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basic python

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Alfredo Oliviero 2024-10-10 18:25:13 +02:00
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@ -11,127 +11,18 @@ We can then define an input `repository` field
and configure the *deploy script* to git clone the repository and install the dependencies, using the placeholder `{{repository}}` to refer the input repository field and configure the *deploy script* to git clone the repository and install the dependencies, using the placeholder `{{repository}}` to refer the input repository field
```sh ```sh
git clone {{repository}} git clone {{repository}} repo
cd sortapp
pip install -r requirements.txt pip install -r requirements.txt
``` ```
then the *run script* will run it passing the required parameters then the *run script* will run it passing the required parameters
```json ```sh
{ cd repo
"inputs": { python myapp.py
"ccpimage": {
"id": "ccpimage",
"title": "Runtime",
"description": "the standard 3.19.19 python docker image",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "url",
"contentMediaType": "text/plain",
"default": "python:3.9.19",
"readOnly": true
}
}
}
}
``` ```
## Execution Parameters resulting in the json
all the parameters and configurations needed for the execution of the algorithms are defined in the input sections
```json
{
"inputs": {
"baseurl": {
"id": "baseurl",
"title": "Base URL",
"description": "The base URL of the REST API",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "url",
"contentMediaType": "text/plain",
"default": "https://REST_API_URL/process/",
"readOnly": true
}
},
"service": {
"id": "service",
"title": "Service name",
"description": "The name of the service",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": null,
"contentMediaType": "text/plain",
"default": "my_custom_service"
}
},
"file": {
"id": "file",
"title": "Input file",
"description": "The input file to be annotated",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "file",
"contentMediaType": "text/plain",
"default": ""
}
},
"contenttype": {
"id": "contenttype",
"title": "Content type",
"description": "The content type of the input file",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": null,
"contentMediaType": "text/plain",
"default": "text/plain",
"enum": [
"text/plain",
"application/pdf",
"text/html"
]
}
},
"credentials": {
"id": "credentials",
"title": "Credentials",
"description": "The Basic auth credentials",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "secret",
"contentMediaType": "text/plain",
"default": "XXXYYYZZZ"
}
}
}
}
```
the "readOnly": true/false parameter defines what is binded in the definiton of the ccp method (readonly=true, only the `baseurl` input in the given example)
and what is parametric (readonly=false, or not defined in the input schema)
the given example uses special input parameters that will be explained in next sections
* [credentials](./03_4_credentials.md)
* [file upload](./03_1_input_file.md)
## Execution
the implementation of the algorithms is totally defined in the deploy-script and in the execute-script
```json ```json
{ {
@ -140,120 +31,19 @@ the implementation of the algorithms is totally defined in the deploy-script and
{ {
"name": "deploy-script", "name": "deploy-script",
"value": [ "value": [
"echo {{file}} | base64 -d > /ccp_data/input" "git clone {{repository}} repo" ,
]
},
{
"name": "execute-script",
"value": [
"wget {{baseurl}}/{{service}}?annotations={{annotations}} --post-file /ccp_data/input --header \"Authorization: Basic {{credentials}}\" --header \"Content-Type: {{contenttype}}\" --header \"Accept: application/json\" -O /ccp_data/annotated.json"
]
},
{
"name": "undeploy-script",
"value": []
}
]
}
}
```
full example
```json
{
"title": "Python example",
"description": "basic python example",
"version": "1.0.0",
"jobControlOptions": "async-execute",
"keywords": [
"python",
"example"
],
"id": "2a59f2ec-9771-44d0-80dc-13f3deb863ed",
"metadata": [
{
"role": "category",
"title": "examples"
},
{
"title": "Alfredo Oliviero",
"role": "author",
"href": "https://accounts.d4science.org/auth/admin/realms/d4science/users/b20300b9-d2d7-4ef8-b164-917f661f7ee0"
}
],
"inputs": {
"ccpimage": {
"id": "ccpimage",
"title": "Runtime",
"description": "The image of the runtime to use for method execution. This depends on the infrastructure specific protocol for interacting with registries.",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "none",
"contentMediaType": "text/plain",
"default": "python:3.9.19",
"readOnly": true
}
},
"repository": {
"id": "repository",
"title": "repository url",
"description": "url of the repository of the python application",
"minOccurs": 1,
"maxOccurs": 1,
"schema": {
"type": "string",
"format": "url",
"contentMediaType": "text/plain",
"default": "https://code-repo.d4science.org/gCubeSystem/sortapp.git",
"readOnly": true
}
}
},
"outputs": {},
"additionalParameters": {
"parameters": [
{
"name": "deploy-script",
"value": [
"git clone {{repository}}",
"cd sortapp",
"pip install -r requirements.txt" "pip install -r requirements.txt"
] ]
}, },
{ {
"name": "execute-script", "name": "execute-script",
"value": [ "value": [
"cd sortapp/", "cd repo",
"python sortapp.py" "python myapp.py"
]
},
{
"name": "undeploy-script",
"value": []
},
{
"name": "lifecycle",
"value": [
{
"time": "2024-10-04T15:30:06.183Z",
"type": "created",
"user": "https://accounts.d4science.org/auth/admin/realms/d4science/users/b20300b9-d2d7-4ef8-b164-917f661f7ee0",
"context": "%2Fd4science.research-infrastructures.eu%2FD4Research%2FFOSSR-Lab"
}
] ]
} }
] ]
}, },
"links": [
{
"rel": "compatibleWith",
"title": "D4Science production Infrastructure",
"href": "infrastructures/d4science-prod-swarm"
}
]
} }
``` ```