From fdc70f1ddc2367b0a92db471a763003d506280cd Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 14 Aug 2026 08:54:25 -0500 Subject: [PATCH 01/35] Added cli/fhir_transform.py and transform_utils.py --- gen3/cli/fhir_transform.py | 116 +++++++++ gen3/transform_utils.py | 469 +++++++++++++++++++++++++++++++++++++ 2 files changed, 585 insertions(+) create mode 100644 gen3/cli/fhir_transform.py create mode 100644 gen3/transform_utils.py diff --git a/gen3/cli/fhir_transform.py b/gen3/cli/fhir_transform.py new file mode 100644 index 00000000..1ad9f376 --- /dev/null +++ b/gen3/cli/fhir_transform.py @@ -0,0 +1,116 @@ +import yaml +from itertools import islice, repeat +import orjson +from fhirpathpy import evaluate +import click +import os, glob +import time +from datetime import datetime, timezone +import shutil +import pathlib +import hashlib +from concurrent.futures import ProcessPoolExecutor +from cdislogging import get_logger +from gen3.utils import make_folders_for_filename +from transform_utils import * + +logging = get_logger("fhir_tagger", log_level="info") +TMP_ROOT = pathlib.Path(".fhir_transform/tmp") + + +@click.group() +def fhir(): + """Commands for FHIR data processing""" + pass + + +@click.command( + context_settings={"help_option_names": ["-h", "--help"]}, + help="Tag Bulk FHIR data with Gen3 compatible authorization tags", +) +@click.argument( + "input_file", + type=click.Path(exists=True, dir_okay=False, readable=True), + metavar="input_file", +) +@click.argument( + "output_file", type=click.Path(dir_okay=False, writable=True), metavar="output_file" +) +@click.argument( + "config", + type=click.Path(exists=True, dir_okay=False, readable=True), + metavar="config", +) +@click.option( + "-b", + "--batch_size", + type=int, + default=10000, + show_default=True, + metavar="batch_size", + help="batch size for chunking", +) +@click.option( + "-w", + "--workers", + type=int, + default=8, + show_default=True, + metavar="workers", + help="number of parallel processes", +) +@click.option( + "--force", + is_flag=True, + help="Remove all intermediate files for this run before exiting even if run crashes", +) +def cli( + input_file: str | os.PathLike[str], + output_file: str | os.PathLike[str], + config: str | os.PathLike[str], + workers: int, + batch_size: int, + force: bool, +): + """ + CLI implementation of fhir_tagger. + + Args: + input_file (str): Input .ndjson file + output_file (str): Output file name + config (str): .yaml file with authorization rules + batch_size (int): numb er of lines per chunk + workers (int): number of parallel processes + force (bool): remove all intermediate files for this run before exiting even if it crashes + """ + fhir_tagger(input_file, output_file, config, workers, batch_size, force) + + +@click.command( + context_settings={"help_option_names": ["-h", "--help"]}, + help="Remove all intermediate files in the tmp folder from previous runs", +) +@click.option( + "--dry-run", + is_flag=True, + help="Used with --cleanup, report what would be deleted with --cleanup without deleting the files", +) +@click.option( + "--force", + is_flag=True, + help="Remove temporary directory ignoring status of each directory", +) +def cleanup(dry_run: bool, force: bool): + """ + Remove all intermediate files in the tmp folder from previous runs + + Args: + dry_run (bool): If True, list the files that would be removed, but not actually remove them + force (bool): Delete all intermediate directories disregarding the status + """ + + sweep(dry_run=dry_run, force=force) + + +fhir.add_command(cli, name="transform") +fhir.add_command(cleanup, name="cleanup") diff --git a/gen3/transform_utils.py b/gen3/transform_utils.py new file mode 100644 index 00000000..72ebd1fb --- /dev/null +++ b/gen3/transform_utils.py @@ -0,0 +1,469 @@ +import yaml +from itertools import islice, repeat +import orjson +from fhirpathpy import evaluate +import click +import os, glob +import time +from datetime import datetime, timezone +import shutil +import pathlib +import hashlib +from concurrent.futures import ProcessPoolExecutor +from cdislogging import get_logger +from gen3.utils import make_folders_for_filename + +logging = get_logger("fhir_tagger", log_level="info") +TMP_ROOT = pathlib.Path(".fhir_transform/tmp") + + +class Gen3FHIRAuthzTagger: + """ + The tagger used to tag FHIR data with appropriate Gen3 compatible authorizations given the rules in a config.yaml file. + + Example: + tagger = Gen3FHIRAuthzTagger(config_path=config) #create instance of tagger + tagger.relevant_authz_rules(os.path.basename(input_file).split(".")[0]) #keep only relevant rules for the resource type + authz_tags = tagger.determine_authz(record) #generate tags + out = orjson.dumps(tagger.tag_resource(record, authz_tags)) #tag resources + + """ + + def __init__(self, config_path: str | os.PathLike[str], custom_hook=None): + """ + Initialize instance of the tagger. + + Args: + config_path (str): the name/path of the config.yaml file + custom_hook (?): ??? + """ + + with open(config_path, "r") as f: + self.config = yaml.safe_load(f) + self.custom_hook = custom_hook + + def relevant_authz_rules(self, resource_type: str): + """ + Filters only the revlevant from the config.yaml file given the resource type. + + Args: + resource_type (str): the resource type in the .ndjson file + + """ + resource_rules = [] + for rule in self.config.get("rules", []): + if rule["resource_type"] == resource_type: + resource_rules.append(rule) + self.rules = resource_rules + + def determine_authz(self, resource: dict) -> str: + """ + Determines the correct authorization given the resource type and condition + + Args: + resource (dict): the resource dictionary (a line of the .ndjson file) + + Returns: + The appropriate rule/authorization for the resource + + """ + + # use custom hook if provided + if self.custom_hook: + hook_result = self.custom_hook(resource) + if hook_result: + return hook_result + + # check global catch-all fallback + if "global_authz" in self.config: + return self.config["global_authz"] + + # resource_type = resource.get("resourceType") + + # check static rules engine via FHIRPath + # for rule in self.config.get("rules", []): + # if rule["resource_type"] == resource_type: + # match = evaluate(resource, rule["condition"]) #how to process in bulk + # if match and match[0] is True: + # return rule["authz"] + for rule in self.rules: + match = evaluate(resource, rule["condition"]) + if match and match[0] is True: # FIXME: what if multiple conditions match? + return rule["authz"] + + return None #### FIXME this is just for testing purposes ##### + raise ValueError( + f"No authorization tag mapping found for resource ID: {resource.get('id')}" + ) + + def tag_resource(self, resource: dict, authz: str) -> dict: + """ + Injects the authz path directly into the standard FHIR meta block + + + FIXME: match Gen3 FHIR Proxy service requirements here + + Args: + resource (dict): the resource dictionary (a line of the .ndjson file) + authz (str): the authorization string to tag the resource with + + Returns: + resource (dict): tagged resource with the appropriate authz string + """ + + if "meta" not in resource: + resource["meta"] = {} + if "security" not in resource["meta"]: + resource["meta"]["security"] = [] + + gen3_security_tag = { + "system": "http://gen3.org/authz", + "code": authz, + "display": f"Gen3 Policy Path: {authz}", + } + + if gen3_security_tag not in resource["meta"]["security"]: + resource["meta"]["security"].append(gen3_security_tag) + + return resource + + +def get_md5hash(input_file: str | os.PathLike[str]) -> str: + """ + Returns the md5 hash of the input .ndjson file to create a unique folder per file + + Args: + input_file (str): Input ndjson file to transform + + Returns: + digest (str): md5 hash of the input .ndjson file + + """ + with open(input_file, "rb") as f: + digest = hashlib.file_digest(f, "md5").hexdigest() + return digest + + +def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: + """ + Check if directory is new or needs to be rerun. Returns true if directory doesn't exist, if .config.json doesn't exist, or if the the config.yaml file, + batch_size, or output_file name have changed. + + Args: + directory (str): path of the directory linked to the .ndjson file + record (dict): the configuration of the current run, used to compare to what is already saved in the folder + + Returns: + status (bool): returns whether the directory is new/has to be reset or not + """ + + if not pathlib.Path(directory).is_dir(): + return True + + try: + params = orjson.loads(pathlib.Path(directory, ".config.json").read_bytes()) + except: + return True + + if ( + record["config_hash"] != params["config_hash"] + or record["batch_size"] != params["batch_size"] + or record["output_file"] != params["output_file"] + ): + return True + + return False + + +def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: + """ + Check if transformation in this directory is completed. + + Args: + directory (str): path of the directory linked to the .ndjson file + record (dict): the configuration of the current run, used to compare to what is already saved in the folder + + Returns: + status (bool): returns whether the transformation has beencompleted + """ + try: + params = orjson.loads(pathlib.Path(directory, ".config.json").read_bytes()) + if ( + record["config_hash"] != params["config_hash"] + or record["batch_size"] != params["batch_size"] + or record["output_file"] != params["output_file"] + ): + return False + except: + return False + + # check if output file is the same and if exists + if ( + record["output_file"] == params["output_file"] + and pathlib.Path(record["output_file"]).is_file() + and pathlib.Path(record["output_file"]).stat().st_size != 0 + ): + logging.info(f"File already tagged. Locate file here: {record['output_file']}") + return True + + return False + + +def _resume_run(directory: str | os.PathLike[str], record: dict) -> bool: + """ + Check if transformation needs to be resumed. Returns True if there are chunk files remaining in the directory. + + Args: + directory (str): path of the directory linked to the .ndjson file + record (dict): the configuration of the current run, used to compare to what is already saved in the folder + + Returns: + status (bool): returns whether the transformation needs to be resumed + """ + # check for .chunk files --> tagging incomplete + if any(pathlib.Path(directory).glob("*.chunk")): + return True + return False + + +def _merge_needed(directory: str | os.PathLike[str], record: dict) -> bool: + """ + Check if .done files have been merged to the final output file. Returns True if .done files remaining in the directory. + + Args: + directory (str): path of the directory linked to the .ndjson file + record (dict): the configuration of the current run, used to compare to what is already saved in the folder + + Returns: + status (bool): returns whether the transformed .done files have to be merged + """ + # check for .done files --> merge incomplete + if any(pathlib.Path(directory).glob("*.done")): + return True + return False + + +def sweep(dry_run: bool = False, force: bool = False) -> int: + """ + Remove run dirs whose owning process is gone. + + Args: + dry_run (bool): If True, lists all directories which would be removed, but not actually remove them + force (bool): If True, delete the whole temporary directory disregarding the status + + Output: + count(int): number of directories deleted + """ + + if not TMP_ROOT.is_dir(): + logging.info("Nothing to clean") + return 0 + + # force to delete everything disregarding status + if force: + shutil.rmtree(TMP_ROOT, ignore_errors=True) + return + + count = 0 + for run_dir in sorted(TMP_ROOT.glob("*")): + if not run_dir.is_dir(): + continue + + logging.info(f"{'would remove' if dry_run else 'removed '} {run_dir}") + if not dry_run: + shutil.rmtree(run_dir, ignore_errors=True) + count += 1 + + logging.info(f"{count} stale run dir(s)") + return count + + +def split_file( + input_file: str | os.PathLike[str], + batch_size: int, + output_dir: str | os.PathLike[str], +): + """ + Split ndjson file into manageable batch-sized chunks + + Args: + input_file (str): input .ndjson file to split + batch_size (int): batch size of each chunk + output_dir (str): the path to the directory where to write all the intermediate files to + + """ + start = time.time() + with open(input_file, "rb") as fin: + for i, lines in enumerate(iter(lambda: list(islice(fin, batch_size)), [])): + # with open(f"chunk_{i:05d}.chunk", "wb") as out: + with open( + f"{output_dir}/{pathlib.Path(input_file).stem}_{i:05d}.chunk", "wb" + ) as out: + out.writelines(lines) + logging.info( + f"Split chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" + ) + + +def transform_chunk( + input_file: str | os.PathLike[str], + tagger: object, + output_dir: str | os.PathLike[str], +): + """ + Tag each resource entry with appropriate Gen3 authorization tag based on rules in a config.yaml file + + Args: + input_file (str): .chunk file to transform + tagger (object): The tagger instance to use for tagging the resources + output_dir (str): The directory path of where to write the intermediate files to + """ + with open(input_file, "rb") as fin, open( + os.path.join(output_dir, f"{os.path.basename(input_file)}.done"), "wb" + ) as fout: + out = bytearray() + for r in fin: + + if not r.strip(): + continue + + record = orjson.loads(r) + authz_tags = tagger.determine_authz(record) # generate tags + out += orjson.dumps( + tagger.tag_resource(record, authz_tags) + ) # tag resources) + out += b"\n" + fout.write(out) + os.remove(input_file) # delete chunk file once it has been transformed + + +def merge_chunks( + input_files: list[str | os.PathLike[str]], output_file: str | os.PathLike[str] +): + """ + Merge all tagged files back to one ndjson file + + Args: + input_files (list[str]): Tagged files to merge together + output_file (str): output_file to write the tagged ndjson + + """ + start = time.time() + print(output_file) + with open(f"{output_file}", "wb") as fout: + for f in sorted(input_files): + with open(f, "rb") as fin: + shutil.copyfileobj(fin, fout) + logging.info( + f"merge chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" + ) + for f in input_files: + os.remove(f) # remove .done files once merge completed + + +def fhir_tagger( + input_file: str | os.PathLike[str], + output_file: str | os.PathLike[str], + config: str | os.PathLike[str], + workers: int, + batch_size: int, + force: bool = False, +): + """ + + Stream-transform Bulk FHIR data to Gen3 compatible data with authorization tagging. + Parallelized line by line tagging with batched I/O + + Args: + input_file (str): Input .ndjson file + output_file (str): Output file name + config (str): .yaml file with authorization rules + batch_size (int): number of lines per chunk + workers (int): number of parallel processes + force (bool): remove all intermediate files for this run before exiting even if it crashes + """ + + start_time = time.time() + + # check if input and output file are the same + if os.path.realpath(input_file) == os.path.realpath(output_file): + raise click.UsageError("input_file and output_file must be different") + + make_folders_for_filename(TMP_ROOT) # only necessary the first time its run + + # make temp directories + hash = get_md5hash(input_file) + output_dir = f"{TMP_ROOT}/{os.path.basename(input_file).split('.')[0]}_{hash}" + + record = { + "timestamp": datetime.now(timezone.utc).isoformat(), + "input_file": input_file, + "output_file": output_file, + "config_hash": get_md5hash(config), + "batch_size": batch_size, + } + + try: + logging.info("Checking status of file") + + # if done, skip + if _is_done(output_dir, record): + return + + # if new file or new config/batch_size, reset folder + if _is_new(output_dir, record): + logging.info("New folder, creating directory and chunking") + make_folders_for_filename(f"{output_dir}/.config.json") + pathlib.Path(f"{output_dir}/.config.json").write_bytes( + orjson.dumps(record, default=str) + ) + # split into chunks + logging.info(f"Chunking {input_file} into {batch_size}-sized batches...") + split_file(input_file, batch_size, output_dir) + + # initialize tagger + tagger = Gen3FHIRAuthzTagger(config_path=config) # create instance of tagger + tagger.relevant_authz_rules( + os.path.basename(input_file).split(".")[0] + ) # keep only relevant rules for the resource type + + # if not fully transformed or new/reset, resume + if not _merge_needed(output_dir, record): + chunk_files = glob.glob( + os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.chunk") + ) # paths for chunk files + + # parallelize transform + logging.info("Transforming chunks...") + start = time.time() + with ProcessPoolExecutor(max_workers=workers) as pool: + for _ in pool.map( + transform_chunk, chunk_files, repeat(tagger), repeat(output_dir) + ): + pass + logging.info( + f"Transform chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" + ) + + # merge back to one ndjson file + transformed_files = glob.glob( + os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.done") + ) # paths for transformed files + logging.info(f"Merging chunks to {output_file}...") + merge_chunks(transformed_files, output_file) + + elapsed_time = time.time() - start_time + logging.info(f"Tagged file -> {output_file}") + # logging.info(f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}") + logging.info( + f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}" + ) + if force: + shutil.rmtree(output_dir, ignore_errors=True) + + except BaseException as e: + logging.error(e) + if force: + shutil.rmtree(output_dir, ignore_errors=True) + else: + logging.error("run failed; intermediates left in %s", output_dir) From 134df1303e3e4de87a0ff47b8a12507107de0907 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 14 Aug 2026 11:46:04 -0500 Subject: [PATCH 02/35] Add fhir_transform cli, utils, and tests --- gen3/cli/fhir_transform.py | 4 +- gen3/transform_utils.py | 9 +- tests/test_fhirtransform.py | 347 ++++++++++++++++++++++++++++++++++++ 3 files changed, 356 insertions(+), 4 deletions(-) create mode 100644 tests/test_fhirtransform.py diff --git a/gen3/cli/fhir_transform.py b/gen3/cli/fhir_transform.py index 1ad9f376..0a84e7e7 100644 --- a/gen3/cli/fhir_transform.py +++ b/gen3/cli/fhir_transform.py @@ -44,7 +44,7 @@ def fhir(): @click.option( "-b", "--batch_size", - type=int, + type=click.IntRange(min=1), default=10000, show_default=True, metavar="batch_size", @@ -53,7 +53,7 @@ def fhir(): @click.option( "-w", "--workers", - type=int, + type=click.IntRange(min=1), default=8, show_default=True, metavar="workers", diff --git a/gen3/transform_utils.py b/gen3/transform_utils.py index 72ebd1fb..b94fee53 100644 --- a/gen3/transform_utils.py +++ b/gen3/transform_utils.py @@ -292,6 +292,8 @@ def split_file( output_dir (str): the path to the directory where to write all the intermediate files to """ + if batch_size < 1: + raise ValueError(f"batch_size must be >= 1, got {batch_size}") start = time.time() with open(input_file, "rb") as fin: for i, lines in enumerate(iter(lambda: list(islice(fin, batch_size)), [])): @@ -365,8 +367,8 @@ def fhir_tagger( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], config: str | os.PathLike[str], - workers: int, batch_size: int, + workers: int = 8, force: bool = False, ): """ @@ -384,7 +386,10 @@ def fhir_tagger( """ start_time = time.time() - + if batch_size < 1: + raise ValueError(f"batch_size must be >= 1, got {batch_size}") + if workers < 1: + raise ValueError(f"workers must be >= 1, got {workers}, default is 8") # check if input and output file are the same if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") diff --git a/tests/test_fhirtransform.py b/tests/test_fhirtransform.py new file mode 100644 index 00000000..199332d0 --- /dev/null +++ b/tests/test_fhirtransform.py @@ -0,0 +1,347 @@ +import pytest +import math +from transform_utils import Gen3FHIRAuthzTagger, _is_new, _is_done, _resume_run, _merge_needed, sweep, split_file, transform_chunk, merge_chunks, fhir_tagger +import pathlib +import os +import orjson +import subprocess +import sys +import shutil + + +TMP_ROOT = pathlib.Path("./outputs") +TAGGER = Gen3FHIRAuthzTagger("config.yaml") +SRC = TMP_ROOT / "test_Patient.ndjson" +IN = TMP_ROOT / "Patient.ndjson" +OUT = os.path.join(TMP_ROOT, "output.ndjson") +BATCH_SIZE = 1 +BASE_RECORD = { + "timestamp":"2026-08-12T21:00:20.677168+00:00", + "input_file":"output/fhir/Patient.ndjson", + "output_file":"outputs/test_status/status.ndjson", + "config_hash":"9c61e70e3ea403e3daf1ee795036253c", + "batch_size":1} + +os.makedirs(TMP_ROOT, exist_ok=True) + + +def mock_state( + directory, + *, + config="match", # "match" | None (no file) | dict (custom) | str (raw bytes) + chunks=0, + done=0, + output=None, # None | "empty" | "full" + record=None, +): + """ + Returns (directory, record) with the directory populated as described. + The record's output_file always points inside TMP_ROOT + """ + record = dict(record or BASE_RECORD) + out = pathlib.Path(directory) / "status.ndjson" + record["output_file"] = str(out) + + + shutil.rmtree(directory, ignore_errors=True) + directory.mkdir(parents=True) + + if config == "match": + params = dict(record) + elif isinstance(config, dict): + params = dict(record) + params.update(config) + else: + params = None + + if params is not None: + (directory / ".config.json").write_bytes(orjson.dumps(params)) + elif isinstance(config, str) and config != "match": + (directory / ".config.json").write_text(config, encoding="utf-8") + + for i in range(chunks): + (directory / f"chunk_{i:03d}.chunk").write_text("{}\n", encoding="utf-8") + for i in range(done): + (directory / f"chunk_{i:03d}.done").write_text("{}\n", encoding="utf-8") + + + if output == "empty": + out.touch() + elif output == "full": + out.write_text('{"id":1}\n', encoding="utf-8") + + + return directory, record + +def test_fhir_output(): + src = [orjson.loads(line) + for line in pathlib.Path(SRC).read_bytes().splitlines() + if line.strip()] + fhir_tagger(IN, OUT, "config.yaml", 8, BATCH_SIZE) + out = [orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip()] + + assert len(src) == len(out) + assert {r["id"] for r in src} == {r["id"] for r in out} + assert [ {k: v for k, v in r.items() if k != "meta.security"} for r in out ] == src + + +def test_chunking(): + split_file(IN, BATCH_SIZE, TMP_ROOT) + chunks = list(TMP_ROOT.glob("*.chunk")) + fin = [orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip()] + expected = math.ceil(len(fin) / BATCH_SIZE) + assert len(chunks) == expected, f"expected {expected} chunks, found {len(chunks)}" + recombined = [orjson.loads(line) for p in sorted(chunks) for line in p.read_bytes().splitlines() if line.strip()] + assert recombined == fin + +def test_transform(): + TAGGER.relevant_authz_rules(os.path.basename(IN).split(".")[0]) + chunks = list(TMP_ROOT.glob("*.chunk")) + for c in chunks: + transform_chunk(c, TAGGER, TMP_ROOT) + transformed = list(TMP_ROOT.glob("*.done")) + assert len(transformed) == len(chunks) + assert len(list(TMP_ROOT.glob("*.chunk"))) == 0 + + +def test_merge(): + transformed = list(TMP_ROOT.glob("*.done")) + transformed_sum = sum(len([l for l in pathlib.Path(c).read_bytes().splitlines() if l.strip()]) for c in transformed) + merge_chunks(transformed, OUT) + merged = pathlib.Path(OUT).read_text(encoding="utf-8") + fin = [orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip()] + fout = fin = [orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip()] + assert os.path.exists(OUT) + assert pathlib.Path(OUT).stat().st_size > 0 + assert len(list(TMP_ROOT.glob("*.done"))) == 0 + assert len(fout) == transformed_sum + assert len(fout) == len(fin) + assert merged.endswith("\n"), "file does not end with a newline" + assert not merged.endswith("\n\n"), "file ends with a blank line" + for i, line in enumerate(merged.split("\n")[:-1]): + assert line.strip(), f"blank line at index {i}" + orjson.loads(line) # every line independently parses + + +def test_is_new(): + tmp_path = TMP_ROOT / "test_new" + #directory missing + assert _is_new(TMP_ROOT / "does_not_exist", BASE_RECORD) is True + + #no config file + directory, record = mock_state(tmp_path, config=None) + assert _is_new(directory, record) is True + + #check corrupt config file + directory, record = mock_state(tmp_path, config="{not valid json") + assert _is_new(directory, record) is True + + #check empty config file + directory, record = mock_state(tmp_path, config="") + assert _is_new(directory, record) is True + + #check if not new when everything matches + directory, record = mock_state(tmp_path, config="match") + assert _is_new(directory, record) is False + + #check when config changed + directory, record = mock_state(tmp_path, config={"config_hash": "different"}) + assert _is_new(directory, record) is True + + #check when batch_size changed + directory, record = mock_state(tmp_path, config={"batch_size": 50}) + assert _is_new(directory, record) is True + + #check when output filename changed + directory, record = mock_state(tmp_path, config={"output_file": "/tmp/somewhere_else.ndjson"}) + assert _is_new(directory, record) is True + + + +def test_is_done(): + tmp_path = TMP_ROOT / "test_done" + + #config matches but output is empty + directory, record = mock_state(tmp_path, config="match", output="empty") + assert _is_done(directory, record) is False + + #config matches but no output + directory, record = mock_state(tmp_path, config="match", output=None) + assert _is_done(directory, record) is False + + #output full but no config file + directory, record = mock_state(tmp_path, config=None, output="full") + assert _is_done(directory, record) is False + + #output full but config file is corrupt + directory, record = mock_state(tmp_path, config="{bad", output="full") + assert _is_done(directory, record) is False + + #output full batch_size changed + directory, record = mock_state(tmp_path, config={"batch_size": 50}, output="full") + assert _is_done(directory, record) is False + + #output full but config changed + directory, record = mock_state(tmp_path, config={"config_hash": "different"}, output="full") + assert _is_done(directory, record) is False + + #output full but output filename changed + directory, record = mock_state(tmp_path, config={"output_file": "/tmp/somewhere_else.ndjson"}, output="full") + assert _is_done(directory, record) is False + + #config matches and output is full + directory, record = mock_state(tmp_path, config="match", output="full") + assert _is_done(directory, record) is True + + +def test_resume_run(): + tmp_path = TMP_ROOT / "test_resume" + #no chunk files in directory + directory, record = mock_state(tmp_path, chunks=0) + assert _resume_run(directory, record) is False + + #leftover chunks + directory, record = mock_state(tmp_path, chunks=3) + assert _resume_run(directory, record) is True + + directory, record = mock_state(tmp_path, chunks=1) + assert _resume_run(directory, record) is True + + #no chunks but .done remaining + directory, record = mock_state(tmp_path, chunks=0, done=3) + assert _resume_run(directory, record) is False + + #directory is missing + assert _resume_run(TMP_ROOT / "gone", BASE_RECORD) is False + + #ignored similarly named files + directory, record = mock_state(tmp_path) + (directory / "chunk").write_text("", encoding="utf-8") + (directory / "notes.chunk.csv").write_text("", encoding="utf-8") + assert _resume_run(directory, record) is False + + #non recursive + directory, record = mock_state(tmp_path) + (directory / "nested").mkdir() + (directory / "nested" / "a.chunk").write_text("", encoding="utf-8") + assert _resume_run(directory, record) is False + +def test_merge_needed(): + tmp_path = TMP_ROOT / "outputs" / "test_merge" + #no merge on clean directory + directory, record = mock_state(tmp_path, done=0) + assert _merge_needed(directory, record) is False + + #merge when done files left + directory, record = mock_state(tmp_path, done=3) + assert _merge_needed(directory, record) is True + + #no merge when directory missing + assert _merge_needed(TMP_ROOT / "gone", BASE_RECORD) is False + +def test_status(): + """Tests for overlap in different statuses""" + tmp_path = TMP_ROOT / "test_status" + #fresh directory + directory, record = mock_state(tmp_path, config="match") + assert _is_new(directory, record) is False + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is False + + #need to resume + directory, record = mock_state(tmp_path, config="match", chunks=2, done=3) + assert _is_new(directory, record) is False + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is True + + #merge needed + directory, record = mock_state(tmp_path, config="match", chunks=0, done=5) + assert _is_new(directory, record) is False + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is True + + #fully complete + directory, record = mock_state(tmp_path, config="match", output="full") + assert _is_done(directory, record) is True + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is False + + #new and done are mutually exclusive + for cfg in ["match", None, {"config_hash": "x"}, {"batch_size": 1}]: + directory, record = mock_state(TMP_ROOT / str(id(cfg)), config=cfg, output="full") + assert not (_is_new(directory, record) and _is_done(directory, record)) + + +def test_cli(): + """Run the CLI and return the CompletedProcess.""" + args = ["--input", IN, "--output", OUT, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + + assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" + records = [orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip()] + in_records = [orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip()] + assert len(records) == len(in_records) + assert all("security" in r.get("meta", {}) for r in records) + +@pytest.mark.parametrize("bad", [0, -1, None, "bad"]) +def test_invalid_chunk_size_is_rejected(bad): + out = TMP_ROOT / "cli_test" / "cli_out.ndjson" + + args = ["--input", IN, "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(bad)] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + assert result.returncode != 0 + assert not pathlib.Path(out).exists(), "rejected the argument but still wrote output" + + +def test_missing_input_file_fails_cleanly(): + out = TMP_ROOT / "cli_test" / "nope.ndjson" + args = ["--input", "nope.ndjson", "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + assert result.returncode != 0 + assert "Traceback" not in result.stderr, "raw traceback instead of an error message" + assert not pathlib.Path(out).exists() + +#depends on whether or not we want the script to create new output directories +def test_output_directory_does_not_exist(): + out = TMP_ROOT / "missing_dir" / "out.ndjson" + args = ["--input", IN, "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + assert result.returncode != 0 + assert "Traceback" not in result.stderr From 92d603ee304beebcb6c9c654b4555dd3570c04f6 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 14 Aug 2026 11:54:48 -0500 Subject: [PATCH 03/35] Remove unnecessary imports --- gen3/cli/fhir_transform.py | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/gen3/cli/fhir_transform.py b/gen3/cli/fhir_transform.py index 0a84e7e7..945fbe93 100644 --- a/gen3/cli/fhir_transform.py +++ b/gen3/cli/fhir_transform.py @@ -1,17 +1,8 @@ -import yaml -from itertools import islice, repeat -import orjson from fhirpathpy import evaluate import click -import os, glob -import time -from datetime import datetime, timezone -import shutil +import os import pathlib -import hashlib -from concurrent.futures import ProcessPoolExecutor from cdislogging import get_logger -from gen3.utils import make_folders_for_filename from transform_utils import * logging = get_logger("fhir_tagger", log_level="info") From 44940a93ee16d9142b5405f83ea30deb29fb7210 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Tue, 18 Aug 2026 16:11:12 -0500 Subject: [PATCH 04/35] Add documentation, format tests, integrate into gen3 cli, add test_data files --- docs/howto/fhir.md | 14 + gen3/cli/__main__.py | 2 + gen3/cli/{fhir_transform.py => fhir.py} | 4 +- gen3/{transform_utils.py => fhir.py} | 10 +- tests/test_data/fhir_Patient.ndjson | 22 + tests/test_data/test_fhir_Patient.ndjson | 22 + tests/test_fhir_transform.py | 561 +++++++++++++++++++++++ tests/test_fhirtransform.py | 347 -------------- 8 files changed, 630 insertions(+), 352 deletions(-) create mode 100644 docs/howto/fhir.md rename gen3/cli/{fhir_transform.py => fhir.py} (97%) rename gen3/{transform_utils.py => fhir.py} (98%) create mode 100644 tests/test_data/fhir_Patient.ndjson create mode 100644 tests/test_data/test_fhir_Patient.ndjson create mode 100644 tests/test_fhir_transform.py delete mode 100644 tests/test_fhirtransform.py diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md new file mode 100644 index 00000000..e86c744f --- /dev/null +++ b/docs/howto/fhir.md @@ -0,0 +1,14 @@ +## FHIR + +The fhir commands can be invoked as follows + +`gen3 fhir COMMAND [ARGS] [OPTIONS]` + +For a list of commands and options run + +`gen3 fhir --help` + +For example, the following tags the 'Patient.ndjson' file with Gen3 authorization and outputs 'gen3_Patient.ndjson' using the authorization rules from 'config.yaml' + +`gen3 fhir transform Patient.ndjson gen3_Patient.ndjson config.yaml --batch_size 10000 --workers 8 ` + diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 995bfda6..8d071881 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -15,6 +15,7 @@ import gen3.cli.drs_pull as drs_pull import gen3.cli.users as users import gen3.cli.wrap as wrap +import gen3.cli.fhir as fhir import gen3 from gen3 import logging as sdklogging from gen3.cli import nih @@ -145,4 +146,5 @@ def main( main.add_command(nih.nih) main.add_command(users.users) main.add_command(wrap.run) +main.add_command(fhir.fhir) main() diff --git a/gen3/cli/fhir_transform.py b/gen3/cli/fhir.py similarity index 97% rename from gen3/cli/fhir_transform.py rename to gen3/cli/fhir.py index 945fbe93..cea3bc01 100644 --- a/gen3/cli/fhir_transform.py +++ b/gen3/cli/fhir.py @@ -3,9 +3,9 @@ import os import pathlib from cdislogging import get_logger -from transform_utils import * +from gen3.fhir import * -logging = get_logger("fhir_tagger", log_level="info") +logging = get_logger("fhir_transform", log_level="info") TMP_ROOT = pathlib.Path(".fhir_transform/tmp") diff --git a/gen3/transform_utils.py b/gen3/fhir.py similarity index 98% rename from gen3/transform_utils.py rename to gen3/fhir.py index b94fee53..7165dce9 100644 --- a/gen3/transform_utils.py +++ b/gen3/fhir.py @@ -13,7 +13,7 @@ from cdislogging import get_logger from gen3.utils import make_folders_for_filename -logging = get_logger("fhir_tagger", log_level="info") +logging = get_logger("fhir_transform", log_level="info") TMP_ROOT = pathlib.Path(".fhir_transform/tmp") @@ -351,8 +351,12 @@ def merge_chunks( """ start = time.time() - print(output_file) - with open(f"{output_file}", "wb") as fout: + out = pathlib.Path(output_file) + + # creates all directories in path if dont exist + out.parent.mkdir(parents=True, exist_ok=True) + + with open(out, "wb") as fout: for f in sorted(input_files): with open(f, "rb") as fin: shutil.copyfileobj(fin, fout) diff --git a/tests/test_data/fhir_Patient.ndjson b/tests/test_data/fhir_Patient.ndjson new file mode 100644 index 00000000..2900dbef --- /dev/null +++ b/tests/test_data/fhir_Patient.ndjson @@ -0,0 +1,22 @@ +{"resourceType":"Patient","id":"29afd833-3a8d-43cf-e62b-29e8e3304297","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]},"text":{"status":"generated","div":"
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"},"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2106-3","display":"White"}},{"url":"text","valueString":"White"}]},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2186-5","display":"Not Hispanic or Latino"}},{"url":"text","valueString":"Not Hispanic or Latino"}]},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Lavette209 Batz141"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"F"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Dracut","state":"Massachusetts","country":"US"}},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":10.965902765543907},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":59.03409723445609}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"7a3658df-2d10-69de-e8bf-bc9a67b80923"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR","display":"Medical Record Number"}],"text":"Medical Record Number"},"system":"http://hospital.smarthealthit.org","value":"7a3658df-2d10-69de-e8bf-bc9a67b80923"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"SS","display":"Social Security Number"}],"text":"Social Security Number"},"system":"http://hl7.org/fhir/sid/us-ssn","value":"999-19-3821"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"DL","display":"Driver's license number"}],"text":"Driver's license number"},"system":"urn:oid:2.16.840.1.113883.4.3.25","value":"S99952842"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"PPN","display":"Passport Number"}],"text":"Passport Number"},"system":"http://hl7.org/fhir/sid/passport-USA","value":"X09895870X"}],"name":[{"use":"official","family":"Blanda868","given":["Priscilla527","Gladis186"],"prefix":["Mrs."]},{"use":"maiden","family":"Conroy74","given":["Priscilla527","Gladis186"],"prefix":["Mrs."]}],"telecom":[{"system":"phone","value":"555-907-8608","use":"home"}],"gender":"female","birthDate":"1955-07-02","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.23008713518161},{"url":"longitude","valueDecimal":-71.10123050478171}]}],"line":["632 Brekke Promenade"],"city":"Quincy","state":"MA","postalCode":"02186","country":"US"}],"maritalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus","code":"M","display":"Married"}],"text":"Married"},"multipleBirthBoolean":false,"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en-US","display":"English (United States)"}],"text":"English (United States)"}}]} diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py new file mode 100644 index 00000000..e5dfb1a3 --- /dev/null +++ b/tests/test_fhir_transform.py @@ -0,0 +1,561 @@ +import pytest +import math +from transform_utils import ( + Gen3FHIRAuthzTagger, + _is_new, + _is_done, + _resume_run, + _merge_needed, + split_file, + transform_chunk, + merge_chunks, + fhir_tagger, +) +import pathlib +import os +import orjson +import subprocess +import sys +import shutil + +TMP_ROOT = pathlib.Path("./test_data/fhir_outputs") +TAGGER = Gen3FHIRAuthzTagger("config.yaml") +SRC = "test_data" / "test_fhir_Patient.ndjson" +IN = "test_data" / "fhir_Patient.ndjson" +OUT = os.path.join(TMP_ROOT, "fhir_output_Patient.ndjson") +BATCH_SIZE = 1 +BASE_RECORD = { + "timestamp": "2026-08-12T21:00:20.677168+00:00", + "input_file": "output/fhir/Patient.ndjson", + "output_file": "outputs/test_status/status.ndjson", + "config_hash": "9c61e70e3ea403e3daf1ee795036253c", + "batch_size": 1, +} + +os.makedirs(TMP_ROOT, exist_ok=True) + + +def mock_state( + directory, + config="match", + chunks=0, + done=0, + output=None, + record=None, +): + """ + Build an on-disk run directory and return (directory, record). + + Args: + tmp_path (Path): parent directory; a fresh subdir is created under it + config: "match" -> .config.json equal to record + dict -> record updated with these overrides + str -> written verbatim (for malformed-JSON cases) + None -> no .config.json written + chunks (int): number of chunk_NNN.chunk files + done (int): number of chunk_NNN.done files (indices align with chunks) + output: None -> no output file, "empty" -> touched, "full" -> one row + record (dict): base record; defaults to BASE_RECORD + + Returns: + (Path, dict) + """ + + record = dict(record or BASE_RECORD) + out = pathlib.Path(directory) / "status.ndjson" + record["output_file"] = str(out) + + shutil.rmtree(directory, ignore_errors=True) + directory.mkdir(parents=True) + + if config == "match": + params = dict(record) + elif isinstance(config, dict): + params = dict(record) + params.update(config) + else: + params = None + + if params is not None: + (directory / ".config.json").write_bytes(orjson.dumps(params)) + elif isinstance(config, str) and config != "match": + (directory / ".config.json").write_text(config, encoding="utf-8") + + for i in range(chunks): + (directory / f"chunk_{i:03d}.chunk").write_text("{}\n", encoding="utf-8") + for i in range(done): + (directory / f"chunk_{i:03d}.done").write_text("{}\n", encoding="utf-8") + + if output == "empty": + out.touch() + elif output == "full": + out.write_text('{"id":1}\n', encoding="utf-8") + + return directory, record + + +def test_fhir_output(): + """Tests that output file matches the input file with the only difference being the tags""" + src = [ + orjson.loads(line) + for line in pathlib.Path(SRC).read_bytes().splitlines() + if line.strip() + ] + fhir_tagger(IN, OUT, "config.yaml", 8, BATCH_SIZE) + out = [ + orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip() + ] + + # check that output matched input in everything other than the tags + assert len(src) == len( + out + ), "Length of the output file does not match the length of the input file" + assert {r["id"] for r in src} == { + r["id"] for r in out + }, "IDs in the output file do not match the IDs in the input file. Order not maintained" + assert [ + {k: v for k, v in r.items() if k != "meta.security"} for r in out + ] == src, "Content of the output file does not match the content of the input file (other than the security tags)" + + +def test_chunking(): + """Tests that number of chunks is correct and the recombined chunks match the input file""" + split_file(IN, BATCH_SIZE, TMP_ROOT) + chunks = list(TMP_ROOT.glob("*.chunk")) + fin = [ + orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] + expected = math.ceil(len(fin) / BATCH_SIZE) + + # number of chunk files matches expected + assert len(chunks) == expected, f"Expected {expected} chunks, found {len(chunks)}" + recombined = [ + orjson.loads(line) + for p in sorted(chunks) + for line in p.read_bytes().splitlines() + if line.strip() + ] + # chunks recombine to match input file + assert ( + recombined == fin + ), "Recombined chunks do not match the content of the input file" + + +def test_transform(): + """Asserts transform_chunk creates the same number of .done files as .chunk and no .chunk files remain once transformation is completed""" + TAGGER.relevant_authz_rules(os.path.basename(IN).split(".")[0]) + chunks = list(TMP_ROOT.glob("*.chunk")) + for c in chunks: + transform_chunk(c, TAGGER, TMP_ROOT) + transformed = list(TMP_ROOT.glob("*.done")) + + # same number of transformed files as chunk files + assert len(transformed) == len( + chunks + ), f"Expected same number of transformed .done files as number of .chunk files after transformation completed, found {len(transformed)}" + # all .chunk files deleted after transformation completed + assert ( + len(list(TMP_ROOT.glob("*.chunk"))) == 0 + ), f"Expected 0 chunks after transformation completed, found {len(list(TMP_ROOT.glob("*.chunk")))}" + + +def test_merge(): + """Asserts that after merge is completed, the output file exists and is not empty, there are no .done files remaining, + the length of the output matches the sum of the transformed files and the input file, and the file is not corrupt/formatting is correct + """ + transformed = list(TMP_ROOT.glob("*.done")) + transformed_sum = sum( + len([l for l in pathlib.Path(c).read_bytes().splitlines() if l.strip()]) + for c in transformed + ) + merge_chunks(transformed, OUT) + merged = pathlib.Path(OUT).read_text(encoding="utf-8") + fin = [ + orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] + fout = fin = [ + orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip() + ] + + # output file exists after merge + assert os.path.exists(OUT), "Output file was not created" + # output file is not empty after merge + assert pathlib.Path(OUT).stat().st_size > 0, "Output file empty" + # no leftover .done files after merge completed + assert ( + len(list(TMP_ROOT.glob("*.done"))) == 0 + ), f"Expected 0 .done files after transformation completed, found {len(list(TMP_ROOT.glob("*.done")))}" + # output file is the same length as the combined transformed files and the length of the input file + assert ( + len(fout) == transformed_sum == len(fin) + ), "The length of the output file does not math the sum of the .done files and the input file" + # check formatting of output file + assert merged.endswith("\n"), "File does not end with a newline" + assert not merged.endswith("\n\n"), "File ends with a blank line" + for i, line in enumerate(merged.split("\n")[:-1]): + assert line.strip(), f"blank line at index {i}" + orjson.loads(line) # every line independently parses + + +class Test_is_new: + """Tests the logic of the run/directory being marked as new (_is_new(directory, record) returns True)""" + + tmp_path = TMP_ROOT / "test_new" + + def test_is_new_with_missing_directory(self): + # directory missing + assert _is_new(TMP_ROOT / "does_not_exist", BASE_RECORD) is True + + def test_is_new_directory_has_no_config_file(self): + # no config file + directory, record = mock_state(self.tmp_path, config=None) + assert _is_new(directory, record) is True + + def test_is_new_directory_has_corrupt_config_file(self): + # check corrupt config file + directory, record = mock_state(self.tmp_path, config="{not valid json") + assert _is_new(directory, record) is True + + def test_is_new_directory_has_empty_config_file(self): + # check empty config file + directory, record = mock_state(self.tmp_path, config="") + assert _is_new(directory, record) is True + + def test_is_not_new_when_config_matches(self): + # check if not new when everything matches + directory, record = mock_state(self.tmp_path, config="match") + assert _is_new(directory, record) is False + + def test_is_new_when_config_changed(self): + # check when config changed + directory, record = mock_state( + self.tmp_path, config={"config_hash": "different"} + ) + assert _is_new(directory, record) is True + + @pytest.mark.parametrize("batch_size", [0, 100, 50, 4]) + def test_is_new_when_batch_size_changed(self, batch_size): + # check when batch_size changed + directory, record = mock_state(self.tmp_path, config={"batch_size": batch_size}) + assert _is_new(directory, record) is True + + def test_is_new_when_output_filename_changed(self): + # check when output filename changed + directory, record = mock_state( + self.tmp_path, config={"output_file": "/tmp/somewhere_else.ndjson"} + ) + assert _is_new(directory, record) is True + + +class Test_is_done: + """Tests the logic of the run/directory being marked as done (_is_done(directory, record) returns True)""" + + tmp_path = TMP_ROOT / "test_done" + + def test_is_done_with_matching_config_and_empty_output(self): + # config matches but output is empty + directory, record = mock_state(self.tmp_path, config="match", output="empty") + assert _is_done(directory, record) is False + + def test_is_done_with_matching_config_and_no_output(self): + # config matches but no output + directory, record = mock_state(self.tmp_path, config="match", output=None) + assert _is_done(directory, record) is False + + def test_is_done_with_no_config_and_full_output(self): + # output full but no config file + directory, record = mock_state(self.tmp_path, config=None, output="full") + assert _is_done(directory, record) is False + + def test_is_done_with_corrupt_config_and_full_output(self): + # output full but config file is corrupt + directory, record = mock_state(self.tmp_path, config="{bad", output="full") + assert _is_done(directory, record) is False + + @pytest.mark.parametrize("batch_size", [0, 100, 50, 4]) + def test_is_done_with_full_output_and_different_batch_size(self, batch_size): + # output full batch_size changed + directory, record = mock_state( + self.tmp_path, config={"batch_size": batch_size}, output="full" + ) + assert _is_done(directory, record) is False + + def test_is_done_with_full_output_and_different_config_hash(self): + # output full but config changed + directory, record = mock_state( + self.tmp_path, config={"config_hash": "different"}, output="full" + ) + assert _is_done(directory, record) is False + + def test_is_done_with_full_output_and_different_output_filename(self): + # output full but output filename changed + directory, record = mock_state( + self.tmp_path, + config={"output_file": "/tmp/somewhere_else.ndjson"}, + output="full", + ) + assert _is_done(directory, record) is False + + def test_is_done_with_full_output_and_matching_config(self): + # config matches and output is full + directory, record = mock_state(self.tmp_path, config="match", output="full") + assert _is_done(directory, record) is True + + +class Test_resume_run: + """Tests the logic of the run/directory being marked as need to resume run (_resume_run(directory, record) returns True)""" + + tmp_path = TMP_ROOT / "test_resume" + + def test_resume_run_with_no_chunk_files(self): + # no chunk files in directory + directory, record = mock_state(self.tmp_path, chunks=0) + assert _resume_run(directory, record) is False + + @pytest.mark.parametrize("chunk_files", [4, 20, 57, 100]) + def test_resume_run_with_leftover_chunk_files(self, chunk_files): + # leftover chunks + directory, record = mock_state(self.tmp_path, chunks=chunk_files) + assert _resume_run(directory, record) is True + + @pytest.mark.parametrize("done_files", [0, 20, 57, 100]) + def test_resume_run_with_leftover_done_files_and_no_chunk_files(self, done_files): + # no chunks but .done remaining + directory, record = mock_state(self.tmp_path, chunks=0, done=done_files) + assert _resume_run(directory, record) is False + + @pytest.mark.parametrize(["chunk_files", "done_files"], [(5, 10), (12, 5), (7, 7)]) + def test_resume_run_with_leftover_done_files_and_chunk_files( + self, chunk_files, done_files + ): + # both .chunk and .done remaining + directory, record = mock_state( + self.tmp_path, chunks=chunk_files, done=done_files + ) + assert _resume_run(directory, record) is True + + def test_resume_run_when_directory_missing(self): + # directory is missing + assert _resume_run(TMP_ROOT / "gone", BASE_RECORD) is False + + def test_resume_run_ignores_similarly_named_files(self): + # ignored similarly named files + directory, record = mock_state(self.tmp_path) + (directory / "chunk").write_text("", encoding="utf-8") + (directory / "notes.chunk.csv").write_text("", encoding="utf-8") + assert _resume_run(directory, record) is False + + def test_resume_run_is_nonrecursive(self): + # non recursive + directory, record = mock_state(self.tmp_path) + (directory / "nested").mkdir() + (directory / "nested" / "a.chunk").write_text("", encoding="utf-8") + assert _resume_run(directory, record) is False + + +class Test_merge_needed: + """Tests the logic of the run/directory being marked as merge needed (_merge_needed(directory, record) returns True)""" + + tmp_path = TMP_ROOT / "outputs" / "test_merge" + + def test_merge_needed_when_no_done_files_remaining(self): + # no merge on clean directory + directory, record = mock_state(self.tmp_path, done=0) + assert _merge_needed(directory, record) is False + + @pytest.mark.parametrize("done_files", [5, 20, 57, 100]) + def test_merge_needed_when_done_files_remaining(self, done_files): + # merge when done files left + directory, record = mock_state(self.tmp_path, done=done_files) + assert _merge_needed(directory, record) is True + + @pytest.mark.parametrize( + ["chunk_files", "done_files"], [(5, 2), (5, 5), (5, 7), (1, 10)] + ) + def test_merge_needed_when_chunk_and_done_files_remaining( + self, chunk_files, done_files + ): + # no merge when both chunk and done files left + directory, record = mock_state( + self.tmp_path, chunks=chunk_files, done=done_files + ) + assert _merge_needed(directory, record) is False + + def test_merge_needed_when_directory_missing(self): + # no merge when directory missing + assert _merge_needed(TMP_ROOT / "gone", BASE_RECORD) is False + + +class Test_status: + """Tests for overlap in different statuses""" + + tmp_path = TMP_ROOT / "test_status" + + def test_fresh_directory(self): + # fresh directory + directory, record = mock_state(self.tmp_path, config="match") + assert _is_new(directory, record) is True + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is False + + def test_need_to_resume_overlap(self): + # need to resume + directory, record = mock_state(self.tmp_path, config="match", chunks=2, done=3) + assert _is_new(directory, record) is False + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is True + + def test_merge_needed_overlap(self): + # merge needed + directory, record = mock_state(self.tmp_path, config="match", chunks=0, done=5) + assert _is_new(directory, record) is False + assert _is_done(directory, record) is False + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is True + + def test_run_complete(self): + # fully complete + directory, record = mock_state(self.tmp_path, config="match", output="full") + assert _is_done(directory, record) is True + assert _resume_run(directory, record) is False + assert _merge_needed(directory, record) is False + assert _is_new(directory, record) is False + + @pytest.mark.parametrize( + "state", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] + ) + def test_new_and_done_are_mutually_exclusive(self, state): + # new and done are mutually exclusive + directory, record = mock_state( + TMP_ROOT / str(id(state)), config=state, output="full" + ) + assert not (_is_new(directory, record) and _is_done(directory, record)) + + +def test_cli(): + """Run the CLI and return the CompletedProcess.""" + args = [ + "--input", + IN, + "--output", + OUT, + "--chunk-size", + "--config", + "config.yaml", + "--batch_size", + str(BATCH_SIZE), + ] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" + records = [ + orjson.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip() + ] + in_records = [ + orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] + assert len(records) == len( + in_records + ), "Output number of records doesn't match the input number of records" + assert all( + "security" in r.get("meta", {}) for r in records + ), "Security tags missing" + + +@pytest.mark.parametrize("bad", [0, -1, None, "bad"]) +def test_invalid_batch_size_is_rejected(bad): + """Assert invalid batch_size is rejected and raises an error""" + out = TMP_ROOT / "cli_test" / "cli_out.ndjson" + + args = [ + "--input", + IN, + "--output", + out, + "--chunk-size", + "--config", + "config.yaml", + "--batch_size", + str(bad), + ] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + assert result.returncode != 0, "Function accept invalid batch_size" + assert not pathlib.Path( + out + ).exists(), "Rejected the argument but still wrote output" + + +def test_missing_input_file_fails_cleanly(): + """Asserts error is raised if missing input file passed as argument""" + out = TMP_ROOT / "cli_test" / "nope.ndjson" + args = [ + "--input", + "nope.ndjson", + "--output", + out, + "--chunk-size", + "--config", + "config.yaml", + "--batch_size", + str(BATCH_SIZE), + ] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + assert result.returncode != 0, "Function accepts non-existent input file" + assert "Traceback" not in result.stderr, "Raw traceback instead of an error message" + assert not pathlib.Path( + out + ).exists(), "Output file written even though invalid input file passed" + + +def test_output_directory_does_not_exist(): + """Test response if output directory doesn't exists. Directory (and parents) should be created if missing""" + out = TMP_ROOT / "missing_dir" / "out.ndjson" + args = [ + "--input", + IN, + "--output", + out, + "--chunk-size", + "--config", + "config.yaml", + "--batch_size", + str(BATCH_SIZE), + ] + result = subprocess.run( + [sys.executable, "fhir transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + + assert result.returncode == 0, "Raises error instead of creating output directory" + assert pathlib.Path(out).exists(), "Process not completed, output file not written" diff --git a/tests/test_fhirtransform.py b/tests/test_fhirtransform.py deleted file mode 100644 index 199332d0..00000000 --- a/tests/test_fhirtransform.py +++ /dev/null @@ -1,347 +0,0 @@ -import pytest -import math -from transform_utils import Gen3FHIRAuthzTagger, _is_new, _is_done, _resume_run, _merge_needed, sweep, split_file, transform_chunk, merge_chunks, fhir_tagger -import pathlib -import os -import orjson -import subprocess -import sys -import shutil - - -TMP_ROOT = pathlib.Path("./outputs") -TAGGER = Gen3FHIRAuthzTagger("config.yaml") -SRC = TMP_ROOT / "test_Patient.ndjson" -IN = TMP_ROOT / "Patient.ndjson" -OUT = os.path.join(TMP_ROOT, "output.ndjson") -BATCH_SIZE = 1 -BASE_RECORD = { - "timestamp":"2026-08-12T21:00:20.677168+00:00", - "input_file":"output/fhir/Patient.ndjson", - "output_file":"outputs/test_status/status.ndjson", - "config_hash":"9c61e70e3ea403e3daf1ee795036253c", - "batch_size":1} - -os.makedirs(TMP_ROOT, exist_ok=True) - - -def mock_state( - directory, - *, - config="match", # "match" | None (no file) | dict (custom) | str (raw bytes) - chunks=0, - done=0, - output=None, # None | "empty" | "full" - record=None, -): - """ - Returns (directory, record) with the directory populated as described. - The record's output_file always points inside TMP_ROOT - """ - record = dict(record or BASE_RECORD) - out = pathlib.Path(directory) / "status.ndjson" - record["output_file"] = str(out) - - - shutil.rmtree(directory, ignore_errors=True) - directory.mkdir(parents=True) - - if config == "match": - params = dict(record) - elif isinstance(config, dict): - params = dict(record) - params.update(config) - else: - params = None - - if params is not None: - (directory / ".config.json").write_bytes(orjson.dumps(params)) - elif isinstance(config, str) and config != "match": - (directory / ".config.json").write_text(config, encoding="utf-8") - - for i in range(chunks): - (directory / f"chunk_{i:03d}.chunk").write_text("{}\n", encoding="utf-8") - for i in range(done): - (directory / f"chunk_{i:03d}.done").write_text("{}\n", encoding="utf-8") - - - if output == "empty": - out.touch() - elif output == "full": - out.write_text('{"id":1}\n', encoding="utf-8") - - - return directory, record - -def test_fhir_output(): - src = [orjson.loads(line) - for line in pathlib.Path(SRC).read_bytes().splitlines() - if line.strip()] - fhir_tagger(IN, OUT, "config.yaml", 8, BATCH_SIZE) - out = [orjson.loads(line) - for line in pathlib.Path(OUT).read_bytes().splitlines() - if line.strip()] - - assert len(src) == len(out) - assert {r["id"] for r in src} == {r["id"] for r in out} - assert [ {k: v for k, v in r.items() if k != "meta.security"} for r in out ] == src - - -def test_chunking(): - split_file(IN, BATCH_SIZE, TMP_ROOT) - chunks = list(TMP_ROOT.glob("*.chunk")) - fin = [orjson.loads(line) - for line in pathlib.Path(IN).read_bytes().splitlines() - if line.strip()] - expected = math.ceil(len(fin) / BATCH_SIZE) - assert len(chunks) == expected, f"expected {expected} chunks, found {len(chunks)}" - recombined = [orjson.loads(line) for p in sorted(chunks) for line in p.read_bytes().splitlines() if line.strip()] - assert recombined == fin - -def test_transform(): - TAGGER.relevant_authz_rules(os.path.basename(IN).split(".")[0]) - chunks = list(TMP_ROOT.glob("*.chunk")) - for c in chunks: - transform_chunk(c, TAGGER, TMP_ROOT) - transformed = list(TMP_ROOT.glob("*.done")) - assert len(transformed) == len(chunks) - assert len(list(TMP_ROOT.glob("*.chunk"))) == 0 - - -def test_merge(): - transformed = list(TMP_ROOT.glob("*.done")) - transformed_sum = sum(len([l for l in pathlib.Path(c).read_bytes().splitlines() if l.strip()]) for c in transformed) - merge_chunks(transformed, OUT) - merged = pathlib.Path(OUT).read_text(encoding="utf-8") - fin = [orjson.loads(line) - for line in pathlib.Path(IN).read_bytes().splitlines() - if line.strip()] - fout = fin = [orjson.loads(line) - for line in pathlib.Path(OUT).read_bytes().splitlines() - if line.strip()] - assert os.path.exists(OUT) - assert pathlib.Path(OUT).stat().st_size > 0 - assert len(list(TMP_ROOT.glob("*.done"))) == 0 - assert len(fout) == transformed_sum - assert len(fout) == len(fin) - assert merged.endswith("\n"), "file does not end with a newline" - assert not merged.endswith("\n\n"), "file ends with a blank line" - for i, line in enumerate(merged.split("\n")[:-1]): - assert line.strip(), f"blank line at index {i}" - orjson.loads(line) # every line independently parses - - -def test_is_new(): - tmp_path = TMP_ROOT / "test_new" - #directory missing - assert _is_new(TMP_ROOT / "does_not_exist", BASE_RECORD) is True - - #no config file - directory, record = mock_state(tmp_path, config=None) - assert _is_new(directory, record) is True - - #check corrupt config file - directory, record = mock_state(tmp_path, config="{not valid json") - assert _is_new(directory, record) is True - - #check empty config file - directory, record = mock_state(tmp_path, config="") - assert _is_new(directory, record) is True - - #check if not new when everything matches - directory, record = mock_state(tmp_path, config="match") - assert _is_new(directory, record) is False - - #check when config changed - directory, record = mock_state(tmp_path, config={"config_hash": "different"}) - assert _is_new(directory, record) is True - - #check when batch_size changed - directory, record = mock_state(tmp_path, config={"batch_size": 50}) - assert _is_new(directory, record) is True - - #check when output filename changed - directory, record = mock_state(tmp_path, config={"output_file": "/tmp/somewhere_else.ndjson"}) - assert _is_new(directory, record) is True - - - -def test_is_done(): - tmp_path = TMP_ROOT / "test_done" - - #config matches but output is empty - directory, record = mock_state(tmp_path, config="match", output="empty") - assert _is_done(directory, record) is False - - #config matches but no output - directory, record = mock_state(tmp_path, config="match", output=None) - assert _is_done(directory, record) is False - - #output full but no config file - directory, record = mock_state(tmp_path, config=None, output="full") - assert _is_done(directory, record) is False - - #output full but config file is corrupt - directory, record = mock_state(tmp_path, config="{bad", output="full") - assert _is_done(directory, record) is False - - #output full batch_size changed - directory, record = mock_state(tmp_path, config={"batch_size": 50}, output="full") - assert _is_done(directory, record) is False - - #output full but config changed - directory, record = mock_state(tmp_path, config={"config_hash": "different"}, output="full") - assert _is_done(directory, record) is False - - #output full but output filename changed - directory, record = mock_state(tmp_path, config={"output_file": "/tmp/somewhere_else.ndjson"}, output="full") - assert _is_done(directory, record) is False - - #config matches and output is full - directory, record = mock_state(tmp_path, config="match", output="full") - assert _is_done(directory, record) is True - - -def test_resume_run(): - tmp_path = TMP_ROOT / "test_resume" - #no chunk files in directory - directory, record = mock_state(tmp_path, chunks=0) - assert _resume_run(directory, record) is False - - #leftover chunks - directory, record = mock_state(tmp_path, chunks=3) - assert _resume_run(directory, record) is True - - directory, record = mock_state(tmp_path, chunks=1) - assert _resume_run(directory, record) is True - - #no chunks but .done remaining - directory, record = mock_state(tmp_path, chunks=0, done=3) - assert _resume_run(directory, record) is False - - #directory is missing - assert _resume_run(TMP_ROOT / "gone", BASE_RECORD) is False - - #ignored similarly named files - directory, record = mock_state(tmp_path) - (directory / "chunk").write_text("", encoding="utf-8") - (directory / "notes.chunk.csv").write_text("", encoding="utf-8") - assert _resume_run(directory, record) is False - - #non recursive - directory, record = mock_state(tmp_path) - (directory / "nested").mkdir() - (directory / "nested" / "a.chunk").write_text("", encoding="utf-8") - assert _resume_run(directory, record) is False - -def test_merge_needed(): - tmp_path = TMP_ROOT / "outputs" / "test_merge" - #no merge on clean directory - directory, record = mock_state(tmp_path, done=0) - assert _merge_needed(directory, record) is False - - #merge when done files left - directory, record = mock_state(tmp_path, done=3) - assert _merge_needed(directory, record) is True - - #no merge when directory missing - assert _merge_needed(TMP_ROOT / "gone", BASE_RECORD) is False - -def test_status(): - """Tests for overlap in different statuses""" - tmp_path = TMP_ROOT / "test_status" - #fresh directory - directory, record = mock_state(tmp_path, config="match") - assert _is_new(directory, record) is False - assert _is_done(directory, record) is False - assert _resume_run(directory, record) is False - assert _merge_needed(directory, record) is False - - #need to resume - directory, record = mock_state(tmp_path, config="match", chunks=2, done=3) - assert _is_new(directory, record) is False - assert _is_done(directory, record) is False - assert _resume_run(directory, record) is True - - #merge needed - directory, record = mock_state(tmp_path, config="match", chunks=0, done=5) - assert _is_new(directory, record) is False - assert _is_done(directory, record) is False - assert _resume_run(directory, record) is False - assert _merge_needed(directory, record) is True - - #fully complete - directory, record = mock_state(tmp_path, config="match", output="full") - assert _is_done(directory, record) is True - assert _resume_run(directory, record) is False - assert _merge_needed(directory, record) is False - - #new and done are mutually exclusive - for cfg in ["match", None, {"config_hash": "x"}, {"batch_size": 1}]: - directory, record = mock_state(TMP_ROOT / str(id(cfg)), config=cfg, output="full") - assert not (_is_new(directory, record) and _is_done(directory, record)) - - -def test_cli(): - """Run the CLI and return the CompletedProcess.""" - args = ["--input", IN, "--output", OUT, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] - result = subprocess.run( - [sys.executable, "fhir transform", *args], - capture_output=True, - text=True, - timeout=60, - ) - - - assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" - records = [orjson.loads(line) - for line in pathlib.Path(OUT).read_bytes().splitlines() - if line.strip()] - in_records = [orjson.loads(line) - for line in pathlib.Path(IN).read_bytes().splitlines() - if line.strip()] - assert len(records) == len(in_records) - assert all("security" in r.get("meta", {}) for r in records) - -@pytest.mark.parametrize("bad", [0, -1, None, "bad"]) -def test_invalid_chunk_size_is_rejected(bad): - out = TMP_ROOT / "cli_test" / "cli_out.ndjson" - - args = ["--input", IN, "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(bad)] - result = subprocess.run( - [sys.executable, "fhir transform", *args], - capture_output=True, - text=True, - timeout=60, - ) - - assert result.returncode != 0 - assert not pathlib.Path(out).exists(), "rejected the argument but still wrote output" - - -def test_missing_input_file_fails_cleanly(): - out = TMP_ROOT / "cli_test" / "nope.ndjson" - args = ["--input", "nope.ndjson", "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] - result = subprocess.run( - [sys.executable, "fhir transform", *args], - capture_output=True, - text=True, - timeout=60, - ) - assert result.returncode != 0 - assert "Traceback" not in result.stderr, "raw traceback instead of an error message" - assert not pathlib.Path(out).exists() - -#depends on whether or not we want the script to create new output directories -def test_output_directory_does_not_exist(): - out = TMP_ROOT / "missing_dir" / "out.ndjson" - args = ["--input", IN, "--output", out, "--chunk-size", "--config", "config.yaml", "--batch_size", str(BATCH_SIZE)] - result = subprocess.run( - [sys.executable, "fhir transform", *args], - capture_output=True, - text=True, - timeout=60, - ) - - assert result.returncode != 0 - assert "Traceback" not in result.stderr From aab4d544acdd1107c1bedec30ff841c3edd66c63 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Tue, 18 Aug 2026 18:36:35 -0500 Subject: [PATCH 05/35] Fix and add tests, create folder even if output_file path doesn't exist --- docs/howto/.devTest.md.swp | Bin 0 -> 12288 bytes gen3/fhir.py | 3 ++ .../{fhir_Patient.ndjson => Patient.ndjson} | 0 tests/test_fhir_transform.py | 46 +++++++----------- 4 files changed, 21 insertions(+), 28 deletions(-) create mode 100644 docs/howto/.devTest.md.swp rename tests/test_data/{fhir_Patient.ndjson => Patient.ndjson} (100%) diff --git a/docs/howto/.devTest.md.swp b/docs/howto/.devTest.md.swp new file mode 100644 index 0000000000000000000000000000000000000000..790a93b95b709dc08b901bcb5086153e00f4a8bb GIT binary patch literal 12288 zcmeI2&u<$=6vwAUg7TvU!2#4FF*uh*@_N&xL~2lxLK51bxQ!aO6rtiwcE{dr)-%h_ ztc@w9rT0=0h`#_NE(n$Xf>I;|5*)Z7^*~Q>fIoom+g+z_sH$G6#?m+bF*9%8eCEC9 zM0uOjr&pT%aATU`@f2g9AGmn# z(%42X+-cXncLW@P`ysHG&CVPwQhlQKB7f%TQ}?sT&2a=A0Y|_Qa0DCyN5Bzq1RQ|} zgn&(Vv5Pp%?&>_ps^?uho~yU+$q{e_905nb5pV~H7?=mvBNx(E%R0BS>TLlaO9+7CSfJp}EB{@TabpU`FK zL+AqZJoFs&EOcuxV}C$5p&y|e(D%@F=v(L-^cnOibQQV`Y3MBUCUge+@(ISifIfjf zhOR!&*hkRsk1_TO^c8dk%AljrA!r|T>ruwOfxddpH7)fFs}tI06qKfsKs~mTGCUA5P>Pdfe+31C1bw zM}xGEt#r7JB;TM_8=OXC!>=>+|?cWMYCZuC6df`=2vfwKHk*#PTC#PNt#mwlNb; zhYgc&_F{|iKxg6P+Q}0~PcAgu#}}H*b&hwhFE6&LcjSIs=}@-G;uPCq3AT@7#yZ(E z2Chyno@h2t9A9srI=NcsBDc{Lqo38p1-zV;Dok~(?2$X>X0ii+qjo1w+RQ8R+rmr3$0^Q>;mJwRyvQS$#xvp=6MZgknNtdA{17%1DzzYpw{jU2ok(F!MZYhqPpz$%Q(*6AF%Yp54`9jMRcmhCm*R#54$D zjg1?l8O3 zUg1rFFfkZJtO#2LU(sF4`*CJ-k#MQ-N-Jten9)J0*`qUviOxV~XBcD|srjDmo0en)k>b$_*p4ejG@|bdu1BZs1p2ofk0< zTpANBcIM;8vA(>2PPa|w$Py5x(ROAPBO@%Fw<2ViFb4g$*rh^HY|@4Og|!tfftwoz`INzB6)Igp)$Ea1m_Mqgv4RsQVqU*L z`lu**MeSm%)I5zK?8`)_MNlSj5i_x=>fE}t2n-5Us?5bH@dbpaA6XmUfIen47Y9-t zH^Vo|vc5s_Gn#2BOj3{$U5Q<2QIKbF(X6j-qszpg(T#1CZ_)(^TA^aw0%3VnuQcpe zPd#B!rw|*q8fc_L{{HBOykZm9(uGeH#|hHKSWZ=kqPcJ>ld0yD_@02T6%wxGfOn*@ zNNO`hfm(!fkZ47jg>%rN`u5RA$F1P4RPakD%cC~n)U3Z5D_@{^_TdLPw~5Af#{OGC z${Z(;?^;1B3t@$EEDHLlG_=!g bool: Returns: status (bool): returns whether the transformed .done files have to be merged """ + # if any .chunk remaining, run is incomplete + if any(pathlib.Path(directory).glob("*.chunk")): + return False # check for .done files --> merge incomplete if any(pathlib.Path(directory).glob("*.done")): return True diff --git a/tests/test_data/fhir_Patient.ndjson b/tests/test_data/Patient.ndjson similarity index 100% rename from tests/test_data/fhir_Patient.ndjson rename to tests/test_data/Patient.ndjson diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index e5dfb1a3..b4a1e347 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -20,8 +20,8 @@ TMP_ROOT = pathlib.Path("./test_data/fhir_outputs") TAGGER = Gen3FHIRAuthzTagger("config.yaml") -SRC = "test_data" / "test_fhir_Patient.ndjson" -IN = "test_data" / "fhir_Patient.ndjson" +SRC = pathlib.Path("test_data/test_fhir_Patient.ndjson") +IN = pathlib.Path("test_data/Patient.ndjson") OUT = os.path.join(TMP_ROOT, "fhir_output_Patient.ndjson") BATCH_SIZE = 1 BASE_RECORD = { @@ -96,6 +96,11 @@ def mock_state( def test_fhir_output(): """Tests that output file matches the input file with the only difference being the tags""" + fin = [ + orjson.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] src = [ orjson.loads(line) for line in pathlib.Path(SRC).read_bytes().splitlines() @@ -109,15 +114,16 @@ def test_fhir_output(): ] # check that output matched input in everything other than the tags - assert len(src) == len( + assert len(fin) == len( out ), "Length of the output file does not match the length of the input file" - assert {r["id"] for r in src} == { + assert {r["id"] for r in fin} == { r["id"] for r in out }, "IDs in the output file do not match the IDs in the input file. Order not maintained" - assert [ - {k: v for k, v in r.items() if k != "meta.security"} for r in out - ] == src, "Content of the output file does not match the content of the input file (other than the security tags)" + assert [{k: v for k, v in r.items() if k != "meta"} for r in out] == [ + {k: v for k, v in r.items() if k != "meta"} for r in fin + ], "Content of the output file does not match the content of the input file (other than the security tags)" + assert src == out, "Output file does not match source file" def test_chunking(): @@ -401,7 +407,7 @@ class Test_status: def test_fresh_directory(self): # fresh directory - directory, record = mock_state(self.tmp_path, config="match") + directory, record = mock_state(self.tmp_path, config=None) assert _is_new(directory, record) is True assert _is_done(directory, record) is False assert _resume_run(directory, record) is False @@ -444,18 +450,14 @@ def test_new_and_done_are_mutually_exclusive(self, state): def test_cli(): """Run the CLI and return the CompletedProcess.""" args = [ - "--input", IN, - "--output", OUT, - "--chunk-size", - "--config", "config.yaml", "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - [sys.executable, "fhir transform", *args], + ["fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -486,18 +488,14 @@ def test_invalid_batch_size_is_rejected(bad): out = TMP_ROOT / "cli_test" / "cli_out.ndjson" args = [ - "--input", IN, - "--output", out, - "--chunk-size", - "--config", "config.yaml", "--batch_size", str(bad), ] result = subprocess.run( - [sys.executable, "fhir transform", *args], + ["fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -513,18 +511,14 @@ def test_missing_input_file_fails_cleanly(): """Asserts error is raised if missing input file passed as argument""" out = TMP_ROOT / "cli_test" / "nope.ndjson" args = [ - "--input", "nope.ndjson", - "--output", out, - "--chunk-size", - "--config", "config.yaml", "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - [sys.executable, "fhir transform", *args], + ["fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -540,18 +534,14 @@ def test_output_directory_does_not_exist(): """Test response if output directory doesn't exists. Directory (and parents) should be created if missing""" out = TMP_ROOT / "missing_dir" / "out.ndjson" args = [ - "--input", IN, - "--output", out, - "--chunk-size", - "--config", "config.yaml", "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - [sys.executable, "fhir transform", *args], + ["fhir", "transform", *args], capture_output=True, text=True, timeout=60, From c66e8559989d42aa1e839791e456a96204825ab3 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 19 Aug 2026 13:13:56 -0500 Subject: [PATCH 06/35] Pass all tests, modify multiprocessing to not cause issues with gen3, remove unecessary dependencies --- docs/howto/.devTest.md.swp | Bin 12288 -> 0 bytes gen3/fhir.py | 29 +- poetry.lock | 2686 ++++++++++++----- pyproject.toml | 4 +- tests/test_data/fhir_config.yaml | 39 + tests/test_fhir_transform.py | 58 +- tests/tests/outputs/empty_file | 0 .../outputs/indexing-output-manifest.csv | 2 + tests/tests/outputs/input.csv | 4 + tests/tests/outputs/object-manifest.csv | 4 + tests/tests/outputs/tmp_output_file.csv | 2 + tests/tests/outputs/tmp_output_file_info.csv | 5 + 12 files changed, 1976 insertions(+), 857 deletions(-) delete mode 100644 docs/howto/.devTest.md.swp create mode 100644 tests/test_data/fhir_config.yaml create mode 100644 tests/tests/outputs/empty_file create mode 100644 tests/tests/outputs/indexing-output-manifest.csv create mode 100644 tests/tests/outputs/input.csv create mode 100644 tests/tests/outputs/object-manifest.csv create mode 100644 tests/tests/outputs/tmp_output_file.csv create mode 100644 tests/tests/outputs/tmp_output_file_info.csv diff --git a/docs/howto/.devTest.md.swp b/docs/howto/.devTest.md.swp deleted file mode 100644 index 790a93b95b709dc08b901bcb5086153e00f4a8bb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI2&u<$=6vwAUg7TvU!2#4FF*uh*@_N&xL~2lxLK51bxQ!aO6rtiwcE{dr)-%h_ ztc@w9rT0=0h`#_NE(n$Xf>I;|5*)Z7^*~Q>fIoom+g+z_sH$G6#?m+bF*9%8eCEC9 zM0uOjr&pT%aATU`@f2g9AGmn# z(%42X+-cXncLW@P`ysHG&CVPwQhlQKB7f%TQ}?sT&2a=A0Y|_Qa0DCyN5Bzq1RQ|} zgn&(Vv5Pp%?&>_ps^?uho~yU+$q{e_905nb5pV~H7?=mvBNx(E%R0BS>TLlaO9+7CSfJp}EB{@TabpU`FK zL+AqZJoFs&EOcuxV}C$5p&y|e(D%@F=v(L-^cnOibQQV`Y3MBUCUge+@(ISifIfjf zhOR!&*hkRsk1_TO^c8dk%AljrA!r|T>ruwOfxddpH7)fFs}tI06qKfsKs~mTGCUA5P>Pdfe+31C1bw zM}xGEt#r7JB;TM_8=OXC!>=>+|?cWMYCZuC6df`=2vfwKHk*#PTC#PNt#mwlNb; zhYgc&_F{|iKxg6P+Q}0~PcAgu#}}H*b&hwhFE6&LcjSIs=}@-G;uPCq3AT@7#yZ(E z2Chyno@h2t9A9srI=NcsBDc{Lqo38p1-zV;Dok~(?2$X>X0ii+qjo1w+RQ8R+rmr3$0^Q>;mJwRyvQS$#xvp=6MZgknNtdA{17%1DzzYpw{jU2ok(F!MZYhqPpz$%Q(*6AF%Yp54`9jMRcmhCm*R#54$D zjg1?l8O3 zUg1rFFfkZJtO#2LU(sF4`*CJ-k#MQ-N-Jten9)J0*`qUviOxV~XBcD|srjDmo0en)k>b$_*p4ejG@|bdu1BZs1p2ofk0< zTpANBcIM;8vA(>2PPa|w$Py5x(ROAPBO@%Fw<2ViFb4g$*rh^HY|@4Og|!tfftwoz`INzB6)Igp)$Ea1m_Mqgv4RsQVqU*L z`lu**MeSm%)I5zK?8`)_MNlSj5i_x=>fE}t2n-5Us?5bH@dbpaA6XmUfIen47Y9-t zH^Vo|vc5s_Gn#2BOj3{$U5Q<2QIKbF(X6j-qszpg(T#1CZ_)(^TA^aw0%3VnuQcpe zPd#B!rw|*q8fc_L{{HBOykZm9(uGeH#|hHKSWZ=kqPcJ>ld0yD_@02T6%wxGfOn*@ zNNO`hfm(!fkZ47jg>%rN`u5RA$F1P4RPakD%cC~n)U3Z5D_@{^_TdLPw~5Af#{OGC z${Z(;?^;1B3t@$EEDHLlG_=!g dict: return resource +def json_dumps(obj, default=None) -> bytes: + """Compact UTF-8 JSON bytes. Stand-in for orjson.dumps.""" + return json.dumps( + obj, + ensure_ascii=False, + allow_nan=False, + separators=(",", ":"), + default=default, + ).encode("utf-8") def get_md5hash(input_file: str | os.PathLike[str]) -> str: """ @@ -161,7 +170,7 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: return True try: - params = orjson.loads(pathlib.Path(directory, ".config.json").read_bytes()) + params = json.loads(pathlib.Path(directory, ".config.json").read_bytes()) except: return True @@ -187,7 +196,7 @@ def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: status (bool): returns whether the transformation has beencompleted """ try: - params = orjson.loads(pathlib.Path(directory, ".config.json").read_bytes()) + params = json.loads(pathlib.Path(directory, ".config.json").read_bytes()) if ( record["config_hash"] != params["config_hash"] or record["batch_size"] != params["batch_size"] @@ -332,9 +341,9 @@ def transform_chunk( if not r.strip(): continue - record = orjson.loads(r) + record = json.loads(r) authz_tags = tagger.determine_authz(record) # generate tags - out += orjson.dumps( + out += json_dumps( tagger.tag_resource(record, authz_tags) ) # tag resources) out += b"\n" @@ -426,8 +435,8 @@ def fhir_tagger( if _is_new(output_dir, record): logging.info("New folder, creating directory and chunking") make_folders_for_filename(f"{output_dir}/.config.json") - pathlib.Path(f"{output_dir}/.config.json").write_bytes( - orjson.dumps(record, default=str) + pathlib.Path(f"{output_dir}/.config.json").write_text( + json.dumps(record, default=str), encoding="utf-8" ) # split into chunks logging.info(f"Chunking {input_file} into {batch_size}-sized batches...") @@ -448,7 +457,7 @@ def fhir_tagger( # parallelize transform logging.info("Transforming chunks...") start = time.time() - with ProcessPoolExecutor(max_workers=workers) as pool: + with ThreadPoolExecutor(max_workers=workers) as pool: for _ in pool.map( transform_chunk, chunk_files, repeat(tagger), repeat(output_dir) ): diff --git a/poetry.lock b/poetry.lock index 6fd94941..40a6749b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. 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[package.extras] check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] @@ -3312,10 +4343,31 @@ enabler = ["pytest-enabler (>=2.2)"] test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] +[[package]] +name = "zipp" +version = "4.1.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.10" +groups = ["main"] +markers = "python_version >= \"3.11\"" +files = [ + {file = "zipp-4.1.0-py3-none-any.whl", hash = "sha256:25ad4e16390cd314347dd8f1de67a2ac538ae658ed4ab9db16029c07c188e97f"}, + {file = "zipp-4.1.0.tar.gz", hash = "sha256:4cb57381f544315db7688e976e922a2b18cdb513d21cc194eb42232ba2a3e602"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.14)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=3.4)"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy (>=1.0.1) ; platform_python_implementation != \"PyPy\""] + [extras] -fhir = ["fhirclient"] +fhir = ["fhirclient", "fhirpathpy"] [metadata] lock-version = "2.1" python-versions = ">=3.9, <4" -content-hash = "0ef223739ee0f4e9faf3bf60aa2c6ca6ea2757f7b84023e93c838109379a6915" +content-hash = "b28ee99d364a5d6ca5360637cb65611edaa9ac8c09140570dbb031d1e8ad9c28" diff --git a/pyproject.toml b/pyproject.toml index 17982f82..25e21071 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,9 +42,10 @@ gen3users = "*" # A list of all of the optional dependencies, some of which are included in the # below `extras`. They can be opted into by apps. fhirclient = { version = "*", optional = true } +fhirpathpy = { version = "*", optional = true } [tool.poetry.extras] -fhir = ["fhirclient"] +fhir = ["fhirclient", "fhirpathpy"] [tool.poetry.group.dev.dependencies] pytest = "^6.0.0" @@ -53,6 +54,7 @@ requests-mock = "*" cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" } indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" } deptry = "^0.23.1" +setuptools = "<82" [tool.poetry.scripts] gen3 = "gen3.cli.__main__:main" diff --git a/tests/test_data/fhir_config.yaml b/tests/test_data/fhir_config.yaml new file mode 100644 index 00000000..89b26936 --- /dev/null +++ b/tests/test_data/fhir_config.yaml @@ -0,0 +1,39 @@ +version: "1.0" + + +# Global Override (Applies to all resources if used) +# global_authz: "/programs/NCI/projects/TargetedStudyA" + + +# Conditional Field-Level Routing (Per Resource Type) +rules: + - resource_type: "Patient" + condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" + authz: "/programs/Alpha/projects/Main" + + - resource_type: "Patient" + condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" + authz: "/programs/Alpha/projects/Main" + + - resource_type: "Observation" + condition: "Observation.code.coding.where(code = '9876-5').exists()" + authz: "/programs/Restricted/projects/Genomics" + + - resource_type: "Specimen" + condition: "Specimen.status = 'unavailable'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Specimen" + condition: "Specimen.status = 'available'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Specimen" + condition: "Specimen.Type = 'Blood specimen (specimen)'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Patient" + condition: "Patient.gender = 'male'" + authz: "/programs/Alpha/projects/Biobank" + + + diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index b4a1e347..704f3428 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -1,6 +1,6 @@ import pytest import math -from transform_utils import ( +from gen3.fhir import ( Gen3FHIRAuthzTagger, _is_new, _is_done, @@ -13,21 +13,21 @@ ) import pathlib import os -import orjson +import json import subprocess -import sys import shutil -TMP_ROOT = pathlib.Path("./test_data/fhir_outputs") -TAGGER = Gen3FHIRAuthzTagger("config.yaml") -SRC = pathlib.Path("test_data/test_fhir_Patient.ndjson") -IN = pathlib.Path("test_data/Patient.ndjson") +TMP_ROOT = pathlib.Path("./tests/test_data/fhir_outputs") +SRC = pathlib.Path("./tests/test_data/test_fhir_Patient.ndjson") +IN = pathlib.Path("./tests/test_data/Patient.ndjson") OUT = os.path.join(TMP_ROOT, "fhir_output_Patient.ndjson") +CONFIG_SRC = pathlib.Path("./tests/test_data/fhir_config.yaml") +TAGGER = Gen3FHIRAuthzTagger(CONFIG_SRC) BATCH_SIZE = 1 BASE_RECORD = { "timestamp": "2026-08-12T21:00:20.677168+00:00", - "input_file": "output/fhir/Patient.ndjson", - "output_file": "outputs/test_status/status.ndjson", + "input_file": "./tests/test_data/Patient.ndjson", + "output_file": "./tests/test_data/fhir_outputs/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1, } @@ -77,7 +77,7 @@ def mock_state( params = None if params is not None: - (directory / ".config.json").write_bytes(orjson.dumps(params)) + (directory / ".config.json").write_text(json.dumps(params),encoding="utf-8") elif isinstance(config, str) and config != "match": (directory / ".config.json").write_text(config, encoding="utf-8") @@ -97,18 +97,18 @@ def mock_state( def test_fhir_output(): """Tests that output file matches the input file with the only difference being the tags""" fin = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() if line.strip() ] src = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(SRC).read_bytes().splitlines() if line.strip() ] - fhir_tagger(IN, OUT, "config.yaml", 8, BATCH_SIZE) + fhir_tagger(IN, OUT, CONFIG_SRC, 8, BATCH_SIZE) out = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() if line.strip() ] @@ -131,7 +131,7 @@ def test_chunking(): split_file(IN, BATCH_SIZE, TMP_ROOT) chunks = list(TMP_ROOT.glob("*.chunk")) fin = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() if line.strip() ] @@ -140,7 +140,7 @@ def test_chunking(): # number of chunk files matches expected assert len(chunks) == expected, f"Expected {expected} chunks, found {len(chunks)}" recombined = [ - orjson.loads(line) + json.loads(line) for p in sorted(chunks) for line in p.read_bytes().splitlines() if line.strip() @@ -181,12 +181,12 @@ def test_merge(): merge_chunks(transformed, OUT) merged = pathlib.Path(OUT).read_text(encoding="utf-8") fin = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() if line.strip() ] fout = fin = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() if line.strip() ] @@ -208,7 +208,7 @@ def test_merge(): assert not merged.endswith("\n\n"), "File ends with a blank line" for i, line in enumerate(merged.split("\n")[:-1]): assert line.strip(), f"blank line at index {i}" - orjson.loads(line) # every line independently parses + json.loads(line) # every line independently parses class Test_is_new: @@ -452,12 +452,12 @@ def test_cli(): args = [ IN, OUT, - "config.yaml", + CONFIG_SRC, "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - ["fhir", "transform", *args], + ["gen3", "fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -465,12 +465,12 @@ def test_cli(): assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" records = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() if line.strip() ] in_records = [ - orjson.loads(line) + json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() if line.strip() ] @@ -490,12 +490,12 @@ def test_invalid_batch_size_is_rejected(bad): args = [ IN, out, - "config.yaml", + CONFIG_SRC, "--batch_size", str(bad), ] result = subprocess.run( - ["fhir", "transform", *args], + ["gen3", "fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -513,12 +513,12 @@ def test_missing_input_file_fails_cleanly(): args = [ "nope.ndjson", out, - "config.yaml", + CONFIG_SRC, "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - ["fhir", "transform", *args], + ["gen3", "fhir", "transform", *args], capture_output=True, text=True, timeout=60, @@ -536,12 +536,12 @@ def test_output_directory_does_not_exist(): args = [ IN, out, - "config.yaml", + CONFIG_SRC, "--batch_size", str(BATCH_SIZE), ] result = subprocess.run( - ["fhir", "transform", *args], + ["gen3", "fhir", "transform", *args], capture_output=True, text=True, timeout=60, diff --git a/tests/tests/outputs/empty_file b/tests/tests/outputs/empty_file new file mode 100644 index 00000000..e69de29b diff --git a/tests/tests/outputs/indexing-output-manifest.csv b/tests/tests/outputs/indexing-output-manifest.csv new file mode 100644 index 00000000..e314d402 --- /dev/null +++ b/tests/tests/outputs/indexing-output-manifest.csv @@ -0,0 +1,2 @@ +guid authz md5 package_contents record_type size urls +testprefix:d50731a4-63ce-437e-ada6-bfe600681f74 "[""/open""]" 473d83400bc1bc9dc635e334faddf33c "[{""file_name"": ""file.text""}]" object 363455714 s3://my-data-bucket/dg.1234/path/file.text diff --git a/tests/tests/outputs/input.csv b/tests/tests/outputs/input.csv new file mode 100644 index 00000000..6dd07fc7 --- /dev/null +++ b/tests/tests/outputs/input.csv @@ -0,0 +1,4 @@ +guid,urls,authz,acl,md5,file_size,file_name +,gs://foo/bar,programs/foo/projects/bar,,a1234567891234567890123456789012,42, +,gs://foo/bar,programs/foo/projects/bar,,x1234567891234567890123456789012,42, +,gs://foo/bar,programs/foo/projects/bar,,f1234567891234567890123456789012,234, diff --git a/tests/tests/outputs/object-manifest.csv b/tests/tests/outputs/object-manifest.csv new file mode 100644 index 00000000..464c9363 --- /dev/null +++ b/tests/tests/outputs/object-manifest.csv @@ -0,0 +1,4 @@ +guid,urls,authz,acl,md5,file_size,file_name +dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b,gs://test/test.txt s3://testaws/aws/test.txt,/programs/DEV/projects/test,DEV test,a1234567891234567890123456789012,123, +,gs://foo/bar,programs/foo/projects/bar,,51234567891234567890123456789012,42, +dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce,gs://test/test4%20space.txt s3://test/test4%20space.txt,/programs/DEV/projects/test4 /programs/DEV/projects/test4bak,DEV test4,f1234567891234567890123456789012,345, diff --git a/tests/tests/outputs/tmp_output_file.csv b/tests/tests/outputs/tmp_output_file.csv new file mode 100644 index 00000000..a8734c46 --- /dev/null +++ b/tests/tests/outputs/tmp_output_file.csv @@ -0,0 +1,2 @@ +https://data.midrc.org|gen3_node_property|Case.data_submission_guid,https://data.midrc.org|gen3_node_property|Case.submitter_id,https://data.midrc.org|masked_n3c_id|Masked N3C ID,https://gen3.biodatacatalyst.nhlbi.nih.gov|gen3_node_property|Subject.submitter_id +foobar,A01-00888,123dfj4ia5oi*@a,phs002363.v1_RC-1358 diff --git a/tests/tests/outputs/tmp_output_file_info.csv b/tests/tests/outputs/tmp_output_file_info.csv new file mode 100644 index 00000000..d8064e10 --- /dev/null +++ b/tests/tests/outputs/tmp_output_file_info.csv @@ -0,0 +1,5 @@ +commons_url,identifier_name,description +https://gen3.biodatacatalyst.nhlbi.nih.gov,Subject.submitter_id,These identifiers are constructed as part of the data ingestion process in BDCat and concatenate the study and version with the study-provided subject ID (with a _ delimiting). +https://data.midrc.org,Case.submitter_id,The uniquely assigned case identifier in MIDRC. +https://data.midrc.org,Case.data_submission_guid,The identifier for this subject as provided by the site’s submission of Datavant tokens to MIDRC. +https://data.midrc.org,Masked N3C ID,Masked National COVID Consortium ID provided by a Linkage Honest Broker to the MIDRC system. From 404be39734dec0092e747a4b4025a7dfaab3e5bd Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 19 Aug 2026 13:20:21 -0500 Subject: [PATCH 07/35] test md --- docs/howto/{fhir.md => test.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/howto/{fhir.md => test.md} (100%) diff --git a/docs/howto/fhir.md b/docs/howto/test.md similarity index 100% rename from docs/howto/fhir.md rename to docs/howto/test.md From 8899bef0fdcfbef6b69d91ad6391694608d555bc Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 19 Aug 2026 13:20:42 -0500 Subject: [PATCH 08/35] Add fhir.md --- docs/howto/{test.md => fhir.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/howto/{test.md => fhir.md} (100%) diff --git a/docs/howto/test.md b/docs/howto/fhir.md similarity index 100% rename from docs/howto/test.md rename to docs/howto/fhir.md From 3f861f6f06582aeaca7525ee364178ab63450fca Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 19 Aug 2026 13:36:37 -0500 Subject: [PATCH 09/35] Black formatting --- tests/test_fhir_transform.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 704f3428..df3ba7bb 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -77,7 +77,7 @@ def mock_state( params = None if params is not None: - (directory / ".config.json").write_text(json.dumps(params),encoding="utf-8") + (directory / ".config.json").write_text(json.dumps(params), encoding="utf-8") elif isinstance(config, str) and config != "match": (directory / ".config.json").write_text(config, encoding="utf-8") From d8ae042b32b39713a60b2162dff7ab5d05ccd91d Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 21 Aug 2026 19:40:59 -0500 Subject: [PATCH 10/35] Fix pull request comments --- .../.config.json | 1 + .../.config.json | 1 + .../Patient_00000.chunk | 8 ++ .../Patient_00000.chunk.done | 0 .../Patient_00001.chunk | 8 ++ .../Patient_00002.chunk | 6 ++ .../Patient_00002.chunk.done | 0 docs/howto/fhir.md | 18 +++- gen3/cli/fhir.py | 5 +- gen3/fhir.py | 81 +++++++++-------- poetry.lock | 90 ++++++++++++------- tests/test_data/Patient.ndjson | 33 +++---- tests/test_data/README.md | 3 + tests/test_data/fhir_config.yaml | 4 + .../fhir_outputs/4468389968/status.ndjson | 1 + .../fhir_outputs/4468589200/.config.json | 1 + .../fhir_outputs/4468589200/status.ndjson | 1 + .../fhir_outputs/4479924304/status.ndjson | 1 + .../fhir_outputs/4480123536/.config.json | 1 + .../fhir_outputs/4480123536/status.ndjson | 1 + .../fhir_outputs/4519770192/status.ndjson | 1 + .../fhir_outputs/4519969424/.config.json | 1 + .../fhir_outputs/4519969424/status.ndjson | 1 + .../fhir_outputs/4575344720/status.ndjson | 1 + .../fhir_outputs/4575543952/.config.json | 1 + .../fhir_outputs/4575543952/status.ndjson | 1 + .../fhir_outputs/4655229824/.config.json | 1 + .../fhir_outputs/4655229824/status.ndjson | 1 + .../fhir_outputs/4655230016/.config.json | 1 + .../fhir_outputs/4655230016/status.ndjson | 1 + .../fhir_outputs/4666907648/.config.json | 1 + .../fhir_outputs/4666907648/status.ndjson | 1 + .../fhir_outputs/4666907840/.config.json | 1 + .../fhir_outputs/4666907840/status.ndjson | 1 + .../fhir_outputs/4707028416/.config.json | 1 + .../fhir_outputs/4707028416/status.ndjson | 1 + .../fhir_outputs/4707031680/.config.json | 1 + .../fhir_outputs/4707031680/status.ndjson | 1 + .../fhir_outputs/4763137088/.config.json | 1 + .../fhir_outputs/4763137088/status.ndjson | 1 + .../fhir_outputs/4763137280/.config.json | 1 + .../fhir_outputs/4763137280/status.ndjson | 1 + .../fhir_outputs/fhir_output_Patient.ndjson | 11 +++ .../fhir_outputs/missing_dir/out.ndjson | 11 +++ .../outputs/test_merge/.config.json | 1 + .../outputs/test_merge/chunk_000.chunk | 1 + .../outputs/test_merge/chunk_000.done | 1 + .../outputs/test_merge/chunk_001.done | 1 + .../outputs/test_merge/chunk_002.done | 1 + .../outputs/test_merge/chunk_003.done | 1 + .../outputs/test_merge/chunk_004.done | 1 + .../outputs/test_merge/chunk_005.done | 1 + .../outputs/test_merge/chunk_006.done | 1 + .../outputs/test_merge/chunk_007.done | 1 + .../outputs/test_merge/chunk_008.done | 1 + .../outputs/test_merge/chunk_009.done | 1 + .../fhir_outputs/test_done/.config.json | 1 + .../fhir_outputs/test_done/status.ndjson | 1 + .../fhir_outputs/test_new/.config.json | 1 + .../fhir_outputs/test_resume/.config.json | 1 + .../fhir_outputs/test_resume/nested/a.chunk | 0 .../fhir_outputs/test_status/.config.json | 1 + .../fhir_outputs/test_status/status.ndjson | 1 + tests/test_data/test_fhir_Patient.ndjson | 33 +++---- tests/test_fhir_transform.py | 5 +- 65 files changed, 245 insertions(+), 119 deletions(-) create mode 100644 .fhir_transform/tmp/Patient_4460d7077b0c90cdc50452d577ab8f6d/.config.json create mode 100644 .fhir_transform/tmp/Patient_d5798eeb457ecc355a59d696d68a871c/.config.json create mode 100644 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FHIR is an important standard for working with Electronic Health Records (EHR) and we have started development of a Gen3 FHIR Proxy service. The overall goal is to allow users to seamlessly ingest data into an existing FHIR server. Gen3 is working on adding support for FHIR and this tool will help with data preparation and interaction in the future. + The fhir commands can be invoked as follows @@ -12,3 +15,16 @@ For example, the following tags the 'Patient.ndjson' file with Gen3 authorizatio `gen3 fhir transform Patient.ndjson gen3_Patient.ndjson config.yaml --batch_size 10000 --workers 8 ` + +The authorization configuration file has to be in yaml format and can have multiple conditions, e.g: + +```yaml +rules: + - resource_type: "Patient" + condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" + authz: "/programs/Alpha/projects/Main" + + - resource_type: "Patient" + condition: "Patient.managingOrganization.reference = 'Organization/site-alpha' and Patient.gender = 'male'" + authz: "/programs/Alpha/projects/Main" +``` diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index cea3bc01..e272107e 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -1,11 +1,10 @@ -from fhirpathpy import evaluate import click import os import pathlib from cdislogging import get_logger from gen3.fhir import * -logging = get_logger("fhir_transform", log_level="info") +logging = get_logger(__name__) TMP_ROOT = pathlib.Path(".fhir_transform/tmp") @@ -100,7 +99,7 @@ def cleanup(dry_run: bool, force: bool): force (bool): Delete all intermediate directories disregarding the status """ - sweep(dry_run=dry_run, force=force) + cleanup_fhir_transform_artifacts(dry_run=dry_run, force=force) fhir.add_command(cli, name="transform") diff --git a/gen3/fhir.py b/gen3/fhir.py index 0056c5a8..32201605 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -9,12 +9,14 @@ import shutil import pathlib import hashlib -from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor +from concurrent.futures import ThreadPoolExecutor from cdislogging import get_logger from gen3.utils import make_folders_for_filename +from collections.abc import Callable -logging = get_logger("fhir_transform", log_level="info") +logging = get_logger(__name__) TMP_ROOT = pathlib.Path(".fhir_transform/tmp") +GEN3_PATH = "http://gen3.org/authz" class Gen3FHIRAuthzTagger: @@ -29,13 +31,17 @@ class Gen3FHIRAuthzTagger: """ - def __init__(self, config_path: str | os.PathLike[str], custom_hook=None): + def __init__( + self, + config_path: str | os.PathLike[str], + custom_hook: Callable[[dict], dict] | None = None, + ): """ Initialize instance of the tagger. Args: config_path (str): the name/path of the config.yaml file - custom_hook (?): ??? + custom_hook (Callable): used for authorization instead of the configuration if called """ with open(config_path, "r") as f: @@ -64,7 +70,7 @@ def determine_authz(self, resource: dict) -> str: resource (dict): the resource dictionary (a line of the .ndjson file) Returns: - The appropriate rule/authorization for the resource + authz (str): The appropriate rule/authorization for the resource """ @@ -78,20 +84,21 @@ def determine_authz(self, resource: dict) -> str: if "global_authz" in self.config: return self.config["global_authz"] - # resource_type = resource.get("resourceType") - - # check static rules engine via FHIRPath - # for rule in self.config.get("rules", []): - # if rule["resource_type"] == resource_type: - # match = evaluate(resource, rule["condition"]) #how to process in bulk - # if match and match[0] is True: - # return rule["authz"] + matches = [] for rule in self.rules: match = evaluate(resource, rule["condition"]) - if match and match[0] is True: # FIXME: what if multiple conditions match? - return rule["authz"] + # FIXME: what if multiple conditions match?, add error if multiple conditions match -->user makes necessary changes + if match and match[0] is True: + matches.append(rule) + + if len(matches) > 1: + raise ValueError( + f"Resource {resource.get('id')!r} matched {len(matches)} authorization conditions; expected at most 1. Conflicting: {[m["condition"] for m in matches]}" + ) + + elif len(matches) == 1: + return matches[0]["authz"] - return None #### FIXME this is just for testing purposes ##### raise ValueError( f"No authorization tag mapping found for resource ID: {resource.get('id')}" ) @@ -100,8 +107,7 @@ def tag_resource(self, resource: dict, authz: str) -> dict: """ Injects the authz path directly into the standard FHIR meta block - - FIXME: match Gen3 FHIR Proxy service requirements here + Must match Gen3 FHIR Proxy service requirements here Args: resource (dict): the resource dictionary (a line of the .ndjson file) @@ -117,7 +123,7 @@ def tag_resource(self, resource: dict, authz: str) -> dict: resource["meta"]["security"] = [] gen3_security_tag = { - "system": "http://gen3.org/authz", + "system": GEN3_PATH, "code": authz, "display": f"Gen3 Policy Path: {authz}", } @@ -129,7 +135,7 @@ def tag_resource(self, resource: dict, authz: str) -> dict: def json_dumps(obj, default=None) -> bytes: - """Compact UTF-8 JSON bytes. Stand-in for orjson.dumps.""" + """Compact UTF-8 JSON bytes.""" return json.dumps( obj, ensure_ascii=False, @@ -173,7 +179,7 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: try: params = json.loads(pathlib.Path(directory, ".config.json").read_bytes()) - except: + except (OSError, ValueError): return True if ( @@ -205,7 +211,7 @@ def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: or record["output_file"] != params["output_file"] ): return False - except: + except (OSError, ValueError): return False # check if output file is the same and if exists @@ -257,7 +263,7 @@ def _merge_needed(directory: str | os.PathLike[str], record: dict) -> bool: return False -def sweep(dry_run: bool = False, force: bool = False) -> int: +def cleanup_fhir_transform_artifacts(dry_run: bool = False, force: bool = False) -> int: """ Remove run dirs whose owning process is gone. @@ -311,7 +317,6 @@ def split_file( start = time.time() with open(input_file, "rb") as fin: for i, lines in enumerate(iter(lambda: list(islice(fin, batch_size)), [])): - # with open(f"chunk_{i:05d}.chunk", "wb") as out: with open( f"{output_dir}/{pathlib.Path(input_file).stem}_{i:05d}.chunk", "wb" ) as out: @@ -344,11 +349,14 @@ def transform_chunk( continue record = json.loads(r) - authz_tags = tagger.determine_authz(record) # generate tags - out += json_dumps(tagger.tag_resource(record, authz_tags)) # tag resources) + # generate tags + authz_tags = tagger.determine_authz(record) + # tag resources + out += json_dumps(tagger.tag_resource(record, authz_tags)) out += b"\n" fout.write(out) - os.remove(input_file) # delete chunk file once it has been transformed + # delete chunk file once it has been transformed + os.remove(input_file) def merge_chunks( @@ -375,8 +383,9 @@ def merge_chunks( logging.info( f"merge chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" ) + # remove .done files once merge completed for f in input_files: - os.remove(f) # remove .done files once merge completed + os.remove(f) def fhir_tagger( @@ -410,7 +419,8 @@ def fhir_tagger( if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") - make_folders_for_filename(TMP_ROOT) # only necessary the first time its run + # only necessary the first time its run + make_folders_for_filename(TMP_ROOT) # make temp directories hash = get_md5hash(input_file) @@ -443,16 +453,16 @@ def fhir_tagger( split_file(input_file, batch_size, output_dir) # initialize tagger - tagger = Gen3FHIRAuthzTagger(config_path=config) # create instance of tagger - tagger.relevant_authz_rules( - os.path.basename(input_file).split(".")[0] - ) # keep only relevant rules for the resource type + tagger = Gen3FHIRAuthzTagger(config_path=config) + # keep only relevant rules for the resource type + tagger.relevant_authz_rules(os.path.basename(input_file).split(".")[0]) # if not fully transformed or new/reset, resume if not _merge_needed(output_dir, record): + # paths for chunk files chunk_files = glob.glob( os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.chunk") - ) # paths for chunk files + ) # parallelize transform logging.info("Transforming chunks...") @@ -469,13 +479,12 @@ def fhir_tagger( # merge back to one ndjson file transformed_files = glob.glob( os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.done") - ) # paths for transformed files + ) logging.info(f"Merging chunks to {output_file}...") merge_chunks(transformed_files, output_file) elapsed_time = time.time() - start_time logging.info(f"Tagged file -> {output_file}") - # logging.info(f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}") logging.info( f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}" ) diff --git a/poetry.lock b/poetry.lock index 40a6749b..58e253e4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -443,6 +443,18 @@ files = [ {file = "asyncio-3.4.3.tar.gz", hash = "sha256:83360ff8bc97980e4ff25c964c7bd3923d333d177aa4f7fb736b019f26c7cb41"}, ] +[[package]] +name = "atomicwrites" +version = "1.4.1" +description = "Atomic file writes." +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["dev"] +markers = "sys_platform == \"win32\"" +files = [ + {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, +] + [[package]] name = "attrs" version = "26.1.0" @@ -3342,6 +3354,18 @@ files = [ {file = "psycopg2-2.9.12.tar.gz", hash = "sha256:1dedb1c7a1d8552c4a6044c6b1c41a52e6a8e2d144af83eccac758076b1b7c15"}, ] +[[package]] +name = "py" +version = "1.11.0" +description = "library with cross-python path, ini-parsing, io, code, log facilities" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +groups = ["dev"] +files = [ + {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"}, + {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"}, +] + [[package]] name = "pycparser" version = "2.23" @@ -3368,21 +3392,6 @@ files = [ {file = "pycparser-3.0.tar.gz", hash = "sha256:600f49d217304a5902ac3c37e1281c9fe94e4d0489de643a9504c5cdfdfc6b29"}, ] -[[package]] -name = "pygments" -version = "2.21.0" -description = "Pygments is a syntax highlighting package written in Python." -optional = false -python-versions = ">=3.9" -groups = ["dev"] -files = [ - {file = "pygments-2.21.0-py3-none-any.whl", hash = "sha256:2363c69b61c4a97c838da3b130dcd6468f4848992b21a82f2a63ec34377137d9"}, - {file = "pygments-2.21.0.tar.gz", hash = "sha256:610ca751c9bc2492b38eb9a38a7fbc93edbbb2d7182edaf34e66ae493dee5c8c"}, -] - -[package.extras] -windows-terminal = ["colorama (>=0.4.6)"] - [[package]] name = "pyjwt" version = "2.13.0" @@ -3485,47 +3494,48 @@ files = [ [[package]] name = "pytest" -version = "8.4.2" +version = "6.2.5" description = "pytest: simple powerful testing with Python" optional = false -python-versions = ">=3.9" +python-versions = ">=3.6" groups = ["dev"] files = [ - {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"}, - {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"}, + {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"}, + {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"}, ] [package.dependencies] -colorama = {version = ">=0.4", markers = "sys_platform == \"win32\""} -exceptiongroup = {version = ">=1", markers = "python_version < \"3.11\""} -iniconfig = ">=1" -packaging = ">=20" -pluggy = ">=1.5,<2" -pygments = ">=2.7.2" -tomli = {version = ">=1", markers = "python_version < \"3.11\""} +atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} +attrs = ">=19.2.0" +colorama = {version = "*", markers = "sys_platform == \"win32\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=0.12,<2.0" +py = ">=1.8.2" +toml = "*" [package.extras] -dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"] +testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"] [[package]] name = "pytest-cov" -version = "7.1.0" +version = "6.3.0" description = "Pytest plugin for measuring coverage." optional = false python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "pytest_cov-7.1.0-py3-none-any.whl", hash = "sha256:a0461110b7865f9a271aa1b51e516c9a95de9d696734a2f71e3e78f46e1d4678"}, - {file = "pytest_cov-7.1.0.tar.gz", hash = "sha256:30674f2b5f6351aa09702a9c8c364f6a01c27aae0c1366ae8016160d1efc56b2"}, + {file = "pytest_cov-6.3.0-py3-none-any.whl", hash = "sha256:440db28156d2468cafc0415b4f8e50856a0d11faefa38f30906048fe490f1749"}, + {file = "pytest_cov-6.3.0.tar.gz", hash = "sha256:35c580e7800f87ce892e687461166e1ac2bcb8fb9e13aea79032518d6e503ff2"}, ] [package.dependencies] -coverage = {version = ">=7.10.6", extras = ["toml"]} +coverage = {version = ">=7.5", extras = ["toml"]} pluggy = ">=1.2" -pytest = ">=7" +pytest = ">=6.2.5" [package.extras] -testing = ["process-tests", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] [[package]] name = "python-dateutil" @@ -3868,6 +3878,18 @@ test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3 timezone = ["python-dateutil"] url = ["furl (>=0.4.1)"] +[[package]] +name = "toml" +version = "0.10.2" +description = "Python Library for Tom's Obvious, Minimal Language" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +groups = ["dev"] +files = [ + {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, + {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, +] + [[package]] name = "tomli" version = "2.4.1" @@ -4370,4 +4392,4 @@ fhir = ["fhirclient", "fhirpathpy"] [metadata] lock-version = "2.1" python-versions = ">=3.9, <4" -content-hash = "b28ee99d364a5d6ca5360637cb65611edaa9ac8c09140570dbb031d1e8ad9c28" +content-hash = "c1d70ec18b3a0f058872ccc01bdb94b39a4abc641e6d2cd5381b232e9ecee23a" diff --git a/tests/test_data/Patient.ndjson b/tests/test_data/Patient.ndjson index 2900dbef..3f7eadee 100644 --- a/tests/test_data/Patient.ndjson +++ b/tests/test_data/Patient.ndjson @@ -1,22 +1,11 @@ -{"resourceType":"Patient","id":"29afd833-3a8d-43cf-e62b-29e8e3304297","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]},"text":{"status":"generated","div":"
Generated by Synthea.Version identifier: 7e08387\n . Person seed: 3003857191016678351 Population seed: 1786567397036
"},"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2106-3","display":"White"}},{"url":"text","valueString":"White"}]},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2186-5","display":"Not Hispanic or Latino"}},{"url":"text","valueString":"Not Hispanic or Latino"}]},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Dollie671 Watsica258"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"M"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Dedham","state":"Massachusetts","country":"US"}},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":0.039166437590039176},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":16.96083356240996}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"29afd833-3a8d-43cf-e62b-29e8e3304297"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR","display":"Medical Record Number"}],"text":"Medical Record Number"},"system":"http://hospital.smarthealthit.org","value":"29afd833-3a8d-43cf-e62b-29e8e3304297"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"SS","display":"Social Security Number"}],"text":"Social Security Number"},"system":"http://hl7.org/fhir/sid/us-ssn","value":"999-56-4415"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"DL","display":"Driver's license number"}],"text":"Driver's license number"},"system":"urn:oid:2.16.840.1.113883.4.3.25","value":"S99985705"}],"name":[{"use":"official","family":"Jones311","given":["Jacinto644","Jody426"]}],"telecom":[{"system":"phone","value":"555-581-7273","use":"home"}],"gender":"male","birthDate":"2008-12-10","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.40294972224185},{"url":"longitude","valueDecimal":-71.16554059410517}]}],"line":["792 Hickle Corner Unit 26"],"city":"Cambridge","state":"MA","postalCode":"02139","country":"US"}],"maritalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus","code":"S","display":"Never Married"}],"text":"Never Married"},"multipleBirthBoolean":false,"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en-US","display":"English (United States)"}],"text":"English (United States)"}}]} -{"resourceType":"Patient","id":"90231f2a-e358-1e57-dec1-c9b532385fe5","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]},"text":{"status":"generated","div":"
Generated by Synthea.Version identifier: 7e08387\n . Person seed: -8060564638999765417 Population seed: 1786567397036
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Generated by Synthea.Version identifier: 7e08387\n . Person seed: -1734388560971211700 Population seed: 1787357879264
"},"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2106-3","display":"White"}},{"url":"text","valueString":"White"}]},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2186-5","display":"Not Hispanic or Latino"}},{"url":"text","valueString":"Not Hispanic or Latino"}]},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Kimbery217 Upton904"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"F"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Somerville","state":"Massachusetts","country":"US"}},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":0.26807940704490096},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":61.7319205929551}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"e7ee36cb-00cf-5c4c-b80e-877c7489052c"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR","display":"Medical Record Number"}],"text":"Medical Record Number"},"system":"http://hospital.smarthealthit.org","value":"e7ee36cb-00cf-5c4c-b80e-877c7489052c"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"SS","display":"Social Security Number"}],"text":"Social Security Number"},"system":"http://hl7.org/fhir/sid/us-ssn","value":"999-64-5456"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"DL","display":"Driver's license number"}],"text":"Driver's license number"},"system":"urn:oid:2.16.840.1.113883.4.3.25","value":"S99974911"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"PPN","display":"Passport Number"}],"text":"Passport Number"},"system":"http://hl7.org/fhir/sid/passport-USA","value":"X35070122X"}],"name":[{"use":"official","family":"Hintz995","given":["Adaline602","Loni302"],"prefix":["Mrs."]},{"use":"maiden","family":"Thiel172","given":["Adaline602","Loni302"],"prefix":["Mrs."]}],"telecom":[{"system":"phone","value":"555-489-2752","use":"home"}],"gender":"female","birthDate":"1963-09-18","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":41.892429019677074},{"url":"longitude","valueDecimal":-71.330141761167}]}],"line":["862 Maggio Manor Unit 77"],"city":"Attleboro","state":"MA","postalCode":"02861","country":"US"}],"maritalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus","code":"M","display":"Married"}],"text":"Married"},"multipleBirthBoolean":false,"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en-US","display":"English (United States)"}],"text":"English (United States)"}}]} diff --git a/tests/test_data/README.md b/tests/test_data/README.md new file mode 100644 index 00000000..7742f517 --- /dev/null +++ b/tests/test_data/README.md @@ -0,0 +1,3 @@ +### FHIR Test Data + +The files Patient.ndjson and test_fhir_Patient.ndjson are synthetically generated using Synthea with US Core Implementation Guide for FHIR R4 (https://github.com/synthetichealth/synthea.git). The configuration file (fhir_config.yaml) was created accordingly for testing. \ No newline at end of file diff --git a/tests/test_data/fhir_config.yaml b/tests/test_data/fhir_config.yaml index 89b26936..d2362f2c 100644 --- a/tests/test_data/fhir_config.yaml +++ b/tests/test_data/fhir_config.yaml @@ -34,6 +34,10 @@ rules: - resource_type: "Patient" condition: "Patient.gender = 'male'" authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Patient" + condition: "Patient.gender = 'female'" + authz: "/programs/Restricted/projects/Genomics" diff --git a/tests/test_data/fhir_outputs/4468389968/status.ndjson b/tests/test_data/fhir_outputs/4468389968/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4468389968/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4468589200/.config.json b/tests/test_data/fhir_outputs/4468589200/.config.json new file mode 100644 index 00000000..3621a261 --- /dev/null +++ b/tests/test_data/fhir_outputs/4468589200/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4468589200/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4468589200/status.ndjson b/tests/test_data/fhir_outputs/4468589200/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4468589200/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4479924304/status.ndjson b/tests/test_data/fhir_outputs/4479924304/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4479924304/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4480123536/.config.json b/tests/test_data/fhir_outputs/4480123536/.config.json new file mode 100644 index 00000000..338a7317 --- /dev/null +++ b/tests/test_data/fhir_outputs/4480123536/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4480123536/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4480123536/status.ndjson b/tests/test_data/fhir_outputs/4480123536/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4480123536/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4519770192/status.ndjson b/tests/test_data/fhir_outputs/4519770192/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4519770192/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4519969424/.config.json b/tests/test_data/fhir_outputs/4519969424/.config.json new file mode 100644 index 00000000..d8919a68 --- /dev/null +++ b/tests/test_data/fhir_outputs/4519969424/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4519969424/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4519969424/status.ndjson b/tests/test_data/fhir_outputs/4519969424/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4519969424/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4575344720/status.ndjson b/tests/test_data/fhir_outputs/4575344720/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4575344720/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4575543952/.config.json b/tests/test_data/fhir_outputs/4575543952/.config.json new file mode 100644 index 00000000..86dde948 --- /dev/null +++ b/tests/test_data/fhir_outputs/4575543952/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4575543952/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4575543952/status.ndjson b/tests/test_data/fhir_outputs/4575543952/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4575543952/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4655229824/.config.json b/tests/test_data/fhir_outputs/4655229824/.config.json new file mode 100644 index 00000000..dcdfcdfa --- /dev/null +++ b/tests/test_data/fhir_outputs/4655229824/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4655229824/status.ndjson", "config_hash": "x", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4655229824/status.ndjson b/tests/test_data/fhir_outputs/4655229824/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4655229824/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4655230016/.config.json b/tests/test_data/fhir_outputs/4655230016/.config.json new file mode 100644 index 00000000..c06a6646 --- /dev/null +++ b/tests/test_data/fhir_outputs/4655230016/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4655230016/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4655230016/status.ndjson b/tests/test_data/fhir_outputs/4655230016/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4655230016/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4666907648/.config.json b/tests/test_data/fhir_outputs/4666907648/.config.json new file mode 100644 index 00000000..839b78f8 --- /dev/null +++ b/tests/test_data/fhir_outputs/4666907648/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4666907648/status.ndjson", "config_hash": "x", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4666907648/status.ndjson b/tests/test_data/fhir_outputs/4666907648/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4666907648/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4666907840/.config.json b/tests/test_data/fhir_outputs/4666907840/.config.json new file mode 100644 index 00000000..ee7e7020 --- /dev/null +++ b/tests/test_data/fhir_outputs/4666907840/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4666907840/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4666907840/status.ndjson b/tests/test_data/fhir_outputs/4666907840/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4666907840/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4707028416/.config.json b/tests/test_data/fhir_outputs/4707028416/.config.json new file mode 100644 index 00000000..2576d16c --- /dev/null +++ b/tests/test_data/fhir_outputs/4707028416/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4707028416/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4707028416/status.ndjson b/tests/test_data/fhir_outputs/4707028416/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4707028416/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4707031680/.config.json b/tests/test_data/fhir_outputs/4707031680/.config.json new file mode 100644 index 00000000..8f4ca193 --- /dev/null +++ b/tests/test_data/fhir_outputs/4707031680/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4707031680/status.ndjson", "config_hash": "x", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4707031680/status.ndjson b/tests/test_data/fhir_outputs/4707031680/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4707031680/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4763137088/.config.json b/tests/test_data/fhir_outputs/4763137088/.config.json new file mode 100644 index 00000000..f09f5af8 --- /dev/null +++ b/tests/test_data/fhir_outputs/4763137088/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4763137088/status.ndjson", "config_hash": "x", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4763137088/status.ndjson b/tests/test_data/fhir_outputs/4763137088/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4763137088/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/4763137280/.config.json b/tests/test_data/fhir_outputs/4763137280/.config.json new file mode 100644 index 00000000..b1d40b43 --- /dev/null +++ b/tests/test_data/fhir_outputs/4763137280/.config.json @@ -0,0 +1 @@ +{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/4763137280/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4763137280/status.ndjson b/tests/test_data/fhir_outputs/4763137280/status.ndjson new file mode 100644 index 00000000..6804b58c --- /dev/null +++ b/tests/test_data/fhir_outputs/4763137280/status.ndjson @@ -0,0 +1 @@ +{"id":1} diff --git a/tests/test_data/fhir_outputs/fhir_output_Patient.ndjson b/tests/test_data/fhir_outputs/fhir_output_Patient.ndjson new file mode 100644 index 00000000..f055fe93 --- /dev/null +++ b/tests/test_data/fhir_outputs/fhir_output_Patient.ndjson @@ -0,0 +1,11 @@ +{"resourceType":"Patient","id":"ce6763b2-b910-ed94-e3d6-56dc6de45153","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"],"security":[{"system":"http://gen3.org/authz","code":"/programs/Restricted/projects/Genomics","display":"Gen3 Policy Path: /programs/Restricted/projects/Genomics"}]},"text":{"status":"generated","div":"
Generated by Synthea.Version identifier: 7e08387\n . Person seed: -3573778160034976364 Population seed: 1787357879264
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Generated by Synthea.Version identifier: 7e08387\n . Person seed: -7086630366302974330 Population seed: 1787357879264
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Generated by Synthea.Version identifier: 7e08387\n . Person seed: -1734388560971211700 Population seed: 1787357879264
"},"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2106-3","display":"White"}},{"url":"text","valueString":"White"}]},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity","extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2186-5","display":"Not Hispanic or Latino"}},{"url":"text","valueString":"Not Hispanic or Latino"}]},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Kimbery217 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Number"},"system":"http://hl7.org/fhir/sid/us-ssn","value":"999-64-5456"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"DL","display":"Driver's license number"}],"text":"Driver's license number"},"system":"urn:oid:2.16.840.1.113883.4.3.25","value":"S99974911"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"PPN","display":"Passport Number"}],"text":"Passport Number"},"system":"http://hl7.org/fhir/sid/passport-USA","value":"X35070122X"}],"name":[{"use":"official","family":"Hintz995","given":["Adaline602","Loni302"],"prefix":["Mrs."]},{"use":"maiden","family":"Thiel172","given":["Adaline602","Loni302"],"prefix":["Mrs."]}],"telecom":[{"system":"phone","value":"555-489-2752","use":"home"}],"gender":"female","birthDate":"1963-09-18","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":41.892429019677074},{"url":"longitude","valueDecimal":-71.330141761167}]}],"line":["862 Maggio Manor Unit 77"],"city":"Attleboro","state":"MA","postalCode":"02861","country":"US"}],"maritalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus","code":"M","display":"Married"}],"text":"Married"},"multipleBirthBoolean":false,"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en-US","display":"English (United States)"}],"text":"English (United States)"}}]} diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index df3ba7bb..7488df64 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -32,7 +32,10 @@ "batch_size": 1, } -os.makedirs(TMP_ROOT, exist_ok=True) + +@pytest.fixture(scope="session") +def tmp_root(tmp_path_factory): + return tmp_path_factory.mktemp(TMP_ROOT) def mock_state( From 76c6797790770bbf224119fc46fd16601da6bb8e Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 21 Aug 2026 19:41:47 -0500 Subject: [PATCH 11/35] Delete test outputs --- tests/test_data/fhir_outputs/4468389968/status.ndjson | 1 - tests/test_data/fhir_outputs/4468589200/.config.json | 1 - tests/test_data/fhir_outputs/4468589200/status.ndjson | 1 - tests/test_data/fhir_outputs/4479924304/status.ndjson | 1 - tests/test_data/fhir_outputs/4480123536/.config.json | 1 - tests/test_data/fhir_outputs/4480123536/status.ndjson | 1 - tests/test_data/fhir_outputs/4519770192/status.ndjson | 1 - 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"tests/test_data/fhir_outputs/4468589200/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/4468589200/status.ndjson b/tests/test_data/fhir_outputs/4468589200/status.ndjson deleted file mode 100644 index 6804b58c..00000000 --- a/tests/test_data/fhir_outputs/4468589200/status.ndjson +++ /dev/null @@ -1 +0,0 @@ -{"id":1} diff --git a/tests/test_data/fhir_outputs/4479924304/status.ndjson b/tests/test_data/fhir_outputs/4479924304/status.ndjson deleted file mode 100644 index 6804b58c..00000000 --- a/tests/test_data/fhir_outputs/4479924304/status.ndjson +++ /dev/null @@ -1 +0,0 @@ -{"id":1} diff --git a/tests/test_data/fhir_outputs/4480123536/.config.json b/tests/test_data/fhir_outputs/4480123536/.config.json deleted file mode 100644 index 338a7317..00000000 --- a/tests/test_data/fhir_outputs/4480123536/.config.json +++ /dev/null @@ -1 +0,0 @@ -{"timestamp": 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b/tests/test_data/fhir_outputs/test_status/.config.json deleted file mode 100644 index 5bb46cc7..00000000 --- a/tests/test_data/fhir_outputs/test_status/.config.json +++ /dev/null @@ -1 +0,0 @@ -{"timestamp": "2026-08-12T21:00:20.677168+00:00", "input_file": "./tests/test_data/Patient.ndjson", "output_file": "tests/test_data/fhir_outputs/test_status/status.ndjson", "config_hash": "9c61e70e3ea403e3daf1ee795036253c", "batch_size": 1} \ No newline at end of file diff --git a/tests/test_data/fhir_outputs/test_status/status.ndjson b/tests/test_data/fhir_outputs/test_status/status.ndjson deleted file mode 100644 index 6804b58c..00000000 --- a/tests/test_data/fhir_outputs/test_status/status.ndjson +++ /dev/null @@ -1 +0,0 @@ -{"id":1} From a34ed6c878d820044b0427c44da4de3da292fe24 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 21 Aug 2026 20:01:15 -0500 Subject: [PATCH 12/35] Remove setuptools dependency from pyproject.toml --- docs/howto/devTest.md | 19 +- poetry.lock | 4395 ----------------------------------------- pyproject.toml | 1 - 3 files changed, 2 insertions(+), 4413 deletions(-) delete mode 100644 poetry.lock diff --git a/docs/howto/devTest.md b/docs/howto/devTest.md index e4b6a518..97b4ec7a 100644 --- a/docs/howto/devTest.md +++ b/docs/howto/devTest.md @@ -1,25 +1,11 @@ ## Dev-Test -### Set up Python Virtual Environment - -You can set up a Python development environment with a virtual environment: - -```bash -python3 -m venv py3 -``` - -Make sure that you have the virtual environment activated: - -```bash -. py3/bin/activate -``` - ### Install poetry To use the latest code in this repo (or to develop new features) you can clone this repo, install `poetry`: ``` -curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python - +curl -sSL https://install.python-poetry.org | python3 - ``` and then use `poetry` to install this package: @@ -34,8 +20,7 @@ poetry install -vv Local development like this: ``` -poetry shell 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"pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[[package]] +name = "zipp" +version = "4.1.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.10" +groups = ["main"] +markers = "python_version >= \"3.11\"" +files = [ + {file = "zipp-4.1.0-py3-none-any.whl", hash = "sha256:25ad4e16390cd314347dd8f1de67a2ac538ae658ed4ab9db16029c07c188e97f"}, + {file = "zipp-4.1.0.tar.gz", hash = "sha256:4cb57381f544315db7688e976e922a2b18cdb513d21cc194eb42232ba2a3e602"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.14)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=3.4)"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy (>=1.0.1) ; platform_python_implementation != \"PyPy\""] + +[extras] +fhir = ["fhirclient", "fhirpathpy"] + +[metadata] +lock-version = "2.1" +python-versions = ">=3.9, <4" +content-hash = "5427abd980289fe1fa0ff36a96a19679fb7c1bbf0a9df7c7896347a98f0818ea" diff --git a/pyproject.toml b/pyproject.toml index 50968d8a..bdf54bef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,12 +48,13 @@ fhirpathpy = { version = "*", optional = true } fhir = ["fhirclient", "fhirpathpy"] [tool.poetry.group.dev.dependencies] -pytest = "^6.0.0" +pytest = "^7.0" pytest-cov = "*" requests-mock = "*" cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" } indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" } deptry = "^0.23.1" +setuptools = "<82" [tool.poetry.scripts] gen3 = "gen3.cli.__main__:main" From 8e0174c43d6a5e3b483ca59f2f94e16d1e024f08 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Sat, 22 Aug 2026 10:17:21 -0500 Subject: [PATCH 14/35] Remove FIXME --- gen3/fhir.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gen3/fhir.py b/gen3/fhir.py index 32201605..c9330352 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -87,7 +87,7 @@ def determine_authz(self, resource: dict) -> str: matches = [] for rule in self.rules: match = evaluate(resource, rule["condition"]) - # FIXME: what if multiple conditions match?, add error if multiple conditions match -->user makes necessary changes + if match and match[0] is True: matches.append(rule) From 6192216b02a9b7263a99b5f39003901db9b14b69 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Mon, 24 Aug 2026 18:30:05 -0500 Subject: [PATCH 15/35] Fix default working directory and directory creation, imports, renamed functions, included more details in --help --- docs/howto/fhir.md | 8 +++--- gen3/cli/fhir.py | 37 ++++++++++++++++++++++------ gen3/fhir.py | 42 +++++++++++++++++++++++--------- tests/test_data/fhir_config.yaml | 4 --- tests/test_fhir_transform.py | 5 ++-- 5 files changed, 68 insertions(+), 28 deletions(-) diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md index 66f4f940..cbf8f45f 100644 --- a/docs/howto/fhir.md +++ b/docs/howto/fhir.md @@ -24,7 +24,9 @@ rules: condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" authz: "/programs/Alpha/projects/Main" - - resource_type: "Patient" - condition: "Patient.managingOrganization.reference = 'Organization/site-alpha' and Patient.gender = 'male'" - authz: "/programs/Alpha/projects/Main" + - resource_type: "Specimen" + condition: ""Specimen.status = 'available' and Specimen.Type = 'Blood specimen (specimen)'"" + authz: "/programs/Alpha/projects/Biobank" ``` + +And example config.yaml file can be found in [Config reference](tests/test_data/fhir_config.yaml) diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index e272107e..ac63ca23 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -5,8 +5,6 @@ from gen3.fhir import * logging = get_logger(__name__) -TMP_ROOT = pathlib.Path(".fhir_transform/tmp") - @click.group() def fhir(): @@ -16,7 +14,13 @@ def fhir(): @click.command( context_settings={"help_option_names": ["-h", "--help"]}, - help="Tag Bulk FHIR data with Gen3 compatible authorization tags", + help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. + + \b + input_file (str): Input .ndjson file with Bulk FHIR data, one resource type per file + output_file (str): Output file name, also an .ndjson file + config (str): .yaml file with authorization rules, see docs/howto/fhir.md for more details on formatting + """, ) @click.argument( "input_file", @@ -31,6 +35,14 @@ def fhir(): type=click.Path(exists=True, dir_okay=False, readable=True), metavar="config", ) + +@click.option( + "--work_dir", + type=click.Path(), + metavar="work_dir", + help=f"Specify which working directory to clean, if not specified the default ({DEFAULT_WORK_DIR}) will be cleaned. Can also be set as an environment variable: GEN3_FHIR_WORK_DIR", +) + @click.option( "-b", "--batch_size", @@ -59,27 +71,35 @@ def cli( output_file: str | os.PathLike[str], config: str | os.PathLike[str], workers: int, + work_dir: str | os.PathLike[str], batch_size: int, force: bool, ): """ - CLI implementation of fhir_tagger. + CLI implementation of tag_fhir_resources_with_authz. Args: input_file (str): Input .ndjson file output_file (str): Output file name config (str): .yaml file with authorization rules - batch_size (int): numb er of lines per chunk + work_dir (str): Working directory to save intermediate files for each run + batch_size (int): number of lines per chunk workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ - fhir_tagger(input_file, output_file, config, workers, batch_size, force) + tag_fhir_resources_with_authz(input_file, output_file, config, batch_size, work_dir, workers, force) @click.command( context_settings={"help_option_names": ["-h", "--help"]}, help="Remove all intermediate files in the tmp folder from previous runs", ) +@click.option( + "--work_dir", + type=click.Path(), + metavar="work_dir", + help=f"Specify which working directory to clean, if not specified the default ({DEFAULT_WORK_DIR}) will be cleaned. Can also be set as an environment variable: GEN3_FHIR_WORK_DIR", +) @click.option( "--dry-run", is_flag=True, @@ -90,16 +110,17 @@ def cli( is_flag=True, help="Remove temporary directory ignoring status of each directory", ) -def cleanup(dry_run: bool, force: bool): +def cleanup(work_dir, dry_run: bool, force: bool): """ Remove all intermediate files in the tmp folder from previous runs Args: + work_dir (str): Working directory to save intermediate files for each run dry_run (bool): If True, list the files that would be removed, but not actually remove them force (bool): Delete all intermediate directories disregarding the status """ - cleanup_fhir_transform_artifacts(dry_run=dry_run, force=force) + cleanup_fhir_transform_artifacts(work_dir,dry_run=dry_run, force=force) fhir.add_command(cli, name="transform") diff --git a/gen3/fhir.py b/gen3/fhir.py index c9330352..337e17f6 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -9,13 +9,13 @@ import shutil import pathlib import hashlib -from concurrent.futures import ThreadPoolExecutor +from concurrent.futures import ThreadPoolExecutor, ProcessPoolExecutor from cdislogging import get_logger from gen3.utils import make_folders_for_filename from collections.abc import Callable logging = get_logger(__name__) -TMP_ROOT = pathlib.Path(".fhir_transform/tmp") +DEFAULT_WORK_DIR = "~/.cache/gen3/fhir_transform" GEN3_PATH = "http://gen3.org/authz" @@ -133,6 +133,19 @@ def tag_resource(self, resource: dict, authz: str) -> dict: return resource +def resolve_work_dir(work_dir: str | os.PathLike[str] | None = None, clean: bool = False) -> pathlib.Path: + root = pathlib.Path( + work_dir or os.environ.get("GEN3_FHIR_WORK_DIR") or DEFAULT_WORK_DIR + ).expanduser() + + if not clean: + root.mkdir(parents=True, exist_ok=True) + + # 0o700 makes it only only readable by owner and not everyone else (which is important + # for potentially shared machines and potential FHIR PHI) + root.chmod(0o700) + + return root def json_dumps(obj, default=None) -> bytes: """Compact UTF-8 JSON bytes.""" @@ -174,6 +187,7 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: status (bool): returns whether the directory is new/has to be reset or not """ + if not pathlib.Path(directory).is_dir(): return True @@ -203,6 +217,7 @@ def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: Returns: status (bool): returns whether the transformation has beencompleted """ + try: params = json.loads(pathlib.Path(directory, ".config.json").read_bytes()) if ( @@ -211,6 +226,7 @@ def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: or record["output_file"] != params["output_file"] ): return False + except (OSError, ValueError): return False @@ -263,7 +279,7 @@ def _merge_needed(directory: str | os.PathLike[str], record: dict) -> bool: return False -def cleanup_fhir_transform_artifacts(dry_run: bool = False, force: bool = False) -> int: +def cleanup_fhir_transform_artifacts(work_dir, dry_run: bool = False, force: bool = False) -> int: """ Remove run dirs whose owning process is gone. @@ -274,18 +290,18 @@ def cleanup_fhir_transform_artifacts(dry_run: bool = False, force: bool = False) Output: count(int): number of directories deleted """ - - if not TMP_ROOT.is_dir(): + working_dir = resolve_work_dir(work_dir, clean=True) + if not working_dir.is_dir(): logging.info("Nothing to clean") return 0 # force to delete everything disregarding status if force: - shutil.rmtree(TMP_ROOT, ignore_errors=True) + shutil.rmtree(working_dir, ignore_errors=True) return count = 0 - for run_dir in sorted(TMP_ROOT.glob("*")): + for run_dir in sorted(working_dir.glob("*")): if not run_dir.is_dir(): continue @@ -388,11 +404,12 @@ def merge_chunks( os.remove(f) -def fhir_tagger( +def tag_fhir_resources_with_authz( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], config: str | os.PathLike[str], - batch_size: int, + batch_size: int = 10000, + work_dir: str | os.PathLike[str] = DEFAULT_WORK_DIR, workers: int = 8, force: bool = False, ): @@ -406,6 +423,7 @@ def fhir_tagger( output_file (str): Output file name config (str): .yaml file with authorization rules batch_size (int): number of lines per chunk + work_dir (str): static work directory where all run directories are stored workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ @@ -420,11 +438,11 @@ def fhir_tagger( raise click.UsageError("input_file and output_file must be different") # only necessary the first time its run - make_folders_for_filename(TMP_ROOT) + working_dir = resolve_work_dir(work_dir) # make temp directories hash = get_md5hash(input_file) - output_dir = f"{TMP_ROOT}/{os.path.basename(input_file).split('.')[0]}_{hash}" + output_dir = f"{working_dir}/{os.path.basename(input_file).split('.')[0]}_{hash}" record = { "timestamp": datetime.now(timezone.utc).isoformat(), @@ -444,6 +462,8 @@ def fhir_tagger( # if new file or new config/batch_size, reset folder if _is_new(output_dir, record): logging.info("New folder, creating directory and chunking") + if pathlib.Path(output_dir).exists(): + shutil.rmtree(output_dir) make_folders_for_filename(f"{output_dir}/.config.json") pathlib.Path(f"{output_dir}/.config.json").write_text( json.dumps(record, default=str), encoding="utf-8" diff --git a/tests/test_data/fhir_config.yaml b/tests/test_data/fhir_config.yaml index d2362f2c..1f8b1099 100644 --- a/tests/test_data/fhir_config.yaml +++ b/tests/test_data/fhir_config.yaml @@ -11,10 +11,6 @@ rules: condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" authz: "/programs/Alpha/projects/Main" - - resource_type: "Patient" - condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" - authz: "/programs/Alpha/projects/Main" - - resource_type: "Observation" condition: "Observation.code.coding.where(code = '9876-5').exists()" authz: "/programs/Restricted/projects/Genomics" diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 7488df64..1dcf5f02 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -9,7 +9,8 @@ split_file, transform_chunk, merge_chunks, - fhir_tagger, + tag_fhir_resources_with_authz, + DEFAULT_WORK_DIR ) import pathlib import os @@ -109,7 +110,7 @@ def test_fhir_output(): for line in pathlib.Path(SRC).read_bytes().splitlines() if line.strip() ] - fhir_tagger(IN, OUT, CONFIG_SRC, 8, BATCH_SIZE) + tag_fhir_resources_with_authz(IN, OUT, CONFIG_SRC, BATCH_SIZE, TMP_ROOT, 8, ) out = [ json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() From 6b5f3194018e9497fc0b0a5d72c68f2a152a13cd Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 10:44:17 -0500 Subject: [PATCH 16/35] Remove test outputs, fix typos, add assertions, change to SHA-256 hash, update function descriptions --- gen3/cli/fhir.py | 8 ++++---- gen3/fhir.py | 11 ++++++----- tests/test_fhir_transform.py | 3 ++- tests/tests/outputs/empty_file | 0 tests/tests/outputs/indexing-output-manifest.csv | 2 -- tests/tests/outputs/input.csv | 4 ---- tests/tests/outputs/object-manifest.csv | 4 ---- tests/tests/outputs/tmp_output_file.csv | 2 -- tests/tests/outputs/tmp_output_file_info.csv | 5 ----- 9 files changed, 12 insertions(+), 27 deletions(-) delete mode 100644 tests/tests/outputs/empty_file delete mode 100644 tests/tests/outputs/indexing-output-manifest.csv delete mode 100644 tests/tests/outputs/input.csv delete mode 100644 tests/tests/outputs/object-manifest.csv delete mode 100644 tests/tests/outputs/tmp_output_file.csv delete mode 100644 tests/tests/outputs/tmp_output_file_info.csv diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index ac63ca23..9da4b95b 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -71,7 +71,7 @@ def cli( output_file: str | os.PathLike[str], config: str | os.PathLike[str], workers: int, - work_dir: str | os.PathLike[str], + work_dir: str | os.PathLike[str]| None, batch_size: int, force: bool, ): @@ -87,7 +87,7 @@ def cli( workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ - tag_fhir_resources_with_authz(input_file, output_file, config, batch_size, work_dir, workers, force) + tag_fhir_resources_with_authz(input_file=input_file, output_file=output_file, config=config, batch_size=batch_size, work_dir=work_dir, workers=workers, force=force) @click.command( @@ -103,7 +103,7 @@ def cli( @click.option( "--dry-run", is_flag=True, - help="Used with --cleanup, report what would be deleted with --cleanup without deleting the files", + help="Report what would be deleted with --cleanup without deleting the files", ) @click.option( "--force", @@ -120,7 +120,7 @@ def cleanup(work_dir, dry_run: bool, force: bool): force (bool): Delete all intermediate directories disregarding the status """ - cleanup_fhir_transform_artifacts(work_dir,dry_run=dry_run, force=force) + cleanup_fhir_transform_artifacts(work_dir=work_dir, dry_run=dry_run, force=force) fhir.add_command(cli, name="transform") diff --git a/gen3/fhir.py b/gen3/fhir.py index 337e17f6..7c3b3106 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -143,7 +143,8 @@ def resolve_work_dir(work_dir: str | os.PathLike[str] | None = None, clean: bool # 0o700 makes it only only readable by owner and not everyone else (which is important # for potentially shared machines and potential FHIR PHI) - root.chmod(0o700) + if root.is_dir(): + root.chmod(0o700) return root @@ -158,19 +159,19 @@ def json_dumps(obj, default=None) -> bytes: ).encode("utf-8") -def get_md5hash(input_file: str | os.PathLike[str]) -> str: +def get_sha256hash(input_file: str | os.PathLike[str]) -> str: """ - Returns the md5 hash of the input .ndjson file to create a unique folder per file + Returns the SHA-256 hash of the input .ndjson file to create a unique folder per file Args: input_file (str): Input ndjson file to transform Returns: - digest (str): md5 hash of the input .ndjson file + digest (str): SHA-256 hash of the input .ndjson file """ with open(input_file, "rb") as f: - digest = hashlib.file_digest(f, "md5").hexdigest() + digest = hashlib.file_digest(f, "sha256").hexdigest() return digest diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 1dcf5f02..14380519 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -189,7 +189,7 @@ def test_merge(): for line in pathlib.Path(IN).read_bytes().splitlines() if line.strip() ] - fout = fin = [ + fout = [ json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() if line.strip() @@ -467,6 +467,7 @@ def test_cli(): timeout=60, ) + assert result.returncode == 0, "CLI run failed" assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" records = [ json.loads(line) diff --git a/tests/tests/outputs/empty_file b/tests/tests/outputs/empty_file deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/tests/outputs/indexing-output-manifest.csv b/tests/tests/outputs/indexing-output-manifest.csv deleted file mode 100644 index e314d402..00000000 --- a/tests/tests/outputs/indexing-output-manifest.csv +++ /dev/null @@ -1,2 +0,0 @@ -guid authz md5 package_contents record_type size urls -testprefix:d50731a4-63ce-437e-ada6-bfe600681f74 "[""/open""]" 473d83400bc1bc9dc635e334faddf33c "[{""file_name"": ""file.text""}]" object 363455714 s3://my-data-bucket/dg.1234/path/file.text diff --git a/tests/tests/outputs/input.csv b/tests/tests/outputs/input.csv deleted file mode 100644 index 6dd07fc7..00000000 --- a/tests/tests/outputs/input.csv +++ /dev/null @@ -1,4 +0,0 @@ -guid,urls,authz,acl,md5,file_size,file_name -,gs://foo/bar,programs/foo/projects/bar,,a1234567891234567890123456789012,42, -,gs://foo/bar,programs/foo/projects/bar,,x1234567891234567890123456789012,42, -,gs://foo/bar,programs/foo/projects/bar,,f1234567891234567890123456789012,234, diff --git a/tests/tests/outputs/object-manifest.csv b/tests/tests/outputs/object-manifest.csv deleted file mode 100644 index 464c9363..00000000 --- a/tests/tests/outputs/object-manifest.csv +++ /dev/null @@ -1,4 +0,0 @@ -guid,urls,authz,acl,md5,file_size,file_name -dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b,gs://test/test.txt s3://testaws/aws/test.txt,/programs/DEV/projects/test,DEV test,a1234567891234567890123456789012,123, -,gs://foo/bar,programs/foo/projects/bar,,51234567891234567890123456789012,42, -dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce,gs://test/test4%20space.txt s3://test/test4%20space.txt,/programs/DEV/projects/test4 /programs/DEV/projects/test4bak,DEV test4,f1234567891234567890123456789012,345, diff --git a/tests/tests/outputs/tmp_output_file.csv b/tests/tests/outputs/tmp_output_file.csv deleted file mode 100644 index a8734c46..00000000 --- a/tests/tests/outputs/tmp_output_file.csv +++ /dev/null @@ -1,2 +0,0 @@ -https://data.midrc.org|gen3_node_property|Case.data_submission_guid,https://data.midrc.org|gen3_node_property|Case.submitter_id,https://data.midrc.org|masked_n3c_id|Masked N3C ID,https://gen3.biodatacatalyst.nhlbi.nih.gov|gen3_node_property|Subject.submitter_id -foobar,A01-00888,123dfj4ia5oi*@a,phs002363.v1_RC-1358 diff --git a/tests/tests/outputs/tmp_output_file_info.csv b/tests/tests/outputs/tmp_output_file_info.csv deleted file mode 100644 index d8064e10..00000000 --- a/tests/tests/outputs/tmp_output_file_info.csv +++ /dev/null @@ -1,5 +0,0 @@ -commons_url,identifier_name,description -https://gen3.biodatacatalyst.nhlbi.nih.gov,Subject.submitter_id,These identifiers are constructed as part of the data ingestion process in BDCat and concatenate the study and version with the study-provided subject ID (with a _ delimiting). -https://data.midrc.org,Case.submitter_id,The uniquely assigned case identifier in MIDRC. -https://data.midrc.org,Case.data_submission_guid,The identifier for this subject as provided by the site’s submission of Datavant tokens to MIDRC. -https://data.midrc.org,Masked N3C ID,Masked National COVID Consortium ID provided by a Linkage Honest Broker to the MIDRC system. From d00ecf5e4944265cb249a782e8e9e5ef17e54c58 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 10:52:20 -0500 Subject: [PATCH 17/35] Fix hash bug --- .gitignore | 1 + gen3/fhir.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 2b0627bb..b3b7ed62 100644 --- a/.gitignore +++ b/.gitignore @@ -109,6 +109,7 @@ schema.json # pytest outputs tests/outputs +tests/test_data/fhir_outputs *.sq3 gen3/tools/indexing/tmp/ diff --git a/gen3/fhir.py b/gen3/fhir.py index 7c3b3106..3ffa8067 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -442,14 +442,14 @@ def tag_fhir_resources_with_authz( working_dir = resolve_work_dir(work_dir) # make temp directories - hash = get_md5hash(input_file) + hash = get_sha256hash(input_file) output_dir = f"{working_dir}/{os.path.basename(input_file).split('.')[0]}_{hash}" record = { "timestamp": datetime.now(timezone.utc).isoformat(), "input_file": input_file, "output_file": output_file, - "config_hash": get_md5hash(config), + "config_hash": get_sha256hash(config), "batch_size": batch_size, } From 8339418b23f60b8afce195cdef0938e676bd4a6a Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 12:12:07 -0500 Subject: [PATCH 18/35] Add unit test for global authz and fix tmp_path --- tests/test_data/fhir_config.yaml | 4 +- tests/test_data/fhir_global_config.yaml | 39 ++++++++ tests/test_fhir_transform.py | 117 ++++++++++++++++-------- 3 files changed, 119 insertions(+), 41 deletions(-) create mode 100644 tests/test_data/fhir_global_config.yaml diff --git a/tests/test_data/fhir_config.yaml b/tests/test_data/fhir_config.yaml index 1f8b1099..24a0fc3c 100644 --- a/tests/test_data/fhir_config.yaml +++ b/tests/test_data/fhir_config.yaml @@ -1,8 +1,8 @@ version: "1.0" -# Global Override (Applies to all resources if used) -# global_authz: "/programs/NCI/projects/TargetedStudyA" +##Global Override (Applies to all resources if used) +#global_authz: "/programs/NCI/projects/TargetedStudyA" # Conditional Field-Level Routing (Per Resource Type) diff --git a/tests/test_data/fhir_global_config.yaml b/tests/test_data/fhir_global_config.yaml new file mode 100644 index 00000000..e7893f06 --- /dev/null +++ b/tests/test_data/fhir_global_config.yaml @@ -0,0 +1,39 @@ +version: "1.0" + + +#Global Override (Applies to all resources if used) +global_authz: "/programs/NCI/projects/TargetedStudyA" + + +# Conditional Field-Level Routing (Per Resource Type) +rules: + - resource_type: "Patient" + condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" + authz: "/programs/Alpha/projects/Main" + + - resource_type: "Observation" + condition: "Observation.code.coding.where(code = '9876-5').exists()" + authz: "/programs/Restricted/projects/Genomics" + + - resource_type: "Specimen" + condition: "Specimen.status = 'unavailable'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Specimen" + condition: "Specimen.status = 'available'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Specimen" + condition: "Specimen.Type = 'Blood specimen (specimen)'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Patient" + condition: "Patient.gender = 'male'" + authz: "/programs/Alpha/projects/Biobank" + + - resource_type: "Patient" + condition: "Patient.gender = 'female'" + authz: "/programs/Restricted/projects/Genomics" + + + diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 14380519..04faa316 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -17,12 +17,15 @@ import json import subprocess import shutil +import yaml + TMP_ROOT = pathlib.Path("./tests/test_data/fhir_outputs") SRC = pathlib.Path("./tests/test_data/test_fhir_Patient.ndjson") IN = pathlib.Path("./tests/test_data/Patient.ndjson") OUT = os.path.join(TMP_ROOT, "fhir_output_Patient.ndjson") CONFIG_SRC = pathlib.Path("./tests/test_data/fhir_config.yaml") +GLOBAL_CONFIG_SRC = pathlib.Path("./tests/test_data/fhir_global_config.yaml") TAGGER = Gen3FHIRAuthzTagger(CONFIG_SRC) BATCH_SIZE = 1 BASE_RECORD = { @@ -35,8 +38,11 @@ @pytest.fixture(scope="session") -def tmp_root(tmp_path_factory): - return tmp_path_factory.mktemp(TMP_ROOT) +def tmp_root(): + root = pathlib.Path(__file__).parent / "test_data" / "fhir_outputs" + shutil.rmtree(root, ignore_errors=True) + root.mkdir(parents=True) + return root def mock_state( @@ -98,7 +104,7 @@ def mock_state( return directory, record -def test_fhir_output(): +def test_fhir_output(tmp_root): """Tests that output file matches the input file with the only difference being the tags""" fin = [ json.loads(line) @@ -110,7 +116,7 @@ def test_fhir_output(): for line in pathlib.Path(SRC).read_bytes().splitlines() if line.strip() ] - tag_fhir_resources_with_authz(IN, OUT, CONFIG_SRC, BATCH_SIZE, TMP_ROOT, 8, ) + tag_fhir_resources_with_authz(IN, OUT, CONFIG_SRC, BATCH_SIZE, tmp_root, 8) out = [ json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() @@ -130,10 +136,10 @@ def test_fhir_output(): assert src == out, "Output file does not match source file" -def test_chunking(): +def test_chunking(tmp_root): """Tests that number of chunks is correct and the recombined chunks match the input file""" - split_file(IN, BATCH_SIZE, TMP_ROOT) - chunks = list(TMP_ROOT.glob("*.chunk")) + split_file(IN, BATCH_SIZE, tmp_root) + chunks = list(tmp_root.glob("*.chunk")) fin = [ json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() @@ -155,13 +161,13 @@ def test_chunking(): ), "Recombined chunks do not match the content of the input file" -def test_transform(): +def test_transform(tmp_root): """Asserts transform_chunk creates the same number of .done files as .chunk and no .chunk files remain once transformation is completed""" TAGGER.relevant_authz_rules(os.path.basename(IN).split(".")[0]) - chunks = list(TMP_ROOT.glob("*.chunk")) + chunks = list(tmp_root.glob("*.chunk")) for c in chunks: - transform_chunk(c, TAGGER, TMP_ROOT) - transformed = list(TMP_ROOT.glob("*.done")) + transform_chunk(c, TAGGER, tmp_root) + transformed = list(tmp_root.glob("*.done")) # same number of transformed files as chunk files assert len(transformed) == len( @@ -169,15 +175,15 @@ def test_transform(): ), f"Expected same number of transformed .done files as number of .chunk files after transformation completed, found {len(transformed)}" # all .chunk files deleted after transformation completed assert ( - len(list(TMP_ROOT.glob("*.chunk"))) == 0 - ), f"Expected 0 chunks after transformation completed, found {len(list(TMP_ROOT.glob("*.chunk")))}" + len(list(tmp_root.glob("*.chunk"))) == 0 + ), f"Expected 0 chunks after transformation completed, found {len(list(tmp_root.glob("*.chunk")))}" -def test_merge(): +def test_merge(tmp_root): """Asserts that after merge is completed, the output file exists and is not empty, there are no .done files remaining, the length of the output matches the sum of the transformed files and the input file, and the file is not corrupt/formatting is correct """ - transformed = list(TMP_ROOT.glob("*.done")) + transformed = list(tmp_root.glob("*.done")) transformed_sum = sum( len([l for l in pathlib.Path(c).read_bytes().splitlines() if l.strip()]) for c in transformed @@ -201,8 +207,8 @@ def test_merge(): assert pathlib.Path(OUT).stat().st_size > 0, "Output file empty" # no leftover .done files after merge completed assert ( - len(list(TMP_ROOT.glob("*.done"))) == 0 - ), f"Expected 0 .done files after transformation completed, found {len(list(TMP_ROOT.glob("*.done")))}" + len(list(tmp_root.glob("*.done"))) == 0 + ), f"Expected 0 .done files after transformation completed, found {len(list(tmp_root.glob("*.done")))}" # output file is the same length as the combined transformed files and the length of the input file assert ( len(fout) == transformed_sum == len(fin) @@ -218,11 +224,12 @@ def test_merge(): class Test_is_new: """Tests the logic of the run/directory being marked as new (_is_new(directory, record) returns True)""" - tmp_path = TMP_ROOT / "test_new" + def __init__(self,tmp_root): + self.tmp_path = tmp_root / "test_new" - def test_is_new_with_missing_directory(self): + def test_is_new_with_missing_directory(self, tmp_root): # directory missing - assert _is_new(TMP_ROOT / "does_not_exist", BASE_RECORD) is True + assert _is_new(tmp_root/ "does_not_exist", BASE_RECORD) is True def test_is_new_directory_has_no_config_file(self): # no config file @@ -268,7 +275,8 @@ def test_is_new_when_output_filename_changed(self): class Test_is_done: """Tests the logic of the run/directory being marked as done (_is_done(directory, record) returns True)""" - tmp_path = TMP_ROOT / "test_done" + def __init__(self,tmp_root): + self.tmp_path = tmp_root / "test_done" def test_is_done_with_matching_config_and_empty_output(self): # config matches but output is empty @@ -322,8 +330,8 @@ def test_is_done_with_full_output_and_matching_config(self): class Test_resume_run: """Tests the logic of the run/directory being marked as need to resume run (_resume_run(directory, record) returns True)""" - - tmp_path = TMP_ROOT / "test_resume" + def __init__(self,tmp_root): + self.tmp_path = tmp_root / "test_resume" def test_resume_run_with_no_chunk_files(self): # no chunk files in directory @@ -352,9 +360,9 @@ def test_resume_run_with_leftover_done_files_and_chunk_files( ) assert _resume_run(directory, record) is True - def test_resume_run_when_directory_missing(self): + def test_resume_run_when_directory_missing(self, tmp_root): # directory is missing - assert _resume_run(TMP_ROOT / "gone", BASE_RECORD) is False + assert _resume_run(tmp_root / "gone", BASE_RECORD) is False def test_resume_run_ignores_similarly_named_files(self): # ignored similarly named files @@ -373,8 +381,8 @@ def test_resume_run_is_nonrecursive(self): class Test_merge_needed: """Tests the logic of the run/directory being marked as merge needed (_merge_needed(directory, record) returns True)""" - - tmp_path = TMP_ROOT / "outputs" / "test_merge" + def __init__(self,tmp_root): + self.tmp_path = tmp_root / "outputs" / "test_merge" def test_merge_needed_when_no_done_files_remaining(self): # no merge on clean directory @@ -399,15 +407,15 @@ def test_merge_needed_when_chunk_and_done_files_remaining( ) assert _merge_needed(directory, record) is False - def test_merge_needed_when_directory_missing(self): + def test_merge_needed_when_directory_missing(self, tmp_root): # no merge when directory missing - assert _merge_needed(TMP_ROOT / "gone", BASE_RECORD) is False + assert _merge_needed(tmp_root / "gone", BASE_RECORD) is False class Test_status: """Tests for overlap in different statuses""" - - tmp_path = TMP_ROOT / "test_status" + def __init__(self,tmp_root): + self.tmp_path = tmp_root / "test_status" def test_fresh_directory(self): # fresh directory @@ -443,10 +451,10 @@ def test_run_complete(self): @pytest.mark.parametrize( "state", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] ) - def test_new_and_done_are_mutually_exclusive(self, state): + def test_new_and_done_are_mutually_exclusive(self, state, tmp_root): # new and done are mutually exclusive directory, record = mock_state( - TMP_ROOT / str(id(state)), config=state, output="full" + tmp_root / str(id(state)), config=state, output="full" ) assert not (_is_new(directory, record) and _is_done(directory, record)) @@ -488,9 +496,9 @@ def test_cli(): @pytest.mark.parametrize("bad", [0, -1, None, "bad"]) -def test_invalid_batch_size_is_rejected(bad): +def test_invalid_batch_size_is_rejected(bad, tmp_root): """Assert invalid batch_size is rejected and raises an error""" - out = TMP_ROOT / "cli_test" / "cli_out.ndjson" + out = tmp_root / "cli_test" / "cli_out.ndjson" args = [ IN, @@ -512,9 +520,9 @@ def test_invalid_batch_size_is_rejected(bad): ).exists(), "Rejected the argument but still wrote output" -def test_missing_input_file_fails_cleanly(): +def test_missing_input_file_fails_cleanly(tmp_root): """Asserts error is raised if missing input file passed as argument""" - out = TMP_ROOT / "cli_test" / "nope.ndjson" + out = tmp_root / "cli_test" / "nope.ndjson" args = [ "nope.ndjson", out, @@ -535,9 +543,9 @@ def test_missing_input_file_fails_cleanly(): ).exists(), "Output file written even though invalid input file passed" -def test_output_directory_does_not_exist(): +def test_output_directory_does_not_exist(tmp_root): """Test response if output directory doesn't exists. Directory (and parents) should be created if missing""" - out = TMP_ROOT / "missing_dir" / "out.ndjson" + out = tmp_root / "missing_dir" / "out.ndjson" args = [ IN, out, @@ -554,3 +562,34 @@ def test_output_directory_does_not_exist(): assert result.returncode == 0, "Raises error instead of creating output directory" assert pathlib.Path(out).exists(), "Process not completed, output file not written" + + +def test_global_config_overrides_other_rules(tmp_root): + """Assert global authorization overrides any other rules""" + out = tmp_root / "global_config" / "out.ndjson" + args = [ + IN, + out, + GLOBAL_CONFIG_SRC, + "--batch_size", + str(BATCH_SIZE), + ] + result = subprocess.run( + ["gen3", "fhir", "transform", *args], + capture_output=True, + text=True, + timeout=60, + ) + assert result.returncode == 0, "Run fails" + assert pathlib.Path(out).exists(), "Process not completed, output file not written" + tagged_file = [ + json.loads(line) + for line in pathlib.Path(out).read_bytes().splitlines() + if line.strip() + ] + with open(GLOBAL_CONFIG_SRC, "r") as f: + config = yaml.safe_load(f) + + for rec in tagged_file: + security = (rec.get("meta")).get("security")[0].get("code") + assert security == config["global_authz"], "File not tagged with global authorization" From 9cbf8baa25ad2325860ab7496feeb285cb2c8608 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 12:25:47 -0500 Subject: [PATCH 19/35] Comment out all parrallelization code --- docs/howto/fhir.md | 3 ++- gen3/cli/fhir.py | 24 ++++++++++++------------ gen3/fhir.py | 31 +++++++++++++++++-------------- 3 files changed, 31 insertions(+), 27 deletions(-) diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md index cbf8f45f..6c3e2680 100644 --- a/docs/howto/fhir.md +++ b/docs/howto/fhir.md @@ -24,9 +24,10 @@ rules: condition: "Patient.managingOrganization.reference = 'Organization/site-alpha'" authz: "/programs/Alpha/projects/Main" +#Example with multiple conditions - resource_type: "Specimen" condition: ""Specimen.status = 'available' and Specimen.Type = 'Blood specimen (specimen)'"" authz: "/programs/Alpha/projects/Biobank" ``` -And example config.yaml file can be found in [Config reference](tests/test_data/fhir_config.yaml) +And example config.yaml file can be found in [fhir_config.yaml](tests/test_data/fhir_config.yaml) diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index 9da4b95b..ebe38837 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -52,15 +52,15 @@ def fhir(): metavar="batch_size", help="batch size for chunking", ) -@click.option( - "-w", - "--workers", - type=click.IntRange(min=1), - default=8, - show_default=True, - metavar="workers", - help="number of parallel processes", -) +# @click.option( +# "-w", +# "--workers", +# type=click.IntRange(min=1), +# default=8, +# show_default=True, +# metavar="workers", +# help="number of parallel processes", +# ) @click.option( "--force", is_flag=True, @@ -70,7 +70,7 @@ def cli( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], config: str | os.PathLike[str], - workers: int, + #workers: int, work_dir: str | os.PathLike[str]| None, batch_size: int, force: bool, @@ -84,10 +84,10 @@ def cli( config (str): .yaml file with authorization rules work_dir (str): Working directory to save intermediate files for each run batch_size (int): number of lines per chunk - workers (int): number of parallel processes + ###workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ - tag_fhir_resources_with_authz(input_file=input_file, output_file=output_file, config=config, batch_size=batch_size, work_dir=work_dir, workers=workers, force=force) + tag_fhir_resources_with_authz(input_file=input_file, output_file=output_file, config=config, batch_size=batch_size, work_dir=work_dir, force=force) @click.command( diff --git a/gen3/fhir.py b/gen3/fhir.py index 3ffa8067..f10faacb 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -9,7 +9,6 @@ import shutil import pathlib import hashlib -from concurrent.futures import ThreadPoolExecutor, ProcessPoolExecutor from cdislogging import get_logger from gen3.utils import make_folders_for_filename from collections.abc import Callable @@ -372,8 +371,8 @@ def transform_chunk( out += json_dumps(tagger.tag_resource(record, authz_tags)) out += b"\n" fout.write(out) - # delete chunk file once it has been transformed - os.remove(input_file) + # delete chunk file once it has been transformed + os.remove(input_file) def merge_chunks( @@ -411,13 +410,13 @@ def tag_fhir_resources_with_authz( config: str | os.PathLike[str], batch_size: int = 10000, work_dir: str | os.PathLike[str] = DEFAULT_WORK_DIR, - workers: int = 8, + #workers: int = 8, force: bool = False, ): """ Stream-transform Bulk FHIR data to Gen3 compatible data with authorization tagging. - Parallelized line by line tagging with batched I/O + Line by line tagging with batched I/O Args: input_file (str): Input .ndjson file @@ -425,15 +424,15 @@ def tag_fhir_resources_with_authz( config (str): .yaml file with authorization rules batch_size (int): number of lines per chunk work_dir (str): static work directory where all run directories are stored - workers (int): number of parallel processes + ###workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ - + start_time = time.time() if batch_size < 1: raise ValueError(f"batch_size must be >= 1, got {batch_size}") - if workers < 1: - raise ValueError(f"workers must be >= 1, got {workers}, default is 8") + # if workers < 1: + # raise ValueError(f"workers must be >= 1, got {workers}, default is 8") # check if input and output file are the same if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") @@ -488,11 +487,15 @@ def tag_fhir_resources_with_authz( # parallelize transform logging.info("Transforming chunks...") start = time.time() - with ThreadPoolExecutor(max_workers=workers) as pool: - for _ in pool.map( - transform_chunk, chunk_files, repeat(tagger), repeat(output_dir) - ): - pass + ### FUTURE implement multiprocessing + # with ProcessPoolExecutor(max_workers=workers) as pool: + # for _ in pool.map( + # transform_chunk, chunk_files, repeat(tagger), repeat(output_dir) + # ): + # pass + for chunk in chunk_files: + transform_chunk(chunk, tagger, output_dir) + logging.info( f"Transform chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" ) From 8f5eee53932d5b8f481e10d49f57e1233aa44216 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 12:32:43 -0500 Subject: [PATCH 20/35] Remove _resume_run from all code --- gen3/fhir.py | 17 ---------- tests/test_fhir_transform.py | 66 +++++------------------------------- 2 files changed, 8 insertions(+), 75 deletions(-) diff --git a/gen3/fhir.py b/gen3/fhir.py index f10faacb..650813bf 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -242,23 +242,6 @@ def _is_done(directory: str | os.PathLike[str], record: dict) -> bool: return False -def _resume_run(directory: str | os.PathLike[str], record: dict) -> bool: - """ - Check if transformation needs to be resumed. Returns True if there are chunk files remaining in the directory. - - Args: - directory (str): path of the directory linked to the .ndjson file - record (dict): the configuration of the current run, used to compare to what is already saved in the folder - - Returns: - status (bool): returns whether the transformation needs to be resumed - """ - # check for .chunk files --> tagging incomplete - if any(pathlib.Path(directory).glob("*.chunk")): - return True - return False - - def _merge_needed(directory: str | os.PathLike[str], record: dict) -> bool: """ Check if .done files have been merged to the final output file. Returns True if .done files remaining in the directory. diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 04faa316..3c1740e0 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -4,7 +4,6 @@ Gen3FHIRAuthzTagger, _is_new, _is_done, - _resume_run, _merge_needed, split_file, transform_chunk, @@ -328,56 +327,6 @@ def test_is_done_with_full_output_and_matching_config(self): assert _is_done(directory, record) is True -class Test_resume_run: - """Tests the logic of the run/directory being marked as need to resume run (_resume_run(directory, record) returns True)""" - def __init__(self,tmp_root): - self.tmp_path = tmp_root / "test_resume" - - def test_resume_run_with_no_chunk_files(self): - # no chunk files in directory - directory, record = mock_state(self.tmp_path, chunks=0) - assert _resume_run(directory, record) is False - - @pytest.mark.parametrize("chunk_files", [4, 20, 57, 100]) - def test_resume_run_with_leftover_chunk_files(self, chunk_files): - # leftover chunks - directory, record = mock_state(self.tmp_path, chunks=chunk_files) - assert _resume_run(directory, record) is True - - @pytest.mark.parametrize("done_files", [0, 20, 57, 100]) - def test_resume_run_with_leftover_done_files_and_no_chunk_files(self, done_files): - # no chunks but .done remaining - directory, record = mock_state(self.tmp_path, chunks=0, done=done_files) - assert _resume_run(directory, record) is False - - @pytest.mark.parametrize(["chunk_files", "done_files"], [(5, 10), (12, 5), (7, 7)]) - def test_resume_run_with_leftover_done_files_and_chunk_files( - self, chunk_files, done_files - ): - # both .chunk and .done remaining - directory, record = mock_state( - self.tmp_path, chunks=chunk_files, done=done_files - ) - assert _resume_run(directory, record) is True - - def test_resume_run_when_directory_missing(self, tmp_root): - # directory is missing - assert _resume_run(tmp_root / "gone", BASE_RECORD) is False - - def test_resume_run_ignores_similarly_named_files(self): - # ignored similarly named files - directory, record = mock_state(self.tmp_path) - (directory / "chunk").write_text("", encoding="utf-8") - (directory / "notes.chunk.csv").write_text("", encoding="utf-8") - assert _resume_run(directory, record) is False - - def test_resume_run_is_nonrecursive(self): - # non recursive - directory, record = mock_state(self.tmp_path) - (directory / "nested").mkdir() - (directory / "nested" / "a.chunk").write_text("", encoding="utf-8") - assert _resume_run(directory, record) is False - class Test_merge_needed: """Tests the logic of the run/directory being marked as merge needed (_merge_needed(directory, record) returns True)""" @@ -422,29 +371,30 @@ def test_fresh_directory(self): directory, record = mock_state(self.tmp_path, config=None) assert _is_new(directory, record) is True assert _is_done(directory, record) is False - assert _resume_run(directory, record) is False assert _merge_needed(directory, record) is False - def test_need_to_resume_overlap(self): - # need to resume - directory, record = mock_state(self.tmp_path, config="match", chunks=2, done=3) + @pytest.mark.parametrize( + ["chunk_files", "done_files"], [(5, 2), (5, 5), (5, 7), (1, 10)] + ) + def test_need_to_resume_overlap(self, chunk_files, done_files): + directory, record = mock_state(self.tmp_path, config="match", chunks=chunk_files, done=done_files) assert _is_new(directory, record) is False assert _is_done(directory, record) is False - assert _resume_run(directory, record) is True + @pytest.mark.parametrize( + "chunks", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] + ) def test_merge_needed_overlap(self): # merge needed directory, record = mock_state(self.tmp_path, config="match", chunks=0, done=5) assert _is_new(directory, record) is False assert _is_done(directory, record) is False - assert _resume_run(directory, record) is False assert _merge_needed(directory, record) is True def test_run_complete(self): # fully complete directory, record = mock_state(self.tmp_path, config="match", output="full") assert _is_done(directory, record) is True - assert _resume_run(directory, record) is False assert _merge_needed(directory, record) is False assert _is_new(directory, record) is False From 9cdf886cc7f216a61a75a35eede2aa3b0a7d50ae Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 12:52:48 -0500 Subject: [PATCH 21/35] Fix exception handling --- gen3/fhir.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gen3/fhir.py b/gen3/fhir.py index 650813bf..31785b75 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -495,12 +495,15 @@ def tag_fhir_resources_with_authz( logging.info( f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}" ) + if force: shutil.rmtree(output_dir, ignore_errors=True) - except BaseException as e: + except Exception as e: logging.error(e) if force: shutil.rmtree(output_dir, ignore_errors=True) else: logging.error("run failed; intermediates left in %s", output_dir) + raise + From 818c537c6d1c70a0a97948f9a2aa1c8d46bc68b8 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 14:00:00 -0500 Subject: [PATCH 22/35] Fix resource_type check --- gen3/cli/fhir.py | 2 +- gen3/fhir.py | 54 ++++++++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 53 insertions(+), 3 deletions(-) diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index ebe38837..bac12977 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -17,7 +17,7 @@ def fhir(): help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. \b - input_file (str): Input .ndjson file with Bulk FHIR data, one resource type per file + input_file (str): Input .ndjson file with Bulk FHIR data, MUST be one resource type per file output_file (str): Output file name, also an .ndjson file config (str): .yaml file with authorization rules, see docs/howto/fhir.md for more details on formatting """, diff --git a/gen3/fhir.py b/gen3/fhir.py index 31785b75..040d7a30 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -173,6 +173,51 @@ def get_sha256hash(input_file: str | os.PathLike[str]) -> str: digest = hashlib.file_digest(f, "sha256").hexdigest() return digest +def get_resource_type(input_file, sample=5): + """ + Check resource type within the input .ndjson file by reading the first few and last few lines + + Args: + input_file(str): Input ndjson file to be transformed + sample(int): number of lines to read + + Returns: + resource_type(str): Resource type contained within the ndjson (one per file) + + """ + + path = pathlib.Path(input_file) + size = path.stat().st_size + + with path.open("rb") as f: + head = list(islice((ln for ln in f if ln.strip()), sample)) + if not head: + raise ValueError(f"{path}: file has no records") + + #calculate approximate offset from end of file, guards from concatnated files with different resource types + f.seek(max(0, size - max(len(ln) for ln in head) * sample * 2)) + # drop [0]: a partial line mid-file, or a line the head already has + tail = [ln for ln in f.read().split(b"\n")[1:] if ln.strip()][-sample:] + + if len(tail) < sample: + f.seek(0) + tail = [ln for ln in f.read().split(b"\n") if ln.strip()][-sample:] + + types = set() + for raw in head + tail: + try: + rec = json.loads(raw.decode("utf-8-sig")) + except json.JSONDecodeError as e: + raise ValueError(f"{path}: malformed JSON in sampled line: {e}") from e + if not isinstance(rec, dict) or "resourceType" not in rec: + raise ValueError(f"{path}: sampled line has no 'resourceType' field") + types.add(rec["resourceType"]) + + if len(types) == 1: + return types.pop() + else: + raise ValueError(f"Expected 1 resource type per file, got {len(types)} types: {sorted(types)} in {input_file}.") + def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: """ @@ -420,6 +465,10 @@ def tag_fhir_resources_with_authz( if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") + #check if input file is empty + if pathlib.Path(input_file).stat().st_size == 0: + raise ValueError(f"{input_file}: file is empty") + # only necessary the first time its run working_dir = resolve_work_dir(work_dir) @@ -458,7 +507,8 @@ def tag_fhir_resources_with_authz( # initialize tagger tagger = Gen3FHIRAuthzTagger(config_path=config) # keep only relevant rules for the resource type - tagger.relevant_authz_rules(os.path.basename(input_file).split(".")[0]) + resource_type = get_resource_type(input_file) + tagger.relevant_authz_rules(resource_type) # if not fully transformed or new/reset, resume if not _merge_needed(output_dir, record): @@ -504,6 +554,6 @@ def tag_fhir_resources_with_authz( if force: shutil.rmtree(output_dir, ignore_errors=True) else: - logging.error("run failed; intermediates left in %s", output_dir) + logging.error("Run failed; intermediates left in %s", output_dir) raise From dd2abb218f25b522b0e5676a47d9920abdd73158 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 16:55:25 -0500 Subject: [PATCH 23/35] Use fhirpathpy.compile instead of fhirpathpy.evaluate for speed up. --- gen3/fhir.py | 42 ++++++++++++++++++++++++++++++------------ 1 file changed, 30 insertions(+), 12 deletions(-) diff --git a/gen3/fhir.py b/gen3/fhir.py index 040d7a30..e576e2e8 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -1,7 +1,8 @@ import yaml -from itertools import islice, repeat +from itertools import islice import json -from fhirpathpy import evaluate +from fhirpathpy import compile +from fhirpathpy.models import models import click import os, glob import time @@ -34,6 +35,7 @@ def __init__( self, config_path: str | os.PathLike[str], custom_hook: Callable[[dict], dict] | None = None, + fhir_version: str = "r4", ): """ Initialize instance of the tagger. @@ -41,11 +43,13 @@ def __init__( Args: config_path (str): the name/path of the config.yaml file custom_hook (Callable): used for authorization instead of the configuration if called + fhir_version (str): FHIR model version """ with open(config_path, "r") as f: self.config = yaml.safe_load(f) self.custom_hook = custom_hook + self.model = models[fhir_version] def relevant_authz_rules(self, resource_type: str): """ @@ -55,11 +59,25 @@ def relevant_authz_rules(self, resource_type: str): resource_type (str): the resource type in the .ndjson file """ - resource_rules = [] + self.rules = [] for rule in self.config.get("rules", []): - if rule["resource_type"] == resource_type: - resource_rules.append(rule) - self.rules = resource_rules + if rule['resource_type'] != resource_type: + continue + try: + match = compile(rule["condition"], model=self.model) + match({"resourceType": resource_type}) + except Exception as e: + raise ValueError( + f"invalid FHIRPath for authz {rule.get('authz')!r}: " + f"{rule['condition']!r}: {e}" + ) from e + self.rules.append({**rule, "match": match}) + + if not self.rules: + raise ValueError( + f"no authz rules configured for resource type {resource_type!r}" + ) + def determine_authz(self, resource: dict) -> str: """ @@ -79,16 +97,16 @@ def determine_authz(self, resource: dict) -> str: if hook_result: return hook_result - # check global catch-all fallback + # check global catch-all override if "global_authz" in self.config: return self.config["global_authz"] matches = [] - for rule in self.rules: - match = evaluate(resource, rule["condition"]) - - if match and match[0] is True: - matches.append(rule) + matches = [ + rule + for rule in self.rules + if (result := rule["match"](resource)) and result[0] is True + ] if len(matches) > 1: raise ValueError( From 157eb947a33e5d9574609f516a6d4dea06c53d34 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Thu, 27 Aug 2026 17:01:02 -0500 Subject: [PATCH 24/35] Add check for if output file exists and is not empty for _is_new. --- gen3/fhir.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gen3/fhir.py b/gen3/fhir.py index e576e2e8..65ffb98b 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -266,6 +266,9 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: ): return True + if not pathlib.Path(record["output_file"]).is_file() or pathlib.Path(record["output_file"]).stat().st_size == 0: + return True + return False From d7773f66edf0139c4172d251c1ee99feaacb4e31 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Fri, 28 Aug 2026 12:31:07 -0500 Subject: [PATCH 25/35] Fix poetry dependencies --- poetry.lock | 171 ++++++++++++++++++++++++++++++++++++++----------- pyproject.toml | 15 ++--- 2 files changed, 140 insertions(+), 46 deletions(-) diff --git a/poetry.lock b/poetry.lock index 11ba5535..ffc48b70 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1041,20 +1041,17 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "click" -version = "8.4.2" +version = "8.5.0" description = "Composable command line interface toolkit" optional = false 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platform_python_implementation != \"PyPy\""] + [[package]] name = "six" version = "1.17.0" @@ -3859,7 +3954,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["dev"] -markers = "python_version < \"3.11\"" +markers = "python_version < \"3.15\"" files = [ {file = "tomli-2.4.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:f8f0fc26ec2cc2b965b7a3b87cd19c5c6b8c5e5f436b984e85f486d652285c30"}, {file = "tomli-2.4.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4ab97e64ccda8756376892c53a72bd1f964e519c77236368527f758fbc36a53a"}, @@ -4030,14 +4125,14 @@ watchdog = ["watchdog (>=2.3)"] [[package]] name = "xmltodict" -version = "0.13.0" +version = "0.15.1" description = "Makes working with XML feel like you are working with JSON" optional = false -python-versions = ">=3.4" +python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, - {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"}, + {file = "xmltodict-0.15.1-py2.py3-none-any.whl", hash = "sha256:dcd84b52f30a15be5ac4c9099a0cb234df8758624b035411e329c5c1e7a49089"}, + {file = "xmltodict-0.15.1.tar.gz", hash = "sha256:3d8d49127f3ce6979d40a36dbcad96f8bab106d232d24b49efdd4bd21716983c"}, ] [[package]] @@ -4354,4 +4449,4 @@ fhir = ["fhirclient", "fhirpathpy"] [metadata] lock-version = "2.1" python-versions = ">=3.9, <4" -content-hash = "5427abd980289fe1fa0ff36a96a19679fb7c1bbf0a9df7c7896347a98f0818ea" +content-hash = "c7a5259a1333638085d79398f73cc644325ea65abf924cf4d82b84a286303f5f" diff --git a/pyproject.toml b/pyproject.toml index bdf54bef..d5d3cca8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "gen3" homepage = "https://gen3.org/" -version = "4.28.3" +version = "4.29.0" description = "Gen3 CLI and Python SDK" authors = ["Center for Translational Data Science at the University of Chicago "] license = "Apache-2.0" @@ -20,23 +20,23 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.9, <4" requests = "*" -indexclient = "^2.3.0" +indexclient = ">=2.3.0" drsclient = ">=0.3.0" aiohttp = "*" backoff = "*" -cdislogging = "^1.1.0" +cdislogging = ">=1.1.0" click = "*" importlib_metadata = ">=8,<9" jsonschema = "*" # FIXME updating to >=0.6.0 breaks a few tests dataclasses-json = "<=0.5.9" pypfb = ">=0.6.2" -tqdm = "^4.61.2" +tqdm = ">=4.61.2" humanfriendly ="*" python-dateutil = "*" aiofiles = "*" pandas = ">=1.4.2" -xmltodict = "^0.13.0" +xmltodict = ">=0.13.0" gen3users = "*" # A list of all of the optional dependencies, some of which are included in the @@ -48,13 +48,12 @@ fhirpathpy = { version = "*", optional = true } fhir = ["fhirclient", "fhirpathpy"] [tool.poetry.group.dev.dependencies] -pytest = "^7.0" +pytest = ">=7.0" pytest-cov = "*" requests-mock = "*" cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" } indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" } -deptry = "^0.23.1" -setuptools = "<82" +deptry = ">=0.23.1" [tool.poetry.scripts] gen3 = "gen3.cli.__main__:main" From 82e871009109ca4b8d7a43cdd02f0b3e50d19a25 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Sat, 29 Aug 2026 09:18:36 -0500 Subject: [PATCH 26/35] Remove all parallelization code and make fhir import optional in cli --- gen3/cli/__main__.py | 40 ++++++- gen3/cli/fhir.py | 11 -- gen3/fhir.py | 18 +--- poetry.lock | 244 +++++++++++++++++++++---------------------- 4 files changed, 162 insertions(+), 151 deletions(-) diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 8d071881..50d5af3b 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -15,7 +15,6 @@ import gen3.cli.drs_pull as drs_pull import gen3.cli.users as users import gen3.cli.wrap as wrap -import gen3.cli.fhir as fhir import gen3 from gen3 import logging as sdklogging from gen3.cli import nih @@ -34,7 +33,7 @@ def get(self): return self._cache -@click.group() +@click.group(epilog="FHIR commands require extras. See: poetry install --all-extras") @click.option( "--auth", "auth_config", @@ -146,5 +145,40 @@ def main( main.add_command(nih.nih) main.add_command(users.users) main.add_command(wrap.run) -main.add_command(fhir.fhir) + +#optional fhir subcommand dependent on whether user installed FHIR extras +try: + import gen3.cli.fhir as fhir + main.add_command(fhir.fhir) +except ImportError: + @click.group(name="fhir") + def fhir(): + """Commands for FHIR data processing: transform & cleanup""" + raise click.ClickException("Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras") + + @fhir.command(name="transform", + context_settings={"help_option_names": ["-h", "--help"]}, + help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. + + \b + input_file (str): Input .ndjson file with Bulk FHIR data, MUST be one resource type per file + output_file (str): Output file name, also an .ndjson file + config (str): .yaml file with authorization rules, see docs/howto/fhir.md for more details on formatting + """, + ) + def cli(): + """ + CLI implementation of tag_fhir_resources_with_authz. + """ + + @fhir.command(name="cleanup", + context_settings={"help_option_names": ["-h", "--help"]}, + help="Remove all intermediate files in the tmp folder from previous runs", + ) + def cleanup(): + """ + Remove all intermediate files in the tmp folder from previous runs + """ + main.add_command(fhir) + main() diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index bac12977..c6983439 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -52,15 +52,6 @@ def fhir(): metavar="batch_size", help="batch size for chunking", ) -# @click.option( -# "-w", -# "--workers", -# type=click.IntRange(min=1), -# default=8, -# show_default=True, -# metavar="workers", -# help="number of parallel processes", -# ) @click.option( "--force", is_flag=True, @@ -70,7 +61,6 @@ def cli( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], config: str | os.PathLike[str], - #workers: int, work_dir: str | os.PathLike[str]| None, batch_size: int, force: bool, @@ -84,7 +74,6 @@ def cli( config (str): .yaml file with authorization rules work_dir (str): Working directory to save intermediate files for each run batch_size (int): number of lines per chunk - ###workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ tag_fhir_resources_with_authz(input_file=input_file, output_file=output_file, config=config, batch_size=batch_size, work_dir=work_dir, force=force) diff --git a/gen3/fhir.py b/gen3/fhir.py index 65ffb98b..008ae5d5 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -459,7 +459,6 @@ def tag_fhir_resources_with_authz( config: str | os.PathLike[str], batch_size: int = 10000, work_dir: str | os.PathLike[str] = DEFAULT_WORK_DIR, - #workers: int = 8, force: bool = False, ): """ @@ -473,16 +472,13 @@ def tag_fhir_resources_with_authz( config (str): .yaml file with authorization rules batch_size (int): number of lines per chunk work_dir (str): static work directory where all run directories are stored - ###workers (int): number of parallel processes force (bool): remove all intermediate files for this run before exiting even if it crashes """ start_time = time.time() if batch_size < 1: raise ValueError(f"batch_size must be >= 1, got {batch_size}") - # if workers < 1: - # raise ValueError(f"workers must be >= 1, got {workers}, default is 8") - # check if input and output file are the same + if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") @@ -541,12 +537,7 @@ def tag_fhir_resources_with_authz( # parallelize transform logging.info("Transforming chunks...") start = time.time() - ### FUTURE implement multiprocessing - # with ProcessPoolExecutor(max_workers=workers) as pool: - # for _ in pool.map( - # transform_chunk, chunk_files, repeat(tagger), repeat(output_dir) - # ): - # pass + for chunk in chunk_files: transform_chunk(chunk, tagger, output_dir) @@ -572,9 +563,6 @@ def tag_fhir_resources_with_authz( except Exception as e: logging.error(e) - if force: - shutil.rmtree(output_dir, ignore_errors=True) - else: - logging.error("Run failed; intermediates left in %s", output_dir) + logging.error("Run failed; intermediates left in %s", output_dir) raise diff --git a/poetry.lock b/poetry.lock index ffc48b70..c64658cd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1188,134 +1188,134 @@ toml = 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"sha256:077f0964087883176ff6ab9b074694cae29f8c708273b13ca62c183c6ed716cd"}, ] [package.extras] From 9c42dd75a49c212ca51e0fc1ea7c774f241000a1 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Sat, 29 Aug 2026 09:51:34 -0500 Subject: [PATCH 27/35] Add helper function for tag_fhir_resources_with_authz and fix tmp_root in the unit tests --- gen3/fhir.py | 128 ++++++++++++++++++++--------------- tests/test_fhir_transform.py | 93 +++++++++++++------------ 2 files changed, 119 insertions(+), 102 deletions(-) diff --git a/gen3/fhir.py b/gen3/fhir.py index 008ae5d5..583e7677 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -452,6 +452,76 @@ def merge_chunks( for f in input_files: os.remove(f) +def tag_fhir_resource_pipeline( + input_file: str | os.PathLike[str], + output_file: str | os.PathLike[str], + config: str | os.PathLike[str], + output_dir: str | os.PathLike[str], + record: dict, + batch_size: int = 10000, +): + """ + + Stream-transform Bulk FHIR data to Gen3 compatible data with authorization tagging. + Line by line tagging with batched I/O + + Args: + input_file (str): Input .ndjson file + output_file (str): Output file name + config (str): .yaml file with authorization rules + batch_size (int): number of lines per chunk + output_dir (str): static work directory where all run directories are stored + record (dict): the record/information for the current run (.config.json) + """ + logging.info("Checking status of file") + + # if done, skip + if _is_done(output_dir, record): + return + + # if new file or new config/batch_size, reset folder + if _is_new(output_dir, record): + logging.info("New folder, creating directory and chunking") + if pathlib.Path(output_dir).exists(): + shutil.rmtree(output_dir) + make_folders_for_filename(f"{output_dir}/.config.json") + pathlib.Path(f"{output_dir}/.config.json").write_text( + json.dumps(record, default=str), encoding="utf-8" + ) + # split into chunks + logging.info(f"Chunking {input_file} into {batch_size}-sized batches...") + split_file(input_file, batch_size, output_dir) + + # initialize tagger + tagger = Gen3FHIRAuthzTagger(config_path=config) + # keep only relevant rules for the resource type + resource_type = get_resource_type(input_file) + tagger.relevant_authz_rules(resource_type) + + # if not fully transformed or new/reset, resume + if not _merge_needed(output_dir, record): + # paths for chunk files + chunk_files = glob.glob( + os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.chunk") + ) + + # parallelize transform + logging.info("Transforming chunks...") + start = time.time() + + for chunk in chunk_files: + transform_chunk(chunk, tagger, output_dir) + + logging.info( + f"Transform chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" + ) + + # merge back to one ndjson file + transformed_files = glob.glob( + os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.done") + ) + logging.info(f"Merging chunks to {output_file}...") + merge_chunks(transformed_files, output_file) def tag_fhir_resources_with_authz( input_file: str | os.PathLike[str], @@ -462,9 +532,8 @@ def tag_fhir_resources_with_authz( force: bool = False, ): """ - + End-to-end pipeline for FHIR resource tagging. Stream-transform Bulk FHIR data to Gen3 compatible data with authorization tagging. - Line by line tagging with batched I/O Args: input_file (str): Input .ndjson file @@ -502,62 +571,11 @@ def tag_fhir_resources_with_authz( } try: - logging.info("Checking status of file") - - # if done, skip - if _is_done(output_dir, record): - return - - # if new file or new config/batch_size, reset folder - if _is_new(output_dir, record): - logging.info("New folder, creating directory and chunking") - if pathlib.Path(output_dir).exists(): - shutil.rmtree(output_dir) - make_folders_for_filename(f"{output_dir}/.config.json") - pathlib.Path(f"{output_dir}/.config.json").write_text( - json.dumps(record, default=str), encoding="utf-8" - ) - # split into chunks - logging.info(f"Chunking {input_file} into {batch_size}-sized batches...") - split_file(input_file, batch_size, output_dir) - - # initialize tagger - tagger = Gen3FHIRAuthzTagger(config_path=config) - # keep only relevant rules for the resource type - resource_type = get_resource_type(input_file) - tagger.relevant_authz_rules(resource_type) - - # if not fully transformed or new/reset, resume - if not _merge_needed(output_dir, record): - # paths for chunk files - chunk_files = glob.glob( - os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.chunk") - ) - - # parallelize transform - logging.info("Transforming chunks...") - start = time.time() - - for chunk in chunk_files: - transform_chunk(chunk, tagger, output_dir) - - logging.info( - f"Transform chunks total time: {(time.strftime('%H:%M:%S', time.gmtime(time.time() - start)))}" - ) - - # merge back to one ndjson file - transformed_files = glob.glob( - os.path.join(output_dir, f"{pathlib.Path(input_file).stem}_*.done") - ) - logging.info(f"Merging chunks to {output_file}...") - merge_chunks(transformed_files, output_file) - + tag_fhir_resource_pipeline(input_file = input_file, output_file = output_file, config = config, output_dir = output_dir, record = record, batch_size=batch_size) elapsed_time = time.time() - start_time logging.info(f"Tagged file -> {output_file}") logging.info( - f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}" - ) - + f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}") if force: shutil.rmtree(output_dir, ignore_errors=True) diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 3c1740e0..920d7b93 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -19,12 +19,12 @@ import yaml -TMP_ROOT = pathlib.Path("./tests/test_data/fhir_outputs") -SRC = pathlib.Path("./tests/test_data/test_fhir_Patient.ndjson") -IN = pathlib.Path("./tests/test_data/Patient.ndjson") -OUT = os.path.join(TMP_ROOT, "fhir_output_Patient.ndjson") -CONFIG_SRC = pathlib.Path("./tests/test_data/fhir_config.yaml") -GLOBAL_CONFIG_SRC = pathlib.Path("./tests/test_data/fhir_global_config.yaml") +TMP_ROOT = pathlib.Path(__file__).parent / "test_data" / "fhir_outputs" +SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/test_fhir_Patient.ndjson") +IN = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/Patient.ndjson") +OUT = pathlib.Path(f"{TMP_ROOT}/fhir_output_Patient.ndjson") +CONFIG_SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/fhir_config.yaml") +GLOBAL_CONFIG_SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/fhir_global_config.yaml") TAGGER = Gen3FHIRAuthzTagger(CONFIG_SRC) BATCH_SIZE = 1 BASE_RECORD = { @@ -38,10 +38,9 @@ @pytest.fixture(scope="session") def tmp_root(): - root = pathlib.Path(__file__).parent / "test_data" / "fhir_outputs" - shutil.rmtree(root, ignore_errors=True) - root.mkdir(parents=True) - return root + shutil.rmtree(TMP_ROOT, ignore_errors=True) + TMP_ROOT.mkdir(parents=True) + def mock_state( @@ -103,7 +102,7 @@ def mock_state( return directory, record -def test_fhir_output(tmp_root): +def test_fhir_output(): """Tests that output file matches the input file with the only difference being the tags""" fin = [ json.loads(line) @@ -115,7 +114,7 @@ def test_fhir_output(tmp_root): for line in pathlib.Path(SRC).read_bytes().splitlines() if line.strip() ] - tag_fhir_resources_with_authz(IN, OUT, CONFIG_SRC, BATCH_SIZE, tmp_root, 8) + tag_fhir_resources_with_authz(IN, OUT, CONFIG_SRC, BATCH_SIZE, TMP_ROOT, 8) out = [ json.loads(line) for line in pathlib.Path(OUT).read_bytes().splitlines() @@ -135,10 +134,10 @@ def test_fhir_output(tmp_root): assert src == out, "Output file does not match source file" -def test_chunking(tmp_root): +def test_chunking(): """Tests that number of chunks is correct and the recombined chunks match the input file""" - split_file(IN, BATCH_SIZE, tmp_root) - chunks = list(tmp_root.glob("*.chunk")) + split_file(IN, BATCH_SIZE, TMP_ROOT) + chunks = list(TMP_ROOT.glob("*.chunk")) fin = [ json.loads(line) for line in pathlib.Path(IN).read_bytes().splitlines() @@ -160,13 +159,13 @@ def test_chunking(tmp_root): ), "Recombined chunks do not match the content of the input file" -def test_transform(tmp_root): +def test_transform(): """Asserts transform_chunk creates the same number of .done files as .chunk and no .chunk files remain once transformation is completed""" TAGGER.relevant_authz_rules(os.path.basename(IN).split(".")[0]) - chunks = list(tmp_root.glob("*.chunk")) + chunks = list(TMP_ROOT.glob("*.chunk")) for c in chunks: - transform_chunk(c, TAGGER, tmp_root) - transformed = list(tmp_root.glob("*.done")) + transform_chunk(c, TAGGER, TMP_ROOT) + transformed = list(TMP_ROOT.glob("*.done")) # same number of transformed files as chunk files assert len(transformed) == len( @@ -174,15 +173,15 @@ def test_transform(tmp_root): ), f"Expected same number of transformed .done files as number of .chunk files after transformation completed, found {len(transformed)}" # all .chunk files deleted after transformation completed assert ( - len(list(tmp_root.glob("*.chunk"))) == 0 - ), f"Expected 0 chunks after transformation completed, found {len(list(tmp_root.glob("*.chunk")))}" + len(list(TMP_ROOT.glob("*.chunk"))) == 0 + ), f"Expected 0 chunks after transformation completed, found {len(list(TMP_ROOT.glob("*.chunk")))}" -def test_merge(tmp_root): +def test_merge(): """Asserts that after merge is completed, the output file exists and is not empty, there are no .done files remaining, the length of the output matches the sum of the transformed files and the input file, and the file is not corrupt/formatting is correct """ - transformed = list(tmp_root.glob("*.done")) + transformed = list(TMP_ROOT.glob("*.done")) transformed_sum = sum( len([l for l in pathlib.Path(c).read_bytes().splitlines() if l.strip()]) for c in transformed @@ -206,8 +205,8 @@ def test_merge(tmp_root): assert pathlib.Path(OUT).stat().st_size > 0, "Output file empty" # no leftover .done files after merge completed assert ( - len(list(tmp_root.glob("*.done"))) == 0 - ), f"Expected 0 .done files after transformation completed, found {len(list(tmp_root.glob("*.done")))}" + len(list(TMP_ROOT.glob("*.done"))) == 0 + ), f"Expected 0 .done files after transformation completed, found {len(list(TMP_ROOT.glob("*.done")))}" # output file is the same length as the combined transformed files and the length of the input file assert ( len(fout) == transformed_sum == len(fin) @@ -223,12 +222,12 @@ def test_merge(tmp_root): class Test_is_new: """Tests the logic of the run/directory being marked as new (_is_new(directory, record) returns True)""" - def __init__(self,tmp_root): - self.tmp_path = tmp_root / "test_new" + def __init__(self): + self.tmp_path = TMP_ROOT / "test_new" - def test_is_new_with_missing_directory(self, tmp_root): + def test_is_new_with_missing_directory(self): # directory missing - assert _is_new(tmp_root/ "does_not_exist", BASE_RECORD) is True + assert _is_new(TMP_ROOT/ "does_not_exist", BASE_RECORD) is True def test_is_new_directory_has_no_config_file(self): # no config file @@ -274,8 +273,8 @@ def test_is_new_when_output_filename_changed(self): class Test_is_done: """Tests the logic of the run/directory being marked as done (_is_done(directory, record) returns True)""" - def __init__(self,tmp_root): - self.tmp_path = tmp_root / "test_done" + def __init__(self): + self.tmp_path = TMP_ROOT / "test_done" def test_is_done_with_matching_config_and_empty_output(self): # config matches but output is empty @@ -330,8 +329,8 @@ def test_is_done_with_full_output_and_matching_config(self): class Test_merge_needed: """Tests the logic of the run/directory being marked as merge needed (_merge_needed(directory, record) returns True)""" - def __init__(self,tmp_root): - self.tmp_path = tmp_root / "outputs" / "test_merge" + def __init__(self): + self.tmp_path = TMP_ROOT / "outputs" / "test_merge" def test_merge_needed_when_no_done_files_remaining(self): # no merge on clean directory @@ -356,15 +355,15 @@ def test_merge_needed_when_chunk_and_done_files_remaining( ) assert _merge_needed(directory, record) is False - def test_merge_needed_when_directory_missing(self, tmp_root): + def test_merge_needed_when_directory_missing(self): # no merge when directory missing - assert _merge_needed(tmp_root / "gone", BASE_RECORD) is False + assert _merge_needed(TMP_ROOT / "gone", BASE_RECORD) is False class Test_status: """Tests for overlap in different statuses""" - def __init__(self,tmp_root): - self.tmp_path = tmp_root / "test_status" + def __init__(self): + self.tmp_path = TMP_ROOT / "test_status" def test_fresh_directory(self): # fresh directory @@ -401,10 +400,10 @@ def test_run_complete(self): @pytest.mark.parametrize( "state", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] ) - def test_new_and_done_are_mutually_exclusive(self, state, tmp_root): + def test_new_and_done_are_mutually_exclusive(self, state): # new and done are mutually exclusive directory, record = mock_state( - tmp_root / str(id(state)), config=state, output="full" + TMP_ROOT / str(id(state)), config=state, output="full" ) assert not (_is_new(directory, record) and _is_done(directory, record)) @@ -446,9 +445,9 @@ def test_cli(): @pytest.mark.parametrize("bad", [0, -1, None, "bad"]) -def test_invalid_batch_size_is_rejected(bad, tmp_root): +def test_invalid_batch_size_is_rejected(bad): """Assert invalid batch_size is rejected and raises an error""" - out = tmp_root / "cli_test" / "cli_out.ndjson" + out = TMP_ROOT / "cli_test" / "cli_out.ndjson" args = [ IN, @@ -470,9 +469,9 @@ def test_invalid_batch_size_is_rejected(bad, tmp_root): ).exists(), "Rejected the argument but still wrote output" -def test_missing_input_file_fails_cleanly(tmp_root): +def test_missing_input_file_fails_cleanly(): """Asserts error is raised if missing input file passed as argument""" - out = tmp_root / "cli_test" / "nope.ndjson" + out = TMP_ROOT / "cli_test" / "nope.ndjson" args = [ "nope.ndjson", out, @@ -493,9 +492,9 @@ def test_missing_input_file_fails_cleanly(tmp_root): ).exists(), "Output file written even though invalid input file passed" -def test_output_directory_does_not_exist(tmp_root): +def test_output_directory_does_not_exist(): """Test response if output directory doesn't exists. Directory (and parents) should be created if missing""" - out = tmp_root / "missing_dir" / "out.ndjson" + out = TMP_ROOT / "missing_dir" / "out.ndjson" args = [ IN, out, @@ -514,9 +513,9 @@ def test_output_directory_does_not_exist(tmp_root): assert pathlib.Path(out).exists(), "Process not completed, output file not written" -def test_global_config_overrides_other_rules(tmp_root): +def test_global_config_overrides_other_rules(): """Assert global authorization overrides any other rules""" - out = tmp_root / "global_config" / "out.ndjson" + out = TMP_ROOT / "global_config" / "out.ndjson" args = [ IN, out, From a9a0418fddb3d1f5c460bc1b53da23e045188596 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Mon, 31 Aug 2026 09:02:18 -0500 Subject: [PATCH 28/35] Black formatting --- gen3/cli/__main__.py | 29 ++++++++------ gen3/cli/fhir.py | 14 +++++-- gen3/fhir.py | 75 ++++++++++++++++++++++-------------- tests/test_fhir_transform.py | 33 +++++++++------- 4 files changed, 95 insertions(+), 56 deletions(-) diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 50d5af3b..699a50d6 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -146,19 +146,24 @@ def main( main.add_command(users.users) main.add_command(wrap.run) -#optional fhir subcommand dependent on whether user installed FHIR extras +# optional fhir subcommand dependent on whether user installed FHIR extras try: - import gen3.cli.fhir as fhir + import gen3.cli.fhir as fhir + main.add_command(fhir.fhir) except ImportError: + @click.group(name="fhir") def fhir(): - """Commands for FHIR data processing: transform & cleanup""" - raise click.ClickException("Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras") + """Commands for FHIR data processing: transform & cleanup""" + raise click.ClickException( + "Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras" + ) - @fhir.command(name="transform", - context_settings={"help_option_names": ["-h", "--help"]}, - help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. + @fhir.command( + name="transform", + context_settings={"help_option_names": ["-h", "--help"]}, + help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. \b input_file (str): Input .ndjson file with Bulk FHIR data, MUST be one resource type per file @@ -171,14 +176,16 @@ def cli(): CLI implementation of tag_fhir_resources_with_authz. """ - @fhir.command(name="cleanup", - context_settings={"help_option_names": ["-h", "--help"]}, - help="Remove all intermediate files in the tmp folder from previous runs", + @fhir.command( + name="cleanup", + context_settings={"help_option_names": ["-h", "--help"]}, + help="Remove all intermediate files in the tmp folder from previous runs", ) def cleanup(): """ Remove all intermediate files in the tmp folder from previous runs """ + main.add_command(fhir) - + main() diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index c6983439..b767e8e0 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -6,6 +6,7 @@ logging = get_logger(__name__) + @click.group() def fhir(): """Commands for FHIR data processing""" @@ -35,14 +36,12 @@ def fhir(): type=click.Path(exists=True, dir_okay=False, readable=True), metavar="config", ) - @click.option( "--work_dir", type=click.Path(), metavar="work_dir", help=f"Specify which working directory to clean, if not specified the default ({DEFAULT_WORK_DIR}) will be cleaned. Can also be set as an environment variable: GEN3_FHIR_WORK_DIR", ) - @click.option( "-b", "--batch_size", @@ -61,7 +60,7 @@ def cli( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], config: str | os.PathLike[str], - work_dir: str | os.PathLike[str]| None, + work_dir: str | os.PathLike[str] | None, batch_size: int, force: bool, ): @@ -76,7 +75,14 @@ def cli( batch_size (int): number of lines per chunk force (bool): remove all intermediate files for this run before exiting even if it crashes """ - tag_fhir_resources_with_authz(input_file=input_file, output_file=output_file, config=config, batch_size=batch_size, work_dir=work_dir, force=force) + tag_fhir_resources_with_authz( + input_file=input_file, + output_file=output_file, + config=config, + batch_size=batch_size, + work_dir=work_dir, + force=force, + ) @click.command( diff --git a/gen3/fhir.py b/gen3/fhir.py index 583e7677..202dc649 100644 --- a/gen3/fhir.py +++ b/gen3/fhir.py @@ -59,25 +59,24 @@ def relevant_authz_rules(self, resource_type: str): resource_type (str): the resource type in the .ndjson file """ - self.rules = [] + self.rules = [] for rule in self.config.get("rules", []): - if rule['resource_type'] != resource_type: + if rule["resource_type"] != resource_type: continue try: match = compile(rule["condition"], model=self.model) - match({"resourceType": resource_type}) + match({"resourceType": resource_type}) except Exception as e: raise ValueError( f"invalid FHIRPath for authz {rule.get('authz')!r}: " f"{rule['condition']!r}: {e}" ) from e self.rules.append({**rule, "match": match}) - + if not self.rules: raise ValueError( f"no authz rules configured for resource type {resource_type!r}" ) - def determine_authz(self, resource: dict) -> str: """ @@ -150,21 +149,25 @@ def tag_resource(self, resource: dict, authz: str) -> dict: return resource -def resolve_work_dir(work_dir: str | os.PathLike[str] | None = None, clean: bool = False) -> pathlib.Path: + +def resolve_work_dir( + work_dir: str | os.PathLike[str] | None = None, clean: bool = False +) -> pathlib.Path: root = pathlib.Path( work_dir or os.environ.get("GEN3_FHIR_WORK_DIR") or DEFAULT_WORK_DIR ).expanduser() - + if not clean: root.mkdir(parents=True, exist_ok=True) - # 0o700 makes it only only readable by owner and not everyone else (which is important + # 0o700 makes it only only readable by owner and not everyone else (which is important # for potentially shared machines and potential FHIR PHI) if root.is_dir(): root.chmod(0o700) return root + def json_dumps(obj, default=None) -> bytes: """Compact UTF-8 JSON bytes.""" return json.dumps( @@ -191,28 +194,29 @@ def get_sha256hash(input_file: str | os.PathLike[str]) -> str: digest = hashlib.file_digest(f, "sha256").hexdigest() return digest + def get_resource_type(input_file, sample=5): """ Check resource type within the input .ndjson file by reading the first few and last few lines - + Args: input_file(str): Input ndjson file to be transformed sample(int): number of lines to read - + Returns: resource_type(str): Resource type contained within the ndjson (one per file) - + """ path = pathlib.Path(input_file) size = path.stat().st_size - + with path.open("rb") as f: head = list(islice((ln for ln in f if ln.strip()), sample)) if not head: raise ValueError(f"{path}: file has no records") - #calculate approximate offset from end of file, guards from concatnated files with different resource types + # calculate approximate offset from end of file, guards from concatnated files with different resource types f.seek(max(0, size - max(len(ln) for ln in head) * sample * 2)) # drop [0]: a partial line mid-file, or a line the head already has tail = [ln for ln in f.read().split(b"\n")[1:] if ln.strip()][-sample:] @@ -234,8 +238,10 @@ def get_resource_type(input_file, sample=5): if len(types) == 1: return types.pop() else: - raise ValueError(f"Expected 1 resource type per file, got {len(types)} types: {sorted(types)} in {input_file}.") - + raise ValueError( + f"Expected 1 resource type per file, got {len(types)} types: {sorted(types)} in {input_file}." + ) + def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: """ @@ -250,7 +256,6 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: status (bool): returns whether the directory is new/has to be reset or not """ - if not pathlib.Path(directory).is_dir(): return True @@ -266,9 +271,12 @@ def _is_new(directory: str | os.PathLike[str], record: dict) -> bool: ): return True - if not pathlib.Path(record["output_file"]).is_file() or pathlib.Path(record["output_file"]).stat().st_size == 0: + if ( + not pathlib.Path(record["output_file"]).is_file() + or pathlib.Path(record["output_file"]).stat().st_size == 0 + ): return True - + return False @@ -328,7 +336,9 @@ def _merge_needed(directory: str | os.PathLike[str], record: dict) -> bool: return False -def cleanup_fhir_transform_artifacts(work_dir, dry_run: bool = False, force: bool = False) -> int: +def cleanup_fhir_transform_artifacts( + work_dir, dry_run: bool = False, force: bool = False +) -> int: """ Remove run dirs whose owning process is gone. @@ -452,6 +462,7 @@ def merge_chunks( for f in input_files: os.remove(f) + def tag_fhir_resource_pipeline( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], @@ -474,7 +485,7 @@ def tag_fhir_resource_pipeline( record (dict): the record/information for the current run (.config.json) """ logging.info("Checking status of file") - + # if done, skip if _is_done(output_dir, record): return @@ -523,6 +534,7 @@ def tag_fhir_resource_pipeline( logging.info(f"Merging chunks to {output_file}...") merge_chunks(transformed_files, output_file) + def tag_fhir_resources_with_authz( input_file: str | os.PathLike[str], output_file: str | os.PathLike[str], @@ -543,7 +555,7 @@ def tag_fhir_resources_with_authz( work_dir (str): static work directory where all run directories are stored force (bool): remove all intermediate files for this run before exiting even if it crashes """ - + start_time = time.time() if batch_size < 1: raise ValueError(f"batch_size must be >= 1, got {batch_size}") @@ -551,10 +563,10 @@ def tag_fhir_resources_with_authz( if os.path.realpath(input_file) == os.path.realpath(output_file): raise click.UsageError("input_file and output_file must be different") - #check if input file is empty + # check if input file is empty if pathlib.Path(input_file).stat().st_size == 0: - raise ValueError(f"{input_file}: file is empty") - + raise ValueError(f"{input_file}: file is empty") + # only necessary the first time its run working_dir = resolve_work_dir(work_dir) @@ -571,16 +583,23 @@ def tag_fhir_resources_with_authz( } try: - tag_fhir_resource_pipeline(input_file = input_file, output_file = output_file, config = config, output_dir = output_dir, record = record, batch_size=batch_size) + tag_fhir_resource_pipeline( + input_file=input_file, + output_file=output_file, + config=config, + output_dir=output_dir, + record=record, + batch_size=batch_size, + ) elapsed_time = time.time() - start_time logging.info(f"Tagged file -> {output_file}") logging.info( - f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}") + f"Total time to process: {(time.strftime('%H:%M:%S', time.gmtime(elapsed_time)))}" + ) if force: shutil.rmtree(output_dir, ignore_errors=True) except Exception as e: logging.error(e) logging.error("Run failed; intermediates left in %s", output_dir) - raise - + raise diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 920d7b93..68e9a6dd 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -9,7 +9,7 @@ transform_chunk, merge_chunks, tag_fhir_resources_with_authz, - DEFAULT_WORK_DIR + DEFAULT_WORK_DIR, ) import pathlib import os @@ -18,13 +18,16 @@ import shutil import yaml - TMP_ROOT = pathlib.Path(__file__).parent / "test_data" / "fhir_outputs" -SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/test_fhir_Patient.ndjson") +SRC = pathlib.Path( + f"{pathlib.Path(__file__).parent}/test_data/test_fhir_Patient.ndjson" +) IN = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/Patient.ndjson") OUT = pathlib.Path(f"{TMP_ROOT}/fhir_output_Patient.ndjson") CONFIG_SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/fhir_config.yaml") -GLOBAL_CONFIG_SRC = pathlib.Path(f"{pathlib.Path(__file__).parent}/test_data/fhir_global_config.yaml") +GLOBAL_CONFIG_SRC = pathlib.Path( + f"{pathlib.Path(__file__).parent}/test_data/fhir_global_config.yaml" +) TAGGER = Gen3FHIRAuthzTagger(CONFIG_SRC) BATCH_SIZE = 1 BASE_RECORD = { @@ -40,7 +43,6 @@ def tmp_root(): shutil.rmtree(TMP_ROOT, ignore_errors=True) TMP_ROOT.mkdir(parents=True) - def mock_state( @@ -227,7 +229,7 @@ def __init__(self): def test_is_new_with_missing_directory(self): # directory missing - assert _is_new(TMP_ROOT/ "does_not_exist", BASE_RECORD) is True + assert _is_new(TMP_ROOT / "does_not_exist", BASE_RECORD) is True def test_is_new_directory_has_no_config_file(self): # no config file @@ -326,9 +328,9 @@ def test_is_done_with_full_output_and_matching_config(self): assert _is_done(directory, record) is True - class Test_merge_needed: """Tests the logic of the run/directory being marked as merge needed (_merge_needed(directory, record) returns True)""" + def __init__(self): self.tmp_path = TMP_ROOT / "outputs" / "test_merge" @@ -362,6 +364,7 @@ def test_merge_needed_when_directory_missing(self): class Test_status: """Tests for overlap in different statuses""" + def __init__(self): self.tmp_path = TMP_ROOT / "test_status" @@ -373,16 +376,18 @@ def test_fresh_directory(self): assert _merge_needed(directory, record) is False @pytest.mark.parametrize( - ["chunk_files", "done_files"], [(5, 2), (5, 5), (5, 7), (1, 10)] - ) + ["chunk_files", "done_files"], [(5, 2), (5, 5), (5, 7), (1, 10)] + ) def test_need_to_resume_overlap(self, chunk_files, done_files): - directory, record = mock_state(self.tmp_path, config="match", chunks=chunk_files, done=done_files) + directory, record = mock_state( + self.tmp_path, config="match", chunks=chunk_files, done=done_files + ) assert _is_new(directory, record) is False assert _is_done(directory, record) is False @pytest.mark.parametrize( - "chunks", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] - ) + "chunks", ["match", None, {"config_hash": "x"}, {"batch_size": 1}] + ) def test_merge_needed_overlap(self): # merge needed directory, record = mock_state(self.tmp_path, config="match", chunks=0, done=5) @@ -541,4 +546,6 @@ def test_global_config_overrides_other_rules(): for rec in tagged_file: security = (rec.get("meta")).get("security")[0].get("code") - assert security == config["global_authz"], "File not tagged with global authorization" + assert ( + security == config["global_authz"] + ), "File not tagged with global authorization" From 7b942b00b84ea059e407ddfc561db5f10680e944 Mon Sep 17 00:00:00 2001 From: avantol Date: Mon, 31 Aug 2026 15:13:17 -0500 Subject: [PATCH 29/35] fix(drsclient): remove dep due to out of date sub-deps, implement DRS through API instead --- .secrets.baseline | 12 ++-- gen3/tools/bundle/ingest_manifest.py | 70 ++++++++++++++++++++- poetry.lock | 67 +++----------------- pyproject.toml | 1 - tests/bundle_tests/test_bundle_ingestion.py | 35 ++++++++--- tests/conftest.py | 26 +++----- 6 files changed, 114 insertions(+), 97 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 748400d4..0e8a547f 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -198,35 +198,35 @@ "filename": "tests/bundle_tests/test_bundle_ingestion.py", "hashed_secret": "e1da93616713812cb50e0ac845b1e9e305d949f1", "is_verified": false, - "line_number": 44 + "line_number": 45 }, { "type": "Hex High Entropy String", "filename": "tests/bundle_tests/test_bundle_ingestion.py", "hashed_secret": "47f42f4c34fddab383b817e689dc0fb75af81266", "is_verified": false, - "line_number": 52 + "line_number": 53 }, { "type": "Hex High Entropy String", "filename": "tests/bundle_tests/test_bundle_ingestion.py", "hashed_secret": "300d95dd5d30ab6928ffda6c08c6a129a23e5b39", "is_verified": false, - "line_number": 61 + "line_number": 62 }, { "type": "Hex High Entropy String", "filename": "tests/bundle_tests/test_bundle_ingestion.py", "hashed_secret": "bbe496b7ae06cf635b221afedd43098f4172d7cb", "is_verified": false, - "line_number": 93 + "line_number": 102 }, { "type": "Hex High Entropy String", "filename": "tests/bundle_tests/test_bundle_ingestion.py", "hashed_secret": "968d57fa495dde77707437e3c94f8da2d4074c84", "is_verified": false, - "line_number": 96 + "line_number": 105 } ], "tests/bundle_tests/valid_manifest.csv": [ @@ -656,5 +656,5 @@ } ] }, - "generated_at": "2025-11-07T21:07:45Z" + "generated_at": "2026-08-31T20:13:13Z" } diff --git a/gen3/tools/bundle/ingest_manifest.py b/gen3/tools/bundle/ingest_manifest.py index c798881c..548c8047 100644 --- a/gen3/tools/bundle/ingest_manifest.py +++ b/gen3/tools/bundle/ingest_manifest.py @@ -7,7 +7,8 @@ import traceback import re -from drsclient.client import DrsClient +import requests + from gen3.auth import Gen3Auth from gen3.utils import UUID_FORMAT, SIZE_FORMAT, _verify_format, _standardize_str from gen3.tools.utils import ( @@ -258,6 +259,70 @@ def _write_csv(records, filename="tests/outputs/output_manifest.csv"): return filename +def _create_bundle( + commons_url, + bundles, + name=None, + guid=None, + size=None, + checksums=None, + description=None, + version=None, + aliases=None, + auth=None, + token=None, +): + """ + Create a bundle in indexd. + + Args: + commons_url (str): url of the commons' indexd instance + bundles (list): bundle ids and object guids to include in the bundle + name (str): defaults to the guid if not provided + guid (str): indexd creates one if not provided + size (int): indexd calculates it if not provided + checksums (list): checksums in the form + [{"checksum": "somehash1234", "type": "md5"}]. Indexd calculates an + md5 checksum if not provided + description (str): description of the bundle object + version (str): version of the bundle object + aliases (list): aliases related to the bundle + auth (Gen3Auth or tuple): Gen3Auth or a (username, password) tuple for + indexd basic auth. Takes precedence over `token` + token (str): access token, used only when `auth` is not provided + + Returns: + requests.Response: indexd's response to the bundle creation + """ + data = {"bundles": bundles if bundles is not None else []} + if guid: + data["bundle_id"] = guid + if size: + data["size"] = size + if name: + data["name"] = name + if checksums: + data["checksums"] = checksums + if description: + data["description"] = description + if version: + data["version"] = version + if aliases: + data["aliases"] = aliases + + headers = {"content-type": "application/json"} + if not auth and token: + headers["Authorization"] = "Bearer " + token + + return requests.post( + "{}/bundle".format(commons_url), + data=json.dumps(data), + headers=headers, + auth=auth, + timeout=60, + ) + + def ingest_bundle_manifest( commons_url, manifest_file, @@ -292,7 +357,6 @@ def ingest_bundle_manifest( if not records: return None - drsclient = DrsClient(commons_url, auth=auth, token=token) total = len(records) # Iterate through the records list and post to indexd for start, record in enumerate(records, 1): @@ -303,7 +367,7 @@ def ingest_bundle_manifest( record["bundles"] = _replace_bundle_name_with_guid( record["bundles"], bundle_name_to_guid ) - resp = drsclient.create(**record) + resp = _create_bundle(commons_url, auth=auth, token=token, **record) if resp.status_code != 200: logging.error( diff --git a/poetry.lock b/poetry.lock index c64658cd..25f6bd96 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. [[package]] name = "aiofiles" @@ -380,7 +380,7 @@ version = "4.12.1" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.9" -groups = ["main", "dev"] +groups = ["dev"] markers = "python_version < \"3.11\"" files = [ {file = "anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c"}, @@ -401,7 +401,7 @@ version = "4.14.2" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.10" -groups = ["main", "dev"] +groups = ["dev"] markers = "python_version >= \"3.11\"" files = [ {file = "anyio-4.14.2-py3-none-any.whl", hash = "sha256:9f505dda5ac9f0c8309b5e8bd445a8c2bf7246f3ce950121e45ea15bc41d1494"}, @@ -428,21 +428,6 @@ files = [ {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"}, ] -[[package]] -name = "asyncio" -version = "3.4.3" -description = "reference implementation of PEP 3156" -optional = false -python-versions = "*" -groups = ["main"] -markers = "python_version < \"3.14\"" -files = [ - {file = "asyncio-3.4.3-cp33-none-win32.whl", hash = "sha256:b62c9157d36187eca799c378e572c969f0da87cd5fc42ca372d92cdb06e7e1de"}, - {file = "asyncio-3.4.3-cp33-none-win_amd64.whl", hash = "sha256:c46a87b48213d7464f22d9a497b9eef8c1928b68320a2fa94240f969f6fec08c"}, - {file = "asyncio-3.4.3-py3-none-any.whl", hash = "sha256:c4d18b22701821de07bd6aea8b53d21449ec0ec5680645e5317062ea21817d2d"}, - {file = "asyncio-3.4.3.tar.gz", hash = "sha256:83360ff8bc97980e4ff25c964c7bd3923d333d177aa4f7fb736b019f26c7cb41"}, -] - [[package]] name = "attrs" version = "26.1.0" @@ -1599,49 +1584,13 @@ url = "https://github.com/uc-cdis/dosclient" reference = "1.1.0" resolved_reference = "38c0f1ab42edf3efb1ad6348d7dbdff81b131360" -[[package]] -name = "drsclient" -version = "0.3.2" -description = "GA4GH DRS Client" -optional = false -python-versions = "<4.0,>=3.9" -groups = ["main"] -markers = "python_version < \"3.14\"" -files = [ - {file = "drsclient-0.3.2-py3-none-any.whl", hash = "sha256:e4ba8fe9dc46749ffe6e70956282a0b159e61c5829a134806db8cdf78769c001"}, - {file = "drsclient-0.3.2.tar.gz", hash = "sha256:a3e97362d7dd2fc64ffbf265a11d99dafad7b7e5ef9d0e1fcab8f97f555eb662"}, -] - -[package.dependencies] -asyncio = ">=3.4.3,<4.0.0" -backoff = ">=1.10.0,<2.0.0" -httpx = ">=0.28.1,<1.0.0" -requests = ">=2.23.0,<3.0.0" - -[[package]] -name = "drsclient" -version = "0.4.0" -description = "GA4GH DRS Client" -optional = false -python-versions = "<4,>=3.13" -groups = ["main"] -markers = "python_version >= \"3.14\"" -files = [ - {file = "drsclient-0.4.0-py3-none-any.whl", hash = "sha256:34e5f18b060894cf1402929a84ef96f1c3a80ad07447443dbb575a9324366dff"}, - {file = "drsclient-0.4.0.tar.gz", hash = "sha256:b8fbffbe23fe4e9722f9c511821b7d0c79c8a1ada5a54557e1a0a138894a9422"}, -] - -[package.dependencies] -httpx = ">=0.28.1,<1.0.0" -requests = ">=2.23.0,<3.0.0" - [[package]] name = "exceptiongroup" version = "1.3.1" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" -groups = ["main", "dev"] +groups = ["dev"] markers = "python_version < \"3.11\"" files = [ {file = "exceptiongroup-1.3.1-py3-none-any.whl", hash = "sha256:a7a39a3bd276781e98394987d3a5701d0c4edffb633bb7a5144577f82c773598"}, @@ -2040,7 +1989,7 @@ version = "0.16.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false python-versions = ">=3.8" -groups = ["main", "dev"] +groups = ["dev"] files = [ {file = "h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86"}, {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"}, @@ -2071,7 +2020,7 @@ version = "1.0.9" description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" -groups = ["main", "dev"] +groups = ["dev"] files = [ {file = "httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55"}, {file = "httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8"}, @@ -2093,7 +2042,7 @@ version = "0.28.1" description = "The next generation HTTP client." optional = false python-versions = ">=3.8" -groups = ["main", "dev"] +groups = ["dev"] files = [ {file = "httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad"}, {file = "httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc"}, @@ -4449,4 +4398,4 @@ fhir = ["fhirclient", "fhirpathpy"] [metadata] lock-version = "2.1" python-versions = ">=3.9, <4" -content-hash = "c7a5259a1333638085d79398f73cc644325ea65abf924cf4d82b84a286303f5f" +content-hash = "023bb42c664341112718c84b39f8a2acae75f1b74b1d1a4255547f0a6ae8b890" diff --git a/pyproject.toml b/pyproject.toml index d5d3cca8..b817cadb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,6 @@ classifiers = [ python = ">=3.9, <4" requests = "*" indexclient = ">=2.3.0" -drsclient = ">=0.3.0" aiohttp = "*" backoff = "*" cdislogging = ">=1.1.0" diff --git a/tests/bundle_tests/test_bundle_ingestion.py b/tests/bundle_tests/test_bundle_ingestion.py index 1d63567b..2401cb19 100644 --- a/tests/bundle_tests/test_bundle_ingestion.py +++ b/tests/bundle_tests/test_bundle_ingestion.py @@ -1,7 +1,8 @@ import os import sys from unittest.mock import MagicMock, patch -from drsclient.client import DrsClient + +import requests from gen3.tools.bundle.ingest_manifest import ( _replace_bundle_name_with_guid, @@ -34,7 +35,7 @@ def test_replace_bundle_name_with_guid(): assert list_with_guid == expected_list -def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): +def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_endpoint): """ Test valid manifest """ @@ -75,10 +76,14 @@ def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): # 6 bundles in the manfiest assert len(records) == 6 - resp = drs_client.get("dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933") + resp = requests.get( + "{}/ga4gh/drs/v1/objects/dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933".format( + drs_endpoint + ) + ) assert resp.status_code == 200 - resp1 = drs_client.get_all(endpoint="/bundle") + resp1 = requests.get("{}/bundle".format(drs_endpoint)) assert resp1.status_code == 200 res1 = resp1.json() assert len(res1["records"]) == 6 @@ -86,7 +91,11 @@ def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): for record in res1["records"]: assert record["name"] in ["A", "B", "C", "D", "E", "F"] - resp2 = drs_client.get("dg.xxxx/e366dbca-3c7f-4be6-86e4-c1f8f3e4189d") + resp2 = requests.get( + "{}/ga4gh/drs/v1/objects/dg.xxxx/e366dbca-3c7f-4be6-86e4-c1f8f3e4189d".format( + drs_endpoint + ) + ) rec2 = resp2.json() for checksum in rec2["checksums"]: assert checksum in [ @@ -97,7 +106,11 @@ def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): }, ] - resp3 = drs_client.get("dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933") + resp3 = requests.get( + "{}/ga4gh/drs/v1/objects/dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933".format( + drs_endpoint + ) + ) rec3 = resp3.json() for checksum in rec3["checksums"]: assert checksum in [ @@ -109,7 +122,7 @@ def test_valid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): ] -def test_invalid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): +def test_invalid_ingest_bundle_manifest(gen3_index, indexd_server, drs_endpoint): """ Test invalid manifest """ @@ -149,9 +162,13 @@ def test_invalid_ingest_bundle_manifest(gen3_index, indexd_server, drs_client): assert records == None - resp = drs_client.get("dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933") + resp = requests.get( + "{}/ga4gh/drs/v1/objects/dg.xxxx/590ee63d-2790-477a-bbf8-d53873ca4933".format( + drs_endpoint + ) + ) assert resp.status_code == 404 - resp1 = drs_client.get_all(endpoint="/bundle") + resp1 = requests.get("{}/bundle".format(drs_endpoint)) rec1 = resp1.json() assert len(rec1["records"]) == 0 diff --git a/tests/conftest.py b/tests/conftest.py index f118fe9f..5541e60c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -8,7 +8,6 @@ import pytest import requests -from drsclient.client import DrsClient from cdisutilstest.code.indexd_fixture import ( setup_database, clear_database, @@ -213,26 +212,15 @@ def gen3_query(gen3_auth): @pytest.fixture(scope="function") -def drs_client(indexd_server): +def drs_endpoint(indexd_server): """ - Returns a DrsClient. This will delete any documents, - aliases, or users made by this - client after the test has completed. - Currently the default user is the admin user - Runs once per test. + Returns the base url of an indexd instance with the "user" user created. + This will delete any documents, aliases, or users made against it after the + test has completed. Runs once per test. """ try: - user = create_user("user", "user") + create_user("user", "user") except Exception: - user = ("user", "user") - client = DrsClient(baseurl=indexd_server.baseurl, auth=user) - yield client + pass + yield indexd_server.baseurl clear_database() - - -@pytest.fixture(scope="function") -def drsclient(drs_client): - """ - Mock drsclient - """ - return drs_client From df146ee84a4ed46e9e19d23eb142a13458968c0a Mon Sep 17 00:00:00 2001 From: Dasha Safarian <65255903+dsafarian@users.noreply.github.com> Date: Wed, 2 Sep 2026 17:45:41 -0500 Subject: [PATCH 30/35] Update docs/howto/fhir.md Co-authored-by: Alexander VanTol --- docs/howto/fhir.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md index 6c3e2680..fc36b183 100644 --- a/docs/howto/fhir.md +++ b/docs/howto/fhir.md @@ -1,6 +1,8 @@ ## FHIR -This integration aims to enhance the data ingestion capabilities of Gen3 by integrating a Fast Healthcare Interoperability Resources (FHIR) data ingestion pipeline & tools. FHIR is an important standard for working with Electronic Health Records (EHR) and we have started development of a Gen3 FHIR Proxy service. The overall goal is to allow users to seamlessly ingest data into an existing FHIR server. Gen3 is working on adding support for FHIR and this tool will help with data preparation and interaction in the future. +This integration aims to enhance the data ingestion capabilities of Gen3 by integrating a Fast Healthcare Interoperability Resources (FHIR) data ingestion tools. FHIR is an important standard for working with Electronic Health Records (EHR) and we have started development of a Gen3 FHIR Proxy service. + +Gen3 is working on adding support for FHIR and these tools will help with data preparation. The fhir commands can be invoked as follows From ece2a0a9471f2c84f4ceeb08ff05e2218ec88f77 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 2 Sep 2026 17:56:20 -0500 Subject: [PATCH 31/35] Update fhir.md --- docs/howto/fhir.md | 6 ++++-- gen3/cli/__main__.py | 26 -------------------------- poetry.lock | 10 +++++----- 3 files changed, 9 insertions(+), 33 deletions(-) diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md index 6c3e2680..5022e517 100644 --- a/docs/howto/fhir.md +++ b/docs/howto/fhir.md @@ -1,6 +1,8 @@ ## FHIR -This integration aims to enhance the data ingestion capabilities of Gen3 by integrating a Fast Healthcare Interoperability Resources (FHIR) data ingestion pipeline & tools. FHIR is an important standard for working with Electronic Health Records (EHR) and we have started development of a Gen3 FHIR Proxy service. The overall goal is to allow users to seamlessly ingest data into an existing FHIR server. Gen3 is working on adding support for FHIR and this tool will help with data preparation and interaction in the future. +This integration aims to enhance the data ingestion capabilities of Gen3 by integrating a Fast Healthcare Interoperability Resources (FHIR) data ingestion tools. FHIR is an important standard for working with Electronic Health Records (EHR) and we have started development of a Gen3 FHIR Proxy service. + +Gen3 is working on adding support for FHIR and these tools will help with data preparation. The fhir commands can be invoked as follows @@ -13,7 +15,7 @@ For a list of commands and options run For example, the following tags the 'Patient.ndjson' file with Gen3 authorization and outputs 'gen3_Patient.ndjson' using the authorization rules from 'config.yaml' -`gen3 fhir transform Patient.ndjson gen3_Patient.ndjson config.yaml --batch_size 10000 --workers 8 ` +`gen3 fhir transform Patient.ndjson gen3_Patient.ndjson config.yaml --batch_size 10000` The authorization configuration file has to be in yaml format and can have multiple conditions, e.g: diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 699a50d6..6a851346 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -160,32 +160,6 @@ def fhir(): "Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras" ) - @fhir.command( - name="transform", - context_settings={"help_option_names": ["-h", "--help"]}, - help="""Tag Bulk FHIR data with Gen3 compatible authorization tags. - - \b - input_file (str): Input .ndjson file with Bulk FHIR data, MUST be one resource type per file - output_file (str): Output file name, also an .ndjson file - config (str): .yaml file with authorization rules, see docs/howto/fhir.md for more details on formatting - """, - ) - def cli(): - """ - CLI implementation of tag_fhir_resources_with_authz. - """ - - @fhir.command( - name="cleanup", - context_settings={"help_option_names": ["-h", "--help"]}, - help="Remove all intermediate files in the tmp folder from previous runs", - ) - def cleanup(): - """ - Remove all intermediate files in the tmp folder from previous runs - """ - main.add_command(fhir) main() diff --git a/poetry.lock b/poetry.lock index 25f6bd96..4dd92238 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. [[package]] name = "aiofiles" @@ -397,20 +397,20 @@ trio = ["trio (>=0.31.0) ; python_version < \"3.10\"", "trio (>=0.32.0) ; python [[package]] name = "anyio" -version = "4.14.2" +version = "4.15.0" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.10" groups = ["dev"] markers = "python_version >= \"3.11\"" files = [ - {file = "anyio-4.14.2-py3-none-any.whl", hash = "sha256:9f505dda5ac9f0c8309b5e8bd445a8c2bf7246f3ce950121e45ea15bc41d1494"}, - {file = "anyio-4.14.2.tar.gz", hash = "sha256:cfa139f3ed1a23ee8f88a145ddb5ac7605b8bbfd8592baacd7ce3d8bb4313c7f"}, + {file = "anyio-4.15.0-py3-none-any.whl", hash = "sha256:7ecd9937369ffce8bba0b5ccb9b3a9507b101b0ed50256aecfbab27e6c2acb99"}, + {file = "anyio-4.15.0.tar.gz", hash = "sha256:b5c620ed540725e2579c31b17bb995b3bf02c9281c9cace04c7d186380bab85e"}, ] [package.dependencies] idna = ">=2.8" -typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} +typing_extensions = {version = ">=4.16.0", markers = "python_version < \"3.15\""} [package.extras] trio = ["trio (>=0.32.0)"] From 8b8600636cfa2189ff013f336c0218831bf735b0 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 2 Sep 2026 18:02:35 -0500 Subject: [PATCH 32/35] Update fhir.md --- docs/howto/fhir.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md index 5022e517..698e1d5f 100644 --- a/docs/howto/fhir.md +++ b/docs/howto/fhir.md @@ -28,8 +28,11 @@ rules: #Example with multiple conditions - resource_type: "Specimen" - condition: ""Specimen.status = 'available' and Specimen.Type = 'Blood specimen (specimen)'"" + condition: "Specimen.status = 'available' and Specimen.Type = 'Blood specimen (specimen)'" authz: "/programs/Alpha/projects/Biobank" ``` -And example config.yaml file can be found in [fhir_config.yaml](tests/test_data/fhir_config.yaml) +And example config.yaml file can be found in [fhir_config.yaml](../../tests/test_data/fhir_config.yaml) +To run the fhir transfrom with synthetic test data: + +`poetry run gen3 -vv fhir transform ./tests/test_data/Patient.ndjson ./test_Patient.ndjson ./tests/test_data/fhir_config.yaml` \ No newline at end of file From 50ae4e1a3259994a0518120de0fb7bb6b250192e Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 2 Sep 2026 18:21:18 -0500 Subject: [PATCH 33/35] Fix commands for optional fhir import --- gen3/cli/__main__.py | 11 ++++++----- gen3/cli/fhir.py | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 6a851346..a0fd19ad 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -151,15 +151,16 @@ def main( import gen3.cli.fhir as fhir main.add_command(fhir.fhir) -except ImportError: +except ImportError as e: - @click.group(name="fhir") + @click.group(name="fhir", epilog="Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras") def fhir(): """Commands for FHIR data processing: transform & cleanup""" - raise click.ClickException( - "Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras" - ) + raise main.add_command(fhir) + + + main() diff --git a/gen3/cli/fhir.py b/gen3/cli/fhir.py index b767e8e0..14d9837b 100644 --- a/gen3/cli/fhir.py +++ b/gen3/cli/fhir.py @@ -40,7 +40,7 @@ def fhir(): "--work_dir", type=click.Path(), metavar="work_dir", - help=f"Specify which working directory to clean, if not specified the default ({DEFAULT_WORK_DIR}) will be cleaned. Can also be set as an environment variable: GEN3_FHIR_WORK_DIR", + help=f"Specify which working directory to clean, if not specified the default ({DEFAULT_WORK_DIR}) will be used. Can also be set as an environment variable: GEN3_FHIR_WORK_DIR", ) @click.option( "-b", From d24801591ff3cfa201e9fd874e7c4262f5ad2f68 Mon Sep 17 00:00:00 2001 From: dsafarian Date: Wed, 2 Sep 2026 18:28:54 -0500 Subject: [PATCH 34/35] Fix paths in .config.json for fhir unit test and the pyproject.toml --- poetry.lock | 1201 +++------------------------------- pyproject.toml | 4 +- tests/test_fhir_transform.py | 4 +- 3 files changed, 81 insertions(+), 1128 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4dd92238..c29063bd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -12,19 +12,6 @@ files = [ {file = "aiofiles-25.1.0.tar.gz", hash = "sha256:a8d728f0a29de45dc521f18f07297428d56992a742f0cd2701ba86e44d23d5b2"}, ] -[[package]] -name = "aiohappyeyeballs" -version = "2.6.1" -description = "Happy Eyeballs for asyncio" -optional = false -python-versions = ">=3.9" -groups = ["main"] -markers = "python_version < \"3.11\"" -files = [ - {file = "aiohappyeyeballs-2.6.1-py3-none-any.whl", 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b/pyproject.toml index b817cadb..cdbfe847 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,12 +13,12 @@ classifiers = [ "Intended Audience :: Science/Research", "Intended Audience :: Developers", "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering", ] [tool.poetry.dependencies] -python = ">=3.9, <4" +python = ">=3.10, <4" requests = "*" indexclient = ">=2.3.0" aiohttp = "*" diff --git a/tests/test_fhir_transform.py b/tests/test_fhir_transform.py index 68e9a6dd..9fbdbdda 100644 --- a/tests/test_fhir_transform.py +++ b/tests/test_fhir_transform.py @@ -32,8 +32,8 @@ BATCH_SIZE = 1 BASE_RECORD = { "timestamp": "2026-08-12T21:00:20.677168+00:00", - "input_file": "./tests/test_data/Patient.ndjson", - "output_file": "./tests/test_data/fhir_outputs/status.ndjson", + "input_file": f"{IN}", + "output_file": f"{pathlib.Path(TMP_ROOT)}/status.ndjson", "config_hash": 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Install the 'fhir' extras: poetry install --all-extras") + @click.group( + name="fhir", + epilog="Requires FHIR packages which aren't installed by default. Install the 'fhir' extras: poetry install --all-extras", + ) def fhir(): """Commands for FHIR data processing: transform & cleanup""" raise @@ -161,6 +164,4 @@ def fhir(): main.add_command(fhir) - - main()