1 | from galaxy import model |
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2 | from galaxy.model.item_attrs import * |
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3 | from galaxy.web.base.controller import * |
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4 | from galaxy.web.framework.helpers import time_ago, grids |
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5 | from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor |
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6 | from galaxy.util.odict import odict |
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7 | from galaxy.util.json import from_json_string |
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8 | |
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9 | def format_bool( b ): |
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10 | if b: |
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11 | return "yes" |
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12 | else: |
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13 | return "" |
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14 | |
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15 | class PageListGrid( grids.Grid ): |
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16 | # Custom column. |
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17 | class URLColumn( grids.PublicURLColumn ): |
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18 | def get_value( self, trans, grid, item ): |
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19 | return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) |
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20 | |
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21 | # Grid definition |
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22 | use_panels = True |
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23 | title = "Pages" |
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24 | model_class = model.Page |
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25 | default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } |
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26 | default_sort_key = "-create_time" |
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27 | columns = [ |
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28 | grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), |
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29 | URLColumn( "Public URL" ), |
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30 | grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), |
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31 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), |
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32 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), |
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33 | grids.GridColumn( "Created", key="create_time", format=time_ago ), |
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34 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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35 | ] |
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36 | columns.append( |
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37 | grids.MulticolFilterColumn( |
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38 | "Search", |
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39 | cols_to_filter=[ columns[0], columns[2] ], |
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40 | key="free-text-search", visible=False, filterable="standard" ) |
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41 | ) |
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42 | global_actions = [ |
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43 | grids.GridAction( "Add new page", dict( action='create' ) ) |
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44 | ] |
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45 | operations = [ |
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46 | grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ), |
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47 | grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), |
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48 | grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ), |
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49 | grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), |
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50 | grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ), |
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51 | ] |
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52 | def apply_query_filter( self, trans, query, **kwargs ): |
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53 | return query.filter_by( user=trans.user, deleted=False ) |
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54 | |
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55 | class PageAllPublishedGrid( grids.Grid ): |
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56 | # Grid definition |
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57 | use_panels = True |
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58 | use_async = True |
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59 | title = "Published Pages" |
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60 | model_class = model.Page |
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61 | default_sort_key = "update_time" |
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62 | default_filter = dict( title="All", username="All" ) |
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63 | columns = [ |
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64 | grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), |
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65 | grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), |
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66 | grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), |
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67 | grids.CommunityRatingColumn( "Community Rating", key="rating" ), |
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68 | grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), |
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69 | grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) |
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70 | ] |
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71 | columns.append( |
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72 | grids.MulticolFilterColumn( |
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73 | "Search", |
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74 | cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], |
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75 | key="free-text-search", visible=False, filterable="standard" ) |
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76 | ) |
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77 | def build_initial_query( self, trans, **kwargs ): |
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78 | # Join so that searching history.user makes sense. |
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79 | return trans.sa_session.query( self.model_class ).join( model.User.table ) |
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80 | def apply_query_filter( self, trans, query, **kwargs ): |
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81 | return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) |
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82 | |
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83 | class ItemSelectionGrid( grids.Grid ): |
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84 | """ Base class for pages' item selection grids. """ |
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85 | # Custom columns. |
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86 | class NameColumn( grids.TextColumn ): |
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87 | def get_value(self, trans, grid, item): |
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88 | if hasattr( item, "get_display_name" ): |
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89 | return item.get_display_name() |
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90 | else: |
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91 | return item.name |
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92 | |
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93 | # Grid definition. |
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94 | template = "/page/select_items_grid.mako" |
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95 | async_template = "/page/select_items_grid_async.mako" |
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96 | default_filter = { "deleted" : "False" , "sharing" : "All" } |
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97 | default_sort_key = "-update_time" |
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98 | use_async = True |
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99 | use_paging = True |
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100 | num_rows_per_page = 10 |
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101 | |
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102 | def apply_query_filter( self, trans, query, **kwargs ): |
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103 | return query.filter_by( user=trans.user ) |
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104 | |
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105 | class HistorySelectionGrid( ItemSelectionGrid ): |
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106 | """ Grid for selecting histories. """ |
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107 | # Grid definition. |
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108 | title = "Saved Histories" |
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109 | model_class = model.History |
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110 | columns = [ |
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111 | ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), |
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112 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), |
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113 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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114 | # Columns that are valid for filtering but are not visible. |
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115 | grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), |
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116 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), |
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117 | ] |
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118 | columns.append( |
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119 | grids.MulticolFilterColumn( |
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120 | "Search", |
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121 | cols_to_filter=[ columns[0], columns[1] ], |
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122 | key="free-text-search", visible=False, filterable="standard" ) |
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123 | ) |
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124 | |
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125 | def apply_query_filter( self, trans, query, **kwargs ): |
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126 | return query.filter_by( user=trans.user, purged=False ) |
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127 | |
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128 | class HistoryDatasetAssociationSelectionGrid( ItemSelectionGrid ): |
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129 | """ Grid for selecting HDAs. """ |
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130 | # Grid definition. |
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131 | title = "Saved Datasets" |
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132 | model_class = model.HistoryDatasetAssociation |
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133 | columns = [ |
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134 | ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), |
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135 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), |
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136 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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137 | # Columns that are valid for filtering but are not visible. |
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138 | grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), |
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139 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), |
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140 | ] |
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141 | columns.append( |
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142 | grids.MulticolFilterColumn( |
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143 | "Search", |
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144 | cols_to_filter=[ columns[0], columns[1] ], |
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145 | key="free-text-search", visible=False, filterable="standard" ) |
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146 | ) |
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147 | def apply_query_filter( self, trans, query, **kwargs ): |
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148 | # To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have |
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149 | # a user relation. |
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150 | return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user ) |
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151 | |
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152 | |
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153 | class WorkflowSelectionGrid( ItemSelectionGrid ): |
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154 | """ Grid for selecting workflows. """ |
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155 | # Grid definition. |
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156 | title = "Saved Workflows" |
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157 | model_class = model.StoredWorkflow |
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158 | columns = [ |
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159 | ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), |
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160 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), |
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161 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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162 | # Columns that are valid for filtering but are not visible. |
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163 | grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), |
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164 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), |
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165 | ] |
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166 | columns.append( |
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167 | grids.MulticolFilterColumn( |
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168 | "Search", |
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169 | cols_to_filter=[ columns[0], columns[1] ], |
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170 | key="free-text-search", visible=False, filterable="standard" ) |
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171 | ) |
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172 | |
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173 | class PageSelectionGrid( ItemSelectionGrid ): |
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174 | """ Grid for selecting pages. """ |
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175 | # Grid definition. |
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176 | title = "Saved Pages" |
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177 | model_class = model.Page |
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178 | columns = [ |
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179 | grids.TextColumn( "Title", key="title", filterable="advanced" ), |
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180 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"), |
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181 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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182 | # Columns that are valid for filtering but are not visible. |
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183 | grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), |
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184 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), |
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185 | ] |
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186 | columns.append( |
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187 | grids.MulticolFilterColumn( |
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188 | "Search", |
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189 | cols_to_filter=[ columns[0], columns[1] ], |
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190 | key="free-text-search", visible=False, filterable="standard" ) |
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191 | ) |
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192 | |
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193 | class VisualizationSelectionGrid( ItemSelectionGrid ): |
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194 | """ Grid for selecting visualizations. """ |
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195 | # Grid definition. |
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196 | title = "Saved Visualizations" |
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197 | model_class = model.Visualization |
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198 | columns = [ |
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199 | grids.TextColumn( "Title", key="title", filterable="advanced" ), |
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200 | grids.TextColumn( "Type", key="type" ), |
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201 | grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), |
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202 | grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), |
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203 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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204 | ] |
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205 | columns.append( |
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206 | grids.MulticolFilterColumn( |
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207 | "Search", |
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208 | cols_to_filter=[ columns[0], columns[2] ], |
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209 | key="free-text-search", visible=False, filterable="standard" ) |
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210 | ) |
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211 | |
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212 | class _PageContentProcessor( _BaseHTMLProcessor ): |
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213 | """ Processes page content to produce HTML that is suitable for display. For now, processor renders embedded objects. """ |
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214 | |
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215 | def __init__( self, trans, encoding, type, render_embed_html_fn ): |
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216 | _BaseHTMLProcessor.__init__( self, encoding, type) |
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217 | self.trans = trans |
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218 | self.ignore_content = False |
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219 | self.num_open_tags_for_ignore = 0 |
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220 | self.render_embed_html_fn = render_embed_html_fn |
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221 | |
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222 | def unknown_starttag( self, tag, attrs ): |
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223 | """ Called for each start tag; attrs is a list of (attr, value) tuples. """ |
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224 | |
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225 | # If ignoring content, just increment tag count and ignore. |
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226 | if self.ignore_content: |
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227 | self.num_open_tags_for_ignore += 1 |
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228 | return |
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229 | |
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230 | # Not ignoring tag; look for embedded content. |
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231 | embedded_item = False |
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232 | for attribute in attrs: |
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233 | if ( attribute[0] == "class" ) and ( "embedded-item" in attribute[1].split(" ") ): |
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234 | embedded_item = True |
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235 | break |
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236 | # For embedded content, set ignore flag to ignore current content and add new content for embedded item. |
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237 | if embedded_item: |
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238 | # Set processing attributes to ignore content. |
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239 | self.ignore_content = True |
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240 | self.num_open_tags_for_ignore = 1 |
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241 | |
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242 | # Insert content for embedded element. |
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243 | for attribute in attrs: |
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244 | name = attribute[0] |
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245 | if name == "id": |
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246 | # ID has form '<class_name>-<encoded_item_id>' |
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247 | item_class, item_id = attribute[1].split("-") |
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248 | embed_html = self.render_embed_html_fn( self.trans, item_class, item_id ) |
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249 | self.pieces.append( embed_html ) |
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250 | return |
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251 | |
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252 | # Default behavior: not ignoring and no embedded content. |
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253 | _BaseHTMLProcessor.unknown_starttag( self, tag, attrs ) |
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254 | |
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255 | def handle_data( self, text ): |
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256 | """ Called for each block of plain text. """ |
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257 | if self.ignore_content: |
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258 | return |
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259 | _BaseHTMLProcessor.handle_data( self, text ) |
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260 | |
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261 | def unknown_endtag( self, tag ): |
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262 | """ Called for each end tag. """ |
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263 | |
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264 | # If ignoring content, see if current tag is the end of content to ignore. |
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265 | if self.ignore_content: |
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266 | self.num_open_tags_for_ignore -= 1 |
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267 | if self.num_open_tags_for_ignore == 0: |
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268 | # Done ignoring content. |
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269 | self.ignore_content = False |
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270 | return |
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271 | |
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272 | # Default behavior: |
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273 | _BaseHTMLProcessor.unknown_endtag( self, tag ) |
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274 | |
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275 | class PageController( BaseController, Sharable, UsesAnnotations, UsesHistory, |
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276 | UsesStoredWorkflow, UsesHistoryDatasetAssociation, UsesVisualization, UsesItemRatings ): |
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277 | |
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278 | _page_list = PageListGrid() |
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279 | _all_published_list = PageAllPublishedGrid() |
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280 | _history_selection_grid = HistorySelectionGrid() |
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281 | _workflow_selection_grid = WorkflowSelectionGrid() |
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282 | _datasets_selection_grid = HistoryDatasetAssociationSelectionGrid() |
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283 | _page_selection_grid = PageSelectionGrid() |
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284 | _visualization_selection_grid = VisualizationSelectionGrid() |
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285 | |
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286 | @web.expose |
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287 | @web.require_login() |
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288 | def list( self, trans, *args, **kwargs ): |
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289 | """ List user's pages. """ |
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290 | # Handle operation |
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291 | if 'operation' in kwargs and 'id' in kwargs: |
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292 | session = trans.sa_session |
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293 | operation = kwargs['operation'].lower() |
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294 | ids = util.listify( kwargs['id'] ) |
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295 | for id in ids: |
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296 | item = session.query( model.Page ).get( trans.security.decode_id( id ) ) |
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297 | if operation == "delete": |
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298 | item.deleted = True |
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299 | if operation == "share or publish": |
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300 | return self.sharing( trans, **kwargs ) |
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301 | session.flush() |
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302 | |
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303 | # Build grid HTML. |
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304 | grid = self._page_list( trans, *args, **kwargs ) |
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305 | |
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306 | # Build list of pages shared with user. |
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307 | shared_by_others = trans.sa_session \ |
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308 | .query( model.PageUserShareAssociation ) \ |
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309 | .filter_by( user=trans.get_user() ) \ |
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310 | .join( model.Page.table ) \ |
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311 | .filter( model.Page.deleted == False ) \ |
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312 | .order_by( desc( model.Page.update_time ) ) \ |
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313 | .all() |
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314 | |
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315 | # Render grid wrapped in panels |
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316 | return trans.fill_template( "page/index.mako", grid=grid, shared_by_others=shared_by_others ) |
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317 | |
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318 | @web.expose |
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319 | def list_published( self, trans, *args, **kwargs ): |
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320 | grid = self._all_published_list( trans, *args, **kwargs ) |
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321 | if 'async' in kwargs: |
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322 | return grid |
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323 | else: |
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324 | # Render grid wrapped in panels |
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325 | return trans.fill_template( "page/list_published.mako", grid=grid ) |
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326 | |
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327 | |
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328 | @web.expose |
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329 | @web.require_login( "create pages" ) |
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330 | def create( self, trans, page_title="", page_slug="", page_annotation="" ): |
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331 | """ |
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332 | Create a new page |
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333 | """ |
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334 | user = trans.get_user() |
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335 | page_title_err = page_slug_err = page_annotation_err = "" |
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336 | if trans.request.method == "POST": |
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337 | if not page_title: |
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338 | page_title_err = "Page name is required" |
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339 | elif not page_slug: |
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340 | page_slug_err = "Page id is required" |
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341 | elif not VALID_SLUG_RE.match( page_slug ): |
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342 | page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" |
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343 | elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): |
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344 | page_slug_err = "Page id must be unique" |
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345 | else: |
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346 | # Create the new stored page |
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347 | page = model.Page() |
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348 | page.title = page_title |
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349 | page.slug = page_slug |
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350 | page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' ) |
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351 | self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) |
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352 | page.user = user |
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353 | # And the first (empty) page revision |
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354 | page_revision = model.PageRevision() |
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355 | page_revision.title = page_title |
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356 | page_revision.page = page |
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357 | page.latest_revision = page_revision |
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358 | page_revision.content = "" |
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359 | # Persist |
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360 | session = trans.sa_session |
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361 | session.add( page ) |
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362 | session.flush() |
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363 | # Display the management page |
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364 | ## trans.set_message( "Page '%s' created" % page.title ) |
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365 | return trans.response.send_redirect( web.url_for( action='list' ) ) |
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366 | return trans.show_form( |
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367 | web.FormBuilder( web.url_for(), "Create new page", submit_text="Submit" ) |
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368 | .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) |
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369 | .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, |
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370 | help="""A unique identifier that will be used for |
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371 | public links to this page. A default is generated |
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372 | from the page title, but can be edited. This field |
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373 | must contain only lowercase letters, numbers, and |
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374 | the '-' character.""" ) |
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375 | .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, |
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376 | help="A description of the page; annotation is shown alongside published pages."), |
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377 | template="page/create.mako" ) |
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378 | |
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379 | @web.expose |
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380 | @web.require_login( "edit pages" ) |
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381 | def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ): |
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382 | """ |
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383 | Edit a page's attributes. |
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384 | """ |
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385 | encoded_id = id |
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386 | id = trans.security.decode_id( id ) |
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387 | session = trans.sa_session |
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388 | page = session.query( model.Page ).get( id ) |
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389 | user = trans.user |
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390 | assert page.user == user |
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391 | page_title_err = page_slug_err = page_annotation_err = "" |
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392 | if trans.request.method == "POST": |
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393 | if not page_title: |
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394 | page_title_err = "Page name is required" |
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395 | elif not page_slug: |
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396 | page_slug_err = "Page id is required" |
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397 | elif not VALID_SLUG_RE.match( page_slug ): |
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398 | page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" |
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399 | elif page_slug != page.slug and trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): |
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400 | page_slug_err = "Page id must be unique" |
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401 | elif not page_annotation: |
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402 | page_annotation_err = "Page annotation is required" |
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403 | else: |
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404 | page.title = page_title |
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405 | page.slug = page_slug |
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406 | page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' ) |
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407 | self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) |
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408 | session.flush() |
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409 | # Redirect to page list. |
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410 | return trans.response.send_redirect( web.url_for( action='list' ) ) |
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411 | else: |
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412 | page_title = page.title |
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413 | page_slug = page.slug |
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414 | page_annotation = self.get_item_annotation_str( trans.sa_session, trans.user, page ) |
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415 | if not page_annotation: |
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416 | page_annotation = "" |
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417 | return trans.show_form( |
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418 | web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" ) |
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419 | .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) |
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420 | .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, |
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421 | help="""A unique identifier that will be used for |
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422 | public links to this page. A default is generated |
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423 | from the page title, but can be edited. This field |
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424 | must contain only lowercase letters, numbers, and |
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425 | the '-' character.""" ) |
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426 | .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, |
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427 | help="A description of the page; annotation is shown alongside published pages."), |
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428 | template="page/create.mako" ) |
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429 | |
---|
430 | @web.expose |
---|
431 | @web.require_login( "edit pages" ) |
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432 | def edit_content( self, trans, id ): |
---|
433 | """ |
---|
434 | Render the main page editor interface. |
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435 | """ |
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436 | id = trans.security.decode_id( id ) |
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437 | page = trans.sa_session.query( model.Page ).get( id ) |
---|
438 | assert page.user == trans.user |
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439 | return trans.fill_template( "page/editor.mako", page=page ) |
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440 | |
---|
441 | @web.expose |
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442 | @web.require_login( "use Galaxy pages" ) |
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443 | def sharing( self, trans, id, **kwargs ): |
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444 | """ Handle page sharing. """ |
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445 | |
---|
446 | # Get session and page. |
---|
447 | session = trans.sa_session |
---|
448 | page = trans.sa_session.query( model.Page ).get( trans.security.decode_id( id ) ) |
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449 | |
---|
450 | # Do operation on page. |
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451 | if 'make_accessible_via_link' in kwargs: |
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452 | self._make_item_accessible( trans.sa_session, page ) |
---|
453 | elif 'make_accessible_and_publish' in kwargs: |
---|
454 | self._make_item_accessible( trans.sa_session, page ) |
---|
455 | page.published = True |
---|
456 | elif 'publish' in kwargs: |
---|
457 | page.published = True |
---|
458 | elif 'disable_link_access' in kwargs: |
---|
459 | page.importable = False |
---|
460 | elif 'unpublish' in kwargs: |
---|
461 | page.published = False |
---|
462 | elif 'disable_link_access_and_unpublish' in kwargs: |
---|
463 | page.importable = page.published = False |
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464 | elif 'unshare_user' in kwargs: |
---|
465 | user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) |
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466 | if not user: |
---|
467 | error( "User not found for provided id" ) |
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468 | association = session.query( model.PageUserShareAssociation ) \ |
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469 | .filter_by( user=user, page=page ).one() |
---|
470 | session.delete( association ) |
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471 | |
---|
472 | session.flush() |
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473 | |
---|
474 | return trans.fill_template( "/sharing_base.mako", |
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475 | item=page, use_panels=True ) |
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476 | |
---|
477 | @web.expose |
---|
478 | @web.require_login( "use Galaxy pages" ) |
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479 | def share( self, trans, id, email="", use_panels=False ): |
---|
480 | """ Handle sharing with an individual user. """ |
---|
481 | msg = mtype = None |
---|
482 | page = trans.sa_session.query( model.Page ).get( trans.security.decode_id( id ) ) |
---|
483 | if email: |
---|
484 | other = trans.sa_session.query( model.User ) \ |
---|
485 | .filter( and_( model.User.table.c.email==email, |
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486 | model.User.table.c.deleted==False ) ) \ |
---|
487 | .first() |
---|
488 | if not other: |
---|
489 | mtype = "error" |
---|
490 | msg = ( "User '%s' does not exist" % email ) |
---|
491 | elif other == trans.get_user(): |
---|
492 | mtype = "error" |
---|
493 | msg = ( "You cannot share a page with yourself" ) |
---|
494 | elif trans.sa_session.query( model.PageUserShareAssociation ) \ |
---|
495 | .filter_by( user=other, page=page ).count() > 0: |
---|
496 | mtype = "error" |
---|
497 | msg = ( "Page already shared with '%s'" % email ) |
---|
498 | else: |
---|
499 | share = model.PageUserShareAssociation() |
---|
500 | share.page = page |
---|
501 | share.user = other |
---|
502 | session = trans.sa_session |
---|
503 | session.add( share ) |
---|
504 | self.create_item_slug( session, page ) |
---|
505 | session.flush() |
---|
506 | trans.set_message( "Page '%s' shared with user '%s'" % ( page.title, other.email ) ) |
---|
507 | return trans.response.send_redirect( url_for( controller='page', action='sharing', id=id ) ) |
---|
508 | return trans.fill_template( "/ind_share_base.mako", |
---|
509 | message = msg, |
---|
510 | messagetype = mtype, |
---|
511 | item=page, |
---|
512 | email=email, |
---|
513 | use_panels=use_panels ) |
---|
514 | |
---|
515 | @web.expose |
---|
516 | @web.require_login() |
---|
517 | def save( self, trans, id, content, annotations ): |
---|
518 | id = trans.security.decode_id( id ) |
---|
519 | page = trans.sa_session.query( model.Page ).get( id ) |
---|
520 | assert page.user == trans.user |
---|
521 | |
---|
522 | # Sanitize content |
---|
523 | content = sanitize_html( content, 'utf-8', 'text/html' ) |
---|
524 | |
---|
525 | # Add a new revision to the page with the provided content. |
---|
526 | page_revision = model.PageRevision() |
---|
527 | page_revision.title = page.title |
---|
528 | page_revision.page = page |
---|
529 | page.latest_revision = page_revision |
---|
530 | page_revision.content = content |
---|
531 | |
---|
532 | # Save annotations. |
---|
533 | annotations = from_json_string( annotations ) |
---|
534 | for annotation_dict in annotations: |
---|
535 | item_id = trans.security.decode_id( annotation_dict[ 'item_id' ] ) |
---|
536 | item_class = self.get_class( trans, annotation_dict[ 'item_class' ] ) |
---|
537 | item = trans.sa_session.query( item_class ).filter_by( id=item_id ).first() |
---|
538 | if not item: |
---|
539 | raise RuntimeError( "cannot find annotated item" ) |
---|
540 | text = sanitize_html( annotation_dict[ 'text' ], 'utf-8', 'text/html' ) |
---|
541 | |
---|
542 | # Add/update annotation. |
---|
543 | if item_id and item_class and text: |
---|
544 | # Get annotation association. |
---|
545 | annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item_class.__name__ ) |
---|
546 | annotation_assoc = trans.sa_session.query( annotation_assoc_class ).filter_by( user=trans.get_user() ) |
---|
547 | if item_class == model.History.__class__: |
---|
548 | annotation_assoc = annotation_assoc.filter_by( history=item ) |
---|
549 | elif item_class == model.HistoryDatasetAssociation.__class__: |
---|
550 | annotation_assoc = annotation_assoc.filter_by( hda=item ) |
---|
551 | elif item_class == model.StoredWorkflow.__class__: |
---|
552 | annotation_assoc = annotation_assoc.filter_by( stored_workflow=item ) |
---|
553 | elif item_class == model.WorkflowStep.__class__: |
---|
554 | annotation_assoc = annotation_assoc.filter_by( workflow_step=item ) |
---|
555 | annotation_assoc = annotation_assoc.first() |
---|
556 | if not annotation_assoc: |
---|
557 | # Create association. |
---|
558 | annotation_assoc = annotation_assoc_class() |
---|
559 | item.annotations.append( annotation_assoc ) |
---|
560 | annotation_assoc.user = trans.get_user() |
---|
561 | # Set annotation user text. |
---|
562 | annotation_assoc.annotation = text |
---|
563 | trans.sa_session.flush() |
---|
564 | |
---|
565 | @web.expose |
---|
566 | @web.require_login() |
---|
567 | def display( self, trans, id ): |
---|
568 | id = trans.security.decode_id( id ) |
---|
569 | page = trans.sa_session.query( model.Page ).get( id ) |
---|
570 | if not page: |
---|
571 | raise web.httpexceptions.HTTPNotFound() |
---|
572 | return self.display_by_username_and_slug( trans, page.user.username, page.slug ) |
---|
573 | |
---|
574 | @web.expose |
---|
575 | def display_by_username_and_slug( self, trans, username, slug ): |
---|
576 | """ Display page based on a username and slug. """ |
---|
577 | |
---|
578 | # Get page. |
---|
579 | session = trans.sa_session |
---|
580 | user = session.query( model.User ).filter_by( username=username ).first() |
---|
581 | page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False ).first() |
---|
582 | if page is None: |
---|
583 | raise web.httpexceptions.HTTPNotFound() |
---|
584 | # Security check raises error if user cannot access page. |
---|
585 | self.security_check( trans.get_user(), page, False, True) |
---|
586 | |
---|
587 | # Process page content. |
---|
588 | processor = _PageContentProcessor( trans, 'utf-8', 'text/html', self._get_embed_html ) |
---|
589 | processor.feed( page.latest_revision.content ) |
---|
590 | |
---|
591 | # Get rating data. |
---|
592 | user_item_rating = 0 |
---|
593 | if trans.get_user(): |
---|
594 | user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), page ) |
---|
595 | if user_item_rating: |
---|
596 | user_item_rating = user_item_rating.rating |
---|
597 | else: |
---|
598 | user_item_rating = 0 |
---|
599 | ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, page ) |
---|
600 | |
---|
601 | # Output is string, so convert to unicode for display. |
---|
602 | page_content = unicode( processor.output(), 'utf-8' ) |
---|
603 | return trans.fill_template_mako( "page/display.mako", item=page, item_data=page_content, |
---|
604 | user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings, |
---|
605 | content_only=True ) |
---|
606 | |
---|
607 | @web.expose |
---|
608 | @web.require_login( "use Galaxy pages" ) |
---|
609 | def set_accessible_async( self, trans, id=None, accessible=False ): |
---|
610 | """ Set page's importable attribute and slug. """ |
---|
611 | page = self.get_page( trans, id ) |
---|
612 | |
---|
613 | # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed. |
---|
614 | importable = accessible in ['True', 'true', 't', 'T']; |
---|
615 | if page.importable != importable: |
---|
616 | if importable: |
---|
617 | self._make_item_accessible( trans.sa_session, page ) |
---|
618 | else: |
---|
619 | page.importable = importable |
---|
620 | trans.sa_session.flush() |
---|
621 | return |
---|
622 | |
---|
623 | @web.expose |
---|
624 | @web.require_login( "modify Galaxy items" ) |
---|
625 | def set_slug_async( self, trans, id, new_slug ): |
---|
626 | page = self.get_page( trans, id ) |
---|
627 | if page: |
---|
628 | page.slug = new_slug |
---|
629 | trans.sa_session.flush() |
---|
630 | return page.slug |
---|
631 | |
---|
632 | @web.expose |
---|
633 | @web.require_login( "rate items" ) |
---|
634 | @web.json |
---|
635 | def rate_async( self, trans, id, rating ): |
---|
636 | """ Rate a page asynchronously and return updated community data. """ |
---|
637 | |
---|
638 | page = self.get_page( trans, id, check_ownership=False, check_accessible=True ) |
---|
639 | if not page: |
---|
640 | return trans.show_error_message( "The specified page does not exist." ) |
---|
641 | |
---|
642 | # Rate page. |
---|
643 | page_rating = self.rate_item( trans.sa_session, trans.get_user(), page, rating ) |
---|
644 | |
---|
645 | return self.get_ave_item_rating_data( trans.sa_session, page ) |
---|
646 | |
---|
647 | @web.expose |
---|
648 | def get_embed_html_async( self, trans, id ): |
---|
649 | """ Returns HTML for embedding a workflow in a page. """ |
---|
650 | |
---|
651 | # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code. |
---|
652 | page = self.get_page( trans, id ) |
---|
653 | if page: |
---|
654 | return "Embedded Page '%s'" % page.title |
---|
655 | |
---|
656 | @web.expose |
---|
657 | @web.json |
---|
658 | @web.require_login( "use Galaxy pages" ) |
---|
659 | def get_name_and_link_async( self, trans, id=None ): |
---|
660 | """ Returns page's name and link. """ |
---|
661 | page = self.get_page( trans, id ) |
---|
662 | |
---|
663 | if self.create_item_slug( trans.sa_session, page ): |
---|
664 | trans.sa_session.flush() |
---|
665 | return_dict = { "name" : page.title, "link" : url_for( action="display_by_username_and_slug", username=page.user.username, slug=page.slug ) } |
---|
666 | return return_dict |
---|
667 | |
---|
668 | @web.expose |
---|
669 | @web.require_login("select a history from saved histories") |
---|
670 | def list_histories_for_selection( self, trans, **kwargs ): |
---|
671 | """ Returns HTML that enables a user to select one or more histories. """ |
---|
672 | # Render the list view |
---|
673 | return self._history_selection_grid( trans, **kwargs ) |
---|
674 | |
---|
675 | @web.expose |
---|
676 | @web.require_login("select a workflow from saved workflows") |
---|
677 | def list_workflows_for_selection( self, trans, **kwargs ): |
---|
678 | """ Returns HTML that enables a user to select one or more workflows. """ |
---|
679 | # Render the list view |
---|
680 | return self._workflow_selection_grid( trans, **kwargs ) |
---|
681 | |
---|
682 | @web.expose |
---|
683 | @web.require_login("select a visualization from saved visualizations") |
---|
684 | def list_visualizations_for_selection( self, trans, **kwargs ): |
---|
685 | """ Returns HTML that enables a user to select one or more visualizations. """ |
---|
686 | # Render the list view |
---|
687 | return self._visualization_selection_grid( trans, **kwargs ) |
---|
688 | |
---|
689 | @web.expose |
---|
690 | @web.require_login("select a page from saved pages") |
---|
691 | def list_pages_for_selection( self, trans, **kwargs ): |
---|
692 | """ Returns HTML that enables a user to select one or more pages. """ |
---|
693 | # Render the list view |
---|
694 | return self._page_selection_grid( trans, **kwargs ) |
---|
695 | |
---|
696 | @web.expose |
---|
697 | @web.require_login("select a dataset from saved datasets") |
---|
698 | def list_datasets_for_selection( self, trans, **kwargs ): |
---|
699 | """ Returns HTML that enables a user to select one or more datasets. """ |
---|
700 | # Render the list view |
---|
701 | return self._datasets_selection_grid( trans, **kwargs ) |
---|
702 | |
---|
703 | @web.expose |
---|
704 | @web.require_login("get annotation table for history") |
---|
705 | def get_history_annotation_table( self, trans, id ): |
---|
706 | """ Returns HTML for an annotation table for a history. """ |
---|
707 | history = self.get_history( trans, id, False, True ) |
---|
708 | |
---|
709 | if history: |
---|
710 | datasets = self.get_history_datasets( trans, history ) |
---|
711 | return trans.fill_template( "page/history_annotation_table.mako", history=history, datasets=datasets, show_deleted=False ) |
---|
712 | |
---|
713 | @web.expose |
---|
714 | def get_editor_iframe( self, trans ): |
---|
715 | """ Returns the document for the page editor's iframe. """ |
---|
716 | return trans.fill_template( "page/wymiframe.mako" ) |
---|
717 | |
---|
718 | def get_page( self, trans, id, check_ownership=True, check_accessible=False ): |
---|
719 | """Get a page from the database by id, verifying ownership.""" |
---|
720 | # Load history from database |
---|
721 | id = trans.security.decode_id( id ) |
---|
722 | page = trans.sa_session.query( model.Page ).get( id ) |
---|
723 | if not page: |
---|
724 | err+msg( "Page not found" ) |
---|
725 | else: |
---|
726 | return self.security_check( trans.get_user(), page, check_ownership, check_accessible ) |
---|
727 | |
---|
728 | def _get_embed_html( self, trans, item_class, item_id ): |
---|
729 | """ Returns HTML for embedding an item in a page. """ |
---|
730 | item_class = self.get_class( trans, item_class ) |
---|
731 | if item_class == model.History: |
---|
732 | history = self.get_history( trans, item_id, False, True ) |
---|
733 | history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) |
---|
734 | if history: |
---|
735 | datasets = self.get_history_datasets( trans, history ) |
---|
736 | return trans.fill_template( "history/embed.mako", item=history, item_data=datasets ) |
---|
737 | elif item_class == model.HistoryDatasetAssociation: |
---|
738 | dataset = self.get_dataset( trans, item_id, False, True ) |
---|
739 | dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) |
---|
740 | if dataset: |
---|
741 | data = self.get_data( dataset ) |
---|
742 | return trans.fill_template( "dataset/embed.mako", item=dataset, item_data=data ) |
---|
743 | elif item_class == model.StoredWorkflow: |
---|
744 | workflow = self.get_stored_workflow( trans, item_id, False, True ) |
---|
745 | workflow.annotation = self.get_item_annotation_str( trans.sa_session, workflow.user, workflow ) |
---|
746 | if workflow: |
---|
747 | self.get_stored_workflow_steps( trans, workflow ) |
---|
748 | return trans.fill_template( "workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps ) |
---|
749 | elif item_class == model.Visualization: |
---|
750 | visualization = self.get_visualization( trans, item_id, False, True ) |
---|
751 | visualization.annotation = self.get_item_annotation_str( trans.sa_session, visualization.user, visualization ) |
---|
752 | if visualization: |
---|
753 | return trans.fill_template( "visualization/embed.mako", item=visualization, item_data=None ) |
---|
754 | |
---|
755 | elif item_class == model.Page: |
---|
756 | pass |
---|
757 | |
---|
758 | |
---|
759 | |
---|