From 55531be39fa9f679ef4cfcfec9bf36b6c48f8ad3 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Sat, 28 Feb 2026 15:57:36 +0100 Subject: [PATCH 01/39] remove unused index from auto-curate code --- .../commands/dtc_plugins/auto_curate.py | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index c70df3f..1bf117b 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -2,10 +2,7 @@ import json import logging import re import sys -from itertools import ( - count, - chain, -) +from itertools import chain from typing import ( cast, Iterable, @@ -216,13 +213,10 @@ def auto_curate( continue # Get the first entry an all other entries - for index, (record, _, _, _, total) in track( - zip( - count(), - chain( - [(first_record, None, None, None, None)], - cast(Iterable, record_source), - ), + for record, _, _, _, total in track( + chain( + [(first_record, None, None, None, None)], + cast(Iterable, record_source), ), description=f'processing [green]{label}[/green]', total=total, -- 2.52.0 From 327f37b438a99fcf86850053d8968d59588470dc Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 2 Mar 2026 11:59:15 +0100 Subject: [PATCH 02/39] add `*`-class and --dry-run option to `post-records` --- CHANGELOG.md | 11 ++ .../commands/dtc_plugins/common/__init__.py | 0 .../commands/dtc_plugins/common/prefix.py | 4 + .../commands/dtc_plugins/export.py | 9 +- .../commands/dtc_plugins/post_records.py | 104 ++++++++++++++++-- 5 files changed, 113 insertions(+), 15 deletions(-) create mode 100644 dump_things_pyclient/commands/dtc_plugins/common/__init__.py create mode 100644 dump_things_pyclient/commands/dtc_plugins/common/prefix.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b9cde2..ff50ac1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,14 @@ + +## New features + +- The `dtc` subcommand `post-records` now accepts the class name `*`. If this + class name is given, it will try to infer the class name from the + `schema_type` property of the input records. The command also got the new + options `--ignore-errors` and `--dry-run`. + + + + # 0.2.12 (2026-02-11) ## New features diff --git a/dump_things_pyclient/commands/dtc_plugins/common/__init__.py b/dump_things_pyclient/commands/dtc_plugins/common/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/dump_things_pyclient/commands/dtc_plugins/common/prefix.py b/dump_things_pyclient/commands/dtc_plugins/common/prefix.py new file mode 100644 index 0000000..05fd91a --- /dev/null +++ b/dump_things_pyclient/commands/dtc_plugins/common/prefix.py @@ -0,0 +1,4 @@ + + +def de_prefix(name: str) -> str: + return name.split(':', 1)[-1] diff --git a/dump_things_pyclient/commands/dtc_plugins/export.py b/dump_things_pyclient/commands/dtc_plugins/export.py index 71f7643..e3d22d7 100644 --- a/dump_things_pyclient/commands/dtc_plugins/export.py +++ b/dump_things_pyclient/commands/dtc_plugins/export.py @@ -22,6 +22,7 @@ from ...communicate import ( incoming_read_records, server, ) +from .common.prefix import de_prefix subcommand_name = 'export' @@ -243,7 +244,7 @@ def _store_records( continue break - class_name = _de_prefix(schema_type) + class_name = de_prefix(schema_type) if not keep_schema_type: del record['schema_type'] @@ -265,12 +266,6 @@ def _store_records( return failed -def _de_prefix( - name: str, -): - return name.split(':', 1)[-1] - - def _get_hex_digest( data: str, ) -> str: diff --git a/dump_things_pyclient/commands/dtc_plugins/post_records.py b/dump_things_pyclient/commands/dtc_plugins/post_records.py index 634324f..c04d2c2 100644 --- a/dump_things_pyclient/commands/dtc_plugins/post_records.py +++ b/dump_things_pyclient/commands/dtc_plugins/post_records.py @@ -1,6 +1,7 @@ import json import logging import sys +from codecs import ignore_errors from itertools import count import rich_click as click @@ -13,8 +14,11 @@ from ...communicate import ( collection_write_record, get_session, ) +from .common.prefix import de_prefix +subcommand_name = 'post-records' + logger = logging.getLogger('post-records') console = Console(file=sys.stderr) @@ -40,18 +44,35 @@ console = Console(file=sys.stderr) is_flag=True, help='store record directly in curated area instead of an inbox. (Note: requires a token with curator rights)' ) +@click.option( + '--ignore-errors', + default=False, + is_flag=True, + help='ignore errors when posting a record and continue with remaining records', +) +@click.option( + '--dry-run', '-d', + help='if provided, do not alter any data, instead print what would be done', + default=False, + is_flag=True, +) def cli( obj, service_url, collection, cls, curated, + ignore_errors, + dry_run, ): """Read records of class CLASS from standard input and store them in the collection COLLECTION on the service SERVICE_URL. Records should be - provided in JSON-lines format. Note: all records are assumed to be of class - CLASS. To submit records of multiple classes, the subcommand has to be - invoked multiple times, once for each class. + provided in JSON-lines format. Note: if CLASS is `*` post-records will try + to infer the class from a `schema_type` property in the input records. + Otherwise, all records are + assumed to be of class CLASS. In this case, to submit records of multiple + classes, the + subcommand has to be invoked multiple times, once for each class. If the `--curated`-option is provided, the records will be stored directly in the curated area of the collection without any alterations, i.e, no @@ -62,6 +83,9 @@ def cli( annotated with the submission time and the user that performed the submission. + If any record could not be posted, error information about the failing pids + will be written to stdout in JSON Lines format (one line per faulty record). + A token is required and will be used to authenticate the requests. If the `--curated`-option is provided, the token must have curator-rights.""" @@ -72,6 +96,8 @@ def cli( collection, cls, curated, + ignore_errors, + dry_run, ) ) @@ -82,6 +108,8 @@ def post_records( collection, cls, curated, + ignore_errors, + dry_run, ) -> int: token = obj if token is None: @@ -93,22 +121,40 @@ def post_records( else: write_record = collection_write_record + failed = [] session = get_session() for index, line in zip(count(), track(sys.stdin, console=console)): try: record = json.loads(line) except Exception as e: - console.print( - f'[red]Error: reading JSON record #{index} failed[/red]: {e}', - ) + _handle_json_load_error(failed, index, line) + if ignore_errors: + continue + break + + if cls == '*': + class_name = get_class_from_record(record) + if class_name is None: + _handle_schema_type_error(failed, index, record) + if ignore_errors: + continue + break + else: + class_name = cls + + if dry_run: + if curated: + console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to curated area of collection "{collection}" on "{service_url}"') + else: + console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to token-associated incoming area of collection "{collection}" on "{service_url}"') continue try: write_record( service_url=service_url, collection=collection, - class_name=cls, + class_name=class_name, record=record, token=token, session=session, @@ -121,7 +167,49 @@ def post_records( console.print( f'[red]Error: writing record #{index} with pid {record["pid"]} failed[/red]: {e}', ) + + if failed: + click.echo('\n'.join(failed)) + return 1 return 0 -subcommand_name = 'post-records' +def _handle_json_load_error( + container: list, + index: int, + line: str, +): + console.print(f'[red]Error[/red]: error loading line [red]#{index}[/rec]: {line}') + container.append( + json.dumps( + { + 'status': 'json_load_error', + 'index': index, + 'json': line, + } + ) + ) + + +def _handle_schema_type_error( + container: list, + index: int, + record: dict, +): + console.print(f'[red]Error[/red]: no `schema type` in record [red]#{index}[/red], pid: [red]{record["pid"]}[/red]') + container.append( + json.dumps( + { + 'status': 'class_reading_error', + 'pid': record['pid'], + 'record': record, + 'message': f'could not get class from record {record["pid"]}', + } + ) + ) + + +def get_class_from_record(record: dict) -> str | None: + if 'schema_type' in record: + return de_prefix(record['schema_type']) + return None -- 2.52.0 From 1c45839cfbe6c902a8f7896a35a8f1a816159448 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 09:11:49 +0100 Subject: [PATCH 03/39] add change set creation Create a changeset that contains a one-level hierarchy. The first level is the `label` of the inbox. Below that level all changes from the respective inbox are stored in individual files. The file names are created from the PIDs of the incoming records by replacing `-` with `--` and `/` with `-_`. The double replacements is necessary to prevent name collisions that could otherwise occur if the replacement for `/` is part of a PID. --- .../commands/dtc_plugins/auto_curate.py | 328 +++++++++++++----- 1 file changed, 243 insertions(+), 85 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 1bf117b..5d0b73a 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -1,19 +1,23 @@ import json import logging import re +import subprocess import sys from itertools import chain +from pathlib import Path from typing import ( cast, Iterable, ) import rich_click as click +from requests import Session from rich.console import Console from rich.progress import track from ...communicate import ( HTTPError, + curated_read_record_with_pid, curated_write_record, get_session, incoming_delete_record, @@ -22,6 +26,8 @@ from ...communicate import ( ) +subcommand_name = 'auto-curate' + logger = logging.getLogger('auto-curate') console = Console(file=sys.stderr) @@ -53,6 +59,21 @@ stl_info = False metavar='DEST_TOKEN', help='if provided, this token will be used the authenticate against DEST_SERVICE_URL, which defaults to SERVICE_URL (the default is the token provided via --token)', ) +@click.option( + '--change-set', + metavar='CHANGE_SET_DIR', + help='write a change set to the specified directory instead of modifying data on a server, a change set reflects all changes that would be performed in the destination collection are stored (as git-repo with modifications). ' + '`annotations` are not included in the change set. If the directory does not exist, it will be created. Specifying an existing directory that is not empty is an error. If --change-set is provided, ' + '--destination-service-url, --destination-collection, and --destination-token must not be provided.', + type=click.Path( + exists=False, + file_okay=False, + dir_okay=True, + writable=True, + allow_dash=False, + path_type=Path, + ), +) @click.option( '--pid', '-p', metavar='PID', @@ -93,6 +114,7 @@ def cli( destination_service_url, destination_collection, destination_token, + change_set, pid, exclude, include, @@ -116,6 +138,7 @@ def cli( destination_service_url, destination_collection, destination_token, + change_set, pid, exclude, include, @@ -138,6 +161,7 @@ def auto_curate( destination_service_url, destination_collection, destination_token, + change_set, pid, exclude, include, @@ -151,6 +175,22 @@ def auto_curate( console.print(f'[red]Error[/red]: no token was provided (use --token or DTC_TOKEN environment variable)') return 1 + if change_set: + if destination_collection or destination_service_url or destination_token: + console.print(f'[red]Error[/red]: --change-set must not specified together with --destination-collection, --destination-service-url, or --destination-token') + return 1 + + if change_set.exists(): + if tuple(change_set.glob('*')) != tuple(): + console.print(f'[red]Error[/red]: {change_set} already exists and is not empty') + return 1 + else: + change_set.mkdir() + if dry_run: + console.print(f'INITIALIZING GIT REPO: {change_set}') + else: + subprocess.run(['git', 'init', str(change_set)], check=1) + if destination_collection is None: destination_collection = collection @@ -166,7 +206,7 @@ def auto_curate( # because it includes listing of labels if list_records: if list_labels: - logger.warning('`-l/--list-labels` and `-r/--list-records` defined, ignoring `-l/--list-labels`') + console.print(f'[yellow]Warning[/yellow]: `-l/--list-labels` and `-r/--list-records` defined, ignoring `-l/--list-labels`') list_labels = False output = {} @@ -193,10 +233,6 @@ def auto_curate( output.append(label) continue - if list_records: - output[label] = [] - - # Get the total number of entries for the record_source = incoming_read_records( service_url=service_url, collection=collection, @@ -205,94 +241,61 @@ def auto_curate( session=session, ) - # Get the first entry to find the total number of records + # Get the first entry to find the total number of records in the + # incoming area `label`. try: first_record, _, _, _, total = next(record_source) except StopIteration: console.print(f'no records in incoming area [green]{label}[/green], skipping it') continue - # Get the first entry an all other entries - for record, _, _, _, total in track( - chain( - [(first_record, None, None, None, None)], - cast(Iterable, record_source), - ), - description=f'processing [green]{label}[/green]', - total=total, - console=console, - ): - if list_records: - output[label].append(record) - continue + # Create a source that returns the first entry, all remaining entries, + # and tracks progress. + final_record_source = track( + chain( + [(first_record, None, None, None, None)], + cast(Iterable, record_source), + ), + description=f'processing [green]{label}[/green]', + total=total, + console=console, + ) - if pid: - if record['pid'] not in pid: - logger.debug( - 'ignoring record with non-matching pid: %s', - record['pid']) - continue + if change_set: + result = _update_change_set( + source=final_record_source, + change_set=change_set, + label=label, + destination_service_url=destination_service_url, + destination_collection=destination_collection, + destination_token=destination_token, + pid=pid, + dry_run=dry_run, + session=session, + ) + if result != 0: + return result - # Get the class name from the `schema_type` attribute. This requires - # that the schema type is either stored in the record or that the - # store has a "Schema Type Layer", i.e., the store type is - # `record_dir+stl`, or `sqlite+stl`. - try: - class_name = re.search('([_A-Za-z0-9]*$)', record['schema_type']).group(0) - except (IndexError, KeyError): - global stl_info - console.print(f'[yellow]Warning[/yellow]: ignoring record with pid [yellow]{record["pid"]}[/yellow] because `schema_type` attribute is missing.') - if not stl_info: - console.print( - ' [yellow]Please ensure that `schema_type` is stored in the records. Note: ' - 'if the incoming area store has a backend with a "Schema Type Layer", i.e., ' - '"record_dir+stl" or "sqlite+stl", `schema_type` will not be stored on persistent ' - 'storage and will not be returned when retrieving records from the incoming area. ' - 'dump-things-service <= 5.4.0 circumvented the "Schema Type Layer", therefore they ' - 'will return records without `schema_type` attributes on curator access to ' - 'incoming areas or curated areas. Therefore it might be a good idea to NOT use a ' - '"Schema Type Layer" in collections that shall be auto-curated, when using ' - 'dump-things-service <= 5.4.0.[/yellow]', - ) - stl_info = True - continue + elif list_records: + output[label] = [record for record, _, _, _, _, in final_record_source] + list_records() - if dry_run: - console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to collection "{destination_collection}" on "{destination_service_url}"') - console.print(f'DELETE record [green]"{record["pid"]}"[/green] from inbox "{label}" of collection "{collection}" on "{service_url}"') - continue - - # Store record in destination collection - try: - curated_write_record( - service_url=destination_service_url, - collection=destination_collection, - class_name=class_name, - record=record, - token=destination_token, - session=session, - ) - except HTTPError as e: - console.print( - f'[red]Error[/red]: writing record with pid [green]{record["pid"]}[/green] failed: {e}: {e.response.text}', - ) - return 1 - - # Delete record from incoming area - try: - incoming_delete_record( - service_url=service_url, - collection=collection, - label=label, - pid=record['pid'], - token=curator_token, - session=session, - ) - except HTTPError as e: - console.print( - f'[red]Error[/red]: deleting record with pid [green]{record["pid"]}[/green] failed: {e}: {e.response.text}', - ) - return 1 + else: + result = _curate_records( + final_record_source, + service_url, + collection, + label, + curator_token, + destination_service_url, + destination_collection, + destination_token, + pid, + dry_run, + session, + ) + if result != 0: + return result if output is not None: click.echo(json.dumps(output, ensure_ascii=False)) @@ -300,4 +303,159 @@ def auto_curate( return 0 -subcommand_name = 'auto-curate' +def _curate_records( + source: Iterable, + service_url: str, + collection: str, + label: str, + curator_token: str, + destination_service_url: str, + destination_collection: str, + destination_token: str, + pid: str | None, + dry_run: bool, + session: Session, +) -> int: + for record, _, _, _, _ in source: + if pid: + if record['pid'] not in pid: + logger.debug( + 'ignoring record with non-matching pid: %s', + record['pid']) + continue + + class_name = _get_class_name(record) + if class_name is None: + continue + + if dry_run: + console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to collection "{destination_collection}" on "{destination_service_url}"') + console.print(f'DELETE record [green]"{record["pid"]}"[/green] from inbox "{label}" of collection "{collection}" on "{service_url}"') + continue + + # Store record in destination collection + try: + curated_write_record( + service_url=destination_service_url, + collection=destination_collection, + class_name=class_name, + record=record, + token=destination_token, + session=session, + ) + except HTTPError as e: + console.print( + f'[red]Error[/red]: writing record with pid [green]{record["pid"]}[/green] failed: {e}: {e.response.text}', + ) + return 1 + + # Delete record from incoming area + try: + incoming_delete_record( + service_url=service_url, + collection=collection, + label=label, + pid=record['pid'], + token=curator_token, + session=session, + ) + except HTTPError as e: + console.print( + f'[red]Error[/red]: deleting record with pid [green]{record["pid"]}[/green] failed: {e}: {e.response.text}', + ) + return 1 + return 0 + + +def _get_class_name(record: dict) -> str | None: + """Get the class name from the `schema_type` attribute. + + This requires that the schema type is either stored in the record or that + the store has a "Schema Type Layer", i.e., the store type is + `record_dir+stl`, or `sqlite+stl`. + """ + try: + return re.search('([_A-Za-z0-9]*$)', record['schema_type']).group(0) + except (IndexError, KeyError): + global stl_info + console.print(f'[yellow]Warning[/yellow]: ignoring record with pid [yellow]{record["pid"]}[/yellow] because `schema_type` attribute is missing.') + if not stl_info: + console.print( + ' [yellow]Please ensure that `schema_type` is stored in the records. Note: ' + 'if the incoming area store has a backend with a "Schema Type Layer", i.e., ' + '"record_dir+stl" or "sqlite+stl", `schema_type` will not be stored on persistent ' + 'storage and will not be returned when retrieving records from the incoming area.' + 'dump-things-service circumvents the "Schema Type Layer" on curator access, i.e., ' + 'on access to incoming areas and on access to the curated area. Therefore it ' + 'might return records without `schema_type` attributes on curator access to ' + 'incoming areas or curated areas. To be consistent, it might be a good idea to ' + 'NOT use a "Schema Type Layer" in collections that shall be auto-curated, but ' + 'store `schema_type`-attributes in all records.[/yellow]', + ) + stl_info = True + return None + + +def _update_change_set( + source: Iterable, + change_set: Path, + label: str, + destination_service_url: str, + destination_collection: str, + destination_token: str, + pid: str, + dry_run: bool, + session: Session, +) -> int: + label_dir = change_set / label + label_dir.mkdir(parents=True, exist_ok=True) + + for record, _, _, _, _ in source: + if pid: + if record['pid'] not in pid: + logger.debug( + 'ignoring record with non-matching pid: %s', + record['pid']) + continue + + class_name = _get_class_name(record) + if class_name is None: + continue + + file_path = label_dir / _pid_to_filename(record['pid']) + if dry_run: + console.print(f'STORE record [green]"{record["pid"]}"[/green] of class "{class_name}" from inbox {label} at "{file_path.resolve()}"') + continue + + # Fetch the current curated record from the destination, delete its + # annotations, write it to a file, and add the file to git. + existing_record = curated_read_record_with_pid( + service_url=destination_service_url, + collection=destination_collection, + pid=record['pid'], + token=destination_token, + session=session, + ) + if existing_record: + existing_record.pop('annotations', None) + file_path.write_text( + json.dumps(existing_record, ensure_ascii=False), + encoding='utf8' + ) + else: + file_path.write_text('null\n') + subprocess.run(['git', 'add', str(file_path)], cwd=change_set, check=True) + + # Write the new record without annotations to disk + record.pop('annotations', None) + file_path.write_text( + json.dumps(record, ensure_ascii=False), + encoding='utf8' + ) + + subprocess.run(['git', 'commit', '-m', 'commit curated state'], cwd=change_set, check=True) + return 0 + + +def _pid_to_filename(pid: str) -> str: + return pid.replace('-', '--').replace('/', '-_') -- 2.52.0 From dd52754887fa7d8145a84b8f8108c9c1a260806b Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 09:28:16 +0100 Subject: [PATCH 04/39] add --dry-run handling to change-set code --- .../commands/dtc_plugins/auto_curate.py | 52 ++++++++++++------- 1 file changed, 34 insertions(+), 18 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 5d0b73a..6e9c1e5 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -185,10 +185,10 @@ def auto_curate( console.print(f'[red]Error[/red]: {change_set} already exists and is not empty') return 1 else: - change_set.mkdir() if dry_run: - console.print(f'INITIALIZING GIT REPO: {change_set}') + console.print(f'[DRY_RUN]:INITIALIZING GIT REPO: {change_set}') else: + change_set.mkdir() subprocess.run(['git', 'init', str(change_set)], check=1) if destination_collection is None: @@ -329,8 +329,8 @@ def _curate_records( continue if dry_run: - console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to collection "{destination_collection}" on "{destination_service_url}"') - console.print(f'DELETE record [green]"{record["pid"]}"[/green] from inbox "{label}" of collection "{collection}" on "{service_url}"') + console.print(f'[DRY_RUN]:WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to collection "{destination_collection}" on "{destination_service_url}"') + console.print(f'[DRY_RUN]:DELETE record [green]"{record["pid"]}"[/green] from inbox "{label}" of collection "{collection}" on "{service_url}"') continue # Store record in destination collection @@ -408,7 +408,10 @@ def _update_change_set( session: Session, ) -> int: label_dir = change_set / label - label_dir.mkdir(parents=True, exist_ok=True) + if dry_run: + console.print(f'[DRY_RUN]:CREATING LABEL DIRECTORY: {label_dir}') + else: + label_dir.mkdir(parents=True, exist_ok=True) for record, _, _, _, _ in source: if pid: @@ -423,9 +426,6 @@ def _update_change_set( continue file_path = label_dir / _pid_to_filename(record['pid']) - if dry_run: - console.print(f'STORE record [green]"{record["pid"]}"[/green] of class "{class_name}" from inbox {label} at "{file_path.resolve()}"') - continue # Fetch the current curated record from the destination, delete its # annotations, write it to a file, and add the file to git. @@ -438,22 +438,38 @@ def _update_change_set( ) if existing_record: existing_record.pop('annotations', None) - file_path.write_text( - json.dumps(existing_record, ensure_ascii=False), - encoding='utf8' - ) + if dry_run: + console.print(f'[DRY_RUN]:STORE existing record [green]"{record["pid"]}"[/green] of class "{class_name}" from curated area at "{file_path.resolve()}"') + else: + file_path.write_text( + json.dumps(existing_record, ensure_ascii=False), + encoding='utf8' + ) + else: + if dry_run: + console.print(f'[DRY_RUN]:STORE "null" at "{file_path.resolve()}"') + else: + file_path.write_text('null\n') + + if dry_run: + console.print(f'[DRY_RUN]:GIT ADD {file_path}') else: - file_path.write_text('null\n') subprocess.run(['git', 'add', str(file_path)], cwd=change_set, check=True) # Write the new record without annotations to disk record.pop('annotations', None) - file_path.write_text( - json.dumps(record, ensure_ascii=False), - encoding='utf8' - ) + if dry_run: + console.print(f'[DRY_RUN]:STORE new record [green]"{record["pid"]}"[/green] of class "{class_name}" from inbox {label} at "{file_path.resolve()}"') + else: + file_path.write_text( + json.dumps(record, ensure_ascii=False), + encoding='utf8' + ) - subprocess.run(['git', 'commit', '-m', 'commit curated state'], cwd=change_set, check=True) + if dry_run: + console.print(f'[DRY_RUN]:GIT COMMIT in {change_set}') + else: + subprocess.run(['git', 'commit', '-m', 'commit curated state'], cwd=change_set, check=True) return 0 -- 2.52.0 From 47f208e2f3db16a2f183f892b08d9afbd44e5981 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 09:37:48 +0100 Subject: [PATCH 05/39] add --change-set description to CHANGELOG.md --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ff50ac1..0fe7f40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,13 @@ `schema_type` property of the input records. The command also got the new options `--ignore-errors` and `--dry-run`. - +- The `dtc` subcommand `auto-curate` has the new option + `--change set CHANGE_SET_DIR`. If provided, `auto-curate` will generate a + git repository in `CHANGE_SET_DIR` that contains the that changes that + would be introduced by the curation in thw git worktree. The change set + directory contains one directory layer to separate incoming areas. Within + the individual incoming area directories, incoming records are stored in a + flat hierarchy with their PIDs as filenames. # 0.2.12 (2026-02-11) -- 2.52.0 From 611fd61369beb0286b19ebf712f9692bd150c470 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 10:19:29 +0100 Subject: [PATCH 06/39] ensure change set records end with newline --- dump_things_pyclient/commands/dtc_plugins/auto_curate.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 6e9c1e5..d4ee43e 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -442,7 +442,7 @@ def _update_change_set( console.print(f'[DRY_RUN]:STORE existing record [green]"{record["pid"]}"[/green] of class "{class_name}" from curated area at "{file_path.resolve()}"') else: file_path.write_text( - json.dumps(existing_record, ensure_ascii=False), + json.dumps(existing_record, ensure_ascii=False) + '\n', encoding='utf8' ) else: @@ -462,7 +462,7 @@ def _update_change_set( console.print(f'[DRY_RUN]:STORE new record [green]"{record["pid"]}"[/green] of class "{class_name}" from inbox {label} at "{file_path.resolve()}"') else: file_path.write_text( - json.dumps(record, ensure_ascii=False), + json.dumps(record, ensure_ascii=False) + '\n', encoding='utf8' ) -- 2.52.0 From 8df6a20822a81aaf3e65c595fa7cca0e07c9eddd Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 10:24:52 +0100 Subject: [PATCH 07/39] add dry-run prefix to dry-run output in post-records --- dump_things_pyclient/commands/dtc_plugins/post_records.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/post_records.py b/dump_things_pyclient/commands/dtc_plugins/post_records.py index c04d2c2..16e4c14 100644 --- a/dump_things_pyclient/commands/dtc_plugins/post_records.py +++ b/dump_things_pyclient/commands/dtc_plugins/post_records.py @@ -145,9 +145,9 @@ def post_records( if dry_run: if curated: - console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to curated area of collection "{collection}" on "{service_url}"') + console.print(f'[DRY_RUN]:WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to curated area of collection "{collection}" on "{service_url}"') else: - console.print(f'WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to token-associated incoming area of collection "{collection}" on "{service_url}"') + console.print(f'[DRY_RUN]:WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to token-associated incoming area of collection "{collection}" on "{service_url}"') continue try: -- 2.52.0 From e20ee4d03be334fd967c08a4f869182bc8a5bf3e Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 10:27:37 +0100 Subject: [PATCH 08/39] add exception details to error info in post-records --- dump_things_pyclient/commands/dtc_plugins/post_records.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/post_records.py b/dump_things_pyclient/commands/dtc_plugins/post_records.py index 16e4c14..0b283f8 100644 --- a/dump_things_pyclient/commands/dtc_plugins/post_records.py +++ b/dump_things_pyclient/commands/dtc_plugins/post_records.py @@ -1,7 +1,6 @@ import json import logging import sys -from codecs import ignore_errors from itertools import count import rich_click as click @@ -128,7 +127,7 @@ def post_records( try: record = json.loads(line) except Exception as e: - _handle_json_load_error(failed, index, line) + _handle_json_load_error(failed, index, line, e) if ignore_errors: continue break @@ -178,6 +177,7 @@ def _handle_json_load_error( container: list, index: int, line: str, + exc: Exception, ): console.print(f'[red]Error[/red]: error loading line [red]#{index}[/rec]: {line}') container.append( @@ -186,6 +186,7 @@ def _handle_json_load_error( 'status': 'json_load_error', 'index': index, 'json': line, + 'detail': str(exc), } ) ) -- 2.52.0 From 41ef7df867ac236e64a5d22cf4ff90e17c815e0e Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 10:33:33 +0100 Subject: [PATCH 09/39] update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0fe7f40..9e4e5de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,4 @@ +# 0.2.13 (2026-03-03) ## New features -- 2.52.0 From 866c36c7761e2cbeded5153847281f986a411867 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 10:34:18 +0100 Subject: [PATCH 10/39] fix CHANGELOG.md format --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e4e5de..1c2362f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,6 @@ `import`, and `delete-records`. - Ensure that all `dtc` subcommands return an non-zero exit status on error. - ## Improvements -- 2.52.0 From 95733fd885c2ace76e73111ca0816a4ff363117d Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 14:12:31 +0100 Subject: [PATCH 11/39] store annotations in change sets The annotations that are removed from incoming records are now stored in change sets and can therefore be added when the change set is posted. This keeps the diff small and content-related, while preserveing the annotations. --- .../commands/dtc_plugins/auto_curate.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index d4ee43e..8898928 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -407,12 +407,18 @@ def _update_change_set( dry_run: bool, session: Session, ) -> int: - label_dir = change_set / label + label_dir = change_set / 'records' / label + annotation_dir = change_set / 'annotations' / label if dry_run: console.print(f'[DRY_RUN]:CREATING LABEL DIRECTORY: {label_dir}') else: label_dir.mkdir(parents=True, exist_ok=True) + if dry_run: + console.print(f'[DRY_RUN]:CREATING ANNOTATION DIRECTORY: {annotation_dir}') + else: + annotation_dir.mkdir(parents=True, exist_ok=True) + for record, _, _, _, _ in source: if pid: if record['pid'] not in pid: @@ -426,6 +432,7 @@ def _update_change_set( continue file_path = label_dir / _pid_to_filename(record['pid']) + annotation_path = annotation_dir / _pid_to_filename(record['pid']) # Fetch the current curated record from the destination, delete its # annotations, write it to a file, and add the file to git. @@ -457,7 +464,7 @@ def _update_change_set( subprocess.run(['git', 'add', str(file_path)], cwd=change_set, check=True) # Write the new record without annotations to disk - record.pop('annotations', None) + annotations = record.pop('annotations', None) if dry_run: console.print(f'[DRY_RUN]:STORE new record [green]"{record["pid"]}"[/green] of class "{class_name}" from inbox {label} at "{file_path.resolve()}"') else: @@ -465,6 +472,13 @@ def _update_change_set( json.dumps(record, ensure_ascii=False) + '\n', encoding='utf8' ) + if dry_run: + console.print(f'[DRY_RUN]:STORE annotations for record [green]"{record["pid"]}"[/green] of class "{class_name}" from curated area at "{annotation_path.resolve()}"') + else: + annotation_path.write_text( + json.dumps(annotations, ensure_ascii=False) + '\n', + encoding='utf8' + ) if dry_run: console.print(f'[DRY_RUN]:GIT COMMIT in {change_set}') -- 2.52.0 From a5040bc78d353ee2aebcfbf2a7d0b73b91d2599f Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 3 Mar 2026 15:49:58 +0100 Subject: [PATCH 12/39] add `--post-change-set` option for `dtc auto-curate` --- .../commands/dtc_plugins/auto_curate.py | 106 ++++++++++++++++-- 1 file changed, 99 insertions(+), 7 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 8898928..3045dd9 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -63,8 +63,7 @@ stl_info = False '--change-set', metavar='CHANGE_SET_DIR', help='write a change set to the specified directory instead of modifying data on a server, a change set reflects all changes that would be performed in the destination collection are stored (as git-repo with modifications). ' - '`annotations` are not included in the change set. If the directory does not exist, it will be created. Specifying an existing directory that is not empty is an error. If --change-set is provided, ' - '--destination-service-url, --destination-collection, and --destination-token must not be provided.', + '`annotations` are not included in the change set. If the directory does not exist, it will be created. Specifying an existing directory that is not empty is an error', type=click.Path( exists=False, file_okay=False, @@ -74,6 +73,26 @@ stl_info = False path_type=Path, ), ) +@click.option( + '--post-change-set', + metavar='CHANGE_SET_DIR', + help='read the change set at CHANGE_SET_DIR and post it to the curated area of the given destination server and collection. If --post-change-set is provided, ' + '--change-set must not be provided', + type=click.Path( + exists=True, + file_okay=False, + dir_okay=True, + writable=True, + allow_dash=False, + path_type=Path, + ), +) +@click.option( + '--add-annotations', + help='add annotations when posting a change set. If --post-change-set is not provided, this flag is ignored (true by default)', + default=True, + is_flag=True, +) @click.option( '--pid', '-p', metavar='PID', @@ -115,6 +134,8 @@ def cli( destination_collection, destination_token, change_set, + post_change_set, + add_annotations, pid, exclude, include, @@ -139,6 +160,8 @@ def cli( destination_collection, destination_token, change_set, + post_change_set, + add_annotations, pid, exclude, include, @@ -162,6 +185,8 @@ def auto_curate( destination_collection, destination_token, change_set, + post_change_set, + add_annotations, pid, exclude, include, @@ -176,8 +201,8 @@ def auto_curate( return 1 if change_set: - if destination_collection or destination_service_url or destination_token: - console.print(f'[red]Error[/red]: --change-set must not specified together with --destination-collection, --destination-service-url, or --destination-token') + if post_change_set: + console.print(f'[red]Error[/red]: --change-set and --post-change-set must not be specified together') return 1 if change_set.exists(): @@ -200,6 +225,20 @@ def auto_curate( if destination_token is None: destination_token = curator_token + session = get_session() + + if post_change_set: + result = _post_change_set( + post_change_set, + destination_service_url=destination_service_url, + destination_collection=destination_collection, + destination_token=destination_token, + add_annotations=add_annotations, + dry_run=dry_run, + session=session, + ) + return result + output = None # If --list-labels and --list-records are provided, keep only the latter, @@ -213,7 +252,6 @@ def auto_curate( if list_labels: output = [] - session = get_session() all_labels = incoming_read_labels( service_url=service_url, collection=collection, @@ -273,8 +311,7 @@ def auto_curate( dry_run=dry_run, session=session, ) - if result != 0: - return result + return result elif list_records: output[label] = [record for record, _, _, _, _, in final_record_source] @@ -326,6 +363,7 @@ def _curate_records( class_name = _get_class_name(record) if class_name is None: + console.print(f'[yellow]Warning[/yellow]: could not determine class in record [yellow]{record["pid"]}[/yellow], ignoring it.') continue if dry_run: @@ -489,3 +527,57 @@ def _update_change_set( def _pid_to_filename(pid: str) -> str: return pid.replace('-', '--').replace('/', '-_') + + +def _post_change_set( + post_change_set: Path, + destination_service_url: str, + destination_collection: str, + destination_token: str, + add_annotations: bool, + dry_run: bool, + session: Session, +): + for match in post_change_set.glob('records/*/*'): + try: + record = json.loads(match.read_text()) + except json.JSONDecodeError as jde: + console.print(f'[yellow]Warning[/yellow]: JSON error: {jde} at [yellow]{match}[/yellow], ignoring it.') + continue + + label, file_name = match.parts[-2:] + if add_annotations: + annotation_file = post_change_set / 'annotations' / label / file_name + try: + annotations = json.loads(annotation_file.read_text()) + except json.JSONDecodeError as jde: + console.print(f'[yellow]Warning[/yellow]: JSON error: {jde} at [yellow]{annotation_file}[/yellow], ignoring record.') + continue + record['annotations'] = annotations + + class_name = _get_class_name(record) + if class_name is None: + console.print(f'[yellow]Warning[/yellow]: could not determine class of record [yellow]{record["pid"]}[/yellow], ignoring it.') + continue + + if dry_run: + console.print(f'[DRY_RUN]:WRITE record [green]"{record["pid"]}"[/green] of class "{class_name}" to collection "{destination_collection}" on "{destination_service_url}"') + continue + + # Store record in destination collection + try: + curated_write_record( + service_url=destination_service_url, + collection=destination_collection, + class_name=class_name, + record=record, + token=destination_token, + session=session, + ) + except HTTPError as e: + console.print( + f'[red]Error[/red]: writing record with pid [green]{record["pid"]}[/green] failed: {e}: {e.response.text}', + ) + return 1 + + return 0 -- 2.52.0 From e3e192457ccdf0d7e3e5bd5fe98fff0518afe5e2 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Wed, 4 Mar 2026 09:29:57 +0100 Subject: [PATCH 13/39] rename `--change-set` to `--create-change-set` Rename `--change-set` to `--create-change-set`. Improve validity check to change-set operations when `--list-records` or `--list-labels` is defined. --- .../commands/dtc_plugins/auto_curate.py | 49 +++++++++++-------- 1 file changed, 29 insertions(+), 20 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 3045dd9..96ef8d6 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -60,10 +60,10 @@ stl_info = False help='if provided, this token will be used the authenticate against DEST_SERVICE_URL, which defaults to SERVICE_URL (the default is the token provided via --token)', ) @click.option( - '--change-set', + '--create-change-set', metavar='CHANGE_SET_DIR', - help='write a change set to the specified directory instead of modifying data on a server, a change set reflects all changes that would be performed in the destination collection are stored (as git-repo with modifications). ' - '`annotations` are not included in the change set. If the directory does not exist, it will be created. Specifying an existing directory that is not empty is an error', + help='write a change set to the specified directory instead of modifying data on a server. A change set contains all changes that would be performed in the destination collection (as git-repo with modifications). ' + '`annotations` are not included in the modifications, but are stored separately in the change set directory. If the directory does not exist, it will be created. Specifying an existing directory that is not empty is an error', type=click.Path( exists=False, file_okay=False, @@ -76,8 +76,8 @@ stl_info = False @click.option( '--post-change-set', metavar='CHANGE_SET_DIR', - help='read the change set at CHANGE_SET_DIR and post it to the curated area of the given destination server and collection. If --post-change-set is provided, ' - '--change-set must not be provided', + help='read the change set at CHANGE_SET_DIR and post it to the curated area of the given destination server and collection (--post-change-set and ' + '--create-change-set are mutually exclusive)', type=click.Path( exists=True, file_okay=False, @@ -89,8 +89,8 @@ stl_info = False ) @click.option( '--add-annotations', - help='add annotations when posting a change set. If --post-change-set is not provided, this flag is ignored (true by default)', - default=True, + help='add annotations when posting a change set. By default the annotations will not be added to the records that are posted. If --post-change-set is not provided, this flag is ignored', + default=False, is_flag=True, ) @click.option( @@ -133,7 +133,7 @@ def cli( destination_service_url, destination_collection, destination_token, - change_set, + create_change_set, post_change_set, add_annotations, pid, @@ -159,7 +159,7 @@ def cli( destination_service_url, destination_collection, destination_token, - change_set, + create_change_set, post_change_set, add_annotations, pid, @@ -184,7 +184,7 @@ def auto_curate( destination_service_url, destination_collection, destination_token, - change_set, + create_change_set, post_change_set, add_annotations, pid, @@ -200,21 +200,30 @@ def auto_curate( console.print(f'[red]Error[/red]: no token was provided (use --token or DTC_TOKEN environment variable)') return 1 - if change_set: + if create_change_set: if post_change_set: - console.print(f'[red]Error[/red]: --change-set and --post-change-set must not be specified together') + console.print(f'[red]Error[/red]: --create-change-set and --post-change-set must not be specified together') return 1 - if change_set.exists(): - if tuple(change_set.glob('*')) != tuple(): - console.print(f'[red]Error[/red]: {change_set} already exists and is not empty') + if list_labels or list_records: + console.print(f'[red]Error[/red]: --create-change-set cannot be combined with --list-labels or --list-records') + return 1 + + if create_change_set.exists(): + if tuple(create_change_set.glob('*')) != tuple(): + console.print(f'[red]Error[/red]: {create_change_set} already exists and is not empty') return 1 else: if dry_run: - console.print(f'[DRY_RUN]:INITIALIZING GIT REPO: {change_set}') + console.print(f'[DRY_RUN]:INITIALIZING GIT REPO: {create_change_set}') else: - change_set.mkdir() - subprocess.run(['git', 'init', str(change_set)], check=1) + create_change_set.mkdir() + subprocess.run(['git', 'init', str(create_change_set)], check=1) + + if post_change_set: + if list_labels or list_records: + console.print(f'[red]Error[/red]: --post-change-set cannot be combined with --list-labels or --list-records') + return 1 if destination_collection is None: destination_collection = collection @@ -299,10 +308,10 @@ def auto_curate( console=console, ) - if change_set: + if create_change_set: result = _update_change_set( source=final_record_source, - change_set=change_set, + change_set=create_change_set, label=label, destination_service_url=destination_service_url, destination_collection=destination_collection, -- 2.52.0 From 24ac61707ac9ef0fcab7acaedb8d7fe2357322bd Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Wed, 4 Mar 2026 11:18:41 +0100 Subject: [PATCH 14/39] clean up auto-curate This commit unifies the handling of "normal" curation, change-set-creation and change-set-posting. inbox inclusion- and exclusion-lists are now honored in all three operation modes, i.e., in curating, change-set-creation, and change-set-posting. The commit also fixes some errors. --- .../commands/dtc_plugins/auto_curate.py | 183 ++++++++++++------ 1 file changed, 119 insertions(+), 64 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 96ef8d6..640dee2 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -236,18 +236,6 @@ def auto_curate( session = get_session() - if post_change_set: - result = _post_change_set( - post_change_set, - destination_service_url=destination_service_url, - destination_collection=destination_collection, - destination_token=destination_token, - add_annotations=add_annotations, - dry_run=dry_run, - session=session, - ) - return result - output = None # If --list-labels and --list-records are provided, keep only the latter, @@ -261,12 +249,17 @@ def auto_curate( if list_labels: output = [] - all_labels = incoming_read_labels( - service_url=service_url, - collection=collection, - token=obj, - session=session, - ) + # Get the labels from the service, or from a change set that should be posted. + if post_change_set: + all_labels = _get_change_set_labels(post_change_set) + else: + all_labels = incoming_read_labels( + service_url=service_url, + collection=collection, + token=obj, + session=session, + ) + for label in all_labels: if include and label not in include: logger.debug('ignoring non-included incoming label: %s', label) @@ -280,33 +273,45 @@ def auto_curate( output.append(label) continue - record_source = incoming_read_records( - service_url=service_url, - collection=collection, - label=label, - token=obj, - session=session, - ) + # Get the records from the service, or from a change set that should + # be posted. + if post_change_set: + record_source = _get_change_set_records(post_change_set, label) + final_record_source = track( + record_source, + description=f'processing [green]{label}[/green]', + total=len(record_source), + console=console, + ) - # Get the first entry to find the total number of records in the - # incoming area `label`. - try: - first_record, _, _, _, total = next(record_source) - except StopIteration: - console.print(f'no records in incoming area [green]{label}[/green], skipping it') - continue + else: + record_source = incoming_read_records( + service_url=service_url, + collection=collection, + label=label, + token=obj, + session=session, + ) - # Create a source that returns the first entry, all remaining entries, - # and tracks progress. - final_record_source = track( - chain( - [(first_record, None, None, None, None)], - cast(Iterable, record_source), - ), - description=f'processing [green]{label}[/green]', - total=total, - console=console, - ) + # Get the first entry to find the total number of records in the + # incoming area `label`. + try: + first_record, _, _, _, total = next(record_source) + except StopIteration: + console.print(f'no records in incoming area [green]{label}[/green], skipping it') + continue + + # Create a source that returns the first entry, all remaining entries, + # and tracks progress. + final_record_source = track( + chain( + [(first_record, None, None, None, None)], + cast(Iterable, record_source), + ), + description=f'processing [green]{label}[/green]', + total=total, + console=console, + ) if create_change_set: result = _update_change_set( @@ -320,25 +325,42 @@ def auto_curate( dry_run=dry_run, session=session, ) - return result + if result != 0: + return result elif list_records: output[label] = [record for record, _, _, _, _, in final_record_source] - list_records() + continue + + elif post_change_set: + result = _post_change_set( + final_record_source, + post_change_set=post_change_set, + label=label, + destination_service_url=destination_service_url, + destination_collection=destination_collection, + destination_token=destination_token, + pid=pid, + add_annotations=add_annotations, + dry_run=dry_run, + session=session, + ) + if result != 0: + return result else: result = _curate_records( final_record_source, - service_url, - collection, - label, - curator_token, - destination_service_url, - destination_collection, - destination_token, - pid, - dry_run, - session, + service_url=service_url, + collection=collection, + label=label, + curator_token=curator_token, + destination_service_url=destination_service_url, + destination_collection=destination_collection, + destination_token=destination_token, + pid=pid, + dry_run=dry_run, + session=session, ) if result != 0: return result @@ -450,7 +472,7 @@ def _update_change_set( destination_service_url: str, destination_collection: str, destination_token: str, - pid: str, + pid: str | None, dry_run: bool, session: Session, ) -> int: @@ -505,10 +527,11 @@ def _update_change_set( else: file_path.write_text('null\n') + intra_repo_file_path = Path(*file_path.parts[1:]) if dry_run: - console.print(f'[DRY_RUN]:GIT ADD {file_path}') + console.print(f'[DRY_RUN]:GIT ADD {intra_repo_file_path} (cdw={change_set})') else: - subprocess.run(['git', 'add', str(file_path)], cwd=change_set, check=True) + subprocess.run(['git', 'add', str(intra_repo_file_path)], cwd=change_set, check=True) # Write the new record without annotations to disk annotations = record.pop('annotations', None) @@ -539,22 +562,31 @@ def _pid_to_filename(pid: str) -> str: def _post_change_set( + source: Iterable, post_change_set: Path, + label: str, destination_service_url: str, destination_collection: str, destination_token: str, + pid: str | None, add_annotations: bool, dry_run: bool, session: Session, ): - for match in post_change_set.glob('records/*/*'): - try: - record = json.loads(match.read_text()) - except json.JSONDecodeError as jde: - console.print(f'[yellow]Warning[/yellow]: JSON error: {jde} at [yellow]{match}[/yellow], ignoring it.') + pid_file_name = _pid_to_filename(pid) if pid else None + for file_name in source: + + if pid_file_name and pid_file_name != file_name: + logger.debug('ignoring file with non-matching pid: %s', pid_file_name) + continue + + try: + record_file = post_change_set / 'records' / label / file_name + record = json.loads(record_file.read_text()) + except json.JSONDecodeError as jde: + console.print(f'[yellow]Warning[/yellow]: JSON error: {jde} at [yellow]{record_file}[/yellow], ignoring it.') continue - label, file_name = match.parts[-2:] if add_annotations: annotation_file = post_change_set / 'annotations' / label / file_name try: @@ -590,3 +622,26 @@ def _post_change_set( return 1 return 0 + + +def _get_change_set_labels( + change_set: Path, +) -> tuple[str]: + return tuple( + map( + lambda match: match.name, + change_set.glob(f'records/*') + ) + ) + + +def _get_change_set_records( + change_set: Path, + label: str, +) -> tuple[str]: + return tuple( + map( + lambda match: match.name, + change_set.glob(f'records/{label}/*') + ) + ) -- 2.52.0 From 8e1b0cdcce78aea1b7775d71960c66ea85a36e7b Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Wed, 4 Mar 2026 14:26:47 +0100 Subject: [PATCH 15/39] update CHANGELOG.md --- CHANGELOG.md | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c2362f..3ad8326 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,16 +4,20 @@ - The `dtc` subcommand `post-records` now accepts the class name `*`. If this class name is given, it will try to infer the class name from the - `schema_type` property of the input records. The command also got the new + `schema_type` property of the input records. `post-records` also got the new options `--ignore-errors` and `--dry-run`. -- The `dtc` subcommand `auto-curate` has the new option - `--change set CHANGE_SET_DIR`. If provided, `auto-curate` will generate a - git repository in `CHANGE_SET_DIR` that contains the that changes that - would be introduced by the curation in thw git worktree. The change set - directory contains one directory layer to separate incoming areas. Within - the individual incoming area directories, incoming records are stored in a - flat hierarchy with their PIDs as filenames. +- The `dtc` subcommand `auto-curate` has the new options + `--create-change-set CHANGE_SET_DIR` and `--post-change-set`. With + `--create-change-set`, `auto-curate` will generate a + git repository in `CHANGE_SET_DIR` that contains the changes that + would be introduced by the curation in the git worktree. The records in the + change set have no `annotations`-property, annotations are store separately + in the change set change set. If `--post-change-set` is provided, + `auto-curate` will post the records from the change set to the curated area + of the service. With + the option `--add-annotations` the annotations that were read from the inbox + will be added to the records before they are posted to the service. # 0.2.12 (2026-02-11) -- 2.52.0 From 383bad7ce8a18337f393a1c2d32221fdc64b6770 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Wed, 4 Mar 2026 14:33:08 +0100 Subject: [PATCH 16/39] update doc-string of `auto-curate` --- dump_things_pyclient/commands/dtc_plugins/auto_curate.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 640dee2..7a888a9 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -148,6 +148,14 @@ def cli( collection, or to the curated area of another collection, possibly on another service. + `auto-curate` can create change sets that reflect what changes would be + applied to the destination, if records in inboxes were posted to the + destination. The changes are reflected as worktree diff in a git + repository (annotations are excluded from the diff). + `auto-curate` can also read records from a change set and post them + a service. If required, annotations can be re-added before the records + from the change set are posted to the service. + A token is required and will be used to authenticate the requests. The token must have curator-rights.""" try: -- 2.52.0 From eb72828d200114ed5dbfa9f0acca812fd17e3147 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Wed, 4 Mar 2026 14:37:29 +0100 Subject: [PATCH 17/39] update `--post-change-set` option help-text --- dump_things_pyclient/commands/dtc_plugins/auto_curate.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index 7a888a9..f5e5f87 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -76,7 +76,9 @@ stl_info = False @click.option( '--post-change-set', metavar='CHANGE_SET_DIR', - help='read the change set at CHANGE_SET_DIR and post it to the curated area of the given destination server and collection (--post-change-set and ' + help='read the change set at CHANGE_SET_DIR and post it to the curated area of the given destination server and collection. ' + 'If `--add-annotations` is provided in addition, the annotations that were recorded in the records in the incoming areas ' + 'are added to the respective records before posting them to the destination (--post-change-set and ' '--create-change-set are mutually exclusive)', type=click.Path( exists=True, @@ -89,7 +91,7 @@ stl_info = False ) @click.option( '--add-annotations', - help='add annotations when posting a change set. By default the annotations will not be added to the records that are posted. If --post-change-set is not provided, this flag is ignored', + help='add annotations when posting a change set via `--post-change-set`. By default the annotations will not be added to the records that are posted. If --post-change-set is not provided, this flag is ignored', default=False, is_flag=True, ) -- 2.52.0 From 927ae3ca57792d7987dda66b3ce67d894a103575 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 11:24:42 +0100 Subject: [PATCH 18/39] add a minimal schema for tests --- .../tests/assets/pyclient_testschema.yaml | 117 ++++++++++++++++++ 1 file changed, 117 insertions(+) create mode 100644 dump_things_pyclient/tests/assets/pyclient_testschema.yaml diff --git a/dump_things_pyclient/tests/assets/pyclient_testschema.yaml b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml new file mode 100644 index 0000000..deb0bda --- /dev/null +++ b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml @@ -0,0 +1,117 @@ +name: demo-research-information-schema +description: | + A minimal schema that is compatible with concepts.datalad.org's type + definitions and annotations. +id: https://concepts.datalad.org/s/test-schemas/dump-things-pyclient/unreleased +version: UNRELEASED +license: MIT +prefixes: + rdf: + prefix_prefix: rdf + prefix_reference: http://www.w3.org/1999/02/22-rdf-syntax-ns# + rdfs: + prefix_prefix: rdfs + prefix_reference: http://www.w3.org/2000/01/rdf-schema# + xsd: + prefix_prefix: xsd + prefix_reference: http://www.w3.org/2001/XMLSchema# + test: + prefix_prefix: test + prefix_reference: http://www.example.org/test +emit_prefixes: + - xsd + - test +default_prefix: test +types: + string: + name: string + description: A character string + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + uriorcurie: + name: uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: https://w3id.org/linkml/types + base: URIorCURIE + uri: xsd:anyURI + repr: str + NodeUriOrCurie: + name: NodeUriOrCurie + typeof: uriorcurie + base: str + uri: rdfs:Resource +slots: + family_name: + name: family_name + title: Family name + range: string + given_name: + name: given_name + title: Given name + range: string + annotations: + name: annotations + description: A record of properties of the metadata record on a subject, a collection + of tag/text tuples with the semantics of OWL Annotation. + title: Annotations + range: Annotation + multivalued: true + inlined: true + annotation_tag: + name: annotation_tag + description: A tag identifying an annotation. + title: Tag + range: Thing + annotation_value: + name: annotation_value + description: The actual annotation. + title: Value + range: string + pid: + name: pid + description: Persistent and globally unique identifier of a `Thing`. + title: Persistent identifier + identifier: true + range: uriorcurie + schema_type: + name: schema_type + slot_uri: rdf:type + designates_type: true + range: NodeUriOrCurie +classes: + Person: + name: Person + description: Person agents are people, alive, dead, or fictional. + is_a: Thing + slots: + - family_name + - given_name + ThingMixin: + name: ThingMixin + mixin: true + slots: + - annotations + - schema_type + Thing: + name: Thing + mixins: + - ThingMixin + slots: + - pid + class_uri: dlthings:Thing + Annotation: + name: Annotation + slots: + - annotation_tag + - annotation_value + slot_usage: + annotation_tag: + name: annotation_tag + key: true + range: AnnotationTag + AnnotationTag: + is_a: Thing -- 2.52.0 From f78112c344b4e5a33b07e18937bb2dca45daf793 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 12:37:03 +0100 Subject: [PATCH 19/39] add dump-things-server test fixtures This commit adds fixtures that generate a test dump-things-server that contains one collection, i.e., `collection_1`. The collection uses a `record-dir`-backend and the schema `pyclient_testschema.yaml`. --- dump_things_pyclient/conftest.py | 9 ++ dump_things_pyclient/tests/fixtures.py | 112 +++++++++++++++++++++++++ pyproject.toml | 1 + 3 files changed, 122 insertions(+) create mode 100644 dump_things_pyclient/conftest.py create mode 100644 dump_things_pyclient/tests/fixtures.py diff --git a/dump_things_pyclient/conftest.py b/dump_things_pyclient/conftest.py new file mode 100644 index 0000000..1b850ec --- /dev/null +++ b/dump_things_pyclient/conftest.py @@ -0,0 +1,9 @@ +from dump_things_pyclient.tests.fixtures import ( + dump_stores_simple, + dump_things_service, +) + +__all__ = [ + 'dump_stores_simple', + 'dump_things_service', +] diff --git a/dump_things_pyclient/tests/fixtures.py b/dump_things_pyclient/tests/fixtures.py new file mode 100644 index 0000000..2bfc134 --- /dev/null +++ b/dump_things_pyclient/tests/fixtures.py @@ -0,0 +1,112 @@ +import os +import signal +import socket +import subprocess +import time +from pathlib import Path + +import pytest +import requests +from dump_things_service import config_file_name + + +# String representation of curated- and incoming-path +curated = 'curated' +incoming = 'incoming' + +# Path to a local simple test schema +schema_path = Path(__file__).parent / 'assets' / 'pyclient_testschema.yaml' +schema_path = schema_path.resolve() + +# The global configuration file, all collections and +# staging areas share the same directories. All tokens +# of the same collection share an "incoming_label". +global_config_text = f""" +type: collections +version: 1 +collections: + collection_1: + default_token: basic_access + curated: {curated} + incoming: {incoming} + backend: + type: record_dir + auth_sources: + - type: config + submission_tags: + submitter_id_tag: oxo:NCIT_C54269 + submission_time_tag: https://time.example.com + +tokens: + basic_access: + user_id: tester + collections: + collection_1: + mode: WRITE_COLLECTION + incoming_label: tester + token-curator: + user_id: test_curator + collections: + collection_1: + mode: CURATOR + incoming_label: test_curator +""" + + +collection_1_config = f"""type: records +version: 1 +schema: {schema_path} +format: yaml +idfx: digest-md5 +""" + + +@pytest.fixture(scope='session') +def dump_stores_simple(tmp_path_factory): + tmp_path = tmp_path_factory.mktemp('dump_store') + + # Write the global config file, create collection directories, and write + # the collection config file. + (tmp_path / config_file_name).write_text(global_config_text) + (tmp_path / curated).mkdir(parents=True, exist_ok=True) + (tmp_path / incoming).mkdir(parents=True, exist_ok=True) + (tmp_path / curated / config_file_name).write_text(collection_1_config) + return tmp_path + + +@pytest.fixture(scope='session') +def dump_things_service(dump_stores_simple): + + # Start a server on an unused port + port = _get_unused_port() + process_info = subprocess.Popen( + ['dump-things-service', '--port', str(port), str(dump_stores_simple)], + ) + + # Wait until the server is responding to requests + waited = 1 + while True: + time.sleep(1) + try: + result = requests.get(f'http://127.0.0.1:{port}/server') + if result.status_code == 200: + break + except requests.exceptions.ConnectionError: + waited += 1 + if waited >= 10: + raise Exception from None + continue + + # Give the port to the user + yield port + + os.kill(process_info.pid, signal.SIGTERM) + os.waitpid(process_info.pid, 0) + + +def _get_unused_port() -> int: + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + s.bind(('', 0)) + addr = s.getsockname() + s.close() + return addr[1] diff --git a/pyproject.toml b/pyproject.toml index 7520119..87bd138 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ ttl = [ "dump-things-service>=5.3.0", ] tests = [ + "dump-things-service>=5.3.0", "pytest>=9.0.1", ] -- 2.52.0 From bef9e5b3422eca060bcb36d8abe6a766a1a2c8ff Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 14:38:09 +0100 Subject: [PATCH 20/39] fix an error in the test schema --- dump_things_pyclient/tests/assets/pyclient_testschema.yaml | 1 - dump_things_pyclient/tests/fixtures.py | 3 +++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/dump_things_pyclient/tests/assets/pyclient_testschema.yaml b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml index deb0bda..de77392 100644 --- a/dump_things_pyclient/tests/assets/pyclient_testschema.yaml +++ b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml @@ -102,7 +102,6 @@ classes: - ThingMixin slots: - pid - class_uri: dlthings:Thing Annotation: name: Annotation slots: diff --git a/dump_things_pyclient/tests/fixtures.py b/dump_things_pyclient/tests/fixtures.py index 2bfc134..c9f81a8 100644 --- a/dump_things_pyclient/tests/fixtures.py +++ b/dump_things_pyclient/tests/fixtures.py @@ -91,6 +91,8 @@ def dump_things_service(dump_stores_simple): result = requests.get(f'http://127.0.0.1:{port}/server') if result.status_code == 200: break + msg = f'dump-things-server responded with {result.status_code}: {result.text}' + raise ValueError(msg) except requests.exceptions.ConnectionError: waited += 1 if waited >= 10: @@ -100,6 +102,7 @@ def dump_things_service(dump_stores_simple): # Give the port to the user yield port + # Shut the server down os.kill(process_info.pid, signal.SIGTERM) os.waitpid(process_info.pid, 0) -- 2.52.0 From deb44758e4c88a1c1f91f795c99714c565454f60 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 14:53:28 +0100 Subject: [PATCH 21/39] improve error handling and reporting in post-records --- .../commands/dtc_plugins/post_records.py | 31 ++++++++++++++++--- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/post_records.py b/dump_things_pyclient/commands/dtc_plugins/post_records.py index 0b283f8..1cc750b 100644 --- a/dump_things_pyclient/commands/dtc_plugins/post_records.py +++ b/dump_things_pyclient/commands/dtc_plugins/post_records.py @@ -159,13 +159,15 @@ def post_records( session=session, ) except HTTPError as e: - console.print( - f'[red]Error: writing record #{index} with pid {record["pid"]} failed[/red]: {e}: {e.response.text}', - ) + _handle_http_error(failed, index, line, e) + if ignore_errors: + continue + break except Exception as e: console.print( f'[red]Error: writing record #{index} with pid {record["pid"]} failed[/red]: {e}', ) + raise if failed: click.echo('\n'.join(failed)) @@ -179,7 +181,7 @@ def _handle_json_load_error( line: str, exc: Exception, ): - console.print(f'[red]Error[/red]: error loading line [red]#{index}[/rec]: {line}') + console.print(f'[red]Error[/red]: error loading line [red]#{index}[/red]: {line}') container.append( json.dumps( { @@ -192,6 +194,27 @@ def _handle_json_load_error( ) +def _handle_http_error( + container: list, + index: int, + line: str, + exc: HTTPError, +): + console.print(f'[red]Error[/red]: error writing line [red]#{index}[/red]: {line}') + container.append( + json.dumps( + { + 'status': 'http_error', + 'index': index, + 'json': line, + 'url': exc.request.url, + 'http_status': exc.response.status_code, + 'http_response': exc.response.text, + } + ) + ) + + def _handle_schema_type_error( container: list, index: int, -- 2.52.0 From 9f39aa0f7d7df98fce0ed28763cba232d74fa692 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 14:54:09 +0100 Subject: [PATCH 22/39] add basic tests This commit adds a basic test using `post-records` and `get-records`. --- dump_things_pyclient/tests/fixtures.py | 4 +- dump_things_pyclient/tests/test_basic.py | 67 ++++++++++++++++++++++++ 2 files changed, 69 insertions(+), 2 deletions(-) create mode 100644 dump_things_pyclient/tests/test_basic.py diff --git a/dump_things_pyclient/tests/fixtures.py b/dump_things_pyclient/tests/fixtures.py index c9f81a8..43b75cd 100644 --- a/dump_things_pyclient/tests/fixtures.py +++ b/dump_things_pyclient/tests/fixtures.py @@ -99,8 +99,8 @@ def dump_things_service(dump_stores_simple): raise Exception from None continue - # Give the port to the user - yield port + # Give the port and storage location to the user + yield port, dump_stores_simple # Shut the server down os.kill(process_info.pid, signal.SIGTERM) diff --git a/dump_things_pyclient/tests/test_basic.py b/dump_things_pyclient/tests/test_basic.py new file mode 100644 index 0000000..8636540 --- /dev/null +++ b/dump_things_pyclient/tests/test_basic.py @@ -0,0 +1,67 @@ +import json + +import yaml +from click.testing import CliRunner + +from dump_things_pyclient.commands.dtc import cli + + +def test_dtc_version(): + runner = CliRunner() + result = runner.invoke(cli, ['version']) + assert result.exit_code == 0 + + +def test_dtc_post_get(dump_things_service): + port, store = dump_things_service + + records = tuple( + {"pid": f"test:person_{i}", "given_name": f"gustav_{i}", "family_name": f"maler_{i}"} + for i in range(5) + ) + + runner = CliRunner() + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in records + ) + '\n' + ) + assert result.exit_code == 0 + print(result.output) + + # Check on disk, read all records from disk, check for annotations, + # delete their annotations, and ensure that all records from `records` + # are in there. + inbox = store / 'incoming' / 'tester' / 'Person' + disk_records = tuple( + yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) + for yaml_file in inbox.glob('**/*.yaml') + ) + for record in disk_records: + assert 'annotations' in record + + cleaned_disk_record = tuple( + {k: v for k, v in r.items() if k not in ('annotations', 'schema_type')} + for r in disk_records + ) + + assert all(r in cleaned_disk_record for r in records) + + # Check via get-records, this might return more than + result = runner.invoke( + cli, + ['--token=basic_access', 'get-records', f'http://127.0.0.1:{port}', 'collection_1'], + ) + assert result.exit_code == 0 + returned_records = tuple(json.loads(line) for line in result.output.splitlines()) + assert len(returned_records) == len(records) + + # This assertion relies on the fact that the result of get-records is + # ordered by PID. This is the case because, by default, the server does + # order the results by PID. + assert all( + r[0] == {k: v for k, v in r[1].items() if k not in ('annotations', 'schema_type')} + for r in zip(records, returned_records) + ) -- 2.52.0 From 18789d46f075e1be1db7ba53aecaf0250ca28e8d Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Fri, 6 Mar 2026 17:00:32 +0100 Subject: [PATCH 23/39] update comment --- dump_things_pyclient/tests/test_basic.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dump_things_pyclient/tests/test_basic.py b/dump_things_pyclient/tests/test_basic.py index 8636540..a2fa362 100644 --- a/dump_things_pyclient/tests/test_basic.py +++ b/dump_things_pyclient/tests/test_basic.py @@ -59,8 +59,8 @@ def test_dtc_post_get(dump_things_service): assert len(returned_records) == len(records) # This assertion relies on the fact that the result of get-records is - # ordered by PID. This is the case because, by default, the server does - # order the results by PID. + # ordered by PID. This is the case because the server does order the + # results by PID (by default). assert all( r[0] == {k: v for k, v in r[1].items() if k not in ('annotations', 'schema_type')} for r in zip(records, returned_records) -- 2.52.0 From b4124982672a10f32fbb2f400dc733c8a981897a Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Sat, 7 Mar 2026 02:52:33 +0100 Subject: [PATCH 24/39] add tests for post-records and get-records Add tests for post-records that check the write-interface. Some tests use get-records to fetch records for validation. Add the `Document`-class to test schema. --- .../tests/assets/pyclient_testschema.yaml | 7 + .../tests/test_auto_curate.py | 0 dump_things_pyclient/tests/test_basic.py | 55 ----- .../tests/test_post_records.py | 194 ++++++++++++++++++ 4 files changed, 201 insertions(+), 55 deletions(-) create mode 100644 dump_things_pyclient/tests/test_auto_curate.py create mode 100644 dump_things_pyclient/tests/test_post_records.py diff --git a/dump_things_pyclient/tests/assets/pyclient_testschema.yaml b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml index de77392..75c4dfc 100644 --- a/dump_things_pyclient/tests/assets/pyclient_testschema.yaml +++ b/dump_things_pyclient/tests/assets/pyclient_testschema.yaml @@ -82,6 +82,9 @@ slots: slot_uri: rdf:type designates_type: true range: NodeUriOrCurie + title: + name: title + range: string classes: Person: name: Person @@ -114,3 +117,7 @@ classes: range: AnnotationTag AnnotationTag: is_a: Thing + Document: + is_a: Thing + slots: + - title diff --git a/dump_things_pyclient/tests/test_auto_curate.py b/dump_things_pyclient/tests/test_auto_curate.py new file mode 100644 index 0000000..e69de29 diff --git a/dump_things_pyclient/tests/test_basic.py b/dump_things_pyclient/tests/test_basic.py index a2fa362..4bc7b00 100644 --- a/dump_things_pyclient/tests/test_basic.py +++ b/dump_things_pyclient/tests/test_basic.py @@ -10,58 +10,3 @@ def test_dtc_version(): runner = CliRunner() result = runner.invoke(cli, ['version']) assert result.exit_code == 0 - - -def test_dtc_post_get(dump_things_service): - port, store = dump_things_service - - records = tuple( - {"pid": f"test:person_{i}", "given_name": f"gustav_{i}", "family_name": f"maler_{i}"} - for i in range(5) - ) - - runner = CliRunner() - result = runner.invoke( - cli, - ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], - input='\n'.join( - json.dumps(record, ensure_ascii=False) for record in records - ) + '\n' - ) - assert result.exit_code == 0 - print(result.output) - - # Check on disk, read all records from disk, check for annotations, - # delete their annotations, and ensure that all records from `records` - # are in there. - inbox = store / 'incoming' / 'tester' / 'Person' - disk_records = tuple( - yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) - for yaml_file in inbox.glob('**/*.yaml') - ) - for record in disk_records: - assert 'annotations' in record - - cleaned_disk_record = tuple( - {k: v for k, v in r.items() if k not in ('annotations', 'schema_type')} - for r in disk_records - ) - - assert all(r in cleaned_disk_record for r in records) - - # Check via get-records, this might return more than - result = runner.invoke( - cli, - ['--token=basic_access', 'get-records', f'http://127.0.0.1:{port}', 'collection_1'], - ) - assert result.exit_code == 0 - returned_records = tuple(json.loads(line) for line in result.output.splitlines()) - assert len(returned_records) == len(records) - - # This assertion relies on the fact that the result of get-records is - # ordered by PID. This is the case because the server does order the - # results by PID (by default). - assert all( - r[0] == {k: v for k, v in r[1].items() if k not in ('annotations', 'schema_type')} - for r in zip(records, returned_records) - ) diff --git a/dump_things_pyclient/tests/test_post_records.py b/dump_things_pyclient/tests/test_post_records.py new file mode 100644 index 0000000..eaceda3 --- /dev/null +++ b/dump_things_pyclient/tests/test_post_records.py @@ -0,0 +1,194 @@ +import json + +import yaml +from click.testing import CliRunner + +from dump_things_pyclient.commands.dtc import cli + + +def test_dtc_post_get(dump_things_service): + port, store = dump_things_service + + records = tuple( + {"pid": f"test:person_{i}", "given_name": f"gustav_{i}", "family_name": f"maler_{i}"} + for i in range(5) + ) + + runner = CliRunner() + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in records + ) + '\n' + ) + assert result.exit_code == 0 + + # Check on disk, read all records from disk, check for annotations, + # delete their annotations, and ensure that all records from `records` + # are in there. + inbox = store / 'incoming' / 'tester' / 'Person' + disk_records = tuple( + yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) + for yaml_file in inbox.glob('**/*.yaml') + ) + for record in disk_records: + if record['given_name'].startswith('gustav'): + assert 'annotations' in record + + cleaned_disk_record = tuple( + {k: v for k, v in r.items() if k not in ('annotations', 'schema_type')} + for r in disk_records + ) + + assert all(r in cleaned_disk_record for r in records) + + # Check via get-records, this might return more than the records we just posted + result = runner.invoke( + cli, + [ + '--token=basic_access', + 'get-records', f'http://127.0.0.1:{port}', 'collection_1' + ], + ) + assert result.exit_code == 0 + returned_records = tuple(json.loads(line) for line in result.output.splitlines()) + assert len(returned_records) >= len(records) + + # This assertion relies on the fact that the result of get-records is + # ordered by PID. This is the case because the server does order the + # results by PID (by default). + assert all( + r[0] == {k: v for k, v in r[1].items() if k not in ('annotations', 'schema_type')} + for r in zip(records, returned_records) + ) + + +def test_dtc_post_curated(dump_things_service): + port, store = dump_things_service + + # We add `schema_type` to the test record because the server API code, i.e., + # the fastapi pydantic interface classes that are generated via linkml + # add it automatically. The curated interface does never use a schema_type + # layer, so `schema_type` will end up in the persisted record. Adding it + # to our input record keeps the input and output records consistent, and + # we don't have to care about the schema_type attribute when comparing + # uploaded and downloaded records. + records = tuple( + { + "pid": f"test:person_curated_{i}", + "given_name": f"hans_{i}", + "family_name": f"post_curated_{i}", + 'schema_type': 'test:Person', + } + for i in range(5) + ) + + runner = CliRunner() + result = runner.invoke( + cli, + [ + '--token=token-curator', + 'post-records', '--curated', f'http://127.0.0.1:{port}', 'collection_1', 'Person' + ], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in records + ) + '\n' + ) + assert result.exit_code == 0 + + # Check on disk, read all records from disk, check for annotations, + # delete their annotations, and ensure that all records from `records` + # are in there. + curated = store / 'curated' / 'Person' + disk_records = tuple( + yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) + for yaml_file in curated.glob('**/*.yaml') + ) + # Check that curated access does not add annotations + for record in disk_records: + if record['given_name'].startswith('hans_'): + assert 'annotations' not in record + + # Check that all uploaded records appear verbatim on disk, i.e., that they + # were really uploaded through the `curated`-interface. + assert all(r in disk_records for r in records) + + # Check via get-records, this might return more than the records we just posted + result = runner.invoke( + cli, + [ + '--token=basic_access', + 'get-records', + '--class', 'Person', + f'http://127.0.0.1:{port}', 'collection_1' + ], + ) + assert result.exit_code == 0 + returned_records = tuple(json.loads(line) for line in result.output.splitlines()) + assert len(returned_records) >= len(records) + assert all(r in returned_records for r in records) + + +def test_dtc_post_record_any_class(dump_things_service): + port, store = dump_things_service + + person_records = tuple( + { + "pid": f"test:person_wildcard_{i}", + "given_name": f"johann_{i}", + "family_name": f"post_wildcard_class_{i}", + 'schema_type': 'test:Person', + } + for i in range(3) + ) + document_records = tuple( + { + "pid": f"test:document_wildcard_{i}", + "title": f"document_{i}", + 'schema_type': 'test:Document', + } + for i in range(3) + ) + + runner = CliRunner() + result = runner.invoke( + cli, + [ + '--token=basic_access', + 'post-records', + f'http://127.0.0.1:{port}', 'collection_1', '*', + ], + input='\n'.join( + json.dumps(record, ensure_ascii=False) + for record in person_records + document_records + ) + '\n' + ) + assert result.exit_code == 0 + + # Check that the records were associated with the correct class on disk. + # (This checks the interpretation of the schema_type attribute in the + # input records and the interface implementation). + inbox = store / 'incoming' / 'tester' / 'Person' + disk_records = tuple( + yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) + for yaml_file in inbox.glob('**/*.yaml') + ) + cleaned_disk_record = tuple( + {k: v for k, v in r.items() if k not in ('annotations',)} + for r in disk_records + ) + + assert all(r in cleaned_disk_record for r in person_records) + + inbox = store / 'incoming' / 'tester' / 'Document' + disk_records = tuple( + yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) + for yaml_file in inbox.glob('**/*.yaml') + ) + cleaned_disk_record = tuple( + {k: v for k, v in r.items() if k not in ('annotations',)} + for r in disk_records + ) + + assert all(r in cleaned_disk_record for r in document_records) -- 2.52.0 From 2ffeb186ec2f1078856ab11b436ea14ea602d564 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 9 Mar 2026 09:38:28 +0100 Subject: [PATCH 25/39] remove code duplication in test code This commit factors out a function that reads records from a dumpthings-recorddir backend. --- dump_things_pyclient/tests/common.py | 63 +++++++++++++++++++ .../tests/test_auto_curate.py | 3 + .../tests/test_post_records.py | 33 +++++----- 3 files changed, 82 insertions(+), 17 deletions(-) create mode 100644 dump_things_pyclient/tests/common.py diff --git a/dump_things_pyclient/tests/common.py b/dump_things_pyclient/tests/common.py new file mode 100644 index 0000000..3407f42 --- /dev/null +++ b/dump_things_pyclient/tests/common.py @@ -0,0 +1,63 @@ +from pathlib import Path +from typing import Generator + +import yaml + + +def read_records_from_store( + store: Path, + collection: str = 'collection_1', + incoming: str | None = None, + class_name: str = '*', + remove_keys: list | None = None, +) -> Generator[tuple[Path, str | None, dict], None, None]: + """Read record from a dumpthings-"recorddir" backend + + By default records are read from the curated area. If records should + be read from the incoming area, set `incoming` to a glob expression that + matches the user IDs for which records should be read. Use '*' for all + user IDs (the value of `incoming` is used a glob-expression). + + By default all classes are returned because the glob expression '*' is + used for the classes. If `class_name` is set, the value will be used as + glob expression for classes. For example, `*Document` would match + `XYZDocument` and `Document`. + + If `remove_keys` is not `None`, all keys that are specified in `remove_keys` + will be removed from the records before they are returned. For example, + remove annotations by specifying `['annotations']`. + + Returns tuples of (record_path, user_id or None, cleaned record content) + """ + + config = yaml.safe_load((store / '.dumpthings.yaml').read_text()) + curated_dir = config['collections'][collection]['curated'] + incoming_dir = config['collections'][collection]['incoming'] + + glob_expression = f'{class_name}/**/*.yaml' + if incoming: + base_dir = store / incoming_dir + glob_expression = f'{incoming}/' + glob_expression + else: + base_dir = store / curated_dir + + for record_path in base_dir.glob(glob_expression): + if record_path.name == '.dumpthings.yaml': + continue + if incoming: + base_parts = base_dir.parts + user_id = record_path.parts[len(base_parts)] + else: + user_id = None + record = yaml.safe_load(record_path.read_text()) + if remove_keys: + yield ( + record_path, + user_id, + { + k: v for k, v in record.items() + if k not in remove_keys + }, + ) + else: + yield (record_path, user_id, record) diff --git a/dump_things_pyclient/tests/test_auto_curate.py b/dump_things_pyclient/tests/test_auto_curate.py index e69de29..b4b26b2 100644 --- a/dump_things_pyclient/tests/test_auto_curate.py +++ b/dump_things_pyclient/tests/test_auto_curate.py @@ -0,0 +1,3 @@ + + +from dump_things_pyclient.commands.dtc_plugins.auto_curate import cli diff --git a/dump_things_pyclient/tests/test_post_records.py b/dump_things_pyclient/tests/test_post_records.py index eaceda3..9b2f200 100644 --- a/dump_things_pyclient/tests/test_post_records.py +++ b/dump_things_pyclient/tests/test_post_records.py @@ -4,9 +4,10 @@ import yaml from click.testing import CliRunner from dump_things_pyclient.commands.dtc import cli +from dump_things_pyclient.tests.common import read_records_from_store -def test_dtc_post_get(dump_things_service): +def test_dtc_post_get_end_to_end(dump_things_service): port, store = dump_things_service records = tuple( @@ -24,24 +25,22 @@ def test_dtc_post_get(dump_things_service): ) assert result.exit_code == 0 - # Check on disk, read all records from disk, check for annotations, - # delete their annotations, and ensure that all records from `records` - # are in there. - inbox = store / 'incoming' / 'tester' / 'Person' - disk_records = tuple( - yaml.load(yaml_file.read_text(), Loader=yaml.SafeLoader) - for yaml_file in inbox.glob('**/*.yaml') - ) - for record in disk_records: - if record['given_name'].startswith('gustav'): - assert 'annotations' in record + # Read all records from disk, check for annotations. + for disk_record in map( + lambda t: t[2], + read_records_from_store(store, incoming='tester', class_name='Person') + ): + if disk_record['given_name'].startswith('gustav'): + assert 'annotations' in disk_record - cleaned_disk_record = tuple( - {k: v for k, v in r.items() if k not in ('annotations', 'schema_type')} - for r in disk_records + # Ensure that all records from `records` are on disk + cleaned_disk_records = tuple( + map( + lambda t: t[2], + read_records_from_store(store, incoming='tester', class_name='Person', remove_keys=['annotations', 'schema_type']) + ) ) - - assert all(r in cleaned_disk_record for r in records) + assert all(r in cleaned_disk_records for r in records) # Check via get-records, this might return more than the records we just posted result = runner.invoke( -- 2.52.0 From e553382e7417f9974c0fd924193df1c7c58ea822 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 9 Mar 2026 10:43:53 +0100 Subject: [PATCH 26/39] update metavars for auto-curate options -e and -i --- dump_things_pyclient/commands/dtc_plugins/auto_curate.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index f5e5f87..f6ab1c4 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -102,11 +102,13 @@ stl_info = False ) @click.option( '--exclude', '-e', + metavar='INBOX_LABEL', help='exclude an inbox on the source collection (repeatable)', multiple=True, ) @click.option( '--include', '-i', + metavar='INBOX_LABEL', help='process only the given inbox, all other inboxes are ignored (repeatable, -e/--exclude is applied after inclusion)', multiple=True, ) -- 2.52.0 From a1f0db54c052b609c059bf98870e30ef65ab70f0 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 9 Mar 2026 14:34:56 +0100 Subject: [PATCH 27/39] fix intra repo path and repo initialization This commit fixes two errors in auto-curate that are related to change set-creation. The first error was that a git repository might not be initialized. The second error was the faulty calculation of the intra-repository path of records. --- .../commands/dtc_plugins/auto_curate.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py index f6ab1c4..2611c31 100644 --- a/dump_things_pyclient/commands/dtc_plugins/auto_curate.py +++ b/dump_things_pyclient/commands/dtc_plugins/auto_curate.py @@ -227,10 +227,14 @@ def auto_curate( return 1 else: if dry_run: - console.print(f'[DRY_RUN]:INITIALIZING GIT REPO: {create_change_set}') + console.print(f'[DRY_RUN]:CREATE DIRECORY: {create_change_set}') else: create_change_set.mkdir() - subprocess.run(['git', 'init', str(create_change_set)], check=1) + + if dry_run: + console.print(f'[DRY_RUN]:INITIALIZING GIT REPO: {create_change_set}') + else: + subprocess.run(['git', 'init', str(create_change_set)], check=1) if post_change_set: if list_labels or list_records: @@ -539,7 +543,7 @@ def _update_change_set( else: file_path.write_text('null\n') - intra_repo_file_path = Path(*file_path.parts[1:]) + intra_repo_file_path = file_path.relative_to(change_set) if dry_run: console.print(f'[DRY_RUN]:GIT ADD {intra_repo_file_path} (cdw={change_set})') else: -- 2.52.0 From 74386e48d6177b6da4fb7cb6d1f09f49954ed345 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 9 Mar 2026 14:37:17 +0100 Subject: [PATCH 28/39] use non-prefix IRI for annotations --- dump_things_pyclient/tests/fixtures.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dump_things_pyclient/tests/fixtures.py b/dump_things_pyclient/tests/fixtures.py index 43b75cd..9da0c8f 100644 --- a/dump_things_pyclient/tests/fixtures.py +++ b/dump_things_pyclient/tests/fixtures.py @@ -34,7 +34,7 @@ collections: auth_sources: - type: config submission_tags: - submitter_id_tag: oxo:NCIT_C54269 + submitter_id_tag: https://submitter.example.com submission_time_tag: https://time.example.com tokens: -- 2.52.0 From 453b5d7e3e71016177377c1a37ba3be540094960 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Mon, 9 Mar 2026 14:37:48 +0100 Subject: [PATCH 29/39] add tests for --create-change-set This commit adds tests for the create change set-option of auto-curate. --- .../tests/test_auto_curate.py | 196 +++++++++++++++++- 1 file changed, 195 insertions(+), 1 deletion(-) diff --git a/dump_things_pyclient/tests/test_auto_curate.py b/dump_things_pyclient/tests/test_auto_curate.py index b4b26b2..35d99b5 100644 --- a/dump_things_pyclient/tests/test_auto_curate.py +++ b/dump_things_pyclient/tests/test_auto_curate.py @@ -1,3 +1,197 @@ +import json +import posix +import random +import subprocess +from itertools import chain + +from click.testing import CliRunner + +from dump_things_pyclient.commands.dtc import cli +from dump_things_pyclient.tests.common import read_records_from_store +from pygments.lexers import r -from dump_things_pyclient.commands.dtc_plugins.auto_curate import cli +prefix = 'https://www.example.com/ac_e2e_test/' + + +def _create_unique_records(offset: int, count: int) -> dict[int, dict]: + while True: + pids = tuple(set(random.randrange(offset, offset + 10000) for _ in range(count))) + if len(pids) == count: + break + return { + # NOTE: the order of keys is relevant because there are JSON-string + # comparisons in the change-set tests below. + pid: { + 'schema_type': 'test:Person', + 'pid': prefix + f'person_{pid}', + 'family_name': f'grieg_{pid}', + 'given_name': f'erwin_{pid}', + } + for pid in pids + } + + +def test_auto_curate_basic_end_to_end(dump_things_service): + port, store = dump_things_service + + + new_records = tuple(_create_unique_records(10000, 5).values()) + + # Add records to inbox + runner = CliRunner() + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in new_records + ) + '\n' + ) + assert result.exit_code == 0, 'dtc post-records failed' + + # Ensure that the records do not yet exist in the curated area + stored_curated_records = tuple( + map( + lambda e: e[2], + read_records_from_store(store, class_name='Person', remove_keys=['annotations']) + ) + ) + for record in new_records: + assert record not in stored_curated_records, 'record already exists, possibly a random number collision' + + # Perform auto-curation + result = runner.invoke( + cli, + ['--token=token-curator', 'auto-curate', '-i', 'tester', f'http://127.0.0.1:{port}', 'collection_1'], + ) + assert result.exit_code == 0, 'dtc auto-curate failed' + + # Check that the inbox is empty + stored_inbox_records = tuple( + map( + lambda e: e[2], + read_records_from_store(store, incoming='tester') + ) + ) + assert stored_inbox_records == tuple(), 'Inbox not clean after auto-curation' + + # Check that the records are in the curated area + stored_curated_records = tuple( + map( + lambda e: e[2], + read_records_from_store(store, class_name='Person', remove_keys=['annotations']) + ) + ) + for record in new_records: + assert record in stored_curated_records + + +def test_auto_curate_change_set_end_to_end(dump_things_service, tmp_path_factory): + port, store = dump_things_service + change_set_dir = tmp_path_factory.mktemp('change_set') + + new_records = _create_unique_records(20000, 5) + new_curated_records = _create_unique_records(30000, 5) + + runner = CliRunner() + + # Add new curated records to inbox and auto-curate them to move them to + # the curated area. + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in new_curated_records.values() + ) + '\n' + ) + assert result.exit_code == 0, 'dtc post-records failed' + + # Perform auto-curation + result = runner.invoke( + cli, + ['--token=token-curator', 'auto-curate', '-i', 'tester', f'http://127.0.0.1:{port}', 'collection_1'], + ) + assert result.exit_code == 0, 'dtc auto-curate failed' + + # Modify the record that were auto-curated and upload those together with + # newly created records to the inbox. + modified_curated_records = { + # NOTE: the order of keys is relevant because there are JSON-string + # comparisons in the change-set tests below. + pid: { + 'schema_type': 'test:Person', + 'pid': record['pid'], + 'family_name': record['family_name'], + 'given_name': record['given_name'].replace('erwin', 'edvard'), + } + for pid, record in new_curated_records.items() + } + + # Upload the modified (already curated) records and the new records to the + # inbox. + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) + for record in chain(modified_curated_records.values(), new_records.values()) + ) + '\n' + ) + assert result.exit_code == 0, 'dtc post-records failed' + + # Create a change set + result = runner.invoke( + cli, + [ + '--token=token-curator', + 'auto-curate', + '--create-change-set', str(change_set_dir), + '-i', 'tester', + f'http://127.0.0.1:{port}', 'collection_1', + ], + ) + assert result.exit_code == 0, 'dtc auto-curate --create-change-set failed' + + # Check the number of modified records in the change set + result = subprocess.run( + ['git', 'status', '-s',], + cwd=str(change_set_dir), + check=True, + capture_output=True, + ) + lines = [ + line.strip() + for line in result.stdout.decode().splitlines() + if 'annotations' not in line + ] + assert len(lines) == len(new_records) + len(modified_curated_records), f'unexpected number of modified records: {len(lines)}' + assert all(l.startswith('M records/tester') for l in lines), f'unexpected status for modified records: {lines}' + + # Check for expected diff content + result = subprocess.run( + ['git', 'diff', '-p',], + cwd=str(change_set_dir), + check=True, + capture_output=True, + ) + lines = [line.strip() for line in result.stdout.decode().splitlines()] + # Every diff should be seven lines long, the line at index 5 contains the + # previous content, the line at index 6 contains the new content. + for patch in range(int(len(lines) / 7)): + old = json.loads(lines[(7 * patch) + 5][1:]) + new = json.loads(lines[(7 * patch) + 6][1:]) + pid = int(lines[7 * patch][-5:]) + if pid in new_records: + assert old == None + assert new == new_records[pid] + else: + assert old == new_curated_records[pid] + assert new == modified_curated_records[pid] + + # Check that annotations are stored in the change set + annotations = { + int(p.name[-5:]): json.loads(p.read_text()) + for p in (change_set_dir / 'annotations').glob('tester/*') + } + assert len(annotations) == len(modified_curated_records) + len(new_curated_records) + print(annotations) -- 2.52.0 From 09bb5a39e6f4b53ea1924b3c9c9de94b9e5ae6d3 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 00:09:07 +0100 Subject: [PATCH 30/39] add tests for --post-change-set --- .../tests/test_auto_curate.py | 115 +++++++++++++++++- 1 file changed, 110 insertions(+), 5 deletions(-) diff --git a/dump_things_pyclient/tests/test_auto_curate.py b/dump_things_pyclient/tests/test_auto_curate.py index 35d99b5..0745fdd 100644 --- a/dump_things_pyclient/tests/test_auto_curate.py +++ b/dump_things_pyclient/tests/test_auto_curate.py @@ -86,17 +86,16 @@ def test_auto_curate_basic_end_to_end(dump_things_service): assert record in stored_curated_records -def test_auto_curate_change_set_end_to_end(dump_things_service, tmp_path_factory): +def test_auto_curate_create_change_set_end_to_end(dump_things_service, tmp_path_factory): port, store = dump_things_service - change_set_dir = tmp_path_factory.mktemp('change_set') + change_set_dir = tmp_path_factory.mktemp('create_change_set') new_records = _create_unique_records(20000, 5) new_curated_records = _create_unique_records(30000, 5) - runner = CliRunner() - # Add new curated records to inbox and auto-curate them to move them to # the curated area. + runner = CliRunner() result = runner.invoke( cli, ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], @@ -194,4 +193,110 @@ def test_auto_curate_change_set_end_to_end(dump_things_service, tmp_path_factory for p in (change_set_dir / 'annotations').glob('tester/*') } assert len(annotations) == len(modified_curated_records) + len(new_curated_records) - print(annotations) + + +def test_auto_curate_post_change_set_end_to_end(dump_things_service, tmp_path_factory): + port, store = dump_things_service + change_set_dir = tmp_path_factory.mktemp('post_change_set') + + new_records = _create_unique_records(40000, 5) + + # Add new records to inbox of 'tester'. + runner = CliRunner() + result = runner.invoke( + cli, + ['--token=basic_access', 'post-records', f'http://127.0.0.1:{port}', 'collection_1', 'Person'], + input='\n'.join( + json.dumps(record, ensure_ascii=False) for record in new_records.values() + ) + '\n' + ) + assert result.exit_code == 0, 'dtc post-records failed' + + # Create a change set with the records from 'tester's' inbox + result = runner.invoke( + cli, + [ + '--token=token-curator', + 'auto-curate', + '--create-change-set', str(change_set_dir), + '-i', 'tester', + f'http://127.0.0.1:{port}', 'collection_1', + ], + ) + assert result.exit_code == 0, 'dtc auto-curate --create-change-set failed' + + # Post the changeset without annotations + result = runner.invoke( + cli, + [ + '--token=token-curator', + 'auto-curate', + '--post-change-set', str(change_set_dir), + f'http://127.0.0.1:{port}', 'collection_1', + ], + ) + assert result.exit_code == 0, 'dtc auto-curate --post-change-set failed' + + # Check that new records have been posted without annotations + curated_records = tuple( + map( + lambda e: e[2], + read_records_from_store( + store, + class_name='Person', + ) + ) + ) + + for record in new_records.values(): + assert record in curated_records + for record in curated_records: + assert 'annotations' not in record, f'unexpected annotations in {record}' + + # Post the changeset with annotations + result = runner.invoke( + cli, + [ + '--token=token-curator', + 'auto-curate', + '--post-change-set', str(change_set_dir), + '--add-annotations', + f'http://127.0.0.1:{port}', 'collection_1', + ], + ) + assert result.exit_code == 0, 'dtc auto-curate --post-change-set --add-annotations failed' + + # Check that new records have been posted with annotations + curated_records = tuple( + map( + lambda e: e[2], + read_records_from_store( + store, + class_name='Person', + ) + ) + ) + + # Check that all record content has been posted + cleaned_curated_records = tuple( + { + 'schema_type': r['schema_type'], + 'pid': r['pid'], + 'family_name': r['family_name'], + 'given_name': r['given_name'], + } + for r in curated_records + ) + + for record in new_records.values(): + assert record in cleaned_curated_records + + # Check that annotations were posted. + annotations = { + p.name.replace('-_', '/').replace('--', '-'): json.loads(p.read_text()) + for p in change_set_dir.glob('annotations/tester/*') + } + + for record in curated_records: + assert 'annotations' in record, f'missing annotations in {record}' + assert record['annotations'] == annotations[record['pid']] -- 2.52.0 From 6e08b906835b8d19e35f496a6e68cf354125874d Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 01:32:22 +0100 Subject: [PATCH 31/39] ensure that tests work with additional records This commit makes the tests robust against the presence of other test artifacts in the test store --- .forgejo/workflows/run_tests.yaml | 0 dump_things_pyclient/tests/test_post_records.py | 12 +++++++++--- 2 files changed, 9 insertions(+), 3 deletions(-) create mode 100644 .forgejo/workflows/run_tests.yaml diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml new file mode 100644 index 0000000..e69de29 diff --git a/dump_things_pyclient/tests/test_post_records.py b/dump_things_pyclient/tests/test_post_records.py index 9b2f200..de3c7dd 100644 --- a/dump_things_pyclient/tests/test_post_records.py +++ b/dump_things_pyclient/tests/test_post_records.py @@ -52,16 +52,22 @@ def test_dtc_post_get_end_to_end(dump_things_service): ) assert result.exit_code == 0 returned_records = tuple(json.loads(line) for line in result.output.splitlines()) + + # Due to other tests, there might be more records in the server than the + # ones that we just uploaded assert len(returned_records) >= len(records) # This assertion relies on the fact that the result of get-records is # ordered by PID. This is the case because the server does order the # results by PID (by default). - assert all( - r[0] == {k: v for k, v in r[1].items() if k not in ('annotations', 'schema_type')} - for r in zip(records, returned_records) + cleaned_records = tuple( + {k: v for k, v in r.items() if k not in ('annotations', 'schema_type')} + for r in returned_records ) + for r in records: + assert r in cleaned_records, f'record {r} not found in cleaned records' + def test_dtc_post_curated(dump_things_service): port, store = dump_things_service -- 2.52.0 From 321f41ce38aa97773603cc6a0059f7113d0b9927 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 01:33:47 +0100 Subject: [PATCH 32/39] update locked package versions Ensure that linkml 1.10.0 is used. --- uv.lock | 1489 ++++++++++++++++++++++++++++++------------------------- 1 file changed, 822 insertions(+), 667 deletions(-) diff --git a/uv.lock b/uv.lock index f8bfaef..9d19074 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,12 @@ 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ubuntu-latest + steps: + - name: Check out repository code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + + - name: Install uv + uses: astral-sh/setup-uv@v6 + + - name: Install hatch + run: uv tool install hatch + + - name: Run tests + run: | + hatch run tests:run \ + --ignore=dump_things_service/tests/test_generators.py \ + --ignore=dump_things_service/tests/test_ifabsent_patch.py + + - name: Run generator tests + run: | + hatch run tests:run dump_things_service/tests/test_generators.py + + - name: Run ifabsent-patch tests + run: | + hatch run tests:run dump_things_service/tests/test_ifabsent_patch.py diff --git a/dump_things_pyclient/tests/test_auto_curate.py b/dump_things_pyclient/tests/test_auto_curate.py index 0745fdd..77b9144 100644 --- a/dump_things_pyclient/tests/test_auto_curate.py +++ b/dump_things_pyclient/tests/test_auto_curate.py @@ -251,7 +251,12 @@ def test_auto_curate_post_change_set_end_to_end(dump_things_service, tmp_path_fa for record in new_records.values(): assert record in curated_records for record in curated_records: - assert 'annotations' not in record, f'unexpected annotations in {record}' + try: + record_pid = int(record['pid'][-5:]) + if record_pid in new_records: + assert 'annotations' not in record, f'unexpected annotations in {record}' + except ValueError: + continue # Post the changeset with annotations result = runner.invoke( @@ -298,5 +303,10 @@ def test_auto_curate_post_change_set_end_to_end(dump_things_service, tmp_path_fa } for record in curated_records: - assert 'annotations' in record, f'missing annotations in {record}' - assert record['annotations'] == annotations[record['pid']] + try: + record_pid = int(record['pid'][-5:]) + if record_pid in new_records: + assert 'annotations' in record, f'missing annotations in {record}' + assert record['annotations'] == annotations[record['pid']] + except ValueError: + continue diff --git a/pyproject.toml b/pyproject.toml index 87bd138..5bba445 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,10 +8,10 @@ authors = [ {name="Christian Mönch", email="christian.moench@web.de"}, ] dependencies = [ - "click>=8.3.1", - "pyyaml>=6.0.3", - "requests>=2.32.5", - "rich-click>=1.9.6", + "click", + "pyyaml", + "requests", + "rich-click", ] [project.optional-dependencies] @@ -23,6 +23,14 @@ tests = [ "pytest>=9.0.1", ] +[dependency-groups] +tests = [ + "linkml>=1.10.0", + "linkml-runtime>=1.10.0", + "dump-things-service>=5.3.0", + "pytest>=9.0.1", +] + [project.scripts] dtc = "dump_things_pyclient.commands.dtc:cli" json2ttl = "dump_things_pyclient.commands.json2ttl:main" -- 2.52.0 From 479957f5e056e4404c4cd953ea43fd15e6996d14 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 01:43:48 +0100 Subject: [PATCH 34/39] fix test workflow --- .forgejo/workflows/run_tests.yaml | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index 1716e7e..19b5bc5 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -13,19 +13,6 @@ jobs: - name: Install uv uses: astral-sh/setup-uv@v6 - - name: Install hatch - run: uv tool install hatch - - name: Run tests run: | - hatch run tests:run \ - --ignore=dump_things_service/tests/test_generators.py \ - --ignore=dump_things_service/tests/test_ifabsent_patch.py - - - name: Run generator tests - run: | - hatch run tests:run dump_things_service/tests/test_generators.py - - - name: Run ifabsent-patch tests - run: | - hatch run tests:run dump_things_service/tests/test_ifabsent_patch.py + uv run --extra tests pytest -- 2.52.0 From 5aab35589ac725702a44b4a63d981abeebc14906 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 01:53:38 +0100 Subject: [PATCH 35/39] use python version 3.11.2 for tests --- .forgejo/workflows/run_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index 19b5bc5..f3b3f50 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -9,6 +9,8 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 + with: + python-version: 3.11.2 - name: Install uv uses: astral-sh/setup-uv@v6 -- 2.52.0 From bc344d1823d9ad33fa60e8004ad36608e67dec25 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 02:01:18 +0100 Subject: [PATCH 36/39] do not specify python version for tests explicitly This lets the runner select a version that is locally available. --- .forgejo/workflows/run_tests.yaml | 4 ++-- .python-version | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) delete mode 100644 .python-version diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index f3b3f50..e4081aa 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -9,8 +9,8 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 - with: - python-version: 3.11.2 + #with: + # python-version: 3.11.2 - name: Install uv uses: astral-sh/setup-uv@v6 diff --git a/.python-version b/.python-version deleted file mode 100644 index 24ee5b1..0000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.13 -- 2.52.0 From 58fbe822285eb05d93bd957bb23d35aa84ef7ecb Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 02:03:50 +0100 Subject: [PATCH 37/39] set up git identity before running tests --- .forgejo/workflows/run_tests.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index e4081aa..23f1128 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -7,10 +7,13 @@ jobs: - name: Check out repository code uses: actions/checkout@v4 + - name: Set up git + run : | + git config --global user.email "tester@example.com" + git config --global user.name "Automated Tester" + - name: Set up Python uses: actions/setup-python@v5 - #with: - # python-version: 3.11.2 - name: Install uv uses: astral-sh/setup-uv@v6 -- 2.52.0 From 792f8195c348b6ef9ce9902bc43a21bf261165b8 Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 02:09:23 +0100 Subject: [PATCH 38/39] install the package before running the tests --- .forgejo/workflows/run_tests.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index 23f1128..8581602 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -18,6 +18,10 @@ jobs: - name: Install uv uses: astral-sh/setup-uv@v6 + - name: Install this package + run : | + uv pip install . + - name: Run tests run: | uv run --extra tests pytest -- 2.52.0 From 181813ab4451678ab84723a964310151f531432d Mon Sep 17 00:00:00 2001 From: Christian Monch Date: Tue, 10 Mar 2026 02:11:47 +0100 Subject: [PATCH 39/39] create a virtual environment before running tests --- .forgejo/workflows/run_tests.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.forgejo/workflows/run_tests.yaml b/.forgejo/workflows/run_tests.yaml index 8581602..356a938 100644 --- a/.forgejo/workflows/run_tests.yaml +++ b/.forgejo/workflows/run_tests.yaml @@ -18,6 +18,10 @@ jobs: - name: Install uv uses: astral-sh/setup-uv@v6 + - name: Create virtual environment + run : | + uv venv + - name: Install this package run : | uv pip install . -- 2.52.0