Remove qual and FBC SED-ML files.

In theory, we could figure out what to use for them, but we haven't and need to publish, so don't do this.

fix-entries.py

@@ -24,6 +24,7 @@
 import remove_converted_files_for_non_kinetic_models
 import remove_empty_containers_from_sedml_doc
 import remove_non_sbml
+import remove_qual_and_fbc_sedml
 import remove_unused_sedml_elements
 import remove_urn_sbml_files
 import remove_initial_rdf_file
@@ -209,7 +210,10 @@ def fix_entry(id, convert_files=False, guess_file_name=None, validate_sbml=False
     sbml_filenames.sort()
 
     fix_sbml_validity.run(id, sbml_filenames)
-
+    sedml_filenames = glob.glob(os.path.join(temp_entry_dir, '**', '*.sedml'), recursive=True)
+    sedml_filenames.sort()
+
+    remove_qual_and_fbc_sedml(id, sedml_filenames, sbml_filenames)
     sedml_filenames = glob.glob(os.path.join(temp_entry_dir, '**', '*.sedml'), recursive=True)
     sedml_filenames.sort()
 

remove_qual_and_fbc_sedml.py

@@ -0,0 +1,20 @@
+import os
+
+# Don't use this list; figure it out on the fly (so we're future-proofed)
+#qual_and_fbc_models = ["BIOMD0000000562", "BIOMD0000000592", "BIOMD0000000593", "BIOMD0000001046", "BIOMD0000001061", "BIOMD0000001062", "BIOMD0000001063", "BIOMD0000001064"]
+
+def hasQualOrFBC(sbml_filenames):
+    for filename in sbml_filenames:
+        f = open(filename, "r")
+        for line in f:
+            if "qual:" in line:
+                return True
+            if "fbc:" in line:
+                return True
+    return False
+
+
+def run(id, sedml_filenames, sbml_filenames):
+    if hasQualOrFBC(sbml_filenames):
+        for filename in sedml_filenames:
+            os.remove(filename)