| Name | biomodels JSON |
| Version |
0.3.2
JSON |
| download |
| home_page | |
| Summary | Download from the BioModels API |
| upload_time | 2024-02-03 22:36:36 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.9 |
| license | MIT License Copyright (c) 2023 Mauro Silberberg Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
biomodels
omex
sbml
sed-ml
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# BioModels
`biomodels` is a Python library to download models from [BioModels](https://www.ebi.ac.uk/biomodels/).
Models are cached locally in the OS user cache directory,
so they will not be redownloaded every time.
## Usage
### Get model metadata
The first time we download a file,
it will let us know that it is being downloaded
and cached locally.
```python
>>> import biomodels
>>> metadata = biomodels.get_metadata("BIOMD0000000012") # doctest: +SKIP
Downloading data from 'https://www.ebi.ac.uk/biomodels/model/files/BIOMD0000000012?format=json' to file '.../Caches/biomodels/model/files/BIOMD0000000012'.
SHA256 hash of downloaded file: ...
Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.
```
Later, this file will get fetched from the local cache,
instead of being redownloaded.
```python
>>> metadata = biomodels.get_metadata("BIOMD12") # no need to input the leading zeros
>>> metadata
name description size
-- --------------------------- ----------------------------------- ------
0 BIOMD0000000012_url.xml main 46274
1 BIOMD0000000012-biopax2.owl Auto-generated BioPAX (Level 2) 16748
2 BIOMD0000000012-biopax3.owl Auto-generated BioPAX (Level 3) 23577
3 BIOMD0000000012.m Auto-generated Octave file 4994
4 BIOMD0000000012.pdf Auto-generated PDF file 205156
5 BIOMD0000000012.png Auto-generated Reaction graph (PNG) 39018
6 BIOMD0000000012.sci Auto-generated Scilab file 154
7 BIOMD0000000012.svg Auto-generated Reaction graph (SVG) 35750
8 BIOMD0000000012.vcml Auto-generated VCML file 60183
9 BIOMD0000000012.xpp Auto-generated XPP file 4114
10 BIOMD0000000012_urn.xml Auto-generated SBML file with URNs 47097
```
### Get a particular file
To get a particular file,
you can either pass the filename and model_id:
```python
>>> biomodels.get_file("BIOMD0000000012_url.xml", model_id="BIOMD12")
PosixPath('<CACHE_DIR>/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')
```
or choose one from the metadata:
```python
>>> path = biomodels.get_file(metadata[0])
>>> path
PosixPath('<CACHE_DIR>/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')
```
Then, you can use that `Path` object to load the file:
```python
>>> print(path.read_text())
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" metaid="_153818" level="2" version="3">
...
```
### Get COMBINE archive
If you are interested in all the model files,
it might be better to download the COMBINE archive,
which is a compressed file (260KB vs 500KB for this small model):
```python
>>> omex = biomodels.get_omex("BIOMD12")
>>> omex
location format master
-- --------------------------- --------------------------------------------------------------------- --------
0 https://identifiers.org/combine.specifications/omex False
1 BIOMD0000000012-biopax2.owl https://identifiers.org/combine.specifications/biopax.level-2 False
2 BIOMD0000000012-biopax3.owl https://identifiers.org/combine.specifications/biopax.level-3 False
3 BIOMD0000000012.m https://purl.org/NET/mediatypes/application/x.unknown False
4 BIOMD0000000012.pdf https://purl.org/NET/mediatypes/application/pdf False
5 BIOMD0000000012.png https://purl.org/NET/mediatypes/image/png False
6 BIOMD0000000012.sci https://purl.org/NET/mediatypes/application/x.unknown False
7 BIOMD0000000012.svg https://purl.org/NET/mediatypes/application/xml False
8 BIOMD0000000012.vcml https://purl.org/NET/mediatypes/application/xml False
9 BIOMD0000000012.xpp https://purl.org/NET/mediatypes/application/x.unknown False
10 BIOMD0000000012_manual.png https://purl.org/NET/mediatypes/image/png False
11 BIOMD0000000012_manual.svg https://purl.org/NET/mediatypes/application/xml False
12 BIOMD0000000012_url.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 True
13 BIOMD0000000012_urn.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 False
14 manifest.xml https://identifiers.org/combine.specifications/omex-manifest False
15 metadata.rdf https://identifiers.org/combine.specifications/omex-metadata False
```
We can select a particular file by indexing:
```python
>>> content = omex[12]
>>> content
Content(location='BIOMD0000000012_url.xml', format='https://identifiers.org/combine.specifications/sbml.level-2.version-3', master=True)
```
Then,
you can get a `zipfile.Path` object with the `Content.path` attribute,
and read the contents from the OMEX file:
```python
>>> print(content.path.read_text())
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" metaid="_153818" level="2" version="3">
...
```
## Installation
```
pip install biomodels
```
## Development
We are using pytest for testing,
and pre-commit hooks to format and lint the codebase.
To easily set-up a development environment,
run the following commands:
```
git clone https://github.com/maurosilber/biomodels
cd biomodels
conda env create --file environment-dev.yml
pre-commit install
```
which assume you have git and conda preinstalled.
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model_id=\"BIOMD12\")\nPosixPath('<CACHE_DIR>/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')\n```\n\nor choose one from the metadata:\n\n```python\n>>> path = biomodels.get_file(metadata[0])\n>>> path\nPosixPath('<CACHE_DIR>/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')\n```\n\nThen, you can use that `Path` object to load the file:\n\n```python\n>>> print(path.read_text())\n<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" metaid=\"_153818\" level=\"2\" version=\"3\">\n...\n```\n\n### Get COMBINE archive\n\nIf you are interested in all the model files,\nit might be better to download the COMBINE archive,\nwhich is a compressed file (260KB vs 500KB for this small model):\n\n```python\n>>> omex = biomodels.get_omex(\"BIOMD12\")\n>>> omex\n location format master\n-- --------------------------- --------------------------------------------------------------------- --------\n 0 https://identifiers.org/combine.specifications/omex False\n 1 BIOMD0000000012-biopax2.owl https://identifiers.org/combine.specifications/biopax.level-2 False\n 2 BIOMD0000000012-biopax3.owl https://identifiers.org/combine.specifications/biopax.level-3 False\n 3 BIOMD0000000012.m https://purl.org/NET/mediatypes/application/x.unknown False\n 4 BIOMD0000000012.pdf https://purl.org/NET/mediatypes/application/pdf False\n 5 BIOMD0000000012.png https://purl.org/NET/mediatypes/image/png False\n 6 BIOMD0000000012.sci https://purl.org/NET/mediatypes/application/x.unknown False\n 7 BIOMD0000000012.svg https://purl.org/NET/mediatypes/application/xml False\n 8 BIOMD0000000012.vcml https://purl.org/NET/mediatypes/application/xml False\n 9 BIOMD0000000012.xpp https://purl.org/NET/mediatypes/application/x.unknown False\n10 BIOMD0000000012_manual.png https://purl.org/NET/mediatypes/image/png False\n11 BIOMD0000000012_manual.svg https://purl.org/NET/mediatypes/application/xml False\n12 BIOMD0000000012_url.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 True\n13 BIOMD0000000012_urn.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 False\n14 manifest.xml https://identifiers.org/combine.specifications/omex-manifest False\n15 metadata.rdf https://identifiers.org/combine.specifications/omex-metadata False\n```\n\nWe can select a particular file by indexing:\n\n```python\n>>> content = omex[12]\n>>> content\nContent(location='BIOMD0000000012_url.xml', format='https://identifiers.org/combine.specifications/sbml.level-2.version-3', master=True)\n```\n\nThen,\nyou can get a `zipfile.Path` object with the `Content.path` attribute,\nand read the contents from the OMEX file:\n\n```python\n>>> print(content.path.read_text())\n<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" metaid=\"_153818\" level=\"2\" version=\"3\">\n...\n```\n\n## Installation\n\n```\npip install 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