async def purge(req):
"""
Delete all unreferenced HMMs and hide the rest.
"""
db = req.app["db"]
await virtool.db.hmm.purge(db)
hmm_path = os.path.join(req.app["settings"]["data_path"],
"hmm/profiles.hmm")
try:
await req.app["run_in_thread"](virtool.utils.rm, hmm_path)
except FileNotFoundError:
pass
await db.status.find_one_and_update(
{"_id": "hmm"},
{"$set": {
"installed": None,
"process": None,
"updates": list()
}})
await virtool.db.hmm.fetch_and_update_release(req.app)
return no_content()
async def remove(req):
"""
Remove a job.
"""
db = req.app["db"]
job_id = req.match_info["job_id"]
document = await db.jobs.find_one(job_id)
if not document:
return not_found()
if virtool.jobs.utils.is_running_or_waiting(document):
return conflict("Job is running or waiting and cannot be removed")
# Removed the documents associated with the job ids from the database.
await db.jobs.delete_one({"_id": job_id})
try:
# Calculate the log path and remove the log file. If it exists, return True.
path = os.path.join(req.app["settings"].get("data_path"), "logs", "jobs", job_id + ".log")
await virtool.utils.rm(path)
except OSError:
pass
return no_content()
async def logout(req):
"""
Invalidates the requesting session, effectively logging out the user.
"""
db = req.app["db"]
session_id = req["client"].session_id
if session_id:
await db.sessions.delete_one({"_id": session_id})
return no_content()
async def remove_sequence(req):
"""
Remove a sequence from an isolate.
"""
db = req.app["db"]
otu_id = req.match_info["otu_id"]
isolate_id = req.match_info["isolate_id"]
sequence_id = req.match_info["sequence_id"]
if not await db.sequences.count({"_id": sequence_id}):
return not_found()
old = await virtool.db.otus.join(db, {
"_id": otu_id,
"isolates.id": isolate_id
})
if old is None:
return not_found()
if not await virtool.db.references.check_right(req, old["reference"]["id"],
"modify_otu"):
return insufficient_rights()
isolate = virtool.otus.find_isolate(old["isolates"], isolate_id)
await db.sequences.delete_one({"_id": sequence_id})
await db.otus.update_one({"_id": otu_id}, {
"$set": {
"verified": False
},
"$inc": {
"version": 1
}
})
new = await virtool.db.otus.join(db, otu_id)
await virtool.db.otus.update_verification(db, new)
isolate_name = virtool.otus.format_isolate_name(isolate)
await virtool.db.history.add(
db, "remove_sequence", old, new,
f"Removed sequence {sequence_id} from {isolate_name}",
req["client"].user_id)
return no_content()
async def remove_api_key(req):
db = req.app["db"]
user_id = req["client"].user_id
key_id = req.match_info.get("key_id")
delete_result = await db.keys.delete_one({
"id": key_id,
"user.id": user_id
})
if delete_result.deleted_count == 0:
return not_found()
return no_content()
async def remove(req):
"""
Remove a user.
"""
user_id = req.match_info["user_id"]
if user_id == req["client"].user_id:
return bad_request("Cannot remove own account")
delete_result = await req.app["db"].users.delete_one({"_id": user_id})
if delete_result.deleted_count == 0:
return not_found()
return no_content()
async def remove(req):
"""
Remove a group.
"""
db = req.app["db"]
group_id = req.match_info["group_id"]
delete_result = await db.groups.delete_one({"_id": group_id})
if not delete_result.deleted_count:
return not_found()
await virtool.db.groups.update_member_users(db, group_id, remove=True)
return no_content()
async def remove(req):
db = req.app["db"]
settings = req.app["settings"]
subtraction_id = req.match_info["subtraction_id"]
if await db.samples.count({"subtraction.id": subtraction_id}):
return conflict("Has linked samples")
delete_result = await db.subtraction.delete_one({"_id": subtraction_id})
if delete_result.deleted_count == 0:
return not_found()
index_path = virtool.subtractions.calculate_index_path(settings, subtraction_id)
await req.loop.run_in_executor(None, shutil.rmtree, index_path, True)
return no_content()
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.db.samples.PROJECTION)
if not sample:
return bad_request("Parent sample does not exist")
read, write = virtool.samples.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.db.samples.recalculate_algorithm_tags(db, sample_id)
return no_content()
async def delete_user(req):
db = req.app["db"]
ref_id = req.match_info["ref_id"]
user_id = req.match_info["user_id"]
document = await db.references.find_one(
{
"_id": ref_id,
"users.id": user_id
}, ["groups", "users"])
if document is None:
return not_found()
if not await virtool.db.references.check_right(req, ref_id, "modify"):
return insufficient_rights()
await virtool.db.references.delete_group_or_user(db, ref_id, user_id,
"users")
return no_content()
async def remove(req):
"""
Remove a user.
"""
db = req.app["db"]
user_id = req.match_info["user_id"]
if user_id == req["client"].user_id:
return bad_request("Cannot remove own account")
delete_result = await db.users.delete_one({"_id": user_id})
# Remove user from all references.
await db.references.update_many({}, {"$pull": {"users": {"id": user_id}}})
if delete_result.deleted_count == 0:
return not_found()
return no_content()
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.db.references.check_right(req, document["reference"]["id"], "modify_otu"):
return insufficient_rights()
try:
await virtool.db.history.revert(db, change_id)
except virtool.errors.DatabaseError:
return conflict("Change is already built")
return no_content()
async def remove(req):
"""
Remove a sample document and all associated analyses.
"""
db = req.app["db"]
sample_id = req.match_info["sample_id"]
try:
if not await virtool.db.samples.check_rights(db, sample_id,
req["client"]):
return insufficient_rights()
except virtool.errors.DatabaseError as err:
if "Sample does not exist" in str(err):
return not_found()
raise
await virtool.db.samples.remove_samples(db, req.app["settings"],
[sample_id])
return no_content()
async def remove_all_api_keys(req):
db = req.app["db"]
await db.keys.delete_many({"user.id": req["client"].user_id})
return no_content()
async def remove_isolate(req):
"""
Remove an isolate and its sequences from a otu.
"""
db = req.app["db"]
otu_id = req.match_info["otu_id"]
isolate_id = req.match_info["isolate_id"]
document = await db.otus.find_one({
"_id": otu_id,
"isolates.id": isolate_id
})
if not document:
return not_found()
if not await virtool.db.references.check_right(
req, document["reference"]["id"], "modify_otu"):
return insufficient_rights()
isolates = deepcopy(document["isolates"])
# Get any isolates that have the isolate id to be removed (only one should match!).
isolate_to_remove = virtool.otus.find_isolate(isolates, isolate_id)
# Remove the isolate from the otu' isolate list.
isolates.remove(isolate_to_remove)
new_default = None
# Set the first isolate as default if the removed isolate was the default.
if isolate_to_remove["default"] and len(isolates):
new_default = isolates[0]
new_default["default"] = True
old = await virtool.db.otus.join(db, otu_id, document)
document = await db.otus.find_one_and_update({"_id": otu_id}, {
"$set": {
"isolates": isolates,
"verified": False
},
"$inc": {
"version": 1
}
})
new = await virtool.db.otus.join(db, otu_id, document)
issues = await virtool.db.otus.verify(db, otu_id, joined=new)
if issues is None:
await db.otus.update_one({"_id": otu_id}, {"$set": {"verified": True}})
new["verified"] = True
# Remove any sequences associated with the removed isolate.
await db.sequences.delete_many({
"otu_id": otu_id,
"isolate_id": isolate_id
})
old_isolate_name = virtool.otus.format_isolate_name(isolate_to_remove)
description = f"Removed {old_isolate_name}"
if isolate_to_remove["default"] and new_default:
new_isolate_name = virtool.otus.format_isolate_name(new_default)
description += f" and set {new_isolate_name} as default"
await virtool.db.history.add(db, "remove_isolate", old, new, description,
req["client"].user_id)
return no_content()
