Merge branch 'main' into parallel-creative

biothings · Sep 6, 2024 · 3ee93de · 3ee93de
2 parents e965059 + 14d9b71
commit 3ee93de
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Showing 6 changed files with 49 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -21,7 +21,7 @@ RUN npm i pnpm -g
 # Add additional dependencies in the same line if needed
 #    git: used for clone multiple source repos in our monorepo setup
 #    lz4 python3 make g++: required to build lz4 nodejs package
-RUN apk add --no-cache --virtual build-deps git lz4 python3 make g++
+RUN apk add --no-cache --virtual build-deps git lz4 python3 make g++ py3-setuptools
 RUN apk add --no-cache curl
 COPY --chown=node:node . .
 USER node

diff --git a/docs/REFERENCE.md b/docs/REFERENCE.md
@@ -94,6 +94,14 @@ Several environment variables are supported for various purposes, listed below:
 
 **Description:** Maximum number of records allowable in a single query execution, after which the query will be terminated.
 
+#### `NGD_TIMEOUT_MS`
+
+**Default:** `10000`
+
+**Docker Default:** `10000`
+
+**Description:** Timeout used for the NGD scoring process of results.
+
 #### `NODE_ENV`
 
 **Default:** `development`
@@ -212,4 +220,4 @@ Several environment variables are supported for various purposes, listed below:
 
 **Docker Default:** `true`
 
-**Description:** Run all TRAPI requests in queued thread pools.
+**Description:** Run all TRAPI requests in queued thread pools.
diff --git a/examples/v1.1/query_genes_relate_to_disease_list.json b/examples/v1.1/query_genes_relate_to_disease_list.json
@@ -0,0 +1,26 @@
+{
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "n0": {
+                    "categories": ["biolink:Disease"],
+                    "ids": [
+                            "MONDO:0005737",
+                            "MONDO:0005358",
+                            "MONDO:0020500"
+                    ],
+                    "is_set": true
+                },
+                "n1": {
+                    "categories": ["biolink:Gene"]
+                }
+            },
+            "edges": {
+                "e01": {
+                    "subject": "n0",
+                    "object": "n1"
+                }
+            }
+        }
+    }
+}
diff --git a/packages/types/src/trapi.ts b/packages/types/src/trapi.ts
@@ -3,6 +3,8 @@ export interface TrapiQNode {
   categories?: string[];
   is_set?: boolean;
   constraints?: TrapiAttributeConstraint[];
+  set_interpretation?: string;
+  member_ids?: string[];
 }
 
 export interface TrapiQEdge {
@@ -121,6 +123,7 @@ export interface TrapiAuxiliaryGraph {
 
 export interface TrapiPfocrFigure {
   figureUrl: string;
+  pfocrUrl: string;
   pmc: string;
   matchedCuries: string[];
   score: number;

diff --git a/prod_revisions.txt b/prod_revisions.txt
@@ -2,13 +2,13 @@
 > @biothings-explorer/[email protected] get_rev /Users/jcallaghan/Projects/bte-main
 > ./scripts/get_rev.sh
 
-# Generated from "pnpm run get_rev" on  Tue May 21 16:12:40 EDT 2024
-https://github.com/biothings/bte-server.git c5aecdd c5aecdd860e4ace375bef0a0f16f3131b905ba3f
-https://github.com/biothings/api-respone-transform.js.git 9e89776 9e89776089cf82b2564914aeb627b45b1607b997
-https://github.com/biothings/call-apis.js.git ef7b1f9 ef7b1f92118b19ba0956cef2c279c92cad5e6c5b
-https://github.com/biothings/smartapi-kg.js.git f46b48c f46b48c03ce05f6eae5327340414b0abe2cd00cb
-https://github.com/biothings/bte_trapi_query_graph_handler.git da2271f da2271f65c80c36caa42d16263a0fce3c9609e41
-https://github.com/biothings/node-expansion.git e4bb786 e4bb7865135ffdf8b4fc30b8960888c27d29c337
-https://github.com/biothings/biolink-model.js.git 72d7404 72d74046b1c5ba954363978671df8aa6b6332b03
-https://github.com/biothings/biomedical_id_resolver.js.git e375b08 e375b08f9adea3c8afbdecc91009518d930acdde
+# Generated from "pnpm run get_rev" on  Fri Aug 30 12:53:17 EDT 2024
+https://github.com/biothings/bte-server.git cdb1b8e cdb1b8e2b7fea8c83852db3542de91c03ca7626f
+https://github.com/biothings/api-respone-transform.js.git f5831b9 f5831b9c54ab974f08c2fb476a61c0e1e4629ebb
+https://github.com/biothings/call-apis.js.git 4c59a93 4c59a930a10024e928e6deffa09725551b9579a3
+https://github.com/biothings/smartapi-kg.js.git a328307 a3283077e18145d1865e4a9ba57ef56846d19264
+https://github.com/biothings/bte_trapi_query_graph_handler.git 265360d 265360def22d267d8a621cc4bacd786852e4bcc5
+https://github.com/biothings/node-expansion.git d140a26 d140a264e96d71fc20da90891bd37c4f4d0e06a8
+https://github.com/biothings/biolink-model.js.git 24b8192 24b81923c99269185f39b7d5bee02239931a0f1b
+https://github.com/biothings/biomedical_id_resolver.js.git 8c1f094 8c1f094d7525fb1ddc6502a379ae2e23f9dbfbe5
 https://github.com/biothings/bte-utils.git 84708cf 84708cf8bd138ee85b11fdc4564d5faac1f31539
diff --git a/scripts/stop_server.sh b/scripts/stop_server.sh
@@ -1,6 +1,5 @@
 #!/bin/bash
-
-btepid=$(pgrep -f bte-trapi)
+btepid=$(pgrep -f "(node|nodemon).*/packages/.*/data")
 echo "$btepid" | xargs -n1 pkill -9 -P && echo 'BTE subprocesses stopped.' || true
 echo "$btepid" | xargs -n1 kill -s KILL && echo 'BTE Stopped.'
 [ "$(docker ps -a | grep test-redis)" ] && docker rm test-redis --force > /dev/null 2>&1 && echo 'Containerized redis stopped.'