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 _
13 class DataFileForm(ModelForm):
17 class DataFileInline(admin.TabularInline):
20 raw_id_fields = ('library',)
23 class DataRunOptions(admin.ModelAdmin):
36 'fields': (('flowcell', 'run_status'),
37 ('runfolder_name', 'cycle_start', 'cycle_stop'),
40 ('image_software', 'image_version'),
41 ('basecall_software', 'basecall_version'),
42 ('alignment_software', 'alignment_version'),
46 inlines = [ DataFileInline ]
47 #list_filter = ('run_status', 'run_start_time')
48 admin.site.register(DataRun, DataRunOptions)
51 class FileTypeAdmin(admin.ModelAdmin):
52 list_display = ('name', 'mimetype', 'regex', 'regex_is_valid')
55 'fields': (('name', 'mimetype'),
59 admin.site.register(FileType, FileTypeAdmin)
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)
69 class LaneInline(admin.StackedInline):
71 Controls display of Lanes on the Flowcell form.
76 raw_id_fields = ('library',)
79 'fields': ('lane_number', 'flowcell',
81 ('pM', 'cluster_estimate', 'status'),
86 class LaneOptions(admin.ModelAdmin):
88 Controls display of Lane browser
90 search_fields = ('=flowcell__flowcell_id', 'library__id', 'library__library_name' )
91 list_display = ('flowcell', 'lane_number', 'library', 'comment')
94 'fields': ('lane_number', 'flowcell',
96 ('pM', 'cluster_estimate'))
99 'classes': ('collapse', ),
100 'fields': ('comment', )
103 admin.site.register(Lane, LaneOptions)
105 class FlowCellModelOptions(admin.ModelAdmin):
106 search_fields = ('name',)
107 list_display = ('name', 'fixed_time', 'per_cycle_time', 'isdefault')
109 (None, { 'fields': ('name', 'fixed_time', 'per_cycle_time', 'isdefault') }),
111 admin.site.register(FlowCellModel, FlowCellModelOptions)
113 class FlowCellOptions(admin.ModelAdmin):
115 css = { 'all': ('css/admin_flowcell.css',) }
116 date_hierarchy = "run_date"
118 search_fields = ('flowcell_id',
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')
127 'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
128 ('flowcell_model', 'read_length', 'paired_end', 'control_lane', ),)
130 ('Notes:', { 'fields': ('notes',),}),
136 def formfield_for_dbfield(self, db_field, **kwargs):
137 field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
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"
150 admin.site.register(FlowCell, FlowCellOptions)
152 class ClusterStationOptions(admin.ModelAdmin):
153 list_display = ('name', 'isdefault',)
154 fieldsets = ( ( None, { 'fields': ( 'name', 'isdefault') } ), )
155 admin.site.register(ClusterStation, ClusterStationOptions)
157 class SequencerSelect(Select):
158 def __init__(self, queryset=None, *args, **kwargs):
159 super(SequencerSelect, self).__init__(*args, **kwargs)
160 self.queryset = queryset
162 def render_options(self, choices, selected_choices):
163 # Normalize to strings.
164 selected_choices = set([force_unicode(v) for v in selected_choices])
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>')
173 output.append(self.render_option(selected_choices, option_value, option_label))
174 return u'\n'.join(output)
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])
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>')
190 output.append(self.render_option(selected_choices, option_value, option_label))
191 return u'\n'.join(output)
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)))
203 class SequencerOptions(admin.ModelAdmin):
204 list_display = ('name', 'active', 'isdefault', 'instrument_name', 'model')
205 fieldsets = ( ( None,
207 'name', ('active', 'isdefault'), 'instrument_name', 'serial_number',
208 'model', 'comment') } ), )
210 admin.site.register(Sequencer, SequencerOptions)