async def blast(req):
"""
BLAST a contig sequence that is part of a NuVs result record. The resulting BLAST data will be attached to that
sequence.
"""
db = req.app["db"]
settings = req.app["settings"]
analysis_id = req.match_info["analysis_id"]
sequence_index = int(req.match_info["sequence_index"])
document = await db.analyses.find_one(
{"_id": analysis_id}, ["ready", "workflow", "results", "sample"])
if not document:
return not_found("Analysis not found")
if document["workflow"] != "nuvs":
return conflict("Not a NuVs analysis")
if not document["ready"]:
return conflict("Analysis is still running")
sequence = virtool.analyses.utils.find_nuvs_sequence_by_index(
document, sequence_index)
if sequence is None:
return not_found("Sequence not found")
sample = await db.samples.find_one({"_id": document["sample"]["id"]},
virtool.samples.db.PROJECTION)
if not sample:
return bad_request("Parent sample does not exist")
_, write = virtool.samples.utils.get_sample_rights(sample, req["client"])
if not write:
return insufficient_rights()
# Start a BLAST at NCBI with the specified sequence. Return a RID that identifies the BLAST run.
rid, _ = await virtool.bio.initialize_ncbi_blast(req.app["settings"],
sequence)
blast_data, document = await virtool.analyses.db.update_nuvs_blast(
db, settings, analysis_id, sequence_index, rid)
# Wait on BLAST request as a Task until the it completes on NCBI. At that point the sequence in the DB will be
# updated with the BLAST result.
await aiojobs.aiohttp.spawn(
req,
virtool.bio.wait_for_blast_result(req.app, analysis_id, sequence_index,
rid))
headers = {
"Location": f"/api/analyses/{analysis_id}/{sequence_index}/blast"
}
return json_response(blast_data, headers=headers, status=201)
async def install(req):
"""
Install the latest official HMM database from GitHub.
"""
db = req.app["db"]
user_id = req["client"].user_id
if await db.status.count_documents({"_id": "hmm", "updates.ready": False}):
return conflict("Install already in progress")
process = await virtool.processes.db.register(db, "install_hmms")
document = await db.status.find_one_and_update(
{"_id": "hmm"}, {"$set": {
"process": {
"id": process["id"]
}
}})
release = document.get("release")
if release is None:
return bad_request("Target release does not exist")
update = virtool.github.create_update_subdocument(release, False, user_id)
await db.status.update_one({"_id": "hmm"}, {"$push": {"updates": update}})
await aiojobs.aiohttp.spawn(
req, virtool.hmm.db.install(req.app, process["id"], release, user_id))
return json_response(update)
async def remove(req):
"""
Remove a job.
"""
db = req.app["db"]
job_id = req.match_info["job_id"]
document = await db.jobs.find_one(job_id)
if not document:
return not_found()
if virtool.jobs.is_running_or_waiting(document):
return conflict("Job is running or waiting and cannot be removed")
# Removed the documents associated with the job ids from the database.
await db.jobs.delete_one({"_id": job_id})
try:
# Calculate the log path and remove the log file. If it exists, return True.
path = os.path.join(req.app["settings"]["data_path"], "logs", "jobs", job_id + ".log")
await req.app["run_in_thread"](virtool.utils.rm, path)
except OSError:
pass
return no_content()
async def create_first(req):
"""
Add a first user to the user database.
"""
db = req.app["db"]
data = await req.json()
if await db.users.count_documents({}):
return conflict("Virtool already has at least one user")
if data["user_id"] == "virtool":
return bad_request("Reserved user name: virtool")
error = await virtool.users.checks.check_password_length(req)
if error:
return bad_request(error)
user_id = data["user_id"]
await virtool.users.db.create(db,
user_id,
data["password"],
force_reset=False)
document = await virtool.users.db.edit(db, user_id, administrator=True)
headers = {"Location": f"/api/users/{user_id}"}
session, token = await virtool.users.sessions.create_session(
db, virtool.http.auth.get_ip(req), user_id)
req["client"].authorize(session, is_api=False)
resp = json_response(virtool.utils.base_processor(
{key: document[key]
for key in virtool.users.db.PROJECTION}),
headers=headers,
status=201)
virtool.http.utils.set_session_id_cookie(resp, session["_id"])
virtool.http.utils.set_session_token_cookie(resp, token)
return resp
async def edit(req):
db = req.app["db"]
data = await req.json()
if "password" in data:
error = await virtool.users.checks.check_password_length(req)
if error:
return bad_request(error)
groups = await db.groups.distinct("_id")
if "groups" in data:
missing = [g for g in data["groups"] if g not in groups]
if missing:
return bad_request("Groups do not exist: " + ", ".join(missing))
primary_group = data.get("primary_group")
if primary_group and primary_group not in groups:
return bad_request("Primary group does not exist")
user_id = req.match_info["user_id"]
if "administrator" in data and user_id == req["client"].user_id:
return bad_request(
"Users cannot modify their own administrative status")
try:
document = await virtool.users.db.edit(db, user_id, **data)
except virtool.errors.DatabaseError as err:
if "User does not exist" in str(err):
return not_found("User does not exist")
if "User is not member of group" in str(err):
return conflict("User is not member of group")
raise
projected = virtool.db.utils.apply_projection(document,
virtool.users.db.PROJECTION)
return json_response(virtool.utils.base_processor(projected))
async def remove(req):
"""
Remove an analysis document by its id.
"""
db = req.app["db"]
analysis_id = req.match_info["analysis_id"]
document = await db.analyses.find_one({"_id": analysis_id},
["job", "ready", "sample"])
if not document:
return not_found()
sample_id = document["sample"]["id"]
sample = await db.samples.find_one({"_id": sample_id},
virtool.samples.db.PROJECTION)
if not sample:
return bad_request("Parent sample does not exist")
read, write = virtool.samples.utils.get_sample_rights(
sample, req["client"])
if not read or not write:
return insufficient_rights()
if not document["ready"]:
return conflict("Analysis is still running")
await db.analyses.delete_one({"_id": analysis_id})
path = os.path.join(req.app["settings"]["data_path"], "samples", sample_id,
"analysis", analysis_id)
await req.app["run_in_thread"](virtool.utils.rm, path, True)
await virtool.samples.db.recalculate_workflow_tags(db, sample_id)
return no_content()
async def cancel(req):
"""
Cancel a job.
"""
db = req.app["db"]
job_id = req.match_info["job_id"]
document = await db.jobs.find_one(job_id, ["status"])
if not document:
return not_found()
if not virtool.jobs.is_running_or_waiting(document):
return conflict("Not cancellable")
await req.app["jobs"].cancel(job_id)
document = await db.jobs.find_one(job_id)
return json_response(virtool.utils.base_processor(document))
async def revert(req):
"""
Remove the change document with the given ``change_id`` and any subsequent changes.
"""
db = req.app["db"]
change_id = req.match_info["change_id"]
document = await db.history.find_one(change_id, ["reference"])
if not document:
return not_found()
if not await virtool.references.db.check_right(
req, document["reference"]["id"], "modify_otu"):
return insufficient_rights()
try:
await virtool.history.db.revert(req.app, change_id)
except virtool.errors.DatabaseError:
return conflict("Change is already built")
return no_content()
async def create(req):
"""
Starts a job to rebuild the otus Bowtie2 index on disk. Does a check to make sure there are no unverified
otus in the collection and updates otu history to show the version and id of the new index.
"""
db = req.app["db"]
ref_id = req.match_info["ref_id"]
reference = await db.references.find_one(ref_id, ["groups", "users"])
if reference is None:
return not_found()
if not await virtool.references.db.check_right(req, reference, "build"):
return insufficient_rights()
if await db.indexes.count_documents({"reference.id": ref_id, "ready": False}):
return conflict("Index build already in progress")
if await db.otus.count_documents({"reference.id": ref_id, "verified": False}):
return bad_request("There are unverified OTUs")
if not await db.history.count_documents({"reference.id": ref_id, "index.id": "unbuilt"}):
return bad_request("There are no unbuilt changes")
index_id = await virtool.db.utils.get_new_id(db.indexes)
index_version = await virtool.indexes.db.get_next_version(db, ref_id)
job_id = await virtool.db.utils.get_new_id(db.jobs)
manifest = await virtool.references.db.get_manifest(db, ref_id)
user_id = req["client"].user_id
document = {
"_id": index_id,
"version": index_version,
"created_at": virtool.utils.timestamp(),
"manifest": manifest,
"ready": False,
"has_files": True,
"job": {
"id": job_id
},
"reference": {
"id": ref_id
},
"user": {
"id": user_id
}
}
await db.indexes.insert_one(document)
await db.history.update_many({"index.id": "unbuilt", "reference.id": ref_id}, {
"$set": {
"index": {
"id": index_id,
"version": index_version
}
}
})
# A dict of task_args for the rebuild job.
task_args = {
"ref_id": ref_id,
"user_id": user_id,
"index_id": index_id,
"index_version": index_version,
"manifest": manifest
}
# Create job document.
job = await virtool.jobs.db.create(
db,
req.app["settings"],
"build_index",
task_args,
user_id,
job_id=job_id
)
await req.app["jobs"].enqueue(job["_id"])
headers = {
"Location": "/api/indexes/" + index_id
}
return json_response(virtool.utils.base_processor(document), status=201, headers=headers)