <i>not</i> modify its contents. Use this if Galaxy
|
||||
has incorrectly guessed the type of your dataset.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
<p/>
|
||||
%else:
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">View attributes of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<div class="form-row">
|
||||
<b>Name:</b> ${ldda.name}
|
||||
<div style="clear: both"></div>
|
||||
<b>Info:</b> ${ldda.info}
|
||||
<div style="clear: both"></div>
|
||||
<b>Data Format:</b> ${ldda.ext}
|
||||
<div style="clear: both"></div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<b>${spec.desc}:</b>
|
||||
${ldda.metadata.get( name )}
|
||||
<div style="clear: both"></div>
|
||||
%endif
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<% ldda.refresh() %>
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_library_item_info_for_edit( ldda, library_id )}
|
||||
%elif ldda.library_dataset_dataset_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict=True )}
|
||||
%elif ldda.library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict='folder' )}
|
||||
%else:
|
||||
${render_available_templates( ldda, library_id, restrict=False )}
|
||||
%endif
|
||||
+107
-121
@@ -1,10 +1,17 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info" />
|
||||
<% from galaxy import util %>
|
||||
|
||||
%if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
<%
|
||||
if ldda == ldda.library_dataset.library_dataset_dataset_association:
|
||||
current_version = True
|
||||
else:
|
||||
current_version = False
|
||||
%>
|
||||
|
||||
%if current_version:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
@@ -21,129 +28,108 @@
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<%def name="datatype( ldda, datatypes )">
|
||||
<select name="datatype">
|
||||
%for ext in datatypes:
|
||||
%if ldda.ext == ext:
|
||||
<option value="${ext}" selected="yes">${ext}</option>
|
||||
%else:
|
||||
<option value="${ext}">${ext}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
</%def>
|
||||
<%
|
||||
if ldda.user:
|
||||
uploaded_by = ldda.user.email
|
||||
else:
|
||||
uploaded_by = 'anonymous'
|
||||
%>
|
||||
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_attributes" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>Name:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="name" value="${ldda.name}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Info:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="text" name="info" value="${ldda.info}" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<textarea name="message" rows="3" cols="35">${ldda.message}</textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<div class="form-row">
|
||||
<label>${spec.desc}:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.metadata.get_html_by_name( name )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
<form name="auto_detect" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="submit" name="detect" value="Auto-detect"/>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will inspect the dataset and attempt to correct the above column values if they are not accurate.
|
||||
</div>
|
||||
</form>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">
|
||||
Information about ${ldda.name}
|
||||
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="dataset-${ldda.id}-popup">
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
|
||||
%else:
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
|
||||
%endif
|
||||
## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
|
||||
##%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=ldda.library_dataset ):
|
||||
## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
|
||||
##%endif
|
||||
%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
%if current_version and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
|
||||
%endif
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library_id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
<p/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change data type</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="change_datatype" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, information=True )}" method="post">
|
||||
<input type="hidden" name="id" value="${ldda.id}"/>
|
||||
<div class="form-row">
|
||||
<label>New Type:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${datatype( ldda, datatypes )}
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This will change the datatype of the existing dataset
|
||||
but <i>not</i> modify its contents. Use this if Galaxy
|
||||
has incorrectly guessed the type of your dataset.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
<div class="toolFormBody">
|
||||
<div class="form-row">
|
||||
<label>Message:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.message}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
</div>
|
||||
<p/>
|
||||
%else:
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">View attributes of ${ldda.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<div class="form-row">
|
||||
<b>Name:</b> ${ldda.name}
|
||||
<div style="clear: both"></div>
|
||||
<b>Info:</b> ${ldda.info}
|
||||
<div style="clear: both"></div>
|
||||
<b>Data Format:</b> ${ldda.ext}
|
||||
<div style="clear: both"></div>
|
||||
%for name, spec in ldda.metadata.spec.items():
|
||||
%if spec.visible:
|
||||
<b>${spec.desc}:</b>
|
||||
${ldda.metadata.get( name )}
|
||||
<div style="clear: both"></div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<label>Uploaded by:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${uploaded_by}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Date uploaded:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.create_time.strftime( "%Y-%m-%d" )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Build:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.dbkey}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Miscellaneous information:</lable>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${ldda.info}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div>${ldda.blurb}</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div id="info${ldda.id}" class="historyItemBody">
|
||||
%if ldda.peek != "no peek":
|
||||
<label>Peek:</lable>
|
||||
<div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
|
||||
%endif
|
||||
## Recurse for child datasets
|
||||
%if len( ldda.visible_children ) > 0:
|
||||
<div>
|
||||
There are ${len( ldda.visible_children )} secondary datasets.
|
||||
%for idx, child in enumerate( ldda.visible_children ):
|
||||
${ render_dataset( child, selected, library.deleted ) }
|
||||
%endfor
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<% ldda.refresh() %>
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_existing_library_item_info( ldda, library_id )}
|
||||
%elif ldda.library_dataset_dataset_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict=True )}
|
||||
%elif ldda.library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( ldda, library_id, restrict='folder' )}
|
||||
%else:
|
||||
${render_available_templates( ldda, library_id, restrict=False )}
|
||||
%endif
|
||||
%if ldda.library_dataset_dataset_info_associations:
|
||||
${render_library_item_info( ldda, library_id )}
|
||||
%endif
|
||||
%if current_version:
|
||||
<% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
|
||||
%if expired_lddas:
|
||||
<div class="toolFormTitle">Expired versions of ${ldda.name}</div>
|
||||
%for expired_ldda in expired_lddas:
|
||||
<div class="form-row">
|
||||
<a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a>
|
||||
</div>
|
||||
%endfor
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
%if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
@@ -64,7 +64,7 @@
|
||||
|
||||
<% library_dataset.refresh() %>
|
||||
%if library_dataset.library_dataset_info_associations:
|
||||
${render_existing_library_item_info( library_dataset, library_id )}
|
||||
${render_library_item_info_for_edit( library_dataset, library_id )}
|
||||
%elif library_dataset.folder.library_folder_info_template_associations:
|
||||
${render_available_templates( library_dataset, library_id, restrict='folder' )}
|
||||
%else:
|
||||
|
||||
@@ -1,55 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset:
|
||||
<b><i>This is the latest version of this library dataset</i></b>
|
||||
%else:
|
||||
<font color="red"><b><i>This is an expired version of this library dataset</i></b></font>
|
||||
%endif
|
||||
<p/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this library</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if msg:
|
||||
${render_msg( msg, messagetype )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Set version of ${library_dataset.name}</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="library_dataset_version" action="${h.url_for( controller='library', action='library_dataset', id=library_dataset.id, library_id=library_id, versions=True )}" method="post">
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<div class="form-row">
|
||||
<input type="radio" name="set_lda_id" value="${library_dataset.library_dataset_dataset_association.id}" checked>${library_dataset.name} (current)
|
||||
<a id="dataset-${library_dataset.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="dataset-${library_dataset.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=library_dataset.library_dataset_dataset_association.id, information=True )}">Edit this dataset's information</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=library_dataset.library_dataset_dataset_association.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Replace this dataset with a new version</a>
|
||||
</div>
|
||||
%for ldda in library_dataset.expired_datasets:
|
||||
<br/>
|
||||
<input type="radio" name="set_lda_id" value="${ldda.id}" >${ldda.name}
|
||||
<a id="ldda-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="ldda-${ldda.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">Edit this dataset's information</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
</div>
|
||||
%endfor
|
||||
</div>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%if library_dataset.expired_datasets:
|
||||
<div class="form-row">
|
||||
<input type="submit" name="change_version_button" value="Save"/>
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
@@ -1,7 +1,7 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
@@ -60,7 +60,7 @@
|
||||
|
||||
<% library.refresh() %>
|
||||
%if library.library_info_associations:
|
||||
${render_existing_library_item_info( library, library.id )}
|
||||
${render_library_item_info_for_edit( library, library.id )}
|
||||
%else:
|
||||
${render_available_templates( library, library.id, restrict=False )}
|
||||
%endif
|
||||
|
||||
@@ -130,7 +130,7 @@
|
||||
<textarea name="message" rows="3" cols="35"></textarea>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
This information will be displayed in the library browser
|
||||
This information will be displayed in the "Information" column for this dataset in the library browser
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
|
||||
@@ -2,7 +2,7 @@
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/dataset/security_common.mako" import="render_permission_form" />
|
||||
<%namespace file="/library/common.mako" import="render_available_templates" />
|
||||
<%namespace file="/library/common.mako" import="render_existing_library_item_info" />
|
||||
<%namespace file="/library/common.mako" import="render_library_item_info_for_edit" />
|
||||
|
||||
%if msg:
|
||||
${render_msg( msg, messagetype )}
|
||||
@@ -50,7 +50,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div class="toolForm">
|
||||
${render_existing_library_item_info( library, library.id )}
|
||||
${render_library_item_info_for_edit( library, library.id )}
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
@@ -491,7 +491,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( "1.bed" )
|
||||
self.check_page_for_string( "hg18" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
def test_085_accessing_dataset_with_private_role_restriction( self ):
|
||||
"""Testing accessing a dataset with a private role restriction"""
|
||||
# admin_user should not be able to see 1.bed from the analysis view's access librarys
|
||||
@@ -571,14 +571,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( "2.bed" )
|
||||
self.check_page_for_string( "hg17" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
def test_095_accessing_datasets_with_role_restriction( self ):
|
||||
"""Testing accessing a dataset with a role restriction"""
|
||||
# admin_user should be able to see 2.bed since she is associated with role_two
|
||||
self.home()
|
||||
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( "2.bed" )
|
||||
self.check_page_for_string( "hg17" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
self.logout()
|
||||
# regular_user1 should be able to see 2.bed since she is associated with group_two
|
||||
self.login( email = 'test1@bx.psu.edu' )
|
||||
@@ -586,10 +586,10 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( folder_one.name )
|
||||
self.check_page_for_string( '2.bed' )
|
||||
self.check_page_for_string( "hg17" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
# Check the permissions on the dataset - should be 'access', which only allows viewing the information
|
||||
self.home()
|
||||
self.visit_url( '%s/library/library_dataset_dataset_association?information=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_two.id ) ) )
|
||||
self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_two.id ) ) )
|
||||
self.check_page_for_string( '2.bed' )
|
||||
self.check_page_for_string( 'This is the latest version of this library dataset' )
|
||||
self.check_page_for_string( 'View attributes of 2.bed' )
|
||||
@@ -653,7 +653,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
assert ldda_three is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_three from the database'
|
||||
self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
|
||||
self.check_page_for_string( "3.bed" )
|
||||
self.check_page_for_string( "hg16" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
self.logout()
|
||||
def test_105_access_public_library_dataset( self ):
|
||||
"""Testing accessing a public library dataset"""
|
||||
@@ -663,7 +663,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( library_one.name )
|
||||
self.check_page_for_string( '3.bed' )
|
||||
self.check_page_for_string( "hg16" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
self.logout()
|
||||
# regular_user2 should not be able to see 3.bed
|
||||
self.login( email = 'test2@bx.psu.edu' )
|
||||
@@ -671,7 +671,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( library_one.name )
|
||||
self.check_page_for_string( '3.bed' )
|
||||
self.check_page_for_string( "hg16" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
self.logout()
|
||||
# regular_user3 should not be able to see 3.bed
|
||||
self.login( email = 'test3@bx.psu.edu' )
|
||||
@@ -679,10 +679,10 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( library_one.name )
|
||||
self.check_page_for_string( '3.bed' )
|
||||
self.check_page_for_string( "hg16" )
|
||||
self.check_page_for_string( admin_user.email )
|
||||
# Test selecting "View this dataset's information"
|
||||
self.home()
|
||||
self.visit_url( '%s/library/library_dataset_dataset_association?information=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_three.id ) ) )
|
||||
self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' % ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_three.id ) ) )
|
||||
self.check_page_for_string( '3.bed' )
|
||||
self.check_page_for_string( 'This is the latest version of this library dataset' )
|
||||
self.check_page_for_string( 'View attributes of 3.bed' )
|
||||
|
||||
Reference in New Issue
Block a user