diff --git a/bia-export/README.md b/bia-export/README.md index 2d9787b4..cbe7ee1c 100644 --- a/bia-export/README.md +++ b/bia-export/README.md @@ -36,6 +36,18 @@ Run: This will create `bia-study-metadata.json` using the example test data for studies +Note that with -r (root directory) - local files will be used to generate the export. If using ingest to generate the files, this will usually be: ~/.cache/bia-integrator-data-sm. If no root location is passed, and a study UUID (as opposed to accession ID) is used, then the API will be called to create the files. + +If no Accession ID or UUID is passed, all studies will be processed (either based on all studies in the /study/ directory, or by querying for studies in the api). The studies are exported in order of release date. + +The two points above hold for all export commands for the api. For the website-study export only, there is a optional cache in order to avoid processing all file references every time an export is performed (as this slows down export a lot). E.g. running: + +`poetry run bia-export website-study -o bia-study-metadata.json -c read_cache` + +Will export all studies using the cached aggregation (when avaliable) as the counts for images, files, and the list of different file types. + + + Image Export Run: @@ -48,15 +60,3 @@ Run: `poetry run bia-export datasets-for-website-image S-BIADTEST -o bia-dataset-export.json -r test/input_data` This will create `bia-dataset-export.json` using the example test data. - -Commands to generate the current BIA data ------------------------------------------ - -Study export: - -``` -poetry run bia-export website-study S-BIAD1218 S-BIAD1201 S-BIAD1034 S-BIAD1026 S-BIAD1287 S-BIAD1055 S-BIAD1185 S-BIAD957 S-BIAD748 S-BIAD850 S-BIAD1018 S-BIAD1077 S-BIAD1122 S-BIAD1163 S-BIAD618 S-BIAD620 S-BIAD650 S-BIAD814 S-BIAD825 S-BIAD954 S-BIAD963 S-BIAD1044 S-BIAD1183 S-BIAD627 S-BIAD826 S-BIAD843 S-BIAD845 S-BIAD849 S-BIAD890 S-BIAD1008 S-BIAD1024 S-BIAD1092 S-BIAD1093 S-BIAD1134 S-BIAD1135 S-BIAD1165 S-BIAD1175 S-BIAD1197 S-BIAD1215 S-BIAD1248 S-BIAD1260 S-BIAD663 S-BIAD831 S-BIAD846 S-BIAD851 S-BIAD887 S-BIAD922 S-BIAD928 S-BIAD1005 S-BIAD1009 S-BIAD1057 S-BIAD1079 S-BIAD1083 S-BIAD1088 S-BIAD1091 S-BIAD1099 S-BIAD1104 S-BIAD1168 S-BIAD1169 S-BIAD1193 S-BIAD1203 S-BIAD1268 S-BIAD1284 S-BIAD1323 S-BIAD607 S-BIAD608 S-BIAD610 S-BIAD616 S-BIAD626 S-BIAD661 S-BIAD694 S-BIAD705 S-BIAD800 S-BIAD813 S-BIAD815 S-BIAD823 S-BIAD824 S-BIAD829 S-BIAD830 S-BIAD847 S-BIAD848 S-BIAD852 S-BIAD861 S-BIAD865 S-BIAD866 S-BIAD884 S-BIAD885 S-BIAD904 S-BIAD931 S-BIAD955 S-BIAD970 S-BIAD986 S-BIAD1012 S-BIAD1019 S-BIAD1028 S-BIAD1039 S-BIAD1064 S-BIAD1078 S-BIAD1084 S-BIAD1090 S-BIAD1094 S-BIAD1095 S-BIAD1097 S-BIAD1102 S-BIAD1114 S-BIAD1116 S-BIAD1119 S-BIAD1130 S-BIAD1133 S-BIAD1151 S-BIAD1152 S-BIAD1157 S-BIAD1159 S-BIAD1162 S-BIAD1167 S-BIAD1196 S-BIAD1199 S-BIAD1200 S-BIAD1204 S-BIAD1236 S-BIAD1244 S-BIAD1245 S-BIAD1267 S-BIAD1271 S-BIAD1272 S-BIAD1274 S-BIAD1285 S-BIAD1293 S-BIAD1308 S-BIAD1327 S-BIAD612 S-BIAD633 S-BIAD646 S-BIAD678 S-BIAD680 S-BIAD684 S-BIAD700 S-BIAD720 S-BIAD725 S-BIAD728 S-BIAD770 S-BIAD855 S-BIAD860 S-BIAD862 S-BIAD864 S-BIAD882 S-BIAD886 S-BIAD915 S-BIAD916 S-BIAD965 S-BIAD967 S-BIAD985 S-BIAD987 S-BIAD992 S-BIAD993 S-BIAD1027 S-BIAD1030 S-BIAD1033 S-BIAD1045 S-BIAD1063 S-BIAD1080 S-BIAD1082 S-BIAD1086 S-BIAD1096 S-BIAD1100 S-BIAD1121 S-BIAD1155 S-BIAD1158 S-BIAD1184 S-BIAD1186 S-BIAD1194 S-BIAD1216 S-BIAD1232 S-BIAD1235 S-BIAD1237 S-BIAD1239 S-BIAD1247 S-BIAD1250 S-BIAD1259 S-BIAD1270 S-BIAD1282 S-BIAD1298 S-BIAD1300 S-BIAD1302 S-BIAD1314 S-BIAD1316 S-BIAD1333 S-BIAD602 S-BIAD603 S-BIAD606 S-BIAD609 S-BIAD611 S-BIAD617 S-BIAD619 S-BIAD621 S-BIAD624 S-BIAD647 S-BIAD651 S-BIAD652 S-BIAD657 S-BIAD658 S-BIAD664 S-BIAD668 S-BIAD669 S-BIAD676 S-BIAD679 S-BIAD682 S-BIAD696 S-BIAD703 S-BIAD704 S-BIAD767 S-BIAD769 S-BIAD777 S-BIAD807 S-BIAD808 S-BIAD817 S-BIAD821 S-BIAD822 S-BIAD827 S-BIAD832 S-BIAD840 S-BIAD841 S-BIAD842 S-BIAD844 S-BIAD863 S-BIAD900 S-BIAD901 S-BIAD903 S-BIAD910 S-BIAD913 S-BIAD914 S-BIAD926 S-BIAD930 S-BIAD961 S-BIAD969 S-BIAD976 S-BIAD984 S-BIAD988 S-BIAD999 -o bia-study-metadata.json -r ~/.cache/bia-integrator-data-sm/ -``` - -And similarly for the images and datasets. - diff --git a/bia-export/bia_export/cli.py b/bia-export/bia_export/cli.py index 7072b699..c37b3a61 100644 --- a/bia-export/bia_export/cli.py +++ b/bia-export/bia_export/cli.py @@ -4,8 +4,9 @@ from rich.logging import RichHandler from typing_extensions import Annotated from pathlib import Path +from bia_export.website_export.export_all import get_study_ids from .website_export.studies.transform import transform_study -from .website_export.studies.models import StudyCLIContext +from .website_export.studies.models import StudyCLIContext, CacheUse from .website_export.images.transform import transform_images from .website_export.images.models import ImageCLIContext from .website_export.datasets_for_images.transform import transform_datasets @@ -23,7 +24,16 @@ @app.command() def website_study( - id_list: Annotated[List[str], typer.Argument(help="IDs of the studies to export")], + id_list: Annotated[ + Optional[List[str]], typer.Argument(help="IDs of the studies to export") + ] = None, + output_filename: Annotated[ + Optional[Path], + typer.Option( + "--out_file", + "-o", + ), + ] = Path("bia-study-metadata.json"), root_directory: Annotated[ Optional[Path], typer.Option( @@ -32,24 +42,29 @@ def website_study( help="If root directory specified then use files there, rather than calling API", ), ] = None, - output_filename: Annotated[ - Path, + cache: Annotated[ + Optional[CacheUse], typer.Option( - "--out_file", - "-o", + "--cache", + "-c", ), - ] = Path("bia-images-export.json"), + ] = None, ): if root_directory: abs_root = root_directory.resolve() + if not id_list: + id_list = get_study_ids(root_directory) + studies_map = {} for id in id_list: if root_directory: - context = StudyCLIContext(root_directory=abs_root, accession_id=id) + context = StudyCLIContext( + root_directory=abs_root, accession_id=id, cache_use=cache + ) else: - context = StudyCLIContext(study_uuid=id) + context = StudyCLIContext(study_uuid=id, cache_use=cache) study = transform_study(context) studies_map[study.accession_id] = study.model_dump(mode="json") @@ -61,8 +76,15 @@ def website_study( @app.command() def website_image( id_list: Annotated[ - List[str], typer.Argument(help="Accession ID of the study to export") - ], + Optional[List[str]], typer.Argument(help="Accession IDs of the study to export") + ] = None, + output_filename: Annotated[ + Optional[Path], + typer.Option( + "--out_file", + "-o", + ), + ] = Path("bia-image-export.json"), root_directory: Annotated[ Optional[Path], typer.Option( @@ -71,19 +93,15 @@ def website_image( help="If root directory specified then use files there, rather than calling API", ), ] = None, - output_filename: Annotated[ - Path, - typer.Option( - "--out_file", - "-o", - ), - ] = Path("bia-image-export.json"), ): # NB: currently only exports for ExperimentallyCapturedImages # TODO: get this working for if root_directory: abs_root = root_directory.resolve() + if not id_list: + id_list = get_study_ids(root_directory) + image_map = {} for id in id_list: if root_directory: @@ -101,8 +119,15 @@ def website_image( @app.command() def datasets_for_website_image( id_list: Annotated[ - List[str], typer.Argument(help="Accession ID of the study to export") - ], + Optional[List[str]], typer.Argument(help="Accession IDs of the study to export") + ] = None, + output_filename: Annotated[ + Optional[Path], + typer.Option( + "--out_file", + "-o", + ), + ] = Path("bia-image-export.json"), root_directory: Annotated[ Optional[Path], typer.Option( @@ -111,18 +136,14 @@ def datasets_for_website_image( help="If root directory specified then use files there, rather than calling API", ), ] = None, - output_filename: Annotated[ - Path, - typer.Option( - "--out_file", - "-o", - ), - ] = Path("bia-image-export.json"), ): if root_directory: abs_root = root_directory.resolve() + if not id_list: + id_list = get_study_ids(root_directory) + dataset_map = {} for id in id_list: if root_directory: diff --git a/bia-export/bia_export/website_export/export_all.py b/bia-export/bia_export/website_export/export_all.py new file mode 100644 index 00000000..5ff7961c --- /dev/null +++ b/bia-export/bia_export/website_export/export_all.py @@ -0,0 +1,53 @@ +from glob import glob +from pathlib import Path +from typing import Optional +from bia_export.bia_client import api_client +from bia_integrator_api.models import Study +from .generic_object_retrieval import read_api_json_file +import logging + +logger = logging.getLogger("__main__." + __name__) + + +def find_local_studies(root_path: Path) -> list[Study]: + study_search_path = root_path.joinpath("study", "**/*.json") + file_paths = glob(str(study_search_path), recursive=True) + studies = [] + for file_path in file_paths: + studies.append(read_api_json_file(file_path, Study)) + return studies + + +def fetch_studies_from_api( + page_size: int, agregator_list: list[Study] = None +) -> list[Study]: + if not agregator_list: + agregator_list = [] + start_uuid = None + else: + start_uuid = agregator_list[-1].uuid + + fetched_studies = api_client.get_studies( + page_size=page_size, start_from_uuid=start_uuid + ) + agregator_list += fetched_studies + + if len(fetched_studies) != page_size: + return agregator_list + else: + return fetch_studies_from_api(page_size, agregator_list) + + +def get_study_ids(root_directory: Optional[Path] = None): + if root_directory: + studies_list = find_local_studies(root_directory) + sorted_studies = sorted( + studies_list, key=lambda study: study.release_date, reverse=True + ) + return [study.accession_id for study in sorted_studies] + else: + studies_list = fetch_studies_from_api(page_size=100) + sorted_studies = sorted( + studies_list, key=lambda study: study.release_date, reverse=True + ) + return [study.uuid for study in sorted_studies] diff --git a/bia-export/bia_export/website_export/generic_object_retrieval.py b/bia-export/bia_export/website_export/generic_object_retrieval.py index a20564dd..c7f78a0a 100644 --- a/bia-export/bia_export/website_export/generic_object_retrieval.py +++ b/bia-export/bia_export/website_export/generic_object_retrieval.py @@ -2,6 +2,7 @@ from uuid import UUID from pydantic import BaseModel from pydantic.alias_generators import to_snake +from bia_shared_datamodels.bia_data_model import DocumentMixin from bia_export.bia_client import api_client from .website_models import CLIContext import json @@ -90,19 +91,25 @@ def retrieve_object( def get_all_api_results( - uuid: UUID, api_method, page_size_setting=20 -) -> List[BaseModel]: - object_list = [] - added_objects = api_method(str(uuid), page_size=page_size_setting) - if len(added_objects) > 0: - object_list += added_objects - start_uuid = added_objects[-1].uuid - while page_size_setting == len(added_objects): - added_objects = api_method( - str(uuid), - page_size=page_size_setting, - start_from_uuid=start_uuid, - ) - object_list += added_objects - start_uuid = added_objects[-1].uuid - return object_list + uuid: UUID, + api_method, + page_size_setting=20, + aggregator_list: list[DocumentMixin] = None, +) -> list[DocumentMixin]: + if not aggregator_list: + aggregator_list: list[DocumentMixin] = [] + start_uuid = None + else: + start_uuid = aggregator_list[-1].uuid + + fetched_objects = api_method( + str(uuid), + page_size=page_size_setting, + start_from_uuid=str(start_uuid) if start_uuid else None, + ) + aggregator_list += fetched_objects + + if len(fetched_objects) != page_size_setting: + return aggregator_list + else: + return get_all_api_results(uuid, api_method, page_size_setting, aggregator_list) diff --git a/bia-export/bia_export/website_export/studies/models.py b/bia-export/bia_export/website_export/studies/models.py index 859b2c96..c19d6e45 100644 --- a/bia-export/bia_export/website_export/studies/models.py +++ b/bia-export/bia_export/website_export/studies/models.py @@ -10,8 +10,9 @@ ) from bia_integrator_api import models -from pydantic import BaseModel, Field +from pydantic import Field +from enum import Enum from typing import List, Optional, Type @@ -57,6 +58,11 @@ class Study(models.Study): ) +class CacheUse(Enum): + READ_CACHE = "read_cache" + WRITE_CACHE = "write_cache" + + class StudyCLIContext(CLIContext): dataset_file_aggregate_data: dict = Field( default_factory=dict, @@ -73,3 +79,4 @@ class StudyCLIContext(CLIContext): description="""Tracks e.g. which BioSamples have been displayed in previous dataset sections to determine whether details should default to open or closed.""", ) + cache_use: Optional[CacheUse] = None diff --git a/bia-export/bia_export/website_export/studies/retrieve.py b/bia-export/bia_export/website_export/studies/retrieve.py index eb210761..8570388b 100644 --- a/bia-export/bia_export/website_export/studies/retrieve.py +++ b/bia-export/bia_export/website_export/studies/retrieve.py @@ -9,7 +9,7 @@ ) from pathlib import Path from pydantic.alias_generators import to_snake -from .models import StudyCLIContext +from .models import StudyCLIContext, CacheUse from bia_shared_datamodels import semantic_models, bia_data_model from bia_integrator_api import models as api_models import json @@ -56,15 +56,25 @@ def retrieve_datasets( def retrieve_aggregation_fields( dataset: bia_data_model.DocumentMixin, context: StudyCLIContext ): - if context.root_directory: + + # The cache and the export from local files both store information in context.dataset_file_aggregate_data + if context.root_directory or ( + context.cache_use == CacheUse.READ_CACHE + and context.dataset_file_aggregate_data + and str(dataset.uuid) in context.dataset_file_aggregate_data + ): try: dataset_aggregation_fields = context.dataset_file_aggregate_data[ - dataset.uuid + str(dataset.uuid) ] dataset_aggregation_fields["file_type_aggregation"] = sorted( list(dataset_aggregation_fields["file_type_aggregation"]) ) + if context.cache_use == CacheUse.WRITE_CACHE: + write_to_cache(dataset.uuid, dataset_aggregation_fields) + except KeyError: + logger.warning(f"Could not find aggregate data for dataset: {dataset.uuid}") dataset_aggregation_fields = { "file_count": 0, "image_count": 0, @@ -72,10 +82,12 @@ def retrieve_aggregation_fields( } else: images: List[bia_data_model.Image] = get_all_api_results( - dataset.uuid, api_client.get_image_linking_dataset + dataset.uuid, api_client.get_image_linking_dataset, page_size_setting=500 ) files: List[bia_data_model.FileReference] = get_all_api_results( - dataset.uuid, api_client.get_file_reference_linking_dataset + dataset.uuid, + api_client.get_file_reference_linking_dataset, + page_size_setting=500, ) file_type_aggregation = set() @@ -88,47 +100,91 @@ def retrieve_aggregation_fields( "image_count": len(images), "file_type_aggregation": sorted(list(file_type_aggregation)), } + if context.cache_use == CacheUse.WRITE_CACHE: + write_to_cache(dataset.uuid, dataset_aggregation_fields) return dataset_aggregation_fields -def aggregate_file_list_data(context: StudyCLIContext) -> dict[UUID, dict]: - dataset_counts_map = {} +def write_to_cache(dataset_uuid, aggregation_fields): + logging.info(f"writing to dataset aggregation cache for dataset: {dataset_uuid}") - file_reference_directory = get_source_directory(api_models.FileReference, context) - file_reference_paths = glob(str(file_reference_directory)) - for file_path in file_reference_paths: - with open(file_path, "r") as object_file: + cache_file = ( + Path(__file__) + .parent.parent.parent.parent.join( + "cached_computed_data", "dataset_aggregate_fields.json" + ) + .absolute() + ) + with open(cache_file, "r") as object_file: + try: object_dict = json.load(object_file) - file_reference = api_models.FileReference(**object_dict) - submission_dataset = file_reference.submission_dataset_uuid - file_type = Path(file_reference.file_path).suffix - if submission_dataset not in dataset_counts_map: - dataset_counts_map[submission_dataset] = { - "file_count": 0, - "image_count": 0, - "file_type_aggregation": set(), - } - dataset_counts_map[submission_dataset]["file_count"] += 1 - dataset_counts_map[submission_dataset]["file_type_aggregation"].add(file_type) + except: + object_dict = {} + + object_dict[str(dataset_uuid)] = aggregation_fields - images_directory = get_source_directory(api_models.Image, context) - image_paths = glob(str(images_directory)) + with open(cache_file, "w") as object_file: + object_file.write(json.dumps(object_dict, indent=4)) + + +def aggregate_file_list_data(context: StudyCLIContext) -> None: + if context.cache_use == CacheUse.READ_CACHE: + cache_file = ( + Path(__file__) + .parent.parent.parent.parent.join( + "cached_computed_data", "dataset_aggregate_fields.json" + ) + .absolute() + ) - for image_path in image_paths: - with open(image_path, "r") as object_file: + with open(cache_file, "r") as object_file: object_dict = json.load(object_file) - submission_dataset = object_dict["submission_dataset_uuid"] - file_type = Path(file_reference.file_path).suffix - if submission_dataset not in dataset_counts_map: - dataset_counts_map[submission_dataset] = { - "file_count": 0, - "image_count": 0, - "file_type_aggregation": set(), - } - dataset_counts_map[submission_dataset]["image_count"] += 1 - return dataset_counts_map + context.dataset_file_aggregate_data = object_dict + return None + + if context.root_directory: + dataset_counts_map = {} + file_reference_directory = get_source_directory( + api_models.FileReference, context + ) + file_reference_paths = glob(str(file_reference_directory)) + for file_path in file_reference_paths: + with open(file_path, "r") as object_file: + object_dict = json.load(object_file) + file_reference = api_models.FileReference(**object_dict) + submission_dataset = str(file_reference.submission_dataset_uuid) + file_type = Path(file_reference.file_path).suffix + if submission_dataset not in dataset_counts_map: + dataset_counts_map[submission_dataset] = { + "file_count": 0, + "image_count": 0, + "file_type_aggregation": set(), + } + dataset_counts_map[submission_dataset]["file_count"] += 1 + dataset_counts_map[submission_dataset]["file_type_aggregation"].add( + file_type + ) + + images_directory = get_source_directory(api_models.Image, context) + image_paths = glob(str(images_directory)) + + for image_path in image_paths: + with open(image_path, "r") as object_file: + object_dict = json.load(object_file) + submission_dataset = object_dict["submission_dataset_uuid"] + file_type = Path(file_reference.file_path).suffix + if submission_dataset not in dataset_counts_map: + dataset_counts_map[submission_dataset] = { + "file_count": 0, + "image_count": 0, + "file_type_aggregation": set(), + } + dataset_counts_map[submission_dataset]["image_count"] += 1 + + context.dataset_file_aggregate_data = dataset_counts_map + return None def retrieve_dataset_images( @@ -149,7 +205,7 @@ def retrieve_dataset_images( else: api_images = get_all_api_results( - dataset_uuid, api_client.get_image_linking_dataset + dataset_uuid, api_client.get_image_linking_dataset, page_size_setting=500 ) return api_images diff --git a/bia-export/bia_export/website_export/studies/transform.py b/bia-export/bia_export/website_export/studies/transform.py index ba63958b..c383f7f4 100644 --- a/bia-export/bia_export/website_export/studies/transform.py +++ b/bia-export/bia_export/website_export/studies/transform.py @@ -4,6 +4,7 @@ Dataset, Study, StudyCLIContext, + CacheUse ) from bia_export.website_export.studies.retrieve import ( retrieve_study, @@ -35,8 +36,8 @@ def transform_study(context: StudyCLIContext) -> Study: # Collect file list information prior to creating eid if reading locally to avoid reading them multiple times. # TODO: make transform_study api/local independent: only retreive functions should have to worry about this. - if context.root_directory: - context.dataset_file_aggregate_data = aggregate_file_list_data(context) + if context.root_directory or context.cache_use == CacheUse.READ_CACHE: + aggregate_file_list_data(context) study_dict["dataset"] = transform_datasets(context) @@ -127,7 +128,9 @@ def transform_detail_object( else: detail_dict["default_open"] = False if target_type == BioSample and detail_dict["growth_protocol_uuid"]: - api_growth_protocol = retrieve_object( detail_dict["growth_protocol_uuid"], api_models.Protocol, context) + api_growth_protocol = retrieve_object( + detail_dict["growth_protocol_uuid"], api_models.Protocol, context + ) detail_dict["growth_protocol"] = api_growth_protocol detail = target_type(**detail_dict) diff --git a/bia-export/cached_computed_data/dataset_aggregate_fields.json b/bia-export/cached_computed_data/dataset_aggregate_fields.json new file mode 100644 index 00000000..5f329c3e --- 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