From 4ae60f52c9a24a49c5ac9d99774de90252c53abc Mon Sep 17 00:00:00 2001
From: Kaiwen He <kaiwenhe@uab.edu>
Date: Tue, 5 Nov 2024 11:55:22 -0600
Subject: [PATCH] updated RTX-KG2 to version 2.10.1pre

---
 .../import-rtx-kg2.rkt                            |  2 +-
 .../transform-edge-jsonl.rkt                      | 15 +++++++++++----
 .../transform-rtx-kg2.rkt                         |  6 +++---
 .../neo/neo-low-level/query-low-level-rtx-kg2.rkt |  2 +-
 medikanren2/neo/neo-server/neo-server.rkt         |  2 +-
 5 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2.rkt b/medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2.rkt
index c58adfc2..41d2c1b3 100644
--- a/medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2.rkt
+++ b/medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2.rkt
@@ -2,7 +2,7 @@
 (require "../../dbKanren/dbk/database.rkt"
          racket/list racket/pretty racket/runtime-path)
 
-(define BASE "../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/rtx-kg2-2.10.0pre/")
+(define BASE "../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/rtx-kg2-2.10.1pre/")
 
 (define EDGEPROP_PATH (string-append BASE "rtx_kg2.edgeprop.tsv"))
 (define EDGE_PATH (string-append BASE "rtx_kg2.edge.tsv"))
diff --git a/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-jsonl.rkt b/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-jsonl.rkt
index 7f92579a..7a78e40e 100644
--- a/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-jsonl.rkt
+++ b/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-jsonl.rkt
@@ -84,10 +84,14 @@ ex-rows:
          (printf "finished processing edges\n")
          (printf "the current counters ~s\n\n" counters)]
         [else
-         (let ((subject (hash-ref line 'subject #f))
-               (object (hash-ref line 'object #f))
-               (predicate (hash-ref line 'predicate #f))
-               (robokop-primary_knowledge_source (hash-ref line 'primary_knowledge_source #f)))
+         (let* ((subject (hash-ref line 'subject #f))
+                (object (hash-ref line 'object #f))
+                (predicate (hash-ref line 'predicate #f))
+                ; the following line is for a fix for rtx-kg2 2.10.1pre
+                (predicate (if (and (string? predicate) (string-contains? predicate "biolink:biolink_"))
+                               (string-replace predicate "biolink:biolink_" "biolink:")
+                               predicate)) 
+                (robokop-primary_knowledge_source (hash-ref line 'primary_knowledge_source #f)))
            (if (equal? robokop-primary_knowledge_source "infores:text-mining-provider-targeted")
                (loop id (read-json edges-in))
                (begin
@@ -117,6 +121,9 @@ ex-rows:
                                            value)))
                            (unless (or (equal? "" value) (equal? 'null value))
                              (cond
+                               ; the following line is for a fix for rtx-kg2 2.10.1pre
+                               ((and (equal? propname 'predicate) (string-contains? value "biolink:biolink_"))
+                                (fprintf edge-props-out "~a\t~a\t~a\n" id propname (string-replace value "biolink:biolink_" "biolink:")))
                                ((equal? propname 'qualified_object_aspect)
                                 (fprintf edge-props-out "~a\tobject_aspect_qualifier\t~a\n" id value))
                                ((equal? propname 'qualified_object_direction)
diff --git a/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2.rkt b/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2.rkt
index ae05d8bd..dc075c11 100644
--- a/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2.rkt
+++ b/medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2.rkt
@@ -4,12 +4,12 @@
          "transform-edge-jsonl.rkt"
          "transform-node-jsonl.rkt")
 
-(define BASE "rtx-kg2-2.10.0pre/")
+(define BASE "rtx-kg2-2.10.1pre/")
 
 (transform-generic (string-append "../../neo-data/raw_downloads_from_kge_archive/" BASE)
                    (string-append "../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/" BASE)
-                   "kg2.10.0pre-nodes.jsonl"
-                   "kg2.10.0pre-edges.jsonl"
+                   "kg2-simplified-2.10.1-nodes.jsonl"
+                   "kg2-simplified-2.10.1-edges.jsonl"
                    "rtx_kg2"
                    'rtx-kg2
                    (cons transform-node-jsonl transform-edge-jsonl))
diff --git a/medikanren2/neo/neo-low-level/query-low-level-rtx-kg2.rkt b/medikanren2/neo/neo-low-level/query-low-level-rtx-kg2.rkt
index 05b1f462..267ff72d 100644
--- a/medikanren2/neo/neo-low-level/query-low-level-rtx-kg2.rkt
+++ b/medikanren2/neo/neo-low-level/query-low-level-rtx-kg2.rkt
@@ -24,7 +24,7 @@
  racket/match)
 
 #;(define db-path-under-parent "rtx-kg2-may-9-2024/rtx-kg2-2.9.0pre/rtx-kg2.db")
-(define db-path-under-parent "rtx-kg2-Aug-6-2024/rtx-kg2-2.10.0pre/rtx-kg2.db")
+(define db-path-under-parent "rtx-kg2-oct-30-2024/rtx-kg2-2.10.1pre/rtx-kg2.db")
 
 (match-define
   (list
diff --git a/medikanren2/neo/neo-server/neo-server.rkt b/medikanren2/neo/neo-server/neo-server.rkt
index fb98d6a1..46c388ed 100644
--- a/medikanren2/neo/neo-server/neo-server.rkt
+++ b/medikanren2/neo/neo-server/neo-server.rkt
@@ -29,7 +29,7 @@
 
 (define DEFAULT_PORT 8384)
 
-(define NEO_SERVER_VERSION "1.53")
+(define NEO_SERVER_VERSION "1.54")
 
 ;; Maximum number of results to be returned from *each individual* KP,
 ;; or from mediKanren itself.