From 0435e799976bb37d28981b35bc2e519b4a619656 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <almahmoudresearch@gmail.com>
Date: Wed, 8 Jan 2025 12:15:30 -0500
Subject: [PATCH] Scripts paths

---
 .github/workflows/create_endpoint.yaml                      | 6 +++++-
 .github/workflows/delete_endpoint.yaml                      | 6 +++++-
 hubsingest                                                  | 1 +
 install_hubsingest.sh                                       | 4 ++--
 .../hubsingest_create_endpoint.sh                           | 0
 .../hubsingest_delete_endpoint.sh                           | 0
 6 files changed, 13 insertions(+), 4 deletions(-)
 rename hubsingest_create_endpoint.sh => scripts/hubsingest_create_endpoint.sh (100%)
 rename hubsingest_delete_endpoint.sh => scripts/hubsingest_delete_endpoint.sh (100%)

diff --git a/.github/workflows/create_endpoint.yaml b/.github/workflows/create_endpoint.yaml
index cec38f0..bcf376f 100644
--- a/.github/workflows/create_endpoint.yaml
+++ b/.github/workflows/create_endpoint.yaml
@@ -12,6 +12,9 @@ on:
         required: true
         type: string
 
+env:
+  BIOC_HUBSINGEST_PATH: "${{ github.workspace }}"
+
 jobs:
   create-endpoint:
     runs-on: ubuntu-latest
@@ -36,4 +39,5 @@ jobs:
       
       - name: Create endpoint
         run: |
-          ./hubsingest create_endpoint "${{ inputs.username }}" "${{ inputs.size }}" ${{ secrets[env.SECRET_NAME] }}
+          sudo bash install_hubsingest.sh
+          hubsingest create_endpoint "${{ inputs.username }}" "${{ inputs.size }}" ${{ secrets[env.SECRET_NAME] }}
diff --git a/.github/workflows/delete_endpoint.yaml b/.github/workflows/delete_endpoint.yaml
index 793977b..f147377 100644
--- a/.github/workflows/delete_endpoint.yaml
+++ b/.github/workflows/delete_endpoint.yaml
@@ -8,6 +8,9 @@ on:
         required: true
         type: string
 
+env:
+  BIOC_HUBSINGEST_PATH: "${{ github.workspace }}"
+
 jobs:
   delete-endpoint:
     runs-on: ubuntu-latest
@@ -27,4 +30,5 @@ jobs:
       
       - name: Delete endpoint
         run: |
-          ./hubsingest delete_endpoint "${{ inputs.username }}"
+          sudo bash install_hubsingest.sh
+          hubsingest delete_endpoint "${{ inputs.username }}"
diff --git a/hubsingest b/hubsingest
index 1566d0b..c78c73d 100755
--- a/hubsingest
+++ b/hubsingest
@@ -1,4 +1,5 @@
 #!/bin/bash
+HUBSINGESTPATH=${BIOC_HUBSINGEST_PATH:-/usr/local/bin/hubsingest}
 
 case "$1" in
   create_endpoint)
diff --git a/install_hubsingest.sh b/install_hubsingest.sh
index 7c3ca0b..a0fec49 100644
--- a/install_hubsingest.sh
+++ b/install_hubsingest.sh
@@ -3,8 +3,8 @@ HUBSINGESTPATH=${BIOC_HUBSINGEST_PATH:-/usr/local/bin/hubsingest}
 mkdir -p $HUBSINGESTPATH
 
 curl -o $HUBSINGESTPATH/hubsingest https://raw.githubusercontent.com/Bioconductor/hubsingest/refs/heads/devel/hubsingest
-curl -o $HUBSINGESTPATH/hubsingest_create_endpoint.sh https://raw.githubusercontent.com/Bioconductor/hubsingest/refs/heads/devel/hubsingest_create_endpoint.sh
-curl -o $HUBSINGESTPATH/hubsingest_delete_endpoint.sh https://raw.githubusercontent.com/Bioconductor/hubsingest/refs/heads/devel/hubsingest_delete_endpoint.sh
+curl -o $HUBSINGESTPATH/hubsingest_create_endpoint.sh https://raw.githubusercontent.com/Bioconductor/hubsingest/refs/heads/devel/scripts/hubsingest_create_endpoint.sh
+curl -o $HUBSINGESTPATH/hubsingest_delete_endpoint.sh https://raw.githubusercontent.com/Bioconductor/hubsingest/refs/heads/devel/scripts/hubsingest_delete_endpoint.sh
 
 chmod +x $HUBSINGESTPATH/hubsingest
 echo 'In order to persist the path, you may want to run, and/or add to your `rc` files:'
diff --git a/hubsingest_create_endpoint.sh b/scripts/hubsingest_create_endpoint.sh
similarity index 100%
rename from hubsingest_create_endpoint.sh
rename to scripts/hubsingest_create_endpoint.sh
diff --git a/hubsingest_delete_endpoint.sh b/scripts/hubsingest_delete_endpoint.sh
similarity index 100%
rename from hubsingest_delete_endpoint.sh
rename to scripts/hubsingest_delete_endpoint.sh