First commit
This commit is contained in:
commit
bad7d296d0
|
|
@ -0,0 +1,18 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<projectDescription>
|
||||
<name>simpleobismaps</name>
|
||||
<comment></comment>
|
||||
<projects>
|
||||
</projects>
|
||||
<buildSpec>
|
||||
<buildCommand>
|
||||
<name>org.eclipse.statet.r.resourceProjects.RBuilder</name>
|
||||
<arguments>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
</buildSpec>
|
||||
<natures>
|
||||
<nature>org.eclipse.statet.ide.resourceProjects.Statet</nature>
|
||||
<nature>org.eclipse.statet.r.resourceProjects.R</nature>
|
||||
</natures>
|
||||
</projectDescription>
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
eclipse.preferences.version=1
|
||||
encoding/<project>=UTF-8
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
# Dockerfile
|
||||
#
|
||||
# Author: Giancarlo Panichi
|
||||
###############################################################################
|
||||
|
||||
# Base
|
||||
#FROM rhub/r-minimal:4.2.3
|
||||
FROM r-base:4.2.3
|
||||
|
||||
#r-base
|
||||
RUN apt-get update
|
||||
RUN apt-get install -y 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
|
||||
|
||||
#Clean
|
||||
RUN apt-get clean && rm -rf /var/lib/apt/lists/* && rm -fr /tmp/*
|
||||
|
||||
# copy R script
|
||||
COPY simpleobismapsCCP.R /
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
# 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);
|
||||
|
|
@ -0,0 +1,311 @@
|
|||
# European Union Public Licence V. 1.1
|
||||
|
||||
|
||||
EUPL © the European Community 2007
|
||||
|
||||
|
||||
This European Union Public Licence (the “EUPL”) applies to the Work or Software
|
||||
(as defined below) which is provided under the terms of this Licence. Any use of
|
||||
the Work, other than as authorised under this Licence is prohibited (to the
|
||||
extent such use is covered by a right of the copyright holder of the Work).
|
||||
|
||||
The Original Work is provided under the terms of this Licence when the Licensor
|
||||
(as defined below) has placed the following notice immediately following the
|
||||
copyright notice for the Original Work:
|
||||
|
||||
Licensed under the EUPL V.1.1
|
||||
|
||||
or has expressed by any other mean his willingness to license under the EUPL.
|
||||
|
||||
|
||||
|
||||
## 1. Definitions
|
||||
|
||||
In this Licence, the following terms have the following meaning:
|
||||
|
||||
- The Licence: this Licence.
|
||||
|
||||
- The Original Work or the Software: the software distributed and/or
|
||||
communicated by the Licensor under this Licence, available as Source Code and
|
||||
also as Executable Code as the case may be.
|
||||
|
||||
- Derivative Works: the works or software that could be created by the Licensee,
|
||||
based upon the Original Work or modifications thereof. This Licence does not
|
||||
define the extent of modification or dependence on the Original Work required
|
||||
in order to classify a work as a Derivative Work; this extent is determined by
|
||||
copyright law applicable in the country mentioned in Article 15.
|
||||
|
||||
- The Work: the Original Work and/or its Derivative Works.
|
||||
|
||||
- The Source Code: the human-readable form of the Work which is the most
|
||||
convenient for people to study and modify.
|
||||
|
||||
- The Executable Code: any code which has generally been compiled and which is
|
||||
meant to be interpreted by a computer as a program.
|
||||
|
||||
- The Licensor: the natural or legal person that distributes and/or communicates
|
||||
the Work under the Licence.
|
||||
|
||||
- Contributor(s): any natural or legal person who modifies the Work under the
|
||||
Licence, or otherwise contributes to the creation of a Derivative Work.
|
||||
|
||||
- The Licensee or “You”: any natural or legal person who makes any usage of the
|
||||
Software under the terms of the Licence.
|
||||
|
||||
- Distribution and/or Communication: any act of selling, giving, lending,
|
||||
renting, distributing, communicating, transmitting, or otherwise making
|
||||
available, on-line or off-line, copies of the Work or providing access to its
|
||||
essential functionalities at the disposal of any other natural or legal
|
||||
person.
|
||||
|
||||
|
||||
|
||||
## 2. Scope of the rights granted by the Licence
|
||||
|
||||
The Licensor hereby grants You a world-wide, royalty-free, non-exclusive,
|
||||
sub-licensable licence to do the following, for the duration of copyright vested
|
||||
in the Original Work:
|
||||
|
||||
- use the Work in any circumstance and for all usage, reproduce the Work, modify
|
||||
- the Original Work, and make Derivative Works based upon the Work, communicate
|
||||
- to the public, including the right to make available or display the Work or
|
||||
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|
||||
- Work, distribute the Work or copies thereof, lend and rent the Work or copies
|
||||
- thereof, sub-license rights in the Work or copies thereof.
|
||||
|
||||
Those rights can be exercised on any media, supports and formats, whether now
|
||||
known or later invented, as far as the applicable law permits so.
|
||||
|
||||
In the countries where moral rights apply, the Licensor waives his right to
|
||||
exercise his moral right to the extent allowed by law in order to make effective
|
||||
the licence of the economic rights here above listed.
|
||||
|
||||
The Licensor grants to the Licensee royalty-free, non exclusive usage rights to
|
||||
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|
||||
rights granted on the Work under this Licence.
|
||||
|
||||
|
||||
|
||||
## 3. Communication of the Source Code
|
||||
|
||||
The Licensor may provide the Work either in its Source Code form, or as
|
||||
Executable Code. If the Work is provided as Executable Code, the Licensor
|
||||
provides in addition a machine-readable copy of the Source Code of the Work
|
||||
along with each copy of the Work that the Licensor distributes or indicates, in
|
||||
a notice following the copyright notice attached to the Work, a repository where
|
||||
the Source Code is easily and freely accessible for as long as the Licensor
|
||||
continues to distribute and/or communicate the Work.
|
||||
|
||||
|
||||
|
||||
## 4. Limitations on copyright
|
||||
|
||||
Nothing in this Licence is intended to deprive the Licensee of the benefits from
|
||||
any exception or limitation to the exclusive rights of the rights owners in the
|
||||
Original Work or Software, of the exhaustion of those rights or of other
|
||||
applicable limitations thereto.
|
||||
|
||||
|
||||
|
||||
## 5. Obligations of the Licensee
|
||||
|
||||
The grant of the rights mentioned above is subject to some restrictions and
|
||||
obligations imposed on the Licensee. Those obligations are the following:
|
||||
|
||||
Attribution right: the Licensee shall keep intact all copyright, patent or
|
||||
trademarks notices and all notices that refer to the Licence and to the
|
||||
disclaimer of warranties. The Licensee must include a copy of such notices and a
|
||||
copy of the Licence with every copy of the Work he/she distributes and/or
|
||||
communicates. The Licensee must cause any Derivative Work to carry prominent
|
||||
notices stating that the Work has been modified and the date of modification.
|
||||
|
||||
Copyleft clause: If the Licensee distributes and/or communicates copies of the
|
||||
Original Works or Derivative Works based upon the Original Work, this
|
||||
Distribution and/or Communication will be done under the terms of this Licence
|
||||
or of a later version of this Licence unless the Original Work is expressly
|
||||
distributed only under this version of the Licence. The Licensee (becoming
|
||||
Licensor) cannot offer or impose any additional terms or conditions on the Work
|
||||
or Derivative Work that alter or restrict the terms of the Licence.
|
||||
|
||||
Compatibility clause: If the Licensee Distributes and/or Communicates Derivative
|
||||
Works or copies thereof based upon both the Original Work and another work
|
||||
licensed under a Compatible Licence, this Distribution and/or Communication can
|
||||
be done under the terms of this Compatible Licence. For the sake of this clause,
|
||||
“Compatible Licence” refers to the licences listed in the appendix attached to
|
||||
this Licence. Should the Licensee’s obligations under the Compatible Licence
|
||||
conflict with his/her obligations under this Licence, the obligations of the
|
||||
Compatible Licence shall prevail.
|
||||
|
||||
Provision of Source Code: When distributing and/or communicating copies of the
|
||||
Work, the Licensee will provide a machine-readable copy of the Source Code or
|
||||
indicate a repository where this Source will be easily and freely available for
|
||||
as long as the Licensee continues to distribute and/or communicate the Work.
|
||||
|
||||
Legal Protection: This Licence does not grant permission to use the trade names,
|
||||
trademarks, service marks, or names of the Licensor, except as required for
|
||||
reasonable and customary use in describing the origin of the Work and
|
||||
reproducing the content of the copyright notice.
|
||||
|
||||
|
||||
|
||||
## 6. Chain of Authorship
|
||||
|
||||
The original Licensor warrants that the copyright in the Original Work granted
|
||||
hereunder is owned by him/her or licensed to him/her and that he/she has the
|
||||
power and authority to grant the Licence.
|
||||
|
||||
Each Contributor warrants that the copyright in the modifications he/she brings
|
||||
to the Work are owned by him/her or licensed to him/her and that he/she has the
|
||||
power and authority to grant the Licence.
|
||||
|
||||
Each time You accept the Licence, the original Licensor and subsequent
|
||||
Contributors grant You a licence to their contributions to the Work, under the
|
||||
terms of this Licence.
|
||||
|
||||
|
||||
|
||||
## 7. Disclaimer of Warranty
|
||||
|
||||
The Work is a work in progress, which is continuously improved by numerous
|
||||
contributors. It is not a finished work and may therefore contain defects or
|
||||
“bugs” inherent to this type of software development.
|
||||
|
||||
For the above reason, the Work is provided under the Licence on an “as is” basis
|
||||
and without warranties of any kind concerning the Work, including without
|
||||
limitation merchantability, fitness for a particular purpose, absence of defects
|
||||
or errors, accuracy, non-infringement of intellectual property rights other than
|
||||
copyright as stated in Article 6 of this Licence.
|
||||
|
||||
This disclaimer of warranty is an essential part of the Licence and a condition
|
||||
for the grant of any rights to the Work.
|
||||
|
||||
|
||||
|
||||
## 8. Disclaimer of Liability
|
||||
|
||||
Except in the cases of wilful misconduct or damages directly caused to natural
|
||||
persons, the Licensor will in no event be liable for any direct or indirect,
|
||||
material or moral, damages of any kind, arising out of the Licence or of the use
|
||||
of the Work, including without limitation, damages for loss of goodwill, work
|
||||
stoppage, computer failure or malfunction, loss of data or any commercial
|
||||
damage, even if the Licensor has been advised of the possibility of such
|
||||
damage. However, the Licensor will be liable under statutory product liability
|
||||
laws as far such laws apply to the Work.
|
||||
|
||||
|
||||
|
||||
## 9. Additional agreements
|
||||
|
||||
While distributing the Original Work or Derivative Works, You may choose to
|
||||
conclude an additional agreement to offer, and charge a fee for, acceptance of
|
||||
support, warranty, indemnity, or other liability obligations and/or services
|
||||
consistent with this Licence. However, in accepting such obligations, You may
|
||||
act only on your own behalf and on your sole responsibility, not on behalf of
|
||||
the original Licensor or any other Contributor, and only if You agree to
|
||||
indemnify, defend, and hold each Contributor harmless for any liability incurred
|
||||
by, or claims asserted against such Contributor by the fact You have accepted
|
||||
any such warranty or additional liability.
|
||||
|
||||
|
||||
|
||||
## 10. Acceptance of the Licence
|
||||
|
||||
The provisions of this Licence can be accepted by clicking on an icon “I agree”
|
||||
placed under the bottom of a window displaying the text of this Licence or by
|
||||
affirming consent in any other similar way, in accordance with the rules of
|
||||
applicable law. Clicking on that icon indicates your clear and irrevocable
|
||||
acceptance of this Licence and all of its terms and conditions.
|
||||
|
||||
Similarly, you irrevocably accept this Licence and all of its terms and
|
||||
conditions by exercising any rights granted to You by Article 2 of this Licence,
|
||||
such as the use of the Work, the creation by You of a Derivative Work or the
|
||||
Distribution and/or Communication by You of the Work or copies thereof.
|
||||
|
||||
|
||||
|
||||
## 11. Information to the public
|
||||
|
||||
In case of any Distribution and/or Communication of the Work by means of
|
||||
electronic communication by You (for example, by offering to download the Work
|
||||
from a remote location) the distribution channel or media (for example, a
|
||||
website) must at least provide to the public the information requested by the
|
||||
applicable law regarding the Licensor, the Licence and the way it may be
|
||||
accessible, concluded, stored and reproduced by the Licensee.
|
||||
|
||||
|
||||
|
||||
## 12. Termination of the Licence
|
||||
|
||||
The Licence and the rights granted hereunder will terminate automatically upon
|
||||
any breach by the Licensee of the terms of the Licence.
|
||||
|
||||
Such a termination will not terminate the licences of any person who has
|
||||
received the Work from the Licensee under the Licence, provided such persons
|
||||
remain in full compliance with the Licence.
|
||||
|
||||
|
||||
|
||||
## 13. Miscellaneous
|
||||
|
||||
Without prejudice of Article 9 above, the Licence represents the complete
|
||||
agreement between the Parties as to the Work licensed hereunder.
|
||||
|
||||
If any provision of the Licence is invalid or unenforceable under applicable
|
||||
law, this will not affect the validity or enforceability of the Licence as a
|
||||
whole. Such provision will be construed and/or reformed so as necessary to make
|
||||
it valid and enforceable.
|
||||
|
||||
The European Commission may publish other linguistic versions and/or new
|
||||
versions of this Licence, so far this is required and reasonable, without
|
||||
reducing the scope of the rights granted by the Licence. New versions of the
|
||||
Licence will be published with a unique version number.
|
||||
|
||||
All linguistic versions of this Licence, approved by the European Commission,
|
||||
have identical value. Parties can take advantage of the linguistic version of
|
||||
their choice.
|
||||
|
||||
|
||||
|
||||
## 14. Jurisdiction
|
||||
|
||||
Any litigation resulting from the interpretation of this License, arising
|
||||
between the European Commission, as a Licensor, and any Licensee, will be
|
||||
subject to the jurisdiction of the Court of Justice of the European Communities,
|
||||
as laid down in article 238 of the Treaty establishing the European Community.
|
||||
|
||||
Any litigation arising between Parties, other than the European Commission, and
|
||||
resulting from the interpretation of this License, will be subject to the
|
||||
exclusive jurisdiction of the competent court where the Licensor resides or
|
||||
conducts its primary business.
|
||||
|
||||
|
||||
|
||||
## 15. Applicable Law
|
||||
|
||||
This Licence shall be governed by the law of the European Union country where
|
||||
the Licensor resides or has his registered office.
|
||||
|
||||
This licence shall be governed by the Belgian law if:
|
||||
|
||||
- a litigation arises between the European Commission, as a Licensor, and any
|
||||
- Licensee; the Licensor, other than the European Commission, has no residence
|
||||
- or registered office inside a European Union country.
|
||||
|
||||
|
||||
|
||||
## 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
|
||||
|
||||
- Cecill v. 2.0
|
||||
|
|
@ -0,0 +1,94 @@
|
|||
# SimpleOBISMaps
|
||||
|
||||
SimpleOBISMaps is an example written in R that allows you to create an image of the occurrences present in OBIS starting from a file that contains the scientific names and a polygon.
|
||||
|
||||
As can be seen, there are 2 scripts, one to be integrated with the SAI simpleobismapsSAI.R and the other with the CCP simpleobismapsCCP.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 simpleobismapsCCP.R.
|
||||
|
||||
The image created in this way can be executed in a container with the following command:
|
||||
|
||||
```
|
||||
$ docker run -i -t --rm --name simpleobismaps-cont simpleobismaps /bin/sh -c '/bin/mkdir /ccp_data ;/usr/bin/Rscript --vanilla simpleobismapsCCP.R "https://..." "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 simpleobismaps-cont simpleobismaps sh
|
||||
|
||||
# mkdir /ccp_data
|
||||
# Rscript --vanilla simpleobismapsCCP.R "https://..." "POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
|
||||
|
||||
```
|
||||
|
||||
Note in the examples above we added the /ccp_app folder to test the created image locally. In reality this is created by the CCP service and therefore in production there is no need to do it so the command would be like this for integration:
|
||||
|
||||
```
|
||||
/bin/sh -c '/usr/bin/Rscript --vanilla simpleobismapsCCP.R "{{url}}" "{{usedPolygon}}"'
|
||||
```
|
||||
|
||||
|
||||
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 simpleobismaps .
|
||||
```
|
||||
|
||||
### Save Docker Image in file
|
||||
```
|
||||
docker save simpleobismaps | gzip > simpleobismaps.tar.gz
|
||||
```
|
||||
|
||||
### Publish Docker Image on DockerHub
|
||||
Re-tagging an existing local image:
|
||||
|
||||
```
|
||||
docker tag simpleobismaps <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)
|
||||
|
||||
|
|
@ -0,0 +1,721 @@
|
|||
Myxine glutinosa
|
||||
Lampetra fluviatilis
|
||||
Petromyzon marinus
|
||||
Chimaera monstrosa
|
||||
Echinorhinus brucus
|
||||
Squatina squatina
|
||||
Carcharias taurus
|
||||
Sharpnose sevengill shark
|
||||
Bluntnose sixgill shark
|
||||
Bigeyed sixgill shark
|
||||
Bramble shark
|
||||
Gulper shark
|
||||
Dalatias licha
|
||||
Etmopterus spinax
|
||||
Oxynotus centrina
|
||||
Centroscymnus coelolepis
|
||||
Somniosus rostratus
|
||||
Squalus acanthias
|
||||
Squalus blainvillei
|
||||
Squalus megalops
|
||||
Squalus uyato
|
||||
Squatina aculeata
|
||||
Squatina oculata
|
||||
Squatina squatina
|
||||
Galeus atlanticus
|
||||
Galeus melastomus
|
||||
Scyliorhinus canicula
|
||||
Scyliorhinus stellaris
|
||||
Galeorhinus galeus
|
||||
Mustelus asterias
|
||||
Mustelus mustelus
|
||||
Mustelus punctulatus
|
||||
Carcharias taurus
|
||||
Odontaspis ferox
|
||||
Alopias superciliosus
|
||||
Alopias vulpinus
|
||||
Cetorhinus maximus
|
||||
Carcharodon carcharias
|
||||
Isurus oxyrinchus
|
||||
Lamna nasus
|
||||
Carcharhinus altimus
|
||||
Carcharhinus amboinensis
|
||||
Carcharhinus brachyurus
|
||||
Carcharhinus brevipinna
|
||||
Carcharhinus falciformis
|
||||
Carcharhinus limbatus
|
||||
Carcharhinus longimanus
|
||||
Carcharhinus melanopterus
|
||||
Carcharhinus obscurus
|
||||
Carcharhinus plumbeus
|
||||
Galeocerdo cuvier
|
||||
Prionace glauca
|
||||
Rhizoprionodon acutus
|
||||
Sphyrna lewini
|
||||
Sphyrna mokarran
|
||||
Sphyrna tudes
|
||||
Sphyrna zygaena
|
||||
Pristis pectinata
|
||||
Pristis pristis
|
||||
Torpedo fuscomaculata
|
||||
Torpedo marmorata
|
||||
Torpedo nobiliana
|
||||
Torpedo torpedo
|
||||
Glaucostegus halavi
|
||||
Rhinobatos cemiculus
|
||||
Rhinobatos rhinobatos
|
||||
Dipturus batis
|
||||
Dipturus oxyrinchus
|
||||
Leucoraja circularis
|
||||
Leucoraja fullonica
|
||||
Leucoraja melitensis
|
||||
Leucoraja naevus
|
||||
Raja africana
|
||||
Raja asterias
|
||||
Raja brachyura
|
||||
Raja clavata
|
||||
Raja miraletus
|
||||
Raja montagui
|
||||
Raja polystigma
|
||||
Raja radula
|
||||
Raja rondeleti
|
||||
Raja undulata
|
||||
Rostroraja alba
|
||||
Dasyatis centroura
|
||||
Dasyatis chrysonota
|
||||
Dasyatis marmorata
|
||||
Dasyatis pastinaca
|
||||
Dasyatis tortonesei
|
||||
Himantura uarnak
|
||||
Pteroplatytrygon violacea
|
||||
Taeniura grabata
|
||||
Urogymnus asperrimus
|
||||
Gymnura altavela
|
||||
Mobula mobular
|
||||
Myliobatis aquila
|
||||
Pteromylaeus bovinus
|
||||
Rhinoptera marginata
|
||||
Acipenser naccarii
|
||||
Acipenser stellatus
|
||||
Acipenser sturio
|
||||
Huso huso
|
||||
Anguilla anguilla
|
||||
Ariosoma balearicum
|
||||
Conger conger
|
||||
Gnathophis mystax
|
||||
Rhynchoconger trewavasae
|
||||
Chlopsis bicolor
|
||||
Panturichthys fowleri
|
||||
Anarchias euryurus
|
||||
Enchelycore anatina
|
||||
Gymnothorax unicolor
|
||||
Muraena helena
|
||||
Cynoponticus ferox
|
||||
Muraenesox cinereus
|
||||
Nemichthys scolopaceus
|
||||
Facciolella oxyrhyncha
|
||||
Nettastoma melanurum
|
||||
Saurenchelys cancrivora
|
||||
Apterichtus anguiformis
|
||||
Apterichtus caecus
|
||||
Dalophis imberbis
|
||||
Echelus myrus
|
||||
Mystriophis crosnieri
|
||||
Ophichthus ophis
|
||||
Ophichthus rufus
|
||||
Ophisurus serpens
|
||||
Pisodonophis semicinctus
|
||||
Serrivomer brevidentatus
|
||||
Dysomma brevirostre
|
||||
Halosaurus ovenii
|
||||
Notacanthus bonaparte
|
||||
Polyacanthonotus rissoanus
|
||||
Alosa agone
|
||||
Alosa alosa
|
||||
Alosa fallax
|
||||
Dussumieria elopsoides
|
||||
Etrumeus teres
|
||||
Herklotsichthys punctatus
|
||||
Sardina pilchardus
|
||||
Sardinella aurita
|
||||
Sardinella maderensis
|
||||
Spratelloides delicatulus
|
||||
Sprattus sprattus
|
||||
Engraulis encrasicolus
|
||||
Arius parkii
|
||||
Netuma thalassina
|
||||
Plotosus lineatus
|
||||
Argentina sphyraena
|
||||
Alepocephalus rostratus
|
||||
Glossanodon leioglossus
|
||||
Microstoma microstoma
|
||||
Nansenia iberica
|
||||
Nansenia oblita
|
||||
Salmo salar
|
||||
Salmo trutta
|
||||
Argyropelecus hemigymnus
|
||||
Argyropelecus olfersii
|
||||
Maurolicus muelleri
|
||||
Cyclothone braueri
|
||||
Cyclothone microdon
|
||||
Cyclothone pygmaea
|
||||
Gonostoma denudatum
|
||||
Valenciennellus tripunctulatus
|
||||
Bathophilus nigerrimus
|
||||
Bathophilus vaillanti
|
||||
Borostomias antarcticus
|
||||
Chauliodus sloani
|
||||
Stomias boa
|
||||
Ichthyococcus ovatus
|
||||
Vinciguerria attenuata
|
||||
Vinciguerria poweriae
|
||||
Alepisaurus ferox
|
||||
Aulopus filamentosus
|
||||
Chlorophthalmus agassizi
|
||||
Bathysaurus mollis
|
||||
Bathypterois dubius
|
||||
Bathypterois grallator
|
||||
Evermannella balbo
|
||||
Arctozenus rissi
|
||||
Lestidiops jayakari
|
||||
Lestidiops sphyrenoides
|
||||
Lestidium atlanticum
|
||||
Paralepis coregonoides
|
||||
Paralepis speciosa
|
||||
Sudis hyalina
|
||||
Saurida undosquamis
|
||||
Synodus saurus
|
||||
Benthosema glaciale
|
||||
Ceratoscopelus maderensis
|
||||
Diaphus holti
|
||||
Diaphus metopoclampus
|
||||
Diaphus rafinesquii
|
||||
Diogenichthys atlanticus
|
||||
Electrona risso
|
||||
Gonichthys cocco
|
||||
Hygophum benoiti
|
||||
Hygophum hygomii
|
||||
Lampanyctus crocodilus
|
||||
Lampanyctus pusillus
|
||||
Lobianchia dofleini
|
||||
Lobianchia gemellarii
|
||||
Myctophum punctatum
|
||||
Notoscopelus bolini
|
||||
Notoscopelus elongatus
|
||||
Notoscopelus kroyeri
|
||||
Symbolophorus veranyi
|
||||
Zeus faber
|
||||
Zenopsis conchifer
|
||||
Coelorinchus caelorhincus
|
||||
Coelorinchus occa
|
||||
Coryphaenoides guentheri
|
||||
Coryphaenoides mediterraneus
|
||||
Hymenocephalus italicus
|
||||
Nezumia aequalis
|
||||
Nezumia sclerorhynchus
|
||||
Trachyrincus scabrus
|
||||
Merluccius merluccius
|
||||
Eretmophorus kleinenbergi
|
||||
Gadella maraldi
|
||||
Guttigadus latifrons
|
||||
Lepidion guentheri
|
||||
Lepidion lepidion
|
||||
Mora moro
|
||||
Physiculus dalwigki
|
||||
Rhynchogadus hepaticus
|
||||
Phycis blennoides
|
||||
Phycis phycis
|
||||
Gaidropsarus biscayensis
|
||||
Gaidropsarus granti
|
||||
Gaidropsarus mediterraneus
|
||||
Gaidropsarus vulgaris
|
||||
Molva dypterygia
|
||||
Molva macrophthalma
|
||||
Molva molva
|
||||
Gadiculus argenteus
|
||||
Merlangius merlangus
|
||||
Micromesistius poutassou
|
||||
Trisopterus luscus
|
||||
Trisopterus minutus
|
||||
Beryx decadactylus
|
||||
Beryx splendens
|
||||
Sargocentron praslin
|
||||
Sargocentron rubrum
|
||||
Aulotrachichthys sajademalensis
|
||||
Gephyroberyx darwinii
|
||||
Hoplostethus mediterraneus
|
||||
Lampris guttatus
|
||||
Lophotus lacepede
|
||||
Regalecus glesne
|
||||
Trachipterus arcticus
|
||||
Trachipterus trachypterus
|
||||
Zu cristatus
|
||||
Lophius budegassa
|
||||
Lophius piscatorius
|
||||
Chaunax suttkusi
|
||||
Bellottia apoda
|
||||
Cataetyx alleni
|
||||
Cataetyx laticeps
|
||||
Grammonus ater
|
||||
Carapus acus
|
||||
Echiodon dentatus
|
||||
Echiodon drummondii
|
||||
Benthocometes robustus
|
||||
Ophidion barbatum
|
||||
Ophidion rochei
|
||||
Parophidion vassali
|
||||
Chelon labrosus
|
||||
Liza aurata
|
||||
Liza carinata
|
||||
Liza haematocheila
|
||||
Liza ramada
|
||||
Liza saliens
|
||||
Mugil cephalus
|
||||
Oedalechilus labeo
|
||||
Jamie minimus
|
||||
Atherina boyeri
|
||||
Atherina hepsetus
|
||||
Atherina presbyter
|
||||
Atherinomorus lacunosus
|
||||
Belone belone
|
||||
Belone svetovidovi
|
||||
Tylosurus acus
|
||||
Tylosurus choram
|
||||
Scomberesox saurus saurus
|
||||
Cheilopogon exsiliens
|
||||
Cheilopogon furcatus
|
||||
Cheilopogon heterurus
|
||||
Exocoetus obtusirostris
|
||||
Exocoetus volitans
|
||||
Hirundichthys rondeletii
|
||||
Hirundichthys speculiger
|
||||
Parexocoetus mento
|
||||
Hemiramphus far
|
||||
Hyporhamphus affinis
|
||||
Hyporhamphus picarti
|
||||
Aphanius dispar dispar
|
||||
Aphanius fasciatus
|
||||
Aphanius iberus
|
||||
Fistularia commersonii
|
||||
Fistularia petimba
|
||||
Macroramphosus scolopax
|
||||
Entelurus aequoreus
|
||||
Hippocampus fuscus
|
||||
Hippocampus guttulatus
|
||||
Hippocampus hippocampus
|
||||
Minyichthys sentus
|
||||
Nerophis lumbriciformis
|
||||
Nerophis maculatus
|
||||
Nerophis ophidion
|
||||
Syngnathus abaster
|
||||
Syngnathus acus
|
||||
Syngnathus phlegon
|
||||
Syngnathus rostellatus
|
||||
Syngnathus taenionotus
|
||||
Syngnathus tenuirostris
|
||||
Syngnathus typhle
|
||||
Anthias anthias
|
||||
Cephalopholis taeniops
|
||||
Epinephelus aeneus
|
||||
Epinephelus caninus
|
||||
Epinephelus coioides
|
||||
Epinephelus costae
|
||||
Epinephelus malabaricus
|
||||
Epinephelus marginatus
|
||||
Hyporthodus haifensis
|
||||
Mycteroperca rubra
|
||||
Serranus atricauda
|
||||
Serranus cabrilla
|
||||
Serranus hepatus
|
||||
Serranus scriba
|
||||
Helicolenus dactylopterus
|
||||
Trachyscorpia cristulata
|
||||
Pontinus kuhlii
|
||||
Pterois miles
|
||||
Scorpaena azorica
|
||||
Scorpaena elongata
|
||||
Scorpaena loppei
|
||||
Scorpaena maderensis
|
||||
Scorpaena notata
|
||||
Scorpaena porcus
|
||||
Scorpaena scrofa
|
||||
Scorpaena stephanica
|
||||
Scorpaenodes arenai
|
||||
Sebastapistes mauritiana
|
||||
Elates ransonnetti
|
||||
Papilloculiceps longiceps
|
||||
Platycephalus indicus
|
||||
Sorsogona prionota
|
||||
Chelidonichthys cuculus
|
||||
Chelidonichthys lucerna
|
||||
Chelidonichthys obscurus
|
||||
Eutrigla gurnardus
|
||||
Lepidotrigla cavillone
|
||||
Lepidotrigla dieuzeidei
|
||||
Trigla lyra
|
||||
Trigloporus lastoviza
|
||||
Peristedion cataphractum
|
||||
Taurulus bubalis
|
||||
Eutelichthys leptochirus
|
||||
Paraliparis murieli
|
||||
Melanostigma atlanticum
|
||||
Cyclopterus lumpus
|
||||
Synagrops japonicus
|
||||
Apogon imberbis
|
||||
Apogon queketti
|
||||
Apogon smithi
|
||||
Apogonichthyoides nigripinnis
|
||||
Apogonichthyoides pharaonis
|
||||
Apogonichthyoides taeniatus
|
||||
Brama brama
|
||||
Callanthias ruber
|
||||
Centracanthus cirrus
|
||||
Spicara maena
|
||||
Spicara smaris
|
||||
Cepola macrophthalma
|
||||
Chaetodon hoefleri
|
||||
Chaetodon melannotus
|
||||
Heniochus intermedius
|
||||
Platax teira
|
||||
Epigonus constanciae
|
||||
Epigonus denticulatus
|
||||
Epigonus telescopus
|
||||
Microichthys coccoi
|
||||
Microichthys sanzoi
|
||||
Parapristipoma humile
|
||||
Parapristipoma octolineatum
|
||||
Plectorhinchus mediterraneus
|
||||
Pomadasys incisus
|
||||
Pomadasys stridens
|
||||
Kyphosus saltatrix
|
||||
Equulites klunzingeri
|
||||
Lobotes surinamensis
|
||||
Lutjanus argentimaculatus
|
||||
Lutjanus jocu
|
||||
Dicentrarchus labrax
|
||||
Dicentrarchus punctatus
|
||||
Mullus barbatus
|
||||
Mullus surmuletus
|
||||
Parupeneus forsskali
|
||||
Pseudupeneus prayensis
|
||||
Upeneus moluccensis
|
||||
Upeneus pori
|
||||
Nemipterus japonicus
|
||||
Nemipterus randalli
|
||||
Pempheris vanicolensis
|
||||
Pomatomus saltatrix
|
||||
Galeoides decadactylus
|
||||
Polyprion americanus
|
||||
Priacanthus arenatus
|
||||
Rachycentron canadum
|
||||
Argyrosomus regius
|
||||
Sciaena umbra
|
||||
Umbrina canariensis
|
||||
Umbrina cirrosa
|
||||
Umbrina ronchus
|
||||
Sillago sihama
|
||||
Boops boops
|
||||
Crenidens crenidens
|
||||
Dentex dentex
|
||||
Dentex gibbosus
|
||||
Dentex macrophthalmus
|
||||
Dentex maroccanus
|
||||
Diplodus annularis
|
||||
Diplodus bellottii
|
||||
Diplodus cervinus
|
||||
Diplodus puntazzo
|
||||
Diplodus sargus
|
||||
Diplodus vulgaris
|
||||
Lithognathus mormyrus
|
||||
Oblada melanura
|
||||
Pagellus acarne
|
||||
Pagellus bellottii
|
||||
Pagellus bogaraveo
|
||||
Pagellus erythrinus
|
||||
Pagrus auriga
|
||||
Pagrus caeruleostictus
|
||||
Pagrus major
|
||||
Pagrus pagrus
|
||||
Rhabdosargus haffara
|
||||
Sarpa salpa
|
||||
Sparus aurata
|
||||
Spondyliosoma cantharus
|
||||
Pelates quadrilineatus
|
||||
Terapon puta
|
||||
Terapon theraps
|
||||
Aphia minuta
|
||||
Bathygobius soporator
|
||||
Buenia affinis
|
||||
Buenia jeffreysii
|
||||
Chromogobius quadrivittatus
|
||||
Chromogobius zebratus
|
||||
Corcyrogobius liechtensteini
|
||||
Coryogalops ocheticus
|
||||
Crystallogobius linearis
|
||||
Deltentosteus collonianus
|
||||
Deltentosteus quadrimaculatus
|
||||
Didogobius bentuvii
|
||||
Didogobius schlieweni
|
||||
Didogobius splechtnai
|
||||
Favonigobius melanobranchus
|
||||
Gammogobius steinitzi
|
||||
Gobius ater
|
||||
Gobius auratus
|
||||
Gobius bucchichi
|
||||
Gobius cobitis
|
||||
Gobius couchi
|
||||
Gobius cruentatus
|
||||
Gobius fallax
|
||||
Gobius geniporus
|
||||
Gobius kolombatovici
|
||||
Gobius niger
|
||||
Gobius paganellus
|
||||
Gobius roulei
|
||||
Gobius strictus
|
||||
Gobius vittatus
|
||||
Gobius xanthocephalus
|
||||
Gobiusculus flavescens
|
||||
Knipowitschia caucasica
|
||||
Knipowitschia panizzae
|
||||
Lebetus guilleti
|
||||
Lesueurigobius friesii
|
||||
Lesueurigobius sanzi
|
||||
Lesueurigobius suerii
|
||||
Millerigobius macrocephalus
|
||||
Neogobius melanostomus[1]
|
||||
Odondebuenia balearica
|
||||
Oxyurichthys papuensis
|
||||
Oxyurichthys petersi
|
||||
Pomatoschistus bathi
|
||||
Pomatoschistus canestrinii
|
||||
Pomatoschistus knerii
|
||||
Pomatoschistus marmoratus
|
||||
Pomatoschistus microps
|
||||
Pomatoschistus minutus
|
||||
Pomatoschistus norvegicus
|
||||
Pomatoschistus pictus
|
||||
Pomatoschistus quagga
|
||||
Pomatoschistus tortonesei
|
||||
Pseudaphya ferreri
|
||||
Silhouettea aegyptia
|
||||
Speleogobius trigloides
|
||||
Thorogobius ephippiatus
|
||||
Thorogobius macrolepis
|
||||
Vanneaugobius dollfusi
|
||||
Vanneaugobius pruvoti
|
||||
Zebrus zebrus
|
||||
Zosterisessor ophiocephalus
|
||||
Aidablennius sphynx
|
||||
Blennius ocellaris
|
||||
Coryphoblennius galerita
|
||||
Hypleurochilus bananensis
|
||||
Lipophrys adriaticus
|
||||
Lipophrys canevae
|
||||
Lipophrys dalmatinus
|
||||
Lipophrys nigriceps
|
||||
Lipophrys pholis
|
||||
Omobranchus punctatus
|
||||
Parablennius gattorugine
|
||||
Parablennius incognitus
|
||||
Parablennius pilicornis
|
||||
Parablennius rouxi
|
||||
Parablennius sanguinolentus
|
||||
Parablennius tentacularis
|
||||
Parablennius zvonimiri
|
||||
Paralipophrys trigloides
|
||||
Petroscirtes ancylodon
|
||||
Salaria basilisca
|
||||
Salaria pavo
|
||||
Scartella cristata
|
||||
Clinitrachus argentatus
|
||||
Tripterygion delaisi
|
||||
Tripterygion melanurum
|
||||
Tripterygion tripteronotum
|
||||
Callionymus fasciatus
|
||||
Callionymus filamentosus
|
||||
Callionymus lyra
|
||||
Callionymus maculatus
|
||||
Callionymus pusillus
|
||||
Callionymus reticulatus
|
||||
Callionymus risso
|
||||
Synchiropus phaeton
|
||||
Apletodon dentatus
|
||||
Apletodon incognitus
|
||||
Apletodon microcephalus
|
||||
Diplecogaster bimaculata
|
||||
Gouania willdenowi
|
||||
Lepadogaster candolii
|
||||
Lepadogaster lepadogaster
|
||||
Lepadogaster purpurea
|
||||
Opeatogenys gracilis
|
||||
Acantholabrus palloni
|
||||
Centrolabrus exoletus
|
||||
Centrolabrus trutta
|
||||
Coris julis
|
||||
Ctenolabrus rupestris
|
||||
Iniistius pavo
|
||||
Labrus bergylta
|
||||
Labrus merula
|
||||
Labrus mixtus
|
||||
Labrus viridis
|
||||
Lappanella fasciata
|
||||
Pteragogus pelycus
|
||||
Symphodus bailloni
|
||||
Symphodus cinereus
|
||||
Symphodus doderleini
|
||||
Symphodus mediterraneus
|
||||
Symphodus melanocercus
|
||||
Symphodus melops
|
||||
Symphodus ocellatus
|
||||
Symphodus roissali
|
||||
Symphodus rostratus
|
||||
Symphodus tinca
|
||||
Thalassoma pavo
|
||||
Xyrichtys novacula
|
||||
Scarus ghobban
|
||||
Sparisoma cretense
|
||||
Abudefduf vaigiensis
|
||||
Chromis chromis
|
||||
Chromis viridis
|
||||
Echeneis naucrates
|
||||
Remora australis
|
||||
Remora brachyptera
|
||||
Remora osteochir
|
||||
Remora remora
|
||||
Coryphaena equiselis
|
||||
Coryphaena hippurus
|
||||
Alectis alexandrinus
|
||||
Alepes djedaba
|
||||
Campogramma glaycos
|
||||
Caranx crysos
|
||||
Caranx hippos
|
||||
Caranx rhonchus
|
||||
Decapterus macarellus
|
||||
Decapterus punctatus
|
||||
Decapterus russelli
|
||||
Elagatis bipinnulata
|
||||
Lichia amia
|
||||
Naucrates ductor
|
||||
Pseudocaranx dentex
|
||||
Selene dorsalis
|
||||
Seriola carpenteri
|
||||
Seriola dumerili
|
||||
Seriola fasciata
|
||||
Seriola rivoliana
|
||||
Trachinotus ovatus
|
||||
Trachurus mediterraneus
|
||||
Trachurus picturatus
|
||||
Trachurus trachurus
|
||||
Centrolophus niger
|
||||
Hyperoglyphe perciformis
|
||||
Schedophilus medusophagus
|
||||
Schedophilus ovalis
|
||||
Cubiceps capensis
|
||||
Cubiceps gracilis
|
||||
Psenes pellucidus
|
||||
Pampus argenteus
|
||||
Stromateus fiatola
|
||||
Sphyraena chrysotaenia
|
||||
Sphyraena flavicauda
|
||||
Sphyraena obtusata
|
||||
Sphyraena sphyraena
|
||||
Sphyraena viridensis
|
||||
Istiophorus platypterus
|
||||
Makaira indica
|
||||
Makaira nigricans
|
||||
Tetrapturus albidus
|
||||
Tetrapturus belone
|
||||
Tetrapturus georgii
|
||||
Xiphias gladius
|
||||
Ruvettus pretiosus
|
||||
Lepidopus caudatus
|
||||
Trichiurus lepturus
|
||||
Acanthocybium solandri
|
||||
Auxis rochei rochei
|
||||
Auxis thazard
|
||||
Euthynnus alletteratus
|
||||
Katsuwonus pelamis
|
||||
Orcynopsis unicolor
|
||||
Rastrelliger kanagurta
|
||||
Sarda sarda
|
||||
Scomber colias
|
||||
Scomber scombrus
|
||||
Scomberomorus commerson
|
||||
Scomberomorus tritor
|
||||
Thunnus alalunga
|
||||
Thunnus thynnus
|
||||
Ammodytes tobianus
|
||||
Champsodon nudivittis
|
||||
Champsodon vorax
|
||||
Gymnammodytes cicerelus
|
||||
Gymnammodytes semisquamatus
|
||||
Pinguipes brasilianus
|
||||
Uranoscopus scaber
|
||||
Echiichthys vipera
|
||||
Trachinus aranaeus
|
||||
Trachinus draco
|
||||
Trachinus radiatus
|
||||
Arnoglossus grohmanni
|
||||
Arnoglossus imperialis
|
||||
Arnoglossus kessleri
|
||||
Arnoglossus laterna
|
||||
Arnoglossus rueppelii
|
||||
Arnoglossus thori
|
||||
Bothus podas
|
||||
Citharus linguatula
|
||||
Platichthys flesus
|
||||
Pleuronectes platessa
|
||||
Lepidorhombus boscii
|
||||
Lepidorhombus whiffiagonis
|
||||
Psetta maxima
|
||||
Scophthalmus rhombus
|
||||
Zeugopterus punctatus
|
||||
Zeugopterus regius
|
||||
Bathysolea profundicola
|
||||
Buglossidium luteum
|
||||
Dicologlossa cuneata
|
||||
Dicologlossa hexophthalma
|
||||
Microchirus azevia
|
||||
Microchirus boscanion
|
||||
Microchirus ocellatus
|
||||
Microchirus variegatus
|
||||
Monochirus hispidus
|
||||
Pegusa impar
|
||||
Pegusa lascaris
|
||||
Solea aegyptiaca
|
||||
Solea senegalensis
|
||||
Solea solea
|
||||
Synaptura lusitanica
|
||||
Synapturichthys kleinii
|
||||
Cynoglossus sinusarabici
|
||||
Symphurus ligulatus
|
||||
Symphurus nigrescens
|
||||
Acanthurus monroviae
|
||||
Luvarus imperialis
|
||||
Siganus luridus
|
||||
Siganus rivulatus
|
||||
Balistes capriscus
|
||||
Cyclichthys spilostylus
|
||||
Diodon hystrix
|
||||
Mola mola
|
||||
Ranzania laevis
|
||||
Stephanolepis diaspros
|
||||
Acanthostracion notacanthus
|
||||
Acanthostracion quadricornis
|
||||
Lactophrys trigonus
|
||||
Tetrosomus gibbosus
|
||||
Tetragonurus cuvieri
|
||||
Arothron hispidus
|
||||
Ephippion guttifer
|
||||
Lagocephalus lagocephalus
|
||||
Lagocephalus sceleratus
|
||||
Lagocephalus spadiceus
|
||||
Lagocephalus suezensis
|
||||
Sphoeroides marmoratus
|
||||
Sphoeroides pachygaster
|
||||
Torquigener flavimaculosus
|
||||
Tylerius spinosissimus
|
||||
Halobatrachus didactylus
|
||||
Gasterosteus aculeatus
|
||||
Dactylopterus volitans
|
||||
Capros aper
|
||||
|
|
|
@ -0,0 +1,68 @@
|
|||
# simpleobisCCP.R
|
||||
# Simple example for CCP integration
|
||||
#
|
||||
# Author: Giancarlo Panichi
|
||||
###############################################################################
|
||||
|
||||
library(robis)
|
||||
library(ggplot2)
|
||||
library(rgeos)
|
||||
library(stringr)
|
||||
|
||||
createplot <- function(sname,usedPolygon){
|
||||
result = tryCatch({
|
||||
result=paste("/ccp_data/",sname,".png",sep="")
|
||||
|
||||
wktP <-readWKT(usedPolygon)
|
||||
print(wktP@bbox)
|
||||
|
||||
#By scientific name and 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)
|
||||
}, warning = function(w) {
|
||||
print(w)
|
||||
}, error = function(e) {
|
||||
print(e)
|
||||
}, finally = {
|
||||
print(paste(sname,"done.", sep=" "))
|
||||
})
|
||||
}
|
||||
|
||||
|
||||
readfile <- function(filename, usedPolygon) {
|
||||
con = file(filename, "r")
|
||||
while ( TRUE ) {
|
||||
line = readLines(con, n = 1)
|
||||
line = str_trim(line)
|
||||
if ( length(line) == 0 ) {
|
||||
break
|
||||
}
|
||||
print(line)
|
||||
createplot(line, usedPolygon)
|
||||
|
||||
}
|
||||
close(con)
|
||||
}
|
||||
|
||||
|
||||
#url="https://data.d4science.net/Y8WK"
|
||||
#usedPolygon="POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
|
||||
main <- function(){
|
||||
args = commandArgs(trailingOnly=TRUE)
|
||||
print(args)
|
||||
|
||||
if (length(args)<=1) {
|
||||
stop("At least two arguments must be supplied", call.=FALSE)
|
||||
}
|
||||
|
||||
filename="fishScientificName.csv"
|
||||
|
||||
url=args[1]
|
||||
usedPolygon=args[2]
|
||||
download.file(url, filename)
|
||||
|
||||
readfile(filename,usedPolygon)
|
||||
}
|
||||
|
||||
main()
|
||||
Loading…
Reference in New Issue