From 52f065a93bd804e0d8c1666c451fa9fd9352fea0 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Wed, 13 May 2026 15:20:20 -0400 Subject: [PATCH 01/10] Linting and testing updates --- pyproject.toml | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f9b46c6..54cfbef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,15 @@ dev = [ [tool.mypy] disallow_untyped_calls = true disallow_untyped_defs = true -exclude = ["tests/"] +exclude = ["tests/", "output/"] + +[[tool.mypy.overrides]] +module = [ + "requests", + "timdex_dataset_api", + "timdex_dataset_api.*", +] +ignore_missing_imports = true [tool.pytest.ini_options] log_level = "INFO" @@ -34,6 +42,7 @@ log_level = "INFO" [tool.ruff] target-version = "py313" line-length = 90 +exclude = ["output"] # enumerate all fixed violations show-fixes = true @@ -41,20 +50,26 @@ show-fixes = true [tool.ruff.lint] select = ["ALL", "PT"] ignore = [ - "COM812", - "D107", - "N812", - "PTH", "C90", + "COM812", "D100", - "D101", + "D101", "D102", "D103", - "D104", + "D104", + "D107", + "EM101", + "EM102", + "G004", + "N812", "PLR0912", - "PLR0913", + "PLR0913", "PLR0915", + "PTH", "S321", + "TD002", + "TD003", + "TRY003" ] # allow autofix behavior for specified rules From 069a3209a10f265f7995a87317d9ca06e8160915 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Wed, 13 May 2026 15:27:15 -0400 Subject: [PATCH 02/10] Read DSpace METS from TIMDEX dataset and extract text bistream information Why these changes are being introduced: This harvester is designed to retrieve fulltext for DSpace theses in TIMDEX with the goal of ultimately writing it back to the TIMDEX dataset associated with particular records. As such, we can read records from the TIMDEX dataset to use as the driver of what records this harvester will harvest for. Additionally, the original DSpace METS is present in the TIDMEX dataset and provides information about DSpace item bitstreams, including the TEXT bitstream we aim to harvest. How this addresses that need: A new module `dfh.timdex_dataset` is created with a class `TIMDEXThesesRecords` that is designed to find DSpace theses records in the TIMDEX dataset, optionally filtered by `run_id`, and parse information from those record's source DSpace METS about bitstreams. The final result is an iterator of TIMDEX records + bitstream information we can use to harvest the fulltext from DSpace. The objects will be used by this harvester to a) harvest fulltext from DSpace and b) write the fulltext back to the TIMDEX dataset associated with the right record. Side effects of this change: * None really, nothing yet depends on this. Relevant ticket(s): * https://mitlibraries.atlassian.net/browse/USE-557 --- dfh/timdex_dataset.py | 239 ++++++++++++++++++ tests/conftest.py | 81 ++++++ .../1721.1-139336-missing-text-filegrp.xml | 215 ++++++++++++++++ ...1721.1-139336-text-file-missing-flocat.xml | 223 ++++++++++++++++ ...721.1-139336-text-filegrp-missing-file.xml | 217 ++++++++++++++++ ...1721.1-139336-text-flocat-missing-href.xml | 224 ++++++++++++++++ tests/fixtures/dspace/mets/1721.1-139336.xml | 225 +++++++++++++++++ .../fixtures/timdex/dspace-1721.1-139336.json | 62 +++++ tests/test_dataset.py | 147 +++++++++++ 9 files changed, 1633 insertions(+) create mode 100644 dfh/timdex_dataset.py create mode 100644 tests/fixtures/dspace/mets/1721.1-139336-missing-text-filegrp.xml create mode 100644 tests/fixtures/dspace/mets/1721.1-139336-text-file-missing-flocat.xml create mode 100644 tests/fixtures/dspace/mets/1721.1-139336-text-filegrp-missing-file.xml create mode 100644 tests/fixtures/dspace/mets/1721.1-139336-text-flocat-missing-href.xml create mode 100644 tests/fixtures/dspace/mets/1721.1-139336.xml create mode 100644 tests/fixtures/timdex/dspace-1721.1-139336.json create mode 100644 tests/test_dataset.py diff --git a/dfh/timdex_dataset.py b/dfh/timdex_dataset.py new file mode 100644 index 0000000..bfea1d0 --- /dev/null +++ b/dfh/timdex_dataset.py @@ -0,0 +1,239 @@ +"""TIMDEX DSpace thesis dataset helpers.""" + +import json +import logging +import os +import re +import xml.etree.ElementTree as ET +from collections.abc import Iterator +from typing import ClassVar, TypedDict + +from timdex_dataset_api import TIMDEXDataset + +logger = logging.getLogger(__name__) + + +class MissingTextBitstreamError(Exception): + """Custom exception to raise when fulltext bistream not found in DSpace METS. + + A typical 'good' METS file will contain a 'fileGrp' section that looks roughly like + the following, allowing us to extract a bitstream UUID for the 'TEXT' bitstream via + an embedded URL: + + ... + + + + + + ... + + If we cannot find this bitstream UUID for any reason, this exception is raised. + """ + + +class TextBitstreamInfo(TypedDict): + uuid: str + href: str + size: int | None + checksum: str | None + checksum_type: str | None + mimetype: str | None + + +class TIMDEXThesesRecords: + """Class to retrieve TIMDEX dataset records of DSpace Theses. + + Theses are determined by looking for "Thesis" in transformed_record.content_type. + """ + + NS: ClassVar[dict[str, str]] = { + "mets": "http://www.loc.gov/METS/", + "xlink": "http://www.w3.org/1999/xlink", + "mods": "http://www.loc.gov/mods/v3", + } + UUID_PATTERN: ClassVar[re.Pattern[str]] = re.compile( + r"[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-" + r"[0-9a-fA-F]{4}-[0-9a-fA-F]{12}" + ) + + def __init__( + self, + dataset_location: str | None = None, + run_id: str | None = None, + limit: int | None = None, + ) -> None: + self.run_id = run_id + self.limit = limit + + self.timdex_dataset = self._init_timdex_dataset(dataset_location) + + def _init_timdex_dataset(self, dataset_location: str | None) -> TIMDEXDataset: + """Init TIMDEXDataset and compose to self. + + If dataset_location is not passed, look to env var TIMDEX_DATASET_LOCATION. + """ + dataset_location = dataset_location or os.getenv("TIMDEX_DATASET_LOCATION") + if not dataset_location: + raise ValueError( + "'dataset_location' must be passed on init " + "or env var 'TIMDEX_DATASET_LOCATION' set" + ) + return TIMDEXDataset(dataset_location) + + def record_and_bitstream_metadata_iter( + self, + ) -> Iterator[dict]: + """Yield TIMDEX DSpace thesis records with their fulltext bitstream info.""" + record_count = 0 + error_count = 0 + for record in self.theses_records(): + record_count += 1 + source_record = record["source_record"] + + # extract fulltext bitstream information from original DSpace METS XML + try: + text_bitstream = self.get_text_bitstream_info_from_source_record( + source_record + ) + except MissingTextBitstreamError as exc: + error_count += 1 + logger.debug( + "Error parsing fulltext bitstream information for " + f"'{record['timdex_record_id']}': {exc}" + ) + continue + + # if bitstream information found, yield metadata package about record + + # fulltext bitstream + yield { + "timdex_record_id": record["timdex_record_id"], + "run_id": record["run_id"], + "run_record_offset": record["run_record_offset"], + "run_date": record["run_date"], + "run_timestamp": record["run_timestamp"], + "fulltext_bitstream": text_bitstream, + } + + logger.debug( + f"TIMDEX dataset DSpace theses: processed={record_count} " + f"yielded={record_count - error_count} " + f"missing_fulltext_bitstream={error_count}" + ) + + def theses_records(self) -> Iterator[dict]: + """Yield current DSpace Theses records.""" + return filter(self.is_thesis_record, self.dspace_records()) + + def dspace_records(self) -> Iterator[dict]: + """Yield current DSpace records. + + Optionally filter to a run id and/or limit number of records yielded. + """ + args = { + "run_id": self.run_id, + "limit": self.limit, + } + records = self.timdex_dataset.records.read_dicts_iter( + table="current_records", + source="dspace", + action="index", + **{key: value for key, value in args.items() if value is not None}, + ) + record_count = 0 + for record in records: + record_count += 1 + record["transformed_record"] = json.loads(record["transformed_record"]) + yield record + logger.debug(f"TIMDEX dataset DSpace records: retrieved={record_count}") + + @classmethod + def is_thesis_record(cls, record: dict) -> bool: + """Determines if a TIMDEX dataset record is a DSpace Theses. + + This is determined by looking at the transformed record and looking for 'Thesis' + in the content_type field. + """ + content_type = record["transformed_record"].get("content_type", []) + return isinstance(content_type, list) and "Thesis" in content_type + + def get_text_bitstream_info_from_source_record( + self, source_record: bytes + ) -> TextBitstreamInfo: + """Extract fulltext bitstream information from DSpace source METS XML.""" + mets = self.get_mets_root(source_record) + return self.get_text_bitstream_info_from_mets(mets) + + def get_mets_root(self, source_record: bytes) -> ET.Element: + """Parse METS XML.""" + try: + root = ET.fromstring(source_record) # noqa: S314 + except ET.ParseError as exc: + msg = f"Could not parse source_record XML: {exc}" + raise ValueError(msg) from exc + + if root.tag == "{http://www.loc.gov/METS/}mets": + return root + mets = root.find(".//mets:mets", self.NS) + if mets is None: + msg = "Could not find METS element in source_record" + raise ValueError(msg) + return mets + + def get_text_bitstream_info_from_mets(self, mets: ET.Element) -> TextBitstreamInfo: + """Extract info about 'TEXT' bitstream in METS XML. + + If a 'TEXT' bitstream cannot be found and/or a DSpace bitstream UUID cannot be + found for any reason, raise a custom MissingTextBitstreamError exception. + """ + file_grp = mets.find('.//mets:fileGrp[@USE="TEXT"]', self.NS) + if file_grp is None: + raise MissingTextBitstreamError("Could not find 'TEXT' fileGrp in METS") + + file_el = file_grp.find("mets:file", self.NS) + if file_el is None: + raise MissingTextBitstreamError("Could not find file in METS 'TEXT' fileGrp") + + flocat = file_el.find("mets:FLocat", self.NS) + if flocat is None: + raise MissingTextBitstreamError("Could not find FLocat in METS 'TEXT' file") + + href = flocat.attrib.get( + "{http://www.w3.org/1999/xlink}href" + ) or flocat.attrib.get("href") + if not href: + raise MissingTextBitstreamError("Could not find href for METS 'TEXT' file") + + bitstream_uuid = self.bitstream_uuid_from_href(href) + return { + "uuid": bitstream_uuid, + "href": href, + "size": self.int_or_none(file_el.attrib.get("SIZE")), + "checksum": file_el.attrib.get("CHECKSUM"), + "checksum_type": file_el.attrib.get("CHECKSUMTYPE"), + "mimetype": file_el.attrib.get("MIMETYPE"), + } + + @classmethod + def bitstream_uuid_from_href(cls, href: str) -> str: + """Extract bitstream UUID from bitstream URL. + + Example URL: + https://.../bitstreams/401e42c9-6ec1-45d4-889b-7689bd5be8c7/download + """ + match = cls.UUID_PATTERN.search(href) + if match is None: + msg = f"Could not find bitstream UUID in href: {href}" + raise MissingTextBitstreamError(msg) + return match.group(0) + + @staticmethod + def int_or_none(value: str | None) -> int | None: + return int(value) if value is not None else None diff --git a/tests/conftest.py b/tests/conftest.py index 42c8c64..4ae83c0 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,6 +1,11 @@ +import json +from pathlib import Path + import pytest from click.testing import CliRunner +from dfh.timdex_dataset import TIMDEXThesesRecords + @pytest.fixture(autouse=True) def _test_env(monkeypatch): @@ -11,3 +16,79 @@ def _test_env(monkeypatch): @pytest.fixture def runner(): return CliRunner() + + +@pytest.fixture +def dspace_mets_fixture_dir(): + return Path(__file__).parent / "fixtures" / "dspace" / "mets" + + +@pytest.fixture +def timdex_fixture_dir(): + return Path(__file__).parent / "fixtures" / "timdex" + + +@pytest.fixture +def dspace_mets_source_record(dspace_mets_fixture_dir): + with open(dspace_mets_fixture_dir / "1721.1-139336.xml", "rb") as file: + return file.read() + + +@pytest.fixture +def dspace_mets_missing_text_filegrp_source_record(dspace_mets_fixture_dir): + with open( + dspace_mets_fixture_dir / "1721.1-139336-missing-text-filegrp.xml", + "rb", + ) as file: + return file.read() + + +@pytest.fixture +def dspace_mets_text_filegrp_missing_file_source_record(dspace_mets_fixture_dir): + with open( + dspace_mets_fixture_dir / "1721.1-139336-text-filegrp-missing-file.xml", + "rb", + ) as file: + return file.read() + + +@pytest.fixture +def dspace_mets_text_file_missing_flocat_source_record(dspace_mets_fixture_dir): + with open( + dspace_mets_fixture_dir / "1721.1-139336-text-file-missing-flocat.xml", + "rb", + ) as file: + return file.read() + + +@pytest.fixture +def dspace_mets_text_flocat_missing_href_source_record(dspace_mets_fixture_dir): + with open( + dspace_mets_fixture_dir / "1721.1-139336-text-flocat-missing-href.xml", + "rb", + ) as file: + return file.read() + + +@pytest.fixture +def timdex_dspace_thesis_record(timdex_fixture_dir): + with open(timdex_fixture_dir / "dspace-1721.1-139336.json", "rb") as file: + return json.loads(file.read()) + + +@pytest.fixture +def dspace_mets_text_bitstream_info(): + bitstream_uuid = "07b3dc83-dc11-4c6d-9ba5-771f0bb141d8" + return { + "uuid": bitstream_uuid, + "href": f"https://dspace.mit.edu/bitstreams/{bitstream_uuid}/download", + "size": 110_423, + "checksum": "c6716e0e5ba7b572948dac054633a665", + "checksum_type": "MD5", + "mimetype": "text/plain", + } + + +@pytest.fixture +def timdex_theses_records(tmp_path): + return TIMDEXThesesRecords(dataset_location=str(tmp_path)) diff --git a/tests/fixtures/dspace/mets/1721.1-139336-missing-text-filegrp.xml b/tests/fixtures/dspace/mets/1721.1-139336-missing-text-filegrp.xml new file mode 100644 index 0000000..9edbddd --- /dev/null +++ b/tests/fixtures/dspace/mets/1721.1-139336-missing-text-filegrp.xml @@ -0,0 +1,215 @@ + + +
+ oai:dspace.mit.edu:1721.1/139336 + 2026-02-19T02:13:49Z + com_1721.1_7582 + com_1721.1_7581 + col_1721.1_131023 +
+ + + + + DSpace at My University + + + + + + + + + advisor + + Amarasinghe, Saman P. + + + + author + + Ramirez, Gabriel L. + + + + department + + Massachusetts Institute of Technology. + Department of Electrical Engineering and Computer + Science + + + + + 2022-01-14T15:04:50Z + + + + + 2022-01-14T15:04:50Z + + + + 2021-06 + + + + https://hdl.handle.net/1721.1/139336 + + Static languages like C++ provide deep compiler + support for optimization and analysis, enabling high + performance at the cost of burdening users with a + low-level interface. DSLs, or domain-specific languages, + have traditionally complemented static languages by adding + custom idioms and optimizations in their particular areas. + Unfortunately, however, static languages are increasingly + sidelined in many domains by dynamic languages such as + Python and Ruby, which, despite their flexibility, suffer + from lower performance. In this thesis, we propose Codon, + a framework for implementing high-performance DSLs based + on Python. Whereas previously achieving high-performance + in dynamic languages has been difficult, often requiring + separate compiled libraries, we provide a robust base for + analysis and optimization on a purely Pythonic base, + bridging the gap between dynamic and static languages. By + combining a purpose-built type checker and novel + intermediate representation, Codon enables developers to + create intrinsically performant, modular DSLs with minimal + implementation effort. We validate this approach by + showcasing several Codon DSLs, all of which achieve + sizeable speed-ups over Python and sometimes even C++. We + further show that Codon can be easily used to implement a + variety of analyses and passes. Thus, Codon enables a new + class of DSLs that maintain dynamism and expressiveness, + without compromising performance. + + + + + In Copyright - + Educational Use Permitted Copyright MIT + + + Codon: A Framework for Pythonic + Domain-Specific Languages + + + Thesis + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/bd70af03-74f2-404f-9a33-ff0f70a98f00/download + + + File + + + MD5 + + + 4906a8bec67791859ff7a3deab2edaee + + + 825497 + + + application/pdf + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf + + + + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/07b3dc83-dc11-4c6d-9ba5-771f0bb141d8/download + + + File + + + MD5 + + + c6716e0e5ba7b572948dac054633a665 + + + 110423 + + + text/plain + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf.txt + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/tests/fixtures/dspace/mets/1721.1-139336-text-file-missing-flocat.xml b/tests/fixtures/dspace/mets/1721.1-139336-text-file-missing-flocat.xml new file mode 100644 index 0000000..dd8b518 --- /dev/null +++ b/tests/fixtures/dspace/mets/1721.1-139336-text-file-missing-flocat.xml @@ -0,0 +1,223 @@ + + +
+ oai:dspace.mit.edu:1721.1/139336 + 2026-02-19T02:13:49Z + com_1721.1_7582 + com_1721.1_7581 + col_1721.1_131023 +
+ + + + + DSpace at My University + + + + + + + + + advisor + + Amarasinghe, Saman P. + + + + author + + Ramirez, Gabriel L. + + + + department + + Massachusetts Institute of Technology. + Department of Electrical Engineering and Computer + Science + + + + + 2022-01-14T15:04:50Z + + + + + 2022-01-14T15:04:50Z + + + + 2021-06 + + + + https://hdl.handle.net/1721.1/139336 + + Static languages like C++ provide deep compiler + support for optimization and analysis, enabling high + performance at the cost of burdening users with a + low-level interface. DSLs, or domain-specific languages, + have traditionally complemented static languages by adding + custom idioms and optimizations in their particular areas. + Unfortunately, however, static languages are increasingly + sidelined in many domains by dynamic languages such as + Python and Ruby, which, despite their flexibility, suffer + from lower performance. In this thesis, we propose Codon, + a framework for implementing high-performance DSLs based + on Python. Whereas previously achieving high-performance + in dynamic languages has been difficult, often requiring + separate compiled libraries, we provide a robust base for + analysis and optimization on a purely Pythonic base, + bridging the gap between dynamic and static languages. By + combining a purpose-built type checker and novel + intermediate representation, Codon enables developers to + create intrinsically performant, modular DSLs with minimal + implementation effort. We validate this approach by + showcasing several Codon DSLs, all of which achieve + sizeable speed-ups over Python and sometimes even C++. We + further show that Codon can be easily used to implement a + variety of analyses and passes. Thus, Codon enables a new + class of DSLs that maintain dynamism and expressiveness, + without compromising performance. + + + + + In Copyright - + Educational Use Permitted Copyright MIT + + + Codon: A Framework for Pythonic + Domain-Specific Languages + + + Thesis + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/bd70af03-74f2-404f-9a33-ff0f70a98f00/download + + + File + + + MD5 + + + 4906a8bec67791859ff7a3deab2edaee + + + 825497 + + + application/pdf + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf + + + + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/07b3dc83-dc11-4c6d-9ba5-771f0bb141d8/download + + + File + + + MD5 + + + c6716e0e5ba7b572948dac054633a665 + + + 110423 + + + text/plain + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf.txt + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/tests/fixtures/dspace/mets/1721.1-139336-text-filegrp-missing-file.xml b/tests/fixtures/dspace/mets/1721.1-139336-text-filegrp-missing-file.xml new file mode 100644 index 0000000..c7e1b42 --- /dev/null +++ b/tests/fixtures/dspace/mets/1721.1-139336-text-filegrp-missing-file.xml @@ -0,0 +1,217 @@ + + +
+ oai:dspace.mit.edu:1721.1/139336 + 2026-02-19T02:13:49Z + com_1721.1_7582 + com_1721.1_7581 + col_1721.1_131023 +
+ + + + + DSpace at My University + + + + + + + + + advisor + + Amarasinghe, Saman P. + + + + author + + Ramirez, Gabriel L. + + + + department + + Massachusetts Institute of Technology. + Department of Electrical Engineering and Computer + Science + + + + + 2022-01-14T15:04:50Z + + + + + 2022-01-14T15:04:50Z + + + + 2021-06 + + + + https://hdl.handle.net/1721.1/139336 + + Static languages like C++ provide deep compiler + support for optimization and analysis, enabling high + performance at the cost of burdening users with a + low-level interface. DSLs, or domain-specific languages, + have traditionally complemented static languages by adding + custom idioms and optimizations in their particular areas. + Unfortunately, however, static languages are increasingly + sidelined in many domains by dynamic languages such as + Python and Ruby, which, despite their flexibility, suffer + from lower performance. In this thesis, we propose Codon, + a framework for implementing high-performance DSLs based + on Python. Whereas previously achieving high-performance + in dynamic languages has been difficult, often requiring + separate compiled libraries, we provide a robust base for + analysis and optimization on a purely Pythonic base, + bridging the gap between dynamic and static languages. By + combining a purpose-built type checker and novel + intermediate representation, Codon enables developers to + create intrinsically performant, modular DSLs with minimal + implementation effort. We validate this approach by + showcasing several Codon DSLs, all of which achieve + sizeable speed-ups over Python and sometimes even C++. We + further show that Codon can be easily used to implement a + variety of analyses and passes. Thus, Codon enables a new + class of DSLs that maintain dynamism and expressiveness, + without compromising performance. + + + + + In Copyright - + Educational Use Permitted Copyright MIT + + + Codon: A Framework for Pythonic + Domain-Specific Languages + + + Thesis + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/bd70af03-74f2-404f-9a33-ff0f70a98f00/download + + + File + + + MD5 + + + 4906a8bec67791859ff7a3deab2edaee + + + 825497 + + + application/pdf + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf + + + + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/07b3dc83-dc11-4c6d-9ba5-771f0bb141d8/download + + + File + + + MD5 + + + c6716e0e5ba7b572948dac054633a665 + + + 110423 + + + text/plain + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf.txt + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/tests/fixtures/dspace/mets/1721.1-139336-text-flocat-missing-href.xml b/tests/fixtures/dspace/mets/1721.1-139336-text-flocat-missing-href.xml new file mode 100644 index 0000000..5717644 --- /dev/null +++ b/tests/fixtures/dspace/mets/1721.1-139336-text-flocat-missing-href.xml @@ -0,0 +1,224 @@ + + +
+ oai:dspace.mit.edu:1721.1/139336 + 2026-02-19T02:13:49Z + com_1721.1_7582 + com_1721.1_7581 + col_1721.1_131023 +
+ + + + + DSpace at My University + + + + + + + + + advisor + + Amarasinghe, Saman P. + + + + author + + Ramirez, Gabriel L. + + + + department + + Massachusetts Institute of Technology. + Department of Electrical Engineering and Computer + Science + + + + + 2022-01-14T15:04:50Z + + + + + 2022-01-14T15:04:50Z + + + + 2021-06 + + + + https://hdl.handle.net/1721.1/139336 + + Static languages like C++ provide deep compiler + support for optimization and analysis, enabling high + performance at the cost of burdening users with a + low-level interface. DSLs, or domain-specific languages, + have traditionally complemented static languages by adding + custom idioms and optimizations in their particular areas. + Unfortunately, however, static languages are increasingly + sidelined in many domains by dynamic languages such as + Python and Ruby, which, despite their flexibility, suffer + from lower performance. In this thesis, we propose Codon, + a framework for implementing high-performance DSLs based + on Python. Whereas previously achieving high-performance + in dynamic languages has been difficult, often requiring + separate compiled libraries, we provide a robust base for + analysis and optimization on a purely Pythonic base, + bridging the gap between dynamic and static languages. By + combining a purpose-built type checker and novel + intermediate representation, Codon enables developers to + create intrinsically performant, modular DSLs with minimal + implementation effort. We validate this approach by + showcasing several Codon DSLs, all of which achieve + sizeable speed-ups over Python and sometimes even C++. We + further show that Codon can be easily used to implement a + variety of analyses and passes. Thus, Codon enables a new + class of DSLs that maintain dynamism and expressiveness, + without compromising performance. + + + + + In Copyright - + Educational Use Permitted Copyright MIT + + + Codon: A Framework for Pythonic + Domain-Specific Languages + + + Thesis + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/bd70af03-74f2-404f-9a33-ff0f70a98f00/download + + + File + + + MD5 + + + 4906a8bec67791859ff7a3deab2edaee + + + 825497 + + + application/pdf + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf + + + + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/07b3dc83-dc11-4c6d-9ba5-771f0bb141d8/download + + + File + + + MD5 + + + c6716e0e5ba7b572948dac054633a665 + + + 110423 + + + text/plain + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf.txt + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/tests/fixtures/dspace/mets/1721.1-139336.xml b/tests/fixtures/dspace/mets/1721.1-139336.xml new file mode 100644 index 0000000..f26935b --- /dev/null +++ b/tests/fixtures/dspace/mets/1721.1-139336.xml @@ -0,0 +1,225 @@ + + +
+ oai:dspace.mit.edu:1721.1/139336 + 2026-02-19T02:13:49Z + com_1721.1_7582 + com_1721.1_7581 + col_1721.1_131023 +
+ + + + + DSpace at My University + + + + + + + + + advisor + + Amarasinghe, Saman P. + + + + author + + Ramirez, Gabriel L. + + + + department + + Massachusetts Institute of Technology. + Department of Electrical Engineering and Computer + Science + + + + + 2022-01-14T15:04:50Z + + + + + 2022-01-14T15:04:50Z + + + + 2021-06 + + + + https://hdl.handle.net/1721.1/139336 + + Static languages like C++ provide deep compiler + support for optimization and analysis, enabling high + performance at the cost of burdening users with a + low-level interface. DSLs, or domain-specific languages, + have traditionally complemented static languages by adding + custom idioms and optimizations in their particular areas. + Unfortunately, however, static languages are increasingly + sidelined in many domains by dynamic languages such as + Python and Ruby, which, despite their flexibility, suffer + from lower performance. In this thesis, we propose Codon, + a framework for implementing high-performance DSLs based + on Python. Whereas previously achieving high-performance + in dynamic languages has been difficult, often requiring + separate compiled libraries, we provide a robust base for + analysis and optimization on a purely Pythonic base, + bridging the gap between dynamic and static languages. By + combining a purpose-built type checker and novel + intermediate representation, Codon enables developers to + create intrinsically performant, modular DSLs with minimal + implementation effort. We validate this approach by + showcasing several Codon DSLs, all of which achieve + sizeable speed-ups over Python and sometimes even C++. We + further show that Codon can be easily used to implement a + variety of analyses and passes. Thus, Codon enables a new + class of DSLs that maintain dynamism and expressiveness, + without compromising performance. + + + + + In Copyright - + Educational Use Permitted Copyright MIT + + + Codon: A Framework for Pythonic + Domain-Specific Languages + + + Thesis + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/bd70af03-74f2-404f-9a33-ff0f70a98f00/download + + + File + + + MD5 + + + 4906a8bec67791859ff7a3deab2edaee + + + 825497 + + + application/pdf + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf + + + + + + + + + + + + + + + URL + + + https://dspace.mit.edu/bitstreams/07b3dc83-dc11-4c6d-9ba5-771f0bb141d8/download + + + File + + + MD5 + + + c6716e0e5ba7b572948dac054633a665 + + + 110423 + + + text/plain + + + + + + Ramirez-glram-meng-eecs-2021-thesis.pdf.txt + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + \ No newline at end of file diff --git a/tests/fixtures/timdex/dspace-1721.1-139336.json b/tests/fixtures/timdex/dspace-1721.1-139336.json new file mode 100644 index 0000000..fdf65df --- /dev/null +++ b/tests/fixtures/timdex/dspace-1721.1-139336.json @@ -0,0 +1,62 @@ +{ + "source": "DSpace@MIT", + "source_link": "https://dspace.mit.edu/handle/1721.1/139336", + "timdex_record_id": "dspace:1721.1-139336", + "title": "Codon: A Framework for Pythonic Domain-Specific Languages", + "citation": "Ramirez, Gabriel L. (2021-06): Codon: A Framework for Pythonic Domain-Specific Languages. Thesis. https://dspace.mit.edu/handle/1721.1/139336", + "content_type": [ + "Thesis" + ], + "contributors": [ + { + "value": "Amarasinghe, Saman P.", + "kind": "advisor" + }, + { + "value": "Ramirez, Gabriel L.", + "kind": "author" + }, + { + "value": "Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science", + "kind": "department" + } + ], + "dates": [ + { + "kind": "Publication date", + "value": "2021-06" + } + ], + "file_formats": [ + "application/pdf" + ], + "format": "electronic resource", + "identifiers": [ + { + "value": "https://hdl.handle.net/1721.1/139336", + "kind": "uri" + } + ], + "links": [ + { + "url": "https://hdl.handle.net/1721.1/139336", + "kind": "Digital object URL", + "text": "Digital object URL" + } + ], + "rights": [ + { + "description": "In Copyright - Educational Use Permitted Copyright MIT", + "kind": "useAndReproduction" + } + ], + "summary": [ + "Static languages like C++ provide deep compiler support for optimization and analysis, enabling high performance at the cost of burdening users with a low-level interface. DSLs, or domain-specific languages, have traditionally complemented static languages by adding custom idioms and optimizations in their particular areas. Unfortunately, however, static languages are increasingly sidelined in many domains by dynamic languages such as Python and Ruby, which, despite their flexibility, suffer from lower performance. In this thesis, we propose Codon, a framework for implementing high-performance DSLs based on Python. Whereas previously achieving high-performance in dynamic languages has been difficult, often requiring separate compiled libraries, we provide a robust base for analysis and optimization on a purely Pythonic base, bridging the gap between dynamic and static languages. By combining a purpose-built type checker and novel intermediate representation, Codon enables developers to create intrinsically performant, modular DSLs with minimal implementation effort. We validate this approach by showcasing several Codon DSLs, all of which achieve sizeable speed-ups over Python and sometimes even C++. We further show that Codon can be easily used to implement a variety of analyses and passes. Thus, Codon enables a new class of DSLs that maintain dynamism and expressiveness, without compromising performance." + ], + "timdex_provenance": { + "source": "dspace", + "run_date": "2026-05-13", + "run_id": "5e11f27e-fe05-44f4-8bcb-5acbdb032cf3", + "run_record_offset": 109979 + } +} \ No newline at end of file diff --git a/tests/test_dataset.py b/tests/test_dataset.py new file mode 100644 index 0000000..c64aaa3 --- /dev/null +++ b/tests/test_dataset.py @@ -0,0 +1,147 @@ +# ruff: noqa: D205 + +import json +import re + +import pytest + +from dfh.timdex_dataset import MissingTextBitstreamError, TIMDEXThesesRecords + + +def test_init_requires_dataset_location(monkeypatch): + monkeypatch.delenv("TIMDEX_DATASET_LOCATION", raising=False) + + with pytest.raises(ValueError, match="dataset_location"): + TIMDEXThesesRecords() + + +def test_theses_records_returns_only_records_with_thesis_content_type( + timdex_theses_records, +): + dspace_records = [ + { + "timdex_record_id": "thesis", + "transformed_record": {"content_type": ["Thesis"]}, + }, + { + "timdex_record_id": "book", + "transformed_record": {"content_type": ["Book"]}, + }, + ] + timdex_theses_records.dspace_records = lambda: iter(dspace_records) + + result = list(timdex_theses_records.theses_records()) + + assert result == [dspace_records[0]] + + +def test_record_and_bitstream_metadata_iter_yields_metadata_and_skips_missing_bitstream( + caplog, + monkeypatch, + dspace_mets_source_record, + dspace_mets_missing_text_filegrp_source_record, + timdex_dspace_thesis_record, + timdex_theses_records, + dspace_mets_text_bitstream_info, +): + caplog.set_level("DEBUG") + timdex_record = timdex_dspace_thesis_record + raw_records = [ + { + "timdex_record_id": timdex_record["timdex_record_id"], + "run_id": timdex_record["timdex_provenance"]["run_id"], + "run_record_offset": timdex_record["timdex_provenance"]["run_record_offset"], + "run_date": timdex_record["timdex_provenance"]["run_date"], + "run_timestamp": "2026-05-13T00:00:00Z", + "source_record": dspace_mets_source_record, + "transformed_record": json.dumps(timdex_record), + }, + { + "timdex_record_id": "dspace:missing-text-filegrp", + "run_id": timdex_record["timdex_provenance"]["run_id"], + "run_record_offset": 2, + "run_date": timdex_record["timdex_provenance"]["run_date"], + "run_timestamp": "2026-05-13T00:00:01Z", + "source_record": dspace_mets_missing_text_filegrp_source_record, + "transformed_record": json.dumps(timdex_record), + }, + ] + monkeypatch.setattr( + timdex_theses_records.timdex_dataset.records, + "read_dicts_iter", + lambda **_: iter(raw_records), + ) + + result = list(timdex_theses_records.record_and_bitstream_metadata_iter()) + + assert "TIMDEX dataset DSpace records: retrieved=2" in caplog.text + assert ( + "Error parsing fulltext bitstream information for 'dspace:missing-text-filegrp': " + "Could not find 'TEXT' fileGrp in METS" in caplog.text + ) + assert ( + "TIMDEX dataset DSpace theses: processed=2 yielded=1 " + "missing_fulltext_bitstream=1" in caplog.text + ) + assert result == [ + { + "timdex_record_id": "dspace:1721.1-139336", + "run_id": timdex_record["timdex_provenance"]["run_id"], + "run_record_offset": 109979, + "run_date": "2026-05-13", + "run_timestamp": "2026-05-13T00:00:00Z", + "fulltext_bitstream": dspace_mets_text_bitstream_info, + }, + ] + + +def test_get_text_bitstream_info_from_source_record( + dspace_mets_source_record, + timdex_theses_records, + dspace_mets_text_bitstream_info, +): + result = timdex_theses_records.get_text_bitstream_info_from_source_record( + dspace_mets_source_record, + ) + + assert result == dspace_mets_text_bitstream_info + + +@pytest.mark.parametrize( + ("source_record_fixture", "message"), + [ + pytest.param( + "dspace_mets_missing_text_filegrp_source_record", + "Could not find 'TEXT' fileGrp in METS", + id="missing-text-filegrp", + ), + pytest.param( + "dspace_mets_text_filegrp_missing_file_source_record", + "Could not find file in METS 'TEXT' fileGrp", + id="text-filegrp-missing-file", + ), + pytest.param( + "dspace_mets_text_file_missing_flocat_source_record", + "Could not find FLocat in METS 'TEXT' file", + id="text-file-missing-flocat", + ), + pytest.param( + "dspace_mets_text_flocat_missing_href_source_record", + "Could not find href for METS 'TEXT' file", + id="text-flocat-missing-href", + ), + ], +) +def test_get_text_bitstream_info_from_source_record_raises_error( + source_record_fixture, + message, + request, + timdex_theses_records, +): + """Parameterized test demonstrates that MissingTextBitstreamError is thrown for a + variety of reasons if a TEXT bistream UUID cannot be identified from the DSpace METS. + """ + source_record = request.getfixturevalue(source_record_fixture) + + with pytest.raises(MissingTextBitstreamError, match=re.escape(message)): + timdex_theses_records.get_text_bitstream_info_from_source_record(source_record) From 7a8d4438db596d8ea45fc36a80212c25511d914f Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Wed, 13 May 2026 15:33:17 -0400 Subject: [PATCH 03/10] Add lightweight DSpace 8 / CRIS client Why these changes are being introduced: There is one primary interaction with the DSpace API: generating pre-signed S3 URLs of bitstreams to download. To do so, we'll need to authenticate and send GET and/or POST requests. How this addresses that need: Instead of importing a fully featured DSpace 8 / CRIS client, a slimmed down version is created here that does three things well: 1. authenticates 2. supports generic, authenticated GET/POST requests 3. opinionation for the one currently known API request we'll make, generating pre-signed URLs Side effects of this change: * This departs from other applications like DSC and DSS which use a community DSpace 8 / CRIS API library. It would be very straight-forward to pivot to using that in the future for this application if needed, but it seems heavier than what we need at the moment. Relevant ticket(s): * https://mitlibraries.atlassian.net/browse/USE-557 --- dfh/dspace.py | 145 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 145 insertions(+) create mode 100644 dfh/dspace.py diff --git a/dfh/dspace.py b/dfh/dspace.py new file mode 100644 index 0000000..1724e34 --- /dev/null +++ b/dfh/dspace.py @@ -0,0 +1,145 @@ +import logging +import os + +import requests + +logger = logging.getLogger(__name__) + + +class DSpaceClient: + """Lightweight DSpace 8 / CRIS client.""" + + def __init__( + self, + *, + api_base: str | None = None, + username: str | None = None, + password: str | None = None, + auth_on_init: bool = True, + ) -> None: + self.api_base = (api_base or os.environ["DSPACE_API_BASE"]).rstrip("/") + self.username = username or os.environ["DSPACE_USERNAME"] + self.password = password or os.environ["DSPACE_PASSWORD"] + + self.session = requests.Session() + self._default_headers = {"Content-type": "application/json"} + + # authenticate on init + if auth_on_init: + self.authenticate() + + def _update_xsrf_token(self, response: requests.Response) -> None: + """Extract DSPACE-XSRF-TOKEN from response and store in session.""" + if "DSPACE-XSRF-TOKEN" in response.headers: + token = response.headers["DSPACE-XSRF-TOKEN"] + logger.debug("Updating XSRF token to %s", token) + self.session.headers.update({"X-XSRF-Token": token}) + self.session.cookies.update({"X-XSRF-Token": token}) + + def authenticate(self, *, retry: bool = False) -> bool: + """Authenticate with the DSpace REST API. + + Posts credentials to ``/authn/login``, handles XSRF token refresh on + 403, and stores the bearer token from the ``Authorization`` response + header into the session. + + Returns True on success, False otherwise. + """ + response = self.session.post( + f"{self.api_base}/authn/login", + data={"user": self.username, "password": self.password}, + ) + self._update_xsrf_token(response) + + if response.status_code == 403: # noqa: PLR2004 + if retry: + logger.error( + "Auth failed after CSRF retry: %s %s", + response.status_code, + response.text, + ) + return False + logger.debug("Retrying auth with refreshed CSRF token") + return self.authenticate(retry=True) + + if response.status_code == 401: # noqa: PLR2004 + logger.error( + "Authentication failure: invalid credentials for %s", + self.username, + ) + return False + + # Store bearer token from response headers + if "Authorization" in response.headers: + self.session.headers.update( + {"Authorization": response.headers["Authorization"]} + ) + + # Verify authentication status + status_r = self.session.get( + f"{self.api_base}/authn/status", + headers=self._default_headers, + ) + if status_r.status_code == 200: # noqa: PLR2004 + status_json = status_r.json() + if status_json.get("authenticated") is True: + logger.info("Authenticated successfully as %s", self.username) + return True + + return False + + def info(self) -> dict: + """Return the top-level API response (available links, etc.).""" + r = self.api_get(self.api_base) + r.raise_for_status() + return r.json() + + def api_get( + self, + url: str, + params: dict | None = None, + ) -> requests.Response: + """GET request with automatic XSRF token refresh.""" + r = self.session.get( + url, + params=params, + headers=self._default_headers, + ) + self._update_xsrf_token(r) + return r + + def api_post( + self, + url: str, + json: dict | None = None, + params: dict | None = None, + ) -> requests.Response: + """POST request with automatic XSRF token refresh.""" + r = self.session.post( + url, + json=json, + params=params, + headers=self._default_headers, + ) + self._update_xsrf_token(r) + return r + + def get_presigned_url_for_bitstream(self, bitstream_uuid: str) -> str: + """Generate a pre-signed S3 S3 download URL for a bistream UUID. + + The URL returned is valid for a limited amount of time and a single request. + """ + response = self.api_get( + f"{self.api_base}/core/bitstreams/{bitstream_uuid}/signedurl" + ) + if response.status_code != 200: # noqa: PLR2004 + raise ValueError( + f"Could not get presigned URL for bitstream '{bitstream_uuid}': " + f"{response.status_code} {response.text}" + ) + signed_url = response.json().get("presignedUrl") + if not signed_url: + raise ValueError( + f"Could not find presigned URL for bitstream '{bitstream_uuid}'" + ) + return signed_url From cc2e0cae47c131fb5637a68c5d496938719f0ef0 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 09:16:13 -0400 Subject: [PATCH 04/10] Handle METS XML parsing error and continue --- dfh/exceptions.py | 28 +++++++++++++++++++++++ dfh/timdex_dataset.py | 36 +++++------------------------- tests/test_dataset.py | 52 ++++++++++++++++++++++++++++++++++++++----- 3 files changed, 81 insertions(+), 35 deletions(-) create mode 100644 dfh/exceptions.py diff --git a/dfh/exceptions.py b/dfh/exceptions.py new file mode 100644 index 0000000..3f9d736 --- /dev/null +++ b/dfh/exceptions.py @@ -0,0 +1,28 @@ +class SourceRecordParseError(ValueError): + """Custom exception to raise when source METS XML cannot be parsed.""" + + +class MissingTextBitstreamError(Exception): + """Custom exception to raise when fulltext bistream not found in DSpace METS. + + A typical 'good' METS file will contain a 'fileGrp' section that looks roughly like + the following, allowing us to extract a bitstream UUID for the 'TEXT' bitstream via + an embedded URL: + + ... + + + + + + ... + + If we cannot find this bitstream UUID for any reason, this exception is raised. + """ diff --git a/dfh/timdex_dataset.py b/dfh/timdex_dataset.py index bfea1d0..5e68232 100644 --- a/dfh/timdex_dataset.py +++ b/dfh/timdex_dataset.py @@ -10,33 +10,9 @@ from timdex_dataset_api import TIMDEXDataset -logger = logging.getLogger(__name__) - +from dfh.exceptions import MissingTextBitstreamError, SourceRecordParseError -class MissingTextBitstreamError(Exception): - """Custom exception to raise when fulltext bistream not found in DSpace METS. - - A typical 'good' METS file will contain a 'fileGrp' section that looks roughly like - the following, allowing us to extract a bitstream UUID for the 'TEXT' bitstream via - an embedded URL: - - ... - - - - - - ... - - If we cannot find this bitstream UUID for any reason, this exception is raised. - """ +logger = logging.getLogger(__name__) class TextBitstreamInfo(TypedDict): @@ -103,7 +79,7 @@ def record_and_bitstream_metadata_iter( text_bitstream = self.get_text_bitstream_info_from_source_record( source_record ) - except MissingTextBitstreamError as exc: + except (MissingTextBitstreamError, SourceRecordParseError) as exc: error_count += 1 logger.debug( "Error parsing fulltext bitstream information for " @@ -125,7 +101,7 @@ def record_and_bitstream_metadata_iter( logger.debug( f"TIMDEX dataset DSpace theses: processed={record_count} " f"yielded={record_count - error_count} " - f"missing_fulltext_bitstream={error_count}" + f"fulltext_bitstream_errors={error_count}" ) def theses_records(self) -> Iterator[dict]: @@ -177,14 +153,14 @@ def get_mets_root(self, source_record: bytes) -> ET.Element: root = ET.fromstring(source_record) # noqa: S314 except ET.ParseError as exc: msg = f"Could not parse source_record XML: {exc}" - raise ValueError(msg) from exc + raise SourceRecordParseError(msg) from exc if root.tag == "{http://www.loc.gov/METS/}mets": return root mets = root.find(".//mets:mets", self.NS) if mets is None: msg = "Could not find METS element in source_record" - raise ValueError(msg) + raise SourceRecordParseError(msg) return mets def get_text_bitstream_info_from_mets(self, mets: ET.Element) -> TextBitstreamInfo: diff --git a/tests/test_dataset.py b/tests/test_dataset.py index c64aaa3..a1d8293 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -5,7 +5,11 @@ import pytest -from dfh.timdex_dataset import MissingTextBitstreamError, TIMDEXThesesRecords +from dfh.timdex_dataset import ( + MissingTextBitstreamError, + SourceRecordParseError, + TIMDEXThesesRecords, +) def test_init_requires_dataset_location(monkeypatch): @@ -35,7 +39,7 @@ def test_theses_records_returns_only_records_with_thesis_content_type( assert result == [dspace_records[0]] -def test_record_and_bitstream_metadata_iter_yields_metadata_and_skips_missing_bitstream( +def test_record_and_bitstream_metadata_iter_yields_metadata_and_skips_bitstream_errors( caplog, monkeypatch, dspace_mets_source_record, @@ -65,6 +69,15 @@ def test_record_and_bitstream_metadata_iter_yields_metadata_and_skips_missing_bi "source_record": dspace_mets_missing_text_filegrp_source_record, "transformed_record": json.dumps(timdex_record), }, + { + "timdex_record_id": "dspace:malformed-source-record", + "run_id": timdex_record["timdex_provenance"]["run_id"], + "run_record_offset": 3, + "run_date": timdex_record["timdex_provenance"]["run_date"], + "run_timestamp": "2026-05-13T00:00:02Z", + "source_record": b"", + "transformed_record": json.dumps(timdex_record), + }, ] monkeypatch.setattr( timdex_theses_records.timdex_dataset.records, @@ -74,14 +87,19 @@ def test_record_and_bitstream_metadata_iter_yields_metadata_and_skips_missing_bi result = list(timdex_theses_records.record_and_bitstream_metadata_iter()) - assert "TIMDEX dataset DSpace records: retrieved=2" in caplog.text + assert "TIMDEX dataset DSpace records: retrieved=3" in caplog.text assert ( "Error parsing fulltext bitstream information for 'dspace:missing-text-filegrp': " "Could not find 'TEXT' fileGrp in METS" in caplog.text ) assert ( - "TIMDEX dataset DSpace theses: processed=2 yielded=1 " - "missing_fulltext_bitstream=1" in caplog.text + "Error parsing fulltext bitstream information for " + "'dspace:malformed-source-record': Could not parse source_record XML:" + in caplog.text + ) + assert ( + "TIMDEX dataset DSpace theses: processed=3 yielded=1 " + "fulltext_bitstream_errors=2" in caplog.text ) assert result == [ { @@ -107,6 +125,30 @@ def test_get_text_bitstream_info_from_source_record( assert result == dspace_mets_text_bitstream_info +@pytest.mark.parametrize( + ("source_record", "message"), + [ + pytest.param( + b"", + "Could not parse source_record XML:", + id="malformed-xml", + ), + pytest.param( + b"", + "Could not find METS element in source_record", + id="missing-mets", + ), + ], +) +def test_get_mets_root_raises_source_record_parse_error( + source_record, + message, + timdex_theses_records, +): + with pytest.raises(SourceRecordParseError, match=re.escape(message)): + timdex_theses_records.get_mets_root(source_record) + + @pytest.mark.parametrize( ("source_record_fixture", "message"), [ From 2b970d277246c099a70d9aee30b31b09a515bdff Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 09:20:26 -0400 Subject: [PATCH 05/10] Fix bistream typo --- dfh/dspace.py | 2 +- dfh/exceptions.py | 2 +- tests/test_dataset.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dfh/dspace.py b/dfh/dspace.py index 1724e34..799c606 100644 --- a/dfh/dspace.py +++ b/dfh/dspace.py @@ -125,7 +125,7 @@ def api_post( return r def get_presigned_url_for_bitstream(self, bitstream_uuid: str) -> str: - """Generate a pre-signed S3 S3 download URL for a bistream UUID. + """Generate a pre-signed S3 S3 download URL for a bitstream UUID. The URL returned is valid for a limited amount of time and a single request. """ diff --git a/dfh/exceptions.py b/dfh/exceptions.py index 3f9d736..b9b04a6 100644 --- a/dfh/exceptions.py +++ b/dfh/exceptions.py @@ -3,7 +3,7 @@ class SourceRecordParseError(ValueError): class MissingTextBitstreamError(Exception): - """Custom exception to raise when fulltext bistream not found in DSpace METS. + """Custom exception to raise when fulltext bitstream not found in DSpace METS. A typical 'good' METS file will contain a 'fileGrp' section that looks roughly like the following, allowing us to extract a bitstream UUID for the 'TEXT' bitstream via diff --git a/tests/test_dataset.py b/tests/test_dataset.py index a1d8293..65f327b 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -181,7 +181,7 @@ def test_get_text_bitstream_info_from_source_record_raises_error( timdex_theses_records, ): """Parameterized test demonstrates that MissingTextBitstreamError is thrown for a - variety of reasons if a TEXT bistream UUID cannot be identified from the DSpace METS. + variety of reasons if a TEXT bitstream UUID cannot be identified from the DSpace METS. """ source_record = request.getfixturevalue(source_record_fixture) From daa0e4462133a38d47508d92bbddb9e9255077c1 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 09:22:02 -0400 Subject: [PATCH 06/10] Raise error on DSpaceClient authentication failure --- dfh/dspace.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dfh/dspace.py b/dfh/dspace.py index 799c606..ac01683 100644 --- a/dfh/dspace.py +++ b/dfh/dspace.py @@ -25,8 +25,9 @@ def __init__( self._default_headers = {"Content-type": "application/json"} # authenticate on init - if auth_on_init: - self.authenticate() + if auth_on_init: # noqa: SIM102 + if not self.authenticate(): + raise RuntimeError("Could not authenticate DSpaceClient") def _update_xsrf_token(self, response: requests.Response) -> None: """Extract DSPACE-XSRF-TOKEN from response and store in session.""" From fd09ac69b5ee4efc3cb0f6d35a43d22404fd3ac3 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 09:27:57 -0400 Subject: [PATCH 07/10] Explicit add of requests library --- pyproject.toml | 1 + uv.lock | 2 ++ 2 files changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 54cfbef..7a07079 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,6 +9,7 @@ requires-python = ">=3.13" dependencies = [ "click>=8.2.1", + "requests>=2.33.1", "sentry-sdk>=2.34.1", "timdex-dataset-api", ] diff --git a/uv.lock b/uv.lock index 9330f57..6631e7c 100644 --- a/uv.lock +++ b/uv.lock @@ -335,6 +335,7 @@ version = "2.0.0" source = { editable = "." } dependencies = [ { name = "click" }, + { name = "requests" }, { name = "sentry-sdk" }, { name = "timdex-dataset-api" }, ] @@ -352,6 +353,7 @@ dev = [ [package.metadata] requires-dist = [ { name = "click", specifier = ">=8.2.1" }, + { name = "requests", specifier = ">=2.33.1" }, { name = "sentry-sdk", specifier = ">=2.34.1" }, { name = "timdex-dataset-api", git = "https://github.com/MITLibraries/timdex-dataset-api" }, ] From 7b22d327dc4a9dacf9838dcb230df646b97583aa Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 13:56:12 -0400 Subject: [PATCH 08/10] Spelling and naming updates --- dfh/timdex_dataset.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dfh/timdex_dataset.py b/dfh/timdex_dataset.py index 5e68232..9fa61a2 100644 --- a/dfh/timdex_dataset.py +++ b/dfh/timdex_dataset.py @@ -132,7 +132,7 @@ def dspace_records(self) -> Iterator[dict]: @classmethod def is_thesis_record(cls, record: dict) -> bool: - """Determines if a TIMDEX dataset record is a DSpace Theses. + """Determines if a TIMDEX dataset record is a DSpace Thesis. This is determined by looking at the transformed record and looking for 'Thesis' in the content_type field. @@ -143,7 +143,7 @@ def is_thesis_record(cls, record: dict) -> bool: def get_text_bitstream_info_from_source_record( self, source_record: bytes ) -> TextBitstreamInfo: - """Extract fulltext bitstream information from DSpace source METS XML.""" + """Extract TEXT bitstream information from DSpace source METS XML.""" mets = self.get_mets_root(source_record) return self.get_text_bitstream_info_from_mets(mets) From 6e35ea1b1142d2f155f79a12619ded2803d44780 Mon Sep 17 00:00:00 2001 From: Graham Hukill Date: Thu, 14 May 2026 14:20:46 -0400 Subject: [PATCH 09/10] Pivot to using 3rd party dspace client Why these changes are being introduced: There is a relatively new DSpace 8 / CRIS client `dspace-rest-client`, that we are using in other projects. We would benefit from normalizing to use that here as well. Even though are needs are lightweight here, it handles the authentication well and provides an identical surface to work from (the "lightweight" client here in code was cribbed heavily from it to begin with). How this addresses that need: * Removes custom `DSpaceClient` class * Replaces with two functions: one to get a `DSpaceClient` instance and a second to generate a pre-signed bitstream download URL using that client Side effects of this change: * Take on dependencies of the 3rd party client `dspace-rest-python`, but also benefit from the community improvements to auth, dependency updates, etc. Relevant ticket(s): * https://mitlibraries.atlassian.net/browse/USE-557 --- dfh/dspace.py | 179 ++++----------- pyproject.toml | 3 + uv.lock | 589 +++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 633 insertions(+), 138 deletions(-) diff --git a/dfh/dspace.py b/dfh/dspace.py index ac01683..ff5c683 100644 --- a/dfh/dspace.py +++ b/dfh/dspace.py @@ -1,146 +1,49 @@ import logging import os -import requests +from dspace_rest_client.client import DSpaceClient logger = logging.getLogger(__name__) -class DSpaceClient: - """Lightweight DSpace 8 / CRIS client.""" - - def __init__( - self, - *, - api_base: str | None = None, - username: str | None = None, - password: str | None = None, - auth_on_init: bool = True, - ) -> None: - self.api_base = (api_base or os.environ["DSPACE_API_BASE"]).rstrip("/") - self.username = username or os.environ["DSPACE_USERNAME"] - self.password = password or os.environ["DSPACE_PASSWORD"] - - self.session = requests.Session() - self._default_headers = {"Content-type": "application/json"} - - # authenticate on init - if auth_on_init: # noqa: SIM102 - if not self.authenticate(): - raise RuntimeError("Could not authenticate DSpaceClient") - - def _update_xsrf_token(self, response: requests.Response) -> None: - """Extract DSPACE-XSRF-TOKEN from response and store in session.""" - if "DSPACE-XSRF-TOKEN" in response.headers: - token = response.headers["DSPACE-XSRF-TOKEN"] - logger.debug("Updating XSRF token to %s", token) - self.session.headers.update({"X-XSRF-Token": token}) - self.session.cookies.update({"X-XSRF-Token": token}) - - def authenticate(self, *, retry: bool = False) -> bool: - """Authenticate with the DSpace REST API. - - Posts credentials to ``/authn/login``, handles XSRF token refresh on - 403, and stores the bearer token from the ``Authorization`` response - header into the session. - - Returns True on success, False otherwise. - """ - response = self.session.post( - f"{self.api_base}/authn/login", - data={"user": self.username, "password": self.password}, - ) - self._update_xsrf_token(response) - - if response.status_code == 403: # noqa: PLR2004 - if retry: - logger.error( - "Auth failed after CSRF retry: %s %s", - response.status_code, - response.text, - ) - return False - logger.debug("Retrying auth with refreshed CSRF token") - return self.authenticate(retry=True) - - if response.status_code == 401: # noqa: PLR2004 - logger.error( - "Authentication failure: invalid credentials for %s", - self.username, - ) - return False - - # Store bearer token from response headers - if "Authorization" in response.headers: - self.session.headers.update( - {"Authorization": response.headers["Authorization"]} - ) - - # Verify authentication status - status_r = self.session.get( - f"{self.api_base}/authn/status", - headers=self._default_headers, - ) - if status_r.status_code == 200: # noqa: PLR2004 - status_json = status_r.json() - if status_json.get("authenticated") is True: - logger.info("Authenticated successfully as %s", self.username) - return True - - return False - - def info(self) -> dict: - """Return the top-level API response (available links, etc.).""" - r = self.api_get(self.api_base) - r.raise_for_status() - return r.json() - - def api_get( - self, - url: str, - params: dict | None = None, - ) -> requests.Response: - """GET request with automatic XSRF token refresh.""" - r = self.session.get( - url, - params=params, - headers=self._default_headers, - ) - self._update_xsrf_token(r) - return r - - def api_post( - self, - url: str, - json: dict | None = None, - params: dict | None = None, - ) -> requests.Response: - """POST request with automatic XSRF token refresh.""" - r = self.session.post( - url, - json=json, - params=params, - headers=self._default_headers, - ) - self._update_xsrf_token(r) - return r - - def get_presigned_url_for_bitstream(self, bitstream_uuid: str) -> str: - """Generate a pre-signed S3 S3 download URL for a bitstream UUID. - - The URL returned is valid for a limited amount of time and a single request. - """ - response = self.api_get( - f"{self.api_base}/core/bitstreams/{bitstream_uuid}/signedurl" +def get_dspace_client( + *, + api_base: str | None = None, + username: str | None = None, + password: str | None = None, + auth_on_init: bool = True, +) -> DSpaceClient: + """Instantiate a DSpace API client.""" + client = DSpaceClient( + api_endpoint=(api_base or os.environ["DSPACE_API_BASE"]).rstrip("/"), + username=username or os.environ["DSPACE_USERNAME"], + password=password or os.environ["DSPACE_PASSWORD"], + fake_user_agent=True, + ) + if auth_on_init: # noqa: SIM102 + if not client.authenticate(): + raise RuntimeError("Could not authenticate DSpaceClient") + + return client + + +def get_presigned_url_for_bitstream( + dspace_client: DSpaceClient, + bitstream_uuid: str, +) -> str: + """Generate a pre-signed S3 S3 download URL for a bitstream UUID. + + The URL returned is valid for a limited amount of time and a single request. + """ + response = dspace_client.api_get( + f"{dspace_client.API_ENDPOINT}/core/bitstreams/{bitstream_uuid}/signedurl" + ) + if response.status_code != 200: # noqa: PLR2004 + raise ValueError( + f"Could not get presigned URL for bitstream '{bitstream_uuid}': " + f"{response.status_code} {response.text}" ) - if response.status_code != 200: # noqa: PLR2004 - raise ValueError( - f"Could not get presigned URL for bitstream '{bitstream_uuid}': " - f"{response.status_code} {response.text}" - ) - signed_url = response.json().get("presignedUrl") - if not signed_url: - raise ValueError( - f"Could not find presigned URL for bitstream '{bitstream_uuid}'" - ) - return signed_url + signed_url = response.json().get("presignedUrl") + if not signed_url: + raise ValueError(f"Could not find presigned URL for bitstream '{bitstream_uuid}'") + return signed_url diff --git a/pyproject.toml b/pyproject.toml index 7a07079..8119c51 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,6 +9,7 @@ requires-python = ">=3.13" dependencies = [ "click>=8.2.1", + "dspace-rest-client>=0.1.17", "requests>=2.33.1", "sentry-sdk>=2.34.1", "timdex-dataset-api", @@ -31,6 +32,8 @@ exclude = ["tests/", "output/"] [[tool.mypy.overrides]] module = [ + "dspace_rest_client", + "dspace_rest_client.*", "requests", "timdex_dataset_api", "timdex_dataset_api.*", diff --git a/uv.lock b/uv.lock index 6631e7c..761324c 100644 --- a/uv.lock +++ b/uv.lock @@ -62,6 +62,109 @@ wheels = [ { url = 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