From 5f4cef3640f84092e5692e16865002a832b7838c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2026 09:51:26 +0200
Subject: Added a test that creates an ontology

---
 guix.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'guix.scm')

diff --git a/guix.scm b/guix.scm
index 77551cd..5c8519e 100644
--- a/guix.scm
+++ b/guix.scm
@@ -7,12 +7,14 @@
 ;;
 ;; Development shell:
 ;;
-;;   guix shell -L . -C -N -F edirect-25 genecup-gemini coreutils -- genecup --port 4201
+;;   guix shell -L . -C -N -F --expose=$HOME/.config/gemini --share=/export3/PubMed edirect-25 genecup-gemini coreutils -- genecup --port 4201
 ;;
 ;; In a shell you can run
 ;;
-;;   python3 -m unittest tests.test_network_esearch
+;;   guix shell -C -N -F -L . --expose=$HOME/.config/gemini --share=/export3/PubMed edirect-25 genecup-gemini
+;;   env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_network_esearch
 ;;   env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_local_xfetch -v
+;;   env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_network_gemini_ontology
 ;;
 ;; Note: API key is read from ~/.config/gemini/credentials
 ;;
-- 
cgit 1.4.1


From 0ede8df7f295604b09a574dcfa587a31483f1583 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2026 11:55:23 +0200
Subject: Propagate (guix.scm) xargs

---
 guix.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'guix.scm')

diff --git a/guix.scm b/guix.scm
index 5c8519e..2d17801 100644
--- a/guix.scm
+++ b/guix.scm
@@ -286,7 +286,7 @@ GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).")
            go-github-com-surgebase-porter2
            go-golang-org-x-sys
            go-golang-org-x-text))
-    (propagated-inputs (list curl wget grep sed gawk coreutils findutils gzip unzip))
+    (propagated-inputs (list curl wget grep sed gawk coreutils findutils gzip unzip xargs))
     (inputs (list bash-minimal coreutils perl perl-xml-simple python))
     (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/")
     (synopsis "Tools for accessing the NCBI's set of databases")
-- 
cgit 1.4.1