Updates from multi-tenant

bims/__init__.py

@@ -1 +1,3 @@
 from .celery import app as celery_app  # noqa
+
+default_app_config = 'bims.apps.BimsAppConfig'

bims/admin.py

@@ -31,6 +31,7 @@
 
 from django_json_widget.widgets import JSONEditorWidget
 
+from bims.admins.site_setting import SiteSettingAdmin
 from bims.tasks import fetch_vernacular_names
 from bims.utils.endemism import merge_endemism
 from bims.utils.sampling_method import merge_sampling_method
@@ -115,7 +116,8 @@
     TaxonomyUpdateProposal,
     TaxonomyUpdateReviewer,
     CITESListingInfo,
-    ImportTask
+    ImportTask,
+    Invasion
 )
 from bims.models.climate_data import ClimateData
 from bims.utils.fetch_gbif import merge_taxa_data
@@ -364,6 +366,11 @@ def save_model(self, request, obj, form, change):
         obj.save()
 
 
+class InvasionAdmin(OrderedModelAdmin):
+    ordering = ('order',)
+    list_display = ('id', 'move_up_down_links', 'category')
+
+
 class IUCNStatusAdmin(OrderedModelAdmin):
     list_display = ('id', 'get_category_display', 'move_up_down_links',
                     'order', 'sensitive',
@@ -482,7 +489,6 @@ class Media:
     )
     list_filter = (
         ('collection_date', DateRangeFilter),
-        'taxonomy',
         'taxonomy__origin',
         'record_type__name',
         'sampling_method',
@@ -977,6 +983,26 @@ class SearchProcessAdmin(admin.ModelAdmin):
         'category',
         'finished')
 
+    def delete_model(self, request, obj):
+        if obj.locked:
+            self.message_user(
+                request,
+                "This record is locked and cannot be deleted.",
+                level='warning')
+        else:
+            super().delete_model(request, obj)
+
+    def delete_queryset(self, request, queryset):
+        for obj in queryset:
+            if obj.locked:
+                self.message_user(
+                    request,
+                    f"Record with ID {obj.id} is locked and cannot be deleted.",
+                    level='warning')
+        queryset = queryset.filter(locked=False)
+        if queryset:
+            super().delete_queryset(request, queryset)
+
 
 class PageviewAdmin(admin.ModelAdmin):
     date_hierarchy = 'view_time'
@@ -1115,7 +1141,8 @@ class TaxonomyAdmin(admin.ModelAdmin):
 
     raw_id_fields = (
         'parent',
-        'accepted_taxonomy'
+        'accepted_taxonomy',
+        'source_reference'
     )
 
     actions = ['merge_taxa', 'update_taxa', 'fetch_common_names', 'fetch_cites_listing']
@@ -1901,7 +1928,11 @@ class TaxonomyUpdateProposalAdmin(admin.ModelAdmin):
         'original_taxonomy',
         'scientific_name',
         'canonical_name',
-        'status'
+        'status',
+        'created_at'
+    )
+    autocomplete_fields = (
+        'vernacular_names',
     )
 
 
@@ -1916,7 +1947,7 @@ class TaxonomyUpdateReviewerAdmin(admin.ModelAdmin):
 @admin.register(CITESListingInfo)
 class CITESListingInfoAdmin(admin.ModelAdmin):
     list_display = ('appendix', 'effective_at', 'taxonomy')
-    list_filter = ('appendix', 'effective_at', 'taxonomy')
+    list_filter = ('appendix', 'effective_at')
     search_fields = ('annotation', 'taxonomy__name')
     raw_id_fields = ('taxonomy',)
 
@@ -1984,7 +2015,7 @@ class ImportTaskAdmin(admin.ModelAdmin):
 admin.site.register(SpatialScaleGroup, SpatialScaleGroupAdmin)
 admin.site.register(SamplingMethod, SamplingMethodAdmin)
 admin.site.register(SiteImage, SiteImageAdmin)
-admin.site.register(SiteSetting, PreferencesAdmin)
+admin.site.register(SiteSetting, SiteSettingAdmin)
 admin.site.register(GeocontextSetting, PreferencesAdmin)
 admin.site.register(ChemicalRecord, ChemicalRecordAdmin)
 admin.site.register(Chem, ChemAdmin)
@@ -2061,3 +2092,7 @@ class ImportTaskAdmin(admin.ModelAdmin):
     TaxonomyUpdateReviewer,
     TaxonomyUpdateReviewerAdmin
 )
+admin.site.register(
+    Invasion,
+    InvasionAdmin
+)

bims/admins/site_setting.py

@@ -0,0 +1,76 @@
+from django import forms
+from preferences.admin import PreferencesAdmin
+
+from bims.models.site_setting import SiteSetting
+
+SECRET_INPUTS = [
+    'recaptcha_secret_key',
+    'iucn_api_key',
+    'cites_token_api',
+    'virtual_museum_token',
+    'resend_api_key',
+    'github_feedback_token'
+]
+
+
+class SiteSettingAdminForm(forms.ModelForm):
+    class Meta:
+        model = SiteSetting
+        fields = '__all__'
+
+    recaptcha_secret_key = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    iucn_api_key = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    cites_token_api = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    virtual_museum_token = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    resend_api_key = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    github_feedback_token = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    minisass_token = forms.CharField(
+        widget=forms.PasswordInput(render_value=True),
+        required=False
+    )
+
+    def __init__(self, *args, **kwargs):
+        super(SiteSettingAdminForm, self).__init__(*args, **kwargs)
+        if self.instance and self.instance.pk:
+            for secret_input in SECRET_INPUTS:
+                self.fields[secret_input].widget.attrs['placeholder'] = '******'
+                self.fields[secret_input].required = False
+
+
+class SiteSettingAdmin(PreferencesAdmin):
+    form = SiteSettingAdminForm
+
+    def save_model(self, request, obj, form, change):
+        if change:
+            for secret_input in SECRET_INPUTS:
+                if secret_input in form.changed_data:
+                    setattr(obj, secret_input, form.cleaned_data[secret_input])
+                else:
+                    current_value = getattr(obj, secret_input)
+                    setattr(obj, secret_input, current_value)
+        obj.save()
+

bims/api_urls.py

@@ -5,6 +5,8 @@
     IsHarvestingGeocontext, HarvestGeocontextView, ClearHarvestingGeocontextCache,
     GetGeocontextLogLinesView
 )
+from bims.api_views.minisass_observations import MiniSASSObservationsView
+from bims.api_views.invasions import InvasionsList
 from bims.api_views.taxon_update import UpdateTaxon, ReviewTaxonProposal
 from bims.api_views.reference import DeleteRecordsByReferenceId
 # from rest_framework.documentation import include_docs_urls
@@ -26,6 +28,7 @@
     NonBiodiversityLayerList, DownloadLayerData
 )
 from bims.api_views.search_module import SearchModuleAPIView
+
 from bims.api_views.taxon import (
     TaxonDetail,
     FindTaxon,
@@ -117,6 +120,7 @@
 )
 from bims.api_views.wetland_data import WetlandDataApiView
 from bims.views.cites import TaxaCitesStatusAPIView
+from mobile.api_views.taxon_group import TaxonGroupTotalValidated
 
 urlpatterns = [
     re_path(r'^location-type/(?P<pk>[0-9]+)/allowed-geometry/$',
@@ -229,6 +233,9 @@
     re_path(r'^endemism-list/$',
         EndemismList.as_view(),
         name='endemism-list'),
+    re_path(r'^invasions-list/$',
+        InvasionsList.as_view(),
+        name='invasions-list'),
     re_path(r'^spatial-scale-filter-list/$',
         SpatialScaleFilterList.as_view(),
         name='spatial-scale-filter-list'),
@@ -370,4 +377,10 @@
     path('harvesting-geocontext-logs/',
          GetGeocontextLogLinesView.as_view(),
          name='get_log_lines'),
+    path('minisass-observations/',
+         MiniSASSObservationsView.as_view(),
+         name='minisass-observations'),
+    path('taxon-group-validated/<int:id>/',
+         TaxonGroupTotalValidated.as_view(),
+         name='taxon-group-total-validated'),
 ]

bims/api_views/checklist.py

@@ -3,13 +3,24 @@
 from django.conf import settings
 from django.http import Http404
 from preferences import preferences
+from reportlab.lib import colors
+from reportlab.lib.pagesizes import A4, landscape
+from reportlab.lib.styles import getSampleStyleSheet
+from reportlab.lib.units import cm
+from reportlab.platypus import SimpleDocTemplate, TableStyle, Table, Spacer
+from reportlab.platypus.para import Paragraph
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
 from bims.api_views.search import CollectionSearch
+from bims.enums import TaxonomicRank
 from bims.models.taxonomy import Taxonomy
+from bims.utils.domain import get_current_domain
 from bims.models.download_request import DownloadRequest
-from bims.serializers.checklist_serializer import ChecklistSerializer
+from bims.serializers.checklist_serializer import (
+    ChecklistSerializer,
+    ChecklistPDFSerializer
+)
 from bims.utils.url import parse_url_to_filters
 from bims.tasks.checklist import download_checklist
 from bims.tasks.email_csv import send_csv_via_email
@@ -60,11 +71,32 @@ def generate_checklist(download_request_id):
     search = CollectionSearch(filters)
     batch_size = 1000
     collection_records = search.process_search().distinct('taxonomy')
+    module_name = ''
+
+    if collection_records.count() > 0:
+        module_name = collection_records.values_list(
+            'module_group__name',
+            flat=True
+        )[0]
+
+    if (
+        download_request.resource_type and
+        download_request.resource_type.lower() == 'pdf'
+    ):
+        return generate_pdf_checklist(
+            download_request, module_name, collection_records, batch_size)
+    else:
+        return generate_csv_checklist(
+            download_request, module_name, collection_records, batch_size)
+
+
+def generate_csv_checklist(download_request, module_name, collection_records, batch_size):
+    site_domain_name = get_current_domain()
 
     csv_file_path = os.path.join(
         settings.MEDIA_ROOT,
         'checklists',
-        f'checklist_{download_request_id}.csv')
+        f'{site_domain_name}_checklist_{module_name}_{download_request.id}.csv')
     os.makedirs(os.path.dirname(csv_file_path), exist_ok=True)
 
     fieldnames = [key for key in get_serializer_keys(ChecklistSerializer) if key != 'id']
@@ -83,9 +115,88 @@ def generate_checklist(download_request_id):
             batch = collection_records[start:start + batch_size]
             process_batch(batch, writer, written_taxa_ids)
 
-    # Save file path to download_request
     download_request.processing = False
     download_request.request_file = csv_file_path
+    download_request.request_category = f'{module_name} Checklist'
+    download_request.save()
+
+    return True
+
+
+def generate_pdf_checklist(download_request, module_name, collection_records, batch_size):
+    site_domain_name = get_current_domain()
+    pdf_file_path = os.path.join(
+        settings.MEDIA_ROOT,
+        'checklists',
+        f'{site_domain_name}_checklist_{module_name}_{download_request.id}.pdf')
+    os.makedirs(os.path.dirname(pdf_file_path), exist_ok=True)
+
+    written_taxa_ids = set()
+    all_taxa = []
+
+    for start in range(0, collection_records.count(), batch_size):
+        batch = collection_records[start:start + batch_size]
+        record_taxonomy_ids = batch.values_list('taxonomy_id', flat=True)
+        unique_taxonomy_ids = set(record_taxonomy_ids) - written_taxa_ids
+
+        if unique_taxonomy_ids:
+            taxa = Taxonomy.objects.filter(
+                id__in=unique_taxonomy_ids
+            ).filter(
+                rank__in=[
+                    TaxonomicRank.SPECIES.name,
+                    TaxonomicRank.SUBSPECIES.name]
+            )
+            taxon_serializer = ChecklistPDFSerializer(taxa, many=True)
+            for taxon in taxon_serializer.data:
+                written_taxa_ids.add(taxon['id'])
+                del taxon['id']
+                all_taxa.append([
+                    Paragraph(taxon['scientific_name'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['common_name'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['threat_status'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['sources'], getSampleStyleSheet()['Normal'])
+                ])
+
+    # Generate the PDF
+    doc = SimpleDocTemplate(
+        pdf_file_path,
+        pagesize=landscape(A4), topMargin=0.5 * cm, bottomMargin=0.35 * cm)
+    elements = []
+
+    # Define table style
+    style_table = TableStyle([
+        ('BACKGROUND', (0, 0), (-1, 0), '#0D3511'),
+        ('TEXTCOLOR', (0, 0), (-1, 0), colors.white),
+        ('ALIGN', (0, 0), (-1, -1), 'LEFT'),
+        ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
+        ('FONTSIZE', (0, 0), (-1, 0), 11),
+        ('BOTTOMPADDING', (0, 0), (-1, 0), 5),
+        ('BACKGROUND', (0, 1), (-1, -1), colors.white),
+        ('GRID', (0, 0), (-1, -1), 1, colors.black),
+        ('LEFTPADDING', (0, 0), (-1, -1), 5),
+        ('RIGHTPADDING', (0, 0), (-1, -1), 5),
+        ('TOPPADDING', (0, 0), (-1, -1), 5),
+        ('BOTTOMPADDING', (0, 0), (-1, -1), 5),
+    ])
+
+    data = [
+               ['Accepted Scientific name and authority',
+                'Common Name',
+                'Threat Status',
+                'Sources']] + all_taxa
+    table_width = doc.width
+    col_widths = [table_width * 0.35, table_width * 0.30, table_width * 0.15, table_width * 0.30]
+
+    table = Table(data, colWidths=col_widths)
+    table.setStyle(style_table)
+
+    elements.append(table)
+    doc.build(elements)
+
+    download_request.processing = False
+    download_request.request_file = pdf_file_path
+    download_request.request_category = f'{module_name} Checklist'
     download_request.save()
 
     return True