htsworkflow/frontend/experiments/admin.py

   1 from itertools import chain
   2 from htsworkflow.frontend.experiments.models import \
   3      FlowCell, 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 FlowCellOptions(admin.ModelAdmin):
 100     class Media:
 101         css = { 'all': ('css/admin_flowcell.css',) }
 102     date_hierarchy = "run_date"
 103     save_on_top = True
 104     search_fields = ('flowcell_id',
 105         'sequencer__name',
 106         'cluster_station__name',
 107         '=lane__library__id',
 108         'lane__library__library_name')
 109     list_display = ('flowcell_id','run_date','Lanes')
 110     list_filter = ('sequencer','cluster_station', 'paired_end')
 111     fieldsets = (
 112         (None, {
 113           'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
 114                     ('read_length', 'control_lane', 'paired_end'),)
 115         }),
 116         ('Notes:', { 'fields': ('notes',),}),
 117     )
 118     inlines = [
 119       LaneInline,
 120     ]
 121
 122     def formfield_for_dbfield(self, db_field, **kwargs):
 123         field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
 124                                                                    **kwargs)
 125
 126         # Override field attributes
 127         if db_field.name == 'sequencer':
 128             # seems kind of clunky.
 129             # the goal is to replace the default select/combo box with one
 130             # that can strike out disabled options.
 131             attrs = field.widget.widget.attrs
 132             field.widget.widget = SequencerSelect(attrs=attrs, queryset=field.queryset)
 133         elif db_field.name == "notes":
 134             field.widget.attrs["rows"] = "3"
 135         return field
 136 admin.site.register(FlowCell, FlowCellOptions)
 137
 138 class ClusterStationOptions(admin.ModelAdmin):
 139     list_display = ('name', 'isdefault',)
 140     fieldsets = ( ( None, { 'fields': ( 'name', 'isdefault') } ), )
 141 admin.site.register(ClusterStation, ClusterStationOptions)
 142
 143 class SequencerSelect(Select):
 144     def __init__(self, queryset=None, *args, **kwargs):
 145         super(SequencerSelect, self).__init__(*args, **kwargs)
 146         self.queryset = queryset
 147
 148     def render_options(self, choices, selected_choices):
 149         # Normalize to strings.
 150         selected_choices = set([force_unicode(v) for v in selected_choices])
 151         output = []
 152         for option_value, option_label in chain(self.choices, choices):
 153             if isinstance(option_label, (list, tuple)):
 154                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 155                 for option in option_label:
 156                     output.append(self.render_option(selected_choices, *option))
 157                 output.append(u'</optgroup>')
 158             else:
 159                 output.append(self.render_option(selected_choices, option_value, option_label))
 160         return u'\n'.join(output)
 161
 162     # render_options blatently grabbed from 1.3.1 as the 1.2 version
 163     # has render_option, which is what I needed to overload as a
 164     # nested function in render_options
 165     def render_options(self, choices, selected_choices):
 166         # Normalize to strings.
 167         selected_choices = set([force_unicode(v) for v in selected_choices])
 168         output = []
 169         for option_value, option_label in chain(self.choices, choices):
 170             if isinstance(option_label, (list, tuple)):
 171                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 172                 for option in option_label:
 173                     output.append(self.render_option(selected_choices, *option))
 174                 output.append(u'</optgroup>')
 175             else:
 176                 output.append(self.render_option(selected_choices, option_value, option_label))
 177         return u'\n'.join(output)
 178
 179
 180     def render_option(self, selected_choices, option_value, option_label):
 181         disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
 182         option_value = unicode(option_value)
 183         selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
 184         cssclass = "strikeout" if option_value in disabled_sequencers else ''
 185         return u'<option class="%s" value="%s"%s>%s</option>' % (
 186             cssclass, escape(option_value), selected_html,
 187             conditional_escape(force_unicode(option_label)))
 188
 189 class SequencerOptions(admin.ModelAdmin):
 190     list_display = ('name', 'active', 'isdefault', 'instrument_name', 'model')
 191     fieldsets = ( ( None,
 192                     { 'fields': (
 193                         'name', ('active', 'isdefault'), 'instrument_name', 'serial_number',
 194                         'model', 'comment') } ), )
 195
 196 admin.site.register(Sequencer, SequencerOptions)