Merge pull request #335 from NeuroML/feat/issue-329

pynml-archive: add `-sedml`

Author: pgleeson

man/man1/pynml-archive.1

@@ -1,4 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.1.
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
 .TH PYNML-ARCHIVE "1" "April 2024" "pynml-archive v1.2.8" "User Commands"
 .SH NAME
 pynml-archive \- manual page for pynml-archive v1.2.8
@@ -7,13 +7,14 @@ usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
 .TP
 [\-zipfileExtension <zip file extension>]
 [\-filelist [<explicit list of files to create archive of> ...]]
-<NeuroML 2/LEMS file>
+[\-sedml]
+<NeuroML 2/LEMS file/SED\-ML file>
 .PP
 A script to create a COMBINE archive
 .SS "positional arguments:"
 .TP
-<NeuroML 2/LEMS file>
-Name of the NeuroML 2/LEMS main file
+<NeuroML 2/LEMS file/SED\-ML file>
+Name of the NeuroML 2/LEMS/SED\-ML main file
 .SS "options:"
 .TP
 \fB\-h\fR, \fB\-\-help\fR
@@ -23,10 +24,14 @@ show this help message and exit
 Extension to use for archive.
 .TP
 \fB\-zipfileExtension\fR <zip file extension>
-Extension to use for archive.
+Extension to use for archive: .neux by default
 .TP
 \fB\-filelist\fR [<explicit list of files to create archive of> ...]
 Explicit list of files to create archive of.
+.TP
+\fB\-sedml\fR
+Generate SED\-ML file from main LEMS file and use as
+master file.
 .SH "SEE-ALSO"
 .BR pynml (1),
 .BR pynml-archive (1),
@@ -45,4 +50,4 @@ Explicit list of files to create archive of.
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.8 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.8 (libNeuroML v0.5.9, jNeuroML v0.13.0)

pyneuroml/archive/__init__.py

@@ -16,14 +16,16 @@
 
 from pyneuroml.utils import get_model_file_list
 from pyneuroml.utils.cli import build_namespace
+from pyneuroml.runners import run_jneuroml
+from pyneuroml.sedml import validate_sedml_files
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
 
 DEFAULTS = {
     "zipfileName": None,
-    "zipfileExtension": ".neux",
+    "zipfileExtension": None,
     "filelist": [],
 }  # type: typing.Dict[str, typing.Any]
 
@@ -39,8 +41,8 @@ def process_args():
     parser.add_argument(
         "rootfile",
         type=str,
-        metavar="<NeuroML 2/LEMS file>",
-        help="Name of the NeuroML 2/LEMS main file",
+        metavar="<NeuroML 2/LEMS file/SED-ML file>",
+        help="Name of the NeuroML 2/LEMS/SED-ML main file",
     )
 
     parser.add_argument(
@@ -55,7 +57,7 @@ def process_args():
         type=str,
         metavar="<zip file extension>",
         default=DEFAULTS["zipfileExtension"],
-        help="Extension to use for archive.",
+        help="Extension to use for archive: .neux by default",
     )
     parser.add_argument(
         "-filelist",
@@ -64,6 +66,11 @@ def process_args():
         default=DEFAULTS["filelist"],
         help="Explicit list of files to create archive of.",
     )
+    parser.add_argument(
+        "-sedml",
+        action="store_true",
+        help=("Generate SED-ML file from main LEMS file and use as master file."),
+    )
 
     return parser.parse_args()
 
@@ -79,10 +86,32 @@ def main(args=None):
 def cli(a: typing.Optional[typing.Any] = None, **kwargs: str):
     """Main cli caller method"""
     a = build_namespace(DEFAULTS, a, **kwargs)
+
+    rootfile = a.rootfile
+    zipfile_extension = None
+
+    # first generate SED-ML file
+    # use .omex as extension
+    if (
+        a.rootfile.startswith("LEMS") and a.rootfile.endswith(".xml")
+    ) and a.sedml is True:
+        logger.debug("Generating SED-ML file from LEMS file")
+        run_jneuroml("", a.rootfile, "-sedml")
+
+        rootfile = a.rootfile.replace(".xml", ".sedml")
+        zipfile_extension = ".omex"
+
+        # validate the generated file
+        validate_sedml_files([rootfile])
+
+    # if explicitly given, use that
+    if a.zipfile_extension is not None:
+        zipfile_extension = a.zipfile_extension
+
     create_combine_archive(
         zipfile_name=a.zipfile_name,
-        rootfile=a.rootfile,
-        zipfile_extension=a.zipfile_extension,
+        rootfile=rootfile,
+        zipfile_extension=zipfile_extension,
         filelist=a.filelist,
     )
 
@@ -109,7 +138,7 @@ def create_combine_archive(
 
     :param zipfile_name: name of zip file without extension: rootfile if not provided
     :type zipfile_name: str
-    :param rootfile: full path to main root file
+    :param rootfile: full path to main root file (SED-ML/LEMS/NeuroML2)
     :type rootfile: str
     :param zipfile_extension: extension for zip file, starting with ".".
     :type zipfile_extension: str
@@ -177,43 +206,36 @@ def create_combine_archive_manifest(
     with open(manifest, "w") as mf:
         print('<?xml version="1.0" encoding="utf-8"?>', file=mf)
         print(
-            """
-            <omexManifest
-            xmlns="http://identifiers.org/combine.specifications/omex-manifest">
-            """,
+            """<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">""",
             file=mf,
         )
 
         print(
-            """
-            <content location="."
-                format="http://identifiers.org/combine.specifications/omex"/>
-            """,
+            """\t<content location="." format="http://identifiers.org/combine.specifications/omex"/>""",
             file=mf,
         )
 
         for f in filelist:
+            if f.endswith(".xml") and f.startswith("LEMS"):
+                # TODO: check what the string for LEMS should be
+                format_string = "http://identifiers.org/combine.specifications/neuroml"
+            elif f.endswith(".nml"):
+                format_string = "http://identifiers.org/combine.specifications/neuroml"
+            elif f.endswith(".sedml"):
+                format_string = "http://identifiers.org/combine.specifications/sed-ml"
+
             if f == rootfile:
-                print(
-                    f"""
-                    <content location="{f}" master="true"
-                        format="http://identifiers.org/combine.specifications/neuroml"/>
-                    """,
-                    file=mf,
-                )
+                master_string = 'master="true"'
             else:
-                print(
-                    f"""
-                    <content location="{f}"
-                        format="http://identifiers.org/combine.specifications/neuroml"/>
-                    """,
-                    file=mf,
-                )
+                master_string = ""
+
+            print(
+                f"""\t<content location="{f}" {master_string} format="{format_string}"/>""",
+                file=mf,
+            )
 
         print(
-            """
-            </omexManifest>
-            """,
+            """</omexManifest>""",
             file=mf,
             flush=True,
         )

pyneuroml/utils/__init__.py

@@ -8,7 +8,6 @@
 """
 
 import copy
-from datetime import datetime
 import logging
 import math
 import os
@@ -21,14 +20,16 @@
 import time
 import typing
 import zipfile
+from datetime import datetime
 from pathlib import Path
 
+import libsedml
 import neuroml
 import numpy
+import pyneuroml.utils.misc
 from lems.model.model import Model
 from neuroml.loaders import read_neuroml2_file
 from pyneuroml.errors import UNKNOWN_ERR
-import pyneuroml.utils.misc
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -487,7 +488,7 @@ def get_model_file_list(
     This method will take the rootfile, and recursively resolve all the files
     it uses.
 
-    :param rootfile: main NeuroML or LEMS file to resolve
+    :param rootfile: main NeuroML/LEMS/SED-ML file to resolve
     :type rootfile: str
     :param filelist: list of file paths to append to
     :type filelist: list of strings
@@ -554,8 +555,23 @@ def get_model_file_list(
                 continue
             lems_def_dir = get_model_file_list(inc, filelist, rootdir, lems_def_dir)
 
+    elif rootfile.endswith(".sedml"):
+        if pathlib.Path(rootfile).is_absolute():
+            rootdoc = libsedml.readSedMLFromFile(rootfile)
+        else:
+            rootdoc = libsedml.readSedMLFromFile(rootdir + "/" + rootfile)
+
+        # there should only be one model
+        assert rootdoc.getNumModels() == 1
+        model = rootdoc.getModel(0)
+        lems_file = model.getSource()
+        logger.debug(f"Got {lems_file} from SED-ML file {rootdoc}")
+        lems_def_dir = get_model_file_list(lems_file, filelist, rootdir, lems_def_dir)
+
     else:
-        raise ValueError(f"File must have a .xml or .nml extension. We got: {rootfile}")
+        raise ValueError(
+            f"File must have a .xml/.nml/.sedml extension. We got: {rootfile}"
+        )
 
     return lems_def_dir
 

tests/archive/test_archive.py

@@ -17,13 +17,13 @@
     create_combine_archive_manifest,
     get_model_file_list,
 )
+from pyneuroml.runners import run_jneuroml
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
 
 class TestArchiveModule(unittest.TestCase):
-
     """Test the pyneuroml.archive module."""
 
     def test_get_model_file_list(self):
@@ -43,6 +43,22 @@ def test_get_model_file_list(self):
         )
         self.assertEqual(5, len(filelist))
 
+        # a SEDML file in the examples directory
+        dirname = str(thispath.parent.parent.parent)
+        run_jneuroml(
+            "",
+            "LEMS_NML2_Ex5_DetCell.xml",
+            "-sedml",
+            exec_in_dir="examples",
+            max_memory="1G",
+            exit_on_fail=True,
+        )
+        filelist = []
+        get_model_file_list(
+            "LEMS_NML2_Ex5_DetCell.sedml", filelist, dirname + "/examples"
+        )
+        self.assertEqual(6, len(filelist))
+
         # NeuroML file in examples directory
         dirname = str(thispath.parent.parent.parent)
         filelist = []