From 8509d0df1bbf14fb115e9289a48b1edc66edb499 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 28 Oct 2024 13:59:18 -0400 Subject: [PATCH 1/7] feat: add mime_type property to DRS object --- chord_drs/constants.py | 10 +++++ ...4b4aaba9e448_add_object_mime_type_field.py | 32 ++++++++++++++++ chord_drs/models.py | 11 ++++++ chord_drs/routes.py | 17 ++++++--- chord_drs/serialization.py | 2 + tests/test_mime.py | 37 +++++++++++++++++++ tests/test_routes.py | 18 +++++++++ 7 files changed, 121 insertions(+), 6 deletions(-) create mode 100644 chord_drs/migrations/versions/4b4aaba9e448_add_object_mime_type_field.py create mode 100644 tests/test_mime.py diff --git a/chord_drs/constants.py b/chord_drs/constants.py index 34091af..c9ce315 100644 --- a/chord_drs/constants.py +++ b/chord_drs/constants.py @@ -1,3 +1,4 @@ +import re from bento_lib.service_info.helpers import build_service_type __all__ = [ @@ -6,6 +7,8 @@ "SERVICE_ARTIFACT", "DRS_SPEC_VERSION", "SERVICE_TYPE", + "RE_INGESTABLE_MIME_TYPE", + "MIME_OCTET_STREAM", ] BENTO_SERVICE_KIND = "drs" @@ -13,3 +16,10 @@ SERVICE_ARTIFACT = BENTO_SERVICE_KIND DRS_SPEC_VERSION = "1.4.0" # update to match whatever version of the DRS spec is implemented. SERVICE_TYPE = build_service_type("org.ga4gh", SERVICE_ARTIFACT, DRS_SPEC_VERSION) + +RE_INGESTABLE_MIME_TYPE = re.compile( + r"^(application|audio|font|image|model|text|video)" + r"/[a-zA-Z0-9+\-._]+" + r"(;\s?[a-zA-Z0-9\-_.]+=\"?[a-zA-Z0-9\-_./+ ]*\"?)?$" +) +MIME_OCTET_STREAM = "application/octet-stream" diff --git a/chord_drs/migrations/versions/4b4aaba9e448_add_object_mime_type_field.py b/chord_drs/migrations/versions/4b4aaba9e448_add_object_mime_type_field.py new file mode 100644 index 0000000..16ee490 --- /dev/null +++ b/chord_drs/migrations/versions/4b4aaba9e448_add_object_mime_type_field.py @@ -0,0 +1,32 @@ +"""add object mime_type field + +Revision ID: 4b4aaba9e448 +Revises: 5e982af5cde4 +Create Date: 2024-10-28 16:27:17.598861 + +""" +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision = '4b4aaba9e448' +down_revision = '5e982af5cde4' +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table('drs_object', schema=None) as batch_op: + batch_op.add_column(sa.Column('mime_type', sa.String(length=128), nullable=True)) + + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table('drs_object', schema=None) as batch_op: + batch_op.drop_column('mime_type') + + # ### end Alembic commands ### diff --git a/chord_drs/models.py b/chord_drs/models.py index edd5a7f..6d2b18b 100644 --- a/chord_drs/models.py +++ b/chord_drs/models.py @@ -11,6 +11,7 @@ from .backend import get_backend from .backends.minio import MinioBackend +from .constants import RE_INGESTABLE_MIME_TYPE from .utils import drs_file_checksum __all__ = [ @@ -34,6 +35,8 @@ class DrsBlob(Base): name = Column(String(250), nullable=True) description = Column(String(1000), nullable=True) + mime_type = Column(String(128), nullable=True) # if null, MIME type has not been set / isn't known + # Permissions/Bento-specific project & dataset tagging for DRS items # TODO: Make some of these not nullable in the future: project_id = Column(String(64), nullable=True) # Nullable for backwards-compatibility @@ -57,6 +60,7 @@ def __init__(self, *args, **kwargs): self.location = object_to_copy.location self.size = object_to_copy.size self.checksum = object_to_copy.checksum + self.mime_type del kwargs["object_to_copy"] else: location = kwargs.get("location") @@ -70,6 +74,13 @@ def __init__(self, *args, **kwargs): self.name = secure_filename(filename or p.name) new_filename = f"{self.id[:12]}-{self.name}" # TODO: use checksum for filename instead + # MIME type, if set, must be a valid ingestable mime type (not a made up supertype and not, e.g., + # multipart/form-data. + mime_type: str | None = kwargs.get("mime_type") + if mime_type is not None and not RE_INGESTABLE_MIME_TYPE.match(mime_type): + raise ValueError("Invalid MIME type") + self.mime_type = mime_type + backend = get_backend() if not backend: diff --git a/chord_drs/routes.py b/chord_drs/routes.py index 7f06296..3fae4f1 100644 --- a/chord_drs/routes.py +++ b/chord_drs/routes.py @@ -26,7 +26,7 @@ from . import __version__ from .authz import authz_middleware from .backend import get_backend -from .constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE +from .constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE, MIME_OCTET_STREAM from .db import db from .models import DrsBlob from .serialization import build_blob_json @@ -34,7 +34,6 @@ RE_STARTING_SLASH = re.compile(r"^/") -MIME_OCTET_STREAM = "application/octet-stream" CHUNK_SIZE = 1024 * 128 # Read 128 KB at a time drs_service = Blueprint("drs_service", __name__) @@ -253,6 +252,7 @@ def object_download(object_id: str): obj_name = drs_object.name minio_obj = drs_object.return_minio_object() + mime_type = drs_object.mime_type or MIME_OCTET_STREAM if not minio_obj: # Check for "Range" HTTP header @@ -260,7 +260,7 @@ def object_download(object_id: str): if range_header is None: # Early return, no range header so send the whole thing - res = make_response(send_file(drs_object.location, mimetype=MIME_OCTET_STREAM, download_name=obj_name)) + res = make_response(send_file(drs_object.location, mimetype=mime_type, download_name=obj_name)) res.headers["Accept-Ranges"] = "bytes" return res @@ -298,8 +298,8 @@ def generate_bytes(): break # Stream the bytes of the file or file segment from the generator function - r = current_app.response_class(generate_bytes(), status=206, mimetype=MIME_OCTET_STREAM) - r.headers["Content-Length"] = end + 1 - start # byte range is inclusive, so need to add one + r = current_app.response_class(generate_bytes(), status=206, mimetype=mime_type) + r.headers["Content-Length"] = str(end + 1 - start) # byte range is inclusive, so need to add one r.headers["Content-Range"] = f"bytes {start}-{end}/{obj_size}" r.headers["Content-Disposition"] = ( f"attachment; filename*=UTF-8'{urllib.parse.quote(obj_name, encoding='utf-8')}'" @@ -309,7 +309,7 @@ def generate_bytes(): # TODO: Support range headers for MinIO objects - only the local backend supports it for now # TODO: kinda greasy, not really sure we want to support such a feature later on response = make_response( - send_file(minio_obj["Body"], mimetype="application/octet-stream", as_attachment=True, download_name=obj_name) + send_file(minio_obj["Body"], mimetype=mime_type, as_attachment=True, download_name=obj_name) ) response.headers["Content-Length"] = minio_obj["ContentLength"] @@ -327,7 +327,9 @@ def object_ingest(): dataset_id: str | None = data.get("dataset_id") or None # " data_type: str | None = data.get("data_type") or None # " public: bool = data.get("public", "false").strip().lower() == "true" + file = request.files.get("file") + mime_type: str | None = data.get("mime_type") or None # replace blank strings with None logger.info(f"Received ingest request metadata: {data}") @@ -409,6 +411,7 @@ def object_ingest(): drs_object = DrsBlob( **(dict(object_to_copy=object_to_copy) if object_to_copy else dict(location=obj_path)), filename=filename, + mime_type=mime_type, project_id=project_id, dataset_id=dataset_id, data_type=data_type, @@ -417,6 +420,8 @@ def object_ingest(): db.session.add(drs_object) db.session.commit() logger.info(f"Added DRS object: {drs_object}") + except ValueError as e: + raise bad_request_log_mark(str(e)) except Exception as e: # TODO: More specific handling authz_middleware.mark_authz_done(request) logger.error(f"Encountered exception during ingest: {e}") diff --git a/chord_drs/serialization.py b/chord_drs/serialization.py index 72401e6..0287890 100644 --- a/chord_drs/serialization.py +++ b/chord_drs/serialization.py @@ -90,6 +90,8 @@ def build_blob_json( "name": drs_blob.name, # Description should be excluded if null in the database **({"description": drs_blob.description} if drs_blob.description is not None else {}), + # MIME type should be excluded if null in the database + **({"mime_type": drs_blob.mime_type} if drs_blob.mime_type is not None else {}), "id": drs_blob.id, "self_uri": create_drs_uri(drs_blob.id), **({"bento": build_bento_object_json(drs_blob)} if with_bento_properties else {}), diff --git a/tests/test_mime.py b/tests/test_mime.py new file mode 100644 index 0000000..8c5c08f --- /dev/null +++ b/tests/test_mime.py @@ -0,0 +1,37 @@ +import pytest + +from chord_drs.constants import RE_INGESTABLE_MIME_TYPE + + +@pytest.mark.parametrize( + "val", + [ + "image/jpeg", + "video/mp4", + "application/octet-stream", + "application/json+test;charset=UTF-8", + 'application/json+test; charset="UTF-8"', + "text/html", + "text/x-fasta", + "text/plain;charset=UTF-8", + 'text/plain; charset="UTF-8"', + ], +) +def test_ingestable_mime_type_pattern(val: str): + assert RE_INGESTABLE_MIME_TYPE.match(val) is not None + + +@pytest.mark.parametrize( + "val", + [ + "image", + "multipart/form-data", + "text/*", + "image/;;;;;;;;", + "image/jpeg;", + 'text/plain charset="UTF-8"', + "invalid/octet-stream", + ], +) +def test_non_ingestable_mime_type_pattern(val: str): + assert RE_INGESTABLE_MIME_TYPE.match(val) is None diff --git a/tests/test_routes.py b/tests/test_routes.py index 3cef002..a9f71b0 100644 --- a/tests/test_routes.py +++ b/tests/test_routes.py @@ -412,6 +412,17 @@ def test_object_ingest_fail_2(client): assert res.status_code == 400 +@pytest.mark.parametrize("mime_type", ["image/*", "invalid/mime", "text/html;"]) +@responses.activate +def test_object_ingest_bad_mime_type(client, mime_type: str): + authz_everything_true() + res = client.post("/ingest", data={"path": dummy_file_path(), "mime_type": mime_type}) + assert res.status_code == 400 + data = res.get_json() + assert data["code"] == 400 + assert data["errors"] == [{"message": "400 Bad Request: Invalid MIME type"}] + + def _ingest_one(client, existing_id=None, params=None): res = client.post("/ingest", data={"path": dummy_file_path(), **(params or {})}) data = res.get_json() @@ -428,6 +439,13 @@ def test_object_ingest(client): _ingest_one(client) +@responses.activate +def test_object_ingest_with_mime(client): + authz_everything_true() + data = _ingest_one(client, params={"mime_type": "text/plain"}) + assert data["mime_type"] == "text/plain" + + @responses.activate def test_object_ingest_dedup(client): authz_everything_true() From a54a326eaf65fcb39017126374b9b1186e777aa6 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 28 Oct 2024 14:04:10 -0400 Subject: [PATCH 2/7] test: optional fields in DRS object response --- tests/test_routes.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tests/test_routes.py b/tests/test_routes.py index a9f71b0..ef8db86 100644 --- a/tests/test_routes.py +++ b/tests/test_routes.py @@ -436,7 +436,10 @@ def _ingest_one(client, existing_id=None, params=None): @responses.activate def test_object_ingest(client): authz_everything_true() - _ingest_one(client) + data = 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"sha256:b6f687ced5510a9a2474bbae96a4352e5ace5fa34dc44a217b0537fec1db00b4"}, ] [package.dependencies] idna = ">=2.0" multidict = ">=4.0" +propcache = ">=0.2.0" [metadata] lock-version = "2.0" diff --git a/pyproject.toml b/pyproject.toml index 998265b..3e978b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "chord-drs" -version = "0.18.0" +version = "0.19.0" description = "An implementation of a data repository system (as per GA4GH's specs) for the Bento platform." authors = ["David Lougheed "] license = "LGPL-3.0" From 7efe232d3aa9a4bc288b1596e0a943af2e0b0bb3 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 29 Oct 2024 10:05:11 -0400 Subject: [PATCH 4/7] chore: comment on MIME type logic --- chord_drs/routes.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/chord_drs/routes.py b/chord_drs/routes.py index 3fae4f1..bf42e26 100644 --- a/chord_drs/routes.py +++ b/chord_drs/routes.py @@ -252,7 +252,10 @@ def object_download(object_id: str): obj_name = drs_object.name minio_obj = drs_object.return_minio_object() - mime_type = drs_object.mime_type or MIME_OCTET_STREAM + + # DRS objects have a nullable mime_type in the database. If mime_type is None, serve the object as a generic + # application/octet-stream. + mime_type: str = drs_object.mime_type or MIME_OCTET_STREAM if not minio_obj: # Check for "Range" HTTP header From 42887bbb03af0ed1002298ea281f6b59d9cfbd4b Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 30 Oct 2024 13:09:28 -0400 Subject: [PATCH 5/7] fix: copy object mime type if ingesting copy-record --- chord_drs/models.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_drs/models.py b/chord_drs/models.py index 6d2b18b..b2d5965 100644 --- a/chord_drs/models.py +++ b/chord_drs/models.py @@ -60,7 +60,7 @@ def __init__(self, *args, **kwargs): self.location = object_to_copy.location self.size = object_to_copy.size self.checksum = object_to_copy.checksum - self.mime_type + self.mime_type = object_to_copy.mime_type del kwargs["object_to_copy"] else: location = kwargs.get("location") From c5c1302a536abfd923c674e5144f814c3bc2175c Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 31 Oct 2024 10:37:08 -0400 Subject: [PATCH 6/7] chore: comment on MIME pattern --- chord_drs/constants.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/chord_drs/constants.py b/chord_drs/constants.py index c9ce315..d8c6bbb 100644 --- a/chord_drs/constants.py +++ b/chord_drs/constants.py @@ -17,6 +17,9 @@ DRS_SPEC_VERSION = "1.4.0" # update to match whatever version of the DRS spec is implemented. SERVICE_TYPE = build_service_type("org.ga4gh", SERVICE_ARTIFACT, DRS_SPEC_VERSION) +# See https://datatracker.ietf.org/doc/html/rfc2045#section-5.1 +# - only allow discrete-type content types +# - allow parameters specifying encoding and whatnot RE_INGESTABLE_MIME_TYPE = re.compile( r"^(application|audio|font|image|model|text|video)" r"/[a-zA-Z0-9+\-._]+" From 402f293ec2ef5dea0f3dad1d9e254d096cf74f19 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 31 Oct 2024 10:41:58 -0400 Subject: [PATCH 7/7] chore: update MIME comment --- chord_drs/constants.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/chord_drs/constants.py b/chord_drs/constants.py index d8c6bbb..c00ca00 100644 --- a/chord_drs/constants.py +++ b/chord_drs/constants.py @@ -18,11 +18,13 @@ SERVICE_TYPE = build_service_type("org.ga4gh", SERVICE_ARTIFACT, DRS_SPEC_VERSION) # See https://datatracker.ietf.org/doc/html/rfc2045#section-5.1 +# and https://datatracker.ietf.org/doc/html/rfc6838#section-4.2 # - only allow discrete-type content types # - allow parameters specifying encoding and whatnot +# - for a list of currently assigned MIME types, see https://www.iana.org/assignments/media-types/media-types.xhtml RE_INGESTABLE_MIME_TYPE = re.compile( r"^(application|audio|font|image|model|text|video)" - r"/[a-zA-Z0-9+\-._]+" + r"/[a-zA-Z0-9][a-zA-Z0-9!#$&^_\-+.]*" r"(;\s?[a-zA-Z0-9\-_.]+=\"?[a-zA-Z0-9\-_./+ ]*\"?)?$" ) MIME_OCTET_STREAM = "application/octet-stream"