Skip to content

Latest commit

 

History

History
73 lines (63 loc) · 6.25 KB

CONTRIBUTE.md

File metadata and controls

73 lines (63 loc) · 6.25 KB
Raw

Technical Details

At the core, PICCL consists of various independent Nextflow pipeline scripts (the *.nf scripts). These pipeline scripts provide the logic to connect a number of inter-dependent processes and determines the data flow between them. Within these processes, any language may be use to define the scripts that performs the tasks (bash/python/perl/etc...). Typically, a process script invokes a single external tool.

The underlying tools that are invoked are not provided by PICCL itself, but installation and distribution thereof is delegated to LaMachine, upon which PICCL depends. A notable example is the TICCLtools toolset which provides a variety of tools invoked by the TICCL workflow (ticcl.nf).

The exception to the above are some scripts (shell/perl/python/etc) that are not otherwise distributed nor can be considered proper reusable tools out of the scope of PICCL. These are distributed as part of PICCL in in scripts/. This is a fall-back solution that be preferably be kept to a minimum.

PICCL features a RESTful webservice which doubles as a simple webapplication. This provides an interface that exposes some (currently not all!) of the workflows. This webservice is implemented in CLAM. Note that CLAM provides a fairly generic and simplistic user-interface. Considering the envisioned audience for PICCL, a more user-oriented interface that communicates with the PICCL webservice may be desireable but is not currently provided by this project.

For linguistic annotation, the pivot format in PICCL is FoLiA.

Contributor Guidelines

  • The PICCL codebase is maintained in git at https://github.com/LanguageMachines/PICCL
    • Never do any development outside of version control!!!
    • Pull requests welcome!! (direct push access for main project contributors)
    • the master branch corresponds to the latest development version and should serve as the basis for all development
      • do not use this branch for production, always use the latest release (LaMachine takes care of this for you automatically)
      • keep the master branch in a workable state, use separate git branches for intensive development cycles.
      • Regarding development of TICCL, the PICCL master branch is assumed to be compatible with the master branch of TICCL-tools (#35)
  • For development of workflows, consult the Nextflow Documentation. The Nextflow scripting language is an extension of the Groovy programming language (runs on the Java VM) whose syntax has been specialized to ease the writing of computational pipelines in a declarative manner.
    • ticcl.nf has been commented extra to serve as an example
    • The process scripts within Nextflow pipeline scripts should typically invoke only a single external tool, or at least perform a single well-defined task (if you want to invoke a series of tools, use separate processes)
  • To make additional tools available for use in PICCL, consult the documentation on adding new software to LaMachine, installing tools should never be the responsibility of the end-user and rarely that of PICCL itself.
  • To add pipelines to the webinterface, edit the PICCL's webservice configuration script (webservice/picclservice/picclservice.py), where you can define profiles, and wrapper script (webservice/picclservice/picclservice_wrapper.py). Consult the CLAM Documentation for details on how to do this.
  • Report all bugs and feature requests pertaining to pipelines and webservice (or in case you simply don't know) to https://github.com/LanguageMachines/PICCL/issues
  • Integration tests are defined in test.sh and will automatically be run on our continuous integration platform at https://travis-ci.org/LanguageMachines/PICCL after each git push.
    • If you add a feature, we strongly recommend you to add a test.
    • The coverage of the tests is currently seriously sub-optimal!!
    • Tests should be limited in scope so they can be performed quickly, often and with limited resources (no OCRing of whole books!!)
    • Tests on a lower (unit) level are the responsibility of the underlying tools, rather than PICCL
  • Martin Reynaert is the project leader with the final say on what functionality is accepted into PICCL or not.

Setting up a Development Environment

  • Install the development version of LaMachine, in any flavour, and enable PICCL in the installation manifest during the bootstrap procedure (or just run lamachine-add piccl after the fact)
  • The PICCL git repository will be cloned in $LM_SOURCEPATH/PICCL. If you do not have direct push access to the PICCL repository, we recommend you fork https://github.com/LanguageMachines/PICCL and add do a git remote add to track your own branch there.
  • You can always upgrade your LaMachine environment with lamachine-update, but make sure you don't have uncommitted changes (they will be stashed away automatically)!!
  • Run the development webservice as follows: cd $LM_SOURCEPATH/PICCL/webservice && ./startserver_development.sh and connect at http://127.0.0.1:8080. If you are running the LaMachine VM, you may need to stop the automatically started production webserver first with lamachine-stop-webserver as it shares the same port.