admin.py

"""Submit the sequence by user and name of the protein is predicted."""

from django.contrib import admin
from django.contrib.admin.checks import BaseModelAdminChecks
from django.contrib.admin.models import LogEntry
from django.contrib.admin.options import get_content_type_for_model
from django.contrib.contenttypes.admin import GenericStackedInline
from django.utils.html import format_html, mark_safe
from import_export import resources
from import_export.admin import ImportExportModelAdmin

from database.models import (
    PesticidalProteinDatabase,
    PesticidalProteinPrivateDatabase,
)
from namingalgorithm.models import AuditEntry

from .models import Archive, SendEmail, UserSubmission


@admin.register(AuditEntry)
class AuditEntryLogAdmin(admin.ModelAdmin):
    list_display = [
        "action",
        "username",
        "ip",
    ]
    list_filter = [
        "action",
    ]


class LogEntryAdmin(admin.ModelAdmin):
    readonly_fields = (
        "content_type",
        "user",
        "action_time",
        "object_id",
        "object_repr",
        "action_flag",
        "change_message",
    )

    def has_delete_permission(self, request, obj=None):
        return False

    def get_actions(self, request):
        actions = super(LogEntryAdmin, self).get_actions(request)
        del actions["delete_selected"]
        return actions


class ModelAdminLog(GenericStackedInline):
    model = LogEntry

    # All fields are read-only, obviously
    readonly_fields = fields = ["action_time", "user", "change_message"]
    # No extra fields so noone can add new logs
    extra = 0
    # No one can delete logs
    can_delete = False

    # This is a hackity hack! See below
    checks_class = BaseModelAdminChecks

    def change_message(self, obj):
        message = obj.get_change_message()
        return message


class ArchiveResource(resources.ModelResource):
    class Meta:
        model = Archive


class ArchiveAdmin(ImportExportModelAdmin):
    resource_class = ArchiveResource

    search_fields = ["submittersemail", "submittersname"]
    list_display = (
        "submittersname",
        "accession",
        "uploaded",
        # 'admin_user',
        "admin_comments",
    )

    inlines = [ModelAdminLog]

    def save_model(self, request, obj, form, change):
        super().save_model(request, obj, form, change)
        if change:
            change_message = "{} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {}".format(
                obj.submittersname,
                obj.submittersemail,
                obj.name,
                obj.year,
                obj.sequence,
                obj.bacterium,
                obj.bacterium_textbox,
                obj.taxonid,
                obj.accession,
                obj.partnerprotein,
                obj.partnerprotein_textbox,
                obj.toxicto,
                obj.nontoxic,
                obj.dnasequence,
                obj.pdbcode,
                obj.publication,
                obj.admin_user,
                obj.admin_comments,
                obj.comment,
                obj.uploaded,
                obj.predict_name,
                obj.user_provided_proteinname,
            )
            LogEntry.objects.create(
                user=request.user,
                content_type=get_content_type_for_model(obj),
                object_id=obj.id,
                action_flag=2,
                change_message=change_message,
                object_repr=obj.__str__()[:200],
            )


class UserSubmissionResource(resources.ModelResource):
    class Meta:
        model = UserSubmission


class UserSubmissionAdmin(ImportExportModelAdmin):
    resource_class = UserSubmissionResource

    """Submit the sequence by user and name of the protein is predicted."""

    search_fields = ["submittersemail", "submittersname", "accession"]
    list_editable = ("contact_status",)
    list_display = (
        "submittersname",
        "accession_url",
        "naming_algorithm",
        "availability",
        "refresh",
        "send_email",
        "uploaded",
        "contact_status"
    )
    exclude = ["alignresults"]

    inlines = [ModelAdminLog]

    def save_model(self, request, obj, form, change):
        super().save_model(request, obj, form, change)
        if change:
            change_message = "{} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {} - {}".format(
                obj.submittersname,
                obj.submittersemail,
                obj.name,
                obj.year,
                obj.sequence,
                obj.bacterium,
                obj.bacterium_textbox,
                obj.taxonid,
                obj.accession,
                obj.partnerprotein,
                obj.partnerprotein_textbox,
                obj.toxicto,
                obj.nontoxic,
                obj.dnasequence,
                obj.pdbcode,
                obj.publication,
                obj.admin_user,
                obj.admin_comments,
                obj.comment,
                obj.uploaded,
                obj.predict_name,
                obj.user_provided_proteinname,
            )
            LogEntry.objects.create(
                user=request.user,
                content_type=get_content_type_for_model(obj),
                object_id=obj.id,
                action_flag=2,
                change_message=change_message,
                object_repr=obj.__str__()[:200],
            )

    def accession_url(self, obj):
        return format_html(
            '<a href="%s%s" target="_blank">%s</a>'
            % (
                "https://www.ncbi.nlm.nih.gov/protein/",
                obj.accession,
                obj.accession,
            )
        )

    def naming_algorithm(self, obj):
        if ">" in str(obj.sequence).split("\n")[0]:
            obj.sequence = "\n".join(str(obj.sequence).split("\n")[1:])

        """Submit the sequence by user and name of the protein is predicted."""
        return format_html(
            mark_safe(
                '<a href="/run_naming_algorithm/?fulltextarea={0}&submission_id={1}" target="_blank">Naming Algorithm</a>'.format(
                    obj.sequence, obj.id
                )
            )
        )

    def align_results(self, obj):
        """Submit the sequence by user and name of the protein is predicted."""
        if obj.alignresults:
            return format_html(
                '<a href="/align_results/?submission_id={0}" target="_blank">View Result</a>'.format(
                    obj.id)
            )
        return ""

    # def create_public(self, obj):
    #     """Submit the sequence by user and name of the protein is predicted."""
    #     return format_html('<a href="/admin/database/pesticidalproteindatabase/add/?name={0}&sequence={1}" target="_blank">Create Public</a>'.format(obj.predict_name or '', obj.sequence))

    def refresh(self, obj):
        """Submit the sequence by user and name of the protein is predicted."""
        return format_html('<a href="/admin/namingalgorithm/usersubmission/">refresh</a>')

    def send_email(self, obj):
        return format_html(
            '<a href="/admin/contact/?submittersname={0}&submittersemail={1}&accession={2}" target="_blank">Send Email</a>'.format(
                obj.submittersname, obj.submittersemail, obj.accession
            )
        )

    def availability(self, obj):
        accession_number = obj.accession
        if not accession_number:
            return format_html("<body> <p>No accession number</p> </body>")
        public = PesticidalProteinDatabase.objects.filter(
            accession=accession_number)
        private = PesticidalProteinPrivateDatabase.objects.filter(
            accession=accession_number)
        if public:
            print(accession_number)
            return format_html('<body> <p style="color:#FF0000";>Available in Public</p></body>')
        if private:
            return format_html('<body> <p style="color:#FF0000";>Available in Private</p></body>')

    def Pfam(self, obj):
        return format_html()

    naming_algorithm.allow_tags = True
    naming_algorithm.description = "Run the align link for the submission"

    align_results.allow_tags = True
    align_results.description = "View the align results"

    align_results.allow_tags = True
    align_results.description = "Create new data in the database"


class SendEmailAdmin(admin.ModelAdmin):
    list_display = (
        "submittersname",
        "submittersemail",
        "accession",
        "message",
    )

    inlines = [ModelAdminLog]


# class ArchiveAdmin(admin.ModelAdmin):
#     search_fields = ('name', 'year', 'submittersname',
#                      'submittersemail')
#     fields = ('submittersname', 'submittersemail', 'name', 'year', 'sequence', 'bacterium', 'bacterium_textbox', 'taxonid', 'accession', 'partnerprotein', 'partnerprotein_textbox', 'toxicto', 'nontoxic', 'dnasequence', 'pdbcode', 'publication', 'comment', 'uploaded', 'predict_name', 'alignresults', 'terms_conditions')
#     list_display = ('name', 'submittersname',
#                      'accession', 'uploaded',)
#     ordering = ('-uploaded',)
admin.site.register(LogEntry, LogEntryAdmin)
admin.site.register(UserSubmission, UserSubmissionAdmin)
admin.site.register(Archive, ArchiveAdmin)
admin.site.register(SendEmail, SendEmailAdmin)