1 from htsworkflow.frontend.experiments.models import \
2 FlowCell, DataRun, DataFile, FileType, ClusterStation, Sequencer, Lane
3 from django.contrib import admin
4 from django.contrib.admin.widgets import FilteredSelectMultiple
5 from django.forms import ModelForm
6 from django.forms.fields import Field, CharField
7 from django.forms.widgets import TextInput, Select
8 from django.utils.encoding import force_unicode
9 from django.utils.html import escape, conditional_escape
10 from django.utils.translation import ugettext_lazy as _
12 class DataFileForm(ModelForm):
16 class DataFileInline(admin.TabularInline):
19 raw_id_fields = ('library',)
22 class DataRunOptions(admin.ModelAdmin):
35 'fields': (('flowcell', 'run_status'),
36 ('runfolder_name', 'cycle_start', 'cycle_stop'),
39 ('image_software', 'image_version'),
40 ('basecall_software', 'basecall_version'),
41 ('alignment_software', 'alignment_version'),
45 inlines = [ DataFileInline ]
46 #list_filter = ('run_status', 'run_start_time')
47 admin.site.register(DataRun, DataRunOptions)
50 class FileTypeAdmin(admin.ModelAdmin):
51 list_display = ('name', 'mimetype', 'regex')
52 admin.site.register(FileType, FileTypeAdmin)
54 # lane form setup needs to come before Flowcell form config
55 # as flowcell refers to the LaneInline class
56 class LaneForm(ModelForm):
57 comment = CharField(widget=TextInput(attrs={'size':'80'}), required=False)
62 class LaneInline(admin.StackedInline):
64 Controls display of Lanes on the Flowcell form.
69 raw_id_fields = ('library',)
72 'fields': ('lane_number', 'flowcell',
74 ('pM', 'cluster_estimate', 'status'),
79 class LaneOptions(admin.ModelAdmin):
81 Controls display of Lane browser
83 search_fields = ('=flowcell__flowcell_id', 'library__id', 'library__library_name' )
84 list_display = ('flowcell', 'lane_number', 'library', 'comment')
87 'fields': ('lane_number', 'flowcell',
89 ('pM', 'cluster_estimate'))
92 'classes': ('collapse', ),
93 'fields': ('comment', )
96 admin.site.register(Lane, LaneOptions)
98 class FlowCellOptions(admin.ModelAdmin):
100 css = { 'all': ('css/admin_flowcell.css',) }
101 date_hierarchy = "run_date"
103 search_fields = ('flowcell_id',
105 'cluster_station__name',
106 '=lane__library__id',
107 'lane__library__library_name')
108 list_display = ('flowcell_id','run_date','Lanes')
109 list_filter = ('sequencer','cluster_station')
112 'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
113 ('read_length', 'control_lane', 'paired_end'),)
115 ('Notes:', { 'fields': ('notes',),}),
121 def formfield_for_dbfield(self, db_field, **kwargs):
122 field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
125 # Override field attributes
126 if db_field.name == 'sequencer':
127 # seems kind of clunky.
128 # the goal is to replace the default select/combo box with one
129 # that can strike out disabled options.
130 attrs = field.widget.widget.attrs
131 disabled_sequencers = field.queryset.filter(active=False)
132 attrs['disabled_sequencers'] = [ unicode(s.id) for s in disabled_sequencers ]
133 field.widget.widget = SequencerSelect(attrs=attrs)
134 elif db_field.name == "notes":
135 field.widget.attrs["rows"] = "3"
137 admin.site.register(FlowCell, FlowCellOptions)
139 class ClusterStationOptions(admin.ModelAdmin):
140 list_display = ('name', )
141 fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
142 admin.site.register(ClusterStation, ClusterStationOptions)
144 class SequencerSelect(Select):
145 def render_option(self, selected_choices, option_value, option_label):
146 disabled_sequencers = self.attrs.get('disabled_sequencers', [])
147 option_value = unicode(option_value)
148 selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
149 cssclass = "strikeout" if option_value in disabled_sequencers else ''
150 return u'<option class="%s" value="%s"%s>%s</option>' % (
151 cssclass, escape(option_value), selected_html,
152 conditional_escape(force_unicode(option_label)))
154 class SequencerOptions(admin.ModelAdmin):
155 list_display = ('name', 'active', 'instrument_name', 'model')
156 fieldsets = ( ( None,
158 'name', 'active', 'instrument_name', 'serial_number',
159 'model', 'comment') } ), )
161 admin.site.register(Sequencer, SequencerOptions)