basic python
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@ -11,127 +11,18 @@ We can then define an input `repository` field
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and configure the *deploy script* to git clone the repository and install the dependencies, using the placeholder `{{repository}}` to refer the input repository field
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```sh
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git clone {{repository}}
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cd sortapp
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git clone {{repository}} repo
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pip install -r requirements.txt
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```
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then the *run script* will run it passing the required parameters
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```json
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{
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"inputs": {
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"ccpimage": {
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"id": "ccpimage",
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"title": "Runtime",
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"description": "the standard 3.19.19 python docker image",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "url",
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"contentMediaType": "text/plain",
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"default": "python:3.9.19",
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"readOnly": true
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}
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}
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}
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}
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```sh
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cd repo
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python myapp.py
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```
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## Execution Parameters
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all the parameters and configurations needed for the execution of the algorithms are defined in the input sections
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```json
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{
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"inputs": {
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"baseurl": {
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"id": "baseurl",
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"title": "Base URL",
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"description": "The base URL of the REST API",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "url",
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"contentMediaType": "text/plain",
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"default": "https://REST_API_URL/process/",
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"readOnly": true
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}
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},
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"service": {
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"id": "service",
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"title": "Service name",
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"description": "The name of the service",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": null,
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"contentMediaType": "text/plain",
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"default": "my_custom_service"
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}
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},
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"file": {
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"id": "file",
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"title": "Input file",
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"description": "The input file to be annotated",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "file",
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"contentMediaType": "text/plain",
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"default": ""
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}
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},
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"contenttype": {
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"id": "contenttype",
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"title": "Content type",
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"description": "The content type of the input file",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": null,
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"contentMediaType": "text/plain",
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"default": "text/plain",
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"enum": [
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"text/plain",
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"application/pdf",
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"text/html"
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]
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}
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},
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"credentials": {
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"id": "credentials",
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"title": "Credentials",
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"description": "The Basic auth credentials",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "secret",
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"contentMediaType": "text/plain",
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"default": "XXXYYYZZZ"
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}
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}
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}
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}
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```
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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)
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and what is parametric (readonly=false, or not defined in the input schema)
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the given example uses special input parameters that will be explained in next sections
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* [credentials](./03_4_credentials.md)
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* [file upload](./03_1_input_file.md)
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## Execution
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the implementation of the algorithms is totally defined in the deploy-script and in the execute-script
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resulting in the json
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```json
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{
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@ -140,121 +31,20 @@ the implementation of the algorithms is totally defined in the deploy-script and
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{
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"name": "deploy-script",
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"value": [
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"echo {{file}} | base64 -d > /ccp_data/input"
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]
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},
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{
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"name": "execute-script",
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"value": [
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"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"
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]
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},
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{
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"name": "undeploy-script",
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"value": []
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}
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]
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}
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}
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```
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full example
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```json
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{
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"title": "Python example",
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"description": "basic python example",
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"version": "1.0.0",
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"jobControlOptions": "async-execute",
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"keywords": [
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"python",
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"example"
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],
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"id": "2a59f2ec-9771-44d0-80dc-13f3deb863ed",
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"metadata": [
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{
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"role": "category",
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"title": "examples"
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},
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{
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"title": "Alfredo Oliviero",
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"role": "author",
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"href": "https://accounts.d4science.org/auth/admin/realms/d4science/users/b20300b9-d2d7-4ef8-b164-917f661f7ee0"
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}
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],
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"inputs": {
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"ccpimage": {
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"id": "ccpimage",
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"title": "Runtime",
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"description": "The image of the runtime to use for method execution. This depends on the infrastructure specific protocol for interacting with registries.",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "none",
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"contentMediaType": "text/plain",
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"default": "python:3.9.19",
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"readOnly": true
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}
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},
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"repository": {
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"id": "repository",
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"title": "repository url",
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"description": "url of the repository of the python application",
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"minOccurs": 1,
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"maxOccurs": 1,
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"schema": {
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"type": "string",
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"format": "url",
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"contentMediaType": "text/plain",
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"default": "https://code-repo.d4science.org/gCubeSystem/sortapp.git",
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"readOnly": true
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}
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}
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},
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"outputs": {},
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"additionalParameters": {
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"parameters": [
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{
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"name": "deploy-script",
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"value": [
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"git clone {{repository}}",
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"cd sortapp",
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"git clone {{repository}} repo" ,
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"pip install -r requirements.txt"
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]
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},
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{
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"name": "execute-script",
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"value": [
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"cd sortapp/",
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"python sortapp.py"
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]
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},
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{
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"name": "undeploy-script",
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"value": []
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},
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{
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"name": "lifecycle",
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"value": [
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{
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"time": "2024-10-04T15:30:06.183Z",
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"type": "created",
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"user": "https://accounts.d4science.org/auth/admin/realms/d4science/users/b20300b9-d2d7-4ef8-b164-917f661f7ee0",
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"context": "%2Fd4science.research-infrastructures.eu%2FD4Research%2FFOSSR-Lab"
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}
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"cd repo",
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"python myapp.py"
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]
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}
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]
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},
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"links": [
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{
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"rel": "compatibleWith",
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"title": "D4Science production Infrastructure",
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"href": "infrastructures/d4science-prod-swarm"
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}
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]
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}
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```
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example: [WordCloud ](../methods_examples/WordCloud-1.0.0.json)
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example: [WordCloud](../methods_examples/WordCloud-1.0.0.json)
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