From ae5030cb7db74b2ae0acb804b646e0d1afdbd5da Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 29 Jul 2024 17:25:29 -0700 Subject: [PATCH] Adding Property Graph example Fixes #142 Also adding roundtrip when generating schema, catches issues with #141 --- README.md | 5 + docs/howto/google-sheets.md | 2 +- poetry.lock | 2114 +++++++++++++------------ schemasheets/schema_exporter.py | 11 +- schemasheets/schemamaker.py | 143 +- schemasheets/schemasheet_datamodel.py | 5 +- tests/test_example_schemas.py | 42 + 7 files changed, 1281 insertions(+), 1041 deletions(-) create mode 100644 tests/test_example_schemas.py diff --git a/README.md b/README.md index da8fbcc..e64b275 100644 --- a/README.md +++ b/README.md @@ -89,6 +89,11 @@ sheets2linkml personinfo.tsv -o personinfo.yaml We recommend using [COGS](https://linkml.io/schemasheets/howto/google-sheets/) to synchronize your google sheets with local files using a git-like mechanism +## Examples + +- [Person Info Schema](https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=55566104) +- [Movies Property Graph Schema](https://docs.google.com/spreadsheets/d/1oMrzA41tg_nisdWInnqKJrcvv30dOXuwAhznJYYPSB8/edit?gid=1499822522#gid=1499822522) + ## Finding out more * [Schema Sheets Manual](https://linkml.io/schemasheets) diff --git a/docs/howto/google-sheets.md b/docs/howto/google-sheets.md index 53fd9ea..a2efee9 100644 --- a/docs/howto/google-sheets.md +++ b/docs/howto/google-sheets.md @@ -38,7 +38,7 @@ E.g. sheets2linkml --gsheet-id 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ personinfo types prefixes -o personinfo.yaml ``` -__Note__: due to a bug with google sheets API (see [this Stack Overflow question](https://stackoverflow.com/questions/61578295/google-spreadsheet-gviz-query-is-concatenating-first-two-rows-into-header)), this will not work if your sheet has floats/decimals in them. It's not clear if google will ever fix this. If you need decimals, then you should either manually download the sheet to TSV, or use COGS. +__Note__: due to a bug with google sheets API (see [this Stack Overflow question](https://stackoverflow.com/questions/61578295/google-spreadsheet-gviz-query-is-concatenating-first-two-rows-into-header)), this will not work if your sheet has floats/decimals/booleans in them. It's not clear if google will ever fix this. If you need decimals, then you should either manually download the sheet to TSV, or use COGS. ## COGS diff --git a/poetry.lock b/poetry.lock index 72d50b0..1aecfa9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,20 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] [[package]] name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -13,82 +23,87 @@ files = [ [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - 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SubsetDefinition, ClassDefinition, EnumDefinition, \ PermissibleValue, \ - TypeDefinition, Example, Annotation, Prefix + TypeDefinition, Example, Annotation, Prefix, SchemaDefinition from linkml_runtime.utils.formatutils import underscore from linkml_runtime.utils.schemaview import SchemaView from schemasheets.conf.configschema import ColumnSettings from schemasheets.schemamaker import SchemaMaker from schemasheets.schemasheet_datamodel import TableConfig, T_CLASS, T_SLOT, SchemaSheet, T_ENUM, T_PV, T_TYPE, \ - T_SUBSET, T_PREFIX + T_SUBSET, T_PREFIX, T_SCHEMA ROW = Dict[str, Any] @@ -108,7 +108,7 @@ class SchemaExporter: Exports a schema to Schema Sheets TSV format """ schemamaker: SchemaMaker = field(default_factory=lambda: SchemaMaker()) - delimiter = '\t' + delimiter: str = field(default_factory=lambda: '\t') rows: List[ROW] = field(default_factory=lambda: []) def export(self, schemaview: SchemaView, to_file: Union[str, Path], specification: str = None, @@ -229,6 +229,11 @@ def export_element(self, element: Element, parent: Optional[Element], schemaview pk_col = col_name else: continue + elif t == T_SCHEMA: + if isinstance(element, SchemaDefinition): + pk_col = col_name + else: + continue else: raise AssertionError(f"Unexpected type: {t}") if not pk_col: diff --git a/schemasheets/schemamaker.py b/schemasheets/schemamaker.py index 64bf9eb..02a876d 100644 --- a/schemasheets/schemamaker.py +++ b/schemasheets/schemamaker.py @@ -5,6 +5,7 @@ import csv import logging import tempfile +from pathlib import Path from urllib.request import urlopen from copy import copy @@ -13,12 +14,13 @@ from dataclasses import dataclass from typing import List, Union, Any, Dict, Tuple, Generator, TextIO -from linkml_runtime.dumpers import yaml_dumper +from linkml_runtime.dumpers import yaml_dumper, json_dumper from linkml_runtime.linkml_model import Annotation, Example from linkml_runtime.linkml_model.meta import SchemaDefinition, ClassDefinition, Prefix, \ SlotDefinition, EnumDefinition, PermissibleValue, SubsetDefinition, TypeDefinition, Element, Setting from linkml_runtime.utils.schema_as_dict import schema_as_dict from linkml_runtime.utils.schemaview import SchemaView, re +from linkml_runtime.utils.yamlutils import YAMLRoot from schemasheets.schemasheet_datamodel import ColumnConfig, TableConfig, get_configmodel, get_metamodel, COL_NAME, \ DESCRIPTOR, \ @@ -28,6 +30,67 @@ from schemasheets.utils.prefixtool import guess_prefix_expansion +def ensure_path_tokens(path: Union[str, List[str]]) -> List[str]: + if isinstance(path, list): + return path + if "." in path: + return path.split(".") + return [path] + + +def get_attr_via_path_accessor(obj: Union[dict, YAMLRoot], path: Union[str, List[str]]) -> Any: + """ + Given an object and a path, return the value at the end of the path + + :param obj: object + :param path: path + :return: value + """ + toks = ensure_path_tokens(path) + tok = toks[0] + toks = toks[1:] + if isinstance(obj, dict): + v = obj.get(tok, None) + else: + # https://github.com/linkml/linkml/issues/971 + v = getattr(obj, tok, None) + if v and toks: + return get_attr_via_path_accessor(v, toks) + else: + return v + + +def set_attr_via_path_accessor(obj: Union[dict, YAMLRoot], path: Union[str, List[str]], value: Any, depth=0) -> None: + """ + Given an object, a path, and a value, set the value at the end of the path + + :param obj: object + :param path: path + :param value: value + :param depth: recursion depth + :return: None + """ + toks = ensure_path_tokens(path) + tok = toks[0] + toks = toks[1:] + logging.debug(f"[{depth}] Setting attr {tok} / {toks} in {obj} to {value}") + if isinstance(obj, dict): + if not toks: + obj[tok] = value + else: + if tok not in obj: + obj[tok] = {} + logging.info(f"Creating empty dict for: {tok}") + set_attr_via_path_accessor(obj[tok], toks, value, depth+1) + else: + if not toks: + setattr(obj, tok, value) + else: + if not hasattr(obj, tok): + setattr(obj, tok, {}) + set_attr_via_path_accessor(getattr(obj, tok), toks, value, depth+1) + + class SchemaSheetRowException(Exception): pass @@ -45,6 +108,7 @@ class SchemaMaker: default_name: str = None unique_slots: bool = None gsheet_id: str = None + gsheet_cache_dir: str = None table_config_path: str = None base_schema_path: str = None @@ -69,6 +133,8 @@ def create_schema(self, csv_files: Union[str, List[str]], **kwargs) -> SchemaDef csv_files = [csv_files] for f in csv_files: self.merge_sheet(f, **kwargs) + # reconstitute schema + self.schema = SchemaDefinition(**json_dumper.to_dict(self.schema)) self.schema.imports.append('linkml:types') self.schema.prefixes['linkml'] = Prefix('linkml', 'https://w3id.org/linkml/') self._tidy_slot_usage() @@ -88,6 +154,7 @@ def _tidy_slot_usage(self): :return: """ for cn, c in self.schema.classes.items(): + logging.debug(f"Tidying {cn}") inapplicable_slots = [sn for sn, s in c.slot_usage.items() if 'inapplicable' in s.annotations] for sn in inapplicable_slots: c.slots.remove(sn) @@ -118,39 +185,47 @@ def merge_sheet(self, file_name: str, delimiter='\t') -> None: try: self.add_row(row, schemasheet.table_config) line_num += 1 - except ValueError as e: - raise SchemaSheetRowException(f'Error in line {line_num}, row={row}') from e + except (ValueError, AttributeError) as e: + raise SchemaSheetRowException(f"Error in line {line_num}, row={row}\n" + f"Exception:\n{e}") from e def add_row(self, row: Dict[str, Any], table_config: TableConfig): + """ + Add and translate a row from a schema sheet to the current schema. + + A row may represent an instance of a LinkML element, such as a class, slot, type, + or enum. The row may also represent a setting, prefix, or schema-level annotation. + + This is known as the "focal element"(s) of the row. + + :param row: + :param table_config: + :return: + """ for element in self.row_focal_element(row, table_config): if isinstance(element, Prefix): name = element.prefix_prefix elif isinstance(element, PermissibleValue): name = element.text elif isinstance(element, Setting): - # print(f"\n{element = }") name = element.setting_key else: logging.debug(f'EL={element} in {row}') name = element.name logging.debug(f'ADDING: {row} // {name}') for k, v in row.items(): - # print(f"\n{k = }") + # iterate through all column values in the row if k not in table_config.columns: raise ValueError(f'Expected to find {k} in {table_config.columns.keys()}') cc = table_config.columns[k] - # print(f"{cc = }") v = self.normalize_value(v, cc) if v: - # print(f"{v = }") # special case: class-context provided by settings if cc.settings.applies_to_class: actual_element = list(self.row_focal_element(row, table_config, column=k))[0] else: actual_element = element - # print(f"{cc.maps_to = }") - # print(f"{cc = }") - logging.debug(f'SETTING {name} {cc.maps_to} = {v}') + logging.debug(f'SETTING {name}.{cc.maps_to} = {v} // IK={cc.settings.inner_key}') if cc.maps_to == 'cardinality': self.set_cardinality(actual_element, v) elif cc.metaslot: @@ -165,9 +240,10 @@ def add_row(self, row: Dict[str, Any], table_config: TableConfig): anns = yaml.safe_load(v[0]) for ann_key, ann_val in anns.items(): actual_element.annotations[ann_key] = ann_val - elif isinstance(v, list): + elif isinstance(v, list) and not cc.settings.inner_key: + # append to existing list setattr(actual_element, cc.maps_to, getattr(actual_element, cc.maps_to, []) + v) - elif isinstance(v, dict): + elif isinstance(v, dict) and not cc.settings.inner_key: for v_k, v_v in v.items(): curr_dict = getattr(actual_element, cc.maps_to) curr_dict[v_k] = v_v @@ -182,15 +258,9 @@ def add_row(self, row: Dict[str, Any], table_config: TableConfig): # will later be converted to a metamodel object curr_obj = {} setattr(actual_element, cc.maps_to, curr_obj) - if isinstance(curr_obj, dict): - curr_val = curr_obj.get(cc.settings.inner_key, None) - else: - # https://github.com/linkml/linkml/issues/971 - curr_val = getattr(curr_obj, cc.settings.inner_key, None) + curr_val = get_attr_via_path_accessor(curr_obj, cc.settings.inner_key) else: curr_val = getattr(actual_element, cc.maps_to) - # print(f"{curr_val = }") - # print(f"{v = }") if curr_val and curr_val != 'TEMP' and curr_val != v and \ not isinstance(actual_element, SchemaDefinition) and \ @@ -199,14 +269,18 @@ def add_row(self, row: Dict[str, Any], table_config: TableConfig): logging.warning(f'Overwriting value for {k}, was {curr_val}, now {v}') raise ValueError(f'Cannot reset value for {k}, was {curr_val}, now {v}') if cc.settings.inner_key: + obj_to_set = getattr(actual_element, cc.maps_to) if isinstance(getattr(actual_element, cc.maps_to), list): if '|' in v: vs = v.split('|') else: vs = [v] - setattr(actual_element, cc.maps_to, [{cc.settings.inner_key: v} for v in vs]) + for v1 in vs: + set_attr_via_path_accessor(obj_to_set, cc.settings.inner_key, v1) + # setattr(actual_element, cc.maps_to, [{cc.settings.inner_key: v} for v in vs]) else: - getattr(actual_element, cc.maps_to)[cc.settings.inner_key] = v + set_attr_via_path_accessor(obj_to_set, cc.settings.inner_key, v) + # getattr(actual_element, cc.maps_to)[cc.settings.inner_key] = v else: setattr(actual_element, cc.maps_to, v) elif cc.is_element_type: @@ -303,7 +377,7 @@ def row_focal_element(self, row: Dict[str, Any], table_config: TableConfig, else: raise ValueError(f'Unknown metatype: {typ}') if table_config.column_by_element_type is None: - raise ValueError(f'No table_config.column_by_element_type') + raise ValueError(f"""No table_config.column_by_element_type in {row}""") for k, elt_cls in tmap.items(): if k in table_config.column_by_element_type: col = table_config.column_by_element_type[k] @@ -498,7 +572,13 @@ def normalize_value(self, v: str, column_config: ColumnConfig = None) -> Any: v = bmap[v.lower()] else: v = bool(v) - if metaslot and metaslot.multivalued and not column_config.settings.inner_key: + # TODO: use inner_key to look up the actual slot + metaslot_is_multivalued = metaslot and metaslot.multivalued and not column_config.settings.inner_key + if metaslot and column_config.settings.inner_key: + if column_config.settings.internal_separator: + # print(f"ASSUMING MV FOR {column_config.name}") + metaslot_is_multivalued = True + if metaslot_is_multivalued: if not isinstance(v, list): if v is None: v = [] @@ -632,10 +712,21 @@ def ensure_file(self, file_name: str) -> str: def ensure_csvreader(self, file_name: str, delimiter=None) -> str: if self.gsheet_id: url = gsheets_download_url(self.gsheet_id, file_name) + if self.gsheet_cache_dir: + # cache a copy of the file + dir_path = Path(self.gsheet_cache_dir) + dir_path.mkdir(parents=True, exist_ok=True) + path = dir_path / (file_name + '.csv') + stream = urlopen(url) + lines = [line for line in codecs.iterdecode(stream, 'utf-8')] + with open(path, 'w') as f: + f.write("".join(lines)) + stream.close() stream = urlopen(url) text_stream = codecs.iterdecode(stream, 'utf-8') reader = csv.DictReader(text_stream, delimiter=",") yield reader + else: with open(file_name) as file: reader = csv.DictReader(file, delimiter=delimiter) @@ -669,11 +760,13 @@ def ensure_csvreader(self, file_name: str, delimiter=None) -> str: help="Auto-repair schema") @click.option("--gsheet-id", help="Google sheets ID. If this is specified then the arguments MUST be sheet names") +@click.option("--gsheet-cache-dir", + help="Directory to cache google sheets") @click.option("--base-schema-path", help="Base schema yaml file, the base-schema will be merged with the generated schema") @click.option("-v", "--verbose", count=True) @click.argument('tsv_files', nargs=-1) -def convert(tsv_files, gsheet_id, output: TextIO, name, repair, table_config_path: str, use_attributes: bool, +def convert(tsv_files, gsheet_id, gsheet_cache_dir, output: TextIO, name, repair, table_config_path: str, use_attributes: bool, unique_slots: bool, verbose: int, sort_keys: bool, base_schema_path: str): """ Convert schemasheets to a LinkML schema @@ -698,6 +791,7 @@ def convert(tsv_files, gsheet_id, output: TextIO, name, repair, table_config_pat sm = SchemaMaker(use_attributes=use_attributes, unique_slots=unique_slots, gsheet_id=gsheet_id, + gsheet_cache_dir=gsheet_cache_dir, default_name=name, table_config_path=table_config_path, base_schema_path=base_schema_path) @@ -706,7 +800,6 @@ def convert(tsv_files, gsheet_id, output: TextIO, name, repair, table_config_pat schema = sm.repair_schema(schema) schema_dict = schema_as_dict(schema) output.write(yaml.dump(schema_dict, sort_keys=sort_keys)) - # output.write(yaml_dumper.dumps(schema)) if __name__ == '__main__': diff --git a/schemasheets/schemasheet_datamodel.py b/schemasheets/schemasheet_datamodel.py index b3bca45..9056035 100644 --- a/schemasheets/schemasheet_datamodel.py +++ b/schemasheets/schemasheet_datamodel.py @@ -152,7 +152,6 @@ def add_info(self, col: COL_NAME, info: Union[Dict, DESCRIPTOR]) -> None: """ if col not in self.columns: self.columns[col] = ColumnConfig(col) - #print(f'ADDING: {col}') self.columns[col].add_info(info) if self.columns[col].maps_to == 'metatype': if self.metatype_column and self.metatype_column != col: @@ -201,6 +200,7 @@ def from_dictreader(reader: csv.DictReader) -> "SchemaSheet": rows = [] line_num = 1 table_config_rows = [] + descriptor_line_count = 0 for row in reader: logging.debug(f"ROW: {row}") # google sheets @@ -210,6 +210,7 @@ def from_dictreader(reader: csv.DictReader) -> "SchemaSheet": if row[k0].startswith('>'): table_config_rows.append(row) line_num += 1 + descriptor_line_count += 1 for k, v in row.items(): if v is not None and v.startswith('>'): v = v.replace('>', '') @@ -223,6 +224,8 @@ def from_dictreader(reader: csv.DictReader) -> "SchemaSheet": logging.debug(f'Empty val for {k} in line {line_num}') else: rows.append(row) + if descriptor_line_count == 0: + logging.warning(f"No descriptor line found in {line_num} lines. Start line_num = {line_num}") return SchemaSheet(table_config=table_config, table_config_rows=table_config_rows, rows=rows, diff --git a/tests/test_example_schemas.py b/tests/test_example_schemas.py new file mode 100644 index 0000000..fbc75aa --- /dev/null +++ b/tests/test_example_schemas.py @@ -0,0 +1,42 @@ +import os +from pathlib import Path + +import pytest +from linkml_runtime.dumpers import yaml_dumper +from linkml_runtime.utils.schemaview import SchemaView + +from schemasheets.schema_exporter import SchemaExporter +from schemasheets.schemamaker import SchemaMaker +from tests import INPUT_DIR, OUTPUT_DIR + + +@pytest.mark.parametrize("source_dir,init_args,roundtrip,delimiter", [ + ("personinfo-schema", {"use_attributes": True, "unique_slots": True}, True, ","), + ("kg-example-schema", {"use_attributes": False, "unique_slots": True}, True, ","), + ("kg-example-schema", {"use_attributes": True, "unique_slots": True}, True, ","), +]) +def test_example_schema(source_dir, init_args, roundtrip, delimiter): + sm = SchemaMaker(**init_args) + src_dir = Path(INPUT_DIR) / source_dir + # glob csv files from INPUT_DIR/source_dir + csv_files = list(src_dir.glob('*.csv')) + schema = sm.create_schema(csv_files, delimiter=delimiter) + schema = sm.repair_schema(schema) + yaml_dumper.dump(schema, to_file=os.path.join(OUTPUT_DIR, f'{source_dir}.yaml')) + yaml = yaml_dumper.dumps(schema) + sv = SchemaView(yaml) + if roundtrip: + # linkml2sheets, using original sheets as specification + # (note that this ignores the main data in the TSV) + roundtrip_dir = Path(OUTPUT_DIR) / "roundtrip" / source_dir + roundtrip_dir.mkdir(parents=True, exist_ok=True) + # print(f"CSV files: {csv_files}") + for file in csv_files: + exporter = SchemaExporter(schemamaker=sm, delimiter=delimiter) + file = str(file) + file_base = file.split("/")[-1] + to_file = str(roundtrip_dir / file_base) + # print(f"Writing schema to {to_file} using {file}") + exporter.export(sv, specification=file, to_file=to_file) + +