Flag SBML as master, not SEDML files.

Also, export list of SBML Master files, so that list can be used when uploading to biomodels.

create_omex.py

@@ -9,14 +9,15 @@
 
 def process(project_id, project_path, omex_dir, write_omex, sbml_master = None):
     manifest_filename = os.path.join(project_path, 'manifest.xml')
-    sedml_filenames = glob.glob(os.path.join(project_path, '**', '*.sedml'), recursive=True)
-    sedml_locations = [os.path.relpath(path, project_path) for path in sedml_filenames]
+    # sedml_filenames = glob.glob(os.path.join(project_path, '**', '*.sedml'), recursive=True)
+    # sedml_locations = [os.path.relpath(path, project_path) for path in sedml_filenames]
+    master_files = []
     if sbml_master:
-        sedml_locations.append(sbml_master)
+        master_files.append(sbml_master)
     if os.path.exists(manifest_filename):
         #Have to do this, otherwise build_combine_archive creates a new one!
         os.remove(manifest_filename)
-    archive = build_combine_archive(project_path, sedml_locations)
+    archive = build_combine_archive(project_path, master_files)
     if write_omex:
         combine_writer.run(archive, project_path, omex_dir + "/" + project_id + ".omex")
     #Write the new manifest.xml file:

fix-entries.py

@@ -48,13 +48,17 @@
 import tempfile
 import warnings
 import math
+import json
 
 MANUALLY_FIXED_ENTRIES_DIR = os.path.join(os.path.dirname(__file__), 'manual-fixes')
 FINAL_ENTRIES_DIR = os.path.join(os.path.dirname(__file__), 'final')
 OMEX_DIR = os.path.join(os.path.dirname(__file__), 'omex_files')
 
 global_sbml_validation_errors = []
 
+all_masters = {}
+only_masters = False
+
 
 def get_entry_ids():
     """ Get the ids of the entries of BioModels
@@ -165,7 +169,13 @@ def fix_entry(id, convert_files=False, guess_file_name=None, validate_sbml=False
     remove_initial_rdf_file.run(rdf_filenames)
     remove_failed_pdfs.run(pdf_filenames)
     remove_non_sbml.run(id, sbml_filenames)
+
     master_sbml = rename_sbml_files.run(id, sbml_filenames, master_sbml)
+    all_masters[id] = master_sbml
+
+    if only_masters:
+        return
+
     rename_xpp_to_ode.run(xpp_filenames)
 
     # SED-ML files: recreate from COPASI, then fix the model sources.
@@ -254,7 +264,7 @@ def fix_entry(id, convert_files=False, guess_file_name=None, validate_sbml=False
 
     ###################################################
     # Build manifest and create OMEX file
-    create_omex.process(id, temp_entry_dir, OMEX_DIR, False)
+    create_omex.process(id, temp_entry_dir, OMEX_DIR, False, master_sbml)
 
     ###################################################
     # Move temporary directory to final location
@@ -371,3 +381,8 @@ def fix_entry(id, convert_files=False, guess_file_name=None, validate_sbml=False
         git_add_file.write("git add final/" + id + "/*\n")
     git_add_file.write("git add good_pmids.p\n")
     git_add_file.close()
+
+    if only_masters:
+        with open('all_masters.json', 'w') as f:
+            json.dump(all_masters, f)        
+