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Translated values provided by a later babelon file are considered newer and will take precedence.", +) @output_option -def merge(inputs, sort_tables, drop_unknown_columns, output): +def merge(inputs, sort_tables, drop_unknown_columns, update_translations, output): """Merge multiple babelon TSV files into one. Example: @@ -294,7 +300,20 @@ def merge(inputs, sort_tables, drop_unknown_columns, output): # Loop through the rest of the input files and concatenate each DataFrame for input_file in inputs[1:]: df_temp = pd.read_csv(input_file, sep="\t") - df = pd.concat([df, df_temp], axis=0, ignore_index=True) + if update_translations: + merge_keys = ['source_language', 'translation_language', 'subject_id', 'predicate_id'] + + # Create a temporary key for merging + df['temp_key'] = df[merge_keys].apply(lambda x: '_'.join(x.astype(str)), axis=1) + df_temp['temp_key'] = df_temp[merge_keys].apply(lambda x: '_'.join(x.astype(str)), axis=1) + + # Remove rows from df that exist in df_temp (based on the merge keys) + df = df[~df['temp_key'].isin(df_temp['temp_key'])] + + df = pd.concat([df, df_temp], axis=0, ignore_index=True) + df = df.drop('temp_key', axis=1) + else: + df = pd.concat([df, df_temp], axis=0, ignore_index=True) if sort_tables: df = sort_babelon(df) diff --git a/tests/data/translations/hp-cs-small.babelon.tsv b/tests/data/translations/hp-cs-small.babelon.tsv new file mode 100644 index 0000000..c66d48e --- /dev/null +++ b/tests/data/translations/hp-cs-small.babelon.tsv @@ -0,0 +1,4 @@ +source_language translation_language subject_id predicate_id source_value translation_value translation_status +en cs HP:0032768 rdfs:label Focal aware autonomic seizure with pupillary dilation/constriction Fokální autonomní záchvat s dilatací/konstrikcí zornic bez poruchy vědomí CANDIDATE +en cs HP:0032768 IAO:0000115 A focal autonomic seizure with pupillary dilation / constriction characterized by retained awareness throughout the seizure Fokální autonomní záchvat s dilatací/konstrikcí zornic charakterizovaný zachovaným vědomím po celou dobu záchvatu. CANDIDATE +en cs HP:0000001 rdfs:label All Všo OFFICIAL diff --git a/tests/data/translations/hp-cs-update.babelon.tsv b/tests/data/translations/hp-cs-update.babelon.tsv new file mode 100644 index 0000000..a4557a0 --- /dev/null +++ b/tests/data/translations/hp-cs-update.babelon.tsv @@ -0,0 +1,4 @@ +source_language translation_language subject_id predicate_id source_value translation_value translation_status +en cs HP:0032768 rdfs:label Focal aware autonomic seizure with pupillary dilation/constriction Fokální autonomní záchvat s dilatací/konstrikcí zornic bez poruchy vědomí CANDIDATE +en cs HP:0032768 IAO:0000115 A focal autonomic seizure with pupillary dilation / constriction characterized by retained awareness throughout the seizure Fokální autonomní záchvat s dilatací/konstrikcí zornic charakterizovaný zachovaným vědomím po celou dobu záchvatu. CANDIDATE +en cs HP:0000001 rdfs:label All Vše OFFICIAL From bb25de68ed77feaa58e6ae2a5714373deab22418 Mon Sep 17 00:00:00 2001 From: souzadevinicius Date: Mon, 21 Oct 2024 19:51:09 +0100 Subject: [PATCH 2/3] Running lint-fix --- src/babelon/cli.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/src/babelon/cli.py b/src/babelon/cli.py index 6fe6bd8..43592f2 100644 --- a/src/babelon/cli.py +++ b/src/babelon/cli.py @@ -301,17 +301,19 @@ def merge(inputs, sort_tables, drop_unknown_columns, update_translations, output for input_file in inputs[1:]: df_temp = pd.read_csv(input_file, sep="\t") if update_translations: - merge_keys = ['source_language', 'translation_language', 'subject_id', 'predicate_id'] - + merge_keys = ["source_language", "translation_language", "subject_id", "predicate_id"] + # Create a temporary key for merging - df['temp_key'] = df[merge_keys].apply(lambda x: '_'.join(x.astype(str)), axis=1) - df_temp['temp_key'] = df_temp[merge_keys].apply(lambda x: '_'.join(x.astype(str)), axis=1) - + df["temp_key"] = df[merge_keys].apply(lambda x: "_".join(x.astype(str)), axis=1) + df_temp["temp_key"] = df_temp[merge_keys].apply( + lambda x: "_".join(x.astype(str)), axis=1 + ) + # Remove rows from df that exist in df_temp (based on the merge keys) - df = df[~df['temp_key'].isin(df_temp['temp_key'])] - + df = df[~df["temp_key"].isin(df_temp["temp_key"])] + df = pd.concat([df, df_temp], axis=0, ignore_index=True) - df = df.drop('temp_key', axis=1) + df = df.drop("temp_key", axis=1) else: df = pd.concat([df, df_temp], axis=0, ignore_index=True) From 219b6339a6c3ca23fb7dedf903b71a0e0aaee5a6 Mon Sep 17 00:00:00 2001 From: souzadevinicius Date: Mon, 21 Oct 2024 20:00:05 +0100 Subject: [PATCH 3/3] sorting imports --- src/babelon/cli.py | 15 +++++++++------ src/babelon/utils.py | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/src/babelon/cli.py b/src/babelon/cli.py index 43592f2..f6633b8 100644 --- a/src/babelon/cli.py +++ b/src/babelon/cli.py @@ -15,10 +15,10 @@ from babelon.translate import prepare_translation_for_ontology, translate_profile from babelon.translation_profile import statistics_translation_profile from babelon.utils import ( + assemble_xliff_file, drop_unknown_columns_babelon, - sort_babelon, generate_translation_units, - assemble_xliff_file, + sort_babelon, ) info_log = logging.getLogger() @@ -285,7 +285,8 @@ def statistics_translation_profile_command( "--update-translations", type=bool, default=False, - help="If true, duplicate translations for the same term and property are merged. Translated values provided by a later babelon file are considered newer and will take precedence.", + help="""If true, duplicate translations for the same term and property are merged. + "Translated values provided by a later babelon file are considered newer and will take precedence.""", ) @output_option def merge(inputs, sort_tables, drop_unknown_columns, update_translations, output): @@ -342,13 +343,15 @@ def prepare_ontology_for_crowdin(oak_adapter, top_level_term, output): """Merge multiple babelon TSV files into one. Example: - babelon prepare-ontology-for-crowdin --oak-adapter simpleobo:hp-base.obo --top-level-term HP:0000001 -o hp-translation.xliff + babelon prepare-ontology-for-crowdin + --oak-adapter simpleobo:hp-base.obo + --top-level-term HP:0000001 -o hp-translation.xliff """ # noqa: DAR101 adapter = get_adapter(oak_adapter) translation_units = list() - for top_level_term in top_level_term: - for term in adapter.descendants(top_level_term, predicates=[IS_A]): + for t in top_level_term: + for term in adapter.descendants(t, predicates=[IS_A]): label = adapter.label(term) definition = adapter.definition(term) alias_map = adapter.entity_alias_map(term) diff --git a/src/babelon/utils.py b/src/babelon/utils.py index c1a2ca0..5b96325 100644 --- a/src/babelon/utils.py +++ b/src/babelon/utils.py @@ -7,8 +7,8 @@ from pathlib import Path from string import punctuation from typing import TextIO, Union -from xml.etree.ElementTree import Element, SubElement, tostring, fromstring from xml.dom import minidom +from xml.etree.ElementTree import Element, SubElement, fromstring, tostring import pandas as pd import validators