def query(self, current_user_id: Optional[UserIDT], prj_id: int,
for_managing: bool) -> ProjectBO:
if current_user_id is None:
RightsBO.anonymous_wants(self.session, Action.READ, prj_id)
highest_right = ""
else:
current_user, project = RightsBO.user_wants(
self.session, current_user_id,
Action.ADMINISTRATE if for_managing else Action.READ, prj_id)
highest_right = RightsBO.highest_right_on(current_user, prj_id)
ret = ProjectBOSet.get_one(self.session, prj_id)
assert ret is not None
ret.highest_right = highest_right
return ret
def query_history(self, current_user_id: Optional[int], object_id: ObjectIDT) \
-> List[HistoricalClassification]:
the_obj = ObjectBO(self.ro_session, object_id)
if not the_obj.exists():
return []
# Security check
# TODO: dup code
projid = the_obj.header.acquisition.sample.projid
if current_user_id is None:
RightsBO.anonymous_wants(self.ro_session, Action.READ, projid)
else:
_user, project = RightsBO.user_wants(self.session, current_user_id, Action.READ, projid)
assert project is not None
ret = the_obj.get_history()
return ret
def search(self, current_user_id: Optional[UserIDT], project_id: ProjectIDT) -> List[AcquisitionBO]:
# Security check
if current_user_id is None:
project = RightsBO.anonymous_wants(self.ro_session, Action.READ, project_id)
else:
_user, project = RightsBO.user_wants(self.session, current_user_id, Action.READ, project_id)
acquisition_set = DescribedAcquisitionSet(self.ro_session, project_id)
# mappings = ProjectMapping().load_from_project(project)
# ret.map_free_columns(mappings.sample_mappings)
return acquisition_set.list()
def summary(self, current_user_id: Optional[UserIDT], proj_id: ProjectIDT, filters: ProjectFilters,
only_total: bool) -> Tuple[int, Optional[int], Optional[int], Optional[int]]:
"""
Query the given project with given filters, return classification summary, or just grand total if
only_total is set.
"""
# Security check
if current_user_id is None:
RightsBO.anonymous_wants(self.session, Action.READ, proj_id)
# Anonymous can only see validated objects
# TODO: Dup code
# noinspection PyTypeHints
filters.statusfilter = "V" # type:ignore
user_id = -1
else:
user, _project = RightsBO.user_wants(self.session, current_user_id, Action.READ, proj_id)
user_id = user.id
# Prepare a where clause and parameters from filter
object_set: DescribedObjectSet = DescribedObjectSet(self.session, proj_id, filters)
from_, where, params = object_set.get_sql(user_id)
sql = """
SET LOCAL enable_seqscan=FALSE;
SELECT COUNT(*) nbr"""
if only_total:
sql += """, NULL nbr_v, NULL nbr_d, NULL nbr_p"""
else:
sql += """,
COUNT(CASE WHEN obh.classif_qual = 'V' THEN 1 END) nbr_v,
COUNT(CASE WHEN obh.classif_qual = 'D' THEN 1 END) nbr_d,
COUNT(CASE WHEN obh.classif_qual = 'P' THEN 1 END) nbr_p"""
sql += """
FROM """ + from_.get_sql() + " " + where.get_sql()
with CodeTimer("summary: V/D/P for %d using %s " % (proj_id, sql), logger):
res: ResultProxy = self.session.execute(sql, params)
nbr: int
nbr_v: Optional[int]
nbr_d: Optional[int]
nbr_p: Optional[int]
nbr, nbr_v, nbr_d, nbr_p = res.first() # type:ignore
return nbr, nbr_v, nbr_d, nbr_p
def query(self, current_user_id: Optional[int], acquisition_id: AcquisitionIDT) -> Optional[AcquisitionBO]:
ret = AcquisitionBO(self.ro_session, acquisition_id)
if not ret.exists():
return None
assert ret.acquis is not None
# Security check
if current_user_id is None:
project = RightsBO.anonymous_wants(self.ro_session, Action.READ, ret.acquis.sample.projid)
else:
_user, project = RightsBO.user_wants(self.session, current_user_id, Action.READ, ret.acquis.sample.projid)
mappings = ProjectMapping().load_from_project(project)
ret.map_free_columns(mappings.acquisition_mappings)
return ret
def read_taxo_stats(self, current_user_id: Optional[UserIDT],
sample_ids: SampleIDListT) -> List[SampleTaxoStats]:
# Get project IDs for the samples and verify rights
sample_set = EnumeratedSampleSet(self.ro_session, sample_ids)
project_ids = sample_set.get_projects_ids()
# Security check
if current_user_id is None:
[RightsBO.anonymous_wants(self.ro_session, Action.READ, project_id)
for project_id in project_ids]
else:
[RightsBO.user_wants(self.session, current_user_id, Action.READ, project_id)
for project_id in project_ids]
return sample_set.read_taxo_stats()
def search(self, current_user_id: Optional[UserIDT],
project_ids: ProjectIDListT,
orig_id_pattern: str) -> List[SampleBO]:
# Security check
if current_user_id is None:
[RightsBO.anonymous_wants(self.ro_session, Action.READ, project_id)
for project_id in project_ids]
else:
[RightsBO.user_wants(self.session, current_user_id, Action.READ, project_id)
for project_id in project_ids]
sample_set = DescribedSampleSet(self.ro_session, project_ids, orig_id_pattern)
# mappings = ProjectMapping().load_from_project(project)
# ret.map_free_columns(mappings.sample_mappings)
return sample_set.list()
def query(self, current_user_id: Optional[UserIDT], sample_id: SampleIDT) -> Optional[SampleBO]:
ret = SampleBO(self.ro_session, sample_id)
if not ret.exists():
return None
assert ret.sample is not None
assert ret.sample.projid is not None # TODO: Why need this?
# Security check
if current_user_id is None:
project = RightsBO.anonymous_wants(self.ro_session, Action.READ, ret.sample.projid)
else:
_user, project = RightsBO.user_wants(self.session, current_user_id, Action.READ, ret.sample.projid)
mappings = ProjectMapping().load_from_project(project)
ret.map_free_columns(mappings.sample_mappings)
return ret
def query(self, current_user_id: Optional[int], object_id: ObjectIDT) -> Optional[ObjectBO]:
ret = ObjectBO(self.ro_session, object_id)
if not ret.exists():
return None
# Security check
projid = ret.header.acquisition.sample.projid
if current_user_id is None:
project = RightsBO.anonymous_wants(self.session, Action.READ, projid)
else:
_user, project = RightsBO.user_wants(self.session, current_user_id, Action.READ, projid)
assert project is not None
mappings = ProjectMapping().load_from_project(project)
ret.map_free_columns(mappings.object_mappings)
return ret
def query(self, current_user_id: Optional[UserIDT], proj_id: ProjectIDT,
filters: ProjectFilters,
order_field: Optional[str] = None,
window_start: Optional[int] = None,
window_size: Optional[int] = None) \
-> Tuple[ObjectIDWithParentsListT, int]:
"""
Query the given project with given filters, return all IDs.
If provided order_field, the result is sorted by this field.
Ambiguity is solved in a stable (over calls) way.
window_start and window_size allow to select a window of data in the result.
"""
# Security check
if current_user_id is None:
RightsBO.anonymous_wants(self.session, Action.READ, proj_id)
# Anonymous can only see validated objects
# noinspection PyTypeHints
filters.statusfilter = "V" # type:ignore
user_id = -1
else:
user, _project = RightsBO.user_wants(self.session, current_user_id, Action.READ, proj_id)
user_id = user.id
# The order field has an impact on the query
order_clause = self.cook_order_clause(order_field)
# Prepare a where clause and parameters from filter
object_set: DescribedObjectSet = DescribedObjectSet(self.session, proj_id, filters)
from_, where, params = object_set.get_sql(user_id, order_clause)
if "obf." in where.get_sql():
# If the filter needs obj_field data it's more efficient to count with a window function
# than issuing a second query.
extra_col = ", COUNT(objid) OVER() AS total"
else:
# Otherwise, no need for obj_field in count, less DB buffers
extra_col = ", 0 AS total"
# The following hint is needed until we sort out why, time to time, there is a FTS on obj_head
sql = """
SET LOCAL enable_seqscan=FALSE;
SELECT obh.objid, acq.acquisid, sam.sampleid %s
FROM """ % extra_col + from_.get_sql() + " " + where.get_sql()
# Add order & window if relevant
if order_clause is not None:
sql += order_clause.get_sql()
if window_start is not None:
sql += " OFFSET %d" % window_start
if window_size is not None:
sql += " LIMIT %d" % window_size
with CodeTimer("query: for %d using %s " % (proj_id, sql), logger):
res: ResultProxy = self.session.execute(sql, params)
ids = []
total = 0
objid: int
acquisid: int
sampleid: int
for objid, acquisid, sampleid, total in res: # type:ignore
ids.append((objid, acquisid, sampleid, proj_id))
if total == 0:
# Total was not computed or left to 0
total, _nbr_v, _nbr_d, _nbr_p = self.summary(current_user_id, proj_id, filters, True)
return ids, total