Add a docker-compose and start fixing the API

Dockerfile.local

@@ -0,0 +1,12 @@
+FROM docker.io/library/python:3.11-slim
+RUN apt update && apt install -y libxrender1 libxtst6 libxi6
+RUN pip install poetry
+COPY poetry.lock pyproject.toml ./
+RUN poetry config virtualenvs.create false \
+    && poetry install --no-interaction --no-ansi
+RUN mkdir /app /app/data
+RUN adduser --system --no-create-home nonroot
+RUN chown -R nonroot /app/data
+USER nonroot
+WORKDIR /app
+CMD [ "uvicorn", "api:app", "--reload", "--host", "0.0.0.0", "--port", "5000"]

README.md

@@ -13,6 +13,17 @@ The dataset is from the [LOTUS](https://lotus.nprod.net) initiative and [Wikidat
 
 ## Install & use
 
+### The docker compose way (recommended)
+
+```shell
+docker-compose run -it backend python update.py
+docker-compose up
+```
+
+The web server is then available on <http://localhost:3000> and the API on <http://localhost:5000>.
+
+### The manual way
+
 To run it yourself, the source is available at: <https://github.com/lotusnprod/lotus-search>:
 
 - Install dependencies using poetry

api.py

@@ -36,32 +36,32 @@ def get_matching_structures_from_structure_in_item(
     dm: DataModel, item: Item
 ) -> set[int]:
     """Returns all_structures if the item do not filter by structure, else returns the WID of matching structures"""
-    if item.molecule is None and item.structure_wid is None:
+    if item.structure is None and item.structure_wid is None:
         return all_structures
-    elif item.molecule and item.structure_wid:
+    elif item.structure and item.structure_wid:
         raise HTTPException(
             status_code=500,
-            detail=f"You cannot provide both 'molecule' and 'structure_wid'",
+            detail=f"You cannot provide both 'structure' and 'structure_wid'",
         )
     else:
         # This needs to be explained in the API doc
         if item.structure_wid:
             if item.structure_wid in all_structures:
                 return {item.structure_wid}
         else:
-            if item.molecule:
+            if item.structure:
                 if item.substructure_search:
                     try:
-                        results = dm.structure_search_substructure(item.molecule)
+                        results = dm.structure_search_substructure(item.structure)
                         structures = {_id for _id, _ in results}
                     except ValueError:
                         raise HTTPException(
                             status_code=500,
-                            detail=f"The structure given is invalid: {item.molecule}",
+                            detail=f"The structure given is invalid: {item.structure}",
                         )
                 else:
                     try:
-                        results = dm.structure_search(item.molecule)
+                        results = dm.structure_search(item.structure)
                         structures = {
                             _id
                             for _id, score in results
@@ -70,18 +70,18 @@ def get_matching_structures_from_structure_in_item(
                     except ValueError:
                         raise HTTPException(
                             status_code=500,
-                            detail=f"The structure given is invalid: {item.molecule}",
+                            detail=f"The structure given is invalid: {item.structure}",
                         )
             else:
                 structures = all_structures
 
             return structures
 
 
-def get_matching_taxa_from_taxon_in_item(dm: DataModel, item: Item) -> set[int]:
-    """Returns all_taxa if the item do not filter by taxon, else returns the WID of matching taxa"""
+def get_matching_taxa_from_taxon_in_item(dm: DataModel, item: Item) -> set[int] | None:
+    """Returns all_taxa if the item do not filter by taxon, else returns the WID of matching taxa or None if no taxa requested"""
     if item.taxon_wid is None and item.taxon_name is None:
-        return all_taxa
+        return None
     else:
         # This needs to be explained in the API doc
         if item.taxon_wid:
@@ -102,6 +102,9 @@ def get_matching_structures_from_taxon_in_item(dm: DataModel, item: Item) -> set
     # We need to get all the matching taxa
     taxa = get_matching_taxa_from_taxon_in_item(dm, item)
 
+    if taxa is None:
+        return None
+
     # We could have a parameter "recursive" in the query to have all the structures from the parents too
     out = set()
     for taxon in taxa:
@@ -164,13 +167,18 @@ async def search_structures(item: Item) -> StructureResult:
     matching_structures_by_structure = get_matching_structures_from_structure_in_item(
         dm, item
     )
-    # We want the set of all the molecules found in the given taxa
+    # We want the set of all the structures found in the given taxa
     matching_structures_by_taxon = get_matching_structures_from_taxon_in_item(dm, item)
 
     # We want the intersection of both (and we can do the same for the references later)
-    matching_structures = (
-        matching_structures_by_structure & matching_structures_by_taxon
-    )
+    # But if one of the sets is fully empty
+    if matching_structures_by_taxon is None:
+        matching_structures = matching_structures_by_structure
+    else:
+      matching_structures = (
+          matching_structures_by_structure & matching_structures_by_taxon
+      )
+
     return StructureResult(
         ids=matching_structures,
         structures={
@@ -188,13 +196,11 @@ async def search_taxa(item: Item) -> TaxonResult:
     # We want the set of all the taxa matching the query
     matching_taxa_by_taxon = get_matching_taxa_from_taxon_in_item(dm, item)
 
-    # We want the set of all the taxa which have molecules matching the query
+    # We want the set of all the taxa which have structures matching the query
     matching_taxa_by_structure = get_matching_taxa_from_structure_in_item(dm, item)
 
     # We want the intersection of both (and we can do the same for the references later)
     matching_taxa = matching_taxa_by_taxon & matching_taxa_by_structure
-    print(matching_taxa)
-    print(dm.get_dict_of_wid_to_taxon_name(matching_taxa))
 
     return TaxonResult(
         ids=matching_taxa,

doc/example_queries.http

@@ -9,7 +9,14 @@ accept: application/json
 Content-Type: application/json
 
 {
-  "molecule": "CC1C=C(C(=O)C2(C1CC3C4(C2C(=O)C(=C(C4CC(=O)O3)C)OC)C)C)OC"
+  "structure": "CC1C=C(C(=O)C2(C1CC3C4(C2C(=O)C(=C(C4CC(=O)O3)C)OC)C)C)OC"
+}
+###
+POST http://127.0.0.1:5000/v1_0/structures
+accept: application/json
+Content-Type: application/json
+
+{
 }
 
 ###

docker-compose.yml

@@ -0,0 +1,24 @@
+# A docker-compose file for a two services system. One is the backend, with the Dockerfile in this directory
+# the other one is inside frontend.
+
+version: '3.8'
+services:
+  backend:
+    build:
+      context: .
+      dockerfile: Dockerfile.local
+    ports:
+      - "5000:5000"
+    volumes:
+      - .:/app
+      - backend_data:/app/data
+  frontend:
+    build: frontend/
+    ports:
+      - "3000:3000"
+    volumes:
+      - ./frontend/src:/app/src
+    depends_on:
+      - backend
+volumes:
+  backend_data:

frontend/Dockerfile

@@ -0,0 +1,14 @@
+FROM node:21.4
+ENV PNPM_HOME="/pnpm"
+ENV PATH="$PNPM_HOME:$PATH"
+RUN corepack enable
+WORKDIR /app
+COPY package.json .
+RUN pnpm install
+COPY tsconfig.json .
+COPY tsconfig.node.json .
+COPY vite.config.ts .
+COPY package.json .
+COPY pnpm-lock.yaml .
+COPY index.html .
+CMD ["pnpm", "run", "dev"]

frontend/vite.config.ts

@@ -34,9 +34,10 @@ export default defineConfig({
   },
   server: {
     port: 3000,
+    host: "0.0.0.0",
     proxy: {
       '/api': {
-        target: 'http://localhost:5000',
+        target: 'http://backend:5000',
         changeOrigin: true,
         rewrite: (path) => path.replace(/^\/api/, ''),
       }

model.py

@@ -17,7 +17,7 @@
 
 class Item(BaseModel):
     structure_wid: int | None = None
-    molecule: str | None = None
+    structure: str | None = None
     substructure_search: bool | None = None
     similarity_level: float = 1.0
     taxon_wid: int | None = None
@@ -27,7 +27,7 @@ class Item(BaseModel):
             "examples": [
                 {
                     "structure_wid": "27151406",
-                    "molecule": "C=C[C@@H]1[C@@H]2CCOC(=O)C2=CO[C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O",
+                    "structure": "C=C[C@@H]1[C@@H]2CCOC(=O)C2=CO[C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O",
                     "substructure_search": True,
                     "similarity_level": 0.8,
                     "taxon_wid": 158572,