testing

Author: jjacobson95

build/docker/Dockerfile.upload

@@ -6,6 +6,20 @@ RUN python -m pip install --upgrade pip pyyaml requests linkml
 
 RUN apt-get update && apt-get install -y git
 
+# Install necessary system packages: git, curl, and gpg
+RUN apt-get update && \
+    apt-get install -y git curl gnupg && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install GitHub CLI (gh)
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | \
+    gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg && \
+    echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | \
+    tee /etc/apt/sources.list.d/github-cli.list > /dev/null && \
+    apt-get update && \
+    apt-get install -y gh && \
+    rm -rf /var/lib/apt/lists/*
+
 
 RUN git clone https://github.com/PNNL-CompBio/coderdata.git
 WORKDIR /usr/src/app/coderdata

scripts/map_improve_sample_ids.py

@@ -24,9 +24,8 @@ def load_mapping(mapping_file='improve_sample_mapping.json'):
             "samples": []
         }, False
 
-def save_mapping(mapping_data):
+def save_mapping(mapping_data,mapping_file):
     """Saves mapping data to disk as JSON."""
-    mapping_file='tmp/improve_sample_mapping.json'
     with open(mapping_file, 'w') as f:
         json.dump(mapping_data, f, indent=2)
 
@@ -414,7 +413,7 @@ def main():
         key=lambda x: int(x["stable_id"]) if x["stable_id"].isdigit() else x["stable_id"]
     )
     # Save improve_sample_mapping.json
-    save_mapping(mapping_data)
+    save_mapping(mapping_data,mapping_file)
     print(f"improve_sample_mapping.json updated with {len(mapping_data['samples'])} samples.")
     # Determine if any improve_sample_ids were modified
     ids_modified = any(