-from htsworkflow.frontend.experiments.models import FlowCell, DataRun, ClusterStation, Sequencer
+from itertools import chain
+from htsworkflow.frontend.experiments.models import \
+ FlowCell, DataRun, DataFile, FileType, ClusterStation, Sequencer, Lane
from django.contrib import admin
+from django.contrib.admin.widgets import FilteredSelectMultiple
+from django.forms import ModelForm
+from django.forms.fields import Field, CharField
+from django.forms.widgets import TextInput, Select
+from django.utils.encoding import force_unicode
+from django.utils.html import escape, conditional_escape
from django.utils.translation import ugettext_lazy as _
+class DataFileForm(ModelForm):
+ class Meta:
+ model = DataFile
+
+class DataFileInline(admin.TabularInline):
+ model = DataFile
+ form = DataFileForm
+ raw_id_fields = ('library',)
+ extra = 0
+
class DataRunOptions(admin.ModelAdmin):
search_fields = [
+ 'flowcell_id',
'run_folder',
'run_note',
- 'config_params',
- '=fcid__lane_1_library__library_id',
- '=fcid__lane_2_library__library_id',
- '=fcid__lane_3_library__library_id',
- '=fcid__lane_4_library__library_id',
- '=fcid__lane_5_library__library_id',
- '=fcid__lane_6_library__library_id',
- '=fcid__lane_7_library__library_id',
- '=fcid__lane_8_library__library_id'
- ]
+ ]
list_display = [
- 'run_folder',
- 'Flowcell_Info',
+ 'runfolder_name',
+ 'result_dir',
'run_start_time',
- 'main_status',
- 'run_note',
]
- list_filter = ('run_status', 'run_start_time')
+ fieldsets = (
+ (None, {
+ 'fields': (('flowcell', 'run_status'),
+ ('runfolder_name', 'cycle_start', 'cycle_stop'),
+ ('result_dir',),
+ ('last_update_time'),
+ ('image_software', 'image_version'),
+ ('basecall_software', 'basecall_version'),
+ ('alignment_software', 'alignment_version'),
+ ('comment',))
+ }),
+ )
+ inlines = [ DataFileInline ]
+ #list_filter = ('run_status', 'run_start_time')
+admin.site.register(DataRun, DataRunOptions)
+
+
+class FileTypeAdmin(admin.ModelAdmin):
+ list_display = ('name', 'mimetype', 'regex')
+admin.site.register(FileType, FileTypeAdmin)
+
+# lane form setup needs to come before Flowcell form config
+# as flowcell refers to the LaneInline class
+class LaneForm(ModelForm):
+ comment = CharField(widget=TextInput(attrs={'size':'80'}), required=False)
+
+ class Meta:
+ model = Lane
+
+class LaneInline(admin.StackedInline):
+ """
+ Controls display of Lanes on the Flowcell form.
+ """
+ model = Lane
+ extra = 8
+ form = LaneForm
+ raw_id_fields = ('library',)
+ fieldsets = (
+ (None, {
+ 'fields': ('lane_number', 'flowcell',
+ ('library',),
+ ('pM', 'cluster_estimate', 'status'),
+ 'comment',)
+ }),
+ )
+
+class LaneOptions(admin.ModelAdmin):
+ """
+ Controls display of Lane browser
+ """
+ search_fields = ('=flowcell__flowcell_id', 'library__id', 'library__library_name' )
+ list_display = ('flowcell', 'lane_number', 'library', 'comment')
+ fieldsets = (
+ (None, {
+ 'fields': ('lane_number', 'flowcell',
+ ('library'),
+ ('pM', 'cluster_estimate'))
+ }),
+ ('Optional', {
+ 'classes': ('collapse', ),
+ 'fields': ('comment', )
+ }),
+ )
+admin.site.register(Lane, LaneOptions)
class FlowCellOptions(admin.ModelAdmin):
+ class Media:
+ css = { 'all': ('css/admin_flowcell.css',) }
date_hierarchy = "run_date"
save_on_top = True
search_fields = ('flowcell_id',
- 'sequencer',
- 'cluster_station',
- '=lane_1_library__library_id',
- '=lane_2_library__library_id',
- '=lane_3_library__library_id',
- '=lane_4_library__library_id',
- '=lane_5_library__library_id',
- '=lane_6_library__library_id',
- '=lane_7_library__library_id',
- '=lane_8_library__library_id')
+ 'sequencer__name',
+ 'cluster_station__name',
+ '=lane__library__id',
+ 'lane__library__library_name')
list_display = ('flowcell_id','run_date','Lanes')
- list_filter = ('sequencer','cluster_station')
+ list_filter = ('sequencer','cluster_station', 'paired_end')
fieldsets = (
(None, {
- 'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'), ('read_length', 'paired_end'),)
- }),
- ('Lanes:', {
- 'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
+ 'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
+ ('read_length', 'control_lane', 'paired_end'),)
}),
('Notes:', { 'fields': ('notes',),}),
)
+ inlines = [
+ LaneInline,
+ ]
+
+ def formfield_for_dbfield(self, db_field, **kwargs):
+ field = super(FlowCellOptions, self).formfield_for_dbfield(db_field,
+ **kwargs)
+
+ # Override field attributes
+ if db_field.name == 'sequencer':
+ # seems kind of clunky.
+ # the goal is to replace the default select/combo box with one
+ # that can strike out disabled options.
+ attrs = field.widget.widget.attrs
+ field.widget.widget = SequencerSelect(attrs=attrs, queryset=field.queryset)
+ elif db_field.name == "notes":
+ field.widget.attrs["rows"] = "3"
+ return field
+admin.site.register(FlowCell, FlowCellOptions)
class ClusterStationOptions(admin.ModelAdmin):
- list_display = ('name', )
- fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
+ list_display = ('name', 'isdefault',)
+ fieldsets = ( ( None, { 'fields': ( 'name', 'isdefault') } ), )
+admin.site.register(ClusterStation, ClusterStationOptions)
+
+class SequencerSelect(Select):
+ def __init__(self, queryset=None, *args, **kwargs):
+ super(SequencerSelect, self).__init__(*args, **kwargs)
+ self.queryset = queryset
+
+ def render_options(self, choices, selected_choices):
+ # Normalize to strings.
+ selected_choices = set([force_unicode(v) for v in selected_choices])
+ output = []
+ for option_value, option_label in chain(self.choices, choices):
+ if isinstance(option_label, (list, tuple)):
+ output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
+ for option in option_label:
+ output.append(self.render_option(selected_choices, *option))
+ output.append(u'</optgroup>')
+ else:
+ output.append(self.render_option(selected_choices, option_value, option_label))
+ return u'\n'.join(output)
+
+ # render_options blatently grabbed from 1.3.1 as the 1.2 version
+ # has render_option, which is what I needed to overload as a
+ # nested function in render_options
+ def render_options(self, choices, selected_choices):
+ # Normalize to strings.
+ selected_choices = set([force_unicode(v) for v in selected_choices])
+ output = []
+ for option_value, option_label in chain(self.choices, choices):
+ if isinstance(option_label, (list, tuple)):
+ output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
+ for option in option_label:
+ output.append(self.render_option(selected_choices, *option))
+ output.append(u'</optgroup>')
+ else:
+ output.append(self.render_option(selected_choices, option_value, option_label))
+ return u'\n'.join(output)
+
+
+ def render_option(self, selected_choices, option_value, option_label):
+ disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
+ option_value = unicode(option_value)
+ selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
+ cssclass = "strikeout" if option_value in disabled_sequencers else ''
+ return u'<option class="%s" value="%s"%s>%s</option>' % (
+ cssclass, escape(option_value), selected_html,
+ conditional_escape(force_unicode(option_label)))
class SequencerOptions(admin.ModelAdmin):
- list_display = ('name', )
- fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
+ list_display = ('name', 'active', 'isdefault', 'instrument_name', 'model')
+ fieldsets = ( ( None,
+ { 'fields': (
+ 'name', ('active', 'isdefault'), 'instrument_name', 'serial_number',
+ 'model', 'comment') } ), )
-admin.site.register(DataRun, DataRunOptions)
-admin.site.register(FlowCell, FlowCellOptions)
-admin.site.register(ClusterStation, ClusterStationOptions)
admin.site.register(Sequencer, SequencerOptions)
projects / htsworkflow.git / blobdiff