ecotaxa/ecotaxa_front#764 + Some nullity & calls clarification found …

…out while trying last version of mypy.

py/API_models/crud.py

@@ -219,7 +219,8 @@ class _AddedToProject(BaseModel):
  process_free_cols: FreeColT = Field(title="Process free cols", description="Process free columns.", default={},
  example={"nb_images": "t01"})
  bodc_variables: Dict[str, Optional[str]] = Field(title="Expressions for computing standard BODC quantities.",
- description="BODC quantities from columns. Only the 3 keys listed in example are valid.", default={},
+ description="BODC quantities from columns. Only the 3 keys listed in example are valid.",
+ default={},
  example={"subsample_coef": "1/ssm.sub_part",
  "total_water_volume": "sam.tot_vol/1000",
  "individual_volume": "4.0/3.0*math.pi*(math.sqrt(obj.area/math.pi)*ssm.pixel_size)**3"})

py/API_models/helpers/DBtoModel.py

@@ -50,6 +50,7 @@ def _sqlalchemy_to_pydantic(db_model: T, *,
  not_null_cols = set()
  # Build model from ORM fields
  mapper = inspect(db_model)
+ assert mapper is not None
  for attr in mapper.attrs:
  if not isinstance(attr, ColumnProperty):
  continue

py/API_models/taxonomy.py

@@ -30,7 +30,7 @@ class TaxonModel(BaseModel):
  id: int = Field(title="Id", description="The taxon/category IDs.", example=1)
  renm_id: Optional[int] = Field(title="Renm id",
  description="The advised replacement ID if the taxon/category is deprecated.",
- example="null")
+ default=None, example="null")
  name: str = Field(title="Name", description="The taxon/category verbatim name.", example="living")
  type: str = Field(title="Type", description="The taxon/category type, 'M' for Morpho or 'P' for Phylo.",
  example="P")

py/API_operations/Consistency.py

@@ -60,3 +60,4 @@ def check_partial_time_space(self) -> List[str]:
  """
  Objects which are partially located in time/space.
  """
+ return []

py/API_operations/JsonDumper.py

@@ -136,7 +136,7 @@ def _find_what_to_dump(self) -> None:
 
  with CodeTimer("Get IDs:", logger):
  res: Result = self.session.execute(text(sql), params)
- ids = [r['objid'] for r in res]
+ ids = [r['objid'] for r in res.mappings()]
 
  logger.info("NB OBJIDS=%d", len(ids))
 

py/API_operations/Prediction.py

@@ -19,7 +19,6 @@
 from FS.MachineLearningModels import SavedModels
 from FS.Vault import Vault
 from helpers.DynamicLogs import get_logger, LogsSwitcher
-
 # TODO: Move somewhere else
 from .helpers.JobService import JobServiceBase, ArgsDict
 from .helpers.Service import Service
@@ -54,7 +53,6 @@ def run(self, current_user_id: UserIDT) -> PredictionRsp:
  return ret
 
  def init_args(self, args: ArgsDict) -> ArgsDict:
- super().init_args(args)
  args["req"] = self.req.dict()
  args["filters"] = self.filters
  return args

py/API_operations/exports/DarwinCore.py

@@ -413,7 +413,8 @@ def build_meta(self) -> Optional[EMLMeta]:
 
  def get_taxo_coverage(self, project_ids: ProjectIDListT) -> List[EMLTaxonomicClassification]:
  """
- Taxonomic coverage is the list of taxa which can be found in the projects.
+ Taxonomic coverage is the list of taxa which can be found in the projects, regardless
+ of their validation state.
  """
  ret: List[EMLTaxonomicClassification] = []
  # Fetch the used taxa in the projects

py/BO/CommonObjectSets.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # This file is part of Ecotaxa, see license.md in the application root directory for license informations.
-# Copyright (C) 2015-2020 Picheral, Colin, Irisson (UPMC-CNRS)
+# Copyright (C) 2015-2022 Picheral, Colin, Irisson (UPMC-CNRS)
 #
 from API_models.filters import ProjectFiltersDict
 from BO.ObjectSet import DescribedObjectSet

py/BO/Object.py

@@ -82,7 +82,7 @@ def get_history(self) -> HistoricalClassificationListT:
  ObjectsClassifHisto.objid == self.header.objid)
  qry = qry.outerjoin(User)
  qry = qry.outerjoin(Taxonomy, Taxonomy.id == och.classif_id)
- ret = [HistoricalClassification(**rec) for rec in qry]
+ ret = [HistoricalClassification(**rec._mapping) for rec in qry]
  return ret
 
  @staticmethod

py/BO/ObjectSetQueryPlus.py

@@ -284,7 +284,7 @@ def get_row_source(self, ro_session: Session, wrn_fct: Optional[Callable[[str],
  res = ro_session.execute(text(sql), params)
  if self.sum_exp is None:
  # Pure SQL, emit each row
- for a_simple_row in res:
+ for a_simple_row in res.mappings():
  yield dict(a_simple_row)
  else:
  assert self.grouping != ResultGrouping.NO_GROUPING

py/BO/Taxonomy.py

@@ -65,7 +65,7 @@ def find_ids(session: Session, classif_id_seen: List):
  " FROM taxonomy "
  " WHERE id = ANY (:een)")
  res: Result = session.execute(sql, {"een": list(classif_id_seen)})
- return {int(r['id']) for r in res}
+ return {an_id for an_id, in res}
 
  @staticmethod
  def keep_phylo(session: Session, classif_id_seen: ClassifIDListT):

py/DB/helpers/Core.py

@@ -6,4 +6,4 @@
 # SQLAlchemy core imports, for re-export
 #
 
-from sqlalchemy.sql import select, Select
+from sqlalchemy.sql import select, Select, delete, Delete, update, Update

py/DB/helpers/__init__.py

@@ -3,5 +3,4 @@
 # This file is part of Ecotaxa, see license.md in the application root directory for license informations.
 # Copyright (C) 2015-2020 Picheral, Colin, Irisson (UPMC-CNRS)
 #
-from sqlalchemy.engine import Result # type: ignore
-from sqlalchemy.orm import Session
+from sqlalchemy.engine import Result, MappingResult # type: ignore

py/formats/DarwinCore/models.py

@@ -95,6 +95,14 @@ class BasisOfRecordEnum(str, Enum):
  livingSpecimen = 'LivingSpecimen'
 
 
+class IdentificationVerificationEnum(str, Enum):
+ # for identifications generated by an algorithm and not validated by human.
+ predictedByMachine = 'PredictedByMachine'
+ # for identifications generated by an algorithm and verified to be correct by a
+ # human, this is also referred as validated data
+ validatedByHuman = 'ValidatedByHuman'
+
+
 class OccurrenceStatusEnum(str, Enum):
  present = 'present'
  absent = 'absent'
@@ -108,6 +116,13 @@ class DwcOccurrence(BaseModel):
  # Record-level fields
  basisOfRecord: BasisOfRecordEnum = Field(term="http://rs.tdwg.org/dwc/terms/basisOfRecord")
 
+ # identified By # TODO
+
+ identificationVerificationStatus: Optional[IdentificationVerificationEnum] \
+ = Field(term="https://dwc.tdwg.org/list/#dwc_identificationVerificationStatus")
+ # identification References # TODO
+ # associated Media # TODO
+
  # Identification fields
  scientificName: str = Field(term="http://rs.tdwg.org/dwc/terms/scientificName")
  # LSID from WoRMS for EMODnet

py/helpers/fastApiUtils.py

@@ -80,8 +80,8 @@ class BearerOrCookieAuth(OAuth2):
  def __init__(
  self,
  tokenUrl: str,
- scheme_name: str = None,
- scopes: dict = None,
+ scheme_name: Optional[str] = None,
+ scopes: Optional[dict] = None,
  auto_error: bool = True,
  ):
  if not scopes:
@@ -90,7 +90,7 @@ def __init__(
  super().__init__(flows=flows, scheme_name=scheme_name, auto_error=auto_error)
 
  async def __call__(self, request: Request) -> Optional[str]:
- header_authorization: str = request.headers.get("Authorization")
+ header_authorization: Optional[str] = request.headers.get("Authorization")
  session_cookie: Optional[str] = request.cookies.get("session")
 
  header_scheme, header_param = get_authorization_scheme_param(