Neuroglancer admin

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

class neuroglancer.admin.AnnotationSessionAdmin(model, admin_site)

Bases: AtlasAdminModel

Administer the annotation session data.

get_queryset(request)

Return a QuerySet of all model instances that can be edited by the admin site. This is used by changelist_view.

get_urls()

Shows the HTML of the links to go to the graph, and table data.

label(obj)

list_display = ['animal', 'open_neuroglancer', 'annotator', 'label', 'show_points', 'annotation_type', 'created', 'updated']

list_filter = ['annotation_type', 'created', 'updated']

property media

open_neuroglancer(obj)

This method creates an HTML link that allows the user to access Neuroglancer

ordering = ['animal', 'annotation_type', 'created', 'annotator']

search_fields = ['animal__prep_id', 'annotation_type', 'annotator__first_name']

show_points(obj)

Shows the HTML for the link to the graph of data.

view_points_in_session(request, id, *args, **kwargs)

Provides the HTML link to the table data

class neuroglancer.admin.ArchiveSetAdmin(model, admin_site)

Bases: AtlasAdminModel

Class that provides admin capability for managing a region of the brain. This was also called a structure.

actions = [<function restore_archive>]

fields = ['annotation_session', 'created']

get_animal(obj)

get_annotation_type(obj)

get_name(obj)

get_queryset(request)

Return a QuerySet of all model instances that can be edited by the admin site. This is used by changelist_view.

has_add_permission(request, obj=None)

Returns false as the data is readonly

has_change_permission(request, obj=None)

Returns false as the data is readonly

has_delete_permission(request, obj=None)

Returns false as the data is readonly

list_display = ('get_animal', 'get_name', 'get_annotation_type', 'created')

list_filter = ['created', 'annotation_session__annotation_type']

property media

ordering = ['annotation_session__animal__prep_id']

search_fields = ['annotation_session__animal__prep_id']

class neuroglancer.admin.BrainRegionAdmin(model, admin_site)

Bases: AtlasAdminModel, ExportCsvMixin

Class that provides admin capability for managing a region of the brain. This was also called a structure.

created_display(obj)

Formats the date nicely.

list_display = ('abbreviation', 'description', 'active', 'created_display')

list_filter = ['created', 'active']

property media

ordering = ['abbreviation']

readonly_fields = ['created']

search_fields = ['abbreviation', 'description']

class neuroglancer.admin.CellTypeAdmin(model, admin_site)

Bases: AtlasAdminModel, ExportCsvMixin

“This class administers the different type of cells.

created_display(obj)

Formats the date nicely.

list_display = ('cell_type', 'description', 'active')

list_filter = ['created', 'active']

property media

ordering = ['cell_type']

readonly_fields = ['created']

search_fields = ['cell_type', 'description']

class neuroglancer.admin.CompletedTaskAdmin(model, admin_site)

Bases: ModelAdmin

This class is used to admin the completed tasks. These are tasks that are long running and take to long for an HTTP request. They get sent to the supervisord daemon to be run outside the scope of the HTTP request.

display_filter = ['task_name']

has_add_permission(request)

Returns false as it is added by another process.

has_change_permission(request, obj=None)

Returns false as it is added by another process.

list_display = ['task_name', 'run_at', 'attempts', 'has_error', 'creator']

list_filter = ['run_at']

property media

class neuroglancer.admin.MarkedCellWorkflowAdmin(model, admin_site)

Bases: ModelAdmin

This class provides the ability to manage the data entered through Neuroglancer. These are points are entered by an anatomist and are solely for marked cells (premotor, starter etc)

change_list_template = 'markedcell_change_list.html'

changelist_view(request, extra_context=None)

The ‘change list’ admin view for this model.

drilldown_link(obj)

has_add_permission(request, obj=None)

Returns false as this data is just a report

has_change_permission(request, obj=None)

Returns false as it is just a report.

has_delete_permission(request, obj=None)

Returns false as it is just a report.

list_filter = ('cell_type', 'annotation_session__created', 'annotation_session__updated')

marked_cells(obj)

property media

search_fields = ['annotation_session__animal__prep_id', 'annotation_session__annotator__username']

class neuroglancer.admin.PointsAdmin(model, admin_site)

Bases: ModelAdmin

This class may become deprecated, but for now it gets point data from the actual JSON and not the 3 new tables we have that contain x,y,z data.

created_display(obj)

Returns a nicely formatted creation date.

get_queryset(request)

Returns the query set of points where the layer contains annotations

get_urls()

Shows the HTML of the links to go to the graph, and table data.

has_add_permission(request, obj=None)

Returns false as the data is readonly

has_change_permission(request, obj=None)

Returns false as the data is readonly

has_delete_permission(request, obj=None)

Returns false as the data is readonly

list_display = ('animal', 'comments', 'owner', 'show_points', 'updated')

list_filter = ['created', 'updated', 'readonly']

property media

ordering = ['-created']

readonly_fields = ['url', 'created', 'user_date', 'updated']

search_fields = ['comments']

show_points(obj)

Shows the HTML for the link to the graph of data.

view_points_3Dgraph(request, id, *args, **kwargs)

Provides a link to the 3D point graph

Parameters

• request – http request

• id – id of url

• args –

• kwargs –

Returns

3dGraph in a django template

view_points_data(request, id, *args, **kwargs)

Provides the HTML link to the table data

class neuroglancer.admin.StructureComAdmin(model, admin_site)

Bases: ModelAdmin

This class provides the ability to manage the data entered through Neuroglancer. These are points are entered by an anatomist and are solely for the center of mass (COM) for a brain region (structure)

get_queryset(request)

Return a QuerySet of all model instances that can be edited by the admin site. This is used by changelist_view.

get_urls()

Shows the HTML of the links to go to the graph, and table data.

list_display = ('animal', 'annotator', 'created', 'show_com', 'source')

property media

ordering = ('annotation_session__animal__prep_id', 'annotation_session__annotator__username', 'annotation_session__brain_region__abbreviation', 'source')

search_fields = ('annotation_session__animal__prep_id', 'annotation_session__annotator__username', 'annotation_session__brain_region__abbreviation', 'source')

show_com(obj)

Shows the HTML for the link to the graph of data.

view_coms(request, id, *args, **kwargs)

Provides the HTML link to the table data

class neuroglancer.admin.TaskAdmin(model, admin_site)

Bases: ModelAdmin

This admin class is for taking care of the tasks associated with the pre-processing

display_filter = ['task_name']

has_add_permission(request, obj=None)

Returns false as this data comes in from the pre-processing

list_display = ['task_name', 'run_at', 'priority', 'attempts', 'has_error', 'locked_by', 'locked_by_pid_running', 'creator']

property media

search_fields = ['task_name', 'task_params']

class neuroglancer.admin.UrlModelAdmin(model, admin_site)

Bases: ModelAdmin

This class provides the admin backend to the JSON data produced by Neuroglancer. In the original version of Neuroglancer, all the data was stored in the URL, hence the name of this class. The name: ‘UrlModel’ will be changed in future versions.

exclude = ['url']

formfield_overrides = {<class 'django.db.models.fields.CharField'>: {'widget': <django.forms.widgets.TextInput object>}}

has_add_permission(request, obj=None)

Returns false as the data is only added via Neuroglancer

list_display = ('animal', 'open_neuroglancer', 'open_multiuser', 'owner', 'created')

list_filter = ['updated', 'created', 'readonly', <class 'neuroglancer.url_filter.UrlFilter'>]

property media

open_multiuser(obj)

This method creates an HTML link that allows the user to access Neuroglancer in multi user mode.

open_neuroglancer(obj)

This method creates an HTML link that allows the user to access Neuroglancer

ordering = ['-readonly', '-updated']

pretty_url(instance)

Function to display pretty version of the JSON data. It uses the pygments library to make the JSON readable.

Parameters

instance – admin obj

Returns

nicely formatted JSON data that is viewed in the page.

readonly_fields = ['animal', 'pretty_url', 'created', 'user_date', 'updated']

search_fields = ['comments']

neuroglancer.admin.datetime_format(dtime)

A method to return a nicely formatted date and time.

neuroglancer.admin.delete_session(modeladmin, request, queryset)

neuroglancer.admin.get_points_in_session(id)

Shows how many points are in data.

neuroglancer.admin.make_active(modeladmin, request, queryset)

A method to set any object active

Parameters

• request – HTTP request.

• queryset – set of querys used to update.

neuroglancer.admin.make_inactive(modeladmin, request, queryset)

A method to set any object inactive

Parameters

• request – HTTP request.

• queryset – set of querys used to update.

neuroglancer.admin.restore_archive(modeladmin, request, queryset)

This method will restore data from the annotation_points_archive table to the annotations_points table.

1. Set existing data to inactive (quick)

2. Move inactive data to archive (select, insert, slow, use background)

3. Move archived data to existing (select, insert, slow use background)

Parameters

• request – the HTTP request

• queryset – the query set used to fetch data