Add wrapper endpoints

setup.cfg

@@ -74,6 +74,7 @@ web =
     docstring-parser
     indralab_auth_tools @ git+https://github.com/indralab/ui_util.git#egg=indralab_auth_tools&subdirectory=indralab_auth_tools
     pusher
+    markupsafe<2.1.0
 gunicorn =
     gunicorn
 gsea =

src/indra_cogex/apps/chat_page/app/deploy.sh

@@ -61,7 +61,7 @@ echo "Deploying to $S3_URI"
 
 # Copy the content of the dist directory to the S3 bucket
 # See https://awscli.amazonaws.com/v2/documentation/api/latest/reference/s3/sync.html for more details
-aws s3 sync --exact-timestamps --delete dist/ "${S3_URI}"
+aws s3 sync --exact-timestamps --delete dist/ "${S3_URI}" --acl public-read
 echo "Deployment complete"
 echo ""
 

src/indra_cogex/apps/chat_page/app/src/components/AgentModal.vue

@@ -216,8 +216,8 @@ export default {
       }
 
       if (Object.entries(this.lookupData).length === 0) {
-        // Call biolookup.io, e.g. http://biolookup.io/api/lookup/DOID:14330
-        const bioluUrl = `http://biolookup.io/api/lookup/${topNsUpper}:${this.topGrounding[1]}`; // Currently only supports http
+        // Call the biolookup.io wrapper, e.g. https://discovery.indra.bio/biolookup/DOID:14330
+        const bioluUrl = `https://discovery.indra.bio/biolookup/${topNsUpper}:${this.topGrounding[1]}`;
         const bioluResp = await fetch(bioluUrl);
         const bioluData = await bioluResp.json();
         this.lookupData = await bioluData;

src/indra_cogex/apps/chat_page/app/src/components/StmtList.vue

@@ -96,20 +96,22 @@ export default {
         for (let source of Object.keys(metaEntry.sourceCounts)) {
           // If the source is a reader, add it to the readers array
           const lowerSource = source.toLowerCase();
+          const mappedLowerSource =
+            this.$source_mapping[lowerSource] ?? lowerSource;
 
           if (
-            this.$sources.readers.includes(lowerSource) &&
-            !availableSources.readers.includes(lowerSource)
+            this.$sources.readers.includes(mappedLowerSource) &&
+            !availableSources.readers.includes(mappedLowerSource)
           ) {
-            availableSources.readers.push(lowerSource);
+            availableSources.readers.push(mappedLowerSource);
           } else if (
-            this.$sources.databases.includes(lowerSource) &&
-            !availableSources.databases.includes(lowerSource)
+            this.$sources.databases.includes(mappedLowerSource) &&
+            !availableSources.databases.includes(mappedLowerSource)
           ) {
-            availableSources.databases.push(lowerSource);
+            availableSources.databases.push(mappedLowerSource);
           } else if (
-            !this.$sources.databases.includes(lowerSource) &&
-            !this.$sources.readers.includes(lowerSource)
+            !this.$sources.databases.includes(mappedLowerSource) &&
+            !this.$sources.readers.includes(mappedLowerSource)
           ) {
             console.warn(`Unknown source: ${source}`);
           }
@@ -189,7 +191,7 @@ export default {
       return `${firstAgent.name} ${verb} ${restOfAgentsString}`;
     },
     async getEnglishArray() {
-      const indraApi = "http://api.indra.bio:8000/assemblers/english";
+      const indraApi = "https://discovery.indra.bio/get_english_stmts";
       // POST to get the English assembly of the statements
       const response = await fetch(indraApi, {
         method: "POST",

src/indra_cogex/apps/chat_page/app/src/main.js

@@ -62,6 +62,13 @@ app.config.globalProperties.$sources = {
     "acsn",
   ],
 };
+app.config.globalProperties.$source_mapping = {
+  bel: "bel_lc",
+  phosphoelm: "pe",
+  biopax: "pc",
+  virhostnet: "vhn",
+  phosphosite: "psp",
+};
 
 const GStore = reactive({
   xrefs: {},

src/indra_cogex/apps/data_display/__init__.py

@@ -12,10 +12,13 @@
 from http import HTTPStatus
 from typing import Any, Dict, Iterable, List, Optional, Set
 
+import requests
 from flask import Blueprint, Response, abort, jsonify, render_template, request
 from flask_jwt_extended import jwt_optional
+
+from indra.assemblers.english import EnglishAssembler
 from indra.sources.indra_db_rest import IndraDBRestAPIError
-from indra.statements import Statement
+from indra.statements import Statement, stmts_from_json
 from indralab_auth_tools.auth import resolve_auth
 
 from indra_cogex.apps.proxies import client, curation_cache
@@ -173,6 +176,51 @@ def get_stmts():
         abort(Response("Parameter 'stmt_hash' unfilled", status=415))
 
 
+@data_display_blueprint.route("/get_english_stmts", methods=["POST"])
+def get_english_stmts():
+    """Get English statements from a list of INDRA statements in JSON format
+
+    This does the same thing as http://api.indra.bio:8000/assemble/english,
+    we do it here to avoid CORS issues and blocking by the browser
+    when calling http from a https page
+    """
+    stmts_json = request.json.get("statements")
+    if isinstance(stmts_json, dict):
+        stmts_json = [stmts_json]
+    if not stmts_json or not isinstance(stmts_json, list):
+        logger.warning("No statements provided to generate English statements")
+        abort(HTTPStatus.UNPROCESSABLE_ENTITY,
+              "No statements provided, cannot generate English statements from empty list")
+    stmts = stmts_from_json(stmts_json)
+    english = {}
+    for stmt in stmts:
+        english[stmt.uuid] = EnglishAssembler([stmt]).make_model()
+    return jsonify({"sentences": english})
+
+
+@data_display_blueprint.route("/biolookup/<curie>", methods=["GET"])
+def biolookup(curie):
+    """A simple wrapper to biolookup that returns the results as JSON
+
+    We use this wrapper to avoid browser blocking when calling the biolookup
+    service (that's running on http) from a https page.
+
+    Parameters
+    ----------
+    curie :
+        The CURIE to look up
+
+    Returns
+    -------
+    :
+        The JSON response from biolookup
+    """
+    res = requests.get("http://biolookup.io/api/lookup/%s" % curie)
+    if res.status_code != 200:
+        abort(res.status_code, res.text)
+    return jsonify(res.json())
+
+
 # Endpoint for getting evidence
 @data_display_blueprint.route("/expand/<stmt_hash>", methods=["GET"])
 @jwt_optional