From fe3d3bbda9a29470f6adeafc9f2776ce5c0a450d Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Date: Fri, 23 Aug 2024 14:17:49 +0200
Subject: [PATCH]  - can not assume filenames

---
 pyenzyme/sbml/omex.py | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/pyenzyme/sbml/omex.py b/pyenzyme/sbml/omex.py
index 1f86734..c7aba86 100644
--- a/pyenzyme/sbml/omex.py
+++ b/pyenzyme/sbml/omex.py
@@ -67,7 +67,24 @@ def read_sbml_omex(path: Path) -> tuple[Path, Path | None]:
     """
 
     omex = Omex.from_omex(path)
-    sbml_file = omex.get_path("./model.xml")
-    data = omex.get_path("./data.tsv")
+
+    # get first sbml entry in manifest
+    sbml_entry = None
+    for entry in omex.manifest.entries:
+        if '/sbml' in entry.format:
+            sbml_entry = entry.location
+            if entry.master:
+                break
+    sbml_file = omex.get_path(sbml_entry)
+
+
+    # we really need to get all of the data entries from the manifest
+    # but for now just get the first one
+    data_entry = None
+    for entry in omex.manifest.entries:
+        if '/csv' in entry.format or '/tsv' in entry.format:
+            data_entry = entry.location
+            break
+    data = omex.get_path(data_entry)
 
     return sbml_file, data