diff --git a/.gitignore b/.gitignore index 2b0627bb2..b3b7ed624 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/.secrets.baseline b/.secrets.baseline index 748400d46..0e8a547f7 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/docs/howto/devTest.md b/docs/howto/devTest.md index e4b6a5184..97b4ec7a4 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 -poetry install -vv +eval $(poetry env activate) python3 -m pytest ``` diff --git a/docs/howto/fhir.md b/docs/howto/fhir.md new file mode 100644 index 000000000..6c3e2680d --- /dev/null +++ b/docs/howto/fhir.md @@ -0,0 +1,33 @@ +## 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. + + +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 ` + + +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" + +#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 [fhir_config.yaml](tests/test_data/fhir_config.yaml) diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 995bfda62..699a50d6f 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -33,7 +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", @@ -145,4 +145,47 @@ def main( main.add_command(nih.nih) main.add_command(users.users) main.add_command(wrap.run) + +# 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 new file mode 100644 index 000000000..b767e8e06 --- /dev/null +++ b/gen3/cli/fhir.py @@ -0,0 +1,122 @@ +import click +import os +import pathlib +from cdislogging import get_logger +from gen3.fhir import * + +logging = get_logger(__name__) + + +@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. + + \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 + """, +) +@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( + "--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", + type=click.IntRange(min=1), + default=10000, + show_default=True, + metavar="batch_size", + help="batch size for chunking", +) +@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], + work_dir: str | os.PathLike[str] | None, + batch_size: int, + force: bool, +): + """ + 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 + work_dir (str): Working directory to save intermediate files for each run + 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, + ) + + +@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, + help="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(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(work_dir=work_dir, dry_run=dry_run, force=force) + + +fhir.add_command(cli, name="transform") +fhir.add_command(cleanup, name="cleanup") diff --git a/gen3/fhir.py b/gen3/fhir.py new file mode 100644 index 000000000..202dc649e --- /dev/null +++ b/gen3/fhir.py @@ -0,0 +1,605 @@ +import yaml +from itertools import islice +import json +from fhirpathpy import compile +from fhirpathpy.models import models +import click +import os, glob +import time +from datetime import datetime, timezone +import shutil +import pathlib +import hashlib +from cdislogging import get_logger +from gen3.utils import make_folders_for_filename +from collections.abc import Callable + +logging = get_logger(__name__) +DEFAULT_WORK_DIR = "~/.cache/gen3/fhir_transform" +GEN3_PATH = "http://gen3.org/authz" + + +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 = json.dumps(tagger.tag_resource(record, authz_tags)) #tag resources + + """ + + 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. + + 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): + """ + Filters only the revlevant from the config.yaml file given the resource type. + + Args: + resource_type (str): the resource type in the .ndjson file + + """ + self.rules = [] + for rule in self.config.get("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: + """ + Determines the correct authorization given the resource type and condition + + Args: + resource (dict): the resource dictionary (a line of the .ndjson file) + + Returns: + authz (str): 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 override + if "global_authz" in self.config: + return self.config["global_authz"] + + matches = [] + matches = [ + rule + for rule in self.rules + if (result := rule["match"](resource)) and result[0] is True + ] + + 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"] + + 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 + + Must 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": GEN3_PATH, + "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 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) + if root.is_dir(): + root.chmod(0o700) + + return root + + +def json_dumps(obj, default=None) -> bytes: + """Compact UTF-8 JSON bytes.""" + return json.dumps( + obj, + ensure_ascii=False, + allow_nan=False, + separators=(",", ":"), + default=default, + ).encode("utf-8") + + +def get_sha256hash(input_file: str | os.PathLike[str]) -> str: + """ + 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): SHA-256 hash of the input .ndjson file + + """ + with open(input_file, "rb") as f: + 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: + """ + 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 = json.loads(pathlib.Path(directory, ".config.json").read_bytes()) + except (OSError, ValueError): + 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 + + if ( + not pathlib.Path(record["output_file"]).is_file() + or pathlib.Path(record["output_file"]).stat().st_size == 0 + ): + 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 = json.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 (OSError, ValueError): + 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 _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 + """ + # 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 + return False + + +def cleanup_fhir_transform_artifacts( + work_dir, 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 + """ + 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(working_dir, ignore_errors=True) + return + + count = 0 + for run_dir in sorted(working_dir.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 + + """ + 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)), [])): + 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 = json.loads(r) + # 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) + # delete chunk file once it has been transformed + os.remove(input_file) + + +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() + 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) + 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) + + +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], + output_file: str | os.PathLike[str], + config: str | os.PathLike[str], + batch_size: int = 10000, + work_dir: str | os.PathLike[str] = DEFAULT_WORK_DIR, + force: bool = False, +): + """ + End-to-end pipeline for FHIR resource tagging. + Stream-transform Bulk FHIR data to Gen3 compatible data with authorization tagging. + + 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 + 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}") + + 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) + + # make temp directories + 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_sha256hash(config), + "batch_size": batch_size, + } + + 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, + ) + 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)))}" + ) + 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 diff --git a/gen3/tools/bundle/ingest_manifest.py b/gen3/tools/bundle/ingest_manifest.py index c798881cb..548c80475 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 6fd949415..25f6bd961 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 2.3.1 and should not be changed by hand. 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!= \"PyPy\""] + [extras] -fhir = ["fhirclient"] +fhir = ["fhirclient", "fhirpathpy"] [metadata] lock-version = "2.1" python-versions = ">=3.9, <4" -content-hash = "0ef223739ee0f4e9faf3bf60aa2c6ca6ea2757f7b84023e93c838109379a6915" +content-hash = "023bb42c664341112718c84b39f8a2acae75f1b74b1d1a4255547f0a6ae8b890" diff --git a/pyproject.toml b/pyproject.toml index 85368130d..b817cadb4 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" @@ -20,39 +20,39 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.9, <4" requests = "*" -indexclient = "^2.3.0" -drsclient = ">=0.3.0" +indexclient = ">=2.3.0" 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 # 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" +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" +deptry = ">=0.23.1" [tool.poetry.scripts] gen3 = "gen3.cli.__main__:main" diff --git a/tests/bundle_tests/test_bundle_ingestion.py b/tests/bundle_tests/test_bundle_ingestion.py index 1d63567b6..2401cb194 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 f118fe9f5..5541e60c8 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 diff --git a/tests/test_data/Patient.ndjson b/tests/test_data/Patient.ndjson new file mode 100644 index 000000000..3f7eadee6 --- /dev/null +++ b/tests/test_data/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"]},"text":{"status":"generated","div":"
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Generated by Synthea.Version identifier: 7e08387\n . Person seed: 5520122475053699331 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":"2028-9","display":"Asian"}},{"url":"text","valueString":"Asian"}]},{"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":"Jacqui951 Conn188"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"M"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Lowell","state":"Massachusetts","country":"US"}},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":0.6640544347897612},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":51.33594556521024}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"4c9b6a24-ea39-d103-e4a1-21abd7e413cb"},{"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":"4c9b6a24-ea39-d103-e4a1-21abd7e413cb"},{"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":"999-88-4212"},{"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":"S99972968"},{"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":"X70363534X"}],"name":[{"use":"official","family":"Luettgen772","given":["Israel728","Patrick786"],"prefix":["Mr."]}],"telecom":[{"system":"phone","value":"555-603-5046","use":"home"}],"gender":"male","birthDate":"1973-07-01","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.44676298053978},{"url":"longitude","valueDecimal":-71.28937513726791}]}],"line":["1033 Graham Union Unit 56"],"city":"Waltham","state":"MA","postalCode":"02453","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)"}}]} +{"resourceType":"Patient","id":"95de5a4a-0b9d-b18a-19b5-bc98974d3e88","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: -7647575843159559798 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":"2135-2","display":"Hispanic or Latino"}},{"url":"text","valueString":"Hispanic or Latino"}]},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Tien590 Crooks415"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"M"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Winchendon","state":"Massachusetts","country":"US"}},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":3.7791781556879984},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":48.220821844312}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"95de5a4a-0b9d-b18a-19b5-bc98974d3e88"},{"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":"95de5a4a-0b9d-b18a-19b5-bc98974d3e88"},{"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":"999-87-6031"},{"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":"S99918757"},{"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":"X69735301X"}],"name":[{"use":"official","family":"Block661","given":["Merle11","Carrol931"],"prefix":["Mr."],"suffix":["JD"]}],"telecom":[{"system":"phone","value":"555-309-5953","use":"home"}],"gender":"male","birthDate":"1973-12-07","address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.37751970005985},{"url":"longitude","valueDecimal":-71.06290523992102}]}],"line":["190 Yost Ville Apt 65"],"city":"Somerville","state":"MA","postalCode":"02144","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)"}}]} +{"resourceType":"Patient","id":"e7ee36cb-00cf-5c4c-b80e-877c7489052c","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: -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 000000000..7742f5170 --- /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 new file mode 100644 index 000000000..24a0fc3ce --- /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: "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_data/fhir_global_config.yaml b/tests/test_data/fhir_global_config.yaml new file mode 100644 index 000000000..e7893f06f --- /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_data/test_fhir_Patient.ndjson b/tests/test_data/test_fhir_Patient.ndjson new file mode 100644 index 000000000..f055fe935 --- /dev/null +++ b/tests/test_data/test_fhir_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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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_text(json.dumps(params), encoding="utf-8") + 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""" + fin = [ + json.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] + src = [ + json.loads(line) + 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) + out = [ + json.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(fin) == len( + out + ), "Length of the output file does not match the length of the input file" + 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"} 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(): + """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 = [ + json.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 = [ + json.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 = [ + json.loads(line) + for line in pathlib.Path(IN).read_bytes().splitlines() + if line.strip() + ] + fout = [ + json.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}" + json.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)""" + + def __init__(self): + self.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)""" + + 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 + 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_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" + + 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""" + + def __init__(self): + self.tmp_path = TMP_ROOT / "test_status" + + def test_fresh_directory(self): + # fresh directory + directory, record = mock_state(self.tmp_path, config=None) + assert _is_new(directory, record) is True + assert _is_done(directory, record) is False + assert _merge_needed(directory, record) is False + + @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 + + @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 _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 _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 = [ + IN, + OUT, + 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, "CLI run failed" + assert pathlib.Path(OUT).exists(), "CLI exited 0 but wrote no output file" + records = [ + json.loads(line) + for line in pathlib.Path(OUT).read_bytes().splitlines() + if line.strip() + ] + in_records = [ + json.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 = [ + IN, + out, + CONFIG_SRC, + "--batch_size", + str(bad), + ] + result = subprocess.run( + ["gen3", "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 = [ + "nope.ndjson", + out, + 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, "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 = [ + IN, + out, + 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, "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(): + """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"