Start supporting multiple libraries per lane, as needed for the HiSeq

[htsworkflow.git] / htsworkflow / frontend / experiments / admin.py

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index a4a1eef424ebedc0b2877c4a7a1ceaff1f985752..fa0f15d0141a4473fc02098049d47bea1c3f2900 100644 (file)
--- a/htsworkflow/frontend/experiments/admin.py
+++ b/htsworkflow/frontend/experiments/admin.py
@@ -1,99 +1,131 @@
-from htsworkflow.frontend.experiments.models import FlowCell, DataRun, ClusterStation, Sequencer, Lane
+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 CharField
+from django.forms.fields import Field, CharField
 from django.forms.widgets import TextInput
 from django.utils.translation import ugettext_lazy as _
 
-
-class LaneForm(ModelForm):
-    comment = CharField(widget=TextInput(attrs={'size':'80'}), required=False)
-    
+class DataFileForm(ModelForm):
     class Meta:
-        model = Lane
+        model = DataFile
 
-class LaneInline(admin.StackedInline):
-  model = Lane
-  max_num = 8
-  extra = 8
-  form = LaneForm
+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'
-      'fcid__lane_1_library__library_name',
-      'fcid__lane_2_library__library_name',
-      'fcid__lane_3_library__library_name',
-      'fcid__lane_4_library__library_name',
-      'fcid__lane_5_library__library_name',
-      'fcid__lane_6_library__library_name',
-      'fcid__lane_7_library__library_name',
-      'fcid__lane_8_library__library_name'  ]
+      ]
   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'),
+                   ('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):
     date_hierarchy = "run_date"
     save_on_top = True
     search_fields = ('flowcell_id',
         'sequencer__name',
         'cluster_station__name',
-        '=lane__library__library_id',
+        '=lane__library__id',
         'lane__library__library_name')
     list_display = ('flowcell_id','run_date','Lanes')
     list_filter = ('sequencer','cluster_station')
     fieldsets = (
         (None, {
-            'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'), ('read_length', 'paired_end'),)
+          'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'),
+                    ('read_length', 'control_lane', 'paired_end'),)
         }),
-        #('Lanes:', {
-        #   'fields' : (('lane__library__library_id', 'lane__pM', 'lane__cluster_estimate'),)
-        #}),
         ('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 == "notes":
+            field.widget.attrs["rows"] = "3"
+        return field
+admin.site.register(FlowCell, FlowCellOptions)
+
 class ClusterStationOptions(admin.ModelAdmin):
     list_display = ('name', )
     fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
+admin.site.register(ClusterStation, ClusterStationOptions)
 
 class SequencerOptions(admin.ModelAdmin):
     list_display = ('name', )
     fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
-    
-class LaneOptions(admin.ModelAdmin):
-    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(DataRun, DataRunOptions)
-admin.site.register(FlowCell, FlowCellOptions)
-admin.site.register(ClusterStation, ClusterStationOptions)
 admin.site.register(Sequencer, SequencerOptions)
-admin.site.register(Lane, LaneOptions)