htsworkflow/frontend/samples/admin.py

   1 from django.contrib import admin
   2 from django.contrib.admin import widgets
   3 from django.contrib.auth.models import User
   4 from django.contrib.auth.admin import UserAdmin
   5 from django.contrib.auth.forms import UserCreationForm, UserChangeForm
   6 from django.template import Context, Template
   7 from django.db import models
   8 from django.utils.translation import ugettext_lazy as _
   9 from django.forms import TextInput, Textarea
  10
  11 from htsworkflow.frontend.samples.models import \
  12      Antibody, Cellline, Condition, ExperimentType, HTSUser, \
  13      LibraryType, MultiplexIndex, Species, Affiliation, Library, Tag
  14 from htsworkflow.frontend.experiments.models import Lane
  15 from htsworkflow.frontend.inventory.models import PrinterTemplate
  16 from htsworkflow.frontend.bcmagic.utils import print_zpl_socket
  17
  18 # Let's disable those pesky delete everything by accident features.
  19 admin.site.disable_action('delete_selected')
  20
  21 class AffiliationOptions(admin.ModelAdmin):
  22     list_display = ('name','contact','email')
  23     fieldsets = (
  24       (None, {
  25           'fields': (('name','contact','email','users'))
  26       }),
  27     )
  28
  29     # some post 1.0.2 version of django has formfield_overrides
  30     # which would replace this code with:
  31     # formfield_overrids = {
  32     #   models.ManyToMany: { 'widget': widgets.FilteredSelectMultiple }
  33     # }
  34     def formfield_for_dbfield(self, db_field, **kwargs):
  35       if db_field.name == 'users':
  36         kwargs['widget'] = widgets.FilteredSelectMultiple(db_field.verbose_name, (db_field.name in self.filter_vertical))
  37       rv = super(AffiliationOptions, self).formfield_for_dbfield(db_field, **kwargs)
  38     #  print db_field.name, kwargs
  39       return rv
  40
  41 class AntibodyOptions(admin.ModelAdmin):
  42     search_fields = ('antigene','nickname','catalog','antibodies','source','biology','notes')
  43     list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
  44     list_filter = ('antibodies','source')
  45     fieldsets = (
  46       (None, {
  47           'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
  48       }),
  49      )
  50
  51 class CelllineOptions(admin.ModelAdmin):
  52     list_display = ('cellline_name', 'notes')
  53     search_fields = ('cellline_name', 'nickname', 'notes')
  54     fieldsets = (
  55       (None, {
  56           'fields': (('cellline_name','nickname',),('notes'),)
  57       }),
  58      )
  59
  60 class ConditionOptions(admin.ModelAdmin):
  61     list_display = (('condition_name'), ('notes'),)
  62     fieldsets = (
  63       (None, {
  64           'fields': (('condition_name'),('nickname'),('notes'),)
  65       }),
  66      )
  67
  68 class ExperimentTypeOptions(admin.ModelAdmin):
  69   model = ExperimentType
  70   #list_display = ('name',)
  71   #fieldsets = ( (None, { 'fields': ('name',) }), )
  72
  73 class HTSUserCreationForm(UserCreationForm):
  74     class Meta:
  75         model = HTSUser
  76         fields = ("username",'first_name','last_name')
  77
  78 class HTSUserChangeForm(UserChangeForm):
  79     class Meta:
  80         model = HTSUser
  81         fields = ("username",'first_name','last_name')
  82
  83 class HTSUserOptions(UserAdmin):
  84     form = HTSUserChangeForm
  85     add_form = HTSUserCreationForm
  86
  87 class LaneLibraryInline(admin.StackedInline):
  88   model = Lane
  89   extra = 0
  90
  91 class Library_Inline(admin.TabularInline):
  92   model = Library
  93
  94 class LibraryTypeOptions(admin.ModelAdmin):
  95     list_display = ['name', 'is_paired_end', 'can_multiplex']
  96     model = LibraryType
  97
  98 class MultiplexIndexOptions(admin.ModelAdmin):
  99     model = MultiplexIndex
 100     list_display = ['adapter_type', 'multiplex_id', 'sequence']
 101
 102 class LibraryOptions(admin.ModelAdmin):
 103     class Media:
 104         css = {
 105             "all": ("css/wide_account_number.css",)
 106             }
 107
 108     date_hierarchy = "creation_date"
 109     save_as = True
 110     save_on_top = True
 111     search_fields = (
 112         'id',
 113         'library_name',
 114         'cell_line__cellline_name',
 115         'library_species__scientific_name',
 116         'library_species__common_name',
 117     )
 118     list_display = (
 119         'id',
 120         'library_name',
 121         'index_sequence_text',
 122         'affiliation',
 123         'undiluted_concentration',
 124         'gel_cut_size',
 125         'creation_date',
 126     )
 127     list_filter = (
 128         'hidden',
 129         'experiment_type',
 130         'library_type',
 131         #'cell_line',
 132         'stopping_point',
 133         'made_by',
 134         'library_species',
 135         'affiliations',
 136         )
 137     list_display_links = ('id', 'library_name',)
 138     fieldsets = (
 139       (None, {
 140         'fields': (
 141           ('id','library_name','hidden'),
 142           ('library_species', 'experiment_type'),
 143           ('library_type', 'multiplex_id'),
 144           )
 145          }),
 146          ('Experiment Detail:', {
 147             'fields': (('cell_line', 'replicate',),
 148                        ('condition',),
 149                        ('antibody', ),
 150                        ),
 151             'classes': ('collapse',),
 152             }),
 153          ('Creation Information:', {
 154              'fields' : (('made_by', 'creation_date', 'stopping_point'),
 155                          ('amplified_from_sample'),
 156                          ('gel_cut_size', 'insert_size',
 157                           'undiluted_concentration'),
 158                          ('bioanalyzer_concentration','bioanalyzer_image_url'),
 159                          ('bioanalyzer_summary'),
 160                          ('notes'))
 161          }),
 162          ('Library/Project Affiliation:', {
 163              'fields' : (('account_number', 'affiliations'),)
 164          }),
 165          )
 166     inlines = [
 167       LaneLibraryInline,
 168     ]
 169     actions = ['action_print_library_labels']
 170
 171     def action_print_library_labels(self, request, queryset):
 172         """
 173         Django action which prints labels for the selected set of labels from the
 174         Django Admin interface.
 175         """
 176
 177         #Probably should ask if the user really meant to print all selected
 178         # libraries if the count is above X. X=10 maybe?
 179
 180         # Grab the library template
 181         #FIXME: Hardcoding library template name. Not a good idea... *sigh*.
 182         EVIL_HARDCODED_LIBRARY_TEMPLATE_NAME = "Library"
 183
 184         try:
 185             template = PrinterTemplate.objects.get(item_type__name=EVIL_HARDCODED_LIBRARY_TEMPLATE_NAME)
 186         except PrinterTemplate.DoesNotExist:
 187             self.message_user(request, "Could not find a library template with ItemType.name of '%s'" % \
 188                               (EVIL_HARDCODED_LIBRARY_TEMPLATE_NAME))
 189             return
 190
 191         # ZPL Template
 192         t = Template(template.template)
 193
 194         zpl_list = []
 195         #Iterate over selected labels to print
 196         for library in queryset.all():
 197
 198             # Django Template Context
 199             c = Context({'library': library})
 200
 201             # Send rendered template to the printer that the template
 202             #  object has been attached to in the database.
 203             zpl_list.append(t.render(c))
 204
 205         print_zpl_socket(zpl_list, host=template.printer.ip_address)
 206
 207         self.message_user(request, "%s labels printed." % (len(queryset)))
 208
 209     action_print_library_labels.short_description = "Print Labels"
 210
 211     def formfield_for_dbfield(self, db_field, **kwargs):
 212         # Override Field type
 213         if db_field.name in ('affiliations', 'tags'):
 214             kwargs['widget'] = widgets.FilteredSelectMultiple(
 215                 db_field.verbose_name,
 216                 (db_field.name in self.filter_vertical)
 217             )
 218         field = super(LibraryOptions, self).formfield_for_dbfield(db_field,
 219                                                                   **kwargs)
 220         # Override field attributes
 221         if db_field.name == "bioanalyzer_summary":
 222             field.widget.attrs["rows"] = "3"
 223         return field
 224
 225 class SpeciesOptions(admin.ModelAdmin):
 226     fieldsets = (
 227       (None, {
 228           'fields': (('scientific_name', 'common_name'),)
 229       }),
 230     )
 231
 232 class TagOptions(admin.ModelAdmin):
 233     list_display = ('tag_name', 'context')
 234     fieldsets = (
 235         (None, {
 236           'fields': ('tag_name', 'context')
 237           }),
 238         )
 239
 240 admin.site.register(Library, LibraryOptions)
 241 admin.site.register(Affiliation, AffiliationOptions)
 242 admin.site.register(Antibody, AntibodyOptions)
 243 admin.site.register(Cellline, CelllineOptions)
 244 admin.site.register(Condition, ConditionOptions)
 245 admin.site.register(ExperimentType, ExperimentTypeOptions)
 246 #admin.site.register(HTSUser, HTSUserOptions)
 247 admin.site.register(LibraryType, LibraryTypeOptions)
 248 admin.site.register(MultiplexIndex, MultiplexIndexOptions)
 249 admin.site.register(Species, SpeciesOptions)
 250 #admin.site.register(Tag, TagOptions)