diff --git a/CHANGELOG.md b/CHANGELOG.md index 868696a..f01e00b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [0.1.4] + +Feature - Provide interface for using Tabulator as a package, allowing Jupyter notebooks to use Tabulator without handling a `config.json` file + ## [0.1.3] Bug fix - building a table with entity_table now updates the tabulator object's diff --git a/pyproject.toml b/pyproject.toml index bb32b25..3564264 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "rocrate-tabular" -version = "0.1.2" +version = "0.1.4" description = "A Python library to turn RO-Crates into tables" readme = "README.md" requires-python = ">=3.11" diff --git a/src/rocrate_tabular/tabulator.py b/src/rocrate_tabular/tabulator.py index 609f266..d4c1062 100644 --- a/src/rocrate_tabular/tabulator.py +++ b/src/rocrate_tabular/tabulator.py @@ -5,6 +5,8 @@ from pathlib import Path from sqlite_utils import Database from tqdm import tqdm +import difflib +import collections import csv import json import re @@ -106,10 +108,10 @@ def build(self, properties): """Takes the properties of this entity and builds a dictionary to be inserted into the database, plus any junction records required""" self.data["entity_id"] = self.entity_id - self.cf = self.tabulator.cf["tables"][self.table] + self.config = self.tabulator.config["tables"][self.table] self.text_prop = self.tabulator.text_prop - self.expand_props = self.cf.get("expand_props", []) - self.ignore_props = self.cf.get("ignore_props", []) + self.expand_props = self.config.get("expand_props", []) + self.ignore_props = self.config.get("ignore_props", []) for prop_row in properties: prop = prop_row["property_label"] value = prop_row["value"] @@ -144,7 +146,7 @@ def add_expanded_property(self, prop, target): def set_property(self, prop, value, target_id): """Add a property to entity_data, and add the target_id if defined""" - if prop in self.cf["junctions"]: + if prop in self.config["junctions"]: self.set_property_relational(prop, value, target_id) else: self.set_property_numbered(prop, value) @@ -172,27 +174,166 @@ def set_property_relational(self, prop, value, target_id): self.junctions[prop].append(target_id) +class Config(collections.UserDict): + """ + Helper class to provide a default empty config and for pretty display in notebooks. + """ + + def __init__(self, _dict=None): + if not _dict: + self.data = {"export_queries": {}, "tables": {}, "potential_tables": {}} + else: + self.data = _dict + + def _display_(self): + return self.data + + def __getitem__(self, key): + return self.data[key] + + def __setitem__(self, key, value): + self.data[key] = value + + +class OutputList(collections.UserList): + """ + Helper class for pretty output in notebooks. + """ + + def __init__(self, initlist, message=None): + self.message = message + super().__init__(initlist) + + def _repr_markdown_(self): + if self.message: + return self.message + else: + return self[:] + + +class OutputDict(collections.UserDict): + """ + Helper class for pretty output in notebooks. + """ + + def __init__(self, *args, **kwargs): + return dict.__init__(self, *args, **kwargs) + + def _repr_markdown_(self): + if self.message: + return self.message + else: + return self[:] + + class ROCrateTabulator: def __init__(self): self.crate_dir = None self.db_file = None self.db = None self.crate = None - self.cf = None + self.config = Config() self.text_prop = None self.schemaCrate = minimal_crate() self.encodedProps = {} + def use_tables(self, table_names): + if isinstance(table_names, str): + table_names = [table_names] + for table_name in table_names: + if table_name in self.config["tables"]: + raise ROCrateTabulatorException( + f"already generated the `{table_name}` table" + ) + if table_name not in self.config["potential_tables"]: + close_matches = difflib.get_close_matches( + table_name, self.config["potential_tables"] + ) + raise ROCrateTabulatorException( + f"`{table_name}` is not recognised as a potential table. Did you mean: `{close_matches[0]}`?" + ) + self.config["tables"][table_name] = self.config["potential_tables"][ + table_name + ] + del self.config["potential_tables"][table_name] + + message = "### Properties\n" + for table in self.config["tables"]: + props = self.entity_table(table) + self.config["tables"][table]["all_props"] = list(props) + + message += f"
{table}" + message += "
\n\n" + + message += """ +To attempt to expand references from a particular property +and bring the values from linked entities into the primary +table as columns: (example code, replace with your desired table and properties) + +```python +tb.expand_properties("CreativeWork", ["author"]) +``` + +To exlude a property from the table: + +```python +tb.ignore_properties("CreativeWork", ["datePublished"]) +``` + """ + + return OutputList(self.config["tables"], message) + + def ignore_properties(self, table_name, props): + if isinstance(props, str): + props = [props] + for prop in props: + if table_name not in self.config["tables"]: + if table_name in self.config["potential_tables"]: + raise ROCrateTabulatorException( + f'please run `use_tables(["{table_name}"])` before ignoring a property on this table' + ) + else: + close_matches = difflib.get_close_matches( + table_name, self.config["tables"] + ) + raise ROCrateTabulatorException( + f"`{table_name}` is not recognised as a table name. Did you mean `{close_matches[0]}`?" + ) + self.config["tables"][table_name]["ignore_props"].append(prop) + self.config["tables"][table_name]["all_props"].remove(prop) + + def expand_properties(self, table_name, props): + if isinstance(props, str): + props = [props] + for prop in props: + if table_name not in self.config["tables"]: + if table_name in self.config["potential_tables"]: + raise ROCrateTabulatorException( + f'please run `use_tables(["{table_name}"])` before ignoring a property on this table' + ) + else: + close_matches = difflib.get_close_matches( + table_name, self.config["tables"] + ) + raise ROCrateTabulatorException( + f"`{table_name}` is not recognised as a table name. Did you mean `{close_matches[0]}`?" + ) + self.config["tables"][table_name]["expand_props"].append(prop) + self.config["tables"][table_name]["all_props"].remove(prop) + def load_config(self, config_file): """Load config from file""" close_file = False if isinstance(config_file, (str, PathLike)): - config_file = open(config_file, "r") + config_file = open(config_file, "r", encoding="utf-8") close_file = True else: config_file.seek(0) - self.cf = json.load(config_file) + self.config = json.load(config_file) if close_file: config_file.close() @@ -205,25 +346,39 @@ def infer_config(self): raise ROCrateTabulatorException( "Need to run crate_to_db before infer_config" ) - self.cf = {"export_queries": {}, "tables": {}, "potential_tables": {}} + self.config = Config() for attype in self.fetch_types(): - self.cf["potential_tables"][attype] = { + self.config["potential_tables"][attype] = { "all_props": [], "ignore_props": [], "expand_props": [], } + return OutputList( + self.fetch_types(), + f""" +Potential tables: +{", ".join(self.config["potential_tables"].keys())} + +To create your tables run: (example code, replace with your desired tables) +```python +tb.use_tables(["CreativeWork", "Person"]) +``` +""", + ) + def write_config(self, config_file): """Write the config file with any changes made""" close_file = False if isinstance(config_file, (str, PathLike)): - config_file = open(config_file, "w") + config_file = open(config_file, "w", encoding="utf-8") close_file = True else: config_file.seek(0) - json.dump(self.cf, config_file, indent=4) + # `default=dict` makes json.dump pass our Config subclass of UserDict into dict(), making it serialisable + json.dump(self.config, config_file, indent=4, default=dict) if close_file: config_file.close() @@ -366,19 +521,19 @@ def entity_table(self, table, text_prop=None): ) seq += 1 self.db[table].insert_all(entities, pk="entity_id", replace=True, alter=True) - self.cf["tables"][table]["all_props"] = list(allprops) + self.config["tables"][table]["all_props"] = list(allprops) return list(allprops) def entity_table_plan(self, table): """Check entity relations to see if any need to be done as a junction table to avoid huge numbers of expanded columns""" - if "junctions" not in self.cf["tables"][table]: - self.cf["tables"][table]["junctions"] = [] + if "junctions" not in self.config["tables"][table]: + self.config["tables"][table]["junctions"] = [] for prop_counts in self.fetch_relation_counts(table): if prop_counts["n_links"] > MAX_NUMBERED_COLS: label = prop_counts["property_label"] print(f"{table}.{label} > {MAX_NUMBERED_COLS} relations") - self.cf["tables"][table]["junctions"].append(label) + self.config["tables"][table]["junctions"].append(label) # Some helper methods for wrapping SQLite statements @@ -435,9 +590,9 @@ def fetch_relation_counts(self, t): def export_csv(self, rocrate_dir): """Export csvs as configured""" - queries = self.cf["export_queries"] + queries = self.config["export_queries"] # print("Global props", self.global_props) - # self.cf["global_props"] = list(self.global_props) + # self.config["global_props"] = list(self.global_props) # Ensure rocrate_dir exists if it's provided if rocrate_dir is not None: @@ -451,7 +606,7 @@ def export_csv(self, rocrate_dir): csv_path = csv_filename if rocrate_dir is not None: csv_path = Path(rocrate_dir) / csv_filename - with open(csv_path, "w", newline="") as csvfile: + with open(csv_path, "w", newline="", encoding="utf-8") as csvfile: writer = csv.DictWriter( csvfile, fieldnames=result[0].keys(), quoting=csv.QUOTE_MINIMAL ) @@ -600,9 +755,10 @@ def main(args): tb.infer_config() tb.text_prop = args.text - for table in tb.cf["tables"]: + for table in tb.config["tables"]: print(f"Building entity table for {table}") - tb.entity_table(table) + allprops = tb.entity_table(table) + tb.config["tables"][table]["all_props"] = list(allprops) tb.write_config(args.config) print(f""" diff --git a/tests/test_package_interface.py 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