Package org.fairdatapipeline.api

Class Coderun

java.lang.Object
org.fairdatapipeline.api.Coderun
All Implemented Interfaces:
AutoCloseable
public class Coderun extends Object implements AutoCloseable
Java implementation of the FAIR Data Pipeline API

Users should initialise this library using a try-with-resources block or ensure that .close() is explicitly closed when the required file handles have been accessed.

Usage example 

    try (var coderun = new Coderun(configPath, scriptPath, regToken)) {
       ImmutableSamples samples = ImmutableSamples.builder().addSamples(1, 2, 3).rng(rng).build();
       String dataProduct = "animal/dodo";
       String component1 = "example-samples-dodo1";
       Data_product_write dp = coderun.get_dp_for_write(dataProduct, "toml");
       Object_component_write oc1 = dp.getComponent(component1);
       oc1.raise_issue("something is terribly wrong with this component", 10);
       oc1.writeSamples(samples);
     }
Or, to write a CSV file, with issues on the DP and on the Code_repo: 
    try (var coderun = new Coderun(configPath, scriptPath, regToken)) {
       String dataProduct = "human/health";
       Data_product_write dp = coderun.get_dp_for_write(dataProduct, "toml");
       Object_component_write oc1 = dp.getComponent();
       CleanableFileChannel f = oc1.writeFileChannel();
       my_analysis_csv_writer(f);
       Issue i = coderun.raise_issue("something is terribly wrong with this component", 10);
       i.add_components(oc1);
       i.add_fileObjects(coderun.getCode_repo());
     }

  • Constructor Details

    • Coderun

      public Coderun(Path configFilePath)
      Constructor using only configFilePath - scriptPath is read from the config.
      Parameters:
      configFilePath - the Path to the config file, which must be located in the local data store CodeRun folder with timestamp name.

    • Coderun

      public Coderun(Path configFilePath, @Nullable Path scriptPath)
      Constructor using both configFilePath and ScriptPath
      Parameters:
      configFilePath - the Path to the config.yaml file
      scriptPath - the Path to the script file - this may be null if the script path is given in the config file.

      both startup files are usually provided by fair run in the local data registry jobs/{timestamp} folder.

    • Coderun

      public Coderun(Path configFilePath, @Nullable Path scriptPath, @Nullable String registryToken)
      Constructor specifying configPath, scriptPath, and registryToken.
      Parameters:
      configFilePath - the Path to the config.yaml file
      scriptPath - the Path to the script file - this may be null if the script path is given in the config file.

      both startup files are usually provided by fair run in the local data registry jobs/{timestamp} folder.

      registryToken - the authentication token of the local registry (or null if the token is to be read from the config or from ~/.fair/registry/token)

  • Method Details

    • getScript

      public FileObject getScript()
      Access the Submission_script; in order to raise a Submission_script issue.
      Returns:
      the FileObject representing the Submission_script.

      Usage: 

           coderun.getScript.raise_issue("this is a very bad script", 10);
      OR 
           Issue i = coderun.raise_issue("Seriously bad stuff", 10);
     i.add_fileObjects(coderun.getScript(), coderun.getConfig());

    • getConfig

      public FileObject getConfig()
      Access the configuration file (config.yaml); in order to raise a Config issue.
      Returns:
      the FileObject representing the config file.

      Usage: 

           coderun.getConfig.raise_issue("this is a very bad config file", 10);
      OR 
           Issue i = coderun.raise_issue("Seriously bad stuff", 10);
     i.add_fileObjects(coderun.getScript(), coderun.getConfig());

    • getCode_repo

      public FileObject getCode_repo()
      Access the code repository in order to raise a code repository issue.
      Returns:
      the FileObject representing the code repository (which is given in the config file)

      Usage: 

           coderun.getCode_repo.raise_issue("this contains very bad code", 10);
      OR 
           Issue i = coderun.raise_issue("Seriously bad stuff", 10);
     i.add_fileObjects(coderun.getCode_repo(), coderun.getConfig());

    • get_dp_for_read

      public Data_product_read get_dp_for_read(String dataProduct_name)
      Obtain a data product for reading.
      Parameters:
      dataProduct_name - the name of the dataProduct to obtain.
      Returns:
      the data product.

    • get_dp_for_write

      public Data_product_write get_dp_for_write(String dataProduct_name, String extension)
      Obtain a data product for writing.
      Parameters:
      dataProduct_name - the name of the dataProduct to obtain.
      extension - the file extension representing the file type we will write, e.g. csv or toml
      Returns:
      the data product

    • get_dp_for_write

      public Data_product_write get_dp_for_write(String dataProduct_name)
      Obtain a data product for writing. (gets the extension from config)
      Parameters:
      dataProduct_name - the name of the dataProduct to obtain.
      Returns:
      the data product

    • raise_issue

      public Issue raise_issue(String description, Integer severity)
      create an Issue that can be linked to a number of object components and/or fileObjects.
      Parameters:
      description - text description of the issue
      severity - integer representing the severity of the issue, larger integer means more severe
      Returns:
      the Issue

    • close

      public void close()
      Finalize and register the coderun. (this gets called automatically when using Coderun in a try-with-resources block)
      Specified by:
      close in interface AutoCloseable