tox

api/api.py

@@ -3,9 +3,10 @@
 from fastapi import Depends, FastAPI
 from fastapi_versioning import VersionedFastAPI, version
 
-from api.models import (Item, ReferenceInfo, ReferenceResult,
-                        StructureInfo, StructureResult, TaxonInfo, TaxonResult, TripletResult)
-from api.queries import (combine_and_filter_outputs, get_matching_references_from_reference_in_item,
+from api.models import (Item, ReferenceInfo, ReferenceResult, StructureInfo,
+                        StructureResult, TaxonInfo, TaxonResult, TripletResult)
+from api.queries import (combine_and_filter_outputs,
+                         get_matching_references_from_reference_in_item,
                          get_matching_references_from_structure_in_item,
                          get_matching_references_from_taxon_in_item,
                          get_matching_structures_from_reference_in_item,
@@ -55,14 +56,16 @@ async def search_triplets(item: Item, dm: DataModel = Depends(get_dm)) -> Triple
     selected_structures = get_matching_structures_from_structure_in_item(dm, item)
     selected_taxa = get_matching_taxa_from_taxon_in_item(dm, item)
 
-    triplets_set = dm.get_triples_for(reference_ids=selected_references,
-                                      structure_ids=selected_structures,
-                                      taxon_ids=selected_taxa)
+    triplets_set = dm.get_triples_for(
+        reference_ids=selected_references,
+        structure_ids=selected_structures,
+        taxon_ids=selected_taxa,
+    )
 
     if item.limit == 0:
         triplets = list(triplets_set)
     else:
-        triplets = list(triplets_set)[:item.limit]
+        triplets = list(triplets_set)[: item.limit]
 
     return TripletResult(
         triplets=triplets,
@@ -91,7 +94,9 @@ async def search_triplets(item: Item, dm: DataModel = Depends(get_dm)) -> Triple
 
 @app.post("/structures")
 @version(1, 0)
-async def search_structures(item: Item, dm: DataModel = Depends(get_dm)) -> StructureResult:
+async def search_structures(
+    item: Item, dm: DataModel = Depends(get_dm)
+) -> StructureResult:
     matching_structures_by_structure = get_matching_structures_from_structure_in_item(
         dm, item
     )
@@ -100,15 +105,22 @@ async def search_structures(item: Item, dm: DataModel = Depends(get_dm)) -> Stru
         dm, item
     )
 
-    ids = combine_and_filter_outputs([matching_structures_by_reference,
-                                      matching_structures_by_taxon,
-                                      matching_structures_by_structure], limit=item.limit)
+    ids = combine_and_filter_outputs(
+        [
+            matching_structures_by_reference,
+            matching_structures_by_taxon,
+            matching_structures_by_structure,
+        ],
+        limit=item.limit,
+    )
 
     dict_items = dm.get_dict_of_sid_to_smiles(ids)
 
     return StructureResult(
         ids=dict_items.keys(),
-        structures={sid: StructureInfo(smiles=value) for sid, value in dict_items.items()},
+        structures={
+            sid: StructureInfo(smiles=value) for sid, value in dict_items.items()
+        },
         description="Structures matching the query",
         count=len(dict_items),
     )
@@ -121,9 +133,14 @@ async def search_taxa(item: Item, dm: DataModel = Depends(get_dm)) -> TaxonResul
     matching_taxa_by_structure = get_matching_taxa_from_structure_in_item(dm, item)
     matching_taxa_by_reference = get_matching_taxa_from_reference_in_item(dm, item)
 
-    ids = combine_and_filter_outputs([matching_taxa_by_reference,
-                                      matching_taxa_by_structure,
-                                      matching_taxa_by_taxon], limit=item.limit)
+    ids = combine_and_filter_outputs(
+        [
+            matching_taxa_by_reference,
+            matching_taxa_by_structure,
+            matching_taxa_by_taxon,
+        ],
+        limit=item.limit,
+    )
 
     dict_items = dm.get_dict_of_tid_to_taxon_name(ids)
 
@@ -137,7 +154,9 @@ async def search_taxa(item: Item, dm: DataModel = Depends(get_dm)) -> TaxonResul
 
 @app.post("/references")
 @version(1, 0)
-async def search_references(item: Item, dm: DataModel = Depends(get_dm)) -> ReferenceResult:
+async def search_references(
+    item: Item, dm: DataModel = Depends(get_dm)
+) -> ReferenceResult:
     matching_references_by_reference = get_matching_references_from_reference_in_item(
         dm, item
     )
@@ -146,9 +165,14 @@ async def search_references(item: Item, dm: DataModel = Depends(get_dm)) -> Refe
     )
     matching_references_by_taxon = get_matching_references_from_taxon_in_item(dm, item)
 
-    ids = combine_and_filter_outputs([matching_references_by_reference,
-                                      matching_references_by_structure,
-                                      matching_references_by_taxon], limit=item.limit)
+    ids = combine_and_filter_outputs(
+        [
+            matching_references_by_reference,
+            matching_references_by_structure,
+            matching_references_by_taxon,
+        ],
+        limit=item.limit,
+    )
 
     dict_items = dm.get_dict_of_rid_to_reference_doi(ids)
 

api/queries.py

@@ -5,10 +5,14 @@
 from api.models import Item
 from model import DataModel
 
-logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s"
+)
 
 
-def get_matching_references_from_reference_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_references_from_reference_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     """Returns the WID of matching references."""
     references = None
     if item.reference_doi and item.reference_wid:
@@ -31,7 +35,9 @@ def get_matching_references_from_reference_in_item(dm: DataModel, item: Item) ->
     return references
 
 
-def get_matching_structures_from_structure_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_structures_from_structure_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     """Returns the WID of matching structures."""
     structures = None
 
@@ -99,7 +105,10 @@ def get_matching_taxa_from_taxon_in_item(dm: DataModel, item: Item) -> set[int]
 
     return taxa
 
-def get_matching_references_from_structure_in_item(dm: DataModel, item: Item) -> set[int] | None:
+
+def get_matching_references_from_structure_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     structures = get_matching_structures_from_structure_in_item(dm, item)
 
     if structures is None:
@@ -108,7 +117,9 @@ def get_matching_references_from_structure_in_item(dm: DataModel, item: Item) ->
     return dm.get_references_of_structures(structures)
 
 
-def get_matching_references_from_taxon_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_references_from_taxon_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     taxa = get_matching_taxa_from_taxon_in_item(dm, item)
 
     if taxa is None:
@@ -117,7 +128,9 @@ def get_matching_references_from_taxon_in_item(dm: DataModel, item: Item) -> set
     return dm.get_references_of_taxa(taxa)
 
 
-def get_matching_structures_from_reference_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_structures_from_reference_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     references = get_matching_references_from_reference_in_item(dm, item)
 
     if references is None:
@@ -126,7 +139,9 @@ def get_matching_structures_from_reference_in_item(dm: DataModel, item: Item) ->
     return dm.get_structures_of_references(references)
 
 
-def get_matching_structures_from_taxon_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_structures_from_taxon_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     taxa = get_matching_taxa_from_taxon_in_item(dm, item)
 
     if taxa is None:
@@ -142,7 +157,9 @@ def get_matching_structures_from_taxon_in_item(dm: DataModel, item: Item) -> set
     return out
 
 
-def get_matching_taxa_from_structure_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_taxa_from_structure_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     structures = get_matching_structures_from_structure_in_item(dm, item)
 
     if structures is None:
@@ -151,7 +168,9 @@ def get_matching_taxa_from_structure_in_item(dm: DataModel, item: Item) -> set[i
     return dm.get_taxa_of_structures(structures)
 
 
-def get_matching_taxa_from_reference_in_item(dm: DataModel, item: Item) -> set[int] | None:
+def get_matching_taxa_from_reference_in_item(
+    dm: DataModel, item: Item
+) -> set[int] | None:
     references = get_matching_references_from_reference_in_item(dm, item)
 
     if references is None:

doc/api/paths/references/post.yaml

@@ -1,6 +1,6 @@
 post:
   operationId: search_references
-  security: []
+  security: [ ]
   summary: |
     Search references using parameters
   description: |
@@ -23,10 +23,10 @@ post:
     '404':
       description: No reference matching the given search could be found
       content:
-          application/json:
-              schema:
-                type: object
-                properties:
-                    message:
-                      type: string
-                      example: No reference matching the given search could be found
+        application/json:
+          schema:
+            type: object
+            properties:
+              message:
+                type: string
+                example: No reference matching the given search could be found

doc/api/paths/structures/post.yaml

@@ -1,6 +1,6 @@
 post:
   operationId: search_structures
-  security: []
+  security: [ ]
   summary: |
     Search structures using parameters
   description: |
@@ -23,20 +23,20 @@ post:
     '404':
       description: No structure matching the given query search be found
       content:
-          application/json:
-              schema:
-                type: object
-                properties:
-                    message:
-                      type: string
-                      example: No structure matching the given search could be found
+        application/json:
+          schema:
+            type: object
+            properties:
+              message:
+                type: string
+                example: No structure matching the given search could be found
     '500':
       description: The structure given is invalid
       content:
-          application/json:
-              schema:
-                type: object
-                properties:
-                    message:
-                      type: string
-                      example: The structure given is invalid
+        application/json:
+          schema:
+            type: object
+            properties:
+              message:
+                type: string
+                example: The structure given is invalid

doc/api/paths/taxa/post.yaml

@@ -1,6 +1,6 @@
 post:
   operationId: search_taxa
-  security: []
+  security: [ ]
   summary: |
     Search taxa using parameters
   description: |
@@ -23,10 +23,10 @@ post:
     '404':
       description: No taxon matching the given search could be found
       content:
-          application/json:
-              schema:
-                type: object
-                properties:
-                    message:
-                      type: string
-                      example: No taxon matching the given search could be found
+        application/json:
+          schema:
+            type: object
+            properties:
+              message:
+                type: string
+                example: No taxon matching the given search could be found

doc/api/paths/triplets/post.yaml

@@ -1,6 +1,6 @@
 post:
   operationId: search_triplets
-  security: []
+  security: [ ]
   summary: |
     Search triplets using parameters
   description: |
@@ -23,10 +23,10 @@ post:
     '404':
       description: No triplet matching the given search could be found
       content:
-          application/json:
-              schema:
-                type: object
-                properties:
-                    message:
-                      type: string
-                      example: No triplet matching the given search could be found
+        application/json:
+          schema:
+            type: object
+            properties:
+              message:
+                type: string
+                example: No triplet matching the given search could be found

doc/api/schemas/item.yaml

@@ -1,6 +1,6 @@
 title: Item
 type: object
-required: []
+required: [ ]
 properties:
   #' References.
   # TODO

doc/api/schemas/references.yaml

@@ -2,7 +2,7 @@ title: References
 description: |
   References
 type: object
-required: []
+required: [ ]
 properties:
   doi:
     title: DOI

doc/api/schemas/structureResult.yaml

@@ -6,14 +6,14 @@ properties:
     description: |
       IDs
     type: array
-    example: [27151406]
+    example: [ 27151406 ]
   structures:
     title: Structures
     description: |
       Structures
     type: object
     properties:
-      ids: 
+      ids:
         type: integer
         example: 27151406
       structures:

doc/api/schemas/taxa.yaml

@@ -2,7 +2,7 @@ title: Taxa
 description: |
   Taxa
 type: object
-required: []
+required: [ ]
 properties:
   name:
     title: Name

doc/api/schemas/taxonResult.yaml

@@ -6,14 +6,14 @@ properties:
     description: |
       IDs
     type: array
-    example: [158572]
+    example: [ 158572 ]
   taxa:
     title: Taxa
     description: |
       Taxa
     type: object
     properties:
-      ids: 
+      ids:
         type: integer
         example: 158572
       taxa: