Brain admin

This page lists the classes and methods used to administer the ‘Brain’ app in our database portal. This is where the end user can create, retrieve, update and delete (CRUD) metadata associated with the ‘Brain’ app. It does not list the fields (database columns). Look in the models document for the database table model.

class brain.admin.AnimalAdmin(model, admin_site): This class is used to administer the animal. It includes all the metadata entered by the user. The animal class is often used as a key in another table.

class brain.admin.AtlasAdminModel(model, admin_site)

This is used as a base class for most of the other classes. It contains all the common variables that all the tables/objects have. It inherits from the Django base admin model: admin.ModelAdmin

class Media: This is a simple class that defines some CSS attributes for the thumbnails

formfield_for_foreignkey(db_field, request, **kwargs)

Simple formatting for foreign keys

Parameters:

db_field – data row field
request – http request
kwargs – extra args

Returns:

the HTML of the form field

is_active(instance)

A method returning a boolean showing if the data row is active

Parameters:: instance – obj class
Returns:: A boolean

class brain.admin.ExportCsvMixin

A class used by most of the admin categories. It adds formatting to make fields look consistent and also adds the method to export to CSV from each of the ‘Action’ dropdowns in each category.

export_as_csv(request, queryset)

Set the callback function to be executed when the device sends a notification to the client.

Parameters:

request – The http request
queryset – The query used to fetch the CSV data

Returns:

a http response

class brain.admin.HistologyAdmin(model, admin_site)

A class to administer the histology of each animal

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

class brain.admin.InjectionAdmin(model, admin_site)

A class to describe the injections (if any) for each animal. Each animal can have multiple injections.

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

class brain.admin.InjectionVirusAdmin(model, admin_site)

This class describes a many to many relationship between the virus and the injection classes. An animal can multiple injections, with each injection having one or more viruses.

Inheritance:

AtlasAdminModel:: The base admin model

prep_id(instance)

This returns the animal name (string) used as a foreign key in this class.

Parameters:: instance – the obj
Returns:: the prep_id (AKA the animal name) as a string

virus_name(instance)

Gives the description from the virus foreign key

Parameters:: instance – the obj

class brain.admin.LogEntryAdmin(model, admin_site)

This class describes the log objects used during the preprocessing pipeline

Inheritance:

admin.ModelAdmin:: the base Django admin obj

has_add_permission(request)

This data is added by the preprocessing pipeline so can’t be changed here

Parameters:: request – http request
Returns:: False

has_change_permission(request, obj=None)

This data is added by the preprocessing pipeline so can’t be changed here

Parameters:

request – http request
obj – the LogEntry obj

Returns:

False

has_delete_permission(request, obj=None)

This data is added by the preprocessing pipeline so can’t be deleted here

Parameters:

request – http request
obj – the LogEntry obj

Returns:

False

has_view_permission(request, obj=None)

This data can only be viewed by a superuser

Parameters:

request – http request
obj – the LogEntry obj

Returns:

boolean depending on if the user is a super user or not

class brain.admin.ScanRunAdmin(model, admin_site)

This class describes what occurs when the slides are actually scanned. Many of the attributes from this class are used throughout the preprocessing An animal can have multiple scan runs, but usually, there is just one scanning done for each animal.

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

class brain.admin.SectionAdmin(model, admin_site)

This class describes the Section methods and attributes. Sections come from a view and not a table so it needs to be handled a bit differently.

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

class Media

changelist_view(request, extra_context=None): The ‘change list’ admin view for this model.

get_queryset(request, obj=None)

Description of get_queryset - the query starts out with an empty qeuryset ‘prep_id=XXXX’ so the initial page is empty and the user is forced to select one and only one animal. The order is decided upon whether the brain was section from left to right, or right to left. This comes from the histology table: side_sectioned_first and then slide physical ID and scene number

Parameters:

request – http request
obj – section obj

Returns:

the queryset ordered correctly

has_add_permission(request, obj=None)

The add button is not shown as sections are a view and they can’t be added to.

Parameters:

request – http request
obj – the section obj

Returns:

False

has_change_permission(request, obj=None)

The edit button is not shown as sections are a view and they can’t be changed.

Parameters:

request – http request
obj – the section obj

Returns:

False

has_delete_permission(request, obj=None)

The add button is not shown as sections are a view and they can’t be added to.

Parameters:

request – http request
obj – the section obj

Returns:

False

list_display_links = None

section_number(instance)

Description of section_number - this is just an ordered query, so to get the section number, we just use an incrementor

Parameters:: instance – section obj

class brain.admin.SlideAdmin(model, admin_site)

This class describes the admin area for a particular slide. This is used in the QA process and includes the inline TIFF files in the QA form.

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

get_fields(request, obj)

This method fetches the correct number of inline TIFF files that are used in the QA form.

Parameters:

request – http request
obj – the TIFF obj

Returns:

HTML of the fields

get_queryset(request)

Description of get_queryset - returns the active slides

Parameters:: request – http request
Returns:: a query set

has_add_permission(request, obj=None)

Cannot show or use the add button at this stage

Parameters:

request – http request
obj – the TIFF obj

Returns:

False

has_delete_permission(request, obj=None)

Cannot show or use the delete button at this stage.

Parameters:

request – http request
obj – the slide obj

Returns:

False

prep_id(instance)

Returns the animal name that the slide belongs to

Parameters:: instance – the TIFF obj
Returns:: False

response_change(request, obj): Reset all tifs belong to this slide to its original state

save_model(request, obj, form, change)

Description of save_model - overridden method of the save method. When the user changes the scenes via the QA form, the usual save isn’t sufficient so we override it.

Parameters:

self – the admin slide obj
request – the http request
obj – the slide obj
form – the form obj
change – if the form has changed or not.

scene_count(obj)

Determines how many scenes are there for a slide

Parameters:: obj – the slide obj
Returns:: an integer of the number of scenes

class brain.admin.SlideCziToTifAdmin(model, admin_site)

A class to administer the individual scene, AKA the TIFF file.

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.

has_add_permission(request, obj=None)

Cannot show or use the add button at this stage

Parameters:

request – http request
obj – the TIFF obj

Returns:

False

has_delete_permission(request, obj=None)

Cannot show or use the delete button at this stage

Parameters:

request – http request
obj – the TIFF obj

Returns:

False

class brain.admin.TifInline(parent_model, admin_site)

This class is solely used for the database QA. It will display the associated TIFF files for each slide on the slide page.

Inheritance:

admin.TabularInline:: The class that describes how the data is laid out on the page.

formset: alias of TifInlineFormset

get_formset(request, obj=None, **kwargs)

Description of get_formset - sets up the form for the set of TIFF files for each slide

Parameters:

request – http request
obj – the TIFF obj
kwargs – extra args

Returns:

the HTML of the formset

get_queryset(request)

Description of get_queryset - returns just the first channel for each slide. We only need to look at the first channel for QA purposes.

Parameters:: obj – the TIFF obj
Returns:: a query set

has_add_permission(request, obj=None)

TIFF files cannot be added at this stage.

Parameters:

request – http request
obj – the TIFF obj

Returns:

False

has_change_permission(request, obj=None)

TIFF files can be edited at this stage.

Parameters:

request – http request
obj – the TIFF obj

Returns:

True

model: alias of SlideCziToTif

scene_image(obj)

This method tests if there is a PNG file for each scene, and if so, shows it on the QA page for each slide. This is very helpful when the user must decide if the TIFF file is usable.

Parameters:: obj – the TIFF obj
Returns:: HTML that displays a link to the scene PNG file

section_image(obj)

This method shows the TIFF image as a PNG later on in the QA process after it has been cleaned and aligned.

Parameters:: obj – the TIFF obj
Returns:: HTML that displays a link to the scene PNG file

class brain.admin.VirusAdmin(model, admin_site)

A class used to describe a virus. This class can then be a foreign key into the Injection class

Inheritance:

AtlasAdminModel:: The base admin model
ExportCsvMixin:: The class with standard features and CSV exporter method.