BioVeL workshop reduced full workflow

Created: 2013-09-04 16:03:01

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The workflow is a reduced version of the main workflow. It can be used to call web services to support biodiversity research.

It fetches data from GBIF. The occurrences are then used to create a model using OpenModeller, test the model and to project the model.

The projection of the model is currently a "native projection" i.e. it uses the same layers as those used to create the model. The services within the workflow will allow non-native projections

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Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

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

Processors (13)

Name	Type	Description
create_model	workflow
project_model	workflow
select_algorithm	workflow
test_model	workflow
make_configuration_of_create_model	workflow
select_layers	workflow
make_configuration_of_project_model	workflow
allocate_points	beanshell	Script import java.io.StringReader; import java.io.BufferedReader; BufferedReader reader = new BufferedReader(new StringReader(points)); StringBuilder creation_builder = new StringBuilder(); StringBuilder testing_builder = new StringBuilder(); int count = 0; for (String line = reader.readLine(); line != null; line = reader.readLine()) { count++; String[] parts = line.split(","); if (parts.length == 2) { String point = "\n"; if ((count % 10) == 0) { testing_builder.append(point); } else { creation_builder.append(point); } } } String creation_points = creation_builder.toString(); String testing_points = testing_builder.toString();
fetch_species_points_from_gbif	workflow
make_configuration_of_test_model	workflow
extract_model_algorithm	workflow
show_confusion_matrix	workflow
show_layer_in_browser	workflow

Beanshells (9)

Name	Inputs	Outputs
allocate_points	points	creation_points testing_points
change_to_png_url	img_url	png_url
show_in_browser	url	answer
show_gbif_agreement		answer
find_coordinates	longitude latitude	coordinates
Select_layers	xmltext	chosen_layers
create_algorithm_xml	algorithm_id algorithm_version parameter_names parameter_values	createmodel_algorithm
Beanshell	names values	values
create_xpath_to_get_algorithm	in1	out1

Outputs (9)

Name	Description
serialized_model	The serialization of the model that was created, tested and projected.
create_model_log	The log from creating the model. This is only output for information.
img_layer_url	The URL of the result of the model projection. The data referenced by the URL is in ERDAS IMAGINE format
project_model_log	The log from projecting the model. This is only output for information.
test_model_log	The log from testing the model. This is only output for information.
test_model_statistics	An XML document containing statistics for the result of the testing of the model.
provision_statements	A listing of the providers of the data from GBIF and also of any special terms and conditions applied to the data. This information should be carefully examined before any further analysis or publication of the data.
confusion_matrix_acceptability	The answer to whether the confusion matrix from testing was acceptable. This could be used as a basis for looping back to choosing the algorithm and/or setting its parameters.
img_result

Datalinks (25)

Source	Sink
make_configuration_of_create_model:outputString	create_model:createModel_configuration
make_configuration_of_project_model:outputString	project_model:projectModel_configuration
make_configuration_of_test_model:outputString	test_model:testModel_configuration
select_algorithm:algorithm	make_configuration_of_create_model:algorithm_xml
select_layers:Selected_layers	make_configuration_of_create_model:layers
allocate_points:creation_points	make_configuration_of_create_model:points
select_layers:Selected_layers	make_configuration_of_project_model:layers
extract_model_algorithm:model_algorithm	make_configuration_of_project_model:algorithm_xml
fetch_species_points_from_gbif:coordinates	allocate_points:points
species_name	fetch_species_points_from_gbif:species_name
select_layers:Selected_layers	make_configuration_of_test_model:layers
allocate_points:testing_points	make_configuration_of_test_model:points
extract_model_algorithm:model_algorithm	make_configuration_of_test_model:algorithm_xml
create_model:serialized_model	extract_model_algorithm:serialized_model
test_model:test_statistics	show_confusion_matrix:statistics
project_model:projected_layer_url	show_layer_in_browser:img_url
create_model:serialized_model	serialized_model
create_model:output_log	create_model_log
project_model:projected_layer_url	img_layer_url
project_model:output_log	project_model_log
test_model:output_log	test_model_log
test_model:test_statistics	test_model_statistics
fetch_species_points_from_gbif:provision_statements	provision_statements
show_confusion_matrix:answer	confusion_matrix_acceptability
show_layer_in_browser:img_result	img_result

Coordinations (3)

Controller	Target
select_algorithm	select_layers
fetch_species_points_from_gbif	select_algorithm
show_confusion_matrix	make_configuration_of_project_model

Information Workflow Type

Taverna 2

Information Uploader

Aleksandra Pawlik

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Bonn-September 2013

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BioVeL workshop reduced full workflow

Created by Aleksandra Pawlik on Wednesday 04 September 2013 16:03:00 (UTC)

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BioVeL workshop reduced full workflow

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