From e72461194c50d789e6791cf7830009988ed17c0a Mon Sep 17 00:00:00 2001
From: sgosline <sara.gosline@pnnl.gov>
Date: Wed, 10 Jul 2024 09:57:34 -0700
Subject: [PATCH] updated build process

---
 .github/workflows/database-update.yml | 7 ++++++-
 .github/workflows/docker.yml          | 1 +
 build_script.py                       | 4 ++--
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/database-update.yml b/.github/workflows/database-update.yml
index 1e00756..b0418df 100644
--- a/.github/workflows/database-update.yml
+++ b/.github/workflows/database-update.yml
@@ -80,13 +80,18 @@ jobs:
    build-expr:
      #if: github.actor != 'github-actions[bot]'
      runs-on: ubuntu-20.04
+     needs: build-samples
      steps:
        - name: Checkout Repo
          uses: actions/checkout@v3
-       - name: Download artifacts from previous drug gen
+       - name: Download artifacts from sample generation
          uses: actions/download-artifact@v3
+           with:
+           name: samp-files
        - name: Pull sample image
          run: docker pull sgosline/srp-zfexp
+       - name: move chemical list to tmp
+         run: mv samp-files/chemicals.csv .
        - name: Run zfexp python command
          run: |
            docker run -v $PWD:/tmp sgosline/srp-zfexp
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 2645309..a68653a 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -7,6 +7,7 @@ on:
     branches:
       - '**'
     paths:
+      - build_script.py
       - .github/
       - zfBmd/
       - zfExp/
diff --git a/build_script.py b/build_script.py
index 3f310df..7bad162 100644
--- a/build_script.py
+++ b/build_script.py
@@ -167,10 +167,10 @@ def main():
         runExposome(cid)
         runSchemaCheck()
     if args.geneEx:
-        if not os.path.exists("chemicals.csv"):
+        if not os.path.exists("/tmp/chemicals.csv"):
             runSampMap(False,[],smap,cid,emap,cclass,ctfile,fses,desfile)
         
-        runExpression(gex1,'chemicals.csv',ginfo)
+        runExpression(gex1,'/tmp/chemicals.csv',ginfo)
         runSchemaCheck()