X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/55e73facf08cc8651eb71529a2ab4e0657d3c870..7ac1e7337dca972ce93d04e5eccb6f4de9aed141:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 299ad5c0d5..bd32e9f81b 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -12,6 +12,7 @@ import logging import urllib from io import StringIO import sys +import re from typing import (MutableSequence, MutableMapping) @@ -25,7 +26,7 @@ import arvados.collection from cwltool.pack import pack from cwltool.load_tool import fetch_document, resolve_and_validate_document -from cwltool.process import shortname +from cwltool.process import shortname, uniquename from cwltool.workflow import Workflow, WorkflowException, WorkflowStep from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs from cwltool.context import LoadingContext @@ -36,7 +37,7 @@ import ruamel.yaml as yaml from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields, discover_secondary_files, - make_builder, arvados_jobs_image) + make_builder, arvados_jobs_image, FileUpdates) from .pathmapper import ArvPathMapper, trim_listing from .arvtool import ArvadosCommandTool, set_cluster_target from ._version import __version__ @@ -127,65 +128,170 @@ def make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, return json.dumps(doc, sort_keys=True, indent=4, separators=(',',': ')) -def rel_ref(s, baseuri, urlexpander, merged_map): - uri = urlexpander(s, baseuri) - fileuri = urllib.parse.urldefrag(baseuri)[0] - if fileuri in merged_map: - replacements = merged_map[fileuri].resolved - if uri in replacements: - return replacements[uri] +def rel_ref(s, baseuri, urlexpander, merged_map, jobmapper): if s.startswith("keep:"): return s - p1 = os.path.dirname(uri_file_path(baseuri)) + uri = urlexpander(s, baseuri) + + if uri.startswith("keep:"): + return uri + + fileuri = urllib.parse.urldefrag(baseuri)[0] + + for u in (baseuri, fileuri): + if u in merged_map: + replacements = merged_map[u].resolved + if uri in replacements: + return replacements[uri] + + if uri in jobmapper: + return jobmapper.mapper(uri).target + + p1 = os.path.dirname(uri_file_path(fileuri)) p2 = os.path.dirname(uri_file_path(uri)) p3 = os.path.basename(uri_file_path(uri)) + r = os.path.relpath(p2, p1) if r == ".": r = "" + return os.path.join(r, p3) +def is_basetype(tp): + basetypes = ("null", "boolean", "int", "long", "float", "double", "string", "File", "Directory", "record", "array", "enum") + for b in basetypes: + if re.match(b+"(\[\])?\??", tp): + return True + return False -def update_refs(d, baseuri, urlexpander, merged_map, set_block_style, runtimeContext): - if set_block_style and (isinstance(d, CommentedSeq) or isinstance(d, CommentedMap)): - d.fa.set_block_style() +def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix): if isinstance(d, MutableSequence): - for s in d: - update_refs(s, baseuri, urlexpander, merged_map, set_block_style, runtimeContext) + for i, s in enumerate(d): + if prefix and isinstance(s, str): + if s.startswith(prefix): + d[i] = replacePrefix+s[len(prefix):] + else: + update_refs(s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix) elif isinstance(d, MutableMapping): + for field in ("id", "name"): + if isinstance(d.get(field), str) and d[field].startswith("_:"): + # blank node reference, was added in automatically, can get rid of it. + del d[field] + if "id" in d: baseuri = urlexpander(d["id"], baseuri, scoped_id=True) + elif "name" in d and isinstance(d["name"], str): + baseuri = urlexpander(d["name"], baseuri, scoped_id=True) if d.get("class") == "DockerRequirement": dockerImageId = d.get("dockerImageId") or d.get("dockerPull") d["http://arvados.org/cwl#dockerCollectionPDH"] = runtimeContext.cached_docker_lookups.get(dockerImageId) - for s in d: - for field in ("$include", "$import", "location", "run"): - if field in d and isinstance(d[field], str): - d[field] = rel_ref(d[field], baseuri, urlexpander, merged_map) - - if "$schemas" in d: + for field in d: + if field in ("location", "run", "name") and isinstance(d[field], str): + d[field] = rel_ref(d[field], baseuri, urlexpander, merged_map, jobmapper) + continue + + if field in ("$include", "$import") and isinstance(d[field], str): + d[field] = rel_ref(d[field], baseuri, urlexpander, {}, jobmapper) + continue + + for t in ("type", "items"): + if (field == t and + isinstance(d[t], str) and + not is_basetype(d[t])): + d[t] = rel_ref(d[t], baseuri, urlexpander, merged_map, jobmapper) + continue + + if field == "inputs" and isinstance(d["inputs"], MutableMapping): + for inp in d["inputs"]: + if isinstance(d["inputs"][inp], str) and not is_basetype(d["inputs"][inp]): + d["inputs"][inp] = rel_ref(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper) + if isinstance(d["inputs"][inp], MutableMapping): + update_refs(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix) + continue + + if field == "$schemas": for n, s in enumerate(d["$schemas"]): - d["$schemas"][n] = rel_ref(d["$schemas"][n], baseuri, urlexpander, merged_map) + d["$schemas"][n] = rel_ref(d["$schemas"][n], baseuri, urlexpander, merged_map, jobmapper) + continue + + update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix) + + +def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh): + req = copy.deepcopy(req) - update_refs(d[s], baseuri, urlexpander, merged_map, set_block_style, runtimeContext) + for f in req["types"]: + r = f["name"] + path, frag = urllib.parse.urldefrag(r) + rel = rel_ref(r, baseuri, urlexpander, merged_map, jobmapper) + merged_map.setdefault(path, FileUpdates({}, {})) + rename = "keep:%s/%s" %(pdh, rel) + for mm in merged_map: + merged_map[mm].resolved[r] = rename + return req -def new_upload_workflow(arvRunner, tool, job_order, project_uuid, + +def drop_ids(d): + if isinstance(d, MutableSequence): + for i, s in enumerate(d): + drop_ids(s) + elif isinstance(d, MutableMapping): + if "id" in d and d["id"].startswith("file:"): + del d["id"] + + for field in d: + drop_ids(d[field]) + + +def common_prefix(firstfile, all_files): + n = 0 + allmatch = True + if not firstfile: + return "" + + while allmatch and n < len(firstfile)-1: + n += 1 + for f in all_files: + if len(f)-1 < n: + n -= 1 + allmatch = False + break + if f[n] != firstfile[n]: + allmatch = False + break + + while n > 0 and firstfile[n] != "/": + n -= 1 + + if firstfile[n] == "/": + n += 1 + + return firstfile[:n] + + +def upload_workflow(arvRunner, tool, job_order, project_uuid, runtimeContext, uuid=None, submit_runner_ram=0, name=None, merged_map=None, submit_runner_image=None, git_info=None, - set_defaults=False): + set_defaults=False, + jobmapper=None): firstfile = None workflow_files = set() import_files = set() include_files = set() + # The document loader index will have entries for all the files + # that were loaded in the process of parsing the entire workflow + # (including subworkflows, tools, imports, etc). We use this to + # get compose a list of the workflow file dependencies. for w in tool.doc_loader.idx: if w.startswith("file://"): workflow_files.add(urllib.parse.urldefrag(w)[0]) @@ -198,28 +304,25 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, all_files = workflow_files | import_files | include_files - n = 7 - allmatch = True - while allmatch: - n += 1 - for f in all_files: - if len(f)-1 < n: - n -= 1 - allmatch = False - break - if f[n] != firstfile[n]: - allmatch = False - break - - while firstfile[n] != "/": - n -= 1 - - prefix = firstfile[:n+1] - - col = arvados.collection.Collection() - + # Find the longest common prefix among all the file names. We'll + # use this to recreate the directory structure in a keep + # collection with correct relative references. + prefix = common_prefix(firstfile, all_files) + + col = arvados.collection.Collection(api_client=arvRunner.api) + + # Now go through all the files and update references to other + # files. We previously scanned for file dependencies, these are + # are passed in as merged_map. + # + # note about merged_map: we upload dependencies of each process + # object (CommandLineTool/Workflow) to a separate collection. + # That way, when the user edits something, this limits collection + # PDH changes to just that tool, and minimizes situations where + # small changes break container reuse for the whole workflow. + # for w in workflow_files | import_files: - # 1. load YAML + # 1. load the YAML file text = tool.doc_loader.fetch_text(w) if isinstance(text, bytes): @@ -230,49 +333,81 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, yamlloader = schema_salad.utils.yaml_no_ts() result = yamlloader.load(textIO) - set_block_style = False - if result.fa.flow_style(): - set_block_style = True + # If the whole document is in "flow style" it is probably JSON + # formatted. We'll re-export it as JSON because the + # ruamel.yaml round-trip mode is a lie and only preserves + # "block style" formatting and not "flow style" formatting. + export_as_json = result.fa.flow_style() # 2. find $import, $include, $schema, run, location # 3. update field value - update_refs(result, w, tool.doc_loader.expand_url, merged_map, set_block_style, runtimeContext) + update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "") - with col.open(w[n+1:], "wt") as f: - yamlloader.dump(result, stream=f) + # Write the updated file to the collection. + with col.open(w[len(prefix):], "wt") as f: + if export_as_json: + json.dump(result, f, indent=4, separators=(',',': ')) + else: + yamlloader.dump(result, stream=f) + # Also store a verbatim copy of the original files + with col.open(os.path.join("original", w[len(prefix):]), "wt") as f: + f.write(text) + + + # Upload files referenced by $include directives, these are used + # unchanged and don't need to be updated. for w in include_files: - with col.open(w[n+1:], "wb") as f1: - with open(uri_file_path(w), "rb") as f2: - dat = f2.read(65536) - while dat: - f1.write(dat) + with col.open(w[len(prefix):], "wb") as f1: + with col.open(os.path.join("original", w[len(prefix):]), "wb") as f3: + with open(uri_file_path(w), "rb") as f2: dat = f2.read(65536) + while dat: + f1.write(dat) + f3.write(dat) + dat = f2.read(65536) + + # Now collect metadata: the collection name and git properties. toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"]) if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"): toolname = "%s (%s)" % (toolname, git_info.get("http://arvados.org/cwl#gitDescribe")) - toolfile = tool.tool["id"][n+1:] + toolfile = tool.tool["id"][len(prefix):] properties = { "type": "workflow", "arv:workflowMain": toolfile, } - col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties) + if git_info: + for g in git_info: + p = g.split("#", 1)[1] + properties["arv:"+p] = git_info[g] - adjustDirObjs(job_order, trim_listing) - adjustFileObjs(job_order, trim_anonymous_location) - adjustDirObjs(job_order, trim_anonymous_location) + # Check if a collection with the same content already exists in the target project. If so, just use that one. + existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", col.portable_data_hash()], + ["owner_uuid", "=", arvRunner.project_uuid]]).execute(num_retries=arvRunner.num_retries) - # now construct the wrapper + if len(existing["items"]) == 0: + toolname = toolname.replace("/", " ") + col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties) + logger.info("Workflow uploaded to %s", col.manifest_locator()) + else: + logger.info("Workflow uploaded to %s", existing["items"][0]["uuid"]) + + # Now that we've updated the workflow and saved it to a + # collection, we're going to construct a minimal "wrapper" + # workflow which consists of only of input and output parameters + # connected to a single step that runs the real workflow. + + runfile = "keep:%s/%s" % (col.portable_data_hash(), toolfile) step = { "id": "#main/" + toolname, "in": [], "out": [], - "run": "keep:%s/%s" % (col.portable_data_hash(), toolfile), + "run": runfile, "label": name } @@ -291,14 +426,21 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"} hints.append(wf_runner_resources) - # uncomment me - # wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner, - # submit_runner_image or "arvados/jobs:"+__version__, - # runtimeContext) + wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner, + submit_runner_image or "arvados/jobs:"+__version__, + runtimeContext) if submit_runner_ram: wf_runner_resources["ramMin"] = submit_runner_ram + # Remove a few redundant fields from the "job order" (aka input + # object or input parameters). In the situation where we're + # creating or updating a workflow record, any values in the job + # order get copied over as default values for input parameters. + adjustDirObjs(job_order, trim_listing) + adjustFileObjs(job_order, trim_anonymous_location) + adjustDirObjs(job_order, trim_anonymous_location) + newinputs = [] for i in main["inputs"]: inp = {} @@ -347,7 +489,16 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, if main.get("requirements"): wrapper["requirements"].extend(main["requirements"]) if hints: - wrapper["hints"] = main["hints"] + wrapper["hints"] = hints + + # Schema definitions (this lets you define things like record + # types) require a special handling. + + for i, r in enumerate(wrapper["requirements"]): + if r["class"] == "SchemaDefRequirement": + wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash()) + + update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/") doc = {"cwlVersion": "v1.2", "$graph": [wrapper]} @@ -355,7 +506,8 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, for g in git_info: doc[g] = git_info[g] - update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, False, runtimeContext) + # Remove any lingering file references. + drop_ids(wrapper) return doc @@ -380,70 +532,6 @@ def make_workflow_record(arvRunner, doc, name, tool, project_uuid, update_uuid): return call.execute(num_retries=arvRunner.num_retries)["uuid"] -def upload_workflow(arvRunner, tool, job_order, project_uuid, - runtimeContext, uuid=None, - submit_runner_ram=0, name=None, merged_map=None, - submit_runner_image=None, - git_info=None): - - packed = packed_workflow(arvRunner, tool, merged_map, runtimeContext, git_info) - - adjustDirObjs(job_order, trim_listing) - adjustFileObjs(job_order, trim_anonymous_location) - adjustDirObjs(job_order, trim_anonymous_location) - - main = [p for p in packed["$graph"] if p["id"] == "#main"][0] - for inp in main["inputs"]: - sn = shortname(inp["id"]) - if sn in job_order: - inp["default"] = job_order[sn] - - if not name: - name = tool.tool.get("label", os.path.basename(tool.tool["id"])) - - upload_dependencies(arvRunner, name, tool.doc_loader, - packed, tool.tool["id"], - runtimeContext) - - wf_runner_resources = None - - hints = main.get("hints", []) - found = False - for h in hints: - if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources": - wf_runner_resources = h - found = True - break - if not found: - wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"} - hints.append(wf_runner_resources) - - wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner, - submit_runner_image or "arvados/jobs:"+__version__, - runtimeContext) - - if submit_runner_ram: - wf_runner_resources["ramMin"] = submit_runner_ram - - main["hints"] = hints - - wrapper = make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool) - - body = { - "workflow": { - "name": name, - "description": tool.tool.get("doc", ""), - "definition": wrapper - }} - if project_uuid: - body["workflow"]["owner_uuid"] = project_uuid - - if uuid: - call = arvRunner.api.workflows().update(uuid=uuid, body=body) - else: - call = arvRunner.api.workflows().create(body=body) - return call.execute(num_retries=arvRunner.num_retries)["uuid"] - def dedup_reqs(reqs): dedup = {} for r in reversed(reqs): @@ -541,6 +629,7 @@ class ArvadosWorkflow(Workflow): discover_secondary_files(self.arvrunner.fs_access, builder, self.tool["inputs"], joborder) + normalizeFilesDirs(joborder) with Perf(metrics, "subworkflow upload_deps"):