Merge pull request #710 from upconsulting/develop

Develop

.elasticbeanstalk/config.yml

@@ -4,7 +4,8 @@ branch-defaults:
   develop:
     environment: isiscb-develop
 global:
-  application_name: IsisCB
+  application_name: IsisCB Staging Python 3
+  #application_name: IsisCB Celery Staging Python 3 (non worker)
   default_ec2_keyname: isiscb-eb
   default_platform: 64bit Amazon Linux 2015.03 v2.0.1 running Python 2.7
   default_region: us-west-2

isiscb/curation/forms.py

@@ -234,6 +234,36 @@ class Meta(object):
         model = AuthorityValue
         fields = ['value']
 
+class CitationValueForm(forms.ModelForm):
+    value = forms.CharField(label="Citation ID", widget=forms.TextInput(attrs={'data-type':'citation_id'}))
+    citation_name = forms.CharField(label='Name of stored citation', widget=forms.TextInput(attrs={'readonly': True}))
+
+    def __init__(self, *args, **kwargs):
+        super(CitationValueForm, self).__init__(*args, **kwargs)
+        instance = kwargs.get('instance')
+
+        if instance and not self.is_bound:
+            self.fields['value'].initial = instance.pk
+            self.fields['citation_name'].initial = instance.value.title_for_display
+
+    def clean_value(self):
+        value = self.cleaned_data['value']
+
+        try:
+            value = Citation.objects.get(id=value)
+        except:
+            raise forms.ValidationError('Citation record does not exist.')
+
+        return value
+
+    def save(self, *args, **kwargs):
+        self.instance.value = self.cleaned_data.get('value')
+        super(CitationValueForm, self).save(*args, **kwargs)
+
+    class Meta(object):
+        model = CitationValue
+        fields = ['value']
+
 class PartDetailsForm(forms.ModelForm):
     extent_note = forms.CharField(widget=forms.widgets.Textarea({'rows': '1'}), required=False)
 

isiscb/curation/templates/curation/authority_attribute_changeview.html

@@ -122,6 +122,7 @@
                       {{ attribute_form.value_freeform|addcss:"form-control" }}
                     </div>
                 </div>
+                <div id="ajax_errors"></div>
             </div>
         </div>
         <div class="clearfix">
@@ -170,7 +171,7 @@
     var value = $(this).val();
     var container = $('#value_form_container');
     container.empty();
-    var form = $('#form_for_' + value).clone();
+    var form = $('#form_for_' + value).clone(withDataAndEvents=true);
     container.append(form);
 
     // update help text
@@ -205,6 +206,19 @@
       $("#geocode-attr-warning").modal('hide');
       $("#attributeForm").submit();
   })
+
+  $("[data-type='citation_id']").change(function() {
+    $.ajax({
+      url: "{% url 'curation:api_citation' %}" + "?id=" + $("[data-type='citation_id']").val(),
+      success: function(data) {
+        $("#ajax_errors").text("")
+        $("#id_value-citation_name").val(data['title'])
+      },
+      error: function(data) {
+        $("#ajax_errors").html('<i class="fa fa-warning" aria-hidden="true"></i> Citation with provided id could not be found.')
+      }
+    });
+  });
 });
 </script>
 
@@ -265,7 +279,7 @@ <h4 class="modal-title" id="delete-attribute-modal-label">Are you sure?</h4>
                     You are about to delete an attribute of type <span class="text-warning" id="delete-attribute-target-name"></span>. Deletion cannot be undone!
                 </p>
                 {% if attribute.type_controlled.name == country_code_attribute %}
-                <p style="color: #8a6d3b"> 
+                <p style="color: #8a6d3b">
                   This attribute is a country code. You might need to reindex related citations to make sure your changes are reflected on the public site.
                 </p>
                 {% endif %}

isiscb/curation/urls.py

@@ -49,6 +49,8 @@
     re_path(r'^citation/(?P<citation_id>[A-Z0-9]+)/$', views.citation, name='curate_citation'),
     re_path(r'^authority/(?P<authority_id>[A-Z0-9]+)/$', views.authority, name='curate_authority'),
 
+    re_path(r'^api/citation$', views.get_citation_by_id, name='api_citation'),
+
     re_path(r'^timelines$', bulk_change_csv_views.timeline_tasks, name='timeline_tasks'),
     re_path(r'^timelines/(?P<authority_id>[A-Z0-9]+)/delete$', bulk_change_csv_views.timeline_delete, name='delete_timeline'),
 

isiscb/curation/view_helpers.py

@@ -13,6 +13,8 @@ def _create_attribute_value_forms():
             value_forms[at.id] = ISODateValueForm
         elif value_class is AuthorityValue:
             value_forms[at.id] = AuthorityValueForm
+        elif value_class is CitationValue:
+            value_forms[at.id] = CitationValueForm
         else:
             value_forms[at.id] = modelform_factory(value_class,
                                     exclude=('attribute', 'child_class'))

isiscb/curation/views.py

@@ -2136,6 +2136,19 @@ def search_users(request):
     } for u in queryset[:20]]
     return JsonResponse(results, safe=False)
 
+@user_passes_test(lambda u: u.is_superuser or u.is_staff)
+def get_citation_by_id(request):
+    id = request.GET.get('id', None)
+    if not id:
+        return JsonResponse({'citation': None})
+
+    citation = Citation.objects.filter(id=id).first()
+    if not citation:
+        return JsonResponse({}, status=404)
+    return JsonResponse({
+        'id': citation.id,
+        'title': citation.title_for_display,
+    })
 
 @user_passes_test(lambda u: u.is_superuser or u.is_staff)
 def quick_and_dirty_citation_search(request):
@@ -2293,7 +2306,7 @@ def _get_filtered_queryset(request, object_type='CITATION'):
         if 'collection_only' in filter_params:
             filter_params.pop('collection_only')
     filter_params_raw = filter_params.urlencode()#.encode('utf-8')
-    if object_type is 'CITATION':
+    if object_type == 'CITATION':
         _qs = operations.filter_queryset(request.user, Citation.objects.all())
         queryset = CitationFilter(filter_params, queryset=_qs)
     else:

isiscb/isiscb/local_postgresql_settings.py

@@ -327,6 +327,7 @@
 TIMELINE_PUBLICATION_DATE_ATTRIBUTE = os.environ.get('TIMELINE_PUBLICATION_DATE_ATTRIBUTE', "PublicationDate")
 RECORD_SUBTYPE_ATTRIBUTE = os.environ.get('RECORD_SUBTYPE_ATTRIBUTE', "RecordSubType")
 ACCESSED_ATTRIBUTE_NAME = os.environ.get('ACCESSED_ATTRIBUTE_NAME', "LastAccessedDate")
+BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME = os.environ.get('BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME', "BibliographicEssay")
 
 DOI_LINKED_DATA_NAME = os.environ.get('DOI_LINKED_DATA_NAME', "DOI")
 ISBN_LINKED_DATA_NAME = os.environ.get('ISBN_LINKED_DATA_NAME', "ISBN")

isiscb/isiscb/production_settings.py

@@ -412,6 +412,7 @@
 TIMELINE_PUBLICATION_DATE_ATTRIBUTE = os.environ.get('TIMELINE_PUBLICATION_DATE_ATTRIBUTE', "PublicationDate")
 RECORD_SUBTYPE_ATTRIBUTE = os.environ.get('RECORD_SUBTYPE_ATTRIBUTE', "RecordSubType")
 ACCESSED_ATTRIBUTE_NAME = os.environ.get('ACCESSED_ATTRIBUTE_NAME', "LastAccessedDate")
+BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME = os.environ.get('BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME', "BibliographicEssay")
 
 COUNTRY_CODE_ATTRIBUTE = os.environ.get('COUNTRY_CODE_ATTRIBUTE', "CountryCode")
 

isiscb/isiscb/test_settings.py

@@ -321,6 +321,7 @@
 TIMELINE_PUBLICATION_DATE_ATTRIBUTE = os.environ.get('TIMELINE_PUBLICATION_DATE_ATTRIBUTE', "PublicationDate")
 RECORD_SUBTYPE_ATTRIBUTE = os.environ.get('RECORD_SUBTYPE_ATTRIBUTE', "RecordSubType")
 ACCESSED_ATTRIBUTE_NAME = os.environ.get('ACCESSED_ATTRIBUTE_NAME', "LastAccessedDate")
+BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME = os.environ.get('BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME', "BibliographicEssay")
 
 DOI_LINKED_DATA_NAME = os.environ.get('DOI_LINKED_DATA_NAME', "DOI")
 ISBN_LINKED_DATA_NAME = os.environ.get('ISBN_LINKED_DATA_NAME', "ISBN")

isiscb/isisdata/migrations/0095_auto_20210826_0119.py

@@ -0,0 +1,32 @@
+# Generated by Django 3.0.7 on 2021-08-26 01:19
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('contenttypes', '0002_remove_content_type_name'),
+        ('isisdata', '0094_auto_20210717_1853'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='attributetype',
+            name='value_content_type',
+            field=models.ForeignKey(limit_choices_to=models.Q(('model', 'textvalue'), ('model', 'charvalue'), ('model', 'intvalue'), ('model', 'datetimevalue'), ('model', 'datevalue'), ('model', 'floatvalue'), ('model', 'locationvalue'), ('model', 'isodatevalue'), ('model', 'isodaterangevalue'), ('model', 'authorityvalue'), ('model', 'citationvalue'), _connector='OR'), on_delete=django.db.models.deletion.CASCADE, related_name='attribute_value', to='contenttypes.ContentType'),
+        ),
+        migrations.CreateModel(
+            name='CitationValue',
+            fields=[
+                ('value_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='isisdata.Value')),
+                ('name', models.TextField(blank=True, null=True)),
+                ('value', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='isisdata.Citation')),
+            ],
+            options={
+                'verbose_name': 'citation',
+            },
+            bases=('isisdata.value',),
+        ),
+    ]

isiscb/isisdata/models.py

@@ -43,7 +43,8 @@
 VALUETYPES = Q(model='textvalue') | Q(model='charvalue') | Q(model='intvalue') \
             | Q(model='datetimevalue') | Q(model='datevalue') \
             | Q(model='floatvalue') | Q(model='locationvalue') \
-            | Q(model='isodatevalue') | Q(model='isodaterangevalue') | Q(model='authorityvalue')
+            | Q(model='isodatevalue') | Q(model='isodaterangevalue') \
+            | Q(model='authorityvalue') | Q(model='citationvalue')
 
 
 class Value(models.Model):
@@ -533,6 +534,34 @@ def __str__(self):
     class Meta(object):
         verbose_name = 'location'
 
+class CitationValue(Value):
+    """
+    A citation value. Points to an instance of :class:`.Citation`\.
+    """
+    # CHECK: Had to add on_delete so chose cascade -> JD: since we don't delete Authorities at the moment, this is probably fine
+    value = models.ForeignKey('Citation', on_delete=models.CASCADE)
+    name = models.TextField(blank=True, null=True)
+
+    def __unicode__(self):
+        return str(self.value)
+
+    def __str__(self):
+        return str(self.value)
+
+    class Meta(object):
+        verbose_name = 'citation'
+
+    @staticmethod
+    def convert(value):
+        if type(value) is Citation:
+            return value
+
+        try:
+            return Citation.objects.get(pk=value)
+        except ValueError:
+            raise ValidationError('Must be the id of an existing citation.')
+
+
 class AuthorityValue(Value):
     """
     An authority value. Points to an instance of :class:`.Authority`\.

isiscb/isisdata/templates/isisdata/authority_fragments/fragment_authority_info_box.html

@@ -2,6 +2,7 @@
 {% load static %}
 {% load search_filters %}
 {% load authority_filters %}
+{% load citation_filters %}
 {% load facet_filters %}
 
 
@@ -131,8 +132,24 @@ <h3 style="margin-top: 5px;">{{ authority.name }}</h3>
   </script>
   {% endif %}
 
+  {% with authority|get_bibliographic_essays as bib_essays %}
+  {% if bib_essays %}
+  {% for bib_essay in bib_essays %}
+  <p>
+    <strong>There is a bibliographic essay on this topic: "<a href="{% url 'citation' bib_essay.value.cvalue.id %}">{{bib_essay.value.cvalue.title_for_display}}</a>" by {{bib_essay.value.cvalue|get_authors|join_authors:""}}</strong>
+    <!-- todo: list all and link link -->
+    {% if bib_essay.value.cvalue|get_urls %}
+    {% for url in bib_essay.value.cvalue|get_urls %}
+    <br><strong>Link:</strong> {{ url.resource_name }}
+    {% endfor %}
+    {% endif %}
+  </p>
+  {% endfor %}
+  {% endif %}
+  {% endwith %}
+
   {% for attribute in authority.attributes.all %}
-  {% if attribute|is_attribute_visible %}
+  {% if attribute|is_attribute_visible and not attribute|is_bibliographic_essay %}
   <p><strong>{{ attribute.type_controlled.display_name }}:</strong> {% if attribute.value_freeform %}{{ attribute.value_freeform }}{% else %}{{ attribute.value.display }}{% endif %}</p>
   {% endif %}
   {% endfor %}

isiscb/isisdata/templatetags/authority_filters.py

@@ -15,3 +15,15 @@ def is_attribute_visible(attribute):
             return False
 
     return attribute.public
+
+@register.filter
+def is_bibliographic_essay(attribute):
+    return attribute.type_controlled.name==settings.BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME
+
+@register.filter
+def get_bibliographic_essays(authority):
+    return authority.attributes.filter(type_controlled__name=settings.BIBLIOGRAPHIC_ESSAY_ATTRIBUTE_NAME)
+
+@register.filter
+def get_urls(citation):
+    return citation.linkeddata_entries.filter(type_controlled__name=settings.URL_LINKED_DATA_NAME)

isiscb/isisdata/templatetags/citation_filters.py

@@ -46,6 +46,12 @@ def get_editors(citation):
         return citation.acrelation_set.filter(type_controlled__in=['ED'])
     return citation
 
+@register.filter
+def get_authors(citation):
+    if citation:
+        return citation.acrelation_set.filter(type_controlled__in=['AU'], citation__public=True, public=True).order_by('data_display_order')
+    return citation
+
 
 @register.filter
 def join_names_with_postfix(name_list, postfix):

requirements.txt

@@ -1,14 +1,14 @@
 amqp==2.5.2
-asgiref==3.2.7
+#asgiref==3.2.7
 attrs==19.3.0
-awsebcli==3.18.2
+awsebcli==3.20.2
 backports.ssl-match-hostname==3.7.0.1
 bcrypt==3.1.7
 billiard==3.6.3.0
 bleach==3.1.4
 blessed==1.17.4
-boto3==1.12.36
-botocore==1.15.36
+boto3==1.18.35
+botocore==1.21.36
 cached-property==1.5.1
 cachetools==4.0.0
 celery==4.4.2
@@ -21,14 +21,14 @@ colorclass==2.2.0
 confusable-homoglyphs==3.2.0
 cryptography==2.9
 defusedxml==0.6.0
-Django==3.0.7
+Django==3.1.12
 django-allauth==0.41.0
 django-autocomplete-light==3.5.1
 django-braces==1.14.0
 django-celery-results==1.2.1
 django-cors-headers==3.2.1
 django-extensions==2.2.9
-django-filter==2.2.0
+django-filter==2.4.0
 django-guardian==2.2.0
 django-haystack==3.0b1
 django-ipware==2.1.0
@@ -76,7 +76,7 @@ paramiko==2.7.1
 pathspec==0.5.9
 pbr==5.4.4
 pefile==2019.4.18
-Pillow==8.0
+Pillow==8.3.2
 pip-upgrader==1.4.15
 protobuf==3.11.3
 psycopg2-binary==2.8.6
@@ -96,12 +96,12 @@ PyYAML==5.3.1
 rdflib==4.2.2
 redis==3.4.1
 regex==2020.4.4
-requests==2.20.1
+#requests==2.20.1
 requests-oauthlib==1.3.0
 rsa==4.0
 rules==2.2
-s3transfer==0.3.3
-semantic-version==2.5.0
+#s3transfer==0.3.3
+#semantic-version==2.5.0
 six==1.11.0
 smart-open==1.10.0
 social-auth-app-django==3.1.0
@@ -112,7 +112,7 @@ termcolor==1.1.0
 terminaltables==3.1.0
 texttable==1.6.2
 Unidecode==1.1.1
-urllib3==1.24.3
+urllib3==1.26.6
 vine==1.3.0
 wcwidth==0.1.9
 webencodings==0.5.1