X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f3cb43d4be379703a965a1cb14cae5f5c855728f..09cbdc3074b3f1e69c9c537875146f6da0a6ed8f:/sdk/cwl/arvados_cwl/executor.py diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py index 778af58ac3..447c14b8bf 100644 --- a/sdk/cwl/arvados_cwl/executor.py +++ b/sdk/cwl/arvados_cwl/executor.py @@ -17,6 +17,7 @@ import copy import json import re from functools import partial +import subprocess import time import urllib @@ -24,6 +25,7 @@ from cwltool.errors import WorkflowException import cwltool.workflow from schema_salad.sourceline import SourceLine import schema_salad.validate as validate +from schema_salad.ref_resolver import file_uri, uri_file_path import arvados import arvados.config @@ -68,6 +70,10 @@ class RuntimeStatusLoggingHandler(logging.Handler): kind = 'error' elif record.levelno >= logging.WARNING: kind = 'warning' + if kind == 'warning' and record.name == "salad": + # Don't send validation warnings to runtime status, + # they're noisy and unhelpful. + return if kind is not None and self.updatingRuntimeStatus is not True: self.updatingRuntimeStatus = True try: @@ -110,6 +116,9 @@ class ArvCwlExecutor(object): arvargs.output_tags = None arvargs.thread_count = 1 arvargs.collection_cache_size = None + arvargs.git_info = True + arvargs.submit = False + arvargs.defer_downloads = False self.api = api_client self.processes = {} @@ -135,6 +144,8 @@ class ArvCwlExecutor(object): self.fs_access = None self.secret_store = None self.stdout = stdout + self.fast_submit = False + self.git_info = arvargs.git_info if keep_client is not None: self.keep_client = keep_client @@ -201,6 +212,8 @@ The 'jobs' API is no longer supported. self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess, collection_cache=self.collection_cache) + self.defer_downloads = arvargs.submit and arvargs.defer_downloads + validate_cluster_target(self, self.toplevel_runtimeContext) @@ -252,6 +265,11 @@ The 'jobs' API is no longer supported. Called when there's a need to report errors, warnings or just activity statuses, for example in the RuntimeStatusLoggingHandler. """ + + if kind not in ('error', 'warning'): + # Ignore any other status kind + return + with self.workflow_eval_lock: current = None try: @@ -261,32 +279,35 @@ The 'jobs' API is no longer supported. if current is None: return runtime_status = current.get('runtime_status', {}) - if kind in ('error', 'warning'): - updatemessage = runtime_status.get(kind, "") - if not updatemessage: - updatemessage = message - - # Subsequent messages tacked on in detail - updatedetail = runtime_status.get(kind+'Detail', "") - maxlines = 40 - if updatedetail.count("\n") < maxlines: - if updatedetail: - updatedetail += "\n" - updatedetail += message + "\n" - - if detail: - updatedetail += detail + "\n" - - if updatedetail.count("\n") >= maxlines: - updatedetail += "\nSome messages may have been omitted. Check the full log." - - runtime_status.update({ - kind: updatemessage, - kind+'Detail': updatedetail, - }) - else: - # Ignore any other status kind + + original_updatemessage = updatemessage = runtime_status.get(kind, "") + if not updatemessage: + updatemessage = message + + # Subsequent messages tacked on in detail + original_updatedetail = updatedetail = runtime_status.get(kind+'Detail', "") + maxlines = 40 + if updatedetail.count("\n") < maxlines: + if updatedetail: + updatedetail += "\n" + updatedetail += message + "\n" + + if detail: + updatedetail += detail + "\n" + + if updatedetail.count("\n") >= maxlines: + updatedetail += "\nSome messages may have been omitted. Check the full log." + + if updatemessage == original_updatemessage and updatedetail == original_updatedetail: + # don't waste time doing an update if nothing changed + # (usually because we exceeded the max lines) return + + runtime_status.update({ + kind: updatemessage, + kind+'Detail': updatedetail, + }) + try: self.api.containers().update(uuid=current['uuid'], body={ @@ -348,8 +369,8 @@ The 'jobs' API is no longer supported. page = keys[:pageSize] try: proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries) - except Exception: - logger.exception("Error checking states on API server: %s") + except Exception as e: + logger.exception("Error checking states on API server: %s", e) remain_wait = self.poll_interval continue @@ -510,15 +531,82 @@ The 'jobs' API is no longer supported. for req in job_reqs: tool.requirements.append(req) + @staticmethod + def get_git_info(tool): + in_a_git_repo = False + cwd = None + filepath = None + + if tool.tool["id"].startswith("file://"): + # check if git is installed + try: + filepath = uri_file_path(tool.tool["id"]) + cwd = os.path.dirname(filepath) + subprocess.run(["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, check=True, capture_output=True, text=True) + in_a_git_repo = True + except Exception as e: + pass + + gitproperties = {} + + if in_a_git_repo: + git_commit = subprocess.run(["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout + git_date = subprocess.run(["git", "log", "--format=%cD", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout + git_committer = subprocess.run(["git", "log", "--format=%cn <%ce>", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout + git_branch = subprocess.run(["git", "rev-parse", "--abbrev-ref", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout + git_origin = subprocess.run(["git", "remote", "get-url", "origin"], cwd=cwd, capture_output=True, text=True).stdout + git_status = subprocess.run(["git", "status", "--untracked-files=no", "--porcelain"], cwd=cwd, capture_output=True, text=True).stdout + git_describe = subprocess.run(["git", "describe", "--always", "--tags"], cwd=cwd, capture_output=True, text=True).stdout + git_toplevel = subprocess.run(["git", "rev-parse", "--show-toplevel"], cwd=cwd, capture_output=True, text=True).stdout + git_path = filepath[len(git_toplevel):] + + gitproperties = { + "http://arvados.org/cwl#gitCommit": git_commit.strip(), + "http://arvados.org/cwl#gitDate": git_date.strip(), + "http://arvados.org/cwl#gitCommitter": git_committer.strip(), + "http://arvados.org/cwl#gitBranch": git_branch.strip(), + "http://arvados.org/cwl#gitOrigin": git_origin.strip(), + "http://arvados.org/cwl#gitStatus": git_status.strip(), + "http://arvados.org/cwl#gitDescribe": git_describe.strip(), + "http://arvados.org/cwl#gitPath": git_path.strip(), + } + else: + for g in ("http://arvados.org/cwl#gitCommit", + "http://arvados.org/cwl#gitDate", + "http://arvados.org/cwl#gitCommitter", + "http://arvados.org/cwl#gitBranch", + "http://arvados.org/cwl#gitOrigin", + "http://arvados.org/cwl#gitStatus", + "http://arvados.org/cwl#gitDescribe", + "http://arvados.org/cwl#gitPath"): + if g in tool.metadata: + gitproperties[g] = tool.metadata[g] + + return gitproperties + + def set_container_request_properties(self, container, properties): + resp = self.api.container_requests().list(filters=[["container_uuid", "=", container["uuid"]]], select=["uuid", "properties"]).execute(num_retries=self.num_retries) + for cr in resp["items"]: + cr["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in properties.items()}) + self.api.container_requests().update(uuid=cr["uuid"], body={"container_request": {"properties": cr["properties"]}}).execute(num_retries=self.num_retries) + def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None): self.debug = runtimeContext.debug + git_info = self.get_git_info(updated_tool) if self.git_info else {} + if git_info: + logger.info("Git provenance") + for g in git_info: + if git_info[g]: + logger.info(" %s: %s", g.split("#", 1)[1], git_info[g]) + workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"] workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"] controller = self.api.config()["Services"]["Controller"]["ExternalURL"] logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller) - updated_tool.visit(self.check_features) + if not self.fast_submit: + updated_tool.visit(self.check_features) self.pipeline = None self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir) @@ -546,7 +634,10 @@ The 'jobs' API is no longer supported. runtimeContext.intermediate_storage_classes = default_storage_classes if not runtimeContext.name: - runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"]) + self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"]) + if git_info.get("http://arvados.org/cwl#gitDescribe"): + self.name = "%s (%s)" % (self.name, git_info.get("http://arvados.org/cwl#gitDescribe")) + runtimeContext.name = self.name if runtimeContext.copy_deps is None and (runtimeContext.create_workflow or runtimeContext.update_workflow): # When creating or updating workflow record, by default @@ -565,8 +656,9 @@ The 'jobs' API is no longer supported. self.project_uuid = runtimeContext.project_uuid # Upload local file references in the job order. - job_order = upload_job_order(self, "%s input" % runtimeContext.name, - updated_tool, job_order, runtimeContext) + with Perf(metrics, "upload_job_order"): + job_order = upload_job_order(self, "%s input" % runtimeContext.name, + updated_tool, job_order, runtimeContext) # the last clause means: if it is a command line tool, and we # are going to wait for the result, and always_submit_runner @@ -581,19 +673,26 @@ The 'jobs' API is no longer supported. loadingContext = self.loadingContext.copy() loadingContext.do_validate = False - if submitting: + loadingContext.disable_js_validation = True + if submitting and not self.fast_submit: loadingContext.do_update = False # Document may have been auto-updated. Reload the original # document with updating disabled because we want to # submit the document with its original CWL version, not # the auto-updated one. - tool = load_tool(updated_tool.tool["id"], loadingContext) + with Perf(metrics, "load_tool original"): + tool = load_tool(updated_tool.tool["id"], loadingContext) else: tool = updated_tool # Upload direct dependencies of workflow steps, get back mapping of files to keep references. # Also uploads docker images. - merged_map = upload_workflow_deps(self, tool, runtimeContext) + if not self.fast_submit: + logger.info("Uploading workflow dependencies") + with Perf(metrics, "upload_workflow_deps"): + merged_map = upload_workflow_deps(self, tool, runtimeContext) + else: + merged_map = {} # Recreate process object (ArvadosWorkflow or # ArvadosCommandTool) because tool document may have been @@ -602,7 +701,8 @@ The 'jobs' API is no longer supported. loadingContext.loader = tool.doc_loader loadingContext.avsc_names = tool.doc_schema loadingContext.metadata = tool.metadata - tool = load_tool(tool.tool, loadingContext) + with Perf(metrics, "load_tool"): + tool = load_tool(tool.tool, loadingContext) if runtimeContext.update_workflow or runtimeContext.create_workflow: # Create a pipeline template or workflow record and exit. @@ -614,7 +714,8 @@ The 'jobs' API is no longer supported. submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, merged_map=merged_map, - submit_runner_image=runtimeContext.submit_runner_image) + submit_runner_image=runtimeContext.submit_runner_image, + git_info=git_info) self.stdout.write(uuid + "\n") return (None, "success") @@ -676,7 +777,8 @@ The 'jobs' API is no longer supported. priority=runtimeContext.priority, secret_store=self.secret_store, collection_cache_size=runtimeContext.collection_cache_size, - collection_cache_is_default=self.should_estimate_cache_size) + collection_cache_is_default=self.should_estimate_cache_size, + git_info=git_info) else: runtimeContext.runnerjob = tool.tool["id"] @@ -696,6 +798,7 @@ The 'jobs' API is no longer supported. current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) if current_container: logger.info("Running inside container %s", current_container.get("uuid")) + self.set_container_request_properties(current_container, git_info) self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout) self.polling_thread = threading.Thread(target=self.poll_states)