87 lines
2.9 KiB
Markdown
87 lines
2.9 KiB
Markdown
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# SimpleOBIS
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SimpleOBIS is an example written in R that allows you to create an image(occplot.png) of the occurrences present in OBIS starting from a scientific name and a polygon.
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As can be seen, there are 2 scripts, one to be integrated with the SAI simpleobisSAI.R and the other with the CCP simpleobisCCP.R.
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The differences are few between the two scripts only that the CPP takes the parameters directly from the command line.
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Starting from this example, you can first create a docker image in which it is installed the file simpleobisCCP.R.
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The image created in this way can be executed in a container with the following command:
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```
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$ docker run -i -t --rm --name simpleobis-cont simpleobis /bin/sh -c '/usr/bin/Rscript --vanilla simpleobisCCP.R "Sarda sarda" "POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"'
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```
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You can also run it directly from the container shell:
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```
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$ docker run -i -t --rm --name simpleobis-cont simpleobis sh
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root@7f371ac6f420:/# Rscript --vanilla simpleobisCCP.R "Sarda sarda" "POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
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```
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To be able to create an image from this application you need to have Docker and Docker-Compose installed on your machine and the relative python packages, see:
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[Docker](https://docs.docker.com/engine/),
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[Docker-Compose](https://docs.docker.com/compose/install/) and
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## Useful Commands
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### Create Docker Image
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```
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docker build -t simpleobis .
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```
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### Save Docker Image in file
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```
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docker save simpleobis | gzip > simpleobis.tar.gz
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```
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### Publish Docker Image on DockerHub
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Re-tagging an existing local image:
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```
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docker tag simpleobis <hub-user>/<repo-name>[:<tag>]
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```
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Login in DockerHub(use your Docker ID):
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```
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docker login
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```
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Now you can push this repository to the registry designated by its name or tag:
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```
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docker push <hub-user>/<repo-name>:<tag>
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```
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Then logout for security:
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```
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docker logout
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```
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## Authors
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* **Giancarlo Panichi** ([ORCID](http://orcid.org/0000-0001-8375-6644)) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
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## License
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This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LICENSE.md) file for details.
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## About the gCube Framework
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This software is part of the [gCubeFramework](https://www.gcube-system.org/ "gCubeFramework"): an
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open-source software toolkit used for building and operating Hybrid Data
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Infrastructures enabling the dynamic deployment of Virtual Research Environments
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by favouring the realisation of reuse oriented policies.
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The projects leading to this software have received funding from a series of European Union programmes see [FUNDING.md](FUNDING.md)
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