This version of the Lifemapper Makeflow generator splits a single csv file containing multiple taxa into groups such that like taxa are adjacent to each other into files. These files are used as inputs to models (if there are enough points) and projections under different climate scenarios. The workflow is comprised of a large number of independent taxa (pictured). The included dataset contains a number of invalid samples, so the workflow generates a lot of noise. You should expect to see numerous errors like
Exception in thread "main" java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(StringTokenizer.java:349)
at density.Project.projectGrid(Project.java:152)
at density.Project.doProject(Project.java:112)
at density.Project.main(Project.java:522)
and
Warning: Sample at 32.2275, -109.781389 in Conanthalictus_conanthi.csv is outside the bounding box of environmental data, skipping
Warning: Sample at 32.2275, -109.781389 in Conanthalictus_conanthi.csv is outside the bounding box of environmental data, skipping
Warning: Sample at 32.2275, -109.781389 in Conanthalictus_conanthi.csv is outside the bounding box of environmental data, skipping
Warning: Sample at 32.2275, -109.781389 in Conanthalictus_conanthi.csv is outside the bounding box of environmental data, skipping
Warning: Sample at 32.2275, -109.781389 in Conanthalictus_conanthi.csv is outside the bounding box of environmental data, skipping
The workflow will finish successfully after processing as much data as possible. This example requires Java. It may be installed or available through your system's package manager. You can also download Java here.
This example processes a small dataset and only one model/projection scenario with 183 rules in the workflow.
python split.py data/points/small.csv
To run it, make sure Makeflow is in your $PATH and type
makeflow --jx lifemapper.jx
This example runs on a larger dataset with a model scenario and three projection scenarios each.
python split.py data/points/large.csv
This example consists of 3145 rules and runs all three projection scenarios.
makeflow --jx-define 'PROJECTIONS=["data/layers/" + x for x in listdir("data/layers")]' --jx lifemapper.jx