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"integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", - "dev": true + "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" }, "node_modules/yauzl": { "version": "2.10.0", @@ -1649,6 +3018,18 @@ "dependencies": { "buffer-crc32": "~0.2.3" } + }, + "node_modules/yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } } } } diff --git a/client/vscode/package.json b/client/vscode/package.json index b5c45b5..87e3f4c 100644 --- a/client/vscode/package.json +++ b/client/vscode/package.json @@ -65,16 +65,14 @@ "vscode:prepublish": "npm run compile" }, "devDependencies": { - "@types/node": "^8.10.66", - "@types/vscode": "^1.56.0", - "tslint": "^5.20.1", - "tslint-microsoft-contrib": "^6.2.0", - "tsutils": "^3.21.0", - "typescript": "^3.9.9", - "vsce": "^1.64.0" + "@types/node": "^20.12.7", + "@types/vscode": "^1.88.0", + "@vscode/vsce": "^2.26.0", + "eslint": "^9.1.1", + "typescript": "^5.4.5" }, "dependencies": { - "vscode-languageclient": "^6.1.4" + "vscode-languageclient": "^9.0.1" }, "extensionDependencies": [ "broadinstitute.wdl" diff --git a/client/vscode/src/extension.ts b/client/vscode/src/extension.ts index 6da8fab..8ee6e6a 100644 --- a/client/vscode/src/extension.ts +++ b/client/vscode/src/extension.ts @@ -23,7 +23,7 @@ import * as net from "net"; import * as path from "path"; import { promisify } from "util"; import { ExtensionContext, workspace } from "vscode"; -import { LanguageClient, LanguageClientOptions, ServerOptions } from "vscode-languageclient"; +import { LanguageClient, LanguageClientOptions, ServerOptions } from "vscode-languageclient/node"; const version: string = require("../package.json").version; @@ -106,7 +106,7 @@ export async function activate(context: ExtensionContext) { } client.registerProposedFeatures(); - context.subscriptions.push(client.start()); + await client.start(); } export function deactivate() { diff --git a/client/vscode/tslint.json b/client/vscode/tslint.json deleted file mode 100644 index 8a11659..0000000 --- a/client/vscode/tslint.json +++ /dev/null @@ -1,50 +0,0 @@ -{ - "extends": "tslint:recommended", - "rulesDirectory": [ - "./node_modules/tslint-microsoft-contrib" - ], - "rules": { - "max-line-length": { - "options": [ - 100 - ] - }, - "no-console": [ - false, - "error", - "log", - "warn" - ], - "no-unused-expression": true, - "typedef": [ - false, - "arrow-call-signature", - "arrow-parameter", - "call-signature", - "member-variable-declaration", - "parameter", - "property-declaration", - "variable-declaration" - ], - "class-name": true, - "no-unexternalized-strings": [ - false, - { - "messageIndex": 1, - "signatures": [ - "localize", - "nls.localize" - ], - "keyIndex": 0 - } - ], - "semicolon": [ - true, - "always" - ], - "curly": true, - "no-duplicate-variable": true, - "no-var-requires": false, - "triple-equals": true - } -} diff --git a/server/setup.py b/server/setup.py index c02eb76..c690cb0 100644 --- a/server/setup.py +++ b/server/setup.py @@ -21,10 +21,9 @@ 'License :: OSI Approved :: BSD License', 'Operating System :: OS Independent', 'Programming Language :: Python :: 3 :: Only', - 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', ], - python_requires='>=3.7.0', + python_requires='>=3.8', packages=find_packages( exclude=[ 'tests', @@ -38,9 +37,9 @@ 'relative_to': __file__, }, install_requires=[ - 'cromwell-tools == 2.3.0', - 'miniwdl >= 1.1.5', - 'pygls == 0.8.1', + 'cromwell-tools >= 2.4.1', + 'miniwdl >= 1.11.1', + 'pygls >= 1.3.1', ], entry_points={ 'console_scripts': ['wdl-lsp = wdl_lsp.__main__:main'], diff --git a/server/wdl_lsp/server.py b/server/wdl_lsp/server.py index be62ffc..42ac317 100644 --- a/server/wdl_lsp/server.py +++ b/server/wdl_lsp/server.py @@ -2,76 +2,64 @@ ### https://github.com/openlawlibrary/pygls/blob/master/examples/json-extension/server/server.py import asyncio +import sys from bisect import bisect - -from cromwell_tools import api as cromwell_api -from cromwell_tools.cromwell_auth import CromwellAuth -from cromwell_tools.utilities import download - from functools import wraps - -from pygls.features import ( - CODE_ACTION, - DEFINITION, - REFERENCES, - TEXT_DOCUMENT_DID_OPEN, - TEXT_DOCUMENT_DID_CHANGE, - TEXT_DOCUMENT_DID_SAVE, - TEXT_DOCUMENT_WILL_SAVE, - WORKSPACE_DID_CHANGE_CONFIGURATION, - WORKSPACE_DID_CHANGE_WATCHED_FILES, -) -from pygls.server import LanguageServer -from pygls.types import ( - CodeActionParams, - ConfigurationItem, - ConfigurationParams, - Diagnostic, - DiagnosticSeverity, - DidChangeConfigurationParams, - DidOpenTextDocumentParams, - DidChangeTextDocumentParams, - DidSaveTextDocumentParams, - WillSaveTextDocumentParams, - TextDocumentPositionParams, - DidChangeWatchedFiles, - FileChangeType, - MessageType, - Location, - Position, - Range, -) - -from os import environ, name as platform, pathsep +from importlib.metadata import version +from os import environ +from os import name as platform +from os import pathsep from pathlib import Path -import re, sys -from requests import HTTPError from threading import Timer from time import sleep -from typing import Callable, Dict, Iterable, List, Set, Tuple, Union +from typing import (Callable, Dict, Iterable, List, Mapping, Optional, Set, + Tuple, TypedDict, Union) from urllib.parse import urlparse import WDL -from WDL import SourceNode, SourcePosition, Lint +from cromwell_tools import api as cromwell_api +from cromwell_tools.cromwell_auth import CromwellAuth +from cromwell_tools.utilities import download +from lsprotocol.types import (TEXT_DOCUMENT_CODE_ACTION, + TEXT_DOCUMENT_DEFINITION, + TEXT_DOCUMENT_DID_CHANGE, TEXT_DOCUMENT_DID_OPEN, + TEXT_DOCUMENT_DID_SAVE, TEXT_DOCUMENT_REFERENCES, + TEXT_DOCUMENT_WILL_SAVE, + WORKSPACE_DID_CHANGE_CONFIGURATION, + WORKSPACE_DID_CHANGE_WATCHED_FILES, + CodeActionParams, ConfigurationItem, + ConfigurationParams, Diagnostic, + DiagnosticSeverity, DidChangeConfigurationParams, + DidChangeTextDocumentParams, + DidChangeWatchedFilesParams, + DidOpenTextDocumentParams, + DidSaveTextDocumentParams, FileChangeType, + Location, MessageType, Position, Range, + TextDocumentPositionParams, + WillSaveTextDocumentParams) +from pygls.server import LanguageServer +from requests import HTTPError +from WDL import Lint, SourceNode, SourcePosition + +PARSE_DELAY_SEC = 0.5 # delay parsing of WDL until no more keystrokes are sent -PARSE_DELAY_SEC = 0.5 # delay parsing of WDL until no more keystrokes are sent class Server(LanguageServer): - SERVER_NAME = 'wdl' - CONFIG_SECTION = SERVER_NAME + NAME = 'wdl' + CONFIG_SECTION = NAME - CMD_RUN_WDL = SERVER_NAME + '.run' + CMD_RUN_WDL = NAME + '.run' def __init__(self): - super().__init__() + super().__init__(Server.NAME, version('wdl-lsp')) self.wdl_paths: Dict[str, Set[str]] = dict() self.wdl_types: Dict[str, Dict[str, SourcePosition]] = dict() - self.wdl_defs: Dict[str, Dict[SourcePosition, SourcePosition]] = dict() + self.wdl_defs: Dict[str, Mapping[SourcePosition, SourcePosition]] = dict() self.wdl_refs: Dict[str, Dict[SourcePosition, List[SourcePosition]]] = dict() self.wdl_symbols: Dict[str, List[SourcePosition]] = dict() self.aborting_workflows: Set[str] = set() - def catch_error(self, log = False): + def catch_error(self, log=False): def decorator(func: Callable): @wraps(func) def wrapper(*args, **kwargs): @@ -82,36 +70,45 @@ def wrapper(*args, **kwargs): self.show_message_log(str(e), MessageType.Error) else: self.show_message(str(e), MessageType.Error) + return wrapper + return decorator + server = Server() + def _get_client_config(ls: Server): - config = ls.get_configuration(ConfigurationParams([ - ConfigurationItem(section=Server.CONFIG_SECTION) - ])).result() + config = ls.get_configuration( + ConfigurationParams([ConfigurationItem(section=Server.CONFIG_SECTION)]) + ).result() return config[0] + # https://gist.github.com/walkermatt/2871026 def debounce(delay_sec: float, id_arg: Union[int, str]): - """ Decorator that will postpone a functions - execution until after wait seconds - have elapsed since the last time it was invoked. """ + """Decorator that will postpone a functions + execution until after wait seconds + have elapsed since the last time it was invoked.""" + def decorator(func: Callable): @wraps(func) def debounced(*args, **kwargs): if not hasattr(debounced, 'timers'): - debounced.timers: Dict[str, Timer] = dict() + debounced.timers = dict() id = args[id_arg] if isinstance(id_arg, int) else kwargs[id_arg] if id in debounced.timers: debounced.timers[id].cancel() timer = Timer(delay_sec, lambda: func(*args, **kwargs)) - debounced.timers[id] = timer + getattr(debounced, 'timers')[id] = timer timer.start() + return debounced + return decorator + @debounce(PARSE_DELAY_SEC, 1) def parse_wdl(ls: Server, uri: str): ls.show_message_log('Validating ' + uri, MessageType.Info) @@ -119,19 +116,20 @@ def parse_wdl(ls: Server, uri: str): ls.publish_diagnostics(uri, diagnostics) ls.show_message_log( '{} {}'.format('Valid' if wdl else 'Invalid', uri), - MessageType.Info if wdl else MessageType.Warning + MessageType.Info if wdl else MessageType.Warning, ) + def _parse_wdl(ls: Server, uri: str): try: paths = _get_wdl_paths(ls, uri) - doc = asyncio.run( - WDL.load_async(uri, path=paths, read_source=_read_source(ls)) - ) + doc = asyncio.run(WDL.load_async(uri, path=paths, read_source=_read_source(ls))) types = _get_types(doc.children, dict()) ls.wdl_types[uri] = types - ls.wdl_defs[uri], ls.wdl_refs[uri] = _get_links(doc.children, types, dict(), dict()) + ls.wdl_defs[uri], ls.wdl_refs[uri] = _get_links( + doc.children, types, dict(), dict() + ) ls.wdl_symbols[uri] = sorted(_get_symbols(doc.children, [])) return list(_lint_wdl(ls, doc)), doc @@ -146,6 +144,7 @@ def _parse_wdl(ls: Server, uri: str): ls.show_message_log(str(e), MessageType.Error) return [], None + def _read_source(ls: Server): async def read_source(uri: str, path, importer): uri = await WDL.resolve_file_import(uri, path, importer) @@ -153,14 +152,17 @@ async def read_source(uri: str, path, importer): uri = 'file://' + uri source = ls.workspace.get_document(uri).source return WDL.ReadSourceResult(source_text=source, abspath=uri) + return read_source + def _get_symbols(nodes: Iterable[SourceNode], symbols: List[SourcePosition]): for node in nodes: symbols.append(node.pos) _get_symbols(node.children, symbols) return symbols + # find SourcePosition as the minimum bounding box for cursor Position def _find_symbol(ls: Server, uri: str, p: Position): if uri not in ls.wdl_symbols: @@ -168,7 +170,7 @@ def _find_symbol(ls: Server, uri: str, p: Position): symbols = ls.wdl_symbols[uri] best_score = (sys.maxsize, sys.maxsize) - best_sym: SourcePosition = None + best_sym: Optional[SourcePosition] = None line = p.line + 1 col = p.character + 1 @@ -188,13 +190,15 @@ def _find_symbol(ls: Server, uri: str, p: Position): i += 1 return best_sym + def _get_types(nodes: Iterable[SourceNode], types: Dict[str, SourcePosition]): for node in nodes: - if isinstance(node, WDL.StructTypeDef): + if isinstance(node, WDL.Tree.StructTypeDef): types[node.type_id] = node.pos _get_types(node.children, types) return types + def _get_links( nodes: Iterable[SourceNode], types: Dict[str, SourcePosition], @@ -202,26 +206,35 @@ def _get_links( refs: Dict[SourcePosition, List[SourcePosition]], ): for node in nodes: - source: SourcePosition = None - if isinstance(node, WDL.Call): + source: Optional[SourcePosition] = None + if isinstance(node, WDL.Tree.Call) and node.callee is not None: source = node.callee.pos - elif isinstance(node, WDL.Decl) and isinstance(node.type, WDL.Type.StructInstance): + elif isinstance(node, WDL.Tree.Decl) and isinstance( + node.type, WDL.Type.StructInstance + ): source = types[node.type.type_id] elif isinstance(node, WDL.Expr.Ident): ref = node.referee if isinstance(ref, WDL.Tree.Gather): source = ref.final_referee.pos else: - source = ref.pos + source = getattr(ref, 'pos', None) if source is not None: defs[node.pos] = source refs.setdefault(source, []).append(node.pos) _get_links(node.children, types, defs, refs) return defs, refs + SourceLinks = Union[SourcePosition, List[SourcePosition]] -def _find_links(ls: Server, uri: str, pos: Position, links: Dict[str, Dict[SourcePosition, SourceLinks]]): + +def _find_links( + ls: Server, + uri: str, + pos: Position, + links: Mapping[str, Mapping[SourcePosition, SourceLinks]], +): symbol = _find_symbol(ls, uri, pos) if (symbol is None) or (uri not in links): return @@ -229,23 +242,27 @@ def _find_links(ls: Server, uri: str, pos: Position, links: Dict[str, Dict[Sourc if symbol in symbols: return symbols[symbol] + def _find_def(ls: Server, uri: str, pos: Position): link = _find_links(ls, uri, pos, ls.wdl_defs) - if link is not None: + if isinstance(link, SourcePosition): return Location(link.abspath, _get_range(link)) + def _find_refs(ls: Server, uri: str, pos: Position): links = _find_links(ls, uri, pos, ls.wdl_refs) - if links is not None: + if isinstance(links, list): return [Location(link.abspath, _get_range(link)) for link in links] -def _lint_wdl(ls: Server, doc: WDL.Document): + +def _lint_wdl(ls: Server, doc: WDL.Tree.Document): _check_linter_path() warnings = Lint.collect(Lint.lint(doc, descend_imports=False)) _check_linter_available(ls) for pos, _, msg, _ in warnings: yield _diagnostic(msg, pos, DiagnosticSeverity.Warning) + def _check_linter_path(): if getattr(_check_linter_path, 'skip', False): return @@ -257,19 +274,24 @@ def _check_linter_path(): environ['PATH'] = pathsep.join([LOCAL_BIN] + PATH) _check_linter_path.skip = True + def _check_linter_available(ls: Server): if getattr(_check_linter_available, 'skip', False): - return + return if not Lint._shellcheck_available: - ls.show_message(''' + ls.show_message( + """ WDL task command linter is not available on the system PATH. Please install ShellCheck and/or add it to the PATH: https://github.com/koalaman/shellcheck#installing - ''', MessageType.Warning) + """, + MessageType.Warning, + ) _check_linter_available.skip = True -def _get_wdl_paths(ls: Server, wdl_uri: str, reuse_paths = True) -> List[str]: + +def _get_wdl_paths(ls: Server, wdl_uri: str, reuse_paths=True) -> List[str]: ws = ls.workspace if ws.folders: ws_uris = [f for f in ws.folders if wdl_uri.startswith(f)] @@ -290,15 +312,22 @@ def _get_wdl_paths(ls: Server, wdl_uri: str, reuse_paths = True) -> List[str]: wdl_paths.update(ws_paths) return list(wdl_paths) -WDLError = (WDL.Error.ImportError, WDL.Error.SyntaxError, WDL.Error.ValidationError) -def _diagnostic(msg: str, pos: SourcePosition = None, severity = DiagnosticSeverity.Error): +WDLError = Union[ + WDL.Error.ImportError, WDL.Error.SyntaxError, WDL.Error.ValidationError +] + + +def _diagnostic( + msg: str, pos: Optional[SourcePosition] = None, severity=DiagnosticSeverity.Error +): return Diagnostic(_get_range(pos), msg, severity=severity) -def _get_range(p: SourcePosition = None): + +def _get_range(p: Optional[SourcePosition] = None): if p is None: return Range( - Position(), + Position(0, sys.maxsize), Position(0, sys.maxsize), ) else: @@ -307,22 +336,26 @@ def _get_range(p: SourcePosition = None): Position(p.end_line - 1, p.end_column - 1), ) + def _diagnostic_err(e: WDLError): cause = ': {}'.format(e.__cause__) if e.__cause__ else '' msg = str(e) + cause return _diagnostic(msg, e.pos) + @server.thread() @server.feature(TEXT_DOCUMENT_DID_OPEN) @server.catch_error() def did_open(ls: Server, params: DidOpenTextDocumentParams): - parse_wdl(ls, params.textDocument.uri) + parse_wdl(ls, params.text_document.uri) + @server.thread() @server.feature(TEXT_DOCUMENT_DID_CHANGE) @server.catch_error() def did_change(ls: Server, params: DidChangeTextDocumentParams): - parse_wdl(ls, params.textDocument.uri) + parse_wdl(ls, params.text_document.uri) + @server.thread() @server.feature(TEXT_DOCUMENT_DID_SAVE) @@ -330,78 +363,97 @@ def did_change(ls: Server, params: DidChangeTextDocumentParams): def did_save(ls: Server, params: DidSaveTextDocumentParams): pass + @server.thread() @server.feature(TEXT_DOCUMENT_WILL_SAVE) @server.catch_error() def will_save(ls: Server, params: WillSaveTextDocumentParams): pass + @server.feature(WORKSPACE_DID_CHANGE_CONFIGURATION) def did_change_configuration(ls: Server, params: DidChangeConfigurationParams): pass + @server.thread() @server.feature(WORKSPACE_DID_CHANGE_WATCHED_FILES) @server.catch_error() -def did_change_watched_files(ls: Server, params: DidChangeWatchedFiles): +def did_change_watched_files(ls: Server, params: DidChangeWatchedFilesParams): for change in params.changes: - if change.type in [FileChangeType.Created, FileChangeType.Deleted] and \ - change.uri.endswith('.wdl'): + if change.type in [ + FileChangeType.Created, + FileChangeType.Deleted, + ] and change.uri.endswith('.wdl'): _get_wdl_paths(ls, change.uri, reuse_paths=False) + @server.thread() -@server.feature(DEFINITION) +@server.feature(TEXT_DOCUMENT_DEFINITION) @server.catch_error() -def goto_definition(ls: Server, params: TextDocumentPositionParams): - return _find_def(ls, params.textDocument.uri, params.position) +def goto_TEXT_DOCUMENT_DEFINITION(ls: Server, params: TextDocumentPositionParams): + return _find_def(ls, params.text_document.uri, params.position) + @server.thread() -@server.feature(REFERENCES) +@server.feature(TEXT_DOCUMENT_REFERENCES) @server.catch_error() -def find_references(ls: Server, params: TextDocumentPositionParams): - return _find_refs(ls, params.textDocument.uri, params.position) +def find_TEXT_DOCUMENT_REFERENCES(ls: Server, params: TextDocumentPositionParams): + return _find_refs(ls, params.text_document.uri, params.position) + + +class RunWDLParams(TypedDict): + wdl_uri: str -class RunWDLParams: - def __init__(self, wdl_uri: str): - self.wdl_uri = wdl_uri -@server.feature(CODE_ACTION) +@server.feature(TEXT_DOCUMENT_CODE_ACTION) @server.catch_error() def code_action(ls: Server, params: CodeActionParams): - return [{ - 'title': 'Run WDL', - 'kind': Server.CMD_RUN_WDL, - 'command': { - 'command': Server.CMD_RUN_WDL, - 'arguments': [RunWDLParams(params.textDocument.uri)], - }, - }] + return [ + { + 'title': 'Run WDL', + 'kind': Server.CMD_RUN_WDL, + 'command': { + 'command': Server.CMD_RUN_WDL, + 'arguments': [RunWDLParams(wdl_uri=params.text_document.uri)], + }, + } + ] + @server.thread() @server.command(Server.CMD_RUN_WDL) @server.catch_error() def run_wdl(ls: Server, params: Tuple[RunWDLParams]): - wdl_uri = params[0].wdl_uri + wdl_uri = params[0]['wdl_uri'] wdl_path = urlparse(wdl_uri).path _, wdl = _parse_wdl(ls, wdl_uri) if not wdl: - return ls.show_message('Unable to submit: WDL contains error(s)', MessageType.Error) + return ls.show_message( + 'Unable to submit: WDL contains error(s)', MessageType.Error + ) - config = _get_client_config(ls) - auth = CromwellAuth.from_no_authentication(config.cromwell.url) - workflow = cromwell_api.submit( - auth, wdl_path, raise_for_status=True, + cromwell = _get_client_config(ls)['cromwell'] + auth = CromwellAuth.from_no_authentication(cromwell['url']) # type: ignore + workflow = cromwell_api.submit( # type: ignore + auth, + wdl_path, + raise_for_status=True, ).json() id = workflow['id'] title = 'Workflow {} for {}'.format(id, wdl_path) - _progress(ls, 'start', { - 'id': id, - 'title': title, - 'cancellable': True, - 'message': workflow['status'], - }) + _progress( + ls, + 'start', + { + 'id': id, + 'title': title, + 'cancellable': True, + 'message': workflow['status'], + }, + ) status: str = '' while True: @@ -414,63 +466,78 @@ def run_wdl(ls: Server, params: Tuple[RunWDLParams]): elif status == 'Failed': message_type = MessageType.Error else: - _progress(ls, 'report', { - 'id': id, - 'message': status, - }) + _progress( + ls, + 'report', + { + 'id': id, + 'message': status, + }, + ) continue - _progress(ls, 'done', { - 'id': id, - }) + _progress( + ls, + 'done', + { + 'id': id, + }, + ) message = '{}: {}'.format(title, status) ls.show_message(message, message_type) diagnostics = _parse_failures(wdl, id, auth) return ls.publish_diagnostics(wdl_uri, diagnostics) - sleep(config.cromwell.pollSec) + sleep(cromwell['pollSec']) if id in ls.aborting_workflows: - workflow = cromwell_api.abort( - id, auth, raise_for_status=True, + workflow = cromwell_api.abort( # type: ignore + id, + auth, + raise_for_status=True, ).json() ls.aborting_workflows.remove(id) continue try: - workflow = cromwell_api.status( - id, auth, raise_for_status=True, + workflow = cromwell_api.status( # type: ignore + id, + auth, + raise_for_status=True, ).json() except HTTPError as e: ls.show_message_log(str(e), MessageType.Error) + def _progress(ls: Server, action: str, params): ls.send_notification('window/progress/' + action, params) + @server.feature('window/progress/cancel') def abort_workflow(ls: Server, params): ls.aborting_workflows.add(params.id) -def _parse_failures(wdl: WDL.Document, id: str, auth: CromwellAuth): - workflow = cromwell_api.metadata( - id, auth, + +def _parse_failures(wdl: WDL.Tree.Document, id: str, auth: CromwellAuth): + workflow = cromwell_api.metadata( # type: ignore + id, + auth, includeKey=['status', 'executionStatus', 'failures', 'stderr'], expandSubWorkflows=True, raise_for_status=True, ).json() - if workflow['status'] != 'Failed': + if not wdl.workflow or workflow['status'] != 'Failed': return calls = workflow['calls'] if calls: diagnostics: List[Diagnostic] = [] - elements = wdl.workflow.elements for call, attempts in calls.items(): for attempt in attempts: if attempt['executionStatus'] == 'Failed': - pos = _find_call(wdl.workflow.elements, wdl.workflow.name, call) + pos = _find_call(wdl.workflow.children, wdl.workflow.name, call) failures = _collect_failures(attempt['failures'], []) stderr = _download(attempt['stderr']) @@ -485,31 +552,33 @@ def _parse_failures(wdl: WDL.Document, id: str, auth: CromwellAuth): msg = '\n\n'.join(failures) return [_diagnostic(msg)] -class CausedBy: - def __init__(self, causedBy: List['CausedBy'], message: str): - self.causedBy = causedBy - self.message = message -def _collect_failures(causedBy: List[CausedBy], failures: List[str]): +def _collect_failures(causedBy: List[dict], failures: List[str]): for failure in causedBy: if failure['causedBy']: _collect_failures(failure['causedBy'], failures) failures.append(failure['message']) return failures -WorkflowElements = List[Union[WDL.Decl, WDL.Call, WDL.Scatter, WDL.Conditional]] -def _find_call(elements: WorkflowElements, wf_name: str, call_name: str): - found: SourcePosition = None +def _find_call(elements: Iterable[SourceNode], wf_name: str, call_name: str): + found: Optional[SourcePosition] = None for el in elements: if found: break - elif isinstance(el, WDL.Call) and '{}.{}'.format(wf_name, el.name) == call_name: + elif ( + isinstance(el, WDL.Tree.Call) + and '{}.{}'.format(wf_name, el.name) == call_name + ): found = el.pos - elif isinstance(el, WDL.Conditional) or isinstance(el, WDL.Scatter): - found = _find_call(el.elements, wf_name, call_name) + elif isinstance(el, WDL.Tree.Conditional) or isinstance(el, WDL.Tree.Scatter): + found = _find_call(el.children, wf_name, call_name) return found + @server.catch_error(log=True) def _download(url: str): - return str(download(url), 'utf-8') + text = download(url) + if isinstance(text, str): + return text + return str(text, 'utf-8')