From 8a91a07920b995c4f1b9c5e4046687d45fa7db3f Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Fri, 24 Jan 2025 12:11:57 -0500
Subject: [PATCH] fix(build): Remove onload function and setting env variables

---
 R/utils_annotateProteinInfoFromIndra.R | 14 ++++++++------
 R/utils_onLoad.R                       |  7 -------
 2 files changed, 8 insertions(+), 13 deletions(-)
 delete mode 100644 R/utils_onLoad.R

diff --git a/R/utils_annotateProteinInfoFromIndra.R b/R/utils_annotateProteinInfoFromIndra.R
index a2cd554..640876d 100644
--- a/R/utils_annotateProteinInfoFromIndra.R
+++ b/R/utils_annotateProteinInfoFromIndra.R
@@ -1,3 +1,5 @@
+INDRA_API_URL = "https://discovery.indra.bio"
+
 #' Call API to get UniProt IDs from UniProt mnemonic IDs
 #' @param uniprotMnemonicIds list of UniProt mnemonic ids
 #' @return list of UniProt IDs
@@ -33,7 +35,7 @@
         stop("An error occurred converting uniprot mnemonic IDs to character strings: ", e$message)
     })
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/get_uniprot_ids_from_uniprot_mnemonic_ids")
+    apiUrl <- file.path(INDRA_API_URL, "api/get_uniprot_ids_from_uniprot_mnemonic_ids")
 
     requestBody <- list(uniprot_mnemonic_ids = uniprotMnemonicIds)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
@@ -73,7 +75,7 @@
         stop("Input list must not be empty.")
     }
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/get_hgnc_ids_from_uniprot_ids")
+    apiUrl <- file.path(INDRA_API_URL, "api/get_hgnc_ids_from_uniprot_ids")
 
     requestBody <- list(uniprot_ids = uniprotIds)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
@@ -113,7 +115,7 @@
         stop("Input list must not be empty.")
     }
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/get_hgnc_names_from_hgnc_ids")
+    apiUrl <- file.path(INDRA_API_URL, "api/get_hgnc_names_from_hgnc_ids")
 
     requestBody <- list(hgnc_ids = hgncIds)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
@@ -153,7 +155,7 @@
         stop("Input list must not be empty.")
     }
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/is_kinase")
+    apiUrl <- file.path(INDRA_API_URL, "api/is_kinase")
 
     requestBody <- list(genes = genes)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
@@ -193,7 +195,7 @@
         stop("Input list must not be empty.")
     }
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/is_phosphatase")
+    apiUrl <- file.path(INDRA_API_URL, "api/is_phosphatase")
 
     requestBody <- list(genes = genes)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
@@ -233,7 +235,7 @@
         stop("Input list must not be empty.")
     }
 
-    apiUrl <- file.path(Sys.getenv("INDRA_API_URL"), "api/is_transcription_factor")
+    apiUrl <- file.path(INDRA_API_URL, "api/is_transcription_factor")
 
     requestBody <- list(genes = genes)
     requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
diff --git a/R/utils_onLoad.R b/R/utils_onLoad.R
deleted file mode 100644
index a6859b1..0000000
--- a/R/utils_onLoad.R
+++ /dev/null
@@ -1,7 +0,0 @@
-.onLoad <- function(libname, pkgname) {
-
-   if (Sys.getenv("INDRA_API_URL") == "") {
-    Sys.setenv(INDRA_API_URL = "https://discovery.indra.bio")
-  }
-
-}
\ No newline at end of file