\n# biomage-programmatic-interface
### About
This python package provides an easy way to create projects and upload samples into Biomage.
## Installation
To install the package execute the following line:
`pip install biomage-programmatic-interface`
## Usage
In order to use the package you first need to create an account in Biomage (https://scp.biomage.net/) if you don't have one yet.
Then the package is used in the following way:
```python
import biomage_programmatic_interface as bpi
# 1. Authenticate user and create a connection tunnel with the api
# Default instance-url: https://api.scp.biomage.net/
connection = bpi.Connection('email', 'password', 'instance_url')
# 2. Create an experiment
experiment = connection.create_experiment('experiment name')
# 3. Upload samples associated with the experiment
experiment.upload_samples('local/path/to/samples')
```
Once the upload is complete you can navigate to [Biomage](https://scp.biomage.net/) and process your project there.
### `Connection` class
The object accepts 3 parameters:
1. `email` - Biomage email
2. `password` - Biomage password
3. `instance_url` - Biomage instance url
- Copy the url of the Biomage instance *excluding* `https://`
- If the url is https://scp.biomage.net/ enter just the domain name: `scp.biomage.net`
## Development
If you cloned the repository and want to try using your local version, do the following:
- Install the local version of the pip package:
```bash
cd programmatic_interface
make install
```
- Now you can import the package and use your local version
```python
import biomage_programmatic_interface as bpi
```
***NOTE***: There is **NO** need to run `make install` every time you make changes to the package. When the local changes have been saved the changes will be automatically reflected.
### Running with local instance of Cellenics
When creating the `connection` object set the `instance_url` to `local`. Now the programmatic interface will use your local api (https://localhost:3000)
```python
import biomage_programmatic_interface as bpi
conn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'local')
...
```
### Running with staged environment
Set the full path of the instance url (e.g. `https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/`)
```python
import biomage_programmatic_interface as bpi
conn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/')
...
```
*NOTE: the url is that of the api (i.e. `api-`) and not that of the ui*
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"description": "\\n# biomage-programmatic-interface\n\n\n### About\nThis python package provides an easy way to create projects and upload samples into Biomage.\n\n## Installation\nTo install the package execute the following line:\n\n`pip install biomage-programmatic-interface`\n\n## Usage\nIn order to use the package you first need to create an account in Biomage (https://scp.biomage.net/) if you don't have one yet.\n\nThen the package is used in the following way:\n\n```python\nimport biomage_programmatic_interface as bpi\n\n# 1. Authenticate user and create a connection tunnel with the api\n# Default instance-url: https://api.scp.biomage.net/\nconnection = bpi.Connection('email', 'password', 'instance_url')\n\n# 2. Create an experiment\nexperiment = connection.create_experiment('experiment name')\n\n# 3. Upload samples associated with the experiment\nexperiment.upload_samples('local/path/to/samples')\n```\n\nOnce the upload is complete you can navigate to [Biomage](https://scp.biomage.net/) and process your project there.\n\n### `Connection` class\n\nThe object accepts 3 parameters:\n1. `email` - Biomage email\n2. `password` - Biomage password\n3. `instance_url` - Biomage instance url\n\n- Copy the url of the Biomage instance *excluding* `https://`\n- If the url is https://scp.biomage.net/ enter just the domain name: `scp.biomage.net`\n\n\n\n## Development\n\nIf you cloned the repository and want to try using your local version, do the following:\n\n- Install the local version of the pip package:\n```bash\ncd programmatic_interface\nmake install\n```\n\n- Now you can import the package and use your local version\n\n```python\nimport biomage_programmatic_interface as bpi\n```\n\n***NOTE***: There is **NO** need to run `make install` every time you make changes to the package. When the local changes have been saved the changes will be automatically reflected.\n\n### Running with local instance of Cellenics\n\nWhen creating the `connection` object set the `instance_url` to `local`. Now the programmatic interface will use your local api (https://localhost:3000)\n\n```python\nimport biomage_programmatic_interface as bpi\nconn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'local')\n...\n```\n\n### Running with staged environment\nSet the full path of the instance url (e.g. `https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/`) \n\n```python\nimport biomage_programmatic_interface as bpi\nconn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/')\n...\n```\n\n*NOTE: the url is that of the api (i.e. `api-`) and not that of the ui* \n\n\n",
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