added default_open field to details section of datasets

bia-export/bia_export/website_conversion.py

@@ -1,10 +1,13 @@
-
 from pathlib import Path
 import json
 import logging
 from .website_models import (
     Study,
-    ExperimentalImagingDataset
+    ExperimentalImagingDataset,
+    ImageAcquisition,
+    BioSample,
+    SpecimenGrowthProtocol,
+    SpecimenImagingPrepartionProtocol,
 )
 from glob import glob
 from typing import List, Type
@@ -20,88 +23,165 @@ def read_api_json_file(file_path: Path, object_type: Type[BaseModel]) -> BaseMod
     """
     with open(file_path, "r") as object_file:
         object_dict = json.load(object_file)
-    
+
     return object_type(**object_dict)
 
 
-def read_all_json(directory_path: Path, object_type: Type[BaseModel]) -> List[BaseModel]:
+def read_all_json(
+    directory_path: Path, object_type: Type[BaseModel]
+) -> List[BaseModel]:
     object_list = []
     file_paths = glob(str(directory_path))
     for file_path in file_paths:
         object_list.append(read_api_json_file(file_path, object_type))
     return object_list
 
 
-def find_associated_objects(typed_associations: set, directory_path: Path, object_type: Type[BaseModel]) -> List[bia_data_model.UserIdentifiedObject]:
+def find_associated_objects(
+    typed_associations: set,
+    directory_path: Path,
+    object_type: Type[bia_data_model.UserIdentifiedObject],
+) -> List[dict]:
     linked_object = []
 
     if len(typed_associations) == 0:
         return linked_object
-
-    typed_object_in_study: List[bia_data_model.UserIdentifiedObject] = read_all_json(directory_path, object_type)
+
+    typed_object_in_study: List[bia_data_model.UserIdentifiedObject] = read_all_json(
+        directory_path, object_type
+    )
     for object in typed_object_in_study:
         if object.title_id in typed_associations:
-            linked_object.append(object)
+            linked_object.append(object.model_dump())
     return linked_object
 
 
-def create_study(
-        accession_id: str,
-        root_directory: Path
-) -> Study:
-
+def create_study(accession_id: str, root_directory: Path) -> Study:
+
     if root_directory:
-        study_path = root_directory.joinpath(f'studies/{accession_id}.json')
+        study_path = root_directory.joinpath(f"studies/{accession_id}.json")
+
+        logger.info(f"Loading study from {study_path}")
 
-        logger.info(f'Loading study from {study_path}')
-
         api_study = read_api_json_file(study_path, bia_data_model.Study)
     else:
-        #TODO: use client
+        # TODO: use client
         raise NotImplementedError
     study_dict = api_study.model_dump()
-    study_dict["experimental_imaging_component"] = create_experimental_imaging_datasets(accession_id, root_directory)
+    study_dict["experimental_imaging_component"] = create_experimental_imaging_datasets(
+        accession_id, root_directory
+    )
     study = Study(**study_dict)
 
     return study
 
 
-def create_experimental_imaging_datasets(accession_id: str, root_directory: Path = None) -> List[ExperimentalImagingDataset]:
+def create_experimental_imaging_datasets(
+    accession_id: str, root_directory: Path = None
+) -> List[ExperimentalImagingDataset]:
     eid_list = []
     if root_directory:
-
-        eid_directory = root_directory.joinpath(f'experimental_imaging_datasets/{accession_id}/*.json')
 
-        api_eids: List[bia_data_model.ExperimentalImagingDataset] = read_all_json(eid_directory, bia_data_model.ExperimentalImagingDataset)
-
+        eid_directory = root_directory.joinpath(
+            f"experimental_imaging_datasets/{accession_id}/*.json"
+        )
+
+        api_eids: List[bia_data_model.ExperimentalImagingDataset] = read_all_json(
+            eid_directory, bia_data_model.ExperimentalImagingDataset
+        )
+
+        detail_map = {
+            ImageAcquisition: {
+                "source_directory": "image_acquisitions",
+                "association_field": "image_acquisition",
+                "bia_type": bia_data_model.ImageAcquisition,
+                "previously_displayed": set(),
+            },
+            BioSample: {
+                "source_directory": "biosamples",
+                "association_field": "biosample",
+                "bia_type": bia_data_model.BioSample,
+                "previously_displayed": set(),
+            },
+            SpecimenImagingPrepartionProtocol: {
+                "source_directory": "specimen_imaging_preparation_protocols",
+                "association_field": "specimen",
+                "bia_type": bia_data_model.SpecimenImagingPrepartionProtocol,
+                "previously_displayed": set(),
+            },
+            SpecimenGrowthProtocol: {
+                "source_directory": "specimen_growth_protocols",
+                "association_field": "specimen",
+                "bia_type": bia_data_model.SpecimenGrowthProtocol,
+                "previously_displayed": set(),
+            },
+        }
+
+        def process_details_section(
+            root_directory: Path,
+            accession_id: str,
+            detail_map_info: dict,
+            typed_associations: set,
+        ):
+
+            detail_path = root_directory.joinpath(
+                f"{detail_map_info['source_directory']}/{accession_id}/*.json"
+            )
+            detail_linked_to_dataset = find_associated_objects(
+                typed_associations,
+                detail_path,
+                detail_map_info["bia_type"],
+            )
+
+            for detail in detail_linked_to_dataset:
+                if detail["uuid"] not in detail_map_info["previously_displayed"]:
+                    detail["default_open"] = True
+                    detail_map_info["previously_displayed"].add(detail["uuid"])
+                else:
+                    detail["default_open"] = False
+
+            return detail_linked_to_dataset
+
         for eid in api_eids:
             eid_dict = eid.model_dump()
 
             associations = eid.attribute["associations"]
 
-            association_by_type = {"biosample": set(), "image_acquisition": set(), "specimen": set()}
+            association_by_type = {
+                "biosample": set(),
+                "image_acquisition": set(),
+                "specimen": set(),
+            }
             for association in associations:
                 for key in association_by_type.keys():
                     association_by_type[key].add(association[key])
 
-
-            biosample_directory = root_directory.joinpath(f'biosamples/{accession_id}/*.json')
-            sipp_directory = root_directory.joinpath(f'specimen_imaging_preparation_protocols/{accession_id}/*.json')
-            sgp_directory = root_directory.joinpath(f'specimen_growth_protocols/{accession_id}/*.json')
-            ia_directory = root_directory.joinpath(f'image_acquisitions/{accession_id}/*.json')
-
-            biosample_linked_to_dataset = find_associated_objects(association_by_type["biosample"], biosample_directory, bia_data_model.BioSample)
-            sipp_linked_to_dataset = find_associated_objects(association_by_type["specimen"], sipp_directory, bia_data_model.SpecimenImagingPrepartionProtocol)
-            sgps_linked_to_dataset  = find_associated_objects(association_by_type["specimen"], sgp_directory, bia_data_model.SpecimenGrowthProtocol)
-            ia_linked_to_dataset  = find_associated_objects(association_by_type["image_acquisition"], ia_directory, bia_data_model.ImageAcquisition)
-
-            eid_dict["biological_entity"] = biosample_linked_to_dataset
-            eid_dict["specimen_imaging_preparation_protocol"] = sipp_linked_to_dataset
-            eid_dict["specimen_growth_protocol"] = sgps_linked_to_dataset
-            eid_dict["acquisition_process"] = ia_linked_to_dataset
+            eid_dict["biological_entity"] = process_details_section(
+                root_directory,
+                accession_id,
+                detail_map[BioSample],
+                association_by_type["biosample"],
+            )
+            eid_dict["specimen_imaging_preparation_protocol"] = process_details_section(
+                root_directory,
+                accession_id,
+                detail_map[SpecimenImagingPrepartionProtocol],
+                association_by_type["specimen"],
+            )
+            eid_dict["specimen_growth_protocol"] = process_details_section(
+                root_directory,
+                accession_id,
+                detail_map[BioSample],
+                association_by_type["specimen"],
+            )
+            eid_dict["acquisition_process"] = process_details_section(
+                root_directory,
+                accession_id,
+                detail_map[ImageAcquisition],
+                association_by_type["image_acquisition"],
+            )
 
             eid = ExperimentalImagingDataset(**eid_dict)
             eid_list.append(eid)
-        
+
     return eid_list
-

bia-export/bia_export/website_models.py

@@ -1,23 +1,51 @@
 from __future__ import annotations
-from pydantic import Field
+from pydantic import Field, BaseModel
 from typing import List, Optional
 from bia_shared_datamodels import bia_data_model
 
 
 class Study(bia_data_model.Study):
-    experimental_imaging_component: Optional[List[ExperimentalImagingDataset]] = Field(default_factory=list, description="""A dataset of that is associated with the study.""")
+    experimental_imaging_component: Optional[List[ExperimentalImagingDataset]] = Field(
+        default_factory=list,
+        description="""A dataset of that is associated with the study.""",
+    )
+
 
 class ExperimentalImagingDataset(bia_data_model.ExperimentalImagingDataset):
-    acquisition_process: list[bia_data_model.ImageAcquisition] = Field(
+    acquisition_process: list[ImageAcquisition] = Field(
         description="""Processes involved in the creation of the images and files in this dataset."""
     )
-    specimen_imaging_preparation_protocol: list[bia_data_model.SpecimenImagingPrepartionProtocol] = Field(
-        description="""Processes involved in the preprapartion of the samples for imaged."""
+    specimen_imaging_preparation_protocol: list[SpecimenImagingPrepartionProtocol] = (
+        Field(
+            description="""Processes involved in the preprapartion of the samples for imaged."""
+        )
     )
-    biological_entity: list[bia_data_model.BioSample] = Field(
+    biological_entity: list[BioSample] = Field(
         description="""The biological entity or entities that were imaged."""
     )
-    specimen_growth_protocol: Optional[list[bia_data_model.SpecimenGrowthProtocol]] = Field(
-        description="""Processes involved in the growth of the samples that were then imaged."""
+    specimen_growth_protocol: Optional[list[SpecimenGrowthProtocol]] = Field(
+        default_factory=list,
+        description="""Processes involved in the growth of the samples that were then imaged.""",
     )
 
+
+class DetailSection(BaseModel):
+    default_open: bool = Field()
+
+
+class ImageAcquisition(bia_data_model.ImageAcquisition, DetailSection):
+    pass
+
+
+class BioSample(bia_data_model.BioSample, DetailSection):
+    pass
+
+
+class SpecimenGrowthProtocol(bia_data_model.SpecimenGrowthProtocol, DetailSection):
+    pass
+
+
+class SpecimenImagingPrepartionProtocol(
+    bia_data_model.SpecimenImagingPrepartionProtocol, DetailSection
+):
+    pass

bia-export/test/output_data/bia_export.json

@@ -111,6 +111,7 @@
             "submitted_in_study_uuid": "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71",
             "acquisition_process": [
                 {
+                    "default_open": true,
                     "title_id": "Test Primary Screen Image Acquisition",
                     "uuid": "c2e44a1b-a43c-476e-8ddf-8587f4c955b3",
                     "version": 1,
@@ -126,6 +127,7 @@
             ],
             "specimen_imaging_preparation_protocol": [
                 {
+                    "default_open": true,
                     "title_id": "Test specimen 1",
                     "uuid": "7199d730-29f1-4ad8-b599-e9089cbb2d7b",
                     "version": 1,
@@ -139,6 +141,7 @@
             ],
             "biological_entity": [
                 {
+                    "default_open": true,
                     "title_id": "Test Biosample 1",
                     "uuid": "64a67727-4e7c-469a-91c4-6219ae072e99",
                     "version": 1,
@@ -165,6 +168,7 @@
                     ]
                 },
                 {
+                    "default_open": true,
                     "title_id": "Test Biosample 2",
                     "uuid": "6950718c-4917-47a1-a807-11b874e80a23",
                     "version": 1,
@@ -192,6 +196,55 @@
                 }
             ],
             "specimen_growth_protocol": []
+        },
+        {
+            "title_id": "Study Component 2",
+            "uuid": "850a1ca3-9681-4a8a-b625-477936fcb954",
+            "version": 1,
+            "model": {
+                "type_name": "ExperimentalImagingDataset",
+                "version": 1
+            },
+            "description": "Description of study component 2",
+            "attribute": {
+                "associations": [
+                    {
+                        "image_analysis": "Test image analysis",
+                        "image_correlation": null,
+                        "biosample": "Test Biosample 2 ",
+                        "image_acquisition": "Test Primary Screen Image Acquisition",
+                        "specimen": "Test specimen 2"
+                    }
+                ]
+            },
+            "analysis_method": [
+                {
+                    "protocol_description": "Test image analysis",
+                    "features_analysed": "Test image analysis overview"
+                }
+            ],
+            "correlation_method": [],
+            "example_image_uri": [],
+            "submitted_in_study_uuid": "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71",
+            "acquisition_process": [
+                {
+                    "default_open": false,
+                    "title_id": "Test Primary Screen Image Acquisition",
+                    "uuid": "c2e44a1b-a43c-476e-8ddf-8587f4c955b3",
+                    "version": 1,
+                    "model": {
+                        "type_name": "ImageAcquisition",
+                        "version": 1
+                    },
+                    "protocol_description": "Test image acquisition parameters 1",
+                    "imaging_instrument_description": "Test imaging instrument 1",
+                    "fbbi_id": [],
+                    "imaging_method_name": "confocal microscopy"
+                }
+            ],
+            "specimen_imaging_preparation_protocol": [],
+            "biological_entity": [],
+            "specimen_growth_protocol": []
         }
     ]
 }