FetchandDisplaySpecies
Created: 2011-11-27 12:44:23
Last updated: 2011-11-29 15:34:08
This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed.
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Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
| This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed. |
Dependencies (0)
Inputs (6)
| Name |
Description |
| species_name |
This input takes the name of the species that is under investigation. Note that the name is case sensitive. Additionally you should not add a newline to the end of the name
|
| maxlat |
The maximum latitude of the bounding box
|
| maxlong |
The maximum longitude of the bounding box
|
| minlat |
The minimum latitude of the bounding box
|
| minlong |
The minimum longitude of the bounding box
|
| google_earth_command |
This input contains the command used to call Google Earth. Its content will depend upon your operating system and where Google Earth has been installed.
|
Processors (4)
| Name |
Type |
Description |
| check_bounding_box |
localworker |
Scriptimport javax.swing.JOptionPane;
import javax.swing.*;
import java.awt.GridLayout;
import java.util.ArrayList;
int answer = JOptionPane.showConfirmDialog(null, "Is the selection OK?", "Selection confirmation", JOptionPane.YES_NO_OPTION);
if (answer == JOptionPane.NO_OPTION) {
JPanel panel = new JPanel();
panel.setLayout(new GridLayout(4, 2));
JTextField minLatField = new JTextField(minlat, 20);
JTextField maxLatField = new JTextField(maxlat, 20);
JTextField minLongField = new JTextField(minlong, 20);
JTextField maxLongField = new JTextField(maxlong, 20);
panel.add(new JLabel("Minimum latitude"));
panel.add(minLatField);
panel.add(new JLabel("Maximum latitude"));
panel.add(maxLatField);
panel.add(new JLabel("Minimum longitude"));
panel.add(minLongField);
panel.add(new JLabel("Maximum longitude"));
panel.add(maxLongField);
JOptionPane.showOptionDialog(null, panel, null,
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
minlat = minLatField.getText();
maxlat = maxLatField.getText();
minlong = minLongField.getText();
maxlong = maxLongField.getText();
} |
| Fetch_occurrence_data |
rest |
|
| Show_in_google_earth |
externaltool |
|
| show_gbif_agreement |
beanshell |
Scriptimport java.awt.Desktop;
import java.net.URI;
import java.util.ArrayList;
import javax.swing.JOptionPane;
Desktop.getDesktop().browse(new URI("http://data.gbif.org/tutorial/datauseagreement"));
int answer = JOptionPane.showConfirmDialog(null,
"Do you agree to the GBIF data use agreement?",
"Use agreement",
JOptionPane.YES_NO_OPTION);
if (answer != JOptionPane.YES_OPTION) {
throw new RuntimeException("You must agree to the GBIF data use agreement");
}
|
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| show_gbif_agreement |
|
|
answer
|
Outputs (7)
| Name |
Description |
| kml |
The KML corresponding to the occurrences within the selected bounding box
|
| answer |
|
| maxlat |
The maximum latitude selected for the bounding box for occurrences
|
| maxlong |
The maximum longitude selected for the bounding box for occurrences
|
| minlat |
The minimum latitude selected for the bounding box for occurrences
|
| minlong |
The minimum longitude selected for the bounding box for occurrences
|
| agreement_answer |
|
Datalinks (18)
| Source |
Sink |
| maxlat |
check_bounding_box:maxlat |
| maxlong |
check_bounding_box:maxlong |
| minlat |
check_bounding_box:minlat |
| minlong |
check_bounding_box:minlong |
| maxlat |
Fetch_occurrence_data:maxlat |
| maxlong |
Fetch_occurrence_data:maxlong |
| minlat |
Fetch_occurrence_data:minlat |
| minlong |
Fetch_occurrence_data:minlong |
| species_name |
Fetch_occurrence_data:species_name |
| Fetch_occurrence_data:responseBody |
Show_in_google_earth:data |
| google_earth_command |
Show_in_google_earth:open_command |
| Fetch_occurrence_data:responseBody |
kml |
| check_bounding_box:answer |
answer |
| check_bounding_box:maxlat |
maxlat |
| check_bounding_box:maxlong |
maxlong |
| check_bounding_box:minlat |
minlat |
| check_bounding_box:minlong |
minlong |
| show_gbif_agreement:answer |
agreement_answer |
Coordinations (2)
| Controller |
Target |
| Show_in_google_earth |
check_bounding_box |
| show_gbif_agreement |
Fetch_occurrence_data |
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License
All versions of this Workflow are
licensed under:
Version 3 (latest)
(of 3)
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If you are a Windows user, the Google Earth command parameter for the Show in Google Earth service is:
c:\\\\Windows\\System32\\cmd.exe /c
You will also need to set the explicit location for invoking the tool to "default local". You can do this in Taverna Workbench by selecting the Show in Google Earth service in the Workflow Explorer panel; then go to the Details panel and choose "Configure Tool Invocation" and then go to the Location tab and "select an explicit location" From the drop-down menu, choose "default local".
Make sure you have Google Earth installed!