From 3c965fe3f486d34cb0aead132b780ad405a8a1b0 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 21 Feb 2024 00:32:45 +0200 Subject: [PATCH 1/2] Test translation feature --- .gitignore | 1 + poetry.lock | 2693 ++++++++++++++++------------ pyproject.toml | 2 + src/babelon/__init__.py | 1 + src/babelon/babelon_io.py | 1 + src/babelon/cli.py | 147 +- src/babelon/parsers/xliff.py | 5 +- src/babelon/translate.py | 239 +++ src/babelon/translation_profile.py | 5 +- tests/data/hp-testsubset.obo | 49 + tests/test_data.py | 1 + tests/test_translate.py | 69 + tests/test_translation_profile.py | 1 + tox.ini | 2 +- 14 files changed, 1986 insertions(+), 1230 deletions(-) create mode 100644 src/babelon/translate.py create mode 100644 tests/data/hp-testsubset.obo create mode 100644 tests/test_translate.py diff --git a/.gitignore b/.gitignore index eace57d..9ccf9fc 100644 --- a/.gitignore +++ b/.gitignore @@ -93,3 +93,4 @@ tests/data/all_translations/* src/notebooks/.ipynb_checkpoints/babelon_notebook-checkpoint.ipynb .vscode src/notebooks/hpo_notes.xliff +tests/tmp/ \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 73fcedc..e2e657a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,29 +1,40 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"pytest-ruff"] [extras] @@ -3303,4 +3664,4 @@ docs = [] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "2e46fc5f003e053298a62987115fde52bd8b78ae9984ad809260c8926c7154a1" +content-hash = "5c4cdf196a0f074d038db733227d2ed395d7415857d687f5bdfb3c2114df6578" diff --git a/pyproject.toml b/pyproject.toml index 29070ff..c7fbe2a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,8 @@ xmltodict = "^0.13.0" pandas = "^2.0.2" oaklib = "^0.5.9" tabulate = "^0.9.0" +llm = "^0.13.1" +python-dotenv = "^1.0.1" [tool.poetry.group.docs.dependencies] mkdocs = "^1.4.2" diff --git a/src/babelon/__init__.py b/src/babelon/__init__.py index 03e6759..b1a12f8 100644 --- a/src/babelon/__init__.py +++ b/src/babelon/__init__.py @@ -1,4 +1,5 @@ """babelon package.""" + import importlib_metadata try: diff --git a/src/babelon/babelon_io.py b/src/babelon/babelon_io.py index 6716640..5f2b93f 100644 --- a/src/babelon/babelon_io.py +++ b/src/babelon/babelon_io.py @@ -1,4 +1,5 @@ """babelon.io.""" + from babelon.parsers.xliff import XliffParser diff --git a/src/babelon/cli.py b/src/babelon/cli.py index 1ab54fe..22a9dbc 100644 --- a/src/babelon/cli.py +++ b/src/babelon/cli.py @@ -6,13 +6,16 @@ from pathlib import Path import click +import pandas as pd +from oaklib import get_adapter from babelon.babelon_io import parse_file -from babelon.translation_profile import statistics_translation_profile, update_translation_profile +from babelon.translate import prepare_translation_for_ontology, translate_profile +from babelon.translation_profile import statistics_translation_profile info_log = logging.getLogger("info") # Click input options common across commands -input_argument = click.argument("input_path", required=True, type=click.Path()) +input_argument = click.argument("input", required=False, type=click.Path()) input_format_option = click.option( "--input-format", @@ -71,80 +74,106 @@ def babelon(): @input_argument # @input_format_option @output_option -def parse(input_path, output): +def parse(input, output): """Parse a file in one of the supported formats (such as obographs) into an SSSOM TSV file.""" - parse_file(input_path=input_path, output_path=output) + parse_file(input_path=input, output_path=output) -if __name__ == "__main__": - try: - parse(sys.argv[1:]) - except Exception as e: - print(e) +@click.command("translate") +@input_argument +@output_option +def translate(input, output): + """Process a table to translate values.""" + df = pd.read_csv(input, sep="\t") + translated_df = translate_profile(df) + translated_df.to_csv(output, sep="\t", index=False) -@click.command("statistics") +@click.command() +@input_argument +@click.option("--oak-adapter", type=str, help="Oak handle string.") +@click.option("--language-code", type=str, help="ISO code for the target translation language.") @click.option( - "--translation-profile", - "-t", - metavar="PATH", - required=True, - help="Path to translation profile.", - type=Path, + "--term-list", + type=click.Path(exists=True), + help="Path to file containing term ids to be translated.", ) +@click.option("--field", multiple=True, type=str, help="Fields to be translated.") +@output_option +def prepare_translation(input, oak_adapter, language_code, term_list, field, output): + """Translate ontology fields based on the specified language code.""" + ontology = get_adapter(oak_adapter) + if input: + df_babelon = pd.read_csv(input, sep="\t") + else: + df_babelon = None + + terms = None + if term_list: + with open(term_list, "r") as file: + lines = file.readlines() + terms = [line.strip() for line in lines] + + output_profile = prepare_translation_for_ontology( + ontology=ontology, + language_code=language_code, + df_babelon=df_babelon, + terms=terms, + fields=field, + ) + output_profile.to_csv(output, sep="\t", index=False) + + +@click.command("statistics") +@input_argument def statistics_translation_profile_command( - translation_profile: Path, + input: Path, ): - """Takes as an input a babelon profile (TSV) and returns some basic stats: + """Take as an input a babelon profile (TSV) and returns some basic stats. + number of translations by source_language, target_language number of translations by source_language, target_language, predicate_id number of translations by source_language, target_language, translation_status Args: - translation_profile (Path): translation profile + input (Path): translation profile """ - statistics_translation_profile(translation_profile) + statistics_translation_profile(input) -@click.command("update-translation-profile") -@click.option( - "--translation-profile", - "-t", - metavar="PATH", - required=True, - help="Path to translation profile.", - type=Path, -) -@click.option( - "--ontology-file", - "-o", - metavar="PATH", - required=True, - help="Path to ontology file.", - type=Path, -) -@click.option( - "--output", - "-o", - metavar="PATH", - required=True, - help="Path where updated profile will be written.", - type=Path, -) -def update_translation_profile_command( - translation_profile: Path, - ontology_file: Path, - output: Path, -): - """Write update_translation_profile to TSV file. - - Args: - translation_profile (Path): Path to the translation profile - ontology_file (Path): Path to the ontology file - output (Path): Path to the output TSV file - """ - update_translation_profile(translation_profile, ontology_file, output) +@click.command("example") +@input_argument +def example(input): + """Generate an example babelon file for user.""" + data = [ + { + "source_language": "en", + "source_value": "Fever", + "subject_id": "HP:0001945", + "predicate_id": "rdfs:label", + "translation_language": "de", + "translation_value": "", + "translation_status": "NOT_TRANSLATED", + }, + { + "source_language": "en", + "source_value": "Stroke", + "subject_id": "HP:0001297", + "predicate_id": "rdfs:label", + "translation_language": "de", + "translation_value": "", + "translation_status": "NOT_TRANSLATED", + }, + ] + df = pd.DataFrame(data) + + if input: + df.to_csv(input, sep="\t", index=False) + else: + click.echo(df.to_string(index=False)) babelon.add_command(parse) -babelon.add_command(update_translation_profile_command) +babelon.add_command(prepare_translation) babelon.add_command(statistics_translation_profile_command) +babelon.add_command(example) +babelon.add_command(translate) diff --git a/src/babelon/parsers/xliff.py b/src/babelon/parsers/xliff.py index 0ae2460..d35d544 100644 --- a/src/babelon/parsers/xliff.py +++ b/src/babelon/parsers/xliff.py @@ -1,6 +1,6 @@ """xliff.py.""" + import csv -import os from os.path import exists import pandas as pd @@ -11,6 +11,7 @@ class XliffParser: """parser = XliffParser(/tests/data/).""" def __init__(self, input_file_path, output_file_path): + """Initialize XLIFF parser.""" self.input_file = input_file_path self.output_file = output_file_path @@ -101,7 +102,7 @@ def xml_to_tsv(self): csv_line.append(self._remove_redundant_whitespace(line)) csvfile_writer.writerow(csv_line) - return self.output_file + return pd.read_csv(self.output_file, sep="\t") def _remove_redundant_whitespace(self, v: str): if not v: diff --git a/src/babelon/translate.py b/src/babelon/translate.py new file mode 100644 index 0000000..a18ab2c --- /dev/null +++ b/src/babelon/translate.py @@ -0,0 +1,239 @@ +"""Translate Babelon profiles.""" + +import logging +import os +from typing import Dict, List + +import llm +import pandas as pd + + +class Translator: + """A generic translator class.""" + + def translate(self, text, target_language): + """ + Translate the provided text into the target language. + + Args: + text (str): The text to be translated. + target_language (str): The language to translate the text into. + + Raises: + NotImplementedError: If the method is not implemented in the subclass. + """ + raise NotImplementedError("This method should be implemented by subclasses.") + + +class GPT4Translator(Translator): + """A specific translator class that uses GPT-4 for translation.""" + + def translate(self, text_to_translate, language_code): + """ + Translate text using OpenAI's GPT-4 API (hypothetical). + + Args: + text_to_translate (str): The text to be translated. + language_code (str): The target language code (e.g., 'de' for German). + + Returns: + str: The translated text. + """ + # Set up your OpenAI API key + + prompt = f"""Translate the following text into the specified language. +The language code provided is in ISO format. + +- Language Code (ISO format): {language_code} +- Text to Translate: {text_to_translate} + +Please provide the translation. +If no translation can be found for whatever reason, including that the translation +language is the same as the language of the text to translate, return an empty string. +Give no comments, no explanations. Just the translation or an empty string.""" + + # Save the current logging level + original_level = logging.getLogger().getEffectiveLevel() + + # Set the logging level to CRITICAL to silence lower level logs + # There is a lot of noisy putput here.. + logging.getLogger().setLevel(logging.CRITICAL) + + model = llm.get_model("gpt-4-turbo-preview") + model.key = os.environ["OPENAI_API_KEY"] + + try: + response = model.prompt(prompt) + translated_value = response.text() + # Restore the original logging level + logging.getLogger().setLevel(original_level) + return translated_value + except Exception as e: + # Restore the original logging level + logging.getLogger().setLevel(original_level) + print(f"An error occurred: {e}") + return "" + + +def _get_translation_language(translation_language_df, default_language="en"): + if translation_language_df: + return translation_language_df + else: + return default_language + + +def _is_legal_string(value): + if isinstance(value, str): + return value != "" and value.lower() != "nan" + return False + + +def get_translator_model(model="gpt-4"): + """ + Instantiate translator model based on string. + + Args: + model (str): The model to be instatiated. + + Raises: + ValueError: If the model does not exist. + """ + if model == "gpt-4": + return GPT4Translator() + else: + raise ValueError(f"{model} is not a valid translation model!") + + +def translate_profile( + babelon_df: pd.DataFrame, language_code="en", update_existing=False, model="gpt-4" +): + """Iterate through DataFrame rows and translate values.""" + from datetime import datetime + + translator = get_translator_model(model) + + # Get today's date + today = datetime.now() + + # Format the date as YYYY-MM-DD + formatted_date = today.strftime("%Y-%m-%d") + translated_df = babelon_df.copy() + translated_df = translated_df.astype(str) + for index, row in translated_df.iterrows(): + translation_language = _get_translation_language(row["translation_language"], language_code) + source_value = row["source_value"] + if source_value: + existing_translation_value = ( + row["translation_value"] if "translation_value" in row else None + ) + if update_existing or not _is_legal_string(existing_translation_value): + translated_value = translator.translate(source_value, translation_language) + translated_df.at[index, "translation_value"] = translated_value + translated_df.at[index, "translator"] = "wikidata:Q116709136" + translated_df.at[index, "translator_expertise"] = "ALGORITHM" + translated_df.at[index, "comment"] = model + translated_df.at[index, "translation_date"] = formatted_date + translated_df.at[index, "translation_status"] = "candidate" + else: + logging.warning(f"Existing translation {existing_translation_value}, skipping..") + else: + logging.warning(f"No source_value at index {index}, row: {row}") + return translated_df + + +def _create_default_dataframe(): + default_columns = [ + "source_language", + "source_value", + "subject_id", + "predicate_id", + "translation_language", + "translation_value", + "translation_status", + ] + return pd.DataFrame(columns=default_columns) + + +def prepare_translation_for_ontology( + ontology, language_code, df_babelon: pd.DataFrame, terms: List[str], fields: List[str] +): + """Prepare a babelon translation table for an ontology.""" + if df_babelon is None: + df_augmented = _create_default_dataframe() + else: + df_augmented = df_babelon.copy() + + if terms is None: + terms = [] + for entity in ontology.entities(): + terms.append(entity) + + # First, we update the existing records + # If a value has changed in the ontology, we flip the translation status to + # CANDIDATE + + processed: Dict[str, List[str]] = {} + + for index, row in df_augmented.iterrows(): + subject_id = row["subject_id"] + if subject_id not in processed: + processed[subject_id] = [] + predicate_id = row["predicate_id"] + if predicate_id not in processed[subject_id]: + processed[subject_id].append(predicate_id) + source_value = row["source_value"] + term_metadata = ontology.entity_metadata_map(subject_id) + if predicate_id in term_metadata: + ontology_value = term_metadata[predicate_id][0] + if len(term_metadata[predicate_id]) > 1: + logging.warning( + f"{predicate_id} value for {subject_id} is ambiguous," + f"picking first one ({term_metadata[predicate_id]})." + ) + if ontology_value != source_value: + translation_value = row["translation_value"] + df_augmented.at[index, "source_value"] = ontology_value + new_translation_value = ( + "CANDIDATE" if translation_value != "NOT_TRANSLATED" else "NOT_TRANSLATED" + ) + df_augmented.at[index, "translation_language"] = new_translation_value + logging.warning( + f"{predicate_id} value for {subject_id} is {source_value}, " + f"but {ontology_value} in the ontology. Table is updated and " + f"translation status reset to CANDIDATE" + ) + else: + logging.warning( + f"{predicate_id} value for {subject_id} does not exist in ontology. " + f"Keeping value in the translation profile: {source_value}" + ) + + added_rows = [] + for term in terms: + term_metadata = ontology.entity_metadata_map(term) + for field in fields: + if term in processed: + if field in processed[term]: + continue + if field not in term_metadata: + logging.warning(f"{field} does not exist for {term}.") + continue + for source_value in term_metadata[field]: + subject_id = term + data_row = { + "source_language": "en", + "source_value": source_value, + "subject_id": subject_id, + "predicate_id": field, + "translation_language": language_code, + "translation_value": "", + "translation_status": "NOT_TRANSLATED", + } + + added_rows.append(data_row) + + if added_rows: + df_added = pd.DataFrame(added_rows) + df_augmented = pd.concat([df_augmented, df_added], ignore_index=True) + + return df_augmented diff --git a/src/babelon/translation_profile.py b/src/babelon/translation_profile.py index 918afc7..1389415 100644 --- a/src/babelon/translation_profile.py +++ b/src/babelon/translation_profile.py @@ -25,7 +25,7 @@ def update_translation_profile( def table_print(title: str, data: pd.DataFrame): - """Print grouped translation data + """Print grouped translation data. Args: title (str): Table title @@ -45,7 +45,8 @@ def table_print(title: str, data: pd.DataFrame): def statistics_translation_profile(translation_profile: Path) -> None: - """Takes as an input a babelon profile (TSV) and returns some basic stats: + """Take as an input a babelon profile (TSV) and returns some basic stats. + number of translations by source_language, target_language number of translations by source_language, target_language, predicate_id number of translations by source_language, target_language, translation_status diff --git a/tests/data/hp-testsubset.obo b/tests/data/hp-testsubset.obo new file mode 100644 index 0000000..6678966 --- /dev/null +++ b/tests/data/hp-testsubset.obo @@ -0,0 +1,49 @@ +format-version: 1.2 +data-version: hp/releases/2023-04-05 +synonymtypedef: abbreviation "abbreviation" +synonymtypedef: HP:0034334 "allelic_requirement" +synonymtypedef: layperson "layperson term" +synonymtypedef: obsolete_synonym "discarded/obsoleted synonym" +synonymtypedef: plural_form "plural form" +synonymtypedef: uk_spelling "UK spelling" +default-namespace: human_phenotype +ontology: hp.obo +property_value: http://purl.org/dc/terms/license https://hpo.jax.org/app/license +property_value: IAO:0000700 HP:0000001 +property_value: owl:versionInfo "2023-04-05" xsd:string +logical-definition-view-relation: has_part + +[Term] +id: HP:0000001 +name: All +comment: Root of all terms in the Human Phenotype Ontology. +xref: UMLS:C0444868 + +[Term] +id: HP:0001945 +name: Fever +def: "Body temperature elevated above the normal range." [https://orcid.org/0009-0006-4530-3154, PMID:9759682] +comment: Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation. +synonym: "Fever" EXACT layperson [] +is_a: HP:0000001 ! All + +[Term] +id: HP:0001297 +name: Stroke +def: "Sudden impairment of blood flow to a part of the brain due to occlusion or rupture of an artery to the brain." [https://orcid.org/0000-0002-0736-9199] +synonym: "Cerebral vascular events" EXACT [] +is_a: HP:0000001 ! All + +[Term] +id: HP:0001695 +name: Cardiac arrest +def: "An abrupt loss of heart function." [] +is_a: HP:0000001 ! All + +[Term] +id: HP:0001707 +name: Abnormal right ventricle morphology +def: "An abnormality of the right ventricle of the heart." [https://orcid.org/0000-0002-0736-9199] +comment: The function of the right ventricle is to receive blood from the right atrium and to eject blood into the pulmonary artery. +synonym: "Abnormality of the right ventricle" EXACT [] +is_a: HP:0000001 ! All diff --git a/tests/test_data.py b/tests/test_data.py index 8f3b475..2e8f91c 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -5,6 +5,7 @@ from tests.constants import cwd, data_dir test_validate_dir = os.path.join(cwd, "validate_data") +test_out_dir = os.path.join(cwd, "tmp") schema_dir = os.path.join(cwd, os.pardir, "schema") diff --git a/tests/test_translate.py b/tests/test_translate.py new file mode 100644 index 0000000..7a72516 --- /dev/null +++ b/tests/test_translate.py @@ -0,0 +1,69 @@ +"""Tests for translation profile.""" + +import unittest + +import pandas as pd +from dotenv import load_dotenv +from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.resource import OntologyResource + +from babelon.translate import GPT4Translator, prepare_translation_for_ontology, translate_profile + + +def _create_simple_example(): + data = [ + { + "source_language": "en", + "source_value": "Fever", + "subject_id": "HP:0001945", + "predicate_id": "rdfs:label", + "translation_language": "de", + "translation_value": "", + "translation_status": "NOT_TRANSLATED", + }, + { + "source_language": "en", + "source_value": "Stroke", + "subject_id": "HP:0001297", + "predicate_id": "rdfs:label", + "translation_language": "de", + "translation_value": "", + "translation_status": "NOT_TRANSLATED", + }, + ] + return pd.DataFrame(data) + + +class TestTranslationProfile(unittest.TestCase): + """A test case for translation profile functionality.""" + + def setUp(self) -> None: + """Set up the test case.""" + + def test_translate(self): + """Test update_translation_profile.""" + load_dotenv() + translator = GPT4Translator() + translated_value = translator.translate("fever", "de") + self.assertEqual("Fieber", translated_value) + + def test_translate_profile(self): + """Test to see if a small babelon profile can be translated.""" + load_dotenv() + df_babelon = _create_simple_example() + df_translated = translate_profile(df_babelon) + translations = df_translated["translation_value"].tolist() + expected_translations = ["Fieber", "Schlaganfall"] + self.assertEqual(translations, expected_translations) + + def test_prepare_translation_for_ontology(self): + """Test the update method for babelon profiles.""" + resource = OntologyResource(slug="data/hp-testsubset.obo", local=True) + ontology = ProntoImplementation(resource) + terms = ["HP:0001707"] + fields = ["rdfs:label"] + df_babelon = _create_simple_example() + df_augmented = prepare_translation_for_ontology(ontology, "de", df_babelon, terms, fields) + subject_ids = df_augmented["subject_id"].tolist() + expected_subject_ids = ["HP:0001945", "HP:0001297"] + self.assertEquals(expected_subject_ids, subject_ids) diff --git a/tests/test_translation_profile.py b/tests/test_translation_profile.py index 769e354..cc820e7 100644 --- a/tests/test_translation_profile.py +++ b/tests/test_translation_profile.py @@ -1,4 +1,5 @@ """Tests for translation profile.""" + import unittest from babelon.translation_profile import update_translation_status diff --git a/tox.ini b/tox.ini index 1a8b654..568bbad 100644 --- a/tox.ini +++ b/tox.ini @@ -19,7 +19,7 @@ envlist = py [testenv] -whitelist_externals = +allowlist_externals = poetry commands = poetry run pytest From faddd6d66688f7bea3fe57ce5db641d09017f98a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 21 Feb 2024 10:45:28 +0200 Subject: [PATCH 2/2] Refactor xliff parser and fix tests --- src/babelon/babelon_io.py | 9 +- src/babelon/parsers/xliff.py | 301 +++++++++++++++++------------------ tests/test_data.py | 1 + tests/test_parsers.py | 23 +-- tests/test_translate.py | 8 +- 5 files changed, 175 insertions(+), 167 deletions(-) diff --git a/src/babelon/babelon_io.py b/src/babelon/babelon_io.py index 5f2b93f..772528f 100644 --- a/src/babelon/babelon_io.py +++ b/src/babelon/babelon_io.py @@ -1,6 +1,6 @@ """babelon.io.""" -from babelon.parsers.xliff import XliffParser +from babelon.parsers.xliff import xliff_path_to_babelon def parse_file(input_path: str, output_path: str) -> None: @@ -15,8 +15,9 @@ def parse_file(input_path: str, output_path: str) -> None: """ file_extension = input_path.split(".")[-1] if file_extension == "xliff": - parser = XliffParser(input_file_path=input_path, output_file_path=output_path) - parser.xml_to_tsv() - parser.synonym_split() + df_babelon, df_synonym = xliff_path_to_babelon(input_file_path=input_path) + output_path_synonym = str(output_path).replace(".babelon.", ".synonyms.") + df_babelon.to_csv(output_path, sep="\t", index=False) + df_synonym.to_csv(output_path_synonym, sep="\t", index=False) else: raise ValueError(f"File type: {file_extension} not supported.") diff --git a/src/babelon/parsers/xliff.py b/src/babelon/parsers/xliff.py index d35d544..4d58ba4 100644 --- a/src/babelon/parsers/xliff.py +++ b/src/babelon/parsers/xliff.py @@ -1,167 +1,162 @@ """xliff.py.""" -import csv from os.path import exists +from typing import Dict, Tuple import pandas as pd import xmltodict -class XliffParser: - """parser = XliffParser(/tests/data/).""" - - def __init__(self, input_file_path, output_file_path): - """Initialize XLIFF parser.""" - self.input_file = input_file_path - self.output_file = output_file_path - - def xml_to_tsv(self): - """xlm_to_tsv. +def _get_translation_status(translation_status_raw): + """get_translation_status.""" + if translation_status_raw: + if translation_status_raw == "needs-translation": + return "NOT_TRANSLATED" + elif translation_status_raw == "final": + return "OFFICIAL" + elif translation_status_raw == "translated": + return "CANDIDATE" + else: + return translation_status_raw + return "" - Raises: - FileNotFoundError: FileNotFoundError - Returns: - [type]: [description] - """ - if exists(self.input_file): - with open(self.input_file) as fd: - doc = xmltodict.parse(fd.read()) - else: - raise FileNotFoundError(f"Input file:{self.input_file} not found.") - - csvfile = open(self.output_file, "w", encoding="utf-8") - csvfile_writer = csv.writer(csvfile, delimiter="\t") - - csvfile_synonyms = open( - str(self.output_file).replace(".babelon.", ".synonyms."), "w", encoding="utf-8" - ) - csvfile_writer_synonyms = csv.writer(csvfile_synonyms, delimiter="\t") - - # ADD HEADER - csvfile_writer.writerow( - [ - "source_language", - "translation_language", - "subject_id", - "predicate_id", - "source_value", - "translation_value", - "translation_status", - ] - ) - csvfile_writer_synonyms.writerow(["subject_id", "translation_value", "comment"]) +def _synonym_split_value(raw_synonym): + """synonym_split_value.""" + word_list = raw_synonym.split("#") + stripped = [_remove_redundant_whitespace(s) for s in word_list if s] + return stripped - lang = "unknown" - if doc["xliff"]["file"]["body"]["trans-unit"]: - lang = doc["xliff"]["file"]["body"]["trans-unit"][0]["target"]["@xml:lang"] - - csvfile_writer_synonyms.writerow(["ID", f"AL oboInOwl:hasExactSynonym@{lang}", ""]) - - for trans_unit in doc["xliff"]["file"]["body"]["trans-unit"]: - source_language = trans_unit["source"]["@xml:lang"] - translation_language = trans_unit["target"]["@xml:lang"] - translation_status = self.get_translation_status(trans_unit["target"]["@state"]) - # get subject_id and and format - split_string_id_column = trans_unit["@id"] - get_subject_id = split_string_id_column[0:10] - subject_id = get_subject_id.replace("_", ":") - # get predicate_id and format - get_predicate_id = split_string_id_column[11:21] - if get_predicate_id == "label": - predicate_id = get_predicate_id.replace("label", "rdfs:label") - elif get_predicate_id == "definition": - predicate_id = get_predicate_id.replace("definition", "IAO:0000115") - else: - # elif get_predicate_id == 'synonyms': - predicate_id = get_predicate_id.replace("synonyms", "oboInOwl:exactSynonym") - source_value = trans_unit["source"]["#text"] - translational_value = trans_unit["target"]["#text"] - - csv_line = [] - - if predicate_id == "oboInOwl:exactSynonym": - all_synonyms = self.synonym_split_value(translational_value) - subject_id = self._remove_redundant_whitespace(subject_id) - translation_status = self._remove_redundant_whitespace(translation_status) - - for syn in all_synonyms: - csv_line = [subject_id, syn, translation_status] - csvfile_writer_synonyms.writerow(csv_line) - else: - for line in [ - source_language, - translation_language, - subject_id, - predicate_id, - source_value, - translational_value, - translation_status, - ]: - csv_line.append(self._remove_redundant_whitespace(line)) - csvfile_writer.writerow(csv_line) - - return pd.read_csv(self.output_file, sep="\t") - - def _remove_redundant_whitespace(self, v: str): - if not v: - return "" - return ( - v.replace("\n", " ") - .replace("\t", " ") - .replace("\r", "") - .replace(" ", " ") - .replace(" ", " ") - .strip() - ) - - def get_translation_status(self, translation_status_raw): - """get_translation_status.""" - if translation_status_raw: - if translation_status_raw == "needs-translation": - return "NOT_TRANSLATED" - elif translation_status_raw == "final": - return "OFFICIAL" - elif translation_status_raw == "translated": - return "CANDIDATE" - else: - return translation_status_raw +def _remove_redundant_whitespace(v: str): + if not v: return "" + return ( + v.replace("\n", " ") + .replace("\t", " ") + .replace("\r", "") + .replace(" ", " ") + .replace(" ", " ") + .strip() + ) + + +def xliff_path_to_babelon(input_file_path) -> Tuple[pd.DataFrame, pd.DataFrame]: + """Generate a babelon dataframe for translations and a ROBOT template for synonyms from XLIFF file.""" + doc = _load_xliff_as_xmldoc(input_file_path) + return xliff_to_babelon(doc) + + +def xliff_to_babelon(doc: Dict) -> Tuple[pd.DataFrame, pd.DataFrame]: + """Translate the loaded XLIFF document to Babelon TSV in pandas. + + Returns: + Tuple (pd.DataFrame, pd.DataFrame) : a babelon and a synonym dataframe + """ + babelon_data = [] + synonym_data = [] + + if doc["xliff"]["file"]["body"]["trans-unit"]: + lang = doc["xliff"]["file"]["body"]["trans-unit"][0]["target"]["@xml:lang"] + else: + lang = "unknown" - def synonym_split_value(self, raw_synonym): - """synonym_split_value.""" - word_list = raw_synonym.split("#") - stripped = [self._remove_redundant_whitespace(s) for s in word_list if s] - return stripped - - def synonym_split(self): - """synonym_split.""" - df = pd.read_csv(self.output_file, sep="\t") - - output_df = df[0:0] - - for _, row in df.iterrows(): - if row.predicate_id == "oboInOwl:exactSynonym": - word_list = row["source_value"].split("#") - word_list.remove("") - temp_row = row.copy() - if len(word_list) > 1: - for each_word in word_list: - temp_row.source_value = each_word - temp_row.translation_value = each_word - output_df = pd.concat( - [output_df, pd.DataFrame([temp_row.to_dict()])], ignore_index=True - ) - - else: - temp_row.source_value = word_list[0] - temp_row.translation_value = temp_row.translation_value.replace("#", "") - output_df = pd.concat( - [output_df, pd.DataFrame([temp_row.to_dict()])], ignore_index=True - ) - - else: - output_df = pd.concat([output_df, pd.DataFrame([row.to_dict()])], ignore_index=True) - output_df.to_csv(self.output_file, sep="\t", index=False) - return self.output_file + synonym_data.append( + { + "subject_id": "ID", + "translation_value": f"AL oboInOwl:hasExactSynonym@{lang}", + "comment": "", + } + ) + + for trans_unit in doc["xliff"]["file"]["body"]["trans-unit"]: + source_language = trans_unit["source"]["@xml:lang"] + translation_language = trans_unit["target"]["@xml:lang"] + translation_status = _get_translation_status(trans_unit["target"]["@state"]) + # get subject_id and format + split_string_id_column = trans_unit["@id"] + get_subject_id = split_string_id_column[0:10] + subject_id = get_subject_id.replace("_", ":") + # get predicate_id and format + get_predicate_id = split_string_id_column[11:21] + if get_predicate_id == "label": + predicate_id = get_predicate_id.replace("label", "rdfs:label") + elif get_predicate_id == "definition": + predicate_id = get_predicate_id.replace("definition", "IAO:0000115") + else: + # elif get_predicate_id == 'synonyms': + predicate_id = get_predicate_id.replace("synonyms", "oboInOwl:exactSynonym") + source_value = trans_unit["source"]["#text"] + translational_value = trans_unit["target"]["#text"] + + if predicate_id == "oboInOwl:exactSynonym": + all_synonyms = _synonym_split_value(translational_value) + subject_id = _remove_redundant_whitespace(subject_id) + translation_status = _remove_redundant_whitespace(translation_status) + + for syn in all_synonyms: + synonym_data.append( + { + "subject_id": subject_id, + "translation_value": syn, + "comment": translation_status, + } + ) + else: + babelon_data.append( + { + "source_language": _remove_redundant_whitespace(source_language), + "translation_language": _remove_redundant_whitespace(translation_language), + "subject_id": _remove_redundant_whitespace(subject_id), + "predicate_id": _remove_redundant_whitespace(predicate_id), + "source_value": _remove_redundant_whitespace(source_value), + "translational_value": _remove_redundant_whitespace(translational_value), + "translation_status": _remove_redundant_whitespace(translation_status), + } + ) + + df_synonyms = pd.DataFrame(synonym_data) + df_babelon = pd.DataFrame(babelon_data) + + return df_babelon, df_synonyms + + +def _load_xliff_as_xmldoc(input_file_path): + if exists(input_file_path): + with open(input_file_path) as fd: + doc = xmltodict.parse(fd.read()) + else: + raise FileNotFoundError(f"Input file:{input_file_path} not found.") + return doc + + +# +# # TODO this method seems not necessary +# def synonym_split(df_synonym: pd.DataFrame): +# """synonym_split.""" +# +# output_df = df_synonym[0:0] +# +# for _, row in df_synonym.iterrows(): +# if row.predicate_id == "oboInOwl:exactSynonym": +# word_list = row["source_value"].split("#") +# word_list.remove("") +# temp_row = row.copy() +# if len(word_list) > 1: +# for each_word in word_list: +# temp_row.source_value = each_word +# temp_row.translation_value = each_word +# output_df = pd.concat( +# [output_df, pd.DataFrame([temp_row.to_dict()])], ignore_index=True +# ) +# +# else: +# temp_row.source_value = word_list[0] +# temp_row.translation_value = temp_row.translation_value.replace("#", "") +# output_df = pd.concat( +# [output_df, pd.DataFrame([temp_row.to_dict()])], ignore_index=True +# ) +# +# else: +# output_df = pd.concat([output_df, pd.DataFrame([row.to_dict()])], ignore_index=True) +# return output_df diff --git a/tests/test_data.py b/tests/test_data.py index 2e8f91c..0ecd502 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -7,6 +7,7 @@ test_validate_dir = os.path.join(cwd, "validate_data") test_out_dir = os.path.join(cwd, "tmp") schema_dir = os.path.join(cwd, os.pardir, "schema") +env_file = os.path.join(cwd, ".env") def get_test_file(filename: str) -> str: diff --git a/tests/test_parsers.py b/tests/test_parsers.py index f642f0f..b2de522 100644 --- a/tests/test_parsers.py +++ b/tests/test_parsers.py @@ -1,12 +1,10 @@ """Tests for parsers.""" -import os import unittest from xml.dom import minidom # noqa -from babelon.parsers.xliff import XliffParser +from babelon.parsers.xliff import xliff_path_to_babelon from tests.test_data import data_dir as test_data_dir -from tests.test_data import test_out_dir class TestParse(unittest.TestCase): @@ -19,14 +17,21 @@ def setUp(self) -> None: def test_parse_xliff(self): """Test parsing an Xliff XML.""" - out_path = os.path.join(test_out_dir, "test_parse_alignment_minidom.tsv") - parser = XliffParser(input_file_path=self.xliff_file, output_file_path=out_path) + df_babelon, df_synonyms = xliff_path_to_babelon(input_file_path=self.xliff_file) - df = parser.xml_to_tsv() - df.to_csv(out_path, sep="\t") + # out_path_babelon = os.path.join(test_out_dir, "test_parse_xliff.babelon.tsv") + # out_path_synonyms = os.path.join(test_out_dir, "test_parse_xliff.synonyms.tsv") + # df_babelon.to_csv(out_path_babelon, sep="\t") + # df_synonyms.to_csv(out_path_synonyms, sep="\t") self.assertEqual( - len(df), - 646, + len(df_babelon), + 25133, + f"{self.xliff_file} has the wrong number of translations.", + ) + + self.assertEqual( + len(df_synonyms), + 16755, f"{self.xliff_file} has the wrong number of translations.", ) diff --git a/tests/test_translate.py b/tests/test_translate.py index 7a72516..fdd6966 100644 --- a/tests/test_translate.py +++ b/tests/test_translate.py @@ -1,5 +1,6 @@ """Tests for translation profile.""" +import os import unittest import pandas as pd @@ -8,6 +9,8 @@ from oaklib.resource import OntologyResource from babelon.translate import GPT4Translator, prepare_translation_for_ontology, translate_profile +from tests.test_data import data_dir as test_data_dir +from tests.test_data import env_file def _create_simple_example(): @@ -40,6 +43,7 @@ class TestTranslationProfile(unittest.TestCase): def setUp(self) -> None: """Set up the test case.""" + @unittest.skipIf(not os.path.exists(env_file), "Skipping test as .env file does not exist") def test_translate(self): """Test update_translation_profile.""" load_dotenv() @@ -47,6 +51,7 @@ def test_translate(self): translated_value = translator.translate("fever", "de") self.assertEqual("Fieber", translated_value) + @unittest.skipIf(not os.path.exists(env_file), "Skipping test as .env file does not exist") def test_translate_profile(self): """Test to see if a small babelon profile can be translated.""" load_dotenv() @@ -58,7 +63,8 @@ def test_translate_profile(self): def test_prepare_translation_for_ontology(self): """Test the update method for babelon profiles.""" - resource = OntologyResource(slug="data/hp-testsubset.obo", local=True) + test_file = f"{test_data_dir}/hp-testsubset.obo" + resource = OntologyResource(slug=test_file, local=True) ontology = ProntoImplementation(resource) terms = ["HP:0001707"] fields = ["rdfs:label"]