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', 'regex_is_valid')
  53     fieldsets = (
  54         (None, {
  55             'fields': (('name', 'mimetype'),
  56                        ('regex'))
  57             }
  58         )),
  59 admin.site.register(FileType, FileTypeAdmin)
  60
  61 # lane form setup needs to come before Flowcell form config
  62 # as flowcell refers to the LaneInline class
  63 class LaneForm(ModelForm):
  64     comment = CharField(widget=TextInput(attrs={'size':'80'}), required=False)
  65
  66     class Meta:
  67         model = Lane
  68
  69 class LaneInline(admin.StackedInline):
  70     """
  71     Controls display of Lanes on the Flowcell form.
  72     """
  73     model = Lane
  74     extra = 8
  75     form = LaneForm
  76     raw_id_fields = ('library',)
  77     fieldsets = (
  78       (None, {
  79         'fields': ('lane_number', 'flowcell',
  80                    ('library',),
  81                    ('pM', 'cluster_estimate', 'status'),
  82                    'comment',)
  83       }),
  84     )
  85
  86 class LaneOptions(admin.ModelAdmin):
  87     """
  88     Controls display of Lane browser
  89     """
  90     search_fields = ('=flowcell__flowcell_id', 'library__id', 'library__library_name' )
  91     list_display = ('flowcell', 'lane_number', 'library', 'comment')
  92     fieldsets = (
  93       (None, {
  94         'fields': ('lane_number', 'flowcell',
  95                    ('library'),
  96                    ('pM', 'cluster_estimate'))
  97       }),
  98       ('Optional', {
  99         'classes': ('collapse', ),
 100         'fields': ('comment', )
 101       }),
 102     )
 103 admin.site.register(Lane, LaneOptions)
 104
 105 class FlowCellModelOptions(admin.ModelAdmin):
 106     search_fields = ('name',)
 107     list_display = ('name', 'fixed_time', 'per_cycle_time', 'isdefault')
 108     fieldsets = (
 109         (None, { 'fields': ('name', 'fixed_time', 'per_cycle_time', 'isdefault') }),
 110         )
 111 admin.site.register(FlowCellModel, FlowCellModelOptions)
 112
 113 class FlowCellOptions(admin.ModelAdmin):
 114     class Media:
 115         css = { 'all': ('css/admin_flowcell.css',) }
 116     date_hierarchy = "run_date"
 117     save_on_top = True
 118     search_fields = ('flowcell_id',
 119         'sequencer__name',
 120         'cluster_station__name',
 121         '=lane__library__id',
 122         'lane__library__library_name')
 123     list_display = ('flowcell_id','run_date','Lanes')
 124     list_filter = ('sequencer','cluster_station', 'paired_end')
 125     fieldsets = (
 126         (None, {
 127           'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
 128                     ('flowcell_model', 'read_length', 'paired_end', 'control_lane', ),)
 129         }),
 130         ('Notes:', { 'fields': ('notes',),}),
 131     )
 132     inlines = [
 133       LaneInline,
 134     ]
 135
 136     def formfield_for_dbfield(self, db_field, **kwargs):
 137         field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
 138                                                                    **kwargs)
 139
 140         # Override field attributes
 141         if db_field.name == 'sequencer':
 142             # seems kind of clunky.
 143             # the goal is to replace the default select/combo box with one
 144             # that can strike out disabled options.
 145             attrs = field.widget.widget.attrs
 146             field.widget.widget = SequencerSelect(attrs=attrs, queryset=field.queryset)
 147         elif db_field.name == "notes":
 148             field.widget.attrs["rows"] = "3"
 149         return field
 150 admin.site.register(FlowCell, FlowCellOptions)
 151
 152 class ClusterStationOptions(admin.ModelAdmin):
 153     list_display = ('name', 'isdefault',)
 154     fieldsets = ( ( None, { 'fields': ( 'name', 'isdefault') } ), )
 155 admin.site.register(ClusterStation, ClusterStationOptions)
 156
 157 class SequencerSelect(Select):
 158     def __init__(self, queryset=None, *args, **kwargs):
 159         super(SequencerSelect, self).__init__(*args, **kwargs)
 160         self.queryset = queryset
 161
 162     def render_options(self, choices, selected_choices):
 163         # Normalize to strings.
 164         selected_choices = set([force_unicode(v) for v in selected_choices])
 165         output = []
 166         for option_value, option_label in chain(self.choices, choices):
 167             if isinstance(option_label, (list, tuple)):
 168                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 169                 for option in option_label:
 170                     output.append(self.render_option(selected_choices, *option))
 171                 output.append(u'</optgroup>')
 172             else:
 173                 output.append(self.render_option(selected_choices, option_value, option_label))
 174         return u'\n'.join(output)
 175
 176     # render_options blatently grabbed from 1.3.1 as the 1.2 version
 177     # has render_option, which is what I needed to overload as a
 178     # nested function in render_options
 179     def render_options(self, choices, selected_choices):
 180         # Normalize to strings.
 181         selected_choices = set([force_unicode(v) for v in selected_choices])
 182         output = []
 183         for option_value, option_label in chain(self.choices, choices):
 184             if isinstance(option_label, (list, tuple)):
 185                 output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
 186                 for option in option_label:
 187                     output.append(self.render_option(selected_choices, *option))
 188                 output.append(u'</optgroup>')
 189             else:
 190                 output.append(self.render_option(selected_choices, option_value, option_label))
 191         return u'\n'.join(output)
 192
 193
 194     def render_option(self, selected_choices, option_value, option_label):
 195         disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
 196         option_value = unicode(option_value)
 197         selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
 198         cssclass = "strikeout" if option_value in disabled_sequencers else ''
 199         return u'<option class="%s" value="%s"%s>%s</option>' % (
 200             cssclass, escape(option_value), selected_html,
 201             conditional_escape(force_unicode(option_label)))
 202
 203 class SequencerOptions(admin.ModelAdmin):
 204     list_display = ('name', 'active', 'isdefault', 'instrument_name', 'model')
 205     fieldsets = ( ( None,
 206                     { 'fields': (
 207                         'name', ('active', 'isdefault'), 'instrument_name', 'serial_number',
 208                         'model', 'comment') } ), )
 209
 210 admin.site.register(Sequencer, SequencerOptions)