From f8fe25134444131f3e0b8b4a0e1d914423506737 Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Mon, 26 Feb 2024 15:18:07 -0500
Subject: [PATCH] updated dockerfile for chmod and copasi process

---
 Dockerfile                               |  6 ++++--
 biosimulator_processes/copasi_process.py | 16 +++++++++++++++-
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 223d6eb55..652a5ebe4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,8 +77,8 @@
 #
 # CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]
 
-# Use a more specific tag instead of latest for reproducibility
-FROM ubuntu:20.04
+# TODO: Use a more specific tag instead of latest for reproducibility
+FROM ubuntu:latest
 
 ENV DEBIAN_FRONTEND=noninteractive \
     XVFB_RES="1920x1080x24" \
@@ -126,6 +126,8 @@ RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app
 
 USER jupyteruser
 
+RUN chmod +x /app/notebooks
+
 VOLUME /app/data
 
 CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]
diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py
index 1c931a8ce..cb00b6bb5 100644
--- a/biosimulator_processes/copasi_process.py
+++ b/biosimulator_processes/copasi_process.py
@@ -46,11 +46,25 @@
                 set_species,
                 run_time_course,
                 get_compartments,
-                model_info
+                model_info,
+                biomodels
             )
 from process_bigraph import Process, Composite, pf
 
 
+def find_models(term: str):
+    return biomodels.search_for_model(term)
+
+
+def fetch_model(term: str, index: int = 0):
+    """Searrch for models matching the term and return an instantiated model from BioModels.
+
+        TODO: Implement a dynamic search of this
+    """
+
+
+
+
 class CopasiProcess(Process):
     config_schema = {
         'model_file': 'string',