diff options
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 234 |
1 files changed, 213 insertions, 21 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 23e58e9..193a268 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -1,29 +1,91 @@ import argparse import arvados +import arvados.collection import time import subprocess import tempfile import json +import logging +import ruamel.yaml +from bh20sequploader.qc_metadata import qc_metadata +from bh20sequploader.qc_fasta import qc_fasta +import pkg_resources +from schema_salad.sourceline import add_lc_filename -def start_analysis(api, collection, analysis_project, workflow_uuid): +logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S", + level=logging.INFO) +logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) + +def validate_upload(api, collection, validated_project, + fastq_project, fastq_workflow_uuid): + col = arvados.collection.Collection(collection["uuid"]) + + # validate the collection here. Check metadata, etc. + valid = True + + if "metadata.yaml" not in col: + logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) + valid = False + else: + try: + metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) + metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"] + add_lc_filename(metadata_content, metadata_content["id"]) + valid = qc_metadata(metadata_content) and valid + except Exception as e: + logging.warn(e) + valid = False + if not valid: + logging.warn("Failed metadata qc") + + if valid: + tgt = None + for n in ("sequence.fasta", "reads.fastq"): + if n not in col: + continue + with col.open(n) as qf: + tgt = qc_fasta(qf) + if tgt != n: + logging.info("Expected %s but magic says it should be %s", n, tgt) + valid = False + elif tgt == "reads.fastq": + start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) + return False + if tgt is None: + valid = False + logging.warn("Upload '%s' does not contain sequence.fasta or reads.fastq", collection["name"]) + + dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], + ["portable_data_hash", "=", col.portable_data_hash()]]).execute() + if dup["items"]: + # This exact collection has been uploaded before. + valid = False + logging.warn("Upload '%s' is duplicate" % collection["name"]) + + if valid: + logging.info("Added '%s' to validated sequences" % collection["name"]) + # Move it to the "validated" project to be included in the next analysis + api.collections().update(uuid=collection["uuid"], body={ + "owner_uuid": validated_project, + "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute() + else: + pass + # It is invalid, delete it. + #logging.warn("Deleting '%s'" % collection["name"]) + #api.collections().delete(uuid=collection["uuid"]).execute() + + return valid + + +def run_workflow(api, parent_project, workflow_uuid, name, inputobj): project = api.groups().create(body={ "group_class": "project", - "name": "Analysis of %s" % collection["name"], - "owner_uuid": analysis_project, + "name": name, + "owner_uuid": parent_project, }, ensure_unique_name=True).execute() with tempfile.NamedTemporaryFile() as tmp: - inputobj = json.dumps({ - "sequence": { - "class": "File", - "location": "keep:%s/sequence.fasta" % collection["portable_data_hash"] - }, - "metadata": { - "class": "File", - "location": "keep:%s/metadata.jsonld" % collection["portable_data_hash"] - } - }, indent=2) - tmp.write(inputobj.encode('utf-8')) + tmp.write(json.dumps(inputobj, indent=2).encode('utf-8')) tmp.flush() cmd = ["arvados-cwl-runner", "--submit", @@ -32,24 +94,154 @@ def start_analysis(api, collection, analysis_project, workflow_uuid): "--project-uuid=%s" % project["uuid"], "arvwf:%s" % workflow_uuid, tmp.name] - print("Running %s" % ' '.join(cmd)) + logging.info("Running %s" % ' '.join(cmd)) comp = subprocess.run(cmd, capture_output=True) if comp.returncode != 0: - print(comp.stderr.decode('utf-8')) + logging.error(comp.stderr.decode('utf-8')) + + return project + + +def start_fastq_to_fasta(api, collection, + analysis_project, + fastq_workflow_uuid): + newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", { + "fastq_forward": { + "class": "File", + "location": "keep:%s/reads.fastq" % collection["portable_data_hash"] + }, + "metadata": { + "class": "File", + "location": "keep:%s/metadata.yaml" % collection["portable_data_hash"] + }, + "ref_fasta": { + "class": "File", + "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta" + } + }) + api.collections().update(uuid=collection["uuid"], + body={"owner_uuid": newproject["uuid"]}).execute() + +def start_pangenome_analysis(api, + analysis_project, + pangenome_workflow_uuid, + validated_project, + schema_ref): + validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) + inputobj = { + "inputReads": [], + "metadata": [], + "subjects": [], + "metadataSchema": { + "class": "File", + "location": schema_ref + } + } + for v in validated: + inputobj["inputReads"].append({ + "class": "File", + "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] + }) + inputobj["metadata"].append({ + "class": "File", + "location": "keep:%s/metadata.yaml" % v["portable_data_hash"] + }) + inputobj["subjects"].append("http://arvados.org/keep:%s/sequence.fasta" % v["portable_data_hash"]) + run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj) + + +def get_workflow_output_from_project(api, uuid): + cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid], + ["requesting_container_uuid", "=", None]]).execute() + if cr["items"] and cr["items"][0]["output_uuid"]: + return cr["items"][0] else: - api.collections().update(uuid=collection["uuid"], body={"owner_uuid": project['uuid']}).execute() + return None + + +def copy_most_recent_result(api, analysis_project, latest_result_uuid): + most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]], + order="created_at desc", limit=1).execute() + for m in most_recent_analysis["items"]: + wf = get_workflow_output_from_project(api, m["uuid"]) + if wf: + src = api.collections().get(uuid=wf["output_uuid"]).execute() + dst = api.collections().get(uuid=latest_result_uuid).execute() + if src["portable_data_hash"] != dst["portable_data_hash"]: + logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid) + api.collections().update(uuid=latest_result_uuid, + body={"manifest_text": src["manifest_text"], + "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() + break + + +def move_fastq_to_fasta_results(api, analysis_project, uploader_project): + projects = api.groups().list(filters=[['owner_uuid', '=', analysis_project], + ["properties.moved_output", "!=", True]], + order="created_at desc",).execute() + for p in projects["items"]: + wf = get_workflow_output_from_project(api, p["uuid"]) + if wf: + logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"]) + api.collections().update(uuid=wf["output_uuid"], + body={"owner_uuid": uploader_project}).execute() + p["properties"]["moved_output"] = True + api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute() + + +def upload_schema(api, workflow_def_project): + schema_resource = pkg_resources.resource_stream('bh20sequploader.qc_metadata', "bh20seq-schema.yml") + c = arvados.collection.Collection() + with c.open("schema.yml", "wb") as f: + f.write(schema_resource.read()) + pdh = c.portable_data_hash() + wd = api.collections().list(filters=[["owner_uuid", "=", workflow_def_project], + ["portable_data_hash", "=", pdh]]).execute() + if len(wd["items"]) == 0: + c.save_new(owner_uuid=workflow_def_project, name="Metadata schema", ensure_unique_name=True) + return "keep:%s/schema.yml" % pdh + def main(): parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='') - parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') - parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') + parser.add_argument('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') + parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='') + parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='') + parser.add_argument('--workflow-def-project', type=str, default='lugli-j7d0g-5hswinmpyho8dju', help='') + + parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') + parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='') + + parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') args = parser.parse_args() api = arvados.api() + logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) + + schema_ref = upload_schema(api, args.workflow_def_project) + while True: + move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project) + new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute() + at_least_one_new_valid_seq = False for c in new_collections["items"]: - start_analysis(api, c, args.analysis_project, args.workflow_uuid) - time.sleep(10) + at_least_one_new_valid_seq = validate_upload(api, c, + args.validated_project, + args.fastq_project, + args.fastq_workflow_uuid) or at_least_one_new_valid_seq + + if at_least_one_new_valid_seq: + start_pangenome_analysis(api, + args.pangenome_analysis_project, + args.pangenome_workflow_uuid, + args.validated_project, + schema_ref) + + copy_most_recent_result(api, + args.pangenome_analysis_project, + args.latest_result_collection) + + time.sleep(15) |