Add BCO Score to model.

Also added functions and methods for BCO Score.
Updates to the BCO admin panel.
Updates to the `test_data.json` and `local_data.json`
Fix # 310
Changes to be committed:
	modified:   authentication/migrations/0001_initial.py
	modified:   biocompute/admin.py
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	new file:   config/bco_scores.py
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json

Author: HadleyKing

authentication/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 3.2.13 on 2024-03-14 13:52
+# Generated by Django 3.2.13 on 2024-04-11 21:18
 
 from django.conf import settings
 from django.db import migrations, models

biocompute/admin.py

@@ -1,10 +1,44 @@
-"""BioCompute Object Admin Pannel
-"""
-
 from django.contrib import admin
-from biocompute.models import Bco
+from django.utils.html import format_html_join
+from django.utils.safestring import mark_safe
+from .models import Bco, User, Prefix
+
+class BcoAdmin(admin.ModelAdmin):
+    list_display = (
+        'object_id',
+        'owner',
+        'prefix',
+        'state',
+        'score',
+        'last_update',
+        'access_count',
+        'display_authorized_users'
+    )
+    search_fields = ['object_id', 'owner__username', 'state']
+    list_filter = ('state', 'last_update')
+    fieldsets = (
+        (None, {
+            'fields': ('object_id', 'contents')
+        }),
+        ('Permissions', {
+            'fields': ('owner', 'authorized_users')
+        }),
+        ('Details', {
+            'fields': (
+                'prefix',
+                'state',
+                'score',
+                'last_update',
+                'access_count'
+            )
+        }),
+    )
+    filter_horizontal = ('authorized_users',)
 
-# class BioComputeAdmin(admin.ModelAdmin):
-#     list_display = ["", ""]
+    def display_authorized_users(self, obj):
+        """Return a comma-separated list of authorized user names."""
+        return mark_safe(", ".join(
+            [user.username for user in obj.authorized_users.all()]))
+    display_authorized_users.short_description = "Authorized Users"
 
-admin.site.register(Bco)
+admin.site.register(Bco, BcoAdmin)

biocompute/apis.py

@@ -15,7 +15,6 @@
     retrieve_bco,
     user_can_modify_bco,
     user_can_publish_bco,
-    object_id_deconstructor,
 )
 from config.services import (
     legacy_api_converter,
@@ -347,7 +346,7 @@ def post(self, request) -> Response:
             data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
-            response_id = object.get("object_id", index)
+            response_id = object["contents"].get("object_id", index)
             modify_permitted = user_can_modify_bco(response_id, requester)
 
             if modify_permitted is None:
@@ -617,11 +616,12 @@ def post(self, request) -> Response:
                 else:
                     published_bco = publish_draft(bco_instance, requester, object)
                     identifier=published_bco.object_id
+                    score = published_bco.score
                     response_data.append(response_constructor(
                         identifier=identifier,
                         status = "SUCCESS",
                         code= 201,
-                        message= f"BCO {identifier} has been published.",
+                        message= f"BCO {identifier} has been published and assigned {score} as a score.",
                     ))
                     accepted_requests = True
 

biocompute/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 3.2.13 on 2024-04-02 20:08
+# Generated by Django 3.2.13 on 2024-04-11 21:16
 
 from django.conf import settings
 from django.db import migrations, models
@@ -21,6 +21,7 @@ class Migration(migrations.Migration):
                 ('object_id', models.TextField(primary_key=True, serialize=False)),
                 ('contents', models.JSONField()),
                 ('state', models.CharField(choices=[('REFERENCED', 'referenced'), ('PUBLISHED', 'published'), ('DRAFT', 'draft'), ('DELETE', 'delete')], default='DRAFT', max_length=20)),
+                ('score', models.IntegerField(default=0)),
                 ('last_update', models.DateTimeField()),
                 ('access_count', models.IntegerField(default=0)),
                 ('authorized_users', models.ManyToManyField(blank=True, related_name='authorized_bcos', to=settings.AUTH_USER_MODEL)),

biocompute/models.py

@@ -35,6 +35,8 @@ class Bco(models.Model):
         Prefix for the BCO
     state:str
         State of object. REFERENCED, PUBLISHED, DRAFT, and DELETE are currently accepted values.
+    score:int
+        Score assigned to BCO at the time of publishing. 
     last_update: DateTime
         Date Time object for the last database change to this object
     access_count: Int
@@ -44,7 +46,11 @@ class Bco(models.Model):
 
     object_id = models.TextField(primary_key=True)
     contents = models.JSONField()
-    prefix = models.ForeignKey(Prefix, on_delete=models.CASCADE, to_field="prefix")
+    prefix = models.ForeignKey(
+        Prefix,
+        on_delete=models.CASCADE,
+        to_field="prefix"
+    )
     owner = models.ForeignKey(
         User,
         to_field="username",
@@ -56,7 +62,12 @@ class Bco(models.Model):
         related_name="authorized_bcos",
         blank=True
     )
-    state = models.CharField(max_length=20, choices=STATE_CHOICES, default="DRAFT")
+    state = models.CharField(
+        max_length=20,
+        choices=STATE_CHOICES, 
+        default="DRAFT"
+    )
+    score = models.IntegerField(default=0)
     last_update = models.DateTimeField()
     access_count = models.IntegerField(default=0)
 

biocompute/services.py

@@ -281,7 +281,10 @@ def update(self, validated_data):
         )
         bco_instance.contents = validated_data['contents']
         bco_instance.last_update=timezone.now()
-        bco_contents = deepcopy(bco_instance.contents)
+        bco_contents = bco_instance.contents
+        bco_contents["provenance_domain"]["modified"] = datetime_converter(
+            timezone.now()
+        )
         etag = generate_etag(bco_contents)
         bco_instance.contents['etag'] = etag
         bco_instance.save()
@@ -563,7 +566,8 @@ def publish_draft(bco_instance: Bco, user: User, object: dict):
         timezone.now()
     )
     contents["etag"] = generate_etag(contents)
-    new_bco_instance.save()
+    thingk = bco_score(bco_instance=new_bco_instance)
+    import pdb; pdb.set_trace()
 
     if object["delete_draft"] is True:
         deleted = delete_draft(bco_instance=bco_instance, user=user)
@@ -581,4 +585,20 @@ def delete_draft(bco_instance:Bco, user:User,):
         bco_instance.save()
 
     return "deleted"
-  
+
+def bco_score(bco_instance: Bco) -> Bco:
+    """BCO Score 
+
+    Process and score BioCompute Objects (BCOs).
+
+    """
+
+    contents = bco_instance.contents
+    try:
+        usability_domain_length = sum(len(s) for s in contents['usability_domain'])
+        score = {"usability_domain_length": usability_domain_length}
+    except TypeError:
+        score = {"usability_domain_length": 0}
+    bco_instance.score = usability_domain_length
+    
+    return bco_instance

config/bco_scores.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+
+import os
+import django
+import json
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "bcodb.settings")
+django.setup()
+
+from django.db.models import F
+from django.db.models.functions import Length
+from biocompute.models import BCO
+
+def main():
+    """
+    Process and score BioCompute Objects (BCOs) based on the length of their usability_domain.
+
+    This function performs the following steps:
+    1. Fetches all published BCOs from the database, specifically retrieving their object_id and 
+       the contents of their usability_domain.
+    2. Calculates a 'score' for each BCO, which is the sum of the lengths of strings within the 
+       usability_domain field. If the usability_domain is not present or is invalid, a score of 0 is assigned.
+    3. Sorts the BCOs in descending order based on their scores.
+    4. Outputs the sorted list of BCOs, along with their scores, to a JSON file named 'bco_scores.json'.
+
+    The scoring and sorting help in identifying BCOs with more detailed and potentially more useful usability domains.
+    """
+    # Fetching all BCOs with their id and usability_domain
+    bcos = BCO.objects.filter(state='PUBLISHED').annotate(
+        usability_domain=F('contents__usability_domain')
+        ).values('object_id', 'usability_domain')
+
+    bcos_list = list(bcos)
+
+    count = 0
+    for bco in bcos_list:
+
+        try:
+            usability_domain_length = sum(len(s) for s in bco['usability_domain'])
+            count += 1
+            bco['score'] = {
+                "usability_domain_length": usability_domain_length
+            }
+        except TypeError:
+            import pdb; pdb.set_trace()
+            bco['score'] = {
+                "usability_domain_length": 0
+            }
+            count += 1
+
+    sorted_list_of_dicts = sorted(bcos_list, key=lambda d: d['score']['usability_domain_length'], reverse=True)
+
+    with open('bco_scores.json', "w") as file:
+        json.dump(sorted_list_of_dicts, file, indent=4)
+
+if __name__ == "__main__":
+    main()