From 820282b3a0a52e03cfbf0f0998cd41596198ad49 Mon Sep 17 00:00:00 2001 From: YueWang Date: Wed, 3 Dec 2025 14:00:09 -0800 Subject: [PATCH 1/2] uniprot refactor Remove .DS_Store from tests directory Fixing path problems that were preventing module import Removing `tests/` directory from under `tests` UniRef updates lint First steps towards using external IDs for CDM entities organize uniprot.py revise uniprot.py and test_uniprot.py format: apply ruff formatting to uniprot parser change the format format Regenerate uv.lock Uniprot branch file movements Fix formatting / tests / docs update uniref and test uniref reformat uniprot and uniref update uniprot.py and test any data files used by the test should go in test/data formatting uniprot.py Fix UniRef parsing tests and stabilize timestamp handling Remove large uniprot archaea test data directory style: apply Ruff formatting to uniprot-refactor-v2 --- pyproject.toml | 1 + .../parsers/gene_association_file.py | 2 +- .../parsers/shared_identifiers.py | 11 + src/cdm_data_loader_utils/parsers/uniprot.py | 1088 +++++++++------- src/cdm_data_loader_utils/parsers/uniref.py | 436 ++++--- .../parsers/xml_utils.py | 124 ++ tests/parsers/test_shared_identifiers.py | 34 + tests/parsers/test_uniprot.py | 1153 ++++++++--------- tests/parsers/test_uniref.py | 444 ++++--- tests/parsers/test_xml_utils.py | 49 + uv.lock | 384 +++++- 11 files changed, 2321 insertions(+), 1405 deletions(-) create mode 100644 src/cdm_data_loader_utils/parsers/shared_identifiers.py create mode 100644 src/cdm_data_loader_utils/parsers/xml_utils.py create mode 100644 tests/parsers/test_shared_identifiers.py create mode 100644 tests/parsers/test_xml_utils.py diff --git a/pyproject.toml b/pyproject.toml index 11f2ab8..6211954 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -149,6 +149,7 @@ ignore = [ "tests/**/*.py" = ["S101", "T201"] # use of assert "**/__init__.py" = ["D104"] + [tool.ruff.lint.mccabe] # Flag errors (`C901`) whenever the complexity level exceeds 15. max-complexity = 15 diff --git a/src/cdm_data_loader_utils/parsers/gene_association_file.py b/src/cdm_data_loader_utils/parsers/gene_association_file.py index 548de56..cd81647 100644 --- a/src/cdm_data_loader_utils/parsers/gene_association_file.py +++ b/src/cdm_data_loader_utils/parsers/gene_association_file.py @@ -273,7 +273,7 @@ def run( if register: register_table(spark, output_path, table_name=table_name, permanent=permanent) - except Exception as e: + except Exception: logger.exception("Pipeline failed") sys.exit(1) finally: diff --git a/src/cdm_data_loader_utils/parsers/shared_identifiers.py b/src/cdm_data_loader_utils/parsers/shared_identifiers.py new file mode 100644 index 0000000..33b865f --- /dev/null +++ b/src/cdm_data_loader_utils/parsers/shared_identifiers.py @@ -0,0 +1,11 @@ +from cdm_data_loader_utils.parsers.xml_utils import get_text + + +def parse_identifiers_generic(entry, xpath, prefix, ns): + result = [] + for node in entry.findall(xpath, ns): + text = get_text(node) + if not text: + continue + result.append({"identifier": f"{prefix}:{text}", "source": prefix, "description": f"{prefix} accession"}) + return result diff --git a/src/cdm_data_loader_utils/parsers/uniprot.py b/src/cdm_data_loader_utils/parsers/uniprot.py index fa6d6a4..ca4516e 100644 --- a/src/cdm_data_loader_utils/parsers/uniprot.py +++ b/src/cdm_data_loader_utils/parsers/uniprot.py @@ -1,28 +1,37 @@ """ -UniProt XML Delta Lake Ingestion Pipeline. +UniProt XML Delta Lake Ingestion Pipeline ========================================= This script parses UniProt XML (.xml.gz) file and ingests the data into structured Delta Lake tables. Typical usage: -------------- +Use it in Berdle as: python3 src/parsers/uniprot.py \ --xml-url "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_archaea.xml.gz" \ --output-dir "./output" \ --namespace "uniprot_db" \ --batch-size 5000 + +python -m cdm_data_loader_utils.parsers.uniprot \ + --xml-url "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_archaea.xml.gz" \ + --output-dir "tests/data/uniprot_archaea" \ + --namespace "uniprot_db" \ + --batch-size 5000 + + Arguments: ---------- ---xml-url: URL to the UniProt XML .gz file +--xml-url: URL to the UniProt XML .gz file --output-dir: Output directory for Delta tables and logs (default: './output') --namespace: Delta Lake database name (default: 'uniprot_db') ---target-date: Process entries modified/updated since specific date +--target-date: Process entries modified/updated since specific date --batch-size: Number of UniProt entries to process per write batch (default: 5000) Functionality: -------------- -- Downloads the XML file if not present locally +- Downloads the XML file if not present locally - Parses UniProt entries in a memory-efficient streaming fashion - Maps parsed data into standardized CDM tables - Writes all tables as Delta Lake tables, supporting incremental import @@ -38,6 +47,7 @@ import datetime import gzip import json +import logging import os import uuid import xml.etree.ElementTree as ET @@ -46,49 +56,61 @@ import requests from delta import configure_spark_with_delta_pip from pyspark.sql import SparkSession +from pyspark.sql.functions import col, split from pyspark.sql.types import ArrayType, StringType, StructField, StructType -## XML namespace mapping for UniProt entries (used for all XPath queries) -NS = {"u": "https://uniprot.org/uniprot"} +from cdm_data_loader_utils.parsers.shared_identifiers import parse_identifiers_generic +from cdm_data_loader_utils.parsers.xml_utils import clean_dict, find_all_text, get_attr, get_text, parse_db_references +# --------------------------------------------------------------------- +# Logging +# --------------------------------------------------------------------- +logger = logging.getLogger(__name__) +logging.basicConfig( + level=logging.INFO, + format="%(asctime)s | %(levelname)s | %(name)s | %(message)s", +) -def load_existing_identifiers(spark, output_dir, namespace): - """ - Load the existing 'identifiers' Delta table and build a mapping from UniProt accession to CDM entity ID. - This function enables consistent mapping of accessions to CDM IDs across multiple imports, supporting upsert and idempotent workflows. - Returns: - dict: {accession: entity_id} - """ - access_to_cdm_id = {} - id_path = os.path.abspath(os.path.join(output_dir, f"{namespace}_identifiers_delta")) - if os.path.exists(id_path): - try: - # Read identifier and entity_id columns from the Delta table - df = spark.read.format("delta").load(id_path).select("identifier", "entity_id") - for row in df.collect(): - # Identifier field: UniProt:Pxxxxx, extract the actual accession part after the colon - accession = row["identifier"].split(":", 1)[1] - access_to_cdm_id[accession] = row["entity_id"] - except Exception as e: - print(f"Couldn't load identifiers table: {e}") - else: - print(f"No previous identifiers delta at {id_path}.") - return access_to_cdm_id +# --------------------------------------------------------------------- +# XML namespace mapping for UniProt entries (used for all XPath queries) +# --------------------------------------------------------------------- +NS = {"ns": "https://uniprot.org/uniprot"} -def generate_cdm_id() -> str: - """ - Generate a CDM entity_id directly from UniProt accession, using 'CDM:' prefix - Ensures that each accession is mapped to stable and unique CDM entity ID, making it easy to join across different tables by accession. - """ - return f"CDM:{uuid.uuid4()}" +# --------------------------------------------------------------------- +# Stable ID namespace (UUIDv5) +# --------------------------------------------------------------------- +CDM_UUID_NAMESPACE = uuid.UUID("2d3f6e2a-4d7b-4a8c-9c5a-0e0f7b7d9b3a") -def build_datasource_record(xml_url): - """ - Build a provenance record for the UniProt datasource without version extraction. - """ +# --------------------------------------------------------------------- +# CURIE prefixes +# --------------------------------------------------------------------- +PREFIX_TRANSLATION: dict[str, str] = { + "UniProtKB": "UniProt", + "UniProtKB/Swiss-Prot": "UniProt", + "UniProtKB/TrEMBL": "UniProt", + "UniParc": "UniParc", + "RefSeq": "RefSeq", + "EMBL": "EMBL", + "PDB": "PDB", + "ChEBI": "ChEBI", + "Rhea": "Rhea", + "NCBI Taxonomy": "NCBITaxon", + "GeneID": "NCBIGene", + "Ensembl": "Ensembl", + "GO": "GO", +} + + +# ================================ HELPERS ================================= +def delta_table_path(output_dir: str, namespace: str, table: str) -> str: + return os.path.abspath(os.path.join(output_dir, namespace, table)) + + +def build_datasource_record(xml_url: str) -> dict: + """Build a provenance record for the UniProt datasource.""" return { "name": "UniProt import", "source": "UniProt", @@ -98,162 +120,323 @@ def build_datasource_record(xml_url): } -def parse_identifiers(entry, cdm_id): - """ - Extract all accession numbers in the UniProt entry and format them into a CDM identifier structure. - """ - return [ - { - "entity_id": cdm_id, - "identifier": f"UniProt:{acc.text}", - "source": "UniProt", - "description": "UniProt accession", - } - for acc in entry.findall("u:accession", NS) - ] +def save_datasource_record(xml_url: str, output_dir: str) -> dict: + """Generate and save the datasource provenance record as a JSON file.""" + datasource = build_datasource_record(xml_url) + + os.makedirs(output_dir, exist_ok=True) + output_path = os.path.join(output_dir, "datasource.json") + + with open(output_path, "w", encoding="utf-8") as f: + json.dump(datasource, f, indent=2) + + logger.info("Saved datasource record to %s", output_path) + return datasource + + +def download_file( + url: str, + output_path: str, + chunk_size: int = 1024 * 1024, + overwrite: bool = False, +) -> None: + """Download URL -> output_path (streaming)""" + if os.path.exists(output_path) and not overwrite: + logger.info("File already exists, skip download: %s", output_path) + return + + tmp_path = output_path + ".part" + if os.path.exists(tmp_path): + try: + os.remove(tmp_path) + except Exception: + pass + + try: + logger.info("Downloading %s -> %s", url, output_path) + with requests.get(url, stream=True, timeout=120) as r: + r.raise_for_status() + with open(tmp_path, "wb") as f: + for chunk in r.iter_content(chunk_size=chunk_size): + if chunk: + f.write(chunk) + os.replace(tmp_path, output_path) + logger.info("Download complete: %s", output_path) + except Exception: + logger.exception("Failed to download %s", url) + try: + if os.path.exists(tmp_path): + os.remove(tmp_path) + except Exception: + logger.exception("Failed to remove partial download: %s", tmp_path) + raise + + +def prepare_local_xml(xml_url: str, output_dir: str, overwrite: bool = False) -> str: + os.makedirs(output_dir, exist_ok=True) + local_path = os.path.join(output_dir, os.path.basename(xml_url)) + download_file(xml_url, local_path, overwrite=overwrite) + return local_path + + +def stream_uniprot_xml(filepath: str): + """Stream gzipped UniProt XML entries.""" + logger.info("Streaming UniProt XML from: %s", filepath) + with gzip.open(filepath, "rb") as f: + for _, elem in ET.iterparse(f, events=("end",)): + if elem.tag.endswith("entry"): + yield elem + elem.clear() + + +def get_spark_session(namespace: str) -> SparkSession: + """Initialize SparkSession with Delta Lake support, and ensure the target database exists.""" + builder = ( + SparkSession.builder.appName("UniProtDeltaIngestion") + .config("spark.sql.extensions", "io.delta.sql.DeltaSparkSessionExtension") + .config( + "spark.sql.catalog.spark_catalog", + "org.apache.spark.sql.delta.catalog.DeltaCatalog", + ) + .config("spark.databricks.delta.schema.autoMerge.enabled", "true") + ) + spark = configure_spark_with_delta_pip(builder).getOrCreate() + spark.sql(f"CREATE DATABASE IF NOT EXISTS {namespace}") + return spark + + +def normalize_prefix(db_type: str) -> str: + """Map UniProt dbReference @type to a normalized CURIE prefix.""" + return PREFIX_TRANSLATION.get(db_type, db_type.replace(" ", "")) + +def make_curie(db_type: str, db_id: str) -> str: + """Create CURIE with normalized prefix.""" + return f"{normalize_prefix(db_type)}:{db_id}" -def parse_names(entry, cdm_id): + +# ================================ STABLE ID ================================= +def stable_cdm_id_from_uniprot_accession(accession: str, prefix: str = "cdm_prot_") -> str: + u = uuid.uuid5(CDM_UUID_NAMESPACE, f"UniProt:{accession}") + return f"{prefix}{u}" + + +def load_existing_maps( + spark: SparkSession, + output_dir: str, + namespace: str, +) -> tuple[dict[str, str], dict[str, str]]: """ - Extract all protein names from a UniProt element, including - - Top-level elements (generic names) - - and blocks within (full and short names). + Returns: + accession_to_entity_id: accession -> entity_id (from identifiers) + entity_id_to_created: entity_id -> created (from entities) """ - names = [] + accession_to_entity_id: dict[str, str] = {} + entity_id_to_created: dict[str, str] = {} - # Extract all top-level tags - for name_element in entry.findall("u:name", NS): - if name_element.text: - names.append( - { - "entity_id": cdm_id, - "name": name_element.text, - "description": "UniProt protein name", - "source": "UniProt", - } + id_path = os.path.join(output_dir, namespace, "identifiers") + ent_path = os.path.join(output_dir, namespace, "entities") + + if os.path.exists(id_path): + try: + df = ( + spark.read.format("delta") + .load(id_path) + .filter(col("identifier").startswith("UniProt:")) + .select( + split(col("identifier"), ":").getItem(1).alias("accession"), + col("entity_id"), + ) ) + for row in df.toLocalIterator(): + acc = row["accession"] + eid = row["entity_id"] + if acc and eid: + accession_to_entity_id[acc] = eid + logger.info( + "Loaded %d accession->entity_id from %s", + len(accession_to_entity_id), + id_path, + ) + except Exception: + logger.exception("Couldn't load identifiers from %s", id_path) - # Extract recommended and alternative names from block - protein = entry.find("u:protein", NS) - if protein is not None: - for name_type in ["recommended", "alternative"]: - # Directly use findall for simplicity (recommendedName returns single-element list) - name_blocks = protein.findall(f"u:{name_type}Name", NS) - for name in name_blocks: - for name_length in ["full", "short"]: - name_string = name.find(f"u:{name_length}Name", NS) - if name_string is None or not name_string.text: - continue + if os.path.exists(ent_path): + try: + df = spark.read.format("delta").load(ent_path).select("entity_id", "created") + for row in df.toLocalIterator(): + if row["entity_id"] and row["created"]: + entity_id_to_created[row["entity_id"]] = row["created"] + logger.info( + "Loaded %d entity_id->created from %s", + len(entity_id_to_created), + ent_path, + ) + except Exception: + logger.exception("Couldn't load entities from %s", ent_path) + + return accession_to_entity_id, entity_id_to_created + + +# ================================ PARSERS ================================= +def parse_identifiers(entry, cdm_id: str) -> list[dict]: + out = parse_identifiers_generic(entry=entry, xpath="ns:accession", prefix="UniProt", ns=NS) + for row in out: + row["entity_id"] = cdm_id + row.setdefault("source", "UniProt") + row.setdefault("description", "UniProt accession") + return out - names.append( - { - "entity_id": cdm_id, - "name": name_string.text, - "description": f"UniProt {name_type} {name_length} name", - "source": "UniProt", - } - ) + +def _make_name_record(cdm_id: str, name_text: str, description: str) -> dict: + return { + "entity_id": cdm_id, + "name": name_text, + "description": description, + "source": "UniProt", + } + + +def parse_names(entry, cdm_id: str) -> list[dict]: + names: list[dict] = [] + + for txt in find_all_text(entry, "ns:name", NS): + names.append(_make_name_record(cdm_id, txt, "UniProt entry name")) + + protein = entry.find("ns:protein", NS) + if protein is not None: + for tag_name, logical_type in [ + ("recommendedName", "recommended"), + ("alternativeName", "alternative"), + ]: + for name_block in protein.findall(f"ns:{tag_name}", NS): + for xml_tag, length_label in [ + ("fullName", "full"), + ("shortName", "short"), + ]: + elem = name_block.find(f"ns:{xml_tag}", NS) + text = get_text(elem) + if text: + names.append( + _make_name_record( + cdm_id, + text, + f"UniProt {logical_type} {length_label} name", + ) + ) return names -def parse_protein_info(entry, cdm_id): - """ - Extract protein-level metadata from a UniProt XML element. - """ - protein_info = {} - ec_numbers = [] +def parse_protein_info(entry, cdm_id: str) -> dict | None: + protein_info: dict = {} - # Extract EC numbers from and in - protein = entry.find("u:protein", NS) + protein = entry.find("ns:protein", NS) if protein is not None: - # Find EC numbers in recommendedName - rec = protein.find("u:recommendedName", NS) - if rec is not None: - for ec in rec.findall("u:ecNumber", NS): - if ec.text: - ec_numbers.append(ec.text) - - # Find EC numbers in all alternativeNames - for alt in protein.findall("u:alternativeName", NS): - for ec in alt.findall("u:ecNumber", NS): - if ec.text: - ec_numbers.append(ec.text) + ec_paths = ["ns:recommendedName/ns:ecNumber", "ns:alternativeName/ns:ecNumber"] + ec_numbers: list[str] = [] + for path in ec_paths: + ec_numbers.extend(find_all_text(protein, path, NS)) if ec_numbers: - protein_info["ec_numbers"] = ec_numbers + protein_info["ec_numbers"] = ";".join(ec_numbers) - # Extract protein existence evidence type - protein_existence = entry.find("u:proteinExistence", NS) + protein_existence = entry.find("ns:proteinExistence", NS) if protein_existence is not None: protein_info["protein_id"] = cdm_id - protein_info["evidence_for_existence"] = protein_existence.get("type") - - # Extract sequence and sequence-related attributes - seq_elem = entry.find("u:sequence", NS) - if seq_elem is not None and seq_elem.text: - protein_info["length"] = seq_elem.get("length") - protein_info["mass"] = seq_elem.get("mass") - protein_info["checksum"] = seq_elem.get("checksum") - protein_info["modified"] = seq_elem.get("modified") - protein_info["sequence_version"] = seq_elem.get("version") - protein_info["sequence"] = seq_elem.text.strip() - - # Capture the entry's modified/updated date for tracking - entry_modified = entry.attrib.get("modified") or entry.attrib.get("updated") + protein_info["evidence_for_existence"] = get_attr(protein_existence, "type") + + seq_elem = entry.find("ns:sequence", NS) + if seq_elem is not None: + protein_info.update( + clean_dict( + { + "length": get_attr(seq_elem, "length"), + "mass": get_attr(seq_elem, "mass"), + "checksum": get_attr(seq_elem, "checksum"), + "modified": get_attr(seq_elem, "modified"), + "sequence_version": get_attr(seq_elem, "version"), + "sequence": get_text(seq_elem), + } + ) + ) + + entry_modified = get_attr(entry, "modified") or get_attr(entry, "updated") if entry_modified: protein_info["entry_modified"] = entry_modified - # Return the dictionary if any protein info was extracted return protein_info if protein_info else None -def parse_evidence_map(entry): - """ - Parse all elements from a UniProt XML entry and build a mapping - from evidence key to metadata (type, supporting objects, publications). - """ - evidence_map = {} +def parse_evidence_map(entry) -> dict[str, dict]: + evidence_map: dict[str, dict] = {} - # Loop through every element in the entry - for evidence in entry.findall("u:evidence", NS): - key = evidence.get("key") # Unique evidence key (string) - evidence_type = evidence.get("type") # Evidence code/type (e.g., ECO:0000255) + for ev in entry.findall("ns:evidence", NS): + key = get_attr(ev, "key") + if not key: + continue - supporting_objects = [] - publications = [] + evidence_type = get_attr(ev, "type") + pubs: list[str] = [] + others: list[str] = [] - # Check if this evidence has a element with children - source = evidence.find("u:source", NS) + source = ev.find("ns:source", NS) if source is not None: - for dbref in source.findall("u:dbReference", NS): - db_type = dbref.get("type") - db_id = dbref.get("id") - # Add publication references as PubMed or DOI; others as supporting objects - if db_type == "PubMed": - publications.append(f"PMID:{db_id}") - elif db_type == "DOI": - publications.append(f"DOI:{db_id}") + raw_pubs, raw_others = parse_db_references(source, NS) + + normalized_pubs: list[str] = [] + for p in raw_pubs: + up = p.upper() + if up.startswith("PUBMED:"): + _, acc = p.split(":", 1) + normalized_pubs.append(f"PMID:{acc}") else: - supporting_objects.append(f"{db_type}:{db_id}") + normalized_pubs.append(p) - # Store evidence metadata, omitting empty lists for cleanliness - evidence_map[key] = { - "evidence_type": evidence_type, - "supporting_objects": supporting_objects if supporting_objects else None, - "publications": publications if publications else None, - } + pubs = normalized_pubs + others = raw_others + + evidence_map[key] = clean_dict( + { + "evidence_type": evidence_type, + "publications": pubs or None, + "supporting_objects": others or None, + } + ) return evidence_map -def parse_reaction_association(reaction, cdm_id, evidence_map): - associations = [] - for dbref in reaction.findall("u:dbReference", NS): +def _make_association( + cdm_id: str, + obj: str, + predicate: str | None = None, + evidence_key: str | None = None, + evidence_map: dict | None = None, +) -> dict: + assoc = { + "subject": cdm_id, + "object": obj, + "predicate": predicate, + "evidence_type": None, + "supporting_objects": None, + "publications": None, + } + if evidence_key and evidence_map and evidence_key in evidence_map: + assoc.update(evidence_map[evidence_key]) + return clean_dict(assoc) + + +def parse_reaction_association(reaction, cdm_id: str, evidence_map: dict[str, dict]) -> list[dict]: + associations: list[dict] = [] + for dbref in reaction.findall("ns:dbReference", NS): db_type = dbref.get("type") db_id = dbref.get("id") + if not db_type or not db_id: + continue + assoc = { "subject": cdm_id, "predicate": "catalyzes", - "object": f"{db_type}:{db_id}", + "object": make_curie(db_type, db_id), "evidence_type": None, "supporting_objects": None, "publications": None, @@ -261,124 +444,127 @@ def parse_reaction_association(reaction, cdm_id, evidence_map): evidence_key = reaction.get("evidence") if evidence_key and evidence_key in evidence_map: assoc.update(evidence_map[evidence_key]) - associations.append(assoc) + associations.append(clean_dict(assoc)) return associations -def parse_cofactor_association(cofactor, cdm_id): - associations = [] - for dbref in cofactor.findall("u:dbReference", NS): +def parse_cofactor_association(cofactor, cdm_id: str) -> list[dict]: + associations: list[dict] = [] + for dbref in cofactor.findall("ns:dbReference", NS): db_type = dbref.get("type") db_id = dbref.get("id") - assoc = { - "subject": cdm_id, - "predicate": "requires_cofactor", - "object": f"{db_type}:{db_id}", - "evidence_type": None, - "supporting_objects": None, - "publications": None, - } - associations.append(assoc) + if not db_type or not db_id: + continue + associations.append( + clean_dict( + { + "subject": cdm_id, + "predicate": "requires_cofactor", + "object": make_curie(db_type, db_id), + "evidence_type": None, + "supporting_objects": None, + "publications": None, + } + ) + ) return associations -def parse_associations(entry, cdm_id, evidence_map): +def parse_associations(entry, cdm_id: str, evidence_map: dict[str, dict]) -> list[dict]: """ - Parse all relevant associations from a UniProt XML entry for the CDM model. - Only include fields that are not None for each association. + Only keep: + - taxonomy association + - catalytic activity / cofactor associations """ - associations = [] - - def clean(d): - """Remove None-value keys from a dict.""" - return {k: v for k, v in d.items() if v is not None} + associations: list[dict] = [] # Taxonomy association - organism = entry.find("u:organism", NS) + organism = entry.find("ns:organism", NS) if organism is not None: - taxon_ref = organism.find('u:dbReference[@type="NCBI Taxonomy"]', NS) + taxon_ref = organism.find('ns:dbReference[@type="NCBI Taxonomy"]', NS) if taxon_ref is not None: - associations.append( - clean( - { - "subject": cdm_id, - "object": f"NCBITaxon:{taxon_ref.get('id')}", - "predicate": None, - "evidence_type": None, - "supporting_objects": None, - "publications": None, - } - ) - ) - - # Database cross-references with evidence - for dbref in entry.findall("u:dbReference", NS): - db_type = dbref.get("type") - db_id = dbref.get("id") - association = { - "subject": cdm_id, - "object": f"{db_type}:{db_id}", - "predicate": None, - "evidence_type": None, - "supporting_objects": None, - "publications": None, - } - evidence_key = dbref.get("evidence") - if evidence_key and evidence_key in evidence_map: - association.update(evidence_map[evidence_key]) - associations.append(clean(association)) + tax_id = taxon_ref.get("id") + if tax_id: + associations.append(_make_association(cdm_id, f"NCBITaxon:{tax_id}", predicate="in_taxon")) - # Catalytic/cofactor - for comment in entry.findall("u:comment", NS): + # Catalytic activity / cofactor + for comment in entry.findall("ns:comment", NS): comment_type = comment.get("type") if comment_type == "catalytic activity": - # extract catalytic associations - for reaction in comment.findall("u:reaction", NS): - for assoc in parse_reaction_association(reaction, cdm_id, evidence_map): - associations.append(clean(assoc)) + for reaction in comment.findall("ns:reaction", NS): + associations.extend(parse_reaction_association(reaction, cdm_id, evidence_map)) elif comment_type == "cofactor": - # extract cofactor associations - for cofactor in comment.findall("u:cofactor", NS): - for assoc in parse_cofactor_association(cofactor, cdm_id): - associations.append(clean(assoc)) + for cofactor in comment.findall("ns:cofactor", NS): + associations.extend(parse_cofactor_association(cofactor, cdm_id)) + return associations -def parse_publications(entry): - """ - Extract all publication references from a UniProt XML - Returns a list of standardized publication IDs (PMID and DOI). - """ - publications = [] - - # Iterate through all blocks in the entry - for reference in entry.findall("u:reference", NS): - citation = reference.find("u:citation", NS) - if citation is not None: - # Each may have multiple elements (e.g., PubMed, DOI) - for dbref in citation.findall("u:dbReference", NS): - db_type = dbref.get("type") - db_id = dbref.get("id") - # Standardize format for known publication types - if db_type == "PubMed": - publications.append(f"PMID:{db_id}") - elif db_type == "DOI": - publications.append(f"DOI:{db_id}") - - return publications - - -def parse_uniprot_entry(entry, cdm_id, current_timestamp, datasource_name="UniProt import", prev_created=None): - if prev_created: - entity_created = prev_created - entity_updated = current_timestamp - else: - entity_created = current_timestamp - entity_updated = current_timestamp +def parse_cross_references(entry, cdm_id: str) -> list[dict]: + """Generic -> cross_references table.""" + rows: list[dict] = [] + + for dbref in entry.findall("ns:dbReference", NS): + db_type = dbref.get("type") + db_id = dbref.get("id") + if not db_type or not db_id: + continue + + xref_type = normalize_prefix(db_type) + + if ":" in db_id: + xref = db_id + else: + xref = f"{xref_type}:{db_id}" + + rows.append( + clean_dict( + { + "entity_id": cdm_id, + "xref_type": xref_type, + "xref_value": db_id, + "xref": xref, + } + ) + ) + + return rows + + +def parse_publications(entry) -> list[str]: + publications: list[str] = [] + for reference in entry.findall("ns:reference", NS): + citation = reference.find("ns:citation", NS) + if citation is None: + continue + + raw_pubs, _ = parse_db_references(citation, NS) + for p in raw_pubs: + up = p.upper() + if up.startswith("PUBMED:"): + _, acc = p.split(":", 1) + publications.append(f"PMID:{acc}") + elif up.startswith("DOI:"): + _, acc = p.split(":", 1) + publications.append(f"DOI:{acc}") + + return list(dict.fromkeys(publications)) + + +def parse_uniprot_entry( + entry, + cdm_id: str, + current_timestamp: str, + datasource_name: str = "UniProt import", + prev_created: str | None = None, +) -> dict: + entity_created = prev_created or current_timestamp + entity_updated = current_timestamp uniprot_created = entry.attrib.get("created") uniprot_modified = entry.attrib.get("modified") or entry.attrib.get("updated") uniprot_version = entry.attrib.get("version") + entity = { "entity_id": cdm_id, "entity_type": "protein", @@ -389,65 +575,21 @@ def parse_uniprot_entry(entry, cdm_id, current_timestamp, datasource_name="UniPr "uniprot_created": uniprot_created, "uniprot_modified": uniprot_modified, } + evidence_map = parse_evidence_map(entry) + return { "entity": entity, "identifiers": parse_identifiers(entry, cdm_id), "names": parse_names(entry, cdm_id), "protein": parse_protein_info(entry, cdm_id), "associations": parse_associations(entry, cdm_id, evidence_map), + "cross_references": parse_cross_references(entry, cdm_id), "publications": parse_publications(entry), } -def download_file(url, output_path, chunk_size=8192, overwrite=False) -> None: - """ - Download a file from a given URL to a local output path. - """ - # Skip download if file already exists and not overwriting - if os.path.exists(output_path) and not overwrite: - print(f"File '{output_path}' already exists.") - return - - # Stream download to avoid high memory usage - try: - with requests.get(url, stream=True, timeout=60) as response: - response.raise_for_status() - with open(output_path, "wb") as f: - for chunk in response.iter_content(chunk_size=chunk_size): - if chunk: - f.write(chunk) - print(f"Downloaded '{url}' to '{output_path}'") - except Exception as e: - print(f"Failed to download '{url}': {e}") - - if os.path.exists(output_path): - os.remove(output_path) # Remove incomplete file - raise - - -def stream_uniprot_xml(filepath): - """ - Stream and parse UniProt XML entries from a local gzipped file. - Yields each element as soon as it is parsed to avoid loading the entire XML into memory. - """ - # Open the gzipped XML file for reading in binary mode - with gzip.open(filepath, "rb") as f: - # Use iterparse to process XML incrementally, triggering on element end events - context = ET.iterparse(f, events=("end",)) - for _event, element in context: - # Check tag name, ignoring namespace - if element.tag.endswith("entry"): - yield element - element.clear() - - -## ================================ SCHEMA ================================= -""" -Defines the Spark schema for all major CDM tables derived from UniProt XML. -Each schema is tailored for protein entities, identifiers, protein details, names, associations, and linked publications. -""" - +# ================================ SCHEMA ================================= schema_entities = StructType( [ StructField("entity_id", StringType(), False), @@ -505,6 +647,15 @@ def stream_uniprot_xml(filepath): ] ) +schema_cross_references = StructType( + [ + StructField("entity_id", StringType(), False), + StructField("xref_type", StringType(), True), + StructField("xref_value", StringType(), True), + StructField("xref", StringType(), True), + ] +) + schema_publications = StructType( [ StructField("entity_id", StringType(), False), @@ -513,126 +664,74 @@ def stream_uniprot_xml(filepath): ) -def save_batches_to_delta(spark, tables, output_dir, namespace) -> None: - """ - Persist batches of parsed records for each CDM table into Delta Lake format. - - - Each table is saved into a Delta directory named '{namespace}_{table}_delta' in the output folder. - - If the Delta directory exists, append new records. Otherwise, overwrite it. - - Registers the table in the Spark SQL for downstream query. - """ - for table, (records, schema) in tables.items(): - if not records: - continue # Skip all empty tables - - delta_dir = os.path.abspath(os.path.join(output_dir, f"{namespace}_{table}_delta")) - # Use "append" mode if the Delta directory already exists, otherwise "overwrite" - mode = "append" if os.path.exists(delta_dir) else "overwrite" - - print( - f"[DEBUG] Registering table: {namespace}.{table} at {delta_dir} with mode={mode}, record count: {len(records)}" - ) - - try: - df = spark.createDataFrame(records, schema) - df.write.format("delta").mode(mode).option("overwriteSchema", "true").save(delta_dir) - spark.sql(f""" - CREATE TABLE IF NOT EXISTS {namespace}.{table} - USING DELTA - LOCATION '{delta_dir}' - """) - except Exception as e: - print(f"Failed to save {table} to Delta: {e}") - - -def prepare_local_xml(xml_url, output_dir): - """ - Download the remote UniProt XML (.xml.gz) file to the specified local output directory, - unless the file already exists locally. Returns the full local file path. - """ - # Ensure output directory exists - os.makedirs(output_dir, exist_ok=True) - local_xml_path = os.path.join(output_dir, os.path.basename(xml_url)) - # Download only if file does not exist - download_file(xml_url, local_xml_path) - return local_xml_path - - -def save_datasource_record(xml_url, output_dir): - """ - Generate and save the datasource provenance record as a JSON file in the output directory. - """ - datasource = build_datasource_record(xml_url) - os.makedirs(output_dir, exist_ok=True) # Ensure output directory exists - output_path = os.path.join(output_dir, "datasource.json") - with open(output_path, "w") as f: - json.dump(datasource, f, indent=4) - return datasource - - -def get_spark_session(namespace): - """ - Initialize SparkSession with Delta Lake support, and ensure the target database exists. - """ - # Build SparkSession with Delta extensions enabled - builder = ( - SparkSession.builder.appName("DeltaIngestion") - .config("spark.sql.extensions", "io.delta.sql.DeltaSparkSessionExtension") - .config( - "spark.sql.catalog.spark_catalog", - "org.apache.spark.sql.delta.catalog.DeltaCatalog", - ) - ) - spark = configure_spark_with_delta_pip(builder).getOrCreate() - # Ensure the target namespace (database) exists +# ================================ DELTA WRITE ================================= +def ensure_tables_registered(spark: SparkSession, output_dir: str, namespace: str, table_names: list[str]) -> None: spark.sql(f"CREATE DATABASE IF NOT EXISTS {namespace}") - return spark - - -def load_existing_entity(spark, output_dir, namespace): - """ - Load the existing entities_delta Delta table and build a mapping of entity_id to created timestamp. - This mapping is used to support upserts and idempotent writes. - """ - old_created_dict = {} - entities_table_path = os.path.abspath(os.path.join(output_dir, f"{namespace}_entities_delta")) - if os.path.exists(entities_table_path): - try: - # Read only the required columns for efficiency - old_df = spark.read.format("delta").load(entities_table_path).select("entity_id", "created") - for row in old_df.collect(): - old_created_dict[row["entity_id"]] = row["created"] - print(f"Loaded {len(old_created_dict)} existing entity_id records for upsert.") - except Exception as e: - print(f"Couldn't load previous entities delta table: {e}") - else: - print(f"No previous entities delta at {entities_table_path}.") - return old_created_dict + for tbl in table_names: + # delta_dir = os.path.abspath(os.path.join(output_dir, namespace, tbl)) + delta_dir = delta_table_path(output_dir, namespace, tbl) + spark.sql( + f""" + CREATE TABLE IF NOT EXISTS {namespace}.{tbl} + USING DELTA + LOCATION '{delta_dir}' + """ + ) -def parse_entries(local_xml_path, target_date, batch_size, spark, tables, output_dir, namespace, current_timestamp): - """ - Parse UniProt XML entries, write to Delta Lake in batches - Return (processed_entry_count, skipped_entry_count). +def save_batches_to_delta( + spark: SparkSession, + tables: dict[str, tuple[list, StructType]], + output_dir: str, + namespace: str, + mode: str = "append", +) -> None: + for table_name, (records, schema) in tables.items(): + if not records: + continue - """ + # delta_dir = os.path.abspath(os.path.join(output_dir, namespace, table_name)) + delta_dir = delta_table_path(output_dir, namespace, table_name) + df = spark.createDataFrame(records, schema) + writer = df.write.format("delta").mode(mode) + + if mode == "append": + writer = writer.option("mergeSchema", "true") + if mode == "overwrite": + writer = writer.option("overwriteSchema", "true") + + writer.save(delta_dir) + + +## =============================== MAIN PARSING LOOP ================================= +def parse_entries( + local_xml_path: str, + target_date: str | None, + batch_size: int, + spark: SparkSession, + tables: dict[str, tuple[list, StructType]], + output_dir: str, + namespace: str, + current_timestamp: str, + accession_to_entity_id: dict[str, str], + entity_id_to_created: dict[str, str], + mode: str, +) -> tuple[int, int]: target_date_dt = None - - # Convert target_date string to datetime for comparison if provided if target_date: try: target_date_dt = datetime.datetime.strptime(target_date, "%Y-%m-%d") + logger.info("Target date filter enabled: >= %s", target_date) except Exception: - print(f"Invalid target date is {target_date}") + logger.warning("Invalid target date provided: %s (ignored)", target_date) + target_date_dt = None entry_count, skipped = 0, 0 - # Iterate over each element in the XML file for entry_elem in stream_uniprot_xml(local_xml_path): try: - # Get the modification date of the entry mod_date = entry_elem.attrib.get("modified") or entry_elem.attrib.get("updated") - # If target_date is set, skip entries older than target_date + if target_date_dt and mod_date: try: entry_date_dt = datetime.datetime.strptime(mod_date[:10], "%Y-%m-%d") @@ -643,110 +742,197 @@ def parse_entries(local_xml_path, target_date, batch_size, spark, tables, output skipped += 1 continue - # Extract main accession (skip entry if not present) - main_accession_elem = entry_elem.find("u:accession", NS) - if main_accession_elem is None or main_accession_elem.text is None: + main_accession_elem = entry_elem.find("ns:accession", NS) + if main_accession_elem is None or not main_accession_elem.text: skipped += 1 continue - # Generate a unique CDM ID (UUID) for this entry - cdm_id = generate_cdm_id() + accession = main_accession_elem.text.strip() + + cdm_id = accession_to_entity_id.get(accession) or stable_cdm_id_from_uniprot_accession(accession) + prev_created = entity_id_to_created.get(cdm_id) + + record = parse_uniprot_entry(entry_elem, cdm_id, current_timestamp, prev_created=prev_created) - # Parse all sub-objects: entity, identifiers, names, protein, associations, publications - record = parse_uniprot_entry(entry_elem, cdm_id, current_timestamp) tables["entities"][0].append(record["entity"]) tables["identifiers"][0].extend(record["identifiers"]) tables["names"][0].extend(record["names"]) if record["protein"]: tables["proteins"][0].append(record["protein"]) + tables["associations"][0].extend(record["associations"]) - tables["publications"][0].extend( - {"entity_id": record["entity"]["entity_id"], "publication": pub} for pub in record["publications"] - ) + tables["cross_references"][0].extend(record["cross_references"]) + + for pub in record["publications"]: + tables["publications"][0].append( + { + "entity_id": cdm_id, + "publication": pub, + } + ) entry_count += 1 - # Write batch to Delta and clear lists every batch_size entries + if entry_count % batch_size == 0: - save_batches_to_delta(spark, tables, output_dir, namespace) + save_batches_to_delta(spark, tables, output_dir, namespace, mode=mode) for v in tables.values(): v[0].clear() - print(f"{entry_count} entries processed and saved") - except Exception as e: - # If any error occurs in parsing this entry, skip it and count - print(f"Error parsing entry: {e}") + logger.info("Processed and saved %d entries...", entry_count) + + except Exception: + logger.exception("Error parsing UniProt entry, skipping") skipped += 1 - continue - # write remaining records - save_batches_to_delta(spark, tables, output_dir, namespace) + save_batches_to_delta(spark, tables, output_dir, namespace, mode=mode) return entry_count, skipped -def ingest_uniprot(xml_url, output_dir, namespace, target_date=None, batch_size=5000) -> None: - # Generate the timestamp for the current run +def ingest_uniprot( + xml_url: str, + output_dir: str, + namespace: str, + target_date: str | None = None, + batch_size: int = 5000, + mode: str = "append", + overwrite_download: bool = False, +) -> None: current_timestamp = datetime.datetime.now(datetime.UTC).isoformat() - # Prepare local XML - local_xml_path = prepare_local_xml(xml_url, output_dir) - - # Save data source meta information + local_xml_path = prepare_local_xml(xml_url, output_dir, overwrite=overwrite_download) save_datasource_record(xml_url, output_dir) - # Get Spark and the existing CDM entity_id spark = get_spark_session(namespace) + if mode == "append": + accession_to_entity_id, entity_id_to_created = load_existing_maps(spark, output_dir, namespace) + else: + accession_to_entity_id, entity_id_to_created = {}, {} - # Define the table structure (batch storage) - entities, identifiers, names, proteins, associations, publications = ( - [], - [], - [], - [], - [], - [], - ) - tables = { + # accession_to_entity_id, entity_id_to_created = load_existing_maps(spark, output_dir, namespace) + + entities: list[dict] = [] + identifiers: list[dict] = [] + names: list[dict] = [] + proteins: list[dict] = [] + associations: list[dict] = [] + cross_references: list[dict] = [] + publications: list[dict] = [] + + tables: dict[str, tuple[list, StructType]] = { "entities": (entities, schema_entities), "identifiers": (identifiers, schema_identifiers), "names": (names, schema_names), "proteins": (proteins, schema_proteins), "associations": (associations, schema_associations), + "cross_references": (cross_references, schema_cross_references), "publications": (publications, schema_publications), } - # Main cycle processing, transfer to current timestamp + ensure_tables_registered( + spark, + output_dir, + namespace, + [ + "entities", + "identifiers", + "names", + "proteins", + "associations", + "cross_references", + "publications", + ], + ) + + logger.info( + "Starting UniProt ingestion: xml=%s | namespace=%s | mode=%s | batch_size=%d", + xml_url, + namespace, + mode, + batch_size, + ) + entry_count, skipped = parse_entries( - local_xml_path, target_date, batch_size, spark, tables, output_dir, namespace, current_timestamp + local_xml_path=local_xml_path, + target_date=target_date, + batch_size=batch_size, + spark=spark, + tables=tables, + output_dir=output_dir, + namespace=namespace, + current_timestamp=current_timestamp, + accession_to_entity_id=accession_to_entity_id, + entity_id_to_created=entity_id_to_created, + mode=mode, ) - print(f"All entries processed ({entry_count}), skipped {skipped}, writing complete tables.") - spark.sql(f"SHOW TABLES IN {namespace}").show() - spark.sql(f"SELECT COUNT(*) FROM {namespace}.entities").show() - # make sql test in entity table - spark.sql(f"SELECT * FROM {namespace}.entities LIMIT 10").show(truncate=False) + logger.info("Completed parsing UniProt XML. processed=%d skipped=%d", entry_count, skipped) - spark.stop() + logger.info("Verifying Delta tables in namespace `%s`", namespace) + spark.sql(f"SHOW TABLES IN {namespace}").show(truncate=False) - print(f"All Delta tables are created and registered in Spark SQL under `{namespace}`.") + for tbl in [ + "entities", + "identifiers", + "names", + "proteins", + "associations", + "cross_references", + "publications", + ]: + logger.info("Verifying table: %s.%s", namespace, tbl) + spark.sql(f"SELECT COUNT(*) AS row_count FROM {namespace}.{tbl}").show(truncate=False) + spark.sql(f"SELECT * FROM {namespace}.{tbl} LIMIT 5").show(truncate=False) + + spark.stop() + logger.info("Done") +# ================================ CLI ================================= @click.command() @click.option("--xml-url", required=True, help="URL to UniProt XML (.xml.gz)") -@click.option("--output-dir", default="output", help="Output directory for Delta tables") -@click.option("--namespace", default="uniprot_db", help="Delta Lake database name") +@click.option( + "--output-dir", + default="output", + show_default=True, + help="Output directory for Delta tables", +) +@click.option( + "--namespace", + default="uniprot_db", + show_default=True, + help="Delta Lake database name", +) @click.option( "--target-date", default=None, help="Only process entries modified/updated since this date (YYYY-MM-DD)", ) -@click.option("--batch-size", default=5000, help="Batch size for writing Delta tables") -def main(xml_url, output_dir, namespace, target_date, batch_size) -> None: +@click.option( + "--batch-size", + default=5000, + show_default=True, + help="Batch size for writing Delta tables", +) +@click.option( + "--mode", + type=click.Choice(["append", "overwrite"]), + default="append", + show_default=True, +) +@click.option( + "--overwrite-download", + is_flag=True, + help="Force re-download XML even if file exists", +) +def main(xml_url, output_dir, namespace, target_date, batch_size, mode, overwrite_download): ingest_uniprot( xml_url=xml_url, output_dir=output_dir, namespace=namespace, target_date=target_date, batch_size=int(batch_size), + mode=mode, + overwrite_download=overwrite_download, ) diff --git a/src/cdm_data_loader_utils/parsers/uniref.py b/src/cdm_data_loader_utils/parsers/uniref.py index da3327c..6f24bb3 100644 --- a/src/cdm_data_loader_utils/parsers/uniref.py +++ b/src/cdm_data_loader_utils/parsers/uniref.py @@ -1,5 +1,5 @@ """ -UniRef XML Cluster ETL Pipeline. +UniRef XML Cluster ETL Pipeline This script downloads a UniRef100 XML file, parses cluster and member information, and writes the extracted data into Delta Lake tables for downstream analysis. @@ -22,7 +22,12 @@ --output-dir cdm-data-loader-utils/output/uniref100_clusters \ --batch-size 1000 -**Parameters:** +python3 uniref.py \ + --ftp-url https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.xml.gz \ + --output-dir output_uniref \ + --batch-size 1000 + +Parameters: - --ftp-url: UniProt FTP URL to the UniRef100 gzipped XML file. - --output-dir: Output directory where Delta tables will be written. - --batch-size: Number of UniRef entries to process. @@ -30,118 +35,213 @@ """ import gzip + +### ===== logging setup ===== ### +import logging import os import uuid import xml.etree.ElementTree as ET from datetime import datetime -from urllib.request import URLError, urlretrieve - +from urllib.error import URLError +from datetime import timezone +from urllib.request import urlretrieve import click from delta import configure_spark_with_delta_pip from pyspark.sql import SparkSession from pyspark.sql.types import StringType, StructField, StructType +from pathlib import Path + +from cdm_data_loader_utils.parsers.xml_utils import get_text, parse_properties + + +logger = logging.getLogger(__name__) + + +UNIREF_NS = {"ns": "http://uniprot.org/uniref"} +DATA_SOURCE = "UniRef 100/90/50" + + +PREFIX_TRANSLATION = { + "UniProtKB ID": "UniProt", + "UniProtKB accession": "UniProt", + "UniParc ID": "UniParc", + "UniRef90 ID": "UniRef90", + "UniRef50 ID": "UniRef50", + "UniRef100 ID": "UniRef100", +} + + +def generate_dbxref(db: str, acc: str) -> str: + """Generate a database reference that uses BioRegistry prefixes.""" + return f"{PREFIX_TRANSLATION[db]}:{acc}" + + +def cdm_entity_id(value: str, prefix: str = "CDM:") -> str: + """ + Deterministic UUIDv5-based CDM id generator. + + value must be non-empty. + """ + if not value: + raise ValueError("Value must be a non-empty string") + + return f"{prefix}{uuid.uuid5(uuid.NAMESPACE_OID, value)}" + +# timestamp helper +def get_timestamps( + uniref_id: str, + existing_created: dict[str, str], + now: datetime | None = None, +) -> tuple[str, str]: + """ + Return (updated_time, created_time) for a given UniRef cluster ID. + - All timestamps are UTC ISO8601 with timezone (e.g., 2026-01-05T12:34:56+00:00) + - uniref_id must be non-empty (schema invariant) + """ + if not uniref_id: + raise ValueError("get_timestamps: uniref_id must be a non-empty string") -# Generate a unique CDM entity_id based on accession -def cdm_entity_id(accession) -> str | None: - if not accession: - return None - uuid_part = uuid.uuid5(uuid.NAMESPACE_OID, accession) - return f"CDM:{uuid_part}" + now_dt = now or datetime.now(timezone.utc) + updated_time = now_dt.isoformat(timespec="seconds") + created_time = existing_created.get(uniref_id) or updated_time + return updated_time, created_time -# Download a file from the specified URL to the local path if it does not already exist -def download_file(url, local_path) -> None: + +def download_file(url: str, local_path: str, overwrite: bool = False) -> str: """ - If the file is already present at local, the function does nothing. - If the download fails, any partially downloaded file will be removed. + Download URL -> local_path. + - Atomic: downloads to .part then os.replace + - Idempotent: skips if exists unless overwrite=True + Returns the final local_path. """ - if not os.path.exists(local_path): - print(f"Downloading from URL link: {url}") + dst = Path(local_path) + dst.parent.mkdir(parents=True, exist_ok=True) + + if dst.exists() and not overwrite: + logger.info("File already exists, skip download: %s", dst) + return str(dst) + + tmp = dst.with_suffix(dst.suffix + ".part") + + try: + if tmp.exists(): + tmp.unlink() + except Exception: + logger.exception("Failed to remove partial download: %s", tmp) + + logger.info("Downloading %s -> %s", url, dst) + try: + urlretrieve(url, str(tmp)) + os.replace(tmp, dst) + logger.info("Download complete: %s", dst) + return str(dst) + except Exception: + logger.exception("Failed to download %s", url) try: - urlretrieve(url, local_path) - print("Download completed!") - except Exception as e: - print(f"Failed to download {url}: {e}") - if os.path.exists(local_path): - os.remove(local_path) - raise - else: - print(f"File already exists: {local_path}") + if tmp.exists(): + tmp.unlink() + except Exception: + logger.exception("Failed to cleanup tmp file: %s", tmp) + raise -# Load mapping from data_source_entity_id to created timestamp from Delta table -def load_existing_created(spark, entity_table): - existing_created = {} +def load_existing_created(spark: SparkSession, entity_table: str | None) -> dict[str, str]: + """ + Load mapping data_source_entity_id -> created timestamp from the Entity Delta table. + Returns an empty dict if the table does not exist. + """ + existing_created: dict[str, str] = {} if not entity_table: - print("Entity table path not specified.") + logger.warning("Entity table path not specified.") return existing_created try: df = spark.read.format("delta").load(entity_table).select("data_source_entity_id", "created") existing_created = {row["data_source_entity_id"]: row["created"] for row in df.collect()} - print(f"Loaded {len(existing_created)} existing created timestamps.") + logger.info(f"Loaded {len(existing_created)} existing created timestamps from {entity_table}.") except Exception as e: - print(f"No existing Delta table found at {entity_table}. Starting fresh. ({e.__class__.__name__})") + logger.warning(f"No existing Delta table found at {entity_table}. Starting fresh. ({e.__class__.__name__})") return existing_created ##### -------------- List utility function --------------- ##### - - -# Helper function to extract basic cluster info from XML entry element -def extract_cluster(elem, ns): - cluster_id = f"CDM:{uuid.uuid4()}" +def extract_cluster( + elem: ET.Element, + ns: dict[str, str], + uniref_id: str, +) -> tuple[str, str]: + """ + Extract a deterministic CDM cluster_id and the UniRef cluster name. + """ + cluster_id = cdm_entity_id(value=uniref_id) or f"CDM:{uuid.uuid4()}" name_elem = elem.find("ns:name", ns) - name = name_elem.text if name_elem is not None else "UNKNOWN" - return cluster_id, name + name = get_text(elem=name_elem, default="UNKNOWN") or "UNKNOWN" + return cluster_id, name -# Returns tuple of (updated_time, created_time) -def get_timestamps(uniref_id, existing_created, now=None): - now_dt = now or datetime.now() - formatted_now = now_dt.strftime("%Y-%m-%dT%H:%M:%S") - created = existing_created.get(uniref_id) - created_time = (created.split(".")[0] if "." in created else created) if created else formatted_now - return formatted_now, created_time +def get_accession_and_seed(dbref: ET.Element | None, ns: dict[str, str]) -> tuple[str | None, bool]: + """ + Extract UniProtKB accession and is_seed status from a dbReference element. + """ -# Extract UniProtKB accession and is_seed status from a dbReference element -def get_accession_and_seed(dbref, ns): if dbref is None: return None, False - prop_elems = dbref.findall("ns:property", ns) - props = {} - for prop in prop_elems: - t = prop.attrib["type"] - v = prop.attrib["value"] - props[t] = v + props = parse_properties(dbref, ns) + + raw_acc = props.get("UniProtKB accession") + if isinstance(raw_acc, list): + accession = raw_acc[0] if raw_acc else None + else: + accession = raw_acc # string or None + + raw_seed = props.get("isSeed") + if isinstance(raw_seed, list): + is_seed = bool(raw_seed) and raw_seed[0].lower() == "true" + else: + is_seed = raw_seed is not None and raw_seed.lower() == "true" - acc = props.get("UniProtKB accession") or dbref.attrib.get("id") - is_seed = props.get("isSeed", "false").lower() == "true" - return acc, is_seed + return accession, is_seed -# Add both representative and other cluster members into cluster_member_data list -def add_cluster_members(cluster_id, repr_db, elem, cluster_member_data, ns) -> None: - dbrefs = [] +def add_cluster_members( + cluster_id: str, + repr_db: ET.Element | None, + elem: ET.Element, + cluster_member_rows: list[tuple[str, str, str, str, str]], + ns: dict[str, str], +) -> None: + """Populate cluster_member_rows with representative, member records.""" + dbrefs: list[tuple[ET.Element, bool]] = [] if repr_db is not None: dbrefs.append((repr_db, True)) for mem in elem.findall("ns:member/ns:dbReference", ns): dbrefs.append((mem, False)) for dbref, is_representative in dbrefs: - acc, is_seed = get_accession_and_seed(dbref, ns) - if acc: - member_entity_id = cdm_entity_id(acc) - cluster_member_data.append( - (cluster_id, member_entity_id, str(is_representative).lower(), str(is_seed).lower(), "1.0") + accession, is_seed = get_accession_and_seed(dbref, ns) + if not accession: + continue + + member_entity_id = cdm_entity_id(accession) + if not member_entity_id: + continue + + cluster_member_rows.append( + ( + cluster_id, + member_entity_id, + str(is_representative).lower(), + str(is_seed).lower(), + "1.0", # score placeholder ) + ) -# Extract cross-references (UniRef90/50/UniParc) from a dbReference element def extract_cross_refs(dbref, cross_reference_data, ns) -> None: if dbref is None: return @@ -153,83 +253,95 @@ def extract_cross_refs(dbref, cross_reference_data, ns) -> None: cross_reference_data.append((entity_id, i, props[i])) -##### -------------- Parse Uniref XML --------------- ##### +def parse_uniref_entry( + elem: ET.Element, existing_created: dict[str, str], ns: dict[str, str] +) -> dict[str, list[tuple]]: + """ + Parse a single UniRef element into CDM-friendly row tuples. + """ + cluster_rows: list[tuple[str, str, str, str | None, str]] = [] + entity_rows: list[tuple[str, str, str, str, str, str]] = [] + member_rows: list[tuple[str, str, str, str, str]] = [] + xref_rows: list[tuple[str, str, str]] = [] + + uniref_id = elem.attrib.get("id") or "" + + cluster_id, name = extract_cluster(elem, ns, uniref_id) + updated_time, created_time = get_timestamps(uniref_id, existing_created) + + # Cluster table + cluster_rows.append( + ( + cluster_id, + name, + "protein", + None, + DATA_SOURCE, + ) + ) + # Entity table + entity_rows.append( + ( + cluster_id, + uniref_id, + "Cluster", + DATA_SOURCE, + updated_time, + created_time, + ) + ) -def parse_uniref_xml(local_gz, batch_size, existing_created): - """ - Parse UniRef XML (gzipped) and extract cluster, entity, cluster member, UniProtKB member, and cross-reference info. + # Cross references from representative and members + repr_db = elem.find("ns:representativeMember/ns:dbReference", ns) + extract_cross_refs(repr_db, xref_rows, ns) + + for mem in elem.findall("ns:member/ns:dbReference", ns): + extract_cross_refs(mem, xref_rows, ns) - Args: - local_gz (str): Local gzipped UniRef XML path. - batch_size (int): Maximum number of entries to parse. - existing_created (dict): Mapping from UniRef cluster ID to 'created' timestamp for idempotent imports. + # Cluster members (representative + members) + add_cluster_members(cluster_id, repr_db, elem, member_rows, ns) - Returns: - dict: Dictionary with lists for each CDM table + return { + "cluster_data": cluster_rows, + "entity_data": entity_rows, + "cluster_member_data": member_rows, + "cross_reference_data": xref_rows, + } + + +##### -------------- Parse Uniref XML --------------- ##### +def parse_uniref_xml(local_gz: str, batch_size: int, existing_created: dict[str, str]) -> dict[str, list[tuple]]: + """ + Stream-parse UniRef XML (gzipped) and extract CDM-like row tuples. """ - ns = {"ns": "http://uniprot.org/uniref"} # Namespace for XML parsing + ns = UNIREF_NS entry_count = 0 - # Initialize lists to collect parsed rows for different tables - cluster_data = [] - entity_data = [] - cluster_member_data = [] - cross_reference_data = [] + cluster_data: list[tuple] = [] + entity_data: list[tuple] = [] + cluster_member_data: list[tuple] = [] + cross_reference_data: list[tuple] = [] with gzip.open(local_gz, "rb") as f: - # Stream parse the XML to avoid memory issues with big files context = ET.iterparse(f, events=("end",)) for _, elem in context: - if elem.tag.endswith("entry"): - # Cluster basic info - cluster_id, name = extract_cluster(elem, ns) - - # Get UniRef cluster id and timestamps - uniref_id = elem.attrib.get("id") - updated_time, created_time = get_timestamps(uniref_id, existing_created) - - # Populate Cluster and Entity table data - cluster_data.append( - ( - cluster_id, # cluster_id - name, # cluster name - "protein", # entity_type (fixed value) - None, # description (not present) - "UniRef 100", # protocol_id - ) - ) - - entity_data.append( - ( - cluster_id, # entity_id (matches cluster_id) - uniref_id, # data_source_entity_id (UniRef100_xxx) - "Cluster", # entity_type - "UniRef 100", # data_source - updated_time, # updated - created_time, # created - ) - ) - - # Extract UniProtKB member attributes and cross-references - repr_db = elem.find("ns:representativeMember/ns:dbReference", ns) - extract_cross_refs(repr_db, cross_reference_data, ns) - - for mem in elem.findall("ns:member/ns:dbReference", ns): - extract_cross_refs(mem, cross_reference_data, ns) - - # ClusterMember table (representative + members) - add_cluster_members(cluster_id, repr_db, elem, cluster_member_data, ns) - - # Batch size limit - entry_count += 1 - if entry_count >= batch_size: - break - - # Release element to save memory - elem.clear() - - print(f"Parsed {entry_count} clusters") + if not elem.tag.endswith("entry"): + continue + + parsed = parse_uniref_entry(elem, existing_created, ns) + cluster_data.extend(parsed["cluster_data"]) + entity_data.extend(parsed["entity_data"]) + cluster_member_data.extend(parsed["cluster_member_data"]) + cross_reference_data.extend(parsed["cross_reference_data"]) + + entry_count += 1 + if entry_count >= batch_size: + break + + elem.clear() + + logger.info(f"Parsed {entry_count} clusters") return { "cluster_data": cluster_data, "entity_data": entity_data, @@ -238,10 +350,8 @@ def parse_uniref_xml(local_gz, batch_size, existing_created): } -##### -------------- Save dalta table and print the preview --------------- ##### - - -def save_delta_tables(spark, output_dir, data_dict) -> None: +##### -------------- Save delta table and print the preview --------------- ##### +def save_delta_tables(spark, output_dir, data_dict): # Cluster cluster_schema = StructType( [ @@ -255,7 +365,7 @@ def save_delta_tables(spark, output_dir, data_dict) -> None: cluster_df = spark.createDataFrame(data_dict["cluster_data"], cluster_schema) cluster_df.write.format("delta").mode("overwrite").save(os.path.join(output_dir, "Cluster")) - print(f"Cluster Delta table written to: {os.path.join(output_dir, 'Cluster')}") + logger.info(f"Cluster Delta table written to: {os.path.join(output_dir, 'Cluster')}") # Entity entity_schema = StructType( @@ -272,7 +382,7 @@ def save_delta_tables(spark, output_dir, data_dict) -> None: entity_df = spark.createDataFrame(data_dict["entity_data"], entity_schema) entity_table_path = os.path.join(output_dir, "Entity") entity_df.write.format("delta").mode("overwrite").save(entity_table_path) - print(f"Entity Delta table written to: {entity_table_path}") + logger.info(f"Entity Delta table written to: {entity_table_path}") # ClusterMember cluster_member_schema = StructType( @@ -288,7 +398,7 @@ def save_delta_tables(spark, output_dir, data_dict) -> None: cluster_member_df = spark.createDataFrame(data_dict["cluster_member_data"], cluster_member_schema) cluster_member_path = os.path.join(output_dir, "ClusterMember") cluster_member_df.write.format("delta").mode("overwrite").save(cluster_member_path) - print(f"ClusterMember Delta table written to: {cluster_member_path}") + logger.info(f"ClusterMember Delta table written to: {cluster_member_path}") # CrossReference cross_reference_schema = StructType( @@ -302,22 +412,22 @@ def save_delta_tables(spark, output_dir, data_dict) -> None: cross_reference_df = spark.createDataFrame(data_dict["cross_reference_data"], cross_reference_schema) cross_reference_path = os.path.join(output_dir, "CrossReference") cross_reference_df.write.format("delta").mode("overwrite").save(cross_reference_path) - print(f"CrossReference Delta table written to: {cross_reference_path}") + logger.info(f"CrossReference Delta table written to: {cross_reference_path}") # Previews - print("Sample Clusters:") + logger.info("Sample Clusters:") cluster_df.createOrReplaceTempView("Cluster") spark.sql("SELECT * FROM Cluster LIMIT 20").show(truncate=False) - print("Sample Entities:") + logger.info("Sample Entities:") entity_df.createOrReplaceTempView("Entity") spark.sql("SELECT * FROM Entity LIMIT 20").show(truncate=False) - print("Sample ClusterMembers:") + logger.info("Sample ClusterMembers:") cluster_member_df.createOrReplaceTempView("ClusterMember") spark.sql("SELECT * FROM ClusterMember LIMIT 20").show(truncate=False) - print("Sample CrossReferences:") + logger.info("Sample CrossReferences:") cross_reference_df.createOrReplaceTempView("CrossReference") spark.sql("SELECT * FROM CrossReference LIMIT 20").show(truncate=False) @@ -327,17 +437,27 @@ def build_spark_session(): builder = ( SparkSession.builder.appName("UniRef Cluster Extractor") .config("spark.sql.extensions", "io.delta.sql.DeltaSparkSessionExtension") - .config("spark.sql.catalog.spark_catalog", "org.apache.spark.sql.delta.catalog.DeltaCatalog") + .config( + "spark.sql.catalog.spark_catalog", + "org.apache.spark.sql.delta.catalog.DeltaCatalog", + ) ) return configure_spark_with_delta_pip(builder).getOrCreate() -# Click command-line interface for parameter parsing @click.command() @click.option("--ftp-url", required=True, help="FTP URL to UniRef100 XML file") @click.option("--output-dir", required=True, help="Output directory for Delta table") @click.option("--batch-size", default=1000, help="Number of UniRef entries to parse (limit)") -def main(ftp_url, output_dir, batch_size) -> None: +def main(ftp_url, output_dir, batch_size): + # set up logging in CLI context + logging.basicConfig( + level=logging.INFO, + format="%(asctime)s [%(levelname)s] (%(name)s:%(lineno)d %(message)s", + ) + + logger.info("Starting UniRef100/90/50 Import Pipeline") + # Set local path for downloaded gzipped XML file local_gz = os.path.join("/tmp", os.path.basename(ftp_url)) @@ -345,23 +465,31 @@ def main(ftp_url, output_dir, batch_size) -> None: try: download_file(ftp_url, local_gz) except URLError as e: - print(f"Error! Cannot download file: {e.reason}") + logger.error(f"Error! Cannot download file: {e.reason}") return # Start Spark session with Delta Lake support + logger.info("Building Spark session:") spark = build_spark_session() # Load existing entity creation timestamps - entity_table_path = os.path.join(output_dir, "Entity") - existing_created = load_existing_created(spark, entity_table_path) + try: + entity_table_path = os.path.join(output_dir, "Entity") + existing_created = load_existing_created(spark, entity_table_path) + + # Parse the UniRef XML and extract all CDM table data + logger.info("Parsing UniRef XML:") + data_dict = parse_uniref_xml(local_gz, batch_size, existing_created) - # Parse the UniRef XML and extract all CDM table data - data_dict = parse_uniref_xml(local_gz, batch_size, existing_created) + # Write parsed data to Delta tables in output directory + logger.info("Saving Delta tables:") + save_delta_tables(spark, output_dir, data_dict) - # Write parsed data to Delta tables in output directory - save_delta_tables(spark, output_dir, data_dict) + logger.info("UniRef100/90/50 Import Pipeline completed successfully.") - spark.stop() + finally: + spark.stop() + logger.info("Spark session stopped.") if __name__ == "__main__": diff --git a/src/cdm_data_loader_utils/parsers/xml_utils.py b/src/cdm_data_loader_utils/parsers/xml_utils.py new file mode 100644 index 0000000..d916799 --- /dev/null +++ b/src/cdm_data_loader_utils/parsers/xml_utils.py @@ -0,0 +1,124 @@ +""" +Shared XML helper utilities used by UniProt and UniRef parsers. + +This module centralizes common operations: +- Safe text extraction +- Safe attribute extraction +- Property parsing +- Evidence / dbReference parsing +- Cleaning dictionaries +- Deduplicating lists +""" + +import xml.etree.ElementTree as ET +from typing import Any + +# ============================================================ +# Basic Safe Accessors +# ============================================================ + + +def get_text(elem: ET.Element | None, default: str | None = None) -> str | None: + """Return elem.text if exists and non-empty.""" + if elem is None: + return default + if elem.text is None: + return default + text = elem.text.strip() + return text if text else default + + +def get_attr(elem: ET.Element | None, name: str, default: str | None = None) -> str | None: + """Return elem.get(name) safely.""" + if elem is None: + return default + val = elem.get(name) + return val.strip() if isinstance(val, str) else default + + +# ============================================================ +# List / Node Finders +# ============================================================ + + +def find_one(elem: ET.Element, xpath: str, ns: dict[str, str]): + """Return first element matching xpath or None.""" + results = elem.findall(xpath, ns) + return results[0] if results else None + + +def find_all_text(elem: ET.Element, xpath: str, ns: dict[str, str]) -> list[str]: + """Return list of text values from xpath matches (deduped).""" + texts = [] + for node in elem.findall(xpath, ns): + txt = get_text(node) + if txt: + texts.append(txt) + return list(dict.fromkeys(texts)) # preserve order, dedupe + + +def safe_list(x) -> list[Any]: + """Convert None → [].""" + if x is None: + return [] + if isinstance(x, list): + return x + return [x] + + +# ============================================================ +# dbReference / property parsing (shared by UniProt + UniRef) +# ============================================================ + + +def parse_properties(dbref: ET.Element | None, ns: dict[str, str]) -> dict[str, list[str]]: + """ + Extract key/value pairs from blocks. + """ + if dbref is None: + return {} + props = {} + for prop in dbref.findall("ns:property", ns): + ptype = prop.attrib.get("type") + pval = prop.attrib.get("value") + if ptype and pval: + if ptype not in props: + props[ptype] = [] + props[ptype].append(pval) + return props + + +def parse_db_references(elem: ET.Element, ns: dict[str, str], pub_types=("PubMed", "DOI")): + """ + Generic dbReference parser: + - Identify publication IDs (PubMed, DOI) + - Identify other cross-references (dbType:dbId) + """ + publications = [] + others = [] + + for dbref in elem.findall("ns:dbReference", ns): + db_type = dbref.get("type") + db_id = dbref.get("id") + + if not db_type or not db_id: + continue + + if db_type in pub_types: + publications.append(f"{db_type.upper()}:{db_id}") + else: + others.append(f"{db_type}:{db_id}") + + return publications, others + + +# ============================================================ +# Dict Cleaning +# ============================================================ + + +def clean_dict(d: dict[str, Any]) -> dict[str, Any]: + """ + Remove keys whose value is None or empty list. + """ + return {k: v for k, v in d.items() if v not in (None, [], {})} diff --git a/tests/parsers/test_shared_identifiers.py b/tests/parsers/test_shared_identifiers.py new file mode 100644 index 0000000..b76e9af --- /dev/null +++ b/tests/parsers/test_shared_identifiers.py @@ -0,0 +1,34 @@ +import xml.etree.ElementTree as ET + +from cdm_data_loader_utils.parsers.shared_identifiers import parse_identifiers_generic + + +def test_parse_identifiers_generic_basic() -> None: + # + # P12345 + # Q99999 + # + ns = {"ns": "dummy"} + entry = ET.Element("entry") + + a1 = ET.SubElement(entry, "accession") + a1.text = "P12345" + a2 = ET.SubElement(entry, "accession") + a2.text = "Q99999" + + # Add namespace prefix to match xpath + a1.tag = "{dummy}accession" + a2.tag = "{dummy}accession" + + rows = parse_identifiers_generic( + entry=entry, + xpath="ns:accession", + prefix="UniProt", + ns=ns, + ) + + assert len(rows) == 2 + assert rows[0]["identifier"] == "UniProt:P12345" + assert rows[1]["identifier"] == "UniProt:Q99999" + assert rows[0]["source"] == "UniProt" + assert rows[0]["description"] == "UniProt accession" diff --git a/tests/parsers/test_uniprot.py b/tests/parsers/test_uniprot.py index 105fb76..86ffca3 100644 --- a/tests/parsers/test_uniprot.py +++ b/tests/parsers/test_uniprot.py @@ -1,4 +1,4 @@ -"""Tests for the UniProt parser. +""" This file uses pytest to provide parameterized and functional tests for all major UniProt parsing utility functions, ensuring correct parsing and transformation of @@ -16,756 +16,729 @@ - parse_uniprot_entry: Full record parsing, all fields together How to run in the terminal: - PYTHONPATH=src pytest tests/test_uniprot.py + pytest tests/uniprot_refactor/test_uniprot_parsers.py """ import datetime -import re +import json import xml.etree.ElementTree as ET -from typing import Any +from pathlib import Path import pytest from cdm_data_loader_utils.parsers.uniprot import ( build_datasource_record, - generate_cdm_id, parse_associations, + parse_cross_references, parse_evidence_map, parse_identifiers, parse_names, parse_protein_info, - parse_publications, - parse_uniprot_entry, + save_datasource_record, ) -# Regular expression to validate UUID format -UUID_PATTERN = re.compile(r"^[a-f0-9]{8}-[a-f0-9]{4}-[1-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}$", re.IGNORECASE) +NS_URI = "https://uniprot.org/uniprot" + +@pytest.fixture( + params=[ + "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz", + "http://example.org/uniprot_test.xml.gz", + ] +) +def xml_url(request): + return request.param -@pytest.mark.parametrize("n", range(5)) -def test_generate_cdm_id_format(n: int) -> None: - uuid = generate_cdm_id() - assert uuid.startswith("CDM:") - uuid_str = uuid[4:] - assert UUID_PATTERN.match(uuid_str), f"{uuid_str} is not a valid UUID" +def test_build_datasource_record(xml_url): + record = build_datasource_record(xml_url) -## build_datasource_record ## -def test_build_datasource_record() -> None: - url = "https://example.com/uniprot.xml.gz" - record = build_datasource_record(url) + # ---- basic structure ---- assert isinstance(record, dict) - assert set(record.keys()) == {"name", "source", "url", "accessed", "version"} + + # ---- fixed fields ---- assert record["name"] == "UniProt import" assert record["source"] == "UniProt" - assert record["url"] == url - - # check accessed - accessed_dt = datetime.datetime.fromisoformat(record["accessed"]) - now = datetime.datetime.now(datetime.UTC) - delta = abs((now - accessed_dt).total_seconds()) - assert delta < 10 + assert record["url"] == xml_url assert record["version"] == 115 + # ---- accessed field ---- + accessed = record.get("accessed") + assert accessed is not None -@pytest.mark.parametrize("bad_url", [None, ""]) -def test_build_datasource_record_bad(bad_url: str | None) -> None: - record = build_datasource_record(bad_url) - assert record["url"] == bad_url + parsed = datetime.datetime.fromisoformat(accessed) + assert parsed.tzinfo is not None + assert parsed.tzinfo == datetime.UTC -## parse_identifiers function test ## -@pytest.mark.parametrize( - ("xml_str", "cdm_id", "expected"), - [ - ### multiple accessions, expect two dict, every dic use the same cdm_id - ### identifier according to number - ( - """ - - Q9V2L2 - G8ZFP4 - - """, - "CDM:001", - [ - { - "entity_id": "CDM:001", - "identifier": "UniProt:Q9V2L2", - "source": "UniProt", - "description": "UniProt accession", - }, - { - "entity_id": "CDM:001", - "identifier": "UniProt:G8ZFP4", - "source": "UniProt", - "description": "UniProt accession", - }, - ], - ), - ### Use single accession - ( - """ - - X00001 - - """, - "CDM:002", - [ - { - "entity_id": "CDM:002", - "identifier": "UniProt:X00001", - "source": "UniProt", - "description": "UniProt accession", - } - ], - ), - ### No accession - ( - """ - - - """, - "CDM:003", - [], - ), - ], -) -def test_parse_identifiers(xml_str: str, cdm_id: str, expected: list[dict[str, str]]) -> None: +def test_save_datasource_record(tmp_path: Path, xml_url): + """ + save_datasource_record should: + - create output directory if missing + - write datasource.json + - return the same content that is written to disk """ - This approach ensures that parse_identifiers correctly parses and structures identifier data. + output_dir = tmp_path / "output" - The parsed Element object and the provided CDM_id are passed to the parse_identifiers funtion. - The function is expected to extract all relevant identifier information from the XML and return list of dict. + # ---- call function ---- + result = save_datasource_record(xml_url, str(output_dir)) - The test compares the result output with the predefined expected result using an assert statement. + # ---- return value sanity ---- + assert isinstance(result, dict) + assert result["url"] == xml_url + assert result["source"] == "UniProt" + assert result["name"] == "UniProt import" + assert "accessed" in result + assert "version" in result - """ - entry = ET.fromstring(xml_str) - result = parse_identifiers(entry, cdm_id) - assert result == expected + # ---- file existence ---- + output_file = output_dir / "datasource.json" + assert output_file.exists() + assert output_file.is_file() + # ---- file content correctness ---- + with open(output_file, encoding="utf-8") as f: + on_disk = json.load(f) -""" - This parameterized pytest function tests the correctness of the parse_names function for various UniProt XML entry scenarios. + assert on_disk == result - XML string representing a UniProt entry with different protein names: - top-level - recommended names, - alternative names, - combinations, - no names - cdm_id: CDM entry ID +def make_entry(names=None, protein_names=None): + entry = ET.Element(f"{{{NS_URI}}}entry") - Output: - A list of name records with their metadata + # + for n in names or []: + e = ET.SubElement(entry, f"{{{NS_URI}}}name") + e.text = n -""" + # block + if protein_names: + protein = ET.SubElement(entry, f"{{{NS_URI}}}protein") + + for tag, logical in [ + ("recommendedName", "recommended"), + ("alternativeName", "alternative"), + ]: + if logical not in protein_names: + continue + + block = ET.SubElement(protein, f"{{{NS_URI}}}{tag}") + for xml_tag in ["fullName", "shortName"]: + val = protein_names[logical].get(xml_tag.replace("Name", "")) + if val: + e = ET.SubElement(block, f"{{{NS_URI}}}{xml_tag}") + e.text = val + + return entry -## parse_names function test ## @pytest.mark.parametrize( - ("xml_str", "cdm_id", "expected"), + "entry_kwargs, cdm_id, expected", [ - # Only top-level + # Only ( - """ - MainProteinName - """, - "CDM:001", - [ - { - "entity_id": "CDM:001", - "name": "MainProteinName", - "description": "UniProt protein name", - "source": "UniProt", - } - ], - ), - # RecommendedName (fullName and shortName) - ( - """ - - - RecFullName - RecShort - - - """, - "CDM:002", - [ - { - "entity_id": "CDM:002", - "name": "RecFullName", - "description": "UniProt recommended full name", - "source": "UniProt", - }, - { - "entity_id": "CDM:002", - "name": "RecShort", - "description": "UniProt recommended short name", - "source": "UniProt", - }, - ], + {"names": ["ProteinA"]}, + "cdm_1", + { + ("ProteinA", "UniProt entry name"), + }, ), - # AlternativeName (fullName and shortName) + # entry name + recommended full name ( - """ - - - AltFullName1 - AltShort1 - - - AltFullName2 - - - """, - "CDM:003", - [ - { - "entity_id": "CDM:003", - "name": "AltFullName1", - "description": "UniProt alternative full name", - "source": "UniProt", - }, - { - "entity_id": "CDM:003", - "name": "AltShort1", - "description": "UniProt alternative short name", - "source": "UniProt", - }, - { - "entity_id": "CDM:003", - "name": "AltFullName2", - "description": "UniProt alternative full name", - "source": "UniProt", + { + "names": ["ProteinB"], + "protein_names": { + "recommended": {"full": "Rec Full B", "short": None}, }, - ], + }, + "cdm_2", + { + ("ProteinB", "UniProt entry name"), + ("Rec Full B", "UniProt recommended full name"), + }, ), - # Mixed: top-level and + # everything ( - """ - TopLevel - - - MixedFull - - - """, - "CDM:004", - [ - { - "entity_id": "CDM:004", - "name": "TopLevel", - "description": "UniProt protein name", - "source": "UniProt", - }, - { - "entity_id": "CDM:004", - "name": "MixedFull", - "description": "UniProt recommended full name", - "source": "UniProt", + { + "names": ["ProteinC"], + "protein_names": { + "recommended": {"full": "Rec Full C", "short": "Rec Short C"}, + "alternative": {"full": "Alt Full C", "short": "Alt Short C"}, }, - ], - ), - # No names at all - ( - """ - """, - "CDM:005", - [], + }, + "cdm_3", + { + ("ProteinC", "UniProt entry name"), + ("Rec Full C", "UniProt recommended full name"), + ("Rec Short C", "UniProt recommended short name"), + ("Alt Full C", "UniProt alternative full name"), + ("Alt Short C", "UniProt alternative short name"), + }, ), ], ) -def test_parse_names(xml_str: str, cdm_id: str, expected: list[dict[str, str]]) -> None: - entry = ET.fromstring(xml_str) - result = parse_names(entry, cdm_id) - assert result == expected +def test_parse_names_parametrized(entry_kwargs, cdm_id, expected): + entry = make_entry(**entry_kwargs) + rows = parse_names(entry, cdm_id) -""" - - This test ensures parse_protein_info works correctly for different combinations of data - Including cases with no protein info, sequence only, existence only or EC numbers - - This approach thoroughly validates that parse_protein_info can accurately extract, combine and structure metadata field. + # ---- row count ---- + assert len(rows) == len(expected) - Include: - EC Number, - existence evidence, - sequence + # ---- content ---- + observed = {(r["name"], r["description"]) for r in rows} + assert observed == expected -""" + # ---- entity_id and source ---- + for r in rows: + assert r["entity_id"] == cdm_id + assert r["source"] == "UniProt" -## parse_protein_info function test ## @pytest.mark.parametrize( - ("xml_str", "cdm_id", "expected"), + "build_entry, cdm_id, expected", [ - # There are multiple ecNumbers under the recommend names - ( - """ - - - 1.2.3.4 - 5.6.7.8 - - - """, - "CDM:001", - {"ec_numbers": ["1.2.3.4", "5.6.7.8"]}, - ), - # alternativeName has EC Number + # -------------------------------------------------- + # Empty entry -> None + # -------------------------------------------------- ( - """ - - - 3.3.3.3 - - - """, - "CDM:002", - {"ec_numbers": ["3.3.3.3"]}, + lambda: ET.Element(f"{{{NS_URI}}}entry"), + "cdm_1", + None, ), - # If have both proteinExistence evidence and existence + # -------------------------------------------------- + # Only EC numbers + # -------------------------------------------------- ( - """ - - """, - "CDM:003", + lambda: ( + lambda entry: ( + ET.SubElement( + ET.SubElement( + ET.SubElement(entry, f"{{{NS_URI}}}protein"), + f"{{{NS_URI}}}recommendedName", + ), + f"{{{NS_URI}}}ecNumber", + ).__setattr__("text", "1.1.1.1"), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_2", { - "protein_id": "CDM:003", - "evidence_for_existence": "evidence at protein level", + "ec_numbers": "1.1.1.1", }, ), - # Sequence only + # -------------------------------------------------- + # Only sequence + entry modified + # -------------------------------------------------- ( - """ - - MAGNLSKVAAVSGVAAAVLGK - - """, - "CDM:004", + lambda: ( + lambda entry: ( + entry.set("modified", "2024-01-01"), + ET.SubElement( + entry, + f"{{{NS_URI}}}sequence", + { + "length": "100", + "mass": "12345", + "checksum": "ABC", + "version": "2", + }, + ).__setattr__("text", "MKTIIALSY"), + entry, + )[2] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_3", { - "length": "357", + "length": "100", "mass": "12345", - "checksum": "ABCD", - "modified": "2024-05-21", + "checksum": "ABC", "sequence_version": "2", - "sequence": "MAGNLSKVAAVSGVAAAVLGK", + "sequence": "MKTIIALSY", + "entry_modified": "2024-01-01", }, ), - # Combine with three elements: proteinExistence, sequence and ecNumbers + # -------------------------------------------------- + # Everything + # -------------------------------------------------- ( - """ - - - 3.3.3.3 - - - 8.8.8.8 - - - - - MKTLLTGAAT - - """, - "CDM:005", + lambda: ( + lambda entry: ( + entry.set("modified", "2024-02-02"), + # protein + EC + ET.SubElement( + ET.SubElement( + ET.SubElement(entry, f"{{{NS_URI}}}protein"), + f"{{{NS_URI}}}recommendedName", + ), + f"{{{NS_URI}}}ecNumber", + ).__setattr__("text", "3.5.4.4"), + # proteinExistence + ET.SubElement( + entry, + f"{{{NS_URI}}}proteinExistence", + {"type": "evidence at protein level"}, + ), + # sequence + ET.SubElement( + entry, + f"{{{NS_URI}}}sequence", + { + "length": "250", + "mass": "99999", + "checksum": "XYZ", + "modified": "2023-12-01", + "version": "1", + }, + ).__setattr__("text", "MADEUPSEQUENCE"), + entry, + )[4] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_4", { - "ec_numbers": ["3.3.3.3", "8.8.8.8"], - "protein_id": "CDM:005", - "evidence_for_existence": "evidence at transcript level", - "length": "10", - "mass": "1000", + "ec_numbers": "3.5.4.4", + "protein_id": "cdm_4", + "evidence_for_existence": "evidence at protein level", + "length": "250", + "mass": "99999", "checksum": "XYZ", - "modified": "2021-12-01", + "modified": "2023-12-01", "sequence_version": "1", - "sequence": "MKTLLTGAAT", + "sequence": "MADEUPSEQUENCE", + "entry_modified": "2024-02-02", }, ), - # return None - ("""""", "CDM:006", None), ], ) -def test_parse_protein_info(xml_str: str, cdm_id: str, expected: dict[str, Any]) -> None: - entry = ET.fromstring(xml_str) - result = parse_protein_info(entry, cdm_id) - assert result == expected - +def test_parse_protein_info(build_entry, cdm_id, expected): + entry = build_entry() -""" - - This parameterized pytest function verifies the behavior of the parse_evidence_map function - for different UniProt XML entry structures involving evidence elements. - - xml_str: Simulates a UniProt entry with various and sub-structures, - including cases with multiple evidence elements, missing sources, or no evidence at all. - - expected: A dictionary mapping evidence keys to their extracted details—such as evidence type, - supporting objects, and publication references. - - Ensure parse_evidence_map: - Accurately extract evidence keys and types - Correctly classify supporting objects and publication references - Handle entries with absent sources or evidence elements - Represent all relevant evidence metadata in the required structure + result = parse_protein_info(entry, cdm_id) -""" + if expected is None: + assert result is None + else: + assert isinstance(result, dict) + assert result == expected -## parse_evidence_map function test ## @pytest.mark.parametrize( - ("xml_str", "expected"), + "build_xml, expected", [ - # Single evidence，include PubMed and supporting object + # -------------------------------------------------- + # No evidence elements + # -------------------------------------------------- ( - """ - - - - - - - """, - { - "1": { - "evidence_type": "ECO:0000255", - "supporting_objects": ["Ensembl:ENSG00001"], - "publications": ["PMID:123456"], - } - }, + lambda: ET.Element(f"{{{NS_URI}}}entry"), + {}, ), - # multiple evidences + # -------------------------------------------------- + # Evidence without key + # -------------------------------------------------- ( - """ - - - - - - - - - - - """, - { - "E1": { - "evidence_type": "ECO:0000313", - "supporting_objects": None, - "publications": ["PMID:654321"], - }, - "E2": { - "evidence_type": "ECO:0000250", - "supporting_objects": ["PDB:2N7Q"], - "publications": None, - }, - }, + lambda: ( + lambda entry: ( + ET.SubElement(entry, f"{{{NS_URI}}}evidence", {"type": "ECO:0000269"}), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + {}, ), - # no source + # -------------------------------------------------- + # Evidence with key, no source + # -------------------------------------------------- ( - """ - - """, + lambda: ( + lambda entry: ( + ET.SubElement( + entry, + f"{{{NS_URI}}}evidence", + {"key": "1", "type": "ECO:0000313"}, + ), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), { - "X1": { - "evidence_type": "ECO:9999999", - "supporting_objects": None, - "publications": None, + "1": { + "evidence_type": "ECO:0000313", } }, ), - # no evidence - ( - """ - """, - {}, - ), - # one evidence with multiple supporting objects + # -------------------------------------------------- + # Evidence with PUBMED with other refs + # -------------------------------------------------- ( - """ - - - - - - - """, + lambda: ( + lambda entry: ( + lambda ev: ( + ET.SubElement( + ET.SubElement(ev, f"{{{NS_URI}}}source"), + f"{{{NS_URI}}}dbReference", + {"type": "PubMed", "id": "12345"}, + ), + ET.SubElement( + ET.SubElement(ev, f"{{{NS_URI}}}source"), + f"{{{NS_URI}}}dbReference", + {"type": "GO", "id": "GO:0008150"}, + ), + entry, + )[2] + )( + ET.SubElement( + entry, + f"{{{NS_URI}}}evidence", + {"key": "E2", "type": "ECO:0000269"}, + ) + ) + )(ET.Element(f"{{{NS_URI}}}entry")), { - "K1": { + "E2": { "evidence_type": "ECO:0000269", - "supporting_objects": ["Ensembl:ENS1", "RefSeq:RS123"], - "publications": None, + "publications": ["PMID:12345"], } }, ), ], ) -def test_parse_evidence_map(xml_str: str, expected: dict[str, Any]) -> None: - entry = ET.fromstring(xml_str) +def test_parse_evidence_map_parametrized(build_xml, expected): + entry = build_xml() result = parse_evidence_map(entry) - assert result == expected - -""" - - xml_strings: models a UniProt entry with different types of possible associations - cdm_id: uniquely identifies the protein being parsed - evidence_map: supplies external evidence metadata for associations - expected: list of association dictionaries - - Arg: - The function correctly links proteins to organism taxonomy. - Cross-references are properly included, evidence metadata is correctly merged. - Associations derived from catalytic activity and cofactor comments are correctly generated. - All combinations and edge cases are handled robustly. - -""" + assert isinstance(result, dict) + assert result == expected -## parse_associations function test ## @pytest.mark.parametrize( - ("xml_str", "cdm_id", "evidence_map", "expected"), + "build_xml, cdm_id, evidence_map, expected", [ - # organism association（NCBI Taxonomy dbReference） + # -------------------------------------------------- + # Taxonomy association only + # -------------------------------------------------- ( - """ - - - - """, - "CDM:1", + lambda: ( + lambda entry: ( + ET.SubElement( + ET.SubElement(entry, f"{{{NS_URI}}}organism"), + f"{{{NS_URI}}}dbReference", + {"type": "NCBI Taxonomy", "id": "1234"}, + ), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_1", {}, - [{"subject": "CDM:1", "object": "NCBITaxon:9606"}], - ), - # dbReference with evidence key - ( - """ - - """, - "CDM:2", - { - "E1": { - "evidence_type": "ECO:0000250", - "supporting_objects": ["Ensembl:ENS1"], - "publications": ["PMID:1234"], - } - }, [ { - "subject": "CDM:2", - "object": "PDB:2N7Q", - "evidence_type": "ECO:0000250", - "supporting_objects": ["Ensembl:ENS1"], - "publications": ["PMID:1234"], + "subject": "cdm_1", + "object": "NCBITaxon:1234", + "predicate": "in_taxon", } ], ), - # comment catalytic activity (reaction) with evidence key + # -------------------------------------------------- + # Catalytic activity with evidence + # -------------------------------------------------- ( - """ - - - - - - """, - "CDM:3", + lambda: ( + lambda entry: ( + lambda comment: ( + lambda reaction: ( + ET.SubElement( + reaction, + f"{{{NS_URI}}}dbReference", + {"type": "Rhea", "id": "RHEA:12345"}, + ), + entry, + )[1] + )( + ET.SubElement( + comment, + f"{{{NS_URI}}}reaction", + {"evidence": "E1"}, + ) + ) + )( + ET.SubElement( + entry, + f"{{{NS_URI}}}comment", + {"type": "catalytic activity"}, + ) + ) + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_2", { - "E2": { - "evidence_type": "ECO:0000313", - "publications": ["PMID:2222"], + "E1": { + "evidence_type": "ECO:0000269", + "publications": ["PMID:12345"], } }, [ { - "subject": "CDM:3", + "subject": "cdm_2", "predicate": "catalyzes", - "object": "Rhea:12345", - "evidence_type": "ECO:0000313", - "publications": ["PMID:2222"], + "object": "Rhea:RHEA:12345", + "evidence_type": "ECO:0000269", + "publications": ["PMID:12345"], } ], ), - # Comment cofactor without evidence + # -------------------------------------------------- + # Cofactor association + # -------------------------------------------------- ( - """ - - - - - - """, - "CDM:4", + lambda: ( + lambda entry: ( + lambda comment: ( + ET.SubElement( + ET.SubElement( + comment, + f"{{{NS_URI}}}cofactor", + ), + f"{{{NS_URI}}}dbReference", + {"type": "ChEBI", "id": "CHEBI:15377"}, + ), + entry, + )[1] + )( + ET.SubElement( + entry, + f"{{{NS_URI}}}comment", + {"type": "cofactor"}, + ) + ) + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_3", {}, [ { - "subject": "CDM:4", + "subject": "cdm_3", "predicate": "requires_cofactor", "object": "ChEBI:CHEBI:15377", } ], ), - # Several relevant relationship（with organism and dbReference） - ( - """ - - - - - """, - "CDM:5", - {}, - [ - {"subject": "CDM:5", "object": "NCBITaxon:562"}, - {"subject": "CDM:5", "object": "RefSeq:NP_414543"}, - ], - ), - # if it is empty entry, return to [] - ("""""", "CDM:6", {}, []), ], ) -def test_parse_associations( - xml_str: str, cdm_id: str, evidence_map: dict[str, Any], expected: list[dict[str, str]] -) -> None: - entry = ET.fromstring(xml_str) - result = parse_associations(entry, cdm_id, evidence_map) - assert result == expected - +def test_parse_associations_parametrized(build_xml, cdm_id, evidence_map, expected): + entry = build_xml() -""" - - xml_str: Uniprot entry include , , - Refer: PubMed, DOI, GeneBank, DDBJ, EMBL - - Output: List of publication identifier - - Arg: - Extract publication of references - Recognize and format database types ( with prefixing “PMID:”, “DOI:”) - Handle entries with multiple or mixed publication types - Return an empty list if no publication data. + result = parse_associations(entry, cdm_id, evidence_map) -""" + assert isinstance(result, list) + assert result == expected -## parse_publications function test ## @pytest.mark.parametrize( - ("xml_str", "expected"), + "build_xml, cdm_id, expected", [ - # Single PubMed + # -------------------------------------------------- + # No dbReference + # -------------------------------------------------- ( - """ - - - - - - """, - ["PMID:12345"], + lambda: ET.Element(f"{{{NS_URI}}}entry"), + "cdm_1", + [], ), - # Multiple types include (PubMed, DOI, GenBank) + # -------------------------------------------------- + # dbReference with CURIE id + # -------------------------------------------------- ( - """ - - - - - - - - """, - ["PMID:55555", "DOI:10.1000/j.jmb.2020.01.001"], + lambda: ( + lambda entry: ( + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"type": "GO", "id": "GO:0008150"}, + ), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_2", + [ + { + "entity_id": "cdm_2", + "xref_type": "GO", + "xref_value": "GO:0008150", + "xref": "GO:0008150", + } + ], ), - # Multiple references + # -------------------------------------------------- + # dbReference without CURIE (prefix) + # -------------------------------------------------- ( - """ - - - - - - - - - - - """, - ["DOI:10.1000/jmb.123456", "PMID:98765"], + lambda: ( + lambda entry: ( + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"type": "CDD", "id": "cd04253"}, + ), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_3", + [ + { + "entity_id": "cdm_3", + "xref_type": "CDD", + "xref_value": "cd04253", + "xref": "CDD:cd04253", + } + ], + ), + # -------------------------------------------------- + # Mixed dbReferences + # -------------------------------------------------- + ( + lambda: ( + lambda entry: ( + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"type": "GO", "id": "GO:0003674"}, + ), + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"type": "PDB", "id": "1ABC"}, + ), + entry, + )[2] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_4", + [ + { + "entity_id": "cdm_4", + "xref_type": "GO", + "xref_value": "GO:0003674", + "xref": "GO:0003674", + }, + { + "entity_id": "cdm_4", + "xref_type": "PDB", + "xref_value": "1ABC", + "xref": "PDB:1ABC", + }, + ], ), - # dbReference: DDBJ and EMBL + # -------------------------------------------------- + # Missing type or id + # -------------------------------------------------- ( - """ - - - - - - - """, + lambda: ( + lambda entry: ( + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"type": "GO"}, # missing id + ), + ET.SubElement( + entry, + f"{{{NS_URI}}}dbReference", + {"id": "123"}, # missing type + ), + entry, + )[2] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_5", [], ), - # no publication - ("""""", []), ], ) -def test_parse_publications(xml_str: str, expected: list[str]) -> None: - entry = ET.fromstring(xml_str) - result = parse_publications(entry) +def test_parse_cross_references_parametrized(build_xml, cdm_id, expected): + entry = build_xml() + + result = parse_cross_references(entry, cdm_id) + + assert isinstance(result, list) assert result == expected -## parse_uniprot_entry function test ## @pytest.mark.parametrize( - ("xml_str", "datasource_name", "prev_created"), + "build_xml, cdm_id, expected", [ + # -------------------------------------------------- + # No accession + # -------------------------------------------------- ( - """ - - P12345 - ProteinX - - - ProteinX Full Name - - - - - - - - - - - - """, - "UniProt import", - None, + lambda: ET.Element(f"{{{NS_URI}}}entry"), + "cdm_1", + [], + ), + # -------------------------------------------------- + # Single accession + # -------------------------------------------------- + ( + lambda: ( + lambda entry: ( + ET.SubElement(entry, f"{{{NS_URI}}}accession").__setattr__("text", "P12345"), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_2", + [ + { + "entity_id": "cdm_2", + "identifier": "UniProt:P12345", + "source": "UniProt", + "description": "UniProt accession", + } + ], + ), + # -------------------------------------------------- + # Multiple accessions + # -------------------------------------------------- + ( + lambda: ( + lambda entry: ( + ET.SubElement(entry, f"{{{NS_URI}}}accession").__setattr__("text", "Q11111"), + ET.SubElement(entry, f"{{{NS_URI}}}accession").__setattr__("text", "Q22222"), + entry, + )[2] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_3", + [ + { + "entity_id": "cdm_3", + "identifier": "UniProt:Q11111", + "source": "UniProt", + "description": "UniProt accession", + }, + { + "entity_id": "cdm_3", + "identifier": "UniProt:Q22222", + "source": "UniProt", + "description": "UniProt accession", + }, + ], + ), + # -------------------------------------------------- + # parse_identifiers_generic already sets source/description → setdefault + # -------------------------------------------------- + ( + lambda: ( + lambda entry: ( + ET.SubElement(entry, f"{{{NS_URI}}}accession").__setattr__("text", "A0A000"), + entry, + )[1] + )(ET.Element(f"{{{NS_URI}}}entry")), + "cdm_4", + [ + { + "entity_id": "cdm_4", + "identifier": "UniProt:A0A000", + "source": "UniProt", # remains + "description": "UniProt accession", # remains + } + ], ), ], ) -def test_parse_uniprot_entry(xml_str: str, datasource_name: str, prev_created: None) -> None: - entry = ET.fromstring(xml_str) - cdm_id = generate_cdm_id() - - current_timestamp = "2024-07-17T13:00:00Z" - - record = parse_uniprot_entry(entry, cdm_id, current_timestamp, datasource_name, prev_created) - - entity = record["entity"] - assert entity["entity_type"] == "protein" - assert entity["data_source"] == datasource_name - assert entity["version"] == "3" - assert entity["uniprot_created"] == "2020-01-01" - assert entity["uniprot_modified"] == "2021-01-01" - assert entity["entity_id"].startswith("CDM:") - - # identifiers/names/associations/publications - assert isinstance(record["identifiers"], list) - assert isinstance(record["names"], list) - assert isinstance(record["associations"], list) - assert isinstance(record["publications"], list) +def test_parse_identifiers_parametrized(build_xml, cdm_id, expected): + entry = build_xml() + + result = parse_identifiers(entry, cdm_id) + + assert isinstance(result, list) + assert result == expected diff --git a/tests/parsers/test_uniref.py b/tests/parsers/test_uniref.py index 630949c..9ca5360 100644 --- a/tests/parsers/test_uniref.py +++ b/tests/parsers/test_uniref.py @@ -1,284 +1,318 @@ -"""Tests for the UniRef importer.""" +import os +import sys -import datetime as dt -import textwrap -import xml.etree.ElementTree as ET +sys.path.insert(0, os.path.abspath(os.path.dirname(__file__))) +import gzip +import tempfile +import xml.etree.ElementTree as ET +from datetime import datetime, timezone import pytest from cdm_data_loader_utils.parsers.uniref import ( - add_cluster_members, cdm_entity_id, + get_timestamps, extract_cluster, - extract_cross_refs, get_accession_and_seed, - get_timestamps, + add_cluster_members, + extract_cross_refs, + parse_uniref_xml, ) +NS = {"ns": "http://uniprot.org/uniref"} + +# --------------------------------------------------------- +# cdm_entity_id +# --------------------------------------------------------- @pytest.mark.parametrize( - ("accession", "expected_prefix"), - [("A0B0123456", "CDM:"), ("P01234", "CDM:"), ("", None), (None, None)], + "value, should_raise", + [ + ("A0A009HJL9", False), + ("UniRef100_A0A009HJL9", False), + ("", True), + (None, True), + ], ) -def test_cdm_entity_id(accession: str | None, expected_prefix: str | None) -> None: - """Ensure that CDM entities start with the appropriate prefix.""" - result = cdm_entity_id(accession) - if expected_prefix is None: - assert result is None +def test_cdm_entity_id(value, should_raise): + if should_raise: + with pytest.raises(ValueError): + cdm_entity_id(value) else: - assert result.startswith(expected_prefix) + out = cdm_entity_id(value) + assert isinstance(out, str) + assert out.startswith("CDM:") +# --------------------------------------------------------- +# get_timestamps +# --------------------------------------------------------- @pytest.mark.parametrize( - ("xml_str", "expected_name"), + "uniref_id, existing, now, expect_created_same_as_updated", [ ( - "" - "TestName", - "TestName", + "UniRef100_A", + {"UniRef100_A": "2024-01-01T00:00:00+00:00"}, + datetime(2025, 1, 1, 0, 0, 0, tzinfo=timezone.utc), + False, ), ( - "", - "UNKNOWN", + "UniRef100_B", + {}, + datetime(2025, 1, 1, 0, 0, 0, tzinfo=timezone.utc), + True, + ), + ( + "UniRef100_C", + {}, + None, + True, ), ], ) -def test_extract_cluster(xml_str: str, expected_name: str) -> None: - """Test cluster extraction from XML.""" - ns = {"ns": "http://uniprot.org/uniref"} - elem = ET.fromstring(xml_str) - cluster_id, name = extract_cluster(elem, ns) - assert cluster_id.startswith("CDM:") - assert isinstance(cluster_id, str) - assert name == expected_name +def test_get_timestamps(uniref_id, existing, now, expect_created_same_as_updated): + updated, created = get_timestamps(uniref_id, existing, now) + + assert isinstance(updated, str) + assert isinstance(created, str) + assert updated.endswith("+00:00") + if expect_created_same_as_updated: + assert updated == created + else: + assert updated != created + +@pytest.mark.parametrize("bad_id", ["", None]) +def test_get_timestamps_rejects_empty_uniref_id(bad_id): + with pytest.raises(ValueError): + get_timestamps(bad_id, {}, None) + + +# --------------------------------------------------------- +# add_cluster_members +# --------------------------------------------------------- @pytest.mark.parametrize( - ("uniref_id", "existing_created", "now", "expected"), + "repr_xml, member_xmls, expected_count", [ - # Has existing_created ( - "UniRef100_A", - {"UniRef100_A": "2024-01-01T00:00:00"}, - dt.datetime(2025, 1, 1, 0, 0, 0, tzinfo=dt.UTC), - ("2025-01-01T00:00:00", "2024-01-01T00:00:00"), + """ + + + + + """, + [ + """ + + + + """, + """ + + + + """, + ], + 3, ), - # There is no existing_created ( - "UniRef100_B", - {"UniRef100_A": "2024-01-01T00:00:00"}, - dt.datetime(2025, 1, 1, 0, 0, 0, tzinfo=dt.UTC), - ("2025-01-01T00:00:00", "2025-01-01T00:00:00"), + None, + [ + """ + + + + """, + ], + 1, ), - # There is no existing_created，also not provide "now" + (None, [], 0), + ], +) +def test_add_cluster_members(repr_xml, member_xmls, expected_count): + cluster_id = "CDM_CLUSTER" + repr_db = ET.fromstring(repr_xml) if repr_xml else None + + entry = ET.Element("{http://uniprot.org/uniref}entry") + for m in member_xmls: + mem = ET.SubElement(entry, "{http://uniprot.org/uniref}member") + mem.append(ET.fromstring(m)) + + rows = [] + add_cluster_members(cluster_id, repr_db, entry, rows, NS) + + assert len(rows) == expected_count + for r in rows: + assert r[0] == cluster_id + assert r[1].startswith("CDM:") + assert r[4] == "1.0" + + +# --------------------------------------------------------- +# extract_cluster +# --------------------------------------------------------- +@pytest.mark.parametrize( + "xml_str, uniref_id, expected_name", + [ ( - "UniRef100_C", - {}, - None, # The system automatically use the current time - None, # Only assert that the return is a string and they are equal + "Test Cluster Name", + "UniRef100_A", + "Test Cluster Name", + ), + ( + "", + "UniRef100_B", + "UNKNOWN", ), ], ) -def test_get_timestamps(uniref_id: str, existing_created: str, now: dt.datetime, expected: tuple[str] | None) -> None: - """Test timestamps.""" - result = get_timestamps(uniref_id, existing_created, now) - if expected is not None: - assert result == expected - else: - formatted_now, created_time = result - assert formatted_now == created_time - assert isinstance(formatted_now, str) - assert len(formatted_now) == 19 # "YYYY-MM-DDTHH:MM:SS" ---> 19 bites +def test_extract_cluster(xml_str, uniref_id, expected_name): + elem = ET.fromstring(xml_str) + + cluster_id, name = extract_cluster(elem, NS, uniref_id) + + # ---- cluster_id checks ---- + assert isinstance(cluster_id, str) + assert cluster_id.startswith("CDM:") + + # ---- name checks ---- + assert name == expected_name @pytest.mark.parametrize( - ("xml_str", "expected_acc", "expected_is_seed"), + "xml_str, expected_acc, expected_is_seed", [ - # Have accession and isSeed + # accession + isSeed=true ( """ - - - - - """, + + + + + """, "A0A009HJL9", True, ), - # Only accession, no isSeed + # accession only ( """ - - - - """, + + + + """, "A0A241V597", False, ), - # No accession, only id + # no accession ( """ - - """, - "ID_ONLY", + + + + """, + None, + False, + ), + # dbref is None + ( + None, + None, False, ), - # None - (None, None, False), ], ) -def test_get_accession_and_seed(xml_str: str | None, expected_acc: str | None, expected_is_seed: bool) -> None: - """Test parsing of UniRef entries for accession and seed status.""" - ns = {"ns": "http://uniprot.org/uniref"} +def test_get_accession_and_seed(xml_str, expected_acc, expected_is_seed): dbref = ET.fromstring(xml_str) if xml_str else None - acc, is_seed = get_accession_and_seed(dbref, ns) - assert acc == expected_acc - assert is_seed == expected_is_seed + acc, is_seed = get_accession_and_seed(dbref, NS) -def make_entry_with_members(member_xmls: list[str], ns_uri: str = "http://uniprot.org/uniref") -> ET.Element: - """ - Receives a list of xml strings from dbReference, generates an element with child nodes. - """ - entry_elem = ET.Element(f"{{{ns_uri}}}entry") - for dbref_xml in member_xmls: - dbref_elem = ET.fromstring(dbref_xml) - member_elem = ET.SubElement(entry_elem, f"{{{ns_uri}}}member") - member_elem.append(dbref_elem) - return entry_elem + assert acc == expected_acc + assert is_seed == expected_is_seed +# --------------------------------------------------------- +# extract_cross_refs +# --------------------------------------------------------- @pytest.mark.parametrize( - ("repr_xml", "member_xmls", "expected"), + "props, expected", [ - pytest.param( - # representative member, two members - textwrap.dedent(""" - - - - - """), - [ - textwrap.dedent(""" - - - - """), - textwrap.dedent(""" - - - - - """), - ], + ( [ - ("CLUSTER_X", "CDM:", "true", "true", "1.0"), - ("CLUSTER_X", "CDM:", "false", "false", "1.0"), - ("CLUSTER_X", "CDM:", "false", "true", "1.0"), + ("UniProtKB accession", "A0A1"), + ("UniRef90 ID", "UniRef90_X"), + ("UniParc ID", "UPI0001"), ], - id="with-representative-and-members", + { + ("UniRef90 ID", "UniRef90_X"), + ("UniParc ID", "UPI0001"), + }, ), - pytest.param( - # Only memebers, no representative member - None, + ( [ - textwrap.dedent(""" - - - - """) + ("UniProtKB accession", "A0A2"), ], - [("CLUSTER_X", "CDM:", "false", "false", "1.0")], - id="members-only", - ), - pytest.param( - # No members, no representative member - None, - [], - [], - id="no-members", + set(), ), ], ) -def test_add_cluster_members(repr_xml: str | None, member_xmls: list[str], expected: list[tuple[str, ...]]) -> None: - """Test add_cluster_members with various representative/member combinations.""" - ns = {"ns": "http://uniprot.org/uniref"} - cluster_id = "CLUSTER_X" +def test_extract_cross_refs(props, expected): + dbref = ET.Element("{http://uniprot.org/uniref}dbReference", id="UniProtKB:A0A1") - # Structure (representative members) dbReference if it exists - repr_db = ET.fromstring(repr_xml) if repr_xml else None + for k, v in props: + ET.SubElement( + dbref, + "{http://uniprot.org/uniref}property", + type=k, + value=v, + ) - # Structure nodes, and add - elem = make_entry_with_members(member_xmls) + rows = [] + extract_cross_refs(dbref, rows, NS) - # Calling the function under test - cluster_member_data = [] - add_cluster_members(cluster_id, repr_db, elem, cluster_member_data, ns) + got = {(t, v) for _, t, v in rows} + assert got == expected - assert len(cluster_member_data) == len(expected) - for i, (clu_id, cdm_prefix, is_repr, is_seed, score) in enumerate(expected): - out = cluster_member_data[i] - assert out[0] == clu_id, f"Wrong cluster_id at idx {i}: {out[0]}" - assert out[1].startswith(cdm_prefix), f"Wrong entity_id at idx {i}: {out[1]}" - assert out[2] == is_repr, f"Wrong is_representative at idx {i}: {out[2]}" - assert out[3] == is_seed, f"Wrong is_seed at idx {i}: {out[3]}" - assert out[4] == score, f"Wrong score at idx {i}: {out[4]}" + for entity_id, _, _ in rows: + assert entity_id is not None + assert isinstance(entity_id, str) -XREF_TYPES = ["UniRef90 ID", "UniRef50 ID", "UniParc ID"] +# --------------------------------------------------------- +# parse_uniref_xml +# --------------------------------------------------------- +@pytest.mark.parametrize("batch_size", [1, 2]) +def test_parse_uniref_xml_batch(batch_size): + xml = """ + + + A + + + + + + + + B + + + + + + + + """.strip() -@pytest.mark.parametrize( - ("dbref_props", "expected_xrefs"), - [ - ( - # all cross-ref fields present - [ - ("UniRef90 ID", "UniRef90_N8Q6C0"), - ("UniRef50 ID", "UniRef50_A0A7Z7LP76"), - ("UniParc ID", "UPI00044F6C4F"), - ("protein name", "foo"), - ], - [ - ("UniRef90 ID", "UniRef90_N8Q6C0"), - ("UniRef50 ID", "UniRef50_A0A7Z7LP76"), - ("UniParc ID", "UPI00044F6C4F"), - ], - ), - ( - # partial cross-ref - [ - ("UniRef90 ID", "UniRef90_ABC"), - ("protein name", "bar"), - ], - [ - ("UniRef90 ID", "UniRef90_ABC"), - ], - ), - ( - # No cross-ref - [ - ("protein name", "baz"), - ], - [], - ), - ], -) -def test_extract_cross_refs_param(dbref_props: list[tuple[str, str]], expected_xrefs: list[tuple[str, str]]) -> None: - """ - Test that extract_cross_refs correctly extracts all UniRef cross-reference fields. - """ - dbref = ET.Element("{http://uniprot.org/uniref}dbReference", type="UniProtKB ID", id="TEST_ID") - - for t, v in dbref_props: - ET.SubElement(dbref, "{http://uniprot.org/uniref}property", type=t, value=v) - - ns = {"ns": "http://uniprot.org/uniref"} - cross_reference_data = [] - extract_cross_refs(dbref, cross_reference_data, ns) - - entity_id = cdm_entity_id("TEST_ID") - expected = {(entity_id, typ, val) for typ, val in expected_xrefs} - got = set(cross_reference_data) - assert got == expected + with tempfile.TemporaryDirectory() as tmpdir: + gz_path = f"{tmpdir}/uniref_test.xml.gz" + with gzip.open(gz_path, "wb") as gz: + gz.write(xml.encode("utf-8")) + + result = parse_uniref_xml(gz_path, batch_size, {}) + + assert len(result["cluster_data"]) == batch_size + assert len(result["entity_data"]) == batch_size + assert len(result["cluster_member_data"]) == batch_size + assert len(result["cross_reference_data"]) in (0, batch_size) diff --git a/tests/parsers/test_xml_utils.py b/tests/parsers/test_xml_utils.py new file mode 100644 index 0000000..fc6e3ba --- /dev/null +++ b/tests/parsers/test_xml_utils.py @@ -0,0 +1,49 @@ +import xml.etree.ElementTree as ET + +from cdm_data_loader_utils.parsers.xml_utils import ( + clean_dict, + get_attr, + get_text, + parse_db_references, +) + + +def test_get_text_and_get_attr_basic() -> None: + elem = ET.Element("tag", attrib={"id": "123"}) + elem.text = " hello " + + assert get_text(elem) == "hello" + assert get_text(None) is None + assert get_attr(elem, "id") == "123" + assert get_attr(elem, "missing") is None + + +def test_parse_db_references_pub_and_others() -> None: + ns = {"ns": "dummy"} + source = ET.Element("source") + db1 = ET.SubElement(source, "dbReference", attrib={"type": "PubMed", "id": "12345"}) + db2 = ET.SubElement(source, "dbReference", attrib={"type": "DOI", "id": "10.1000/xyz"}) + db3 = ET.SubElement(source, "dbReference", attrib={"type": "PDB", "id": "1ABC"}) + + db1.tag = "{dummy}dbReference" + db2.tag = "{dummy}dbReference" + db3.tag = "{dummy}dbReference" + + pubs, others = parse_db_references(source, ns) + + assert "PUBMED:12345" in pubs + assert "DOI:10.1000/xyz" in pubs + assert "PDB:1ABC" in others + + +def test_clean_dict_removes_nones_and_empty() -> None: + """Test that clean_dict removes None and empty values.""" + d = { + "a": 1, + "b": None, + "c": [], + "d": {}, + "e": "ok", + } + cleaned = clean_dict(d) + assert cleaned == {"a": 1, "e": "ok"} diff --git a/uv.lock b/uv.lock index 0110326..cec3518 100644 --- a/uv.lock +++ b/uv.lock @@ -95,6 +95,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl", hash = "sha256:053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e", size = 7490, upload-time = "2025-07-03T22:54:42.156Z" }, ] +[[package]] +name = "alabaster" +version = "1.0.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/a6/f8/d9c74d0daf3f742840fd818d69cfae176fa332022fd44e3469487d5a9420/alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e", size = 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