fix specimen and biosample export for images (#266)

BioImage-Archive · Dec 10, 2024 · 9d7b766 · 9d7b766
1 parent 7fe65c4
commit 9d7b766
Show file tree

Hide file tree

Showing 2 changed files with 85 additions and 9 deletions.
diff --git a/bia-export/bia_export/website_export/images/transform.py b/bia-export/bia_export/website_export/images/transform.py
@@ -1,5 +1,8 @@
 from typing import List, Type
-from bia_export.website_export.generic_object_retrieval import retrieve_object_list, retrieve_object
+from bia_export.website_export.generic_object_retrieval import (
+    retrieve_object_list,
+    retrieve_object,
+)
 from bia_integrator_api import models as api_models
 from pydantic import BaseModel
 from bia_export.website_export.images.models import (
@@ -75,7 +78,7 @@ def transform_creation_process(
         api_specimen: api_models.Specimen = retrieve_object(
             api_creation_process.subject_specimen_uuid, api_models.Specimen, context
         )
-        website_fields["subject_specimen"] = transform_specimen(api_specimen, context)
+        website_fields["subject"] = transform_specimen(api_specimen, context)
 
     if len(api_creation_process.annotation_method_uuid) > 0:
         api_annotation_method = retrieve_object_list(
@@ -106,8 +109,9 @@ def transform_specimen(
     api_bio_samples = retrieve_object_list(
         api_specimen.sample_of_uuid, api_models.BioSample, context
     )
+    biosamples = []
     for api_bio_sample in api_bio_samples:
-        transform_biosample(api_bio_sample, context)
+        biosamples.append(transform_biosample(api_bio_sample, context))
 
     api_specimen_imaging_preparation_protocols = retrieve_object_list(
         api_specimen.imaging_preparation_protocol_uuid,
@@ -120,7 +124,7 @@ def transform_specimen(
             api_specimen_imaging_preparation_protocols,
             SpecimenImagingPreparationProtocol,
         ),
-        "sample_of": transform_details_object_list(api_bio_samples, BioSample),
+        "sample_of": biosamples,
     }
     return Specimen(**specimen_dict)
 

diff --git a/bia-export/test/output_data/bia_image_export.json b/bia-export/test/output_data/bia_image_export.json
@@ -26,7 +26,6 @@
             ],
             "acquisition_process": [],
             "subject": null,
-            "protocol": [],
             "annotation_method": [
                 {
                     "default_open": true,
@@ -48,7 +47,8 @@
                     ],
                     "annotation_source_indicator": null
                 }
-            ]
+            ],
+            "protocol": []
         },
         "representation": []
     },
@@ -94,9 +94,81 @@
                     ]
                 }
             ],
-            "subject": null,
-            "protocol": [],
-            "annotation_method": []
+            "subject": {
+                "uuid": "dcc18482-fa1a-468f-878f-c00f9cd46376",
+                "version": 1,
+                "model": {
+                    "type_name": "Specimen",
+                    "version": 1
+                },
+                "attribute": [],
+                "imaging_preparation_protocol_uuid": [
+                    "7199d730-29f1-4ad8-b599-e9089cbb2d7b"
+                ],
+                "sample_of_uuid": [
+                    "64a67727-4e7c-469a-91c4-6219ae072e99"
+                ],
+                "imaging_preparation_protocol": [
+                    {
+                        "default_open": true,
+                        "title_id": "Test specimen 1",
+                        "uuid": "7199d730-29f1-4ad8-b599-e9089cbb2d7b",
+                        "version": 1,
+                        "model": {
+                            "type_name": "SpecimenImagingPreparationProtocol",
+                            "version": 2
+                        },
+                        "attribute": [],
+                        "protocol_description": "Test sample preparation protocol 1",
+                        "signal_channel_information": []
+                    }
+                ],
+                "sample_of": [
+                    {
+                        "default_open": true,
+                        "title_id": "Test Biosample 1",
+                        "uuid": "64a67727-4e7c-469a-91c4-6219ae072e99",
+                        "version": 1,
+                        "model": {
+                            "type_name": "BioSample",
+                            "version": 3
+                        },
+                        "attribute": [],
+                        "organism_classification": [
+                            {
+                                "attribute": null,
+                                "common_name": "human",
+                                "scientific_name": "Homo sapiens",
+                                "ncbi_id": null
+                            }
+                        ],
+                        "biological_entity_description": "Test biological entity 1",
+                        "experimental_variable_description": [
+                            "Test experimental entity 1"
+                        ],
+                        "extrinsic_variable_description": [
+                            "Test extrinsic variable 1"
+                        ],
+                        "intrinsic_variable_description": [
+                            "Test intrinsic variable 1\\nwith escaped character"
+                        ],
+                        "growth_protocol_uuid": "a2ce3950-3b28-40b3-a6a5-23c4f7864912",
+                        "growth_protocol": {
+                            "title_id": "Test specimen 1",
+                            "uuid": "a2ce3950-3b28-40b3-a6a5-23c4f7864912",
+                            "version": 2,
+                            "model": {
+                                "type_name": "Protocol",
+                                "version": 1
+                            },
+                            "attribute": [],
+                            "protocol_description": "Test sample growth protocol 1"
+                        }
+                    }
+                ]
+            },
+            "annotation_method": [],
+            "protocol": []
         },
         "representation": [
             {