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Merge remote-tracking branch 'origin/master'
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@mohsenht
mohsenht committed Nov 6, 2024
2 parents eddf683 + 774076b commit 8e80dd6
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Showing 6 changed files with 201 additions and 92 deletions.
21 changes: 21 additions & 0 deletions code/ARAX/NodeSynonymizer/node_synonymizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import string
import sys
import time
import math
from collections import defaultdict, Counter
from typing import Optional, Union, List, Set, Dict, Tuple

Expand Down Expand Up @@ -297,6 +298,15 @@ def get_normalizer_results(self, entities: Optional[Union[str, Set[str], List[st
entities = entities_dict.get("terms")
output_format = entities_dict.get("format")

# Allow the caller to encode the max_synonyms in the input dict (used by web UI)
max_synonyms_raw = entities_dict.get("max_synonyms")
try:
max_synonyms_int = int(max_synonyms_raw)
if max_synonyms_int > 0:
max_synonyms = max_synonyms_int
except:
pass

# Convert any input curies to Set format
entities_set = self._convert_to_set_format(entities)

Expand Down Expand Up @@ -394,6 +404,17 @@ def get_normalizer_results(self, entities: Optional[Union[str, Set[str], List[st
if normalizer_info:
normalizer_info["knowledge_graph"] = self._get_cluster_graph(normalizer_info)

# Attempt to squash NaNs, which are not legal in JSON. Turn them into nulls
if 'knowledge_graph' in normalizer_info and 'edges' in normalizer_info["knowledge_graph"]:
for edge_name, edge_data in normalizer_info["knowledge_graph"]['edges'].items():
if 'attributes' in edge_data:
for attribute in edge_data['attributes']:
try:
if 'value' in attribute and math.isnan(attribute['value']):
attribute['value'] = None
except:
pass

if debug:
print(f"Took {round(time.time() - start, 5)} seconds")
return results_dict
Expand Down
61 changes: 30 additions & 31 deletions code/UI/interactive/araxi.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
// WARNING:
// This file was auto-generated by /mnt/data/orangeboard/devLM/RTX/code/UI/interactive/./dsl2json.py on: 2024-09-11 06:23:47
// This file was auto-generated by /mnt/data/orangeboard/devLM/RTX/code/UI/interactive/./dsl2json.py on: 2024-11-01 01:58:59
//
var araxi_commands = {
"add_qedge()": {
Expand Down Expand Up @@ -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: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.)"
"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-ehr-clinical-connections-kp, infores:automat-ehr-may-treat-kp, 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": {
Expand Down Expand Up @@ -1360,32 +1360,10 @@ var araxi_commands = {
"min": 1,
"max": 5,
"type": "integer",
"description": "The maximum edges to connect two nodes with. If not provided defaults to 2."
},
"qnode_keys": {
"is_required": true,
"examples": [
[
"n01",
"n02"
],
[]
],
"type": "list",
"description": "List with just two qnode keys to connect. example: [n1, n2]"
},
"node_category_constraint": {
"is_required": false,
"examples": [
"biolink:Disease",
"biolink:Gene",
"biolink:ChemicalEntity"
],
"type": "string",
"description": "This constraint will display paths that only pass through the user-specified category."
"description": "The maximum edges to connect two nodes with. If not provided defaults to 4."
}
},
"description": "\nconnect_nodes adds paths between two nodes specified in the query.\n "
"description": "connect_nodes adds paths between two nodes specified in the query."
},
"infer(action=chemical_gene_regulation_graph_expansion)": {
"parameters": {
Expand Down Expand Up @@ -1435,7 +1413,7 @@ var araxi_commands = {
"qedge_id_3"
],
"type": "string",
"description": "The id of the qedge you wish to perform the drug treatment/chemical regulation inference expansion."
"description": "The id of the qedge you wish to perform the chemical-gene regulation inference expansion."
},
"threshold": {
"is_required": false,
Expand Down Expand Up @@ -1506,15 +1484,25 @@ var araxi_commands = {
},
"infer(action=drug_treatment_graph_expansion)": {
"parameters": {
"node_curie": {
"drug_curie": {
"is_required": true,
"examples": [
"CHEMBL.COMPOUND:CHEMBL55643",
"CHEBI:8378",
"RXNORM:1011"
],
"type": "string",
"description": "The CURIE for a drug node used to predict what potential diseases it may treat."
},
"disease_curie": {
"is_required": true,
"examples": [
"DOID:9352",
"MONDO:0005306",
"HP:0001945"
],
"type": "string",
"description": "The curie for the node you wish to predict drugs which will treat."
"description": "The CURIE for a disease node used to predict what potential drugs can potentially treat it."
},
"qedge_id": {
"is_required": false,
Expand All @@ -1524,7 +1512,7 @@ var araxi_commands = {
"qedge_id_3"
],
"type": "string",
"description": "The id of the qedge you wish to perform the drug treatment/chemical regulation inference expansion."
"description": "The id of the qedge you wish to perform the drug-disease treatment inference expansion."
},
"n_drugs": {
"is_required": false,
Expand All @@ -1535,7 +1523,18 @@ var araxi_commands = {
],
"default": 50,
"type": "integer",
"description": "The number of drug nodes to return. If not provided defaults to 50. Considering the response speed, the maximum number of drugs returned is only allowed to be 50."
"description": "Given an interested disease CURIE, the number of drug nodes to return. If not provided defaults to 50. Considering the response speed, the maximum number of drugs returned is only allowed to be 50."
},
"n_diseases": {
"is_required": false,
"examples": [
5,
15,
25
],
"default": 50,
"type": "integer",
"description": "Given an interested drug CURIE, The number of disease nodes to return. If not provided defaults to 50. Considering the response speed, the maximum number of diseases returned is only allowed to be 50."
},
"n_paths": {
"is_required": false,
Expand Down
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