some fixes

lotusnprod · Dec 18, 2023 · a6607c3 · a6607c3
1 parent 3e8797e
commit a6607c3
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Showing 3 changed files with 12 additions and 9 deletions.
diff --git a/api/api.py b/api/api.py
@@ -100,6 +100,7 @@ def get_matching_taxa_from_taxon_in_item(dm: DataModel, item: Item) -> set[int]
                     taxa = dm.get_taxa()
             else:
                 taxa = dm.get_taxa()
+        print(taxa)
 
         return taxa
 
@@ -191,9 +192,9 @@ async def search_structures(item: Item) -> StructureResult:
         )
 
     if item.limit == 0:
-        items = dm.get_dict_of_wid_to_smiles(matching_structures).items()
+        items = list(dm.get_dict_of_wid_to_smiles(matching_structures).items())
     else:
-        items = dm.get_dict_of_wid_to_smiles(matching_structures).items()[: item.limit]
+        items = list(dm.get_dict_of_wid_to_smiles(matching_structures).items())[: item.limit]
 
     return StructureResult(
         ids=matching_structures,
@@ -216,9 +217,9 @@ async def search_taxa(item: Item) -> TaxonResult:
     matching_taxa = matching_taxa_by_taxon & matching_taxa_by_structure
 
     if item.limit == 0:
-        items = dm.get_dict_of_wid_to_taxon_name(matching_taxa).items()
+        items = list(dm.get_dict_of_wid_to_taxon_name(matching_taxa).items())
     else:
-        items = dm.get_dict_of_wid_to_taxon_name(matching_taxa).items()[: item.limit]
+        items = list(dm.get_dict_of_wid_to_taxon_name(matching_taxa).items())[: item.limit]
 
     return TaxonResult(
         ids=matching_taxa,

diff --git a/doc/EXAMPLE_QUERIES.md b/doc/EXAMPLE_QUERIES.md
@@ -5,21 +5,23 @@
 Careful that's taxus anywhere in the name, so you'll get Cephalotaxus as well!
 
 ```shell
-curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:8000/v1_0/structures -d '{"molecule":"Cl", "substructure_search": true, "taxon_name":"Taxus"}'
+curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:5000/v1_0/structures -d '{"structure":"Cl", "substructure_search": true, "taxon_name":"Taxus"}'
 ```
 
 ## Taxa
 
 ### Get all the taxa with gent in their name producing a structure with chlorine in it
 
 ```shell
-curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:8000/v1_0/taxa -d '{"molecule":"Cl", "substructure_search": true, "taxon_name":"gent"}'
+curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:5000/v1_0/taxa -d '{"structure":"Cl", "substructure_search": true, "taxon_name":"Gent"}'
 ```
 
 ### Get all the taxa producing chlorinated structures
 
+#### TODO THIS ONE IS NOT WORKING ANYMORE (FIX IT)
+
 ```shell
-curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:8000/v1_0/taxa -d '{"molecule":"Cl", "substructure_search": true}'
+curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:5000/v1_0/taxa -d '{"structure":"Cl", "substructure_search": true}'
 ```
 
 ## Couples
@@ -29,5 +31,5 @@ curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' ht
 Careful that's taxus anywhere in the name, so you'll get Cephalotaxus as well!
 
 ```shell
-curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:8000/v1_0/couples -d '{"molecule":"O=C(OC1C(=C)C2CC3(O)CC(OC(=O)C)C(=C(C(OC(=O)C)C(OC(=O)C)C2(C)C(OC(=O)C)C1)C3(C)C)C)C=CC=4C=CC=CC4", "taxon_name":"tax"}'
+curl -XPOST -H 'Accept: application/json' -H 'Content-Type: application/json' http://127.0.0.1:5000/v1_0/couples -d '{"structure":"O=C(OC1C(=C)C2CC3(O)CC(OC(=O)C)C(=C(C(OC(=O)C)C(OC(=O)C)C2(C)C(OC(=O)C)C1)C3(C)C)C)C=CC=4C=CC=CC4", "taxon_name":"tax"}'
 ```
diff --git a/update/generate_database_taxo.py b/update/generate_database_taxo.py
@@ -101,7 +101,7 @@ def run(path: Path) -> None:
 
     with open(path / "taxa_all.csv", "r") as f:
         reader = DictReader(f)
-        dict_all_taxa: dict = {row["taxon"]: row["taxon_name"] for row in reader}
+        dict_all_taxa: dict = {int(row["taxon"]): row["taxon_name"] for row in reader}
 
     database = {
         "taxonomy_direct_parents": taxon_direct_parents,