From 4d18f3373b835fe204775bfa35e0f0b07a47cc16 Mon Sep 17 00:00:00 2001 From: Ryunosuke O'Neil Date: Fri, 23 Oct 2026 16:18:15 +0200 Subject: [PATCH 1/5] feat(core): canonical identity of CWL processes A process is identified by the SHA-256 of a canonical form defined over the parsed JSON document, not over any CWL library's output, so that it is deterministic, stable across library upgrades and reproducible by any tool. Ids, doc and label where they are metadata, $namespaces and dirac: hints are dropped; prefixes are expanded to full URIs; lists become maps; fully scoped identifiers are shortened against their scope; type shorthands are expanded and named types written by short name. Each child run body is replaced by its own identity, so a workflow's identity covers its children's (a Merkle tree). pack and unpack convert to and from a self-contained $graph whose components are named by their identity. Documents must be resolved before canonicalisation: $import, $include and any other schema-salad directive is refused, since the identity would not cover what it names and a runner would fetch it. Standard library only. Closes #1106 Part of #1080 --- diracx-core/src/diracx/core/cwl/__init__.py | 25 + diracx-core/src/diracx/core/cwl/canonical.py | 650 +++++++++++++++++++ diracx-core/tests/test_cwl_canonical.py | 442 +++++++++++++ 3 files changed, 1117 insertions(+) create mode 100644 diracx-core/src/diracx/core/cwl/__init__.py create mode 100644 diracx-core/src/diracx/core/cwl/canonical.py create mode 100644 diracx-core/tests/test_cwl_canonical.py diff --git a/diracx-core/src/diracx/core/cwl/__init__.py b/diracx-core/src/diracx/core/cwl/__init__.py new file mode 100644 index 000000000..adcf1b43d --- /dev/null +++ b/diracx-core/src/diracx/core/cwl/__init__.py @@ -0,0 +1,25 @@ +"""Common Workflow Language utilities shared by the client and the services.""" + +from __future__ import annotations + +__all__ = [ + "CANONICAL_VERSION", + "CanonicalProcess", + "canonical_bytes", + "decompose", + "format_reference", + "pack", + "parse_reference", + "unpack", +] + +from .canonical import ( + CANONICAL_VERSION, + CanonicalProcess, + canonical_bytes, + decompose, + format_reference, + pack, + parse_reference, + unpack, +) diff --git a/diracx-core/src/diracx/core/cwl/canonical.py b/diracx-core/src/diracx/core/cwl/canonical.py new file mode 100644 index 000000000..9941209d2 --- /dev/null +++ b/diracx-core/src/diracx/core/cwl/canonical.py @@ -0,0 +1,650 @@ +"""Canonical form and content identity of CWL processes (DX-ADR-004, DX-ADR-007). + +A process is identified by the SHA-256 of its canonical byte form. The form is +defined over the parsed document (a plain JSON value), not over the output of +any CWL library, so that it is deterministic, stable across library upgrades +and reproducible by any tool. Version 1 of the rules: + +1. Only CWL v1.2 is accepted. +2. On every process, ``id``, ``$namespaces`` and ``$schemas`` are dropped: the + identity of a process is its content, not its name or where it was loaded + from. Before that, every key, ``class`` and ``format`` written with a bound + prefix (``edam:format_2572``) is expanded to its full URI, using the + bindings of the process and of the processes enclosing it, so the identity + covers what a prefix means and not which prefix was chosen. The ``dirac`` + prefix is never expanded. +3. ``doc`` and ``label`` are dropped from processes, parameters, steps and + schemas, but kept as names a user chose (a record field, an environment + variable), inside ``default`` values and inside requirements and hints + other than ``SchemaDefRequirement``, where they are data. ``dirac:`` fields, + ``dirac:`` hints and anonymous schema names (``name: _:``) are dropped. + ``dirac:`` data is extracted into transformation columns at submission, so + it is not part of what a parcel runs. +4. ``inputs``, ``outputs``, ``steps`` and a step's ``in`` are written in map + form keyed by their short id; ``requirements`` and ``hints`` in map form + keyed by class. Shorthand values (``x: File``, ``in: {x: source}``) are + expanded to objects. A step's ``out`` is a sorted list of short ids. +5. A fully scoped identifier or reference (``file:///p/x.cwl#main/x``, + ``#main/x``) is shortened to the part after ``#``, without the enclosing + scope, so that absolute ``file://`` URIs never enter the identity. A + relative one is already relative to that scope, as a CWL runner reads it, + and is kept as written. +6. A child ``run`` body is replaced by a reference to its own identity, so the + identity of a workflow covers those of its children (a Merkle tree). Child + bodies are therefore canonicalised before their parents. +7. Type shorthands are expanded, as a CWL runner reads them: ``File[]`` is + ``{type: array, items: File}`` and ``File?`` is ``[null, File]``. A named + type (``SchemaDefRequirement``) and every reference to it are written by + its short name, as are enum symbols and record field names. A + process may only use named types it defines itself, so that its identity + covers their definitions; :func:`pack` scopes them by component + (``#main/Seed``), as a CWL runner requires. +8. The result is serialised as JSON with sorted keys and no whitespace, then + hashed. Numbers use Python's ``json`` rendering, which matches RFC 8785 + for the integers and short decimals CWL documents contain in practice. + +Documents must be resolved before canonicalisation: a schema-salad directive +left in one (``$import``, ``$include``, ``$mixin``, or any other ``$`` key +except a process's ``$namespaces`` and ``$schemas``) is refused, since the +identity would not cover what it refers to and a CWL runner would fetch it. +""" + +from __future__ import annotations + +import copy +import hashlib +import json +from dataclasses import dataclass +from typing import Any + +CANONICAL_VERSION = 1 + +REFERENCE_PREFIX = "proc:sha256-" +PACKED_PREFIX = "#sha256-" + +PROCESS_CLASSES = frozenset( + {"CommandLineTool", "Workflow", "ExpressionTool", "Operation"} +) +PRIMITIVE_TYPES = frozenset( + { + "null", + "boolean", + "int", + "long", + "float", + "double", + "string", + "File", + "Directory", + "Any", + "stdin", + "stdout", + "stderr", + } +) +PROCESS_ONLY_FIELDS = frozenset({"id", "$namespaces", "$schemas"}) +METADATA_FIELDS = frozenset({"doc", "label"}) +DIRAC_PREFIX = "dirac:" +# Fields whose value is a reference to a parameter or step output +REFERENCE_FIELDS = frozenset({"source", "outputSource"}) + + +@dataclass(frozen=True) +class CanonicalProcess: + """One process of a canonicalised tree. + + Attributes: + process_id: SHA-256 of ``body``. + body: Canonical bytes, child ``run`` bodies replaced by references. + children: Identities of the processes ``body`` references, sorted. + """ + + process_id: bytes + body: bytes + children: tuple[bytes, ...] + + +def canonical_bytes(value: Any) -> bytes: + """Serialise a JSON value in canonical form (rule 7). + + Args: + value: Plain JSON value. + + Returns: + UTF-8 JSON with sorted keys and no insignificant whitespace. + """ + return json.dumps( + value, + sort_keys=True, + separators=(",", ":"), + ensure_ascii=False, + allow_nan=False, + ).encode() + + +def format_reference(process_id: bytes) -> str: + """Return the ``run`` reference to a stored process. + + Args: + process_id: Identity of the process. + + Returns: + The reference, e.g. ``proc:sha256-``. + """ + return REFERENCE_PREFIX + process_id.hex() + + +def parse_reference(reference: str) -> bytes: + """Return the identity a ``run`` reference points to. + + Args: + reference: A reference made by :func:`format_reference`. + + Returns: + The 32-byte identity. + + Raises: + ValueError: If ``reference`` is not a process reference. + """ + if not reference.startswith(REFERENCE_PREFIX): + raise ValueError(f"Not a process reference: {reference!r}") + process_id = bytes.fromhex(reference.removeprefix(REFERENCE_PREFIX)) + if len(process_id) != 32: + raise ValueError(f"Not a SHA-256 process reference: {reference!r}") + return process_id + + +def decompose(process: dict[str, Any]) -> tuple[bytes, dict[bytes, CanonicalProcess]]: + """Canonicalise a process and every process nested in it. + + Args: + process: A CWL process as a plain JSON value, with every ``run`` either + an inline body or a process reference. + + Returns: + The identity of ``process`` and every distinct process of the tree, + keyed by identity. + + Raises: + ValueError: If the document is not a CWL v1.2 process, or a ``run`` + path or schema-salad directive has not been resolved. + """ + _check_resolved(process) + nodes: dict[bytes, CanonicalProcess] = {} + root = _decompose(process, nodes, process.get("cwlVersion"), {}) + return root, nodes + + +def pack(root: bytes, nodes: dict[bytes, CanonicalProcess]) -> dict[str, Any]: + """Assemble a tree into one self-contained packed document. + + The root is ``#main`` and every other process is ``#sha256-``, so the + document runs with a stock CWL runner and still names each component by + its identity. + + Args: + root: Identity of the root process. + nodes: Processes of the tree, at least every one reachable from root. + + Returns: + A CWL document with a ``$graph``. + """ + graph = [] + for process_id in _reachable(root, nodes): + body = json.loads(nodes[process_id].body) + body.pop("cwlVersion", None) + body["id"] = "#main" if process_id == root else PACKED_PREFIX + process_id.hex() + _scope_types(body, body["id"]) + for step in (body.get("steps") or {}).values(): + if isinstance(step.get("run"), str): + step["run"] = PACKED_PREFIX + parse_reference(step["run"]).hex() + graph.append(body) + return {"cwlVersion": "v1.2", "$graph": graph} + + +def unpack(packed: dict[str, Any]) -> tuple[bytes, dict[bytes, CanonicalProcess]]: + """Recover the canonical tree from a document made by :func:`pack`. + + Args: + packed: The packed document. + + Returns: + The identity of the root and the processes of the tree. + + Raises: + ValueError: If the document was not made by :func:`pack` or a + component does not match the identity it is filed under. + """ + by_id = {entry["id"]: entry for entry in packed["$graph"]} + nodes: dict[bytes, CanonicalProcess] = {} + # Each entry is verified once, however many steps share it + resolved: dict[str, bytes] = {} + in_progress: set[str] = set() + + def resolve(entry_id: str) -> bytes: + if entry_id in resolved: + return resolved[entry_id] + if entry_id in in_progress: + raise ValueError(f"{entry_id} runs itself") + in_progress.add(entry_id) + body = copy.deepcopy(by_id[entry_id]) + body.pop("id") + _unscope_types(body, entry_id) + body["cwlVersion"] = packed["cwlVersion"] + children = set() + steps = {} + for name, step in (body.get("steps") or {}).items(): + step = dict(step) + if isinstance(step.get("run"), str): + child = resolve(step["run"]) + children.add(child) + step["run"] = format_reference(child) + steps[name] = step + if steps: + body["steps"] = steps + data = canonical_bytes(body) + process_id = hashlib.sha256(data).digest() + if entry_id != "#main" and entry_id != PACKED_PREFIX + process_id.hex(): + raise ValueError(f"{entry_id} does not match its content") + nodes[process_id] = CanonicalProcess(process_id, data, tuple(sorted(children))) + in_progress.discard(entry_id) + resolved[entry_id] = process_id + return process_id + + return resolve("#main"), nodes + + +def _reachable(root: bytes, nodes: dict[bytes, CanonicalProcess]) -> list[bytes]: + order, seen, stack = [], set(), [root] + while stack: + process_id = stack.pop() + if process_id in seen: + continue + seen.add(process_id) + order.append(process_id) + stack.extend(reversed(nodes[process_id].children)) + return order + + +def _check_resolved(value: Any) -> None: + """Refuse schema-salad directives, which would make a runner fetch files.""" + if isinstance(value, dict): + is_process = value.get("class") in PROCESS_CLASSES + for key, item in value.items(): + if str(key).startswith("$") and not ( + is_process and key in PROCESS_ONLY_FIELDS + ): + raise ValueError( + f"Unresolved {key} directive: resolve the document before " + "submitting it" + ) + _check_resolved(item) + elif isinstance(value, list): + for item in value: + _check_resolved(item) + + +def _decompose( + process: dict[str, Any], + nodes: dict[bytes, CanonicalProcess], + cwl_version: Any, + namespaces: dict[str, str], +) -> bytes: + if process.get("class") not in PROCESS_CLASSES: + raise ValueError(f"Not a CWL process: class={process.get('class')!r}") + version = process.get("cwlVersion", cwl_version) + if version != "v1.2": + raise ValueError( + f"Only CWL v1.2 is supported, got {version!r}: upgrade the document " + "with cwl-upgrader" + ) + + namespaces = {**namespaces, **(process.get("$namespaces") or {})} + namespaces.pop(DIRAC_PREFIX.rstrip(":"), None) + process = _qualify(process, namespaces, top=True) + + own_name = _short(str(process.get("id", "")), None) or None + body: dict[str, Any] = {} + children: set[bytes] = set() + for key, value in process.items(): + if key in PROCESS_ONLY_FIELDS or _is_dropped(key): + continue + if key in ("inputs", "outputs"): + body[key] = _parameters(value, own_name) + elif key in ("requirements", "hints"): + classes = _by_class(value, drop_dirac=key == "hints") + if classes: + body[key] = classes + elif key == "steps": + body[key] = { + name: _step( + step, + own_name, + f"{own_name}/{name}" if own_name else name, + nodes, + version, + namespaces, + children, + ) + for name, step in _by_id(value, own_name).items() + } + else: + body[key] = _strip(value) + _name_types(body, own_name) + body["cwlVersion"] = version + + data = canonical_bytes(body) + process_id = hashlib.sha256(data).digest() + nodes[process_id] = CanonicalProcess(process_id, data, tuple(sorted(children))) + return process_id + + +def _step( + step: dict[str, Any], + own_name: str | None, + step_scope: str, + nodes: dict[bytes, CanonicalProcess], + version: Any, + namespaces: dict[str, str], + children: set[bytes], +) -> dict[str, Any]: + out: dict[str, Any] = {} + for key, value in step.items(): + if _is_dropped(key): + continue + if key == "run": + if isinstance(value, dict): + child = _decompose(value, nodes, version, namespaces) + elif isinstance(value, str) and value.startswith(REFERENCE_PREFIX): + child = parse_reference(value) + else: + raise ValueError(f"Unresolved run reference: {value!r}") + children.add(child) + out[key] = format_reference(child) + elif key == "in": + out[key] = { + name: _strip(_refs(spec, own_name)) + for name, spec in _by_id(value, step_scope, shorthand="source").items() + } + elif key == "out": + out[key] = sorted( + _short(item if isinstance(item, str) else item["id"], step_scope) + for item in value + ) + elif key in ("requirements", "hints"): + classes = _by_class(value, drop_dirac=key == "hints") + if classes: + out[key] = classes + else: + out[key] = _strip( + _refs(value, own_name) if key in REFERENCE_FIELDS else value + ) + return out + + +def _type_definitions(body: dict[str, Any]) -> list[dict[str, Any]]: + schema = (body.get("requirements") or {}).get("SchemaDefRequirement") or {} + return [d for d in schema.get("types") or [] if isinstance(d, dict)] + + +def _map_types(body: dict[str, Any], rename) -> None: + """Apply ``rename`` to every type name a process's types refer to.""" + schema = (body.get("requirements") or {}).get("SchemaDefRequirement") + if schema and schema.get("types"): + schema["types"] = [_map_type(d, rename) for d in schema["types"]] + for side in ("inputs", "outputs"): + for spec in (body.get(side) or {}).values(): + if isinstance(spec, dict) and "type" in spec: + spec["type"] = _map_type(spec["type"], rename) + + +def _map_type(value: Any, rename) -> Any: + """Expand shorthands and rename type names in a type or record field.""" + if isinstance(value, str): + return _expand_type(value, rename) + if isinstance(value, list): + union: list[Any] = [] + for member in value: + mapped = _map_type(member, rename) + # File? in a union is null plus File: a union cannot nest + for item in ( + mapped + if isinstance(member, str) and isinstance(mapped, list) + else [mapped] + ): + if item not in union: + union.append(item) + return union + if not isinstance(value, dict): + return value + value = dict(value) + if value.get("type") not in ("record", "enum", "array") and "type" in value: + value["type"] = _map_type(value["type"], rename) + if "items" in value: + value["items"] = _map_type(value["items"], rename) + fields = value.get("fields") + if isinstance(fields, dict): + value["fields"] = {n: _map_type(f, rename) for n, f in fields.items()} + elif isinstance(fields, list): + value["fields"] = [ + {**_map_type(f, rename), "name": _leaf(f["name"])} + if isinstance(f, dict) and "name" in f + else _map_type(f, rename) + for f in fields + ] + if isinstance(value.get("symbols"), list): + value["symbols"] = [_leaf(s) for s in value["symbols"]] + return value + + +def _expand_type(value: str, rename) -> Any: + """``X?`` is ``[null, X]`` and ``X[]`` is ``{type: array, items: X}``.""" + if value.endswith("?"): + return ["null", _expand_type(value.removesuffix("?"), rename)] + if value.endswith("[]"): + return { + "type": "array", + "items": _expand_type(value.removesuffix("[]"), rename), + } + return rename(value) + + +def _leaf(name: Any) -> Any: + """``red`` for an enum symbol or field written ``#main/Colour/red``.""" + if isinstance(name, str) and "#" in name: + return name.split("#", 1)[1].rsplit("/", 1)[-1] + return name + + +def _name_types(body: dict[str, Any], own_name: str | None) -> None: + """Write named types and references to them by short name (rule 7).""" + definitions = _type_definitions(body) + names = set() + for definition in definitions: + definition["name"] = _short(str(definition["name"]), own_name) + names.add(definition["name"]) + + def rename(name: str) -> str: + if name in PRIMITIVE_TYPES: + return name + short = _short(name, own_name) + if short not in names: + raise ValueError( + f"Type {name!r} is not defined by the process using it: define " + "it in that process's own SchemaDefRequirement" + ) + return short + + _map_types(body, rename) + + +def _scope_types(body: dict[str, Any], entry_id: str) -> None: + """Scope a packed component's named types by its id, as runners require.""" + definitions = _type_definitions(body) + names = {definition["name"] for definition in definitions} + if not names: + return + for definition in definitions: + definition["name"] = f"{entry_id}/{definition['name']}" + _map_types(body, lambda n: f"{entry_id}/{n}" if n in names else n) + + +def _unscope_types(body: dict[str, Any], entry_id: str) -> None: + prefix = f"{entry_id}/" + for definition in _type_definitions(body): + definition["name"] = str(definition["name"]).removeprefix(prefix) + _map_types(body, lambda n: n.removeprefix(prefix)) + + +def _qualify(value: Any, namespaces: dict[str, str], *, top: bool = False) -> Any: + """Expand prefixed keys, classes and formats to full URIs (rule 2). + + Nested processes are left alone: they are expanded with their own + bindings, which may rebind a prefix, when they are canonicalised. + """ + if not namespaces: + return value + if isinstance(value, list): + return [_qualify(v, namespaces) for v in value] + if not isinstance(value, dict): + return value + if not top and value.get("class") in PROCESS_CLASSES: + return value + result = {} + for key, item in value.items(): + if key in ("default", "$namespaces"): + result[key] = item + elif key in ("class", "format"): + result[key] = ( + [_expand_name(v, namespaces) for v in item] + if isinstance(item, list) + else _expand_name(item, namespaces) + ) + else: + result[_expand_name(key, namespaces)] = _qualify(item, namespaces) + return result + + +def _expand_name(name: Any, namespaces: dict[str, str]) -> Any: + if not isinstance(name, str): + return name + prefix, sep, rest = name.partition(":") + if sep and prefix in namespaces and not rest.startswith("//"): + return namespaces[prefix] + rest + return name + + +def _parameters(value: Any, own_name: str | None) -> dict[str, Any]: + return { + name: _strip(_refs(spec, own_name)) + for name, spec in _by_id(value, own_name, shorthand="type").items() + } + + +def _by_id( + value: Any, own_name: str | None, shorthand: str | None = None +) -> dict[str, Any]: + """Map form of an id-keyed list (rule 4), with shorthand values expanded.""" + if isinstance(value, dict): + items = [{"id": k, **_expand(v, shorthand)} for k, v in value.items()] + else: + items = [{"id": v} if isinstance(v, str) else v for v in value] + result = {} + for item in items: + item = dict(item) + name = _short(str(item.pop("id")), own_name) + if name in result: + raise ValueError(f"Duplicate id {name!r}") + result[name] = item + return result + + +def _expand(value: Any, shorthand: str | None) -> dict[str, Any]: + # A map-form value that is an object is the parameter (or step input) itself + if isinstance(value, dict) or shorthand is None: + return value + return {shorthand: value} + + +def _by_class(value: Any, *, drop_dirac: bool) -> dict[str, Any]: + """Map form of a requirements or hints list keyed by class (rule 4). + + ``dirac:`` hints are dropped (rule 3). A ``dirac:`` requirement is kept, + so that the policy refuses it: a runner must honour a requirement, and no + CWL runner knows that class. + """ + if isinstance(value, dict): + items = [{"class": k, **(v or {})} for k, v in value.items()] + else: + items = list(value) + result = {} + for item in items: + item = dict(item) + cls = item.pop("class") + if drop_dirac and str(cls).startswith(DIRAC_PREFIX): + continue + result[cls] = _strip(item, metadata=cls == "SchemaDefRequirement") + return result + + +def _refs(value: Any, own_name: str | None) -> Any: + """Shorten the references inside a parameter or step input (rule 5).""" + if isinstance(value, dict): + return { + k: (_shorten_refs(v, own_name) if k in REFERENCE_FIELDS else v) + for k, v in value.items() + } + return _shorten_refs(value, own_name) + + +def _shorten_refs(value: Any, own_name: str | None) -> Any: + if isinstance(value, str): + return _short(value, own_name) + if isinstance(value, list): + return [_short(v, own_name) if isinstance(v, str) else v for v in value] + return value + + +def _short(identifier: str, scope: str | None) -> str: + """Shorten an identifier relative to its enclosing scope (rule 5). + + Only a fully scoped identifier loses the scope: ``s0/out`` in a workflow + whose own name is ``s0`` names the output of its step ``s0``. + """ + if "#" in identifier: + identifier = identifier.split("#", 1)[1] + if scope and identifier.startswith(scope + "/"): + identifier = identifier[len(scope) + 1 :] + elif "://" in identifier or identifier.startswith("_:"): + identifier = identifier.rsplit("/", 1)[-1] + return identifier + + +def _is_dropped(key: str) -> bool: + return key in METADATA_FIELDS or key.startswith(DIRAC_PREFIX) + + +def _strip(value: Any, *, metadata: bool = True) -> Any: + """Drop ``dirac:`` fields, and metadata if asked, at every level (rule 3). + + ``default`` values are user data and kept verbatim, as are the names of a + record's fields in map form. Anonymous schema names (``name: _:``), + which some CWL libraries mint afresh on every load, are dropped. + """ + if isinstance(value, dict): + result = {} + for k, v in value.items(): + if k.startswith(DIRAC_PREFIX) or (metadata and k in METADATA_FIELDS): + continue + if k == "name" and isinstance(v, str) and v.startswith("_:"): + continue + if k == "default": + result[k] = v + elif k == "fields" and isinstance(v, dict): + result[k] = {n: _strip(f, metadata=metadata) for n, f in v.items()} + else: + result[k] = _strip(v, metadata=metadata) + return result + if isinstance(value, list): + return [_strip(v, metadata=metadata) for v in value] + return value diff --git a/diracx-core/tests/test_cwl_canonical.py b/diracx-core/tests/test_cwl_canonical.py new file mode 100644 index 000000000..b9c210b68 --- /dev/null +++ b/diracx-core/tests/test_cwl_canonical.py @@ -0,0 +1,442 @@ +from __future__ import annotations + +import copy +import json + +import pytest + +from diracx.core.cwl import ( + canonical_bytes, + decompose, + format_reference, + pack, + parse_reference, + unpack, +) + + +def merge_tool(command: str = "hadd") -> dict: + return { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "id": "file:///home/someone/prod/merge.cwl#main", + "doc": "Merge files", + "baseCommand": [command], + "inputs": {"input-data": {"type": "File[]", "inputBinding": {"position": 1}}}, + "outputs": {"merged": {"type": "File", "outputBinding": {"glob": "*.root"}}}, + } + + +def workflow(*tools: dict) -> dict: + return { + "cwlVersion": "v1.2", + "class": "Workflow", + "id": "transformation_3", + "label": "MCMerge", + "hints": [{"class": "dirac:Transformation", "group_size": 4}], + "inputs": [{"id": "input-data", "type": "File[]"}], + "outputs": [ + { + "id": "merged", + "type": "File", + "outputSource": f"step{len(tools) - 1}/merged", + } + ], + "steps": [ + { + "id": f"#transformation_3/step{i}", + "run": tool, + "in": {"input-data": "input-data"}, + "out": ["merged"], + } + for i, tool in enumerate(tools) + ], + } + + +def root_id(process: dict) -> bytes: + return decompose(process)[0] + + +def test_same_document_loaded_from_two_places_has_one_identity(): + a, b = merge_tool(), merge_tool() + b["id"] = "file:///tmp/elsewhere/merge.cwl#main" + assert root_id(a) == root_id(b) + + +def test_identity_ignores_formatting_key_order_and_map_vs_list_form(): + a = merge_tool() + b = json.loads(json.dumps(a, sort_keys=True)) + b["inputs"] = [ + {"id": "input-data", "inputBinding": {"position": 1}, "type": "File[]"} + ] + b["outputs"] = [ + {"id": "merged", "type": "File", "outputBinding": {"glob": "*.root"}} + ] + assert root_id(a) == root_id(b) + + +def test_identity_ignores_metadata_and_dirac_hints(): + a = workflow(merge_tool()) + b = copy.deepcopy(a) + b["label"] = "something else" + b["hints"] = [{"class": "dirac:Transformation", "group_size": 8}] + b["inputs"][0]["dirac:Feeder"] = {"name": "Seeds"} + assert root_id(a) == root_id(b) + + +def formatted(prefix: str, uri: str) -> dict: + tool = merge_tool() + tool["$namespaces"] = {prefix: uri} + tool["inputs"]["input-data"]["format"] = f"{prefix}:format_2572" + return tool + + +def test_identity_covers_what_a_prefix_means_not_which_prefix(): + edam = "http://edamontology.org/" + assert root_id(formatted("edam", edam)) == root_id(formatted("e", edam)) + assert root_id(formatted("edam", edam)) != root_id( + formatted("edam", "http://example.org/") + ) + + +def test_nested_processes_inherit_and_may_rebind_prefixes(): + inherited = workflow(formatted("edam", "http://edamontology.org/")) + child = inherited["steps"][0]["run"] + inherited["$namespaces"] = child.pop("$namespaces") + root, nodes = decompose(inherited) + assert root_id(formatted("edam", "http://edamontology.org/")) in nodes + rebound = copy.deepcopy(inherited) + rebound["steps"][0]["run"]["$namespaces"] = {"edam": "http://example.org/"} + assert root_id(rebound) != root + + +def test_fully_scoped_step_ports_match_the_short_form(): + short = workflow(merge_tool()) + short["steps"][0]["out"] = ["merged"] + scoped = copy.deepcopy(short) + scoped["id"] = "file:///home/someone/prod/merge.cwl#transformation_3" + scope = "file:///home/someone/prod/merge.cwl#transformation_3" + scoped["inputs"][0]["id"] = f"{scope}/input-data" + scoped["outputs"][0]["id"] = f"{scope}/merged" + scoped["outputs"][0]["outputSource"] = f"{scope}/step0/merged" + step = scoped["steps"][0] + step["id"] = f"{scope}/step0" + step["in"] = [{"id": f"{scope}/step0/input-data", "source": f"{scope}/input-data"}] + step["out"] = [{"id": f"{scope}/step0/merged"}] + assert root_id(scoped) == root_id(short) + + +def test_a_relative_reference_keeps_a_step_named_like_its_workflow(): + def named(process_id: str) -> dict: + wf = workflow(merge_tool()) + wf["id"] = process_id + wf["steps"][0]["id"] = "s0" + wf["outputs"][0]["outputSource"] = "s0/merged" + return wf + + root, nodes = decompose(named("s0")) + assert json.loads(nodes[root].body)["outputs"]["merged"]["outputSource"] == ( + "s0/merged" + ) + assert root == root_id(named("something-else")) + + +def test_dirac_hints_are_dropped_but_dirac_requirements_are_kept(): + hinted = merge_tool() + hinted["hints"] = {"dirac:Transformation": {"group_size": 4}} + assert root_id(hinted) == root_id(merge_tool()) + required = merge_tool() + required["requirements"] = {"dirac:Unsupported": {}} + root, nodes = decompose(required) + assert "dirac:Unsupported" in json.loads(nodes[root].body)["requirements"] + + on_step = workflow(merge_tool()) + on_step["steps"][0]["hints"] = {"dirac:Transformation": {"group_size": 4}} + on_step["steps"][0]["requirements"] = {"dirac:Unsupported": {}} + root, nodes = decompose(on_step) + step = json.loads(nodes[root].body)["steps"]["step0"] + assert "hints" not in step + assert "dirac:Unsupported" in step["requirements"] + + +def test_anonymous_schema_names_do_not_change_the_identity(): + a, b = merge_tool(), merge_tool() + for tool, name in ((a, "_:16606bec"), (b, "_:ad4e1bb5")): + tool["inputs"]["input-data"]["type"] = { + "type": "array", + "items": "File", + "name": name, + } + assert root_id(a) == root_id(b) + + +def test_what_runs_changes_the_identity(): + assert root_id(merge_tool("hadd")) != root_id(merge_tool("hadd -f")) + renamed = merge_tool() + renamed["inputs"] = {"files": renamed["inputs"]["input-data"]} + assert root_id(renamed) != root_id(merge_tool()) + + +def test_default_values_are_kept_verbatim(): + a, b = merge_tool(), merge_tool() + a["inputs"]["conf"] = {"type": "Any", "default": {"label": "A"}} + b["inputs"]["conf"] = {"type": "Any", "default": {"label": "B"}} + assert root_id(a) != root_id(b) + + +@pytest.mark.parametrize( + "where", + [ + lambda t, v: t.update( + requirements={"EnvVarRequirement": {"envDef": {"label": v, "doc": v}}} + ), + lambda t, v: t["inputs"].update( + seed={"type": {"type": "record", "fields": {"label": v, "doc": "int"}}} + ), + lambda t, v: t.update(hints={"SoftwareRequirement": {"packages": {"doc": v}}}), + ], +) +def test_user_chosen_names_called_doc_or_label_are_kept(where): + a, b = merge_tool(), merge_tool() + where(a, "string") + where(b, "File") + assert root_id(a) != root_id(b) + + +def typed(name: str, reference: str, value_type: str = "int") -> dict: + tool = merge_tool() + tool["requirements"] = { + "SchemaDefRequirement": { + "types": [ + {"name": "#Colour", "type": "enum", "symbols": ["#Colour/red"]}, + { + "name": name, + "type": "record", + "fields": [{"name": "value", "type": value_type}], + }, + ] + } + } + tool["inputs"]["seed"] = {"type": reference} + tool["inputs"]["seeds"] = {"type": f"{reference}[]"} + return tool + + +def test_named_types_are_written_by_short_name(): + root = root_id(typed("Seed", "Seed")) + assert root == root_id(typed("#Seed", "#Seed")) + assert root == root_id(typed("file:///p/merge.cwl#main/Seed", "#main/Seed")) + assert root != root_id(typed("Seed", "Seed", value_type="string")) + body = json.loads(decompose(typed("#main/Seed", "#main/Seed"))[1][root].body) + assert body["inputs"]["seeds"]["type"] == {"type": "array", "items": "Seed"} + assert body["requirements"]["SchemaDefRequirement"]["types"][0]["symbols"] == [ + "red" + ] + + +def test_named_types_must_be_defined_by_the_process_using_them(): + tool = merge_tool() + tool["inputs"]["seed"] = {"type": "Seed"} + with pytest.raises(ValueError, match="not defined by the process"): + decompose(workflow(tool)) + + +def test_pack_scopes_named_types_by_component(): + root, nodes = decompose(workflow(typed("Seed", "Seed"))) + packed = pack(root, nodes) + tool = packed["$graph"][1] + schema = tool["requirements"]["SchemaDefRequirement"]["types"] + assert schema[1]["name"] == tool["id"] + "/Seed" + assert tool["inputs"]["seeds"]["type"]["items"] == tool["id"] + "/Seed" + assert unpack(packed) == (root, nodes) + + +def test_child_change_propagates_to_parents_but_not_siblings(): + before_root, before = decompose(workflow(merge_tool("a"), merge_tool("b"))) + after_root, after = decompose(workflow(merge_tool("a"), merge_tool("c"))) + assert before_root != after_root + assert root_id(merge_tool("a")) in before and root_id(merge_tool("a")) in after + + +def test_shared_child_is_one_node(): + root, nodes = decompose(workflow(merge_tool(), merge_tool())) + assert len(nodes) == 2 + assert nodes[root].children == (root_id(merge_tool()),) + + +def test_child_body_is_a_reference_to_its_identity(): + root, nodes = decompose(workflow(merge_tool())) + body = json.loads(nodes[root].body) + child = parse_reference(body["steps"]["step0"]["run"]) + assert child == root_id(merge_tool()) + assert body["outputs"]["merged"]["outputSource"] == "step0/merged" + + +def test_existing_reference_is_kept_without_its_body(): + child = root_id(merge_tool()) + wf = workflow(merge_tool()) + wf["steps"][0]["run"] = format_reference(child) + assert root_id(wf) == root_id(workflow(merge_tool())) + + +@pytest.mark.parametrize( + "mutate, message", + [ + (lambda p: p.update(cwlVersion="v1.0"), "upgrade"), + (lambda p: p["steps"][0].update(run="tools/merge.cwl"), "Unresolved"), + (lambda p: p.update({"class": "Nope"}), "Not a CWL process"), + ( + lambda p: p.update( + requirements={ + "InitialWorkDirRequirement": { + "listing": [{"entryname": "f", "entry": {"$include": "x"}}] + } + } + ), + r"Unresolved \$include", + ), + ( + lambda p: p["steps"][0]["run"]["inputs"].update( + conf={"type": "Any", "default": {"$import": "conf.yml"}} + ), + r"Unresolved \$import", + ), + (lambda p: p.update({"$base": "http://example.org/"}), r"Unresolved \$base"), + ], +) +def test_rejected_documents(mutate, message): + wf = workflow(merge_tool()) + mutate(wf) + with pytest.raises(ValueError, match=message): + decompose(wf) + + +def test_pack_round_trips_to_the_same_tree(): + root, nodes = decompose(workflow(merge_tool("a"), merge_tool("b"))) + packed = pack(root, nodes) + assert packed["$graph"][0]["id"] == "#main" + assert unpack(packed) == (root, nodes) + + +def test_unpack_rejects_a_tampered_component(): + root, nodes = decompose(workflow(merge_tool())) + packed = pack(root, nodes) + packed["$graph"][1]["baseCommand"] = ["rm", "-rf"] + with pytest.raises(ValueError, match="does not match"): + unpack(packed) + + +def test_unpack_verifies_a_shared_component_once(): + # Each level runs the level below twice: 2**40 paths, 41 components + nodes = decompose(merge_tool())[1] + root = next(iter(nodes)) + for _ in range(40): + level = workflow(merge_tool(), merge_tool()) + for step in level["steps"]: + step["run"] = format_reference(root) + root, own = decompose(level) + nodes.update(own) + assert unpack(pack(root, nodes)) == (root, nodes) + + +def test_unpack_rejects_a_component_that_runs_itself(): + packed = pack(*decompose(workflow(merge_tool()))) + packed["$graph"][0]["steps"]["step0"]["run"] = "#main" + with pytest.raises(ValueError, match="runs itself"): + unpack(packed) + + +def test_source_lists_and_scatter_are_shortened_like_single_sources(): + def scattered(scope: str) -> dict: + wf = workflow(merge_tool()) + wf["requirements"] = { + "ScatterFeatureRequirement": {}, + "MultipleInputFeatureRequirement": {}, + } + wf["inputs"].append({"id": f"{scope}extra", "type": "File[]"}) + step = wf["steps"][0] + step["in"] = { + "input-data": { + "source": [f"{scope}input-data", f"{scope}extra"], + "linkMerge": "merge_flattened", + } + } + step["scatter"] = "input-data" + step["dirac:Group"] = {"size": 4} + return wf + + root, nodes = decompose(scattered("#transformation_3/")) + step = json.loads(nodes[root].body)["steps"]["step0"] + assert step["in"]["input-data"]["source"] == ["input-data", "extra"] + assert step["scatter"] == "input-data" + assert "dirac:Group" not in step + assert root == root_id(scattered("")) + + +@pytest.mark.parametrize( + "short, expanded", + [ + ("File[]", {"type": "array", "items": "File"}), + ("File?", ["null", "File"]), + ("File[]?", ["null", {"type": "array", "items": "File"}]), + ("File[][]", {"type": "array", "items": {"type": "array", "items": "File"}}), + (["File?", "int"], ["null", "File", "int"]), + ], +) +def test_type_shorthands_are_expanded(short, expanded): + a, b = merge_tool(), merge_tool() + a["inputs"]["input-data"]["type"] = short + b["inputs"]["input-data"]["type"] = expanded + root, nodes = decompose(a) + assert root == root_id(b) + body = json.loads(nodes[root].body) + assert body["inputs"]["input-data"]["type"] == expanded + + +def test_union_types_name_their_members(): + a, b = typed("Seed", "Seed"), typed("Seed", "Seed") + b["inputs"]["seed"] = {"type": ["null", "#main/Seed"]} + a["inputs"]["seed"] = {"type": ["null", "Seed"]} + root, nodes = decompose(a) + assert root == root_id(b) + assert json.loads(nodes[root].body)["inputs"]["seed"]["type"] == ["null", "Seed"] + + +def test_a_process_id_without_a_fragment_is_ignored(): + a = merge_tool() + a["id"] = "file:///home/someone/prod/merge.cwl" + assert root_id(a) == root_id(merge_tool()) + + +@pytest.mark.parametrize( + "reference, message", + [ + ("tools/merge.cwl", "Not a process reference"), + ("proc:sha256-abcd", "Not a SHA-256 process reference"), + ], +) +def test_malformed_process_references_are_refused(reference, message): + with pytest.raises(ValueError, match=message): + parse_reference(reference) + + +def test_duplicate_ids_are_refused(): + tool = merge_tool() + tool["inputs"] = [{"id": "x", "type": "File"}, {"id": "#main/x", "type": "File"}] + tool["id"] = "#main" + with pytest.raises(ValueError, match="Duplicate id 'x'"): + decompose(tool) + + +def test_canonical_bytes_are_compact_and_sorted(): + assert canonical_bytes({"b": 1, "a": "é"}) == '{"a":"é","b":1}'.encode() + + +def test_golden_identity(): + # Changing this value means every stored identity changes: bump + # CANONICAL_VERSION and plan the migration instead of editing it. + assert ( + root_id(workflow(merge_tool())).hex() + == "b06bc1e02806b735f5100eff9d5e9b00fb0ea154c0856d3e03b5d500689344a9" + ) From 8679b417f87d11be96e4bf3dcb7067123fe9e44e Mon Sep 17 00:00:00 2001 From: Ryunosuke O'Neil Date: Fri, 23 Oct 2026 16:20:29 +0200 Subject: [PATCH 2/5] ci: run the transformation DB tests on MySQL and MariaDB Unit tests ran on SQLite only, but production runs on MySQL and MariaDB, which differ from SQLite where the transformation tables rely on them. The diracx-db transformation tests now share one fixture that runs each test on SQLite and on every server given by DIRACX_TEST_MYSQL_URL or DIRACX_TEST_MARIADB_URL, and a CI job runs them on MySQL 8.4 and MariaDB 11.4 service containers, pinned by digest. It found one difference already: a failed CHECK constraint is an IntegrityError on SQLite but an OperationalError on MySQL and MariaDB through PyMySQL, so the deltas test now accepts either, matched on the constraint's name. Closes #1108 --- .github/workflows/main.yml | 51 +++++++++++++++++++ diracx-db/tests/transformation/conftest.py | 51 +++++++++++++++++++ .../transformation/test_transformation_db.py | 26 +++------- docs/dev/explanations/components/db.md | 9 ++++ 4 files changed, 118 insertions(+), 19 deletions(-) create mode 100644 diracx-db/tests/transformation/conftest.py diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 0525a9f76..c6d0441ee 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -141,6 +141,57 @@ jobs: - name: Upload coverage report uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1 + pytest-sql-servers: + name: Unit test - diracx-db on MySQL and MariaDB + runs-on: ubuntu-latest + services: + mysql: + image: mysql:8.4@sha256:76f0358884cb92d9a086d24e5671c38048d3fef40f2588703d73eb55392d6b69 + env: + MYSQL_ROOT_PASSWORD: diracx + MYSQL_DATABASE: transformation + ports: + - 3306:3306 + options: >- + --health-cmd "mysqladmin ping -h 127.0.0.1 -pdiracx" + --health-interval 5s --health-timeout 5s --health-retries 30 + mariadb: + image: mariadb:11.4@sha256:250e1609e93c0e6aecf64bfbab2d84d5e89d2481540fe77447ff6c855c3b1873 + env: + MARIADB_ROOT_PASSWORD: diracx + MARIADB_DATABASE: transformation + ports: + - 3307:3306 + options: >- + --health-cmd "healthcheck.sh --connect --innodb_initialized" + --health-interval 5s --health-timeout 5s --health-retries 30 + steps: + - name: Checkout code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + persist-credentials: false + - uses: prefix-dev/setup-pixi@9dabb60412d3d2d967a8d682f7ce01317af40514 # v0.11.0 + with: + run-install: false + post-cleanup: false + - name: Apply workarounds + run: | + # Workaround for https://github.com/prefix-dev/pixi/issues/3762 + sed -i.bak 's@editable = true@editable = false@g' pixi.toml + rm pixi.toml.bak + # Show any changes + git diff + - uses: prefix-dev/setup-pixi@9dabb60412d3d2d967a8d682f7ce01317af40514 # v0.11.0 + with: + cache: false + environments: diracx-db + - name: Run pytest + # The transformation tests run on SQLite, then again on each server + env: + DIRACX_TEST_MYSQL_URL: mysql+aiomysql://root:diracx@127.0.0.1:3306/transformation + DIRACX_TEST_MARIADB_URL: mysql+aiomysql://root:diracx@127.0.0.1:3307/transformation + run: pixi run pytest-diracx-db tests/transformation --no-cov + pytest-integration: needs: resolve-deps runs-on: ubuntu-latest diff --git a/diracx-db/tests/transformation/conftest.py b/diracx-db/tests/transformation/conftest.py new file mode 100644 index 000000000..abe5a608a --- /dev/null +++ b/diracx-db/tests/transformation/conftest.py @@ -0,0 +1,51 @@ +"""Transformation databases the tests run against. + +Every test using ``transformation_db`` runs on SQLite, and also on each real +server given as the SQLAlchemy URL of an empty database the tests may create +tables in, since MySQL and MariaDB differ from SQLite where these tables rely +on them (``JSON`` normalisation, foreign keys, row locks), e.g.:: + + DIRACX_TEST_MYSQL_URL=mysql+aiomysql://root:pw@127.0.0.1:3306/transformation + DIRACX_TEST_MARIADB_URL=mysql+aiomysql://root:pw@127.0.0.1:3307/transformation +""" + +from __future__ import annotations + +import os + +import pytest +from sqlalchemy import event + +from diracx.db.sql import TransformationDB + +SERVERS = { + name: os.environ.get(variable) + for name, variable in [ + ("mysql", "DIRACX_TEST_MYSQL_URL"), + ("mariadb", "DIRACX_TEST_MARIADB_URL"), + ] +} + + +@pytest.fixture(params=["sqlite", *(name for name, url in SERVERS.items() if url)]) +async def transformation_db(request): + db = TransformationDB(SERVERS.get(request.param) or "sqlite+aiosqlite:///:memory:") + async with db.engine_context(): + if request.param == "sqlite": + # SQLite only enforces foreign keys when asked to, per connection + event.listen( + db.engine.sync_engine, + "connect", + lambda dbapi_conn, _: dbapi_conn.cursor().execute( + "PRAGMA foreign_keys=ON" + ), + ) + async with db.engine.begin() as conn: + await conn.run_sync(db.metadata.drop_all) + await conn.run_sync(db.metadata.create_all) + await db.post_create(conn) + try: + yield db + finally: + async with db.engine.begin() as conn: + await conn.run_sync(db.metadata.drop_all) diff --git a/diracx-db/tests/transformation/test_transformation_db.py b/diracx-db/tests/transformation/test_transformation_db.py index 1c23eb954..2f40cf801 100644 --- a/diracx-db/tests/transformation/test_transformation_db.py +++ b/diracx-db/tests/transformation/test_transformation_db.py @@ -1,8 +1,8 @@ from __future__ import annotations import pytest -from sqlalchemy import delete, event, func, insert, select, update -from sqlalchemy.exc import IntegrityError +from sqlalchemy import delete, func, insert, select, update +from sqlalchemy.exc import IntegrityError, OperationalError from uuid_utils import UUID, uuid7 from diracx.core.models.transformation import ( @@ -25,22 +25,6 @@ from diracx.db.sql.utils.counters import counter_locks_table -@pytest.fixture -async def transformation_db(): - db = TransformationDB("sqlite+aiosqlite:///:memory:") - async with db.engine_context(): - # SQLite only enforces foreign keys when asked to, per connection - event.listen( - db.engine.sync_engine, - "connect", - lambda dbapi_conn, _: dbapi_conn.cursor().execute("PRAGMA foreign_keys=ON"), - ) - async with db.engine.begin() as conn: - await conn.run_sync(db.metadata.create_all) - await db.post_create(conn) - yield db - - @pytest.fixture async def transformation_id(transformation_db: TransformationDB) -> UUID: workgraph_id, ownership_id, transformation_id = uuid7(), uuid7(), uuid7() @@ -211,7 +195,11 @@ async def test_data_parcel_deltas_are_never_negative( ) ) - with pytest.raises(IntegrityError): + # SQLite reports a failed CHECK as an integrity error; MySQL and MariaDB, + # through PyMySQL, as an operational one + with pytest.raises( + (IntegrityError, OperationalError), match="DataParcelDeltasNonNegative" + ): async with transformation_db as db: await db.conn.execute( insert(DataParcelDeltas).values( diff --git a/docs/dev/explanations/components/db.md b/docs/dev/explanations/components/db.md index 05fbb57ff..786590f4e 100644 --- a/docs/dev/explanations/components/db.md +++ b/docs/dev/explanations/components/db.md @@ -14,6 +14,15 @@ While the code is designed to be compatible with multiple database systems, only Support for Postgresql or other databases will be added if demand and resources are found. For convenience SQLite is used for testing and development however this should never be used in production. +The `TransformationDB` tests also run on MySQL and MariaDB, which differ from SQLite where those tables rely on them (`JSON` normalisation, foreign keys, error reporting). +Set either variable to the SQLAlchemy URL of an empty database the tests may create tables in, and each test runs on SQLite and on that server; CI does this for MySQL 8.4 and MariaDB 11.4: + +```bash +export DIRACX_TEST_MYSQL_URL="mysql+aiomysql://root:pw@127.0.0.1:3306/transformation" +export DIRACX_TEST_MARIADB_URL="mysql+aiomysql://root:pw@127.0.0.1:3307/transformation" +pixi run pytest-diracx-db tests/transformation +``` + ### Connecting to SQL databases Connections to DiracX DBs are configured using the [SQLAlchemy connection URL format](https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls). From acd6d9320a98a16a180abb01149aabe274314288 Mon Sep 17 00:00:00 2001 From: Ryunosuke O'Neil Date: Fri, 23 Oct 2026 16:21:09 +0200 Subject: [PATCH 3/5] feat(db): store and fetch content-addressed processes in TransformationDB insert_processes stores documents under their content hash with INSERT IGNORE, so concurrent submissions of a shared process are safe, and get_processes fetches them, on the DX-ADR-004 Processes table unchanged. MySQL's JSON type re-sorts keys and reformats numbers, so a stored row is not the bytes that were hashed: what must hold is that the value read back re-hashes to its identity, which the round-trip test checks on SQLite, MySQL and MariaDB. Closes #1109 Part of #1080 --- .../src/diracx/db/sql/transformation/db.py | 52 ++++++++++++-- .../tests/transformation/test_processes.py | 26 +++++++ .../tests/transformation/test_round_trip.py | 69 +++++++++++++++++++ 3 files changed, 141 insertions(+), 6 deletions(-) create mode 100644 diracx-db/tests/transformation/test_processes.py create mode 100644 diracx-db/tests/transformation/test_round_trip.py diff --git a/diracx-db/src/diracx/db/sql/transformation/db.py b/diracx-db/src/diracx/db/sql/transformation/db.py index 4a89a88b2..44a9f463f 100644 --- a/diracx-db/src/diracx/db/sql/transformation/db.py +++ b/diracx-db/src/diracx/db/sql/transformation/db.py @@ -2,13 +2,17 @@ from __future__ import annotations -from sqlalchemy import insert +from collections.abc import Iterable, Mapping +from typing import Any + +from sqlalchemy import insert, select from sqlalchemy.ext.asyncio import AsyncConnection from diracx.db.sql.utils import BaseSQLDB from diracx.db.sql.utils.counters import counter_locks_table, journalled_counters from .schema import Base as TransformationDBBase +from .schema import Processes class TransformationDB(BaseSQLDB): @@ -38,9 +42,45 @@ async def post_create(cls, conn: AsyncConnection) -> None: for row in counter.lock_rows() ] if rows: - await conn.execute( - insert(counter_locks_table(cls.metadata)) - .prefix_with("IGNORE", dialect="mysql") - .prefix_with("OR IGNORE", dialect="sqlite"), - rows, + await conn.execute(_insert_ignore(counter_locks_table(cls.metadata)), rows) + + async def insert_processes(self, processes: Mapping[bytes, dict[str, Any]]) -> None: + """Store process documents under their content hash. + + Storing a document that is already present is a no-op, so concurrent + submissions of a shared process are safe. + + Args: + processes: Documents keyed by content hash. + """ + if processes: + await self.conn.execute( + _insert_ignore(Processes).values( + [{"process_id": k, "process": v} for k, v in processes.items()] + ) ) + + async def get_processes( + self, process_ids: Iterable[bytes] + ) -> dict[bytes, dict[str, Any]]: + """Fetch stored documents by content hash. + + Args: + process_ids: Content hashes to fetch. + + Returns: + The documents found, keyed by content hash. + """ + stmt = select(Processes.process_id, Processes.process).where( + Processes.process_id.in_(list(process_ids)) + ) + return {pid: body for pid, body in await self.conn.execute(stmt)} + + +def _insert_ignore(table): + """``INSERT`` that skips rows whose key already exists.""" + return ( + insert(table) + .prefix_with("IGNORE", dialect="mysql") + .prefix_with("OR IGNORE", dialect="sqlite") + ) diff --git a/diracx-db/tests/transformation/test_processes.py b/diracx-db/tests/transformation/test_processes.py new file mode 100644 index 000000000..a38956ad4 --- /dev/null +++ b/diracx-db/tests/transformation/test_processes.py @@ -0,0 +1,26 @@ +from __future__ import annotations + +from sqlalchemy import func, select + +from diracx.db.sql import TransformationDB +from diracx.db.sql.transformation.schema import Processes + + +async def test_insert_processes_is_idempotent(transformation_db: TransformationDB): + a, b = b"a" * 32, b"b" * 32 + async with transformation_db as db: + await db.insert_processes({a: {"class": "Workflow"}}) + await db.insert_processes({a: {"class": "Workflow"}, b: {"class": "Tool"}}) + await db.insert_processes({}) + count = await db.conn.scalar(select(func.count()).select_from(Processes)) + assert count == 2 + + +async def test_get_processes_returns_only_what_is_stored( + transformation_db: TransformationDB, +): + a = b"a" * 32 + async with transformation_db as db: + await db.insert_processes({a: {"class": "Workflow", "steps": {}}}) + found = await db.get_processes([a, b"z" * 32]) + assert found == {a: {"class": "Workflow", "steps": {}}} diff --git a/diracx-db/tests/transformation/test_round_trip.py b/diracx-db/tests/transformation/test_round_trip.py new file mode 100644 index 000000000..4f007b098 --- /dev/null +++ b/diracx-db/tests/transformation/test_round_trip.py @@ -0,0 +1,69 @@ +"""Stored processes survive a round trip through the database. + +MySQL's JSON type re-sorts keys and reformats documents, so a stored row is +not the bytes that were hashed; what must hold is that the value read back +re-canonicalises to the identity it is stored under. Run against real servers +as described in ``conftest.py``. +""" + +from __future__ import annotations + +from diracx.core.cwl import decompose, format_reference, pack, unpack +from diracx.db.sql import TransformationDB + + +def tool(default) -> dict: + return { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "$namespaces": {"edam": "http://edamontology.org/"}, + "baseCommand": ["lb-prod-run"], + "requirements": { + "SchemaDefRequirement": { + "types": [ + {"name": "Seed", "type": "record", "fields": {"value": "int"}} + ] + }, + "EnvVarRequirement": {"envDef": {"ZETA": "1", "ALPHA": "2"}}, + }, + "inputs": { + "seed": "Seed?", + "data": {"type": "File[]", "format": "edam:format_2572"}, + "conf": {"type": "Any", "default": default}, + }, + "outputs": {"out": {"type": "File[]", "outputBinding": {"glob": "*.sim"}}}, + } + + +def workflow(*runs) -> dict: + return { + "cwlVersion": "v1.2", + "class": "Workflow", + "requirements": {"SubworkflowFeatureRequirement": {}}, + "inputs": {"data": "File[]"}, + "outputs": {}, + "steps": { + f"s{i}": {"run": run, "in": {"data": "data"}, "out": ["out"]} + for i, run in enumerate(runs) + }, + } + + +# Values MySQL is known to normalise: key order, numbers, unicode +AWKWARD = [0.1, 1e-7, 2**53, -0.0, 1.5e300, "ünïcødé", {"z": 1, "a": 2}] + + +async def test_rows_read_back_re_hash_to_their_identity( + transformation_db: TransformationDB, +): + shared = tool("plain") + trees = [decompose(p) for p in (shared, tool(AWKWARD))] + shared_id = trees[0][0] + trees.append(decompose(workflow(format_reference(shared_id), tool(AWKWARD)))) + nodes = {k: v for _, tree in trees for k, v in tree.items()} + async with transformation_db as db: + await db.insert_processes({root: pack(root, nodes) for root, _ in trees}) + async with transformation_db as db: + stored = await db.get_processes([root for root, _ in trees]) + for root, _ in trees: + assert unpack(stored[root])[0] == root From 6404529ba15cc065925eb94ce92ece97642aaf4c Mon Sep 17 00:00:00 2001 From: Ryunosuke O'Neil Date: Fri, 23 Oct 2026 16:18:50 +0200 Subject: [PATCH 4/5] feat(core): what DiracX accepts in a submitted CWL process check_policy checks every process of a canonical tree against rules beyond valid CWL, and lists every violation in one error: - requirements outside an allow-list every backend can honour are refused, on a process and on a step, dirac: requirements included; hints are not restricted; - DockerRequirement is accepted, to run with Apptainer, for an image to pull (dockerPull, dockerImageId); dockerFile, dockerLoad and dockerImport are refused, in hints too, since they build or fetch an image on the worker node; - abstract Operations are refused, since no runner can execute them; - processes larger than 256 kB are refused. Closes #1107 --- diracx-core/src/diracx/core/cwl/__init__.py | 3 + diracx-core/src/diracx/core/cwl/policy.py | 98 ++++++++++++++++++ diracx-core/tests/test_cwl_policy.py | 105 ++++++++++++++++++++ 3 files changed, 206 insertions(+) create mode 100644 diracx-core/src/diracx/core/cwl/policy.py create mode 100644 diracx-core/tests/test_cwl_policy.py diff --git a/diracx-core/src/diracx/core/cwl/__init__.py b/diracx-core/src/diracx/core/cwl/__init__.py index adcf1b43d..0ca425d73 100644 --- a/diracx-core/src/diracx/core/cwl/__init__.py +++ b/diracx-core/src/diracx/core/cwl/__init__.py @@ -5,7 +5,9 @@ __all__ = [ "CANONICAL_VERSION", "CanonicalProcess", + "PolicyViolationError", "canonical_bytes", + "check_policy", "decompose", "format_reference", "pack", @@ -23,3 +25,4 @@ parse_reference, unpack, ) +from .policy import PolicyViolationError, check_policy diff --git a/diracx-core/src/diracx/core/cwl/policy.py b/diracx-core/src/diracx/core/cwl/policy.py new file mode 100644 index 000000000..2974670ef --- /dev/null +++ b/diracx-core/src/diracx/core/cwl/policy.py @@ -0,0 +1,98 @@ +"""What DiracX accepts in a submitted CWL process, beyond being valid CWL. + +Checked on the canonical tree (:func:`.canonical.decompose`), so the same rules +apply wherever a document comes from and whichever tool checks it. +""" + +from __future__ import annotations + +import json + +from .canonical import CanonicalProcess + +# Requirements every backend can honour. Hints are not restricted: a runner +# is free to ignore them. Kept deliberately narrow: loosening it later is +# safe, tightening it would break documents already accepted. +ALLOWED_REQUIREMENTS = frozenset( + { + # Run with Apptainer, which grid sites and compute backends provide + "DockerRequirement", + "EnvVarRequirement", + "InitialWorkDirRequirement", + "InlineJavascriptRequirement", + "LoadListingRequirement", + "MultipleInputFeatureRequirement", + "NetworkAccess", + "ResourceRequirement", + "ScatterFeatureRequirement", + "SchemaDefRequirement", + "ShellCommandRequirement", + "StepInputExpressionRequirement", + "SubworkflowFeatureRequirement", + "ToolTimeLimit", + } +) + +# DockerRequirement fields that make the worker node build an image or fetch +# one from a URL at run time, rather than pull a published one: Apptainer +# cannot build from a Dockerfile there. Refused in hints too, since a runner +# with a container engine acts on a DockerRequirement hint. +UNSUPPORTED_DOCKER_FIELDS = ("dockerFile", "dockerImport", "dockerLoad") + +# Largest canonical form of a single process. A year of LHCb submissions +# peaks below 20 kB; large data belongs in a sandbox, not in the document. +MAX_PROCESS_BYTES = 256 * 1024 + + +class PolicyViolationError(ValueError): + """A process is valid CWL but not something DiracX accepts.""" + + +def check_policy( + nodes: dict[bytes, CanonicalProcess], + *, + allowed_requirements: frozenset[str] = ALLOWED_REQUIREMENTS, + max_process_bytes: int = MAX_PROCESS_BYTES, +) -> None: + """Check every process of a canonical tree against the submission rules. + + Args: + nodes: Processes of the tree, as returned by ``decompose``. + allowed_requirements: Requirement classes accepted. + max_process_bytes: Largest canonical form accepted for one process. + + Raises: + PolicyViolationError: Listing every violation found. + """ + problems = [] + for process_id, node in sorted(nodes.items()): + name = f"process sha256-{process_id.hex()[:12]}" + if len(node.body) > max_process_bytes: + problems.append( + f"{name} is {len(node.body)} bytes, more than {max_process_bytes}; " + "move large content into a sandbox or File input" + ) + body = json.loads(node.body) + if body.get("class") == "Operation": + problems.append( + f"{name} is an Operation: it declares inputs and outputs but no " + "command, expression or steps, so no runner can execute it; " + "replace it with a CommandLineTool, ExpressionTool or Workflow " + "taking and producing the same inputs and outputs" + ) + holders = [body, *(body.get("steps") or {}).values()] + for holder in holders: + requirements = holder.get("requirements") or {} + for cls in sorted(set(requirements) - allowed_requirements): + problems.append(f"{name} requires {cls}, which DiracX does not support") + for classes in (requirements, holder.get("hints") or {}): + docker = classes.get("DockerRequirement") or {} + for field in UNSUPPORTED_DOCKER_FIELDS: + if field in docker: + problems.append( + f"{name} uses DockerRequirement {field}, which would " + "build or fetch an image on the worker node; publish " + "the image to a registry and name it with dockerPull" + ) + if problems: + raise PolicyViolationError("; ".join(problems)) diff --git a/diracx-core/tests/test_cwl_policy.py b/diracx-core/tests/test_cwl_policy.py new file mode 100644 index 000000000..a075549da --- /dev/null +++ b/diracx-core/tests/test_cwl_policy.py @@ -0,0 +1,105 @@ +from __future__ import annotations + +import pytest + +from diracx.core.cwl import PolicyViolationError, check_policy, decompose + + +def tool(**extra) -> dict: + return { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "baseCommand": ["echo"], + "inputs": {}, + "outputs": {}, + **extra, + } + + +def test_supported_requirements_and_any_hint_are_accepted(): + check_policy( + decompose( + tool( + requirements={"InlineJavascriptRequirement": {}}, + hints={"DockerRequirement": {"dockerPull": "alpine"}}, + ) + )[1] + ) + + +def test_unsupported_requirements_are_refused_wherever_they_are(): + workflow = { + "cwlVersion": "v1.2", + "class": "Workflow", + "inputs": {}, + "outputs": {}, + "steps": { + "s0": { + "run": tool(requirements=[{"class": "InplaceUpdateRequirement"}]), + "requirements": {"SoftwareRequirement": {"packages": []}}, + "in": {}, + "out": [], + } + }, + } + with pytest.raises(PolicyViolationError) as e: + check_policy(decompose(workflow)[1]) + assert "InplaceUpdateRequirement" in str(e.value) + assert "SoftwareRequirement" in str(e.value) + + +def test_oversized_processes_are_refused(): + with pytest.raises(PolicyViolationError, match="sandbox"): + check_policy(decompose(tool(arguments=["x" * 1000]))[1], max_process_bytes=500) + + +def test_dirac_requirements_are_refused_but_dirac_hints_are_not(): + check_policy(decompose(tool(hints={"dirac:Transformation": {"group_size": 4}}))[1]) + with pytest.raises(PolicyViolationError, match="dirac:Unsupported"): + check_policy(decompose(tool(requirements={"dirac:Unsupported": {}}))[1]) + + +def test_abstract_operations_are_refused_wherever_they_are(): + operation = { + "cwlVersion": "v1.2", + "class": "Operation", + "inputs": {"x": "File"}, + "outputs": {"y": "File"}, + } + workflow = { + "cwlVersion": "v1.2", + "class": "Workflow", + "inputs": {"x": "File"}, + "outputs": {"y": {"type": "File", "outputSource": "s0/y"}}, + "steps": {"s0": {"run": operation, "in": {"x": "x"}, "out": ["y"]}}, + } + for process in (operation, workflow): + with pytest.raises(PolicyViolationError, match="is an Operation") as e: + check_policy(decompose(process)[1]) + assert "CommandLineTool, ExpressionTool or Workflow" in str(e.value) + + +def test_docker_images_are_accepted_when_pulled(): + for image in ( + "harbor.cta-observatory.org/ctapipe:0.24", + "alpine@sha256:" + "a" * 64, + ): + check_policy( + decompose(tool(requirements={"DockerRequirement": {"dockerPull": image}}))[ + 1 + ] + ) + check_policy( + decompose( + tool(requirements={"DockerRequirement": {"dockerImageId": "ctapipe"}}) + )[1] + ) + + +@pytest.mark.parametrize("field", ["dockerFile", "dockerImport", "dockerLoad"]) +@pytest.mark.parametrize("where", ["requirements", "hints"]) +def test_docker_images_built_or_fetched_on_the_worker_are_refused(field, where): + docker = {"DockerRequirement": {"dockerImageId": "x", field: "x"}} + with pytest.raises(PolicyViolationError, match=f"DockerRequirement {field}") as e: + check_policy(decompose(tool(**{where: docker}))[1]) + assert "dockerPull" in str(e.value) From 4fb2019d5d0bc6750f5a24bc8112df7770bf9e94 Mon Sep 17 00:00:00 2001 From: Ryunosuke O'Neil Date: Fri, 23 Oct 2026 16:25:20 +0200 Subject: [PATCH 5/5] feat(logic): ingest CWL processes, flat per transformation store_process canonicalises a submitted process, checks the policy, and returns at once if it is already stored. Otherwise it inlines any stored process it references, packs the tree into one self-contained $graph, validates every component of it against the CWL v1.2 schema with cwl-utils and stores it: one Processes row per transformation, keyed by the Merkle root, so a parcel's payload is a single read (load_process) and exactly what a stock runner executes. Validation reads nothing but the packed document: any other file or URL is refused rather than fetched on the server. Step input wiring is not checked yet, until a cwl-utils release fixes its static checker (common-workflow-language/cwl-utils#480). The MCSimulation fixture is the JSON the #1080 workgraph resolves to, as the submission endpoint will receive it. Closes #1110 Part of #1080 --- diracx-logic/pyproject.toml | 3 + .../diracx/logic/transformation/__init__.py | 3 + .../diracx/logic/transformation/processes.py | 93 +++ .../diracx/logic/transformation/validation.py | 90 +++ .../fixtures/mc-simulation.json | 494 +++++++++++++ .../transformation/test_mc_simulation.py | 71 ++ .../tests/transformation/test_processes.py | 129 ++++ .../tests/transformation/test_validation.py | 139 ++++ docs/dev/explanations/cwl-process-store.md | 114 +++ mkdocs.yml | 1 + pixi.lock | 694 +++++++++++++++++- 11 files changed, 1817 insertions(+), 14 deletions(-) create mode 100644 diracx-logic/src/diracx/logic/transformation/__init__.py create mode 100644 diracx-logic/src/diracx/logic/transformation/processes.py create mode 100644 diracx-logic/src/diracx/logic/transformation/validation.py create mode 100644 diracx-logic/tests/transformation/fixtures/mc-simulation.json create mode 100644 diracx-logic/tests/transformation/test_mc_simulation.py create mode 100644 diracx-logic/tests/transformation/test_processes.py create mode 100644 diracx-logic/tests/transformation/test_validation.py create mode 100644 docs/dev/explanations/cwl-process-store.md diff --git a/diracx-logic/pyproject.toml b/diracx-logic/pyproject.toml index 0ddfb5949..6bb1e3a5a 100644 --- a/diracx-logic/pyproject.toml +++ b/diracx-logic/pyproject.toml @@ -14,11 +14,14 @@ classifiers = [ ] dependencies = [ "cachetools", + # Validates submitted CWL against the CWL v1.2 schema (DX-ADR-007) + "cwl-utils >=0.45", "diraccommon >=9.0.18", "diracx-core", "diracx-db", "joserfc", "pydantic >=2.10", + "schema-salad >=8.10", "uuid-utils", ] dynamic = ["version"] diff --git a/diracx-logic/src/diracx/logic/transformation/__init__.py b/diracx-logic/src/diracx/logic/transformation/__init__.py new file mode 100644 index 000000000..4d21ee850 --- /dev/null +++ b/diracx-logic/src/diracx/logic/transformation/__init__.py @@ -0,0 +1,3 @@ +from __future__ import annotations + +__all__ = [] diff --git a/diracx-logic/src/diracx/logic/transformation/processes.py b/diracx-logic/src/diracx/logic/transformation/processes.py new file mode 100644 index 000000000..91e9075b3 --- /dev/null +++ b/diracx-logic/src/diracx/logic/transformation/processes.py @@ -0,0 +1,93 @@ +"""Storing and materialising content-addressed CWL processes (DX-ADR-004/007). + +Each transformation's process is stored flat: one ``Processes`` row holding +its whole subgraph as a packed ``$graph`` document, keyed by the Merkle root +of its canonical tree (:mod:`diracx.core.cwl.canonical`). Materialising the +payload a parcel runs is then a single read of that row. + +The packed document names every component by its own identity +(``#sha256-``), so per-component rows, references and lineage indexes can +be derived from stored rows later without changing any identity. + +A ``run`` may reference a process by identity only if that process is itself +stored, i.e. it is the root of a stored row. + +Validation is the expensive step (cwl-utils), so it runs only for processes not +already stored: a process in the store was validated when it was stored. +""" + +from __future__ import annotations + +from typing import Any + +from diracx.core.cwl import CanonicalProcess, check_policy, decompose, pack, unpack +from diracx.db.sql.transformation.db import TransformationDB + +from .validation import validate_packed + + +class ProcessNotFoundError(LookupError): + """A process, or a process it references, is not in the store.""" + + +async def store_process(db: TransformationDB, process: dict[str, Any]) -> bytes: + """Validate a process and store it, deduplicated by content. + + Args: + db: Transformation database, inside a transaction. + process: CWL process as the resolved JSON value a client submits + (the CLI's ``diracx.cli.cwl.load_document``); each ``run`` is an + inline body or a reference to a stored process. + + Returns: + The identity of the process. + + Raises: + ValueError: If the process is not CWL v1.2 or not canonicalisable. + diracx.core.cwl.PolicyViolationError: If it uses something DiracX does + not support. + diracx.logic.transformation.validation.InvalidProcessError: If cwl-utils + rejects it. + ProcessNotFoundError: If it references a process that is not stored. + """ + root, nodes = decompose(process) + check_policy(nodes) + if await db.get_processes([root]): + return root + referenced = {child for node in nodes.values() for child in node.children} + for process_id in sorted(referenced - set(nodes)): + nodes.update(await _load_tree(db, process_id)) + packed = pack(root, nodes) + validate_packed(packed) + await db.insert_processes({root: packed}) + return root + + +async def load_process(db: TransformationDB, process_id: bytes) -> dict[str, Any]: + """Return a stored process as a self-contained packed CWL document. + + Args: + db: Transformation database. + process_id: Identity of the process. + + Returns: + The packed document a parcel runs. + + Raises: + ProcessNotFoundError: If the process is not stored. + """ + found = await db.get_processes([process_id]) + if process_id not in found: + raise ProcessNotFoundError(process_id.hex()) + return found[process_id] + + +async def _load_tree( + db: TransformationDB, process_id: bytes +) -> dict[bytes, CanonicalProcess]: + root, nodes = unpack(await load_process(db, process_id)) + if root != process_id: + raise ValueError( + f"Stored process {process_id.hex()} does not match its content" + ) + return nodes diff --git a/diracx-logic/src/diracx/logic/transformation/validation.py b/diracx-logic/src/diracx/logic/transformation/validation.py new file mode 100644 index 000000000..ba8722b66 --- /dev/null +++ b/diracx-logic/src/diracx/logic/transformation/validation.py @@ -0,0 +1,90 @@ +"""Validate a packed CWL process with cwl-utils (DX-ADR-007). + +Loading the document with cwl-utils' parser checks every component of it +against the CWL v1.2 schema. The packed document is what parcels run, so +validating it validates exactly what will execute. + +The parser reads nothing but the packed document: a reference to any other +file or URL is refused rather than fetched on the server. + +Step inputs wired to outputs of an incompatible type are not checked yet: +cwl-utils' static checker misses them, and rejects valid workflows whose +enums are named differently, until a release includes +common-workflow-language/cwl-utils#480. +""" + +from __future__ import annotations + +import json +import re +import tempfile +from pathlib import Path +from typing import Any +from urllib.parse import urlsplit + +from cwl_utils.parser import LoadingOptions, load_document_by_uri +from schema_salad.exceptions import ValidationException +from schema_salad.fetcher import DefaultFetcher + + +class InvalidProcessError(ValueError): + """A process is not valid CWL v1.2.""" + + +def validate_packed(packed: dict[str, Any]) -> None: + """Check a packed CWL document against the CWL v1.2 schema. + + Args: + packed: Document made by ``diracx.core.cwl.pack``. + + Raises: + InvalidProcessError: With cwl-utils' explanation of what is wrong. + """ + # The $graph fragments resolve against the document's own URI, so the + # parser is given a file to load. Resolved, as the parser resolves + # symbolic links (macOS's /var) in the URIs it compares against. + with tempfile.TemporaryDirectory() as directory: + path = Path(directory).resolve() / "process.cwl" + path.write_text(json.dumps(packed)) + options = LoadingOptions(fetcher=_only(path.as_uri())()) + # One component at a time: loaded whole, the parser reports any + # error as the $graph array failing to match, without the reason + for entry in packed["$graph"]: + try: + load_document_by_uri(path.as_uri() + entry["id"], options) + except Exception as e: + message = _tidy(str(e), directory, entry["id"]) + raise InvalidProcessError(message) from None + + +def _only(allowed: str): + """A fetcher for cwl-utils that reads ``allowed`` and nothing else.""" + + class OnlyFetcher(DefaultFetcher): + def __init__(self) -> None: + super().__init__({}, None) + + def fetch_text(self, url: str, content_types: list[str] | None = None) -> str: + if url.split("#", 1)[0] != allowed: + raise ValidationException(f"Refusing to fetch {url}") + return super().fetch_text(url, content_types) + + def check_exists(self, url: str) -> bool: + # The parser also asks about bare vocabulary terms ("Workflow"), + # which are not locations + if urlsplit(url).scheme and url.split("#", 1)[0] != allowed: + return False + return super().check_exists(url) + + return OnlyFetcher + + +def _tidy(message: str, directory: str, entry_id: str) -> str: + """Name the component, not the temporary file, and drop line wrapping.""" + message = re.sub( + r"`process\.cwl(#[^`]*)?`", lambda m: f"`{m.group(1) or entry_id}`", message + ) + message = re.sub( + r"\S*" + re.escape(Path(directory).name) + r"/process\.cwl[:\d]*", "", message + ) + return re.sub(r"\s+", " ", message).strip() diff --git a/diracx-logic/tests/transformation/fixtures/mc-simulation.json b/diracx-logic/tests/transformation/fixtures/mc-simulation.json new file mode 100644 index 000000000..bc479e088 --- /dev/null +++ b/diracx-logic/tests/transformation/fixtures/mc-simulation.json @@ -0,0 +1,494 @@ +{ + "cwlVersion": "v1.2", + "class": "Workflow", + "id": "MC_2026_Bs2JpsiPhi_Sim12_plain", + "label": "MC simulation", + "doc": "Produce a requested number of events, reconstruct them, and merge the reconstructed files into the deliverable.", + "$namespaces": { + "dirac": "https://diracgrid.org/cwl#" + }, + "requirements": { + "SubworkflowFeatureRequirement": {} + }, + "hints": { + "dirac:Workgraph": { + "schema_version": "1.0", + "type": "MCSimulation", + "target": { + "output": "datasets", + "files": 20 + }, + "output_sandbox": [ + "prodConf_*.json", + "summary*.xml", + "prmon*", + "*.log" + ] + } + }, + "inputs": { + "events": { + "doc": "Seeds, issued until the requested number of events has been produced", + "dirac:Feeder": { + "name": "Seeds", + "args": { + "target_events": 600000, + "events_per_seed": 1000, + "batch": 60000, + "max_in_flight": 300000 + } + }, + "type": { + "type": "array", + "items": [ + "File", + "string" + ] + } + } + }, + "steps": { + "MCSimulation": { + "label": "MCSimulation", + "doc": "Gauss, one seed per job", + "hints": { + "dirac:Transformation": { + "packer": { + "name": "PerInput" + }, + "actions": { + "Finalizing": [ + { + "action": "NoInputProcessedTwice" + } + ] + } + } + }, + "run": { + "cwlVersion": "v1.2", + "class": "Workflow", + "doc": "Gauss, one seed per job.", + "inputs": { + "seed": { + "type": { + "type": "array", + "items": [ + "File", + "string" + ] + } + } + }, + "outputs": { + "sim-files": { + "type": "File[]", + "outputSource": "gauss/output-data" + } + }, + "steps": { + "gauss": { + "run": { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "doc": "Run one LHCb application step described by a prodConf.", + "requirements": { + "InlineJavascriptRequirement": {}, + "InitialWorkDirRequirement": { + "listing": [ + { + "entryname": "prodConf.json", + "entry": "$(inputs[\"prod-conf\"])" + } + ] + } + }, + "baseCommand": [ + "lb-prod-run" + ], + "arguments": [ + "prodConf.json" + ], + "inputs": { + "prod-conf": { + "type": "string", + "doc": "The application, its version and options, as JSON" + }, + "input-data": { + "type": [ + "null", + { + "type": "array", + "items": [ + "File", + "string" + ] + } + ], + "inputBinding": { + "prefix": "--input" + } + }, + "output-glob": { + "type": "string" + } + }, + "outputs": { + "output-data": { + "type": "File[]", + "outputBinding": { + "glob": "$(inputs[\"output-glob\"])" + } + } + } + }, + "in": { + "input-data": "seed", + "prod-conf": { + "default": "{\"application\": {\"name\": \"Gauss\", \"version\": \"v57r1\"}, \"event_type\": \"13144011\"}" + }, + "output-glob": { + "default": "*.sim" + } + }, + "out": [ + "output-data" + ] + } + } + }, + "in": { + "seed": "events" + }, + "out": [ + "sim-files" + ] + }, + "MCReconstruction": { + "label": "MCReconstruction", + "doc": "Boole and Moore over about 3 GB of simulated data per job", + "hints": { + "dirac:Transformation": { + "packer": { + "name": "ByGroupSizeRun", + "args": { + "group_size": 3, + "keep_storage_together": true + } + }, + "actions": { + "Finalizing": [ + { + "action": "NoInputProcessedTwice" + } + ] + } + } + }, + "run": { + "cwlVersion": "v1.2", + "class": "Workflow", + "doc": "Boole and Moore over about 3 GB of simulated data per job.", + "requirements": { + "SubworkflowFeatureRequirement": {} + }, + "inputs": { + "input-data": "File[]" + }, + "outputs": { + "reco-files": { + "type": "File[]", + "outputSource": "digi-reco/reco-files" + } + }, + "steps": { + "digi-reco": { + "run": { + "cwlVersion": "v1.2", + "class": "Workflow", + "doc": "Boole then Moore, inside one job.", + "inputs": { + "input-data": "File[]" + }, + "outputs": { + "reco-files": { + "type": "File[]", + "outputSource": "moore/output-data" + } + }, + "steps": { + "boole": { + "run": { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "doc": "Run one LHCb application step described by a prodConf.", + "requirements": { + "InlineJavascriptRequirement": {}, + "InitialWorkDirRequirement": { + "listing": [ + { + "entryname": "prodConf.json", + "entry": "$(inputs[\"prod-conf\"])" + } + ] + } + }, + "baseCommand": [ + "lb-prod-run" + ], + "arguments": [ + "prodConf.json" + ], + "inputs": { + "prod-conf": { + "type": "string", + "doc": "The application, its version and options, as JSON" + }, + "input-data": { + "type": [ + "null", + { + "type": "array", + "items": [ + "File", + "string" + ] + } + ], + "inputBinding": { + "prefix": "--input" + } + }, + "output-glob": { + "type": "string" + } + }, + "outputs": { + "output-data": { + "type": "File[]", + "outputBinding": { + "glob": "$(inputs[\"output-glob\"])" + } + } + } + }, + "in": { + "input-data": "input-data", + "prod-conf": { + "default": "{\"application\": {\"name\": \"Boole\", \"version\": \"v46r1\"}}" + }, + "output-glob": { + "default": "*.digi" + } + }, + "out": [ + "output-data" + ] + }, + "moore": { + "run": { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "doc": "Run one LHCb application step described by a prodConf.", + "requirements": { + "InlineJavascriptRequirement": {}, + "InitialWorkDirRequirement": { + "listing": [ + { + "entryname": "prodConf.json", + "entry": "$(inputs[\"prod-conf\"])" + } + ] + } + }, + "baseCommand": [ + "lb-prod-run" + ], + "arguments": [ + "prodConf.json" + ], + "inputs": { + "prod-conf": { + "type": "string", + "doc": "The application, its version and options, as JSON" + }, + "input-data": { + "type": [ + "null", + { + "type": "array", + "items": [ + "File", + "string" + ] + } + ], + "inputBinding": { + "prefix": "--input" + } + }, + "output-glob": { + "type": "string" + } + }, + "outputs": { + "output-data": { + "type": "File[]", + "outputBinding": { + "glob": "$(inputs[\"output-glob\"])" + } + } + } + }, + "in": { + "input-data": "boole/output-data", + "prod-conf": { + "default": "{\"application\": {\"name\": \"Moore\", \"version\": \"v57r2\"}}" + }, + "output-glob": { + "default": "*.dst" + } + }, + "out": [ + "output-data" + ] + } + } + }, + "in": { + "input-data": "input-data" + }, + "out": [ + "reco-files" + ] + } + } + }, + "in": { + "input-data": "MCSimulation/sim-files" + }, + "out": [ + "reco-files" + ] + }, + "MCMerge": { + "label": "MCMerge", + "doc": "Merge about 10 GB of reconstructed data per job", + "hints": { + "dirac:Transformation": { + "packer": { + "name": "ByGroupSizeRun", + "args": { + "group_size": 4, + "keep_storage_together": true + } + }, + "actions": { + "Finalizing": [ + { + "action": "NoInputProcessedTwice" + } + ] + } + } + }, + "run": { + "cwlVersion": "v1.2", + "class": "Workflow", + "doc": "Merge about 10 GB of reconstructed data per job.", + "inputs": { + "input-data": "File[]" + }, + "outputs": { + "merged": { + "type": "File[]", + "outputSource": "merge/output-data" + } + }, + "steps": { + "merge": { + "run": { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "doc": "Run one LHCb application step described by a prodConf.", + "requirements": { + "InlineJavascriptRequirement": {}, + "InitialWorkDirRequirement": { + "listing": [ + { + "entryname": "prodConf.json", + "entry": "$(inputs[\"prod-conf\"])" + } + ] + } + }, + "baseCommand": [ + "lb-prod-run" + ], + "arguments": [ + "prodConf.json" + ], + "inputs": { + "prod-conf": { + "type": "string", + "doc": "The application, its version and options, as JSON" + }, + "input-data": { + "type": [ + "null", + { + "type": "array", + "items": [ + "File", + "string" + ] + } + ], + "inputBinding": { + "prefix": "--input" + } + }, + "output-glob": { + "type": "string" + } + }, + "outputs": { + "output-data": { + "type": "File[]", + "outputBinding": { + "glob": "$(inputs[\"output-glob\"])" + } + } + } + }, + "in": { + "input-data": "input-data", + "prod-conf": { + "default": "{\"application\": {\"name\": \"LHCb\", \"version\": \"v57r2\"}, \"merge\": true}" + }, + "output-glob": { + "default": "*.dst" + } + }, + "out": [ + "output-data" + ] + } + } + }, + "in": { + "input-data": "MCReconstruction/reco-files" + }, + "out": [ + "merged" + ] + } + }, + "outputs": { + "datasets": { + "label": "Merged MC datasets", + "outputSource": "MCMerge/merged", + "type": "File[]" + } + } +} diff --git a/diracx-logic/tests/transformation/test_mc_simulation.py b/diracx-logic/tests/transformation/test_mc_simulation.py new file mode 100644 index 000000000..d8aba15f2 --- /dev/null +++ b/diracx-logic/tests/transformation/test_mc_simulation.py @@ -0,0 +1,71 @@ +"""The MCSimulation workgraph of #1080, ingested end to end. + +The workgraph has three transformations, each a Workflow around the same +shared tool; boole-moore runs a nested sub-workflow (the "6-process" case). +The fixture is the JSON a client submits: the YAML files it was resolved from, +and the tests of resolving them, are in diracx-cli. +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from sqlalchemy import func, select + +from diracx.core.cwl import decompose, unpack +from diracx.db.sql import TransformationDB +from diracx.db.sql.transformation.schema import Processes +from diracx.logic.transformation.processes import load_process, store_process +from diracx.logic.transformation.validation import validate_packed + +FIXTURE = Path(__file__).parent / "fixtures" / "mc-simulation.json" + + +@pytest.fixture +async def transformation_db(): + db = TransformationDB("sqlite+aiosqlite:///:memory:") + async with db.engine_context(): + async with db.engine.begin() as conn: + await conn.run_sync(db.metadata.create_all) + yield db + + +def transformations() -> dict[str, dict]: + workgraph = json.loads(FIXTURE.read_text()) + return {name: step["run"] for name, step in workgraph["steps"].items()} + + +async def test_each_transformation_is_one_valid_row( + transformation_db: TransformationDB, +): + runs = transformations() + async with transformation_db as db: + ids = {name: await store_process(db, run) for name, run in runs.items()} + rows = await db.conn.scalar(select(func.count()).select_from(Processes)) + payloads = {name: await load_process(db, pid) for name, pid in ids.items()} + assert set(ids) == {"MCSimulation", "MCReconstruction", "MCMerge"} + assert rows == 3 + for name, payload in payloads.items(): + validate_packed(payload) + assert unpack(payload) == decompose(runs[name]) + + +async def test_tree_shape(transformation_db: TransformationDB): + runs = transformations() + nodes = {name: decompose(run)[1] for name, run in runs.items()} + # wrapper + shared tool; wrapper + sub-workflow + shared tool + assert len(nodes["MCSimulation"]) == 2 + assert len(nodes["MCReconstruction"]) == 3 + shared = set.intersection(*(set(n) for n in nodes.values())) + assert len(shared) == 1, "lb-run-app.cwl is one process in all three" + + +async def test_resubmitting_is_a_no_op(transformation_db: TransformationDB): + async with transformation_db as db: + first = [await store_process(db, run) for run in transformations().values()] + again = [await store_process(db, run) for run in transformations().values()] + rows = await db.conn.scalar(select(func.count()).select_from(Processes)) + assert first == again + assert rows == 3 diff --git a/diracx-logic/tests/transformation/test_processes.py b/diracx-logic/tests/transformation/test_processes.py new file mode 100644 index 000000000..99ba37f0d --- /dev/null +++ b/diracx-logic/tests/transformation/test_processes.py @@ -0,0 +1,129 @@ +from __future__ import annotations + +import pytest +from sqlalchemy import func, select, update + +from diracx.core.cwl import decompose, format_reference, unpack +from diracx.db.sql import TransformationDB +from diracx.db.sql.transformation.schema import Processes +from diracx.logic.transformation.processes import ( + ProcessNotFoundError, + load_process, + store_process, +) + + +@pytest.fixture +async def transformation_db(): + db = TransformationDB("sqlite+aiosqlite:///:memory:") + async with db.engine_context(): + async with db.engine.begin() as conn: + await conn.run_sync(db.metadata.create_all) + yield db + + +def tool(command: str) -> dict: + return { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "baseCommand": [command], + "inputs": {"files": "File[]"}, + "outputs": {"out": {"type": "File", "outputBinding": {"glob": "*"}}}, + } + + +def transformation(*runs) -> dict: + return { + "cwlVersion": "v1.2", + "class": "Workflow", + "inputs": {"files": "File[]"}, + "outputs": {"out": {"type": "File", "outputSource": "s0/out"}}, + "steps": { + f"s{i}": {"run": run, "in": {"files": "files"}, "out": ["out"]} + for i, run in enumerate(runs) + }, + } + + +async def count_processes(db: TransformationDB) -> int: + return await db.conn.scalar(select(func.count()).select_from(Processes)) + + +async def test_store_then_load_round_trips(transformation_db: TransformationDB): + process = transformation(tool("gauss"), tool("boole")) + async with transformation_db as db: + process_id = await store_process(db, process) + packed = await load_process(db, process_id) + assert process_id == decompose(process)[0] + assert unpack(packed) == decompose(process) + + +async def test_one_row_per_transformation_deduplicated( + transformation_db: TransformationDB, +): + async with transformation_db as db: + first = await store_process(db, transformation(tool("hadd"))) + again = await store_process(db, transformation(tool("hadd"))) + other = await store_process(db, transformation(tool("hadd"), tool("hadd"))) + assert first == again != other + assert await count_processes(db) == 2 + + +async def test_reference_to_a_stored_process_is_inlined( + transformation_db: TransformationDB, +): + async with transformation_db as db: + library = await store_process(db, tool("hadd")) + by_reference = await store_process( + db, transformation(format_reference(library)) + ) + inline = await load_process(db, by_reference) + assert by_reference == decompose(transformation(tool("hadd")))[0] + assert len(inline["$graph"]) == 2 + + +async def test_reference_to_an_unknown_process_is_refused( + transformation_db: TransformationDB, +): + async with transformation_db as db: + with pytest.raises(ProcessNotFoundError): + await store_process(db, transformation(format_reference(b"x" * 32))) + + +async def test_loading_an_unknown_process_is_refused( + transformation_db: TransformationDB, +): + async with transformation_db as db: + with pytest.raises(ProcessNotFoundError): + await load_process(db, b"x" * 32) + + +async def test_unresolved_directives_are_refused_before_anything_is_read( + transformation_db: TransformationDB, +): + process = tool("cat") + process["requirements"] = { + "InitialWorkDirRequirement": { + "listing": [{"entryname": "f", "entry": {"$include": "/etc/hosts"}}] + } + } + async with transformation_db as db: + with pytest.raises(ValueError, match=r"Unresolved \$include"): + await store_process(db, process) + assert await count_processes(db) == 0 + + +async def test_a_stored_row_that_does_not_match_its_identity_is_refused( + transformation_db: TransformationDB, +): + async with transformation_db as db: + stored = await store_process(db, tool("hadd")) + other = await store_process(db, tool("cat")) + swapped = (await db.get_processes([other]))[other] + await db.conn.execute( + update(Processes) + .where(Processes.process_id == stored) + .values({Processes.process: swapped}) + ) + with pytest.raises(ValueError, match="does not match its content"): + await store_process(db, transformation(format_reference(stored))) diff --git a/diracx-logic/tests/transformation/test_validation.py b/diracx-logic/tests/transformation/test_validation.py new file mode 100644 index 000000000..a01a98748 --- /dev/null +++ b/diracx-logic/tests/transformation/test_validation.py @@ -0,0 +1,139 @@ +from __future__ import annotations + +import subprocess + +import pytest +from schema_salad.fetcher import DefaultFetcher + +from diracx.core.cwl import decompose, pack +from diracx.logic.transformation.validation import ( + InvalidProcessError, + _only, + validate_packed, +) + + +def workflow(source_type: str, output: dict | None = None) -> dict: + tool = { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "baseCommand": ["hadd"], + "inputs": {"files": {"type": "File[]", "inputBinding": {"position": 1}}}, + "outputs": output or {"out": {"type": "File", "outputBinding": {"glob": "*"}}}, + } + return { + "cwlVersion": "v1.2", + "class": "Workflow", + "inputs": {"files": source_type}, + "outputs": {"out": {"type": "File", "outputSource": "s0/out"}}, + "steps": {"s0": {"run": tool, "in": {"files": "files"}, "out": ["out"]}}, + } + + +def packed(process: dict) -> dict: + return pack(*decompose(process)) + + +def test_valid_process_passes(): + validate_packed(packed(workflow("File[]"))) + + +def test_schema_errors_are_reported_without_the_temporary_path(): + with pytest.raises(InvalidProcessError) as e: + validate_packed( + packed( + workflow("File[]", output={"out": {"type": "File", "outputBinding": 3}}) + ) + ) + assert "process.cwl" not in str(e.value) + + +def test_unknown_fields_are_refused(): + process = workflow("File[]") + process["steps"]["s0"]["run"]["nonsense"] = 1 + with pytest.raises(InvalidProcessError, match="nonsense"): + validate_packed(packed(process)) + + +def test_validation_reads_nothing_but_the_document(tmp_path, monkeypatch): + secret = tmp_path / "secret" + secret.write_text("do not read") + fetched = [] + original = DefaultFetcher.fetch_text + + def spy(self, url, content_types=None): + fetched.append(url) + return original(self, url, content_types) + + monkeypatch.setattr(DefaultFetcher, "fetch_text", spy) + document = packed(workflow("File[]")) + document["$graph"][1]["requirements"] = [ + { + "class": "InitialWorkDirRequirement", + "listing": [{"entryname": "f", "entry": {"$include": secret.as_uri()}}], + } + ] + with pytest.raises(InvalidProcessError): + validate_packed(document) + assert fetched and all(url.endswith("/process.cwl") for url in fetched) + + +def test_expanded_formats_still_validate(): + process = workflow("File[]") + process["$namespaces"] = {"edam": "http://edamontology.org/"} + process["inputs"]["files"] = {"type": "File[]", "format": "edam:format_2572"} + document = packed(process) + assert "http://edamontology.org/format_2572" in str(document) + validate_packed(document) + + +def test_named_types_survive_packing(): + def seed(value_type: str) -> dict: + return { + "SchemaDefRequirement": { + "types": [ + {"name": "Seed", "type": "record", "fields": {"value": value_type}} + ] + } + } + + process = workflow("File[]") + process["requirements"] = seed("string") + process["inputs"]["seed"] = "Seed" + tool = process["steps"]["s0"]["run"] + tool["requirements"] = seed("int") + tool["inputs"]["seed"] = "Seed?" + validate_packed(packed(process)) + + +def test_the_fetcher_sees_no_other_file(tmp_path): + allowed, other = tmp_path / "process.cwl", tmp_path / "other.cwl" + allowed.write_text("{}") + other.write_text("{}") + fetcher = _only(allowed.as_uri())() + assert fetcher.check_exists(allowed.as_uri() + "#main") + assert not fetcher.check_exists(other.as_uri()) + + +def test_validation_starts_no_process(monkeypatch): + def refuse(*args, **kwargs): + raise AssertionError(f"started a process: {args[0]!r}") + + monkeypatch.setattr(subprocess, "Popen", refuse) + process = workflow("File[]") + tool = process["steps"]["s0"]["run"] + tool["requirements"] = {"InlineJavascriptRequirement": {}} + tool["arguments"] = ["$(inputs.files.length + 1)"] + validate_packed(packed(process)) + + +def test_a_docker_image_validates_without_being_pulled(monkeypatch): + def refuse(*args, **kwargs): + raise AssertionError(f"started a process: {args[0]!r}") + + monkeypatch.setattr(subprocess, "Popen", refuse) + process = workflow("File[]") + process["steps"]["s0"]["run"]["requirements"] = { + "DockerRequirement": {"dockerPull": "harbor.cta-observatory.org/ctapipe:0.24"} + } + validate_packed(packed(process)) diff --git a/docs/dev/explanations/cwl-process-store.md b/docs/dev/explanations/cwl-process-store.md new file mode 100644 index 000000000..4ffda4a68 --- /dev/null +++ b/docs/dev/explanations/cwl-process-store.md @@ -0,0 +1,114 @@ +# CWL process store + +Everything DiracX executes is described in CWL ([DX-ADR-007](../../adr/DX-ADR-007_cwl.md)). +When a workgraph is submitted, the process each transformation runs is stored +in the `Processes` table of the `TransformationDB` +([DX-ADR-004](../../adr/DX-ADR-004_schema.md)), keyed by a hash of its content. +This page explains how that identity is computed, how a process gets into the +store, and what a parcel reads back. + +## One row per transformation + +A transformation's process is usually a small `Workflow` around one or more +`CommandLineTool`s, possibly with nested sub-workflows. It is stored **flat**: +one `Processes` row holds the whole subgraph as a packed CWL document +(`$graph`), so materialising the payload a parcel runs is a single +primary-key read, and the row is exactly the document a stock CWL runner +executes. + +The alternative described in the ADR, one row per CWL process with +`ProcessReferences` edges, was measured on a year of LHCb submissions and +gave no saving: almost all variation between jobs is inside the leaf tools, +so the tree deduplicates little, while costing more rows and a recursive query +at dispatch. The benchmark is in `benchmarks/process_store/`. + +## Identity + +A process is identified by the SHA-256 of its canonical form, +`diracx.core.cwl.canonical`, which is defined over the parsed document rather +than over any CWL library's output, so that it is deterministic, stable across +library upgrades and reproducible by any tool. In short (the module docstring +has the full rules, `CANONICAL_VERSION` numbers them): + +- process `id`s, `$namespaces`, `dirac:` fields and hints, and `doc` and + `label` where they are metadata are dropped: the identity is what runs, + not what it is called, where it was loaded from, or how DiracX schedules + it. Prefixes are first expanded to full URIs, so the identity covers what + a prefix means, and names a user chose (an environment variable, a record + field) are kept even when they are called `doc` or `label`; +- lists keyed by `id` or `class` are written as maps, and fully scoped + identifiers are shortened against their scope, so formatting and absolute + `file://` URIs do not matter; +- named types are written by short name, and a process may only use the + named types it defines itself, so its identity covers their definitions; +- each nested `run` body is replaced by its own identity, so a workflow's + identity covers its children's (a Merkle tree); +- the result is JSON with sorted keys and no whitespace. + +The identity of a transformation is the root of that tree. The packed +document names every component by its own identity (`#sha256-`), so the +tree can be recovered from a stored row (`unpack`), and a component index or +per-component rows can be added later without changing any identity. + +The hash is over the value, not the stored bytes: MySQL's `JSON` type +re-sorts keys and reformats numbers, so a row read back is re-canonicalised to +check it, which `diracx-db/tests/transformation/test_round_trip.py` verifies +on MySQL and MariaDB in CI. + +## From files to a stored process + +```mermaid +flowchart LR + files[".cwl files (YAML)"] -->|"resolved by the CLI"| doc["one JSON value"] + doc -->|decompose| tree["canonical tree"] + tree -->|check_policy| tree + tree -->|"already stored?"| done["identity"] + tree -->|pack| packed["packed document"] + packed -->|"validate_packed (cwl-utils)"| store["Processes row"] + store --> done +``` + +1. **Resolve** (in the CLI): the YAML files are read and every step's `run` + path, `$import`, `$include` and `#fragment` is inlined, so that one JSON + value is submitted. References to stored processes (`proc:sha256-`) + are kept. YAML stays in the CLI: services only receive JSON. They refuse + any `$import`, `$include` or other directive left in it, and validation + never reads anything but the packed document. +2. **Canonicalise** (`decompose`): compute the tree and its identities. + Only CWL v1.2 is accepted; older documents are refused with a request to + run `cwl-upgrader`, since upgrading on the server would change what the + user tested. +3. **Policy** (`check_policy`): requirements outside an allow-list that every + backend can honour are refused, `dirac:` requirements included. So are + abstract `Operation`s, which no runner can execute, and processes larger + than 256 kB, whose content belongs in a sandbox or `File` input. Hints are + not restricted. `DockerRequirement` is accepted, to run with Apptainer, + when it names an image to pull (`dockerPull`, `dockerImageId`); its + `dockerFile`, `dockerLoad` and `dockerImport` fields are refused, even in + a hint, since they build or fetch an image on the worker node. +4. **Hash first**: a process already in the store was validated when it was + stored, so resubmitting it costs a lookup. +5. **Validate** (`diracx.logic.transformation.validation.validate_packed`): + cwl-utils' parser loads every component of the packed document, checking + it against the CWL v1.2 schema. Validating the packed document validates + exactly what parcels will run. How step inputs are wired is not checked + yet: cwl-utils' static checker will do that once a release includes + common-workflow-language/cwl-utils#480. +6. **Store**: `INSERT IGNORE`, so concurrent submissions of the same process + are safe. + +A `run` may reference a stored process by identity, provided it is the root +of a stored row; its body is inlined into the new row. + +## Not yet covered + +- per-component rows, lineage ("which transformations contain this tool") and + references to arbitrary components; +- `ProcessRegistry` names and versions, garbage collection, and VO visibility + of stored bodies; +- pinning mutable references inside bodies, such as container tags: a + `dockerPull` tag is accepted as written, so the same identity can name + different software if the tag moves; +- recording `CANONICAL_VERSION` per row; +- checking how step inputs are wired, until cwl-utils' static checker is + fixed. diff --git a/mkdocs.yml b/mkdocs.yml index 971d3a15e..516fa1506 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -247,6 +247,7 @@ nav: - 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