async def find(req):
db = req.app["db"]
ids = req.query.get("ids", False)
if ids:
return json_response(await db.subtraction.distinct("_id"))
host_count = await db.subtraction.count({"is_host": True})
ready_host_count = await db.subtraction.count({"is_host": True, "ready": True})
term = req.query.get("find", None)
db_query = dict()
if term:
db_query.update(compose_regex_query(term, ["_id"]))
data = await paginate(
db.subtraction,
db_query,
req.query,
sort="_id",
projection=virtool.db.subtractions.PROJECTION
)
data.update({
"host_count": host_count,
"ready_host_count": ready_host_count
})
return json_response(data)
async def find(db, names, term, req_query, verified, ref_id=None):
db_query = dict()
if term:
db_query.update(compose_regex_query(term, ["name", "abbreviation"]))
if verified is not None:
db_query["verified"] = virtool.utils.to_bool(verified)
base_query = None
if ref_id is not None:
base_query = {"reference.id": ref_id}
if names is True or names == "true":
cursor = db.otus.find({
**db_query,
**base_query
}, ["name"],
sort=[("name", 1)])
return [virtool.utils.base_processor(d) async for d in cursor]
data = await paginate(db.otus,
db_query,
req_query,
base_query=base_query,
sort="name",
projection=PROJECTION)
data["modified_count"] = len(await db.history.find({
"index.id": "unbuilt"
}, ["otu"]).distinct("otu.name"))
return data
async def find(req):
"""
Return a list of job documents.
"""
db = req.app["db"]
term = req.query.get("term", None)
db_query = dict()
if term:
db_query.update(compose_regex_query(term, ["task", "user.id"]))
data = await paginate(
db.jobs,
db_query,
req.query,
projection=virtool.db.jobs.PROJECTION,
processor=virtool.db.jobs.processor
)
data["documents"].sort(key=lambda d: d["created_at"])
return json_response(data)
async def find_history(req):
"""
Find history changes for a specific index.
"""
db = req.app["db"]
index_id = req.match_info["index_id"]
if not await db.indexes.count({"_id": index_id}):
return not_found()
term = req.query.get("term", None)
db_query = {
"index.id": index_id
}
if term:
db_query.update(compose_regex_query(term, ["otu.name", "user.id"]))
data = await paginate(
db.history,
db_query,
req.query,
sort=[("otu.name", 1), ("otu.version", -1)],
projection=virtool.db.history.LIST_PROJECTION,
reverse=True
)
return json_response(data)
async def find(req):
db = req.app["db"]
term = req.query.get("find", None)
db_query = dict()
if term:
db_query = compose_regex_query(term, ["name", "data_type"])
base_query = virtool.db.references.compose_base_find_query(
req["client"].user_id, req["client"].administrator,
req["client"].groups)
data = await paginate(db.references,
db_query,
req.query,
sort="name",
base_query=base_query,
processor=virtool.utils.base_processor,
projection=virtool.db.references.PROJECTION)
for d in data["documents"]:
latest_build, otu_count, unbuilt_count = await asyncio.gather(
virtool.db.references.get_latest_build(db, d["id"]),
virtool.db.references.get_otu_count(db, d["id"]),
virtool.db.references.get_unbuilt_count(db, d["id"]))
d.update({
"latest_build": latest_build,
"otu_count": otu_count,
"unbuilt_change_count": unbuilt_count
})
return json_response(data)
async def find(req):
"""
Find samples, filtering by data passed as URL parameters.
"""
db = req.app["db"]
v = Validator(QUERY_SCHEMA, allow_unknown=True)
if not v.validate(dict(req.query)):
return invalid_query(v.errors)
query = v.document
rights_filter = [
# The requesting user is the sample owner
{
"user.id": req["client"].user_id
},
# The sample rights allow all users to view the sample.
{
"all_read": True
}
]
if req["client"].groups:
# The sample rights allow owner group members to view the sample and the requesting user is a member of
# the owner group.
rights_filter.append({
"group_read": True,
"group": {
"$in": req["client"].groups
}
})
base_query = {"$or": rights_filter}
db_query = dict()
term = query.get("find", None)
if term:
db_query = compose_regex_query(term, ["name", "user.id"])
data = await paginate(db.samples,
db_query,
req.query,
sort="created_at",
projection=virtool.db.samples.LIST_PROJECTION,
base_query=base_query,
reverse=True)
return json_response(data)
async def find(req):
"""
Get a list of all user documents in the database.
"""
db = req.app["db"]
term = req.query.get("find", None)
db_query = dict()
if term:
db_query.update(compose_regex_query(term, ["_id"]))
data = await paginate(db.users,
db_query,
req.query,
sort="_id",
projection=virtool.db.users.PROJECTION)
return json_response(data)
async def find_analyses(req):
"""
List the analyses associated with the given ``sample_id``.
"""
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"], write=False):
return insufficient_rights()
except virtool.errors.DatabaseError as err:
if "Sample does not exist" in str(err):
return not_found()
raise
term = req.query.get("term", None)
db_query = dict()
if term:
db_query.update(
compose_regex_query(term, ["reference.name", "user.id"]))
base_query = {"sample.id": sample_id}
data = await paginate(db.analyses,
db_query,
req.query,
base_query=base_query,
projection=virtool.db.analyses.PROJECTION,
sort=[("created_at", -1)])
return json_response(data)
async def find(req):
"""
Find HMM annotation documents.
"""
db = req.app["db"]
term = req.query.get("find", None)
db_query = dict()
if term:
db_query.update(compose_regex_query(term, ["names"]))
data = await paginate(db.hmm,
db_query,
req.query,
sort="cluster",
projection=virtool.db.hmm.PROJECTION,
base_query={"hidden": False})
data["status"] = await virtool.db.hmm.get_status(db)
return json_response(data)