Beta deployment and bugfixes

README-podman-quadlets.md

@@ -184,8 +184,14 @@ needed when you want to **reset and fully rebuild** the Qdrant collections.
 
 Requires `pathfinder-qdrant` to be running. Run from the project root so the
 report output path resolves correctly:
+```bash
+systemctl --user status pathfinder-qdrant
+# if required:
+systemctl --user start pathfinder-qdrant
+```
 
 ```bash
+# make sure this is user-owned, not root:
 mkdir -p apps/api/ingest_reports
 
 podman run --rm \
@@ -196,13 +202,28 @@ podman run --rm \
   -v "$PWD/apps/api/ingest_reports:/reports:Z" \
   -w /app/apps/api \
   localhost/pathfinder-api:latest \
-  /bin/sh -lc "uv run python -m veupath_chatbot.services.vectorstore.ingest.wdk_catalog --sites all --reset && \
-               uv run python -m veupath_chatbot.services.vectorstore.ingest.public_strategies --sites all --reset --report-path /reports/ingest_public_strategies_report.jsonl"
+  /bin/sh -lc "uv run python -m veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog --sites all --reset && \
+               uv run python -m veupath_chatbot.integrations.vectorstore.ingest.public_strategies --sites all --reset --report-path /reports/ingest_public_strategies_report.jsonl"
 ```
 
 Both jobs require `OPENAI_API_KEY` (used for embeddings). The second job writes
 a JSONL report to `apps/api/ingest_reports/` (gitignored).
 
+**Beta sites:** if your `VEUPATHDB_SITES_CONFIG` points at `beta-sites.yaml`,
+many WDK endpoints require authentication. Add both variables to
+`~/.config/pathfinder/.env`:
+
+```bash
+# Note: path is inside the container, not on the host
+VEUPATHDB_SITES_CONFIG=/app/apps/api/src/veupath_chatbot/integrations/veupathdb/beta-sites.yaml
+VEUPATHDB_AUTH_TOKEN=your_api_key_here
+```
+
+Logged-in users can find their API key at their VEuPathDB profile page under
+**Service Access** — for example:
+`https://beta.plasmodb.org/plasmo.beta/app/user/profile#serviceAccess`
+(any component site works).
+
 ## Services overview
 
 | Service | Image | Published port | Depends on |

apps/api/src/veupath_chatbot/integrations/veupathdb/beta-sites.yaml

@@ -0,0 +1,111 @@
+# VEuPathDB Beta Sites Configuration
+# Base URLs for beta/staging versions of all VEuPathDB resources.
+# Override this file at runtime with env: VEUPATHDB_SITES_CONFIG=/path/to/your.yaml
+
+sites:
+  # Portal (queries across all component sites)
+  veupathdb:
+    name: VEuPathDB
+    display_name: VEuPathDB Portal (All organisms)
+    base_url: https://beta.veupathdb.org/veupathdb.beta/service
+    project_id: EuPathDB
+    is_portal: true
+
+  # Apicomplexan parasites
+  plasmodb:
+    name: PlasmoDB
+    display_name: PlasmoDB (Plasmodium)
+    base_url: https://beta.plasmodb.org/plasmo.beta/service
+    project_id: PlasmoDB
+    is_portal: false
+
+  toxodb:
+    name: ToxoDB
+    display_name: ToxoDB (Toxoplasma)
+    base_url: https://beta.toxodb.org/toxo.beta/service
+    project_id: ToxoDB
+    is_portal: false
+
+  cryptodb:
+    name: CryptoDB
+    display_name: CryptoDB (Cryptosporidium)
+    base_url: https://beta.cryptodb.org/cryptodb.beta/service
+    project_id: CryptoDB
+    is_portal: false
+
+  piroplasmadb:
+    name: PiroplasmaDB
+    display_name: PiroplasmaDB (Piroplasma)
+    base_url: https://beta.piroplasmadb.org/piro.beta/service
+    project_id: PiroplasmaDB
+    is_portal: false
+
+  # Other protozoan parasites
+  giardiadb:
+    name: GiardiaDB
+    display_name: GiardiaDB (Giardia)
+    base_url: https://beta.giardiadb.org/giardiadb.beta/service
+    project_id: GiardiaDB
+    is_portal: false
+
+  amoebadb:
+    name: AmoebaDB
+    display_name: AmoebaDB (Amoeba)
+    base_url: https://beta.amoebadb.org/amoeba.beta/service
+    project_id: AmoebaDB
+    is_portal: false
+
+  microsporidiadb:
+    name: MicrosporidiaDB
+    display_name: MicrosporidiaDB (Microsporidia)
+    base_url: https://beta.microsporidiadb.org/micro.beta/service
+    project_id: MicrosporidiaDB
+    is_portal: false
+
+  tritrypdb:
+    name: TriTrypDB
+    display_name: TriTrypDB (Kinetoplastids)
+    base_url: https://beta.tritrypdb.org/tritrypdb.beta/service
+    project_id: TriTrypDB
+    is_portal: false
+
+  # Fungi
+  fungidb:
+    name: FungiDB
+    display_name: FungiDB (Fungi)
+    base_url: https://beta.fungidb.org/fungidb.beta/service
+    project_id: FungiDB
+    is_portal: false
+
+  # Hosts and vectors
+  hostdb:
+    name: HostDB
+    display_name: HostDB (Hosts)
+    base_url: https://beta.hostdb.org/hostdb.beta/service
+    project_id: HostDB
+    is_portal: false
+
+  vectorbase:
+    name: VectorBase
+    display_name: VectorBase (Vectors)
+    base_url: https://beta.vectorbase.org/vectorbase.beta/service
+    project_id: VectorBase
+    is_portal: false
+
+  # Orthology
+  orthomcl:
+    name: OrthoMCL
+    display_name: OrthoMCL (Orthologs)
+    base_url: https://beta.orthomcl.org/orthomcl.beta/service
+    project_id: OrthoMCL
+    is_portal: false
+
+# Default site to use
+default_site: veupathdb
+
+# Routing (timeouts for WDK client)
+routing:
+  # Portal timeout (portal can be slow due to fan-out)
+  portal_timeout: 120
+  # Component site timeout
+  component_timeout: 30

docker-compose.yml

@@ -138,7 +138,7 @@ services:
       [
         "/bin/sh",
         "-lc",
-        "uv run python -m veupath_chatbot.services.vectorstore.ingest.wdk_catalog --sites all --reset && uv run python -m veupath_chatbot.services.vectorstore.ingest.public_strategies --sites all --reset --report-path /reports/ingest_public_strategies_report.jsonl"
+        "uv run python -m veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog --sites all --reset && uv run python -m veupath_chatbot.integrations.vectorstore.ingest.public_strategies --sites all --reset --report-path /reports/ingest_public_strategies_report.jsonl"
       ]
     restart: "no"