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simpleobis
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# Base
#FROM rhub/r-minimal:4.2.3
FROM r-base:4.2.3
#r-base
RUN apt-get update
RUN apt-get install apt-utils
RUN apt-get install -y curl
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install libpng++-dev
RUN apt-get install libpng-dev
RUN apt-get install libxml2
RUN apt-get install libxml2-dev
RUN apt-get install fontconfig
RUN apt-get install libfontconfig
RUN apt-get install -y r-cran-rgdal
RUN apt-get install -y r-cran-systemfonts
RUN apt-get install -y r-cran-base64enc
RUN apt-get install -y r-cran-ggplot2
RUN apt-get install -y r-cran-httr
RUN apt-get install -y r-cran-httpuv
RUN apt-get install -y r-cran-fs
RUN apt-get install -y r-cran-sf
RUN apt-get install -y r-cran-raster
RUN apt-get install -y r-cran-maps
RUN apt-get install -y libgeos-dev
RUN install2.r --error --skipinstalled rgeos
RUN install2.r --error --skipinstalled terra
RUN install2.r --error --skipinstalled robis
#robis rgeos
# copy R script
COPY simpleobisCCP.R /

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# Acknowledgments
The projects leading to this software have received funding from a series of European Union programmes including:
- the Sixth Framework Programme for Research and Technological Development
- [DILIGENT](https://cordis.europa.eu/project/id/004260) (grant no. 004260).
- the Seventh Framework Programme for research, technological development and demonstration
- [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488);
- [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019);
- [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465);
- [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644);
- [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754).
- the H2020 research and innovation programme
- [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024);
- [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119);
- [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142);
- [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182);
- [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680);
- [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610);
- [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001);
- [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194);
- [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914);
- [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091);
- [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650);
- [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409);
- [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042);

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# European Union Public Licence V. 1.1
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## 14. Jurisdiction
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## 15. Applicable Law
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## Appendix
“Compatible Licences” according to article 5 EUPL are:
- GNU General Public License (GNU GPL) v. 2
- Open Software License (OSL) v. 2.1, v. 3.0
- Common Public License v. 1.0
- Eclipse Public License v. 1.0
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# SimpleOBIS
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.
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.
The differences are few between the two scripts only that the CPP takes the parameters directly from the command line.
Starting from this example, you can first create a docker image in which it is installed the file simpleobisCCP.R.
The image created in this way can be executed in a container with the following command:
```
$ 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))"'
```
You can also run it directly from the container shell:
```
$ docker run -i -t --rm --name simpleobis-cont simpleobis sh
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))"
```
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:
[Docker](https://docs.docker.com/engine/),
[Docker-Compose](https://docs.docker.com/compose/install/) and
## Useful Commands
### Create Docker Image
```
docker build -t simpleobis .
```
### Save Docker Image in file
```
docker save simpleobis | gzip > simpleobis.tar.gz
```
### Publish Docker Image on DockerHub
Re-tagging an existing local image:
```
docker tag simpleobis <hub-user>/<repo-name>[:<tag>]
```
Login in DockerHub(use your Docker ID):
```
docker login
```
Now you can push this repository to the registry designated by its name or tag:
```
docker push <hub-user>/<repo-name>:<tag>
```
Then logout for security:
```
docker logout
```
## Authors
* **Giancarlo Panichi** ([ORCID](http://orcid.org/0000-0001-8375-6644)) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
## License
This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LICENSE.md) file for details.
## About the gCube Framework
This software is part of the [gCubeFramework](https://www.gcube-system.org/ "gCubeFramework"): an
open-source software toolkit used for building and operating Hybrid Data
Infrastructures enabling the dynamic deployment of Virtual Research Environments
by favouring the realisation of reuse oriented policies.
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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# TODO: Add comment
#
# Author: Giancarlo Panichi
###############################################################################
library(robis)
library(ggplot2)
library(rgeos)
#sname="Sarda sarda"
#usedPolygon="POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
result="occplot.png"
args = commandArgs(trailingOnly=TRUE)
print(args)
if (length(args)<=1) {
stop("At least two arguments must be supplied", call.=FALSE)
}
sname=args[1]
usedPolygon=args[2]
wktP <-readWKT(usedPolygon)
print(wktP@bbox)
#By scientific name adnd geometry
y=occurrence(sname, geometry = usedPolygon)
occplot<-map_ggplot(y, color = "#ff3399")+coord_sf(xlim = wktP@bbox[1,], ylim = wktP@bbox[2,])
ggsave(result, plot = occplot)

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# TODO: Add comment
#
# Author: Giancarlo Panichi
###############################################################################
library(robis)
library(ggplot2)
library(rgeos)
sname="Sarda sarda"
usedPolygon="POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
result="occplot.png"
wktP <-readWKT(usedPolygon)
print(wktP@bbox)
#By scientific name adnd geometry
y=occurrence(sname, geometry = usedPolygon)
occplot<-map_ggplot(y, color = "#ff3399")+coord_sf(xlim = wktP@bbox[1,], ylim = wktP@bbox[2,])
ggsave(result, plot = occplot)