Merge pull request #263 from bento-platform/develop

Version 2.2.7

chord_metadata_service/package.cfg

@@ -1,4 +1,4 @@
 [package]
 name = katsu
-version = 2.2.6
+version = 2.2.7
 authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire

chord_metadata_service/patients/filters.py

@@ -131,6 +131,40 @@ def filter_search(self, qs, name, value):
                                 "phenopackets__hts_files__genome_assembly",
                                 Cast("phenopackets__hts_files__individual_to_sample_identifiers", TextField()),
                                 Cast("phenopackets__hts_files__extra_properties", TextField()),
+
+                                # Experiment fields
+                                "phenopackets__biosamples__experiment__study_type",
+                                "phenopackets__biosamples__experiment__experiment_type",
+                                Cast("phenopackets__biosamples__experiment__experiment_ontology", TextField()),
+                                "phenopackets__biosamples__experiment__molecule",
+                                Cast("phenopackets__biosamples__experiment__molecule_ontology", TextField()),
+                                "phenopackets__biosamples__experiment__library_strategy",
+                                "phenopackets__biosamples__experiment__library_source",
+                                "phenopackets__biosamples__experiment__library_selection",
+                                "phenopackets__biosamples__experiment__library_layout",
+                                "phenopackets__biosamples__experiment__extraction_protocol",
+                                "phenopackets__biosamples__experiment__reference_registry_id",
+                                Cast("phenopackets__biosamples__experiment__extra_properties", TextField()),
+                                # Experiments: Experiment Results fields
+                                "phenopackets__biosamples__experiment__experiment_results__description",
+                                "phenopackets__biosamples__experiment__experiment_results__filename",
+                                "phenopackets__biosamples__experiment__experiment_results__file_format",
+                                "phenopackets__biosamples__experiment__experiment_results__data_output_type",
+                                "phenopackets__biosamples__experiment__experiment_results__usage",
+                                "phenopackets__biosamples__experiment__experiment_results__creation_date",
+                                "phenopackets__biosamples__experiment__experiment_results__created_by",
+                                Cast(
+                                    "phenopackets__biosamples__experiment__experiment_results__extra_properties",
+                                    TextField()
+                                ),
+                                # Experiments: Instrument fields
+                                "phenopackets__biosamples__experiment__instrument__platform",
+                                "phenopackets__biosamples__experiment__instrument__description",
+                                "phenopackets__biosamples__experiment__instrument__model",
+                                Cast(
+                                    "phenopackets__biosamples__experiment__instrument__extra_properties",
+                                    TextField()
+                                ),
                                 )
         ).filter(search=value).distinct("id")
         return qs

chord_metadata_service/phenopackets/serializers.py

@@ -15,6 +15,7 @@
     Interpretation,
 )
 from chord_metadata_service.resources.serializers import ResourceSerializer
+from chord_metadata_service.experiments.serializers import ExperimentSerializer
 from chord_metadata_service.restapi import fhir_utils
 from chord_metadata_service.restapi.serializers import GenericSerializer
 
@@ -156,6 +157,7 @@ class BiosampleSerializer(GenericSerializer):
         read_only=True, many=True, exclude_when_nested=['id', 'biosample'])
     procedure = ProcedureSerializer(exclude_when_nested=['id'])
     variants = VariantSerializer(read_only=True, many=True)
+    experiments = ExperimentSerializer(read_only=True, many=True, source='experiment_set')
 
     class Meta:
         model = Biosample