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MCC APSIS
NACSOS
NACSOS Core
Commits
c38fd486
Commit
c38fd486
authored
2 years ago
by
Tim Repke
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add deletion, listing to resolved annotations
parent
5abf673a
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Pipeline
#882
failed
2 years ago
Stage: build
Stage: test
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1 changed file
server/api/routes/annotations.py
+113
-20
113 additions, 20 deletions
server/api/routes/annotations.py
with
113 additions
and
20 deletions
server/api/routes/annotations.py
+
113
−
20
View file @
c38fd486
from
pydantic
import
BaseModel
from
sqlalchemy
import
select
from
sqlalchemy.orm
import
load_only
from
sqlalchemy.ext.asyncio
import
AsyncSession
from
fastapi
import
APIRouter
,
Depends
,
HTTPException
,
status
as
http_status
,
Query
from
nacsos_data.db.schemas
import
BotAnnotationMetaData
,
BotAnnotation
from
nacsos_data.db.schemas
import
\
BotAnnotationMetaData
,
\
AssignmentScope
,
\
User
,
\
Annotation
from
nacsos_data.models.annotations
import
\
AnnotationSchemeModel
,
\
AssignmentScopeModel
,
\
...
...
@@ -17,8 +22,9 @@ from nacsos_data.models.bot_annotations import \
AnnotationFilters
,
\
BotAnnotationModel
,
\
AnnotationCollection
,
\
BotMetaResolve
,
\
GroupedBotAnnotation
BotMetaResolve
,
\
GroupedBotAnnotation
,
AnnotationCollectionDB
,
BotKind
,
BotAnnotationMetaDataBaseModel
from
nacsos_data.models.users
import
UserModel
from
nacsos_data.models.items
import
AnyItemModel
from
nacsos_data.db.crud.items
import
read_any_item_by_item_id
from
nacsos_data.db.crud.projects
import
read_project_by_id
...
...
@@ -44,10 +50,11 @@ from nacsos_data.db.crud.annotations import \
ItemWithCount
,
\
AssignmentCounts
,
\
UserProjectAssignmentScope
,
\
store_assignments
store_assignments
,
\
store_resolved_bot_annotations
,
update_resolved_bot_annotations
from
nacsos_data.util.annotations.resolve
import
\
AnnotationFilterObject
,
\
get_resolved_item_annotations
get_resolved_item_annotations
,
read_bot_annotations
from
nacsos_data.util.annotations.validation
import
\
merge_scheme_and_annotations
,
\
annotated_scheme_to_annotations
,
\
...
...
@@ -60,8 +67,7 @@ from server.api.errors import \
NoNextAssignmentWarning
,
\
ProjectNotFoundError
,
\
AnnotationSchemeNotFoundError
,
\
MissingInformationError
,
\
NoDataForKeyError
MissingInformationError
from
server.util.security
import
UserPermissionChecker
from
server.data
import
db_engine
...
...
@@ -79,14 +85,17 @@ class AnnotationItem(AnnotatedItem):
@router.get
(
'
/schemes/definition/{annotation_scheme_id}
'
,
response_model
=
AnnotationSchemeModel
|
AnnotationSchemeModel
Flat
)
response_model
=
AnnotationSchemeModel
Flat
|
AnnotationSchemeModel
)
async
def
get_scheme_definition
(
annotation_scheme_id
:
str
,
flat
:
bool
=
Query
(
default
=
False
))
->
AnnotationSchemeModel
|
AnnotationSchemeModelFlat
:
flat
:
bool
=
Query
(
default
=
False
),
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_read
'
)))
\
->
AnnotationSchemeModelFlat
|
AnnotationSchemeModel
:
"""
This endpoint returns the detailed definition of an annotation scheme.
:param annotation_scheme_id: database id of the annotation scheme.
:param flat: True to get the flattened scheme
:param permissions:
:return: a single annotation scheme
"""
scheme
=
await
read_annotation_scheme
(
annotation_scheme_id
=
annotation_scheme_id
,
db_engine
=
db_engine
)
...
...
@@ -331,6 +340,30 @@ async def make_assignments(payload: MakeAssignmentsRequestModel,
return
assignments
@router.get
(
'
/config/scopes/{scheme_id}
'
,
response_model
=
list
[
AssignmentScopeModel
])
async
def
get_assignment_scopes_for_scheme
(
scheme_id
:
str
,
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_read
'
)))
\
->
list
[
AssignmentScopeModel
]:
async
with
db_engine
.
session
()
as
session
:
# type: AsyncSession
return
[
AssignmentScopeModel
.
parse_obj
(
scope
.
__dict__
)
for
scope
in
(
await
session
.
execute
(
select
(
AssignmentScope
)
.
where
(
AssignmentScope
.
annotation_scheme_id
==
scheme_id
))
).
scalars
().
all
()]
@router.get
(
'
/config/annotators/{scheme_id}
'
,
response_model
=
list
[
UserModel
])
async
def
get_annotators_for_scheme
(
scheme_id
:
str
,
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_edit
'
)))
\
->
list
[
UserModel
]:
async
with
db_engine
.
session
()
as
session
:
# type: AsyncSession
return
[
UserModel
.
parse_obj
(
user
.
__dict__
)
for
user
in
(
await
session
.
execute
(
select
(
User
)
.
join
(
Annotation
)
.
distinct
()
.
where
(
Annotation
.
annotation_scheme_id
==
scheme_id
))).
scalars
().
all
()]
class
ResolutionProposalResponse
(
BaseModel
):
collection
:
AnnotationCollection
proposal
:
dict
[
str
,
list
[
GroupedBotAnnotation
]]
...
...
@@ -338,8 +371,9 @@ class ResolutionProposalResponse(BaseModel):
class
SavedResolutionResponse
(
BaseModel
):
name
:
str
meta
:
BotMetaResolve
saved
:
dict
[
str
,
list
[
BotAnnotation
Model
]]
saved
:
dict
[
str
,
list
[
Grouped
BotAnnotation
]]
@router.get
(
'
/config/resolve/
'
,
response_model
=
ResolutionProposalResponse
)
...
...
@@ -391,19 +425,78 @@ async def get_resolved_annotations(strategy: ResolutionMethod,
return
ResolutionProposalResponse
(
collection
=
collection
,
proposal
=
resolved
,
scheme_flat
=
flat_labels
)
class
ResolutionPayload
(
BaseModel
):
name
:
str
strategy
:
ResolutionMethod
filters
:
AnnotationFilters
ignore_order
:
bool
ignore_hierarchy
:
bool
collection
:
AnnotationCollectionDB
bot_annotations
:
list
[
BotAnnotationModel
]
@router.put
(
'
/config/resolve/
'
,
response_model
=
str
)
async
def
save_resolved_annotations
(
data
:
ResolutionPayload
,
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_edit
'
))):
meta_id
=
await
store_resolved_bot_annotations
(
project_id
=
permissions
.
permissions
.
project_id
,
name
=
data
.
name
,
algorithm
=
data
.
strategy
,
filters
=
data
.
filters
,
ignore_hierarchy
=
data
.
ignore_hierarchy
,
ignore_repeat
=
data
.
ignore_order
,
collection
=
data
.
collection
,
bot_annotations
=
data
.
bot_annotations
,
db_engine
=
db_engine
)
return
meta_id
@router.put
(
'
/config/resolve/update
'
)
async
def
update_resolved_annotations
(
bot_annotation_metadata_id
:
str
,
name
:
str
,
bot_annotations
:
list
[
BotAnnotationModel
],
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_edit
'
)))
->
None
:
await
update_resolved_bot_annotations
(
bot_annotation_metadata_id
=
bot_annotation_metadata_id
,
name
=
name
,
bot_annotations
=
bot_annotations
,
db_engine
=
db_engine
)
@router.get
(
'
/config/resolved-list/
'
,
response_model
=
list
[
BotAnnotationMetaDataBaseModel
])
async
def
list_saved_resolved_annotations
(
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_read
'
))):
async
with
db_engine
.
session
()
as
session
:
# type: AsyncSession
exports
=
(
await
session
.
execute
(
select
(
BotAnnotationMetaData
)
.
where
(
BotAnnotationMetaData
.
project_id
==
permissions
.
permissions
.
project_id
,
BotAnnotationMetaData
.
kind
==
BotKind
.
RESOLVE
)
.
options
(
load_only
(
BotAnnotationMetaData
.
bot_annotation_metadata_id
,
BotAnnotationMetaData
.
annotation_scheme_id
,
BotAnnotationMetaData
.
annotation_scope_id
,
BotAnnotationMetaData
.
project_id
,
BotAnnotationMetaData
.
name
,
BotAnnotationMetaData
.
kind
,
BotAnnotationMetaData
.
time_updated
,
BotAnnotationMetaData
.
time_created
))))
\
.
scalars
().
all
()
print
([
BotAnnotationMetaDataBaseModel
.
parse_obj
(
e
.
__dict__
)
for
e
in
exports
])
return
[
BotAnnotationMetaDataBaseModel
.
parse_obj
(
e
.
__dict__
)
for
e
in
exports
]
@router.get
(
'
/config/resolved/:bot_annotation_meta_id
'
,
response_model
=
SavedResolutionResponse
)
async
def
get_saved_resolved_annotations
(
bot_annotation_meta_id
:
str
,
async
def
get_saved_resolved_annotations
(
bot_annotation_meta
data
_id
:
str
,
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_edit
'
))):
bot_annotations
=
await
read_bot_annotations
(
bot_annotation_metadata_id
=
bot_annotation_metadata_id
,
db_engine
=
db_engine
)
async
with
db_engine
.
session
()
as
session
:
# type: AsyncSession
meta
=
await
session
.
get
(
BotAnnotationMetaData
,
bot_annotation_meta_id
)
if
meta
is
None
:
raise
NoDataForKeyError
(
f
'
No `BotAnnotationMetaData` for
"
{
bot_annotation_meta_id
}
"
!
'
)
bot_annotations
=
(
await
session
.
scalars
(
select
(
BotAnnotation
).
where
(
BotAnnotation
.
bot_annotation_metadata_id
==
bot_annotation_meta_id
))).
all
()
meta
:
BotAnnotationMetaData
=
(
await
session
.
execute
(
select
(
BotAnnotationMetaData
)
.
where
(
BotAnnotationMetaData
.
bot_annotation_metadata_id
==
bot_annotation_metadata_id
)))
\
.
scalars
().
one
()
return
SavedResolutionResponse
(
name
=
meta
.
name
,
meta
=
meta
.
meta
,
# FIXME
saved
=
{}
# saved=[BotAnnotationModel.parse_obj(bot_annotation) for bot_annotation in bot_annotations]
saved
=
bot_annotations
)
@router.delete
(
'
/config/resolved/:bot_annotation_meta_id
'
)
async
def
delete_saved_resolved_annotations
(
bot_annotation_metadata_id
:
str
,
permissions
=
Depends
(
UserPermissionChecker
(
'
annotations_edit
'
))):
async
with
db_engine
.
session
()
as
session
:
# type: AsyncSession
meta
:
BotAnnotationMetaData
=
(
await
session
.
execute
(
select
(
BotAnnotationMetaData
)
.
where
(
BotAnnotationMetaData
.
bot_annotation_metadata_id
==
bot_annotation_metadata_id
)))
\
.
scalars
().
one
()
await
session
.
delete
(
meta
)
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