Update package reference for sbmlpbkutils and add option to include C…

…ITATION.cff for annotation of authors

.github/workflows/build.yml

@@ -50,7 +50,11 @@ jobs:
       - name: Annotate SBML
         id: annotate-sbml
         run: |
-          (python sbml-pbk-workflow/src/annotate_sbml.py -f model/${{inputs.model-name}}.sbml model/${{inputs.model-name}}.annotations.csv model/${{inputs.model-name}}.sbml) | tee log/annotate-terms.log
+          if [ -f CITATION.cff ]; then
+            (python sbml-pbk-workflow/src/annotate_sbml.py model/${{inputs.model-name}}.sbml model/${{inputs.model-name}}.annotations.csv model/${{inputs.model-name}}.sbml -c CITATION.cff -f) | tee log/annotate-terms.log
+          else
+            (python sbml-pbk-workflow/src/annotate_sbml.py model/${{inputs.model-name}}.sbml model/${{inputs.model-name}}.annotations.csv model/${{inputs.model-name}}.sbml -f) | tee log/annotate-terms.log
+          fi
         shell: bash
 
       - name: Validate SBML

requirements.txt

@@ -3,4 +3,4 @@ python-libsbml>=5.20.2
 sbmlutils>=0.9.0
 tellurium>=2.2.10
 numpy>=1.26.4
-sbmlpbkutils @ git+https://github.com/jwkruisselbrink/sbml-pbk-utils.git@v0.10.0
+sbmlpbkutils @ git+https://github.com/jwkruisselbrink/sbml-pbk-utils.git@v0.12.0

src/annotate_sbml.py

@@ -14,26 +14,31 @@ def main():
     parser.add_argument("sbml_file", help="Full path to SBML file")
     parser.add_argument("annotations_file", help="Full path to SBML file")
     parser.add_argument("out_file", help="Output file")
+    parser.add_argument("-c", "--cff", type=str, help="CFF file (optional)")
     parser.add_argument("-f", "--force", action="store_true", help="Overwrite existing")
     args = parser.parse_args()
     f_in = Path(args.sbml_file)
     f_ann = Path(args.annotations_file)
+    f_cff = Path(args.cff) if args.cff else None
     f_out = Path(args.out_file)
     if not f_in.is_file():
-        raise FileNotFoundError(f'SBML file [{f_in}] does not exist.')
+        raise FileNotFoundError(f'SBML file [{f_in}] not found.')
     if not f_ann.is_file():
-        raise FileNotFoundError(f'Annotations file [{f_ann}] does not exist.')
+        raise FileNotFoundError(f'Annotations file [{f_ann}] not found.')
+    if f_cff is not None and not f_cff.is_file():
+        raise FileNotFoundError(f'CFF file [{f_cff}] not found.')
     try:
         if not f_out.exists() or args.force:
-            
+
             # Check if output folder exists, otherwise create it
             out_dir = os.path.dirname(f_out)
             if not os.path.exists(out_dir):
                 os.makedirs(out_dir)
 
             # Annotate SBML file
             annotator = PbkModelAnnotator()
-            document = annotator.annotate(f_in, f_ann, logger)
+            document = ls.readSBML(f_in)
+            annotator.annotate(document, f_ann, f_cff, logger)
 
             # Write SBML
             ls.writeSBML(document, str(f_out))

tests/models/simple.CITATION.cff

@@ -0,0 +1,8 @@
+cff-version: 1.2.0
+title: simple
+version: 0.0.1
+authors:
+  - family-names: Doe
+    given-names: John
+    email: [email protected]
+    affiliation: ACME

tests/test_annotate_sbml.py

@@ -12,5 +12,18 @@ def test_simple(self):
         path = pl.Path('./tests/output/simple.annotated.sbml')
         self.assertIsFile(path)
 
+    @patch('sys.argv', [
+        'ant2sbml.py',
+        './tests/models/simple.sbml',
+        './tests/models/simple.annotations.csv',
+        './tests/output/simple.annotated.cff.sbml',
+        '-c', './tests/models/simple.CITATION.cff',
+        '-f'
+    ])
+    def test_simple_cff(self):
+        src.annotate_sbml.main()
+        path = pl.Path('./tests/output/simple.annotated.cff.sbml')
+        self.assertIsFile(path)
+
 if __name__ == '__main__':
     unittest.main()