working on visualization

setup.cfg

@@ -6,7 +6,7 @@ parse = (?P<major>\d+)
 	\.(?P<minor>\d+)
 	\.(?P<patch>\d+)
 	(?P<release>[a]*)(?P<num>\d*)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}{release}{num}
 	{major}.{minor}.{patch}
 tag_name = {new_version}
@@ -15,15 +15,15 @@ tag_name = {new_version}
 name = sbmlutils
 url = https://github.com/matthiaskoenig/sbmlutils
 download_url = https://pypi.org/project/sbmlutils
-project_urls = 
+project_urls =
 	Source Code = https://github.com/matthiaskoenig/sbmlutils
 	Documentation = https://sbmlutils.readthedocs.io
 	Bug Tracker = https://github.com/matthiaskoenig/sbmlutils/issues
 author = Matthias Koenig
 author_email = [email protected]
 maintainer = Matthias Koenig
 maintainer_email = [email protected]
-classifiers = 
+classifiers =
 	Development Status :: 5 - Production/Stable
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
@@ -38,25 +38,25 @@ license = LGPL-3.0
 description = sbmlutils are utilities for working with SBML.
 long_description = file: README.rst
 long_description_content_type = text/x-rst
-keywords = 
+keywords =
 	modeling
 	standardization
 	SBML
 
 [options]
 zip_safe = True
 python_requires = >=3.10
-install_requires = 
+install_requires =
 	pymetadata>=0.4.1
-	
+
 	depinfo
 	rich
 	lxml
 	requests
 	jinja2
 	xmltodict
 	pydantic>2.8
-	
+
 	setuptools  # fix for colorbrewer dependency of py4cytoscape
 	numpy>=1.26.4
 	python-libsbml>=5.20.4
@@ -65,24 +65,24 @@ install_requires =
 	pandas>=2.2.0
 	tabulate>=0.9.0
 	pint>=0.24.3
-	
+
 	markdown-it-py>=3.0.0
 	openpyxl>=3.1.5
 	xmlschema>=3.3.2
 	matplotlib>=3.9
-	py4cytoscape>=1.9.0
-	libroadrunner>=1.27.0
-	
+	py4cytoscape>=1.11.0
+	libroadrunner>=2.7.0
+
 	uvicorn>=0.30.6
 	fastapi>=0.112.0
 	python-multipart>=0.0.9
-tests_require = 
+tests_require =
 	tox>=3.24.3
 	pytest>=7.0.1
-setup_requires = 
+setup_requires =
 	pytest-runner
 packages = find:
-package_dir = 
+package_dir =
 	= src
 include_package_data = True
 
@@ -93,7 +93,7 @@ test = pytest
 where = src
 
 [options.extras_require]
-development = 
+development =
 	pip-tools>=7.4.1
 	black>=24.8.0
 	bump2version>=1.0.1
@@ -105,7 +105,7 @@ development =
 	pytest>=7.4.0
 	pytest-cov>=4.1.0
 	beautifulsoup4>=4.12.3
-docs = 
+docs =
 	sphinx>=3.4.3
 	ipykernel>=5.4.3
 	nbsphinx>=0.8.1
@@ -119,7 +119,7 @@ universal = 1
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = placeholder
-values = 
+values =
 	placeholder
 	a
 

src/sbmlutils/cytoscape.py

@@ -3,12 +3,14 @@
 import os
 import tempfile
 
+import pandas as pd
 
 os.environ["PY4CYTOSCAPE_DETAIL_LOGGER_DIR"] = str(tempfile.gettempdir())
 
 from pathlib import Path  # noqa: E402
-from typing import Any, Union  # noqa: E402
+from typing import Any, Union, Optional  # noqa: E402
 
+import libsbml
 import py4cytoscape as p4c  # type: ignore  # noqa: E402
 from requests.exceptions import RequestException  # noqa: E402
 
@@ -30,19 +32,91 @@ def visualize_antimony(source: Union[Path, str], delete_session: bool = False) -
     visualize_sbml(Path(f_tmp.name), delete_session=delete_session)
 
 
-def visualize_sbml(sbml_path: Path, delete_session: bool = False) -> None:
-    """Visualize SBML networks in cytoscape."""
+def visualize_sbml(sbml_path: Path, delete_session: bool = False) -> Optional[int]:
+    """Visualize SBML networks in cytoscape.
+
+    Returns dictionary with "networks" and "views".
+    """
+    if sbml_path.suffix != ".xml":
+        console.error(f"SBML path {sbml_path} does not have .xml extension")
 
     try:
         console.print(p4c.cytoscape_version_info())
 
         if delete_session:
             p4c.session.close_session(save_before_closing=False)
 
-        p4c.networks.import_network_from_file(str(sbml_path))
+        networks_views = p4c.networks.import_network_from_file(str(sbml_path))
+        console.print(f"{networks_views}")
+        network = networks_views["networks"][1]
+        p4c.set_current_view(network=network)  # set the base network
+        return network
+
+        return networks_views
 
     except RequestException:
         logger.error(
             "Could not connect to a running Cytoscape instance. "
             "Start Cytoscape before running the python script."
         )
+        return None
+
+
+
+
+
+
+
+def read_layout_xml(sbml_path: Path, xml_path: Path) -> pd.DataFrame:
+    """Read own xml layout information form cytoscape."""
+    # read positions
+    df: pd.DataFrame = pd.read_xml(xml_path, xpath="//boundingBox")
+    df = df[['id', 'xpos', 'ypos']]
+    df.rename(columns={"xpos": "x", "ypos": "y"}, inplace=True)
+    df.set_index("id", inplace=True)
+    return df
+
+def apply_layout(network, layout: pd.DataFrame) -> None:
+    """Apply layout information from Cytoscape to SBML networks."""
+
+    # get SUIDs, sbml_id from node table;
+    df_nodes = p4c.get_table_columns(table="node", columns=["sbml id"], network=network)
+    console.print(df_nodes)
+    sid2suid = {row["sbml id"]: suid for suid, row in df_nodes.iterrows()}
+    console.print(sid2suid)
+
+    # FIXME: necessary to check that all sids exist
+    suids = [sid2suid[sid] for sid in layout.index.values]
+    x_values = layout["x"].values.tolist()
+    y_values = layout["y"].values.tolist()
+
+    # set positions
+    # see: https://github.com/cytoscape/py4cytoscape/issues/144
+    p4c.set_node_position_bypass(suids, new_x_locations=x_values, new_y_locations=y_values, network=network)
+    # p4c.set_node_property_bypass(suids, new_values=x_values, visual_property='NODE_X_LOCATION', network=network)
+    # p4c.set_node_property_bypass(suids, new_values=y_values, visual_property='NODE_Y_LOCATION', network=network)
+    p4c.set_current_view(network=network)
+
+    # remove bypass
+    # p4c.clear_node_property_bypass(suids, visual_property='NODE_X_LOCATION', network=network)
+    # p4c.clear_node_property_bypass(suids, visual_property='NODE_Y_LOCATION', network=network)
+
+    # fit content
+    p4c.fit_content()
+
+
+
+if __name__ == "__main__":
+    pass
+    # # visual style
+    # p4c.set_visual_style('Marquee')
+    #
+    # # fit the content
+    # p4c.fit_content()
+
+    # p4c.load_table_data
+
+    # annotations!
+
+    # network_views.export_image
+