dev(WoRMS): add info for deprecated taxon & lineage

Author: grololo06

py/API_models/taxonomy.py

@@ -14,6 +14,11 @@
 
 class TaxaSearchRsp(BaseModel):
     id: int = Field(title="Id", description="The taxon/category IDs.", example=14334)
+    status: str = Field(
+        title="Status",
+        description="The taxon/category status, 'D' for Deprecated, 'A' for Approved or 'N' for Not approved.",
+        example="P",
+    )
     aphia_id: Optional[int] = Field(
         title="Aphia Id",
         description="The Worms aphia_id of the taxon.",
@@ -33,73 +38,8 @@ class TaxaSearchRsp(BaseModel):
         title="Pr",
         description="1 if the taxon is in project list, 0 otherwise.",
         example=0,
-    )# TODO: dataclass_to_model(TaxonBO) to avoid repeated fields
-class TaxonModel_small(BaseModel):
-    __config__ = OrmConfig
-    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.",
-        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",
-    )
-    status: str = Field(
-        title="Status",
-        description="The taxon/category status, 'D' for Deprecated, 'A' for Approved or 'N' for Notapproved.",
-        example="P",
-    )
-    nb_objects: int = Field(
-        title="Nb objects",
-        description="How many objects are classified in this category.",
-        example=34118,
-    )
-    nb_children_objects: int = Field(
-        title="Nb children objects",
-        description="How many objects are classified in this category children (not itself).",
-        example=30091727,
-    )
-    display_name: str = Field(
-        title="Display name",
-        description="The taxon/category display name.",
-        example="living<",
-    )
-    lineage: List[str] = Field(
-        title="Lineage",
-        description="The taxon/category name of ancestors, including self, in first.",
-        example=["living"],
-    )
-    id_lineage: List[int] = Field(
-        title="Id lineage",
-        description="The taxon/category IDs of ancestors, including self, in first.",
-        example=[1],
-    )
-    children: List[int] = Field(
-        title="Children",
-        description="The taxon/category IDs of children.",
-        example=[
-            92952,
-            2,
-            92329,
-            85048,
-            4,
-            93599,
-            93687,
-            85011,
-            92951,
-            93698,
-            84961,
-            92696,
-            3,
-        ],
-    )
+    )  # TODO: dataclass_to_model(TaxonBO) to avoid repeated fields
+
 
 # TODO: dataclass_to_model(TaxonBO) to avoid repeated fields
 class TaxonModel(BaseModel):
@@ -131,7 +71,13 @@ class TaxonModel(BaseModel):
     id_lineage: List[int] = Field(
         title="Id lineage",
         description="The taxon/category IDs of ancestors, including self, in first.",
-        example=[1],    )
+        example=[1],
+    )
+    lineage_status: str = Field(
+        title="Id lineage",
+        description="The taxon ancestors' status, including self, in first.",
+        example="DDAAA",
+    )
     renm_id: Optional[int] = Field(
         title="Renm id",
         description="The advised replacement ID if the taxon/category is deprecated.",
@@ -210,35 +156,12 @@ class TaxonomyTreeStatus(BaseModel):
     )
 
 
-class TaxoWormsModel(BaseModel):
+class AddWormsTaxonModel(BaseModel):
     aphia_id: Optional[int] = Field(
         title="AphiaId",
-        description="The unique numeric aphia_id of the taxon if in Worms.",
+        description="The unique numeric aphia_id of the taxon in WoRMS.",
         example=12876,
     )
-    rank: Optional[str] = Field(
-        title="Rank",
-        description="The rank in Worms of the taxon.",
-        example="Echinodermata X",
-    )
-    name: str = Field(
-        title="Name", description="The name of the taxon.", example="Echinodermata X"
-    )
-    lineage: Dict[str, Any] = Field(
-        title="Taxon Worms lineage",
-        description="The lineage of the taxon in Worms.",
-        example={"2": {"AphiaID": 1, "rank": "Superdomain", "scientificname": "Biota"}},
-    )
-    status: str = Field(
-        title="Worms taxon status",
-        description="The taxon status in worms 'accepted' .",
-        example="accepted",
-    )
-    creator_email: Any = Field(
-        title="Creator email",
-        description="Email of the creator of the taxon.",
-        example="creator.user@emaim.com",
-    )
 
 
 class _Taxo2Model(BaseModel):

py/API_operations/TaxonomyService.py

@@ -92,7 +92,12 @@ def search(
             renm_id = a_rec["rename_to"]
             is_preset = 1 if classif_id in preset else 0
             to_add = TaxaSearchRsp(
-                id=classif_id, renm_id=renm_id, text=a_rec["display_name"], pr=is_preset
+                id=classif_id,
+                aphia_id=a_rec["aphia_id"],
+                status=a_rec["taxostatus"],
+                renm_id=renm_id,
+                text=a_rec["display_name"],
+                pr=is_preset,
             )
             if classif_id in return_order:
                 mru_ret.append(to_add)

py/BO/Taxonomy.py

@@ -30,6 +30,7 @@
 
 logger = get_logger(__name__)
 
+
 class TaxonBO(object):
     """
     Holder of a node of a taxonomy tree. Used for Unieuk tree and for WoRMS one.
@@ -43,6 +44,7 @@ class TaxonBO(object):
         "display_name",
         "lineage",
         "id_lineage",
+        "lineage_status",
         "renm_id",
         "nb_objects",
         "nb_children_objects",
@@ -62,10 +64,11 @@ def __init__(
         nb_children_objects: int,
         lineage: List[str],
         id_lineage: List[ClassifIDT],
-        aphia_id:Optional[int]=None,
-        rank:Optional[str]=None,
-        closest_worms:Optional[int]=None,
-        closest_phylo:Optional[int]=None,
+        lineage_status: str,
+        aphia_id: Optional[int] = None,
+        rank: Optional[str] = None,
+        closest_worms: Optional[int] = None,
+        closest_phylo: Optional[int] = None,
         children: Optional[List[ClassifIDT]] = None,
         rename_id: Optional[int] = None,
     ):
@@ -87,10 +90,11 @@ def __init__(
         self.display_name = display_name
         self.lineage = lineage
         self.id_lineage = id_lineage
-        self.aphia_id=aphia_id
-        self.rank=rank
-        self.closest_worms=closest_worms
-        self.closest_phylo=closest_phylo
+        self.lineage_status = lineage_status
+        self.aphia_id = aphia_id
+        self.rank = rank
+        self.closest_worms = closest_worms
+        self.closest_phylo = closest_phylo
         self.children = children
 
     def top_down_lineage(self, sep: str = ">"):
@@ -117,9 +121,7 @@ def keep_phylo(session: Session, classif_id_seen: ClassifIDListT):
         Return input IDs, for the existing ones with 'P' type.
         """
         sql = text(
-            "SELECT id "
-            "  FROM taxonomy "
-            " WHERE id = ANY (:een) AND taxotype = 'P'"
+            "SELECT id " "  FROM taxonomy " " WHERE id = ANY (:een) AND taxotype = 'P'"
         )
         res: Result = session.execute(sql, {"een": list(classif_id_seen)})
         return {an_id for an_id, in res}
@@ -266,6 +268,7 @@ def query(
                 tf.c.aphia_id,
                 tf.c.rename_to,
                 tf.c.display_name,
+                tf.c.taxostatus,
                 priority,
             ],
             bind=bind,
@@ -494,6 +497,8 @@ def do_deletes(cls, session: Session, to_delete: List[ClassifIDT]) -> None:
                 session.delete(taxon)
         finally:
             session.execute(text("alter table taxonomy enable trigger all"))
+
+
 class TaxonBOSet(object):
     """
     Many taxa.
@@ -548,22 +553,25 @@ def __init__(self, session: Session, taxon_ids: ClassifIDListT):
             cat_type = lst_rec[3]
             cat_status = lst_rec[4]
             rename_id = lst_rec[6]
-            aphia_id : Optional[int]  = lst_rec[2]
-            rank : Optional[str]  = lst_rec[5]
+            aphia_id: Optional[int] = lst_rec[2]
+            rank: Optional[str] = lst_rec[5]
             numf = 7
             lineage_id = [an_id for an_id in lst_rec[0::numf] if an_id is not None]
+            lineage_status = "".join(
+                [a_status for a_status in lst_rec[4::numf] if a_status is not None]
+            )
             lineage = [name for name in lst_rec[1::numf] if name is not None]
-            closest_phylo:Optional[int]=None
-            closest_worms:Optional[int]=None
-            if cat_type=="M":
-                next=[i for i,r in enumerate(lst_rec[3::numf]) if r=="P"]
+            closest_phylo: Optional[int] = None
+            if cat_type == "M":
+                next = [i for i, r in enumerate(lst_rec[3::numf]) if r == "P"]
                 if len(next):
-                    i=next[0]
-                    closest_phylo=lst_rec[0::numf][i]
-            next=[i for i,r in enumerate(lst_rec[2::numf]) if r is not None]
+                    i = next[0]
+                    closest_phylo = lst_rec[0::numf][i]
+            closest_worms: Optional[int] = None
+            next = [i for i, r in enumerate(lst_rec[2::numf]) if r is not None]
             if len(next):
-                i=next[0]
-                closest_worms=lst_rec[0::numf][i]
+                i = next[0]
+                closest_worms = lst_rec[0::numf][i]
             # assert lineage_id[-1] in (1, 84960, 84959), "Unexpected root %s" % str(lineage_id[-1])
             self.taxa.append(
                 TaxonBO(
@@ -574,11 +582,12 @@ def __init__(self, session: Session, taxon_ids: ClassifIDListT):
                     nbobj2,  # type:ignore
                     lineage,
                     lineage_id,  # type:ignore
+                    lineage_status,
                     rename_id=rename_id,
                     aphia_id=aphia_id,
                     rank=rank,
                     closest_worms=closest_worms,
-                    closest_phylo=closest_phylo
+                    closest_phylo=closest_phylo,
                 )
             )
         self.get_children(session)
@@ -603,7 +612,6 @@ def get_cardinalities(self, session: Session):
         for an_id, a_sum in qry:
             bos_per_id[an_id].nb_objects = a_sum
 
-
     def as_list(self) -> List[TaxonBO]:
         return self.taxa
 

py/main.py

@@ -96,7 +96,7 @@
     TaxonomyTreeStatus,
     TaxonUsageModel,
     TaxonCentral,
-    TaxoWormsModel,
+    AddWormsTaxonModel,
 )
 from API_operations.CRUD.Collections import CollectionsService
 from API_operations.CRUD.Constants import ConstantsService
@@ -187,7 +187,7 @@
 
 app = FastAPI(
     title="EcoTaxa",
-    version="0.0.41",
+    version="0.0.42",
     # openapi URL as seen from navigator, this is included when /docs is required
     # which serves swagger-ui JS app. Stay in /api sub-path.
     openapi_url="/api/openapi.json",