htsworkflow/frontend/experiments/admin.py

   1 from itertools import chain
   2 from htsworkflow.frontend.experiments.models import \
   3      FlowCell, FlowCellModel, DataRun, DataFile, FileType, ClusterStation, Sequencer, Lane
   4 from django.contrib import admin
   5 from django.contrib.admin.widgets import FilteredSelectMultiple
   6 from django.forms import ModelForm
   7 from django.forms.fields import Field, CharField
   8 from django.forms.widgets import TextInput, Select
   9 from django.utils.encoding import force_unicode
  10 from django.utils.html import escape, conditional_escape
  11 from django.utils.translation import ugettext_lazy as _
  12
  13 class DataFileForm(ModelForm):
  14     class Meta:
  15         model = DataFile
  16
  17 class DataFileInline(admin.TabularInline):
  18     model = DataFile
  19     form = DataFileForm
  20     raw_id_fields = ('library',)
  21     extra = 0
  22
  23 class DataRunOptions(admin.ModelAdmin):
  24   search_fields = [
  25       'flowcell_id',
  26       'run_folder',
  27       'run_note',
  28       ]
  29   list_display = [
  30       'runfolder_name',
  31       'result_dir',
  32       'run_start_time',
  33   ]
  34   fieldsets = (
  35       (None, {
  36         'fields': (('flowcell', 'run_status'),
  37                    ('runfolder_name', 'cycle_start', 'cycle_stop'),
  38                    ('result_dir',),
  39                    ('last_update_time'),
  40                    ('image_software', 'image_version'),
  41                    ('basecall_software', 'basecall_version'),
  42                    ('alignment_software', 'alignment_version'),
  43                    ('comment',))
  44       }),
  45     )
  46   inlines = [ DataFileInline ]
  47   #list_filter = ('run_status', 'run_start_time')
  48 admin.site.register(DataRun, DataRunOptions)
  49
  50
  51 class FileTypeAdmin(admin.ModelAdmin):
  52     list_display = ('name', 'mimetype', 'regex')
  53 admin.site.register(FileType, FileTypeAdmin)
  54
  55 # lane form setup needs to come before Flowcell form config
  56 # as flowcell refers to the LaneInline class
  57 class LaneForm(ModelForm):
  58     comment = CharField(widget=TextInput(attrs={'size':'80'}), required=False)
  59
  60     class Meta:
  61         model = Lane
  62
  63 class LaneInline(admin.StackedInline):
  64     """
  65     Controls display of Lanes on the Flowcell form.
  66     """
  67     model = Lane
  68     extra = 8
  69     form = LaneForm
  70     raw_id_fields = ('library',)
  71     fieldsets = (
  72       (None, {
  73         'fields': ('lane_number', 'flowcell',
  74                    ('library',),
  75                    ('pM', 'cluster_estimate', 'status'),
  76                    'comment',)
  77       }),
  78     )
  79
  80 class LaneOptions(admin.ModelAdmin):
  81     """
  82     Controls display of Lane browser
  83     """
  84     search_fields = ('=flowcell__flowcell_id', 'library__id', 'library__library_name' )
  85     list_display = ('flowcell', 'lane_number', 'library', 'comment')
  86     fieldsets = (
  87       (None, {
  88         'fields': ('lane_number', 'flowcell',
  89                    ('library'),
  90                    ('pM', 'cluster_estimate'))
  91       }),
  92       ('Optional', {
  93         'classes': ('collapse', ),
  94         'fields': ('comment', )
  95       }),
  96     )
  97 admin.site.register(Lane, LaneOptions)
  98
  99 class FlowCellModelOptions(admin.ModelAdmin):
 100     search_fields = ('name',)
 101     list_display = ('name', 'fixed_time', 'per_cycle_time', 'isdefault')
 102     fieldsets = (
 103         (None, { 'fields': ('name', 'fixed_time', 'per_cycle_time', 'isdefault') }),
 104         )
 105 admin.site.register(FlowCellModel, FlowCellModelOptions)
 106
 107 class FlowCellOptions(admin.ModelAdmin):
 108     class Media:
 109         css = { 'all': ('css/admin_flowcell.css',) }
 110     date_hierarchy = "run_date"
 111     save_on_top = True
 112     search_fields = ('flowcell_id',
 113         'sequencer__name',
 114         'cluster_station__name',
 115         '=lane__library__id',
 116         'lane__library__library_name')
 117     list_display = ('flowcell_id','run_date','Lanes')
 118     list_filter = ('sequencer','cluster_station', 'paired_end')
 119     fieldsets = (
 120         (None, {
 121           'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
 122                     ('flowcell_model', 'read_length', 'paired_end', 'control_lane', ),)
 123         }),
 124         ('Notes:', { 'fields': ('notes',),}),
 125     )
 126     inlines = [
 127       LaneInline,
 128     ]
 129
 130     def formfield_for_dbfield(self, db_field, **kwargs):
 131         field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
 132                                                                    **kwargs)
 133
 134         # Override field attributes
 135         if db_field.name == 'sequencer':
 136             # seems kind of clunky.
 137             # the goal is to replace the default select/combo box with one
 138             # that can strike out disabled options.
 139             attrs = field.widget.widget.attrs
 140             field.widget.widget = SequencerSelect(attrs=attrs, queryset=field.queryset)
 141         elif db_field.name == "notes":
 142             field.widget.attrs["rows"] = "3"
 143         return field
 144 admin.site.register(FlowCell, FlowCellOptions)
 145
 146 class ClusterStationOptions(admin.ModelAdmin):
 147     list_display = ('name', 'isdefault',)
 148     fieldsets = ( ( None, { 'fields': ( 'name', 'isdefault') } ), )
 149 admin.site.register(ClusterStation, ClusterStationOptions)
 150
 151 class SequencerSelect(Select):
 152     def __init__(self, queryset=None, *args, **kwargs):
 153         super(SequencerSelect, self).__init__(*args, **kwargs)
 154         self.queryset = queryset
 155
 156     def render_options(self, choices, selected_choices):
 157         # Normalize to strings.
 158         selected_choices = set([force_unicode(v) for v in selected_choices])
 159         output = []
 160         for option_value, option_label in chain(self.choices, choices):
 161             if isinstance(option_label, (list, tuple)):
 162                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 163                 for option in option_label:
 164                     output.append(self.render_option(selected_choices, *option))
 165                 output.append(u'</optgroup>')
 166             else:
 167                 output.append(self.render_option(selected_choices, option_value, option_label))
 168         return u'\n'.join(output)
 169
 170     # render_options blatently grabbed from 1.3.1 as the 1.2 version
 171     # has render_option, which is what I needed to overload as a
 172     # nested function in render_options
 173     def render_options(self, choices, selected_choices):
 174         # Normalize to strings.
 175         selected_choices = set([force_unicode(v) for v in selected_choices])
 176         output = []
 177         for option_value, option_label in chain(self.choices, choices):
 178             if isinstance(option_label, (list, tuple)):
 179                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 180                 for option in option_label:
 181                     output.append(self.render_option(selected_choices, *option))
 182                 output.append(u'</optgroup>')
 183             else:
 184                 output.append(self.render_option(selected_choices, option_value, option_label))
 185         return u'\n'.join(output)
 186
 187
 188     def render_option(self, selected_choices, option_value, option_label):
 189         disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
 190         option_value = unicode(option_value)
 191         selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
 192         cssclass = "strikeout" if option_value in disabled_sequencers else ''
 193         return u'<option class="%s" value="%s"%s>%s</option>' % (
 194             cssclass, escape(option_value), selected_html,
 195             conditional_escape(force_unicode(option_label)))
 196
 197 class SequencerOptions(admin.ModelAdmin):
 198     list_display = ('name', 'active', 'isdefault', 'instrument_name', 'model')
 199     fieldsets = ( ( None,
 200                     { 'fields': (
 201                         'name', ('active', 'isdefault'), 'instrument_name', 'serial_number',
 202                         'model', 'comment') } ), )
 203
 204 admin.site.register(Sequencer, SequencerOptions)