CU-2e77aae MetaCAT model Predictions

webapp/api/api/admin/__init__.py

@@ -5,13 +5,13 @@
 admin.site.register(Entity)
 admin.site.register(MetaTaskValue)
 admin.site.register(MetaTask)
-admin.site.register(MetaAnnotation)
 admin.site.register(Vocabulary)
 admin.site.register(Relation)
 admin.site.register(EntityRelation)
 admin.site.register(ProjectGroup, ProjectGroupAdmin)
 admin.site.register(ProjectAnnotateEntities, ProjectAnnotateEntitiesAdmin)
 admin.site.register(AnnotatedEntity, AnnotatedEntityAdmin)
+admin.site.register(MetaAnnotation, MetaAnnotationAdmin)
 admin.site.register(ConceptDB, ConceptDBAdmin)
 admin.site.register(Document, DocumentAdmin)
 admin.site.register(ExportedProject, ExportedProjectAdmin)

webapp/api/api/admin/actions.py

@@ -26,8 +26,10 @@ def reset_project(modeladmin, request, queryset):
         # Remove all annotations and cascade to meta anns
         AnnotatedEntity.objects.filter(project=project).delete()
 
-        # Set all validated documents to none
+        # Clear validated_docuents and prepared_documents
         project.validated_documents.clear()
+        project.prepared_documents.clear()
+
 
 
 def download_without_text(modeladmin, request, queryset):

webapp/api/api/admin/models.py

@@ -8,7 +8,7 @@
 from ..models import *
 
 _PROJECT_ANNO_ENTS_SETTINGS_FIELD_ORDER = (
-    'concept_db', 'vocab', 'cdb_search_filter', 'require_entity_validation', 'train_model_on_submit',
+    'concept_db', 'vocab', 'model_pack', 'cdb_search_filter', 'require_entity_validation', 'train_model_on_submit',
     'add_new_entities', 'restrict_concept_lookup', 'terminate_available', 'irrelevant_available',
     'enable_entity_annotation_comments', 'tasks', 'relations'
 )
@@ -43,7 +43,8 @@ class ProjectAnnotateEntitiesAdmin(admin.ModelAdmin):
     actions = [download, download_without_text, download_without_text_with_doc_names, reset_project, clone_projects]
     list_filter = ('members', 'project_status', 'project_locked', 'annotation_classification')
     list_display = ['name']
-    fields = (('group', 'name', 'description', 'annotation_guideline_link', 'members', 'dataset', 'validated_documents') +
+    fields = (('group', 'name', 'description', 'annotation_guideline_link', 'members',
+               'dataset', 'validated_documents', 'prepared_documents') +
               _PROJECT_FIELDS_ORDER +
               _PROJECT_ANNO_ENTS_SETTINGS_FIELD_ORDER)
 
@@ -55,7 +56,7 @@ def formfield_for_foreignkey(self, db_field, request, **kwargs):
     def formfield_for_manytomany(self, db_field, request, **kwargs):
         if db_field.name == 'cdb_search_filter':
             kwargs['queryset'] = ConceptDB.objects.all()
-        if db_field.name == 'validated_documents':
+        if db_field.name in ('validated_documents', 'prepared_documents'):
             project_id = request.path.replace('/admin/api/projectannotateentities/', '').split('/')[0]
             try:
                 proj = ProjectAnnotateEntities.objects.get(id=int(project_id))
@@ -165,7 +166,13 @@ def metacats(self, obj):
 class MetaCATModelAdmin(admin.ModelAdmin):
     model = MetaCATModel
     list_display = ('name', 'meta_cat_dir')
-    list_filter = ['meta_task']
+
+
+class MetaAnnotationAdmin(admin.ModelAdmin):
+    model = MetaAnnotation
+    list_display = ('annotated_entity', 'meta_task', 'meta_task_value', 'acc',
+                    'predicted_meta_task_value', 'validated', 'last_modified')
+    list_filter = ('meta_task', 'meta_task_value', 'predicted_meta_task_value', 'validated')
 
 
 class DocumentAdmin(admin.ModelAdmin):

webapp/api/api/metrics.py

@@ -36,15 +36,21 @@
 def calculate_metrics(project_ids: List[int], report_name: str):
     """
     Computes metrics in a background task
-    :param projects: list of projects to compute metrics for. Uses the 'first' for the CDB, but
-    should be the same CDB, but will still try and compute metrics regardless
+    :param projects: list of projects to compute metrics for.
+        Uses the 'first' for the CDB / vocab or ModelPack,
+        but should be the same CDB, but will still try and compute metrics regardless.
     :return: computed metrics results
     """
     logger.info('Calculating metrics for report: %s', report_name)
     projects = [ProjectAnnotateEntities.objects.filter(id=p_id).first() for p_id in project_ids]
-    cdb = CDB.load(projects[0].concept_db.cdb_file.path)
-    vocab = Vocab.load(projects[0].vocab.vocab_file.path)
-    cat = CAT(cdb, vocab, config=cdb.config)
+    if projects[0].cdb is None:
+        # assume the model pack is set.
+        cat = CAT.load_model_pack(projects[0].model_pack.model_pack.path)
+    else:
+        # assume the cdb / vocab is set in these projects
+        cdb = CDB.load(projects[0].concept_db.cdb_file.path)
+        vocab = Vocab.load(projects[0].vocab.vocab_file.path)
+        cat = CAT(cdb, vocab, config=cdb.config)
     project_data = retrieve_project_data(projects)
     metrics = ProjectMetrics(project_data, cat)
     report = metrics.generate_report()

webapp/api/api/migrations/0082_remove_metacatmodel_meta_task_and_more.py

@@ -0,0 +1,98 @@
+# Generated by Django 5.0.6 on 2024-08-28 10:56
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0081_alter_metatask_name'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='metacatmodel',
+            name='meta_task',
+        ),
+        migrations.AddField(
+            model_name='metaannotation',
+            name='predicted_meta_task_value',
+            field=models.ForeignKey(blank=True, help_text='meta annotation predicted by a MetaAnnotationModel', null=True, on_delete=django.db.models.deletion.CASCADE, related_name='predicted_value', to='api.metataskvalue'),
+        ),
+        migrations.AddField(
+            model_name='metatask',
+            name='prediction_model',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.metacatmodel'),
+        ),
+        migrations.AddField(
+            model_name='project',
+            name='meta_cat_predictions',
+            field=models.BooleanField(default=False, help_text='If MetaTasks are setup on the project and there are associated MetaCATModel instances, display these predictions in the interface to be validated / corrected'),
+        ),
+        migrations.AddField(
+            model_name='projectannotateentities',
+            name='model_pack',
+            field=models.ForeignKey(blank=True, default=None, help_text='A MedCAT model pack. This will raise an exception if both the CDB and Vocab and ModelPack fields are set', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.modelpack'),
+        ),
+        migrations.AddField(
+            model_name='projectgroup',
+            name='meta_cat_predictions',
+            field=models.BooleanField(default=False, help_text='If MetaTasks are setup on the project and there are associated MetaCATModel instances, display these predictions in the interface to be validated / corrected'),
+        ),
+        migrations.AddField(
+            model_name='projectgroup',
+            name='model_pack',
+            field=models.ForeignKey(blank=True, default=None, help_text='A MedCAT model pack. This will raise an exception if both the CDB and Vocab and ModelPack fields are set', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.modelpack'),
+        ),
+        migrations.AlterField(
+            model_name='metaannotation',
+            name='validated',
+            field=models.BooleanField(default=False, help_text='If an annotation is not '),
+        ),
+        migrations.AlterField(
+            model_name='metacatmodel',
+            name='meta_cat_dir',
+            field=models.FilePathField(allow_folders=True, editable=False, help_text='The zip or dir for a MetaCAT model, not editable, is set via a model pack .zip upload'),
+        ),
+        migrations.AlterField(
+            model_name='metacatmodel',
+            name='name',
+            field=models.CharField(help_text='The task name followed by the underlying model impl', max_length=100),
+        ),
+        migrations.AlterField(
+            model_name='projectannotateentities',
+            name='concept_db',
+            field=models.ForeignKey(blank=True, help_text='The MedCAT CDB used to annotate / validate', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.conceptdb'),
+        ),
+        migrations.AlterField(
+            model_name='projectannotateentities',
+            name='tasks',
+            field=models.ManyToManyField(blank=True, default=None, help_text='The set of MetaAnnotation tasks configured for this project, this will default to the set of Tasks configured in a ModelPack if a model pack is used for the project', to='api.metatask'),
+        ),
+        migrations.AlterField(
+            model_name='projectannotateentities',
+            name='vocab',
+            field=models.ForeignKey(blank=True, help_text='The MedCAT Vocab used to annotate / validate', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.vocabulary'),
+        ),
+        migrations.AlterField(
+            model_name='projectgroup',
+            name='cdb_search_filter',
+            field=models.ManyToManyField(blank=True, help_text='The CDB that will be used for concept lookup. This specific CDB should have been "imported" via the CDB admin screen', related_name='project_group_concept_source', to='api.conceptdb'),
+        ),
+        migrations.AlterField(
+            model_name='projectgroup',
+            name='concept_db',
+            field=models.ForeignKey(blank=True, help_text='The MedCAT CDB used to annotate / validate', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.conceptdb'),
+        ),
+        migrations.AlterField(
+            model_name='projectgroup',
+            name='tasks',
+            field=models.ManyToManyField(blank=True, default=None, help_text='The set of MetaAnnotation tasks configured for this project, this will default to the set of Tasks configured in a ModelPack if a model pack is used for the project', to='api.metatask'),
+        ),
+        migrations.AlterField(
+            model_name='projectgroup',
+            name='vocab',
+            field=models.ForeignKey(blank=True, help_text='The MedCAT Vocab used to annotate / validate', null=True, on_delete=django.db.models.deletion.SET_NULL, to='api.vocabulary'),
+        ),
+    ]

webapp/api/api/migrations/0083_project_prepared_documents_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.0.6 on 2024-08-29 11:25
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0082_remove_metacatmodel_meta_task_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='project',
+            name='prepared_documents',
+            field=models.ManyToManyField(blank=True, default=None, help_text='Set automatically on each prep of a document', related_name='prepared_documents', to='api.document'),
+        ),
+        migrations.AlterField(
+            model_name='project',
+            name='validated_documents',
+            field=models.ManyToManyField(blank=True, default=None, help_text='Set automatically on each doc submission', to='api.document'),
+        ),
+    ]

webapp/api/api/model_cache.py

@@ -0,0 +1,127 @@
+import logging
+import os
+from typing import Dict
+
+import pkg_resources
+from medcat.cat import CAT
+from medcat.cdb import CDB
+from medcat.vocab import Vocab
+
+from api.models import ConceptDB
+
+"""
+Module level caches for CDBs, Vocabs and CAT instances.
+"""
+# Maps between IDs and objects
+CDB_MAP = {}
+VOCAB_MAP = {}
+CAT_MAP = {}
+
+
+logger = logging.getLogger(__name__)
+
+
+def get_medcat_from_cdb_vocab(project,
+                              cdb_map: Dict[str, CDB]=CDB_MAP,
+                              vocab_map: Dict[str, Vocab]=VOCAB_MAP,
+                              cat_map: Dict[str, CAT]=CAT_MAP) -> CAT:
+    cdb_id = project.concept_db.id
+    vocab_id = project.vocab.id
+    cat_id = str(cdb_id) + "-" + str(vocab_id)
+    if cat_id in cat_map:
+        cat = cat_map[cat_id]
+    else:
+        if cdb_id in cdb_map:
+            cdb = cdb_map[cdb_id]
+        else:
+            cdb_path = project.concept_db.cdb_file.path
+            try:
+                cdb = CDB.load(cdb_path)
+            except KeyError as ke:
+                mc_v = pkg_resources.get_distribution('medcat').version
+                if int(mc_v.split('.')[0]) > 0:
+                    logger.error('Attempted to load MedCAT v0.x model with MCTrainer v1.x')
+                    raise Exception('Attempted to load MedCAT v0.x model with MCTrainer v1.x',
+                                    'Please re-configure this project to use a MedCAT v1.x CDB or consult the '
+                                    'MedCATTrainer Dev team if you believe this should work') from ke
+                raise
+
+            custom_config = os.getenv("MEDCAT_CONFIG_FILE")
+            if custom_config is not None and os.path.exists(custom_config):
+                cdb.config.parse_config_file(path=custom_config)
+            else:
+                logger.info("No MEDCAT_CONFIG_FILE env var set to valid path, using default config available on CDB")
+            cdb_map[cdb_id] = cdb
+
+        if vocab_id in vocab_map:
+            vocab = vocab_map[vocab_id]
+        else:
+            vocab_path = project.vocab.vocab_file.path
+            vocab = Vocab.load(vocab_path)
+            vocab_map[vocab_id] = vocab
+        cat = CAT(cdb=cdb, config=cdb.config, vocab=vocab)
+        cat_map[cat_id] = cat
+    return cat
+
+
+def get_medcat_from_model_pack(project, cat_map: Dict[str, CAT]=CAT_MAP) -> CAT:
+    model_pack_obj = project.model_pack
+    cat_id = 'mp' + str(model_pack_obj.id)
+    logger.info('Loading model pack from:%s', model_pack_obj.model_pack.path)
+    cat = CAT.load_model_pack(model_pack_obj.model_pack.path)
+    cat_map[cat_id] = cat
+    return cat
+
+
+def get_medcat(project,
+               cdb_map: Dict[str, CDB]=CDB_MAP,
+               vocab_map: Dict[str, Vocab]=VOCAB_MAP,
+               cat_map: Dict[str, CAT]=CAT_MAP):
+    try:
+        if project.model_pack is None:
+            cat = get_medcat_from_cdb_vocab(project, cdb_map, vocab_map, cat_map)
+        else:
+            cat = get_medcat_from_model_pack(project, cat_map)
+        return cat
+    except AttributeError:
+        raise Exception('Failure loading Project ConceptDB, Vocab or Model Pack. Are these set correctly?')
+
+
+def get_cached_medcat(project, cat_map: Dict[str, CAT]=CAT_MAP):
+    if project.concept_db is None or project.vocab is None:
+        return None
+    cdb_id = project.concept_db.id
+    vocab_id = project.vocab.id
+    cat_id = str(cdb_id) + "-" + str(vocab_id)
+    return cat_map.get(cat_id)
+
+
+def clear_cached_medcat(project, cat_map: Dict[str, CAT]=CAT_MAP):
+    cdb_id = project.concept_db.id
+    vocab_id = project.vocab.id
+    cat_id = str(cdb_id) + "-" + str(vocab_id)
+    if cat_id in cat_map:
+        del cat_map[cat_id]
+
+
+def get_cached_cdb(cdb_id: str, cdb_map: Dict[str, CDB]=CDB_MAP) -> CDB:
+    if cdb_id not in cdb_map:
+        cdb_obj = ConceptDB.objects.get(id=cdb_id)
+        cdb = CDB.load(cdb_obj.cdb_file.path)
+        cdb_map[cdb_id] = cdb
+    return cdb_map[cdb_id]
+
+
+def clear_cached_cdb(cdb_id, cdb_map: Dict[str, CDB]=CDB_MAP):
+    if cdb_id in cdb_map:
+        del cdb_map[cdb_id]
+
+
+def is_model_loaded(project,
+                    cdb_map: Dict[str, CDB]=CDB_MAP,
+                    cat_map: Dict[str, CAT]=CAT_MAP):
+    if project.concept_db is None:
+        # model pack is used.
+        return False if not project.model_pack else f'mp{project.model_pack.id}' in cat_map
+    else:
+        return False if not project.concept_db else project.concept_db.id in cdb_map