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
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)
class SeqAnalyzer:
def __init__(self, api, keepclient,
uploader_project,
pangenome_analysis_project,
fastq_project,
validated_project,
workflow_def_project,
pangenome_workflow_uuid,
fastq_workflow_uuid,
exclude_list,
latest_result_collection):
self.api = api
self.keepclient = keepclient
self.uploader_project = uploader_project
self.pangenome_analysis_project = pangenome_analysis_project
self.fastq_project = fastq_project
self.validated_project = validated_project
self.workflow_def_project = workflow_def_project
self.pangenome_workflow_uuid = pangenome_workflow_uuid
self.fastq_workflow_uuid = fastq_workflow_uuid
self.exclude_list = exclude_list
self.latest_result_uuid = latest_result_collection
self.schema_ref = None
def validate_upload(self, collection, revalidate):
if not revalidate and collection["properties"].get("status") in ("validated", "rejected"):
return False
with arvados.collection.CollectionReader(collection["uuid"], api_client=self.api, keep_client=self.keepclient) as col:
# validate the collection here. Check metadata, etc.
logging.info("Validating upload '%s' (%s)" % (collection["name"], collection["uuid"]))
errors = []
if collection["owner_uuid"] != self.validated_project:
dup = self.api.collections().list(filters=[["owner_uuid", "=", self.validated_project],
["portable_data_hash", "=", col.portable_data_hash()]]).execute()
if dup["items"]:
# This exact collection has been uploaded before.
errors.append("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
if not errors:
if "metadata.yaml" not in col:
errors.append("%s missing metadata.yaml" % collection["name"])
else:
try:
with col.open("metadata.yaml") as md:
metadata_content = ruamel.yaml.round_trip_load(md)
metadata_content["id"] = "http://covid19.genenetwork.org/resource/%s" % collection["uuid"]
sample_id = metadata_content["sample"]["sample_id"]
add_lc_filename(metadata_content, metadata_content["id"])
valid = qc_metadata(metadata_content)
if not valid:
errors.append("Failed metadata qc")
except Exception as e:
errors.append(str(e))
existing = self.api.collections().list(filters=[["owner_uuid", "=", self.validated_project],
["properties.sequence_label", "=", sample_id]]).execute()
if not errors:
try:
tgt = None
paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"}
for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
if n not in col:
continue
with col.open(n, 'rb') as qf:
tgt, seqlabel, seq_type = qc_fasta(qf)
if tgt != n and tgt != paired.get(n):
errors.append("Expected %s but magic says it should be %s" % (n, tgt))
elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
self.start_fastq_to_fasta(collection, n, sample_id)
return False
# If it is a FASTA
if sample_id != seqlabel:
errors.append("Expected sample_id == seqlabel, but %s != %s" % (sample_id, seqlabel))
if tgt is None and len(existing["items"]) == 0:
errors.append("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq" % collection["name"])
except Exception as v:
errors.append(str(v))
if errors:
# It is invalid
logging.warn("'%s' (%s) has validation errors: %s" % (
collection["name"], collection["uuid"], "\n".join(errors)))
collection["properties"]["status"] = "rejected"
collection["properties"]["errors"] = errors
self.api.collections().update(uuid=collection["uuid"], body={"properties": collection["properties"]}).execute()
return False
update_from = None
if existing["items"]:
# "collection" is the newly uploaded one we're looking at
update_from = collection
collection = existing["items"][0]
collection["properties"] = update_from["properties"]
if "errors" in collection["properties"]:
del collection["properties"]["errors"]
collection["properties"]["status"] = "validated"
collection["properties"]["sequence_label"] = sample_id
if update_from:
with arvados.collection.Collection(collection["uuid"], api_client=self.api, keep_client=self.keepclient) as update_existing_col:
update_existing_col.copy("metadata.yaml", "metadata.yaml", source_collection=col, overwrite=True)
update_existing_col.save(properties=collection["properties"])
self.api.collections().delete(uuid=update_from["uuid"]).execute()
logging.info("Updated '%s' in validated sequences" % collection["name"])
else:
# Move it to the "validated" project to be included in the next analysis
self.api.collections().update(uuid=collection["uuid"], body={
"owner_uuid": self.validated_project,
"name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime())),
"properties": collection["properties"]}).execute()
logging.info("Added '%s' to validated sequences" % collection["name"])
return True
def run_workflow(self, parent_project, workflow_uuid, name, inputobj):
project = self.api.groups().create(body={
"group_class": "project",
"name": name,
"owner_uuid": parent_project,
}, ensure_unique_name=True).execute()
with tempfile.NamedTemporaryFile() as tmp:
tmp.write(json.dumps(inputobj, indent=2).encode('utf-8'))
tmp.flush()
cmd = ["arvados-cwl-runner",
"--submit",
"--no-wait",
"--project-uuid=%s" % project["uuid"],
"arvwf:%s" % workflow_uuid,
tmp.name]
logging.info("Running %s" % ' '.join(cmd))
comp = subprocess.run(cmd, capture_output=True)
logging.info("Submitted %s", comp.stdout)
if comp.returncode != 0:
logging.error(comp.stderr.decode('utf-8'))
return project
def start_fastq_to_fasta(self, collection,
tgt,
sample_id):
params = {
"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"
},
"sample_id": sample_id
}
if tgt.startswith("reads.fastq"):
params["fastq_forward"] = {
"class": "File",
"location": "keep:%s/%s" % (collection["portable_data_hash"], tgt)
}
elif tgt.startswith("reads_1.fastq"):
params["fastq_forward"] = {
"class": "File",
"location": "keep:%s/reads_1.%s" % (collection["portable_data_hash"], tgt[8:])
}
params["fastq_reverse"] = {
"class": "File",
"location": "keep:%s/reads_2.%s" % (collection["portable_data_hash"], tgt[8:])
}
newproject = self.run_workflow(self.fastq_project, self.fastq_workflow_uuid, "FASTQ to FASTA", params)
self.api.collections().update(uuid=collection["uuid"],
body={"owner_uuid": newproject["uuid"]}).execute()
def start_pangenome_analysis(self):
if self.schema_ref is None:
self.upload_schema()
inputobj = {
"metadataSchema": {
"class": "File",
"location": self.schema_ref
},
"exclude": {
"class": "File",
"location": self.exclude_list
},
"src_project": self.validated_project
}
self.run_workflow(self.pangenome_analysis_project, self.pangenome_workflow_uuid, "Pangenome analysis", inputobj)
def get_workflow_output_from_project(self, uuid, named):
cr = self.api.container_requests().list(filters=[['owner_uuid', '=', uuid],
["requesting_container_uuid", "=", None],
["name", "=", named]]).execute()
if cr["items"] and cr["items"][0]["output_uuid"]:
container = self.api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute()
if container["state"] == "Complete" and container["exit_code"] == 0:
return cr["items"][0]
return None
def copy_most_recent_result(self):
most_recent_analysis = self.api.groups().list(filters=[['owner_uuid', '=', self.pangenome_analysis_project]],
order="created_at desc").execute()
for m in most_recent_analysis["items"]:
wf = self.get_workflow_output_from_project(m["uuid"], "collect-seqs.cwl")
if wf is None:
continue
src = self.api.collections().get(uuid=wf["output_uuid"]).execute()
dst = self.api.collections().get(uuid=self.latest_result_uuid).execute()
if src["portable_data_hash"] != dst["portable_data_hash"]:
logging.info("Copying latest result from '%s' to %s", m["name"], self.latest_result_uuid)
self.api.collections().update(uuid=self.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(self):
projects = arvados.util.list_all(self.api.groups().list,
filters=[['owner_uuid', '=', self.fastq_project],
["properties.moved_output", "!=", True]],
order="created_at asc")
for p in projects:
wf = self.get_workflow_output_from_project(p["uuid"], "fastq2fasta.cwl")
if not wf:
continue
logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"])
col = arvados.collection.Collection(wf["output_uuid"], api_client=self.api, keep_client=self.keepclient)
with col.open("metadata.yaml") as md:
metadata_content = ruamel.yaml.round_trip_load(md)
colprop = col.get_properties()
colprop["sequence_label"] = metadata_content["sample"]["sample_id"]
self.api.collections().update(uuid=wf["output_uuid"],
body={"owner_uuid": self.uploader_project,
"properties": colprop}).execute()
p["properties"]["moved_output"] = True
self.api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
def upload_schema(self):
schema_resource = pkg_resources.resource_stream('bh20sequploader.qc_metadata', "bh20seq-schema.yml")
c = arvados.collection.Collection(api_client=self.api, keep_client=self.keepclient)
with c.open("schema.yml", "wb") as f:
f.write(schema_resource.read())
pdh = c.portable_data_hash()
wd = self.api.collections().list(filters=[["owner_uuid", "=", self.workflow_def_project],
["portable_data_hash", "=", pdh]]).execute()
if len(wd["items"]) == 0:
c.save_new(owner_uuid=self.workflow_def_project, name="Metadata schema", ensure_unique_name=True)
self.schema_ref = "keep:%s/schema.yml" % pdh
def print_status(self, fmt):
pending = arvados.util.list_all(self.api.collections().list, filters=[["owner_uuid", "=", self.uploader_project]])
out = []
status = {}
for p in pending:
prop = p["properties"]
out.append(prop)
if "status" not in prop:
prop["status"] = "pending"
prop["created_at"] = p["created_at"]
prop["uuid"] = p["uuid"]
status[prop["status"]] = status.get(prop["status"], 0) + 1
if fmt == "html":
print(
"""
<html>
<body>
""")
print("<p>Total collections in upload project %s</p>" % len(out))
print("<p>Status %s</p>" % status)
print(
"""
<table>
<tr><th>Collection</th>
<th>Sequence label</th>
<th>Status</th>
<th>Errors</th></tr>
""")
for r in out:
print("<tr valign='top'>")
print("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
print("<td>%s</td>" % r["sequence_label"])
print("<td>%s</td>" % r["status"])
print("<td><pre>%s</pre></td>" % "\n".join(r.get("errors", [])))
print("</tr>")
print(
"""
</table>
</body>
</html>
""")
else:
print(json.dumps(out, indent=2))
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('--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('--exclude-list', type=str, default='keep:lugli-4zz18-tzzhcm6hrf8ci8d/exclude.txt', help='')
parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
parser.add_argument('--kickoff', action="store_true")
parser.add_argument('--no-start-analysis', action="store_true")
parser.add_argument('--once', action="store_true")
parser.add_argument('--print-status', type=str, default=None)
parser.add_argument('--revalidate', action="store_true", default=None)
args = parser.parse_args()
api = arvados.api()
keepclient = arvados.keep.KeepClient(api_client=api)
seqanalyzer = SeqAnalyzer(api, keepclient,
args.uploader_project,
args.pangenome_analysis_project,
args.fastq_project,
args.validated_project,
args.workflow_def_project,
args.pangenome_workflow_uuid,
args.fastq_workflow_uuid,
args.exclude_list,
args.latest_result_collection)
if args.kickoff:
logging.info("Starting a single analysis run")
seqanalyzer.start_pangenome_analysis()
return
if args.print_status:
seqanalyzer.print_status(args.print_status)
exit(0)
logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
while True:
try:
seqanalyzer.move_fastq_to_fasta_results()
new_collections = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", args.uploader_project]])
at_least_one_new_valid_seq = False
for c in new_collections:
at_least_one_new_valid_seq = seqanalyzer.validate_upload(c, args.revalidate) or at_least_one_new_valid_seq
if at_least_one_new_valid_seq and not args.no_start_analysis:
seqanalyzer.start_pangenome_analysis()
seqanalyzer.copy_most_recent_result()
except Exception as e:
logging.exeception("Error in main loop")
if args.once:
break
time.sleep(15)
