{
"cells": [
{
"cell_type": "markdown",
"id": "2e806b7a",
"metadata": {},
"source": [
"Example for creating a COMBINE archive."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "5e7c2a84",
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from pathlib import Path\n",
"\n",
"from pymetadata.console import console\n",
"from pymetadata.omex import EntryFormat, ManifestEntry, Omex"
]
},
{
"cell_type": "markdown",
"id": "565b2c61",
"metadata": {},
"source": [
"Creating an empty archive and adding entry for SBML."
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "b8796964",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"[ ManifestEntry(location='.', format='http://identifiers.org/combine.specifications:omex', master=False),\n",
" ManifestEntry(location='./manifest.xml', format='http://identifiers.org/combine.specifications:omex-manifest', \n",
"master=False),\n",
" ManifestEntry(location='./sbml/hello_world_sbml.xml', \n",
"format='http://identifiers.org/combine.specifications:sbml.level-3.version-2', master=False),\n",
" ManifestEntry(location='./cellml/hello_world_cellml.cellml', \n",
"format='http://identifiers.org/combine.specifications:cellml', master=False),\n",
" ManifestEntry(location='./sbgn/hello_world_sbgn.sbgn', \n",
"format='http://identifiers.org/combine.specifications:sbgn', master=False),\n",
" ManifestEntry(location='./sbgn/hello_world_sbgn.png', format='https://purl.org/NET/mediatypes/image/png', \n",
"master=False),\n",
" ManifestEntry(location='./sedml/hello_world_sedml.sedml', \n",
"format='http://identifiers.org/combine.specifications:sed-ml', master=False)]\n",
"\n"
],
"text/plain": [
"\u001b[1m[\u001b[0m \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'.'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:omex'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./manifest.xml'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:omex-manifest'\u001b[0m, \n",
"\u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbml/hello_world_sbml.xml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sbml.level-3.version-2'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./cellml/hello_world_cellml.cellml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:cellml'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbgn/hello_world_sbgn.sbgn'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sbgn'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbgn/hello_world_sbgn.png'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'https://purl.org/NET/mediatypes/image/png'\u001b[0m, \n",
"\u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sedml/hello_world_sedml.sedml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sed-ml'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m\n"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"WARNING Existing omex is overwritten: omex.py:680\n",
" '/home/vboxuser/Documents/compbiolibs/combine-notebooks/results/combine_hello_world.omex' \n",
"\n"
],
"text/plain": [
"\u001b[31mWARNING \u001b[0m Existing omex is overwritten: \u001b]8;id=296905;file:///home/vboxuser/.local/lib/python3.10/site-packages/pymetadata/omex.py\u001b\\\u001b[2momex.py\u001b[0m\u001b]8;;\u001b\\\u001b[2m:\u001b[0m\u001b]8;id=280012;file:///home/vboxuser/.local/lib/python3.10/site-packages/pymetadata/omex.py#680\u001b\\\u001b[2m680\u001b[0m\u001b]8;;\u001b\\\n",
" \u001b[32m'/home/vboxuser/Documents/compbiolibs/combine-notebooks/results/combine_hello_world.omex'\u001b[0m \u001b[2m \u001b[0m\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"def create_omex(omex_path: Path, results_dir: Path) -> None:\n",
" \"\"\"Create OMEX archive of resources.\"\"\"\n",
" omex = Omex()\n",
" omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbml/hello_world_sbml.xml\",\n",
" format=EntryFormat.SBML_L3V2,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbml.xml\",\n",
" )\n",
"\n",
" omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./cellml/hello_world_cellml.cellml\",\n",
" format=EntryFormat.CELLML,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_cellml.cellml\",\n",
" )\n",
"\n",
" \"\"\"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./biopax/repressilator_biopax.owl\",\n",
" format=EntryFormat.BIOPAX,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"repressilator_biopax.owl\",\n",
" )\"\"\"\n",
"\n",
" omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbgn/hello_world_sbgn.sbgn\",\n",
" format=EntryFormat.SBGN,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbgn.sbgn\",\n",
" )\n",
" omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbgn/hello_world_sbgn.png\",\n",
" format=EntryFormat.PNG,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbgn.png\",\n",
" )\n",
"\n",
" omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sedml/hello_world_sedml.sedml\",\n",
" format=EntryFormat.SEDML,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sedml.sedml\"\n",
" # FIXME: add the model relative and test\n",
" )\n",
"\n",
" console.print(omex)\n",
" omex.to_omex(omex_path)\n",
"\n",
"\n",
"if __name__ == \"__main__\":\n",
" from combine_notebooks import RESULTS_DIR\n",
"\n",
" create_omex(omex_path=RESULTS_DIR / \"combine_hello_world.omex\", results_dir=RESULTS_DIR)\n",
"\n",
" # "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0cc8164b",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}