async def purge(req):
"""
Delete all unreferenced HMMs and hide the rest.
"""
db = req.app["db"]
await virtool.hmm.db.purge(db, req.app["settings"])
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.hmm.db.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.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 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.samples.db.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.samples.db.remove_samples(
db,
req.app["settings"],
[sample_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_documents({"_id": sequence_id}):
return not_found()
document = await db.otus.find_one({"_id": otu_id, "isolates.id": isolate_id}, ["reference"])
if document is None:
return not_found()
if not await virtool.references.db.check_right(req, document["reference"]["id"], "modify_otu"):
return insufficient_rights()
await asyncio.shield(virtool.otus.sequences.remove(
req.app,
otu_id,
isolate_id,
sequence_id,
req["client"].user_id
))
return no_content()
async def remove_all_api_keys(req):
"""
Remove all API keys for the session account.
"""
await req.app["db"].keys.delete_many({"user.id": req["client"].user_id})
return no_content()
async def remove(req):
db = req.app["db"]
settings = req.app["settings"]
subtraction_id = req.match_info["subtraction_id"]
updated_count = await asyncio.shield(virtool.subtractions.db.delete(req.app, subtraction_id))
if updated_count == 0:
return not_found()
return no_content()
async def remove_api_key(req):
db = req.app["db"]
user_id = req["client"].user_id
key_id = req.match_info["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 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.groups.db.update_member_users(db, group_id, remove=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.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 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.references.db.check_right(req, ref_id, "modify"):
return insufficient_rights()
await virtool.references.db.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.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()
