- Rename quick_defs.json to .js since it is a Javascript file (#2365)

- Add quick-links to external URLs for ClinicalTrials and DrugApprovals KPs in Settings (#2346) - Update some of those URLs to TRAPI 1.5 endpoints - Update ARAXi DSL helper JSON - Add "Total" row to Testing summary view
RTXteam · Sep 14, 2024 · 641d570 · 641d570
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diff --git a/code/UI/interactive/araxi.js b/code/UI/interactive/araxi.js
@@ -1,5 +1,5 @@
 // WARNING:
-// This file was auto-generated by /mnt/data/orangeboard/devLM/RTX/code/UI/interactive/./dsl2json.py on: 2024-07-25 01:50:08
+// This file was auto-generated by /mnt/data/orangeboard/devLM/RTX/code/UI/interactive/./dsl2json.py on: 2024-09-11 06:23:47
 //
 var araxi_commands = {
   "add_qedge()": {
@@ -208,7 +208,7 @@ var araxi_commands = {
         "description": "Whether to omit supporting data on nodes/edges in the results (e.g., publications, description, etc.)."
       }
     },
-    "description": "This command will expand (aka, answer/fill) your query graph in an edge-by-edge fashion, intelligently selecting which KPs to use for each edge. It selects KPs from the SmartAPI Registry based on the meta information provided by their TRAPI APIs, whether they have an endpoint running a matching TRAPI version, and whether they have an endpoint with matching maturity. For each QEdge, it queries the selected KPs concurrently; it will timeout for a particular KP if it decides it's taking too long to respond (this KP timeout can be controlled by the user). You may also optionally specify a particular KP to use via the 'kp' parameter (described below).\n\nCurrent candidate KPs include (for TRAPI 1.5, maturity 'development'): \ninfores:answer-coalesce, infores:automat-binding-db, infores:automat-cam-kp, infores:automat-ctd, infores:automat-drug-central, infores:automat-genome-alliance, infores:automat-gtex, infores:automat-gtopdb, infores:automat-gwas-catalog, infores:automat-hetionet, infores:automat-hgnc, infores:automat-hmdb, infores:automat-human-goa, infores:automat-icees-kg, infores:automat-intact, infores:automat-monarchinitiative, infores:automat-panther, infores:automat-pharos, infores:automat-reactome, infores:automat-robokop, infores:automat-string-db, infores:automat-ubergraph, infores:automat-viral-proteome, infores:cohd, infores:connections-hypothesis, infores:gelinea, infores:genetics-data-provider, infores:knowledge-collaboratory, infores:molepro, infores:openpredict, infores:rtx-kg2, infores:service-provider-trapi, infores:spoke. \n\n(Note that this list of KPs may change unexpectedly based on the SmartAPI registry.)"
+    "description": "This command will expand (aka, answer/fill) your query graph in an edge-by-edge fashion, intelligently selecting which KPs to use for each edge. It selects KPs from the SmartAPI Registry based on the meta information provided by their TRAPI APIs, whether they have an endpoint running a matching TRAPI version, and whether they have an endpoint with matching maturity. For each QEdge, it queries the selected KPs concurrently; it will timeout for a particular KP if it decides it's taking too long to respond (this KP timeout can be controlled by the user). You may also optionally specify a particular KP to use via the 'kp' parameter (described below).\n\nCurrent candidate KPs include (for TRAPI 1.5, maturity 'development'): \ninfores:answer-coalesce, infores:automat-binding-db, infores:automat-cam-kp, infores:automat-ctd, infores:automat-drug-central, infores:automat-genome-alliance, infores:automat-gtex, infores:automat-gtopdb, infores:automat-gwas-catalog, infores:automat-hetionet, infores:automat-hgnc, infores:automat-hmdb, infores:automat-human-goa, infores:automat-icees-kg, infores:automat-intact, infores:automat-monarchinitiative, infores:automat-panther, infores:automat-pharos, infores:automat-reactome, infores:automat-robokop, infores:automat-string-db, infores:automat-ubergraph, infores:automat-viral-proteome, infores:cohd, infores:connections-hypothesis, infores:gelinea, infores:genetics-data-provider, infores:knowledge-collaboratory, infores:molepro, infores:multiomics-clinicaltrials, infores:multiomics-drugapprovals, infores:multiomics-microbiome, infores:multiomics-multiomics, infores:openpredict, infores:rtx-kg2, infores:service-provider-trapi, infores:spoke. \n\n(Note that this list of KPs may change unexpectedly based on the SmartAPI registry.)"
   },
   "overlay(action=add_node_pmids)": {
     "parameters": {
@@ -1374,15 +1374,15 @@ var araxi_commands = {
         "type": "list",
         "description": "List with just two qnode keys to connect. example: [n1, n2]"
       },
-      "result_as": {
+      "node_category_constraint": {
         "is_required": false,
         "examples": [
-          "betweenness_centrality",
-          "all_in_one",
-          "one_by_one"
+          "biolink:Disease",
+          "biolink:Gene",
+          "biolink:ChemicalEntity"
         ],
         "type": "string",
-        "description": "It determines how to receive the results. For instance, one_by_one means that it will return each path in one subgraph. The default value is betweenness_centrality"
+        "description": "This constraint will display paths that only pass through the user-specified category."
       }
     },
     "description": "\nconnect_nodes adds paths between two nodes specified in the query.\n                    "

diff --git a/code/UI/interactive/dsl2json.py b/code/UI/interactive/dsl2json.py
@@ -1,3 +1,4 @@
+#!/mnt/data/python/Python-3.9.18/bin/python3
 import datetime
 import importlib
 import json

diff --git a/code/UI/interactive/index.html b/code/UI/interactive/index.html
@@ -14,7 +14,7 @@
 <script src="//unpkg.com/timelines-chart"></script>
 
 <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
-<script src="/rtxcomplete/data/quick_def.json"></script>
+<script src="/rtxcomplete/data/quick_def.js"></script>
 <script src="/rtxcomplete/bootstrap.js"></script>
 <script src="/rtxcomplete/bootstrap3-typeahead.js"></script>
 <script src="/rtxcomplete/rtxcomplete.js"></script>
@@ -552,13 +552,15 @@ <h3 style="margin-bottom:0px;">EXTERNAL API (post query):</h3>
     <input type="button" class="qprob p0" value="ClinicalRiskKP" onClick="update_url('EXT','https://api.bte.ncats.io/v1/smartapi/d86a24f6027ffe778f84ba10a7a1861a');"/>
     <input type="button" class="qprob scod" value="COHD" onClick="update_url('EXT','https://cohd.io/api');"/>
     <input type="button" class="qprob p0" value="DrugResponseKP" onClick="update_url('EXT','https://api.bte.ncats.io/v1/smartapi/adf20dd6ff23dfe18e8e012bde686e31');"/>
-    <input type="button" class="qprob sgen" value="GeneticsKP" onClick="update_url('EXT','https://translator.broadinstitute.org/genetics_provider/trapi/v1.4');"/>
+    <input type="button" class="qprob sgen" value="GeneticsKP" onClick="update_url('EXT','https://translator.broadinstitute.org/genetics_provider/trapi/v1.5');"/>
     <input type="button" class="qprob p1" value="ICEES-Asthma" onClick="update_url('EXT','https://icees.renci.org:16339');"/>
     <input type="button" class="qprob p1" value="ICEES-DILI" onClick="update_url('EXT','https://icees.renci.org:16341');"/>
-    <input type="button" class="qprob smol" value="MolePro" onClick="update_url('EXT','https://translator.broadinstitute.org/molepro/trapi/v1.4');"/>
-    <input type="button" class="qprob srtx" value="RTX-KG2" onClick="update_url('EXT','https://arax.ncats.io/api/rtxkg2/v1.4');"/>
+    <input type="button" class="qprob smol" value="MolePro" onClick="update_url('EXT','https://translator.broadinstitute.org/molepro/trapi/v1.5');"/>
+    <input type="button" class="qprob srtx" value="RTX-KG2" onClick="update_url('EXT','https://arax.ncats.io/api/rtxkg2/v1.5');"/>
     <input type="button" class="qprob p0" value="TumorGeneMutationKP" onClick="update_url('EXT','https://api.bte.ncats.io/v1/smartapi/5219cefb9d2b8d5df08c3a956fdd20f3');"/>
     <input type="button" class="qprob p0" value="WellnessKP" onClick="update_url('EXT','https://api.bte.ncats.io/v1/smartapi/02af7d098ab304e80d6f4806c3527027');"/>
+    <input type="button" class="qprob p3" value="ClinicalTrialsKP" onClick="update_url('EXT','https://multiomics.rtx.ai:9990/ctkp');"/>
+    <input type="button" class="qprob p5" value="DrugApprovalsKP" onClick="update_url('EXT','https://multiomics.rtx.ai:9990/dakp');"/>
     <br><br>
   </div>
 

diff --git a/code/UI/interactive/rtx.js b/code/UI/interactive/rtx.js
@@ -7025,6 +7025,7 @@ function displayARSResults(parentnode,arsdata) {
     for (var agent of arsdata['ara_list']) {
 	stats[agent] = {};
 	stats[agent]['PASSED'] = 0;
+	stats[agent]['TOTAL'] = 0;
     }
 
     var tdiv = document.createElement("div");
@@ -7212,6 +7213,7 @@ function displayARSResults(parentnode,arsdata) {
     }
     sumtable.appendChild(tr);
 
+    stats.status_list['TOTAL'] = 1;
     for (var status in stats.status_list) {
 	tr = document.createElement("tr");
         tr.className = 'hoverable';
@@ -7238,6 +7240,9 @@ function displayARSResults(parentnode,arsdata) {
 	    span.innerHTML = status.split(":")[1];
 	    span.className = 'explevel p3';
 	}
+	else if (status == 'TOTAL') {
+	    tr.style.borderTop = "2px solid black";
+	}
         td.appendChild(span);
 	tr.appendChild(td);
 
@@ -7267,6 +7272,9 @@ function displayARSResults(parentnode,arsdata) {
 		td.appendChild(span);
 	    }
 	    tr.appendChild(td);
+
+	    if (status != 'TOTAL' && stats[agent][status]!=null)
+		stats[agent]['TOTAL'] += stats[agent][status];
 	}
 	sumtable.appendChild(tr);
     }

diff --git a/code/UI/interactive/rtx.version b/code/UI/interactive/rtx.version
@@ -1 +1 @@
-Demanding Praying mantis
+Urban Otter
diff --git a/code/autocomplete/data/quick_def.json b/code/autocomplete/data/quick_def.json