From 18d853cd32f5b6af3ffe00f16c7e4b77e992b093 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Mon, 29 Apr 2024 18:17:53 -0700 Subject: [PATCH] code update and an example of why DRY is important! i just haven't figured out how to not duplicate code between my example plugin and the book yet, but that's a work in progress. --- book/plugins/tutorials/add-pipeline.md | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/book/plugins/tutorials/add-pipeline.md b/book/plugins/tutorials/add-pipeline.md index a9f8910..6576a4e 100644 --- a/book/plugins/tutorials/add-pipeline.md +++ b/book/plugins/tutorials/add-pipeline.md @@ -145,19 +145,21 @@ Here's the final Pipeline registration code that I ended up with in my `plugin_s ```python plugin.pipelines.register_function( function=align_and_summarize, - inputs=_align_and_summarize_inputs, - parameters=_align_and_summarize_parameters, + inputs=_nw_align_inputs, + parameters=_nw_align_parameters, outputs=_align_and_summarize_outputs, - input_descriptions=_align_and_summarize_input_descriptions, - parameter_descriptions=_align_and_summarize_parameter_descriptions, + input_descriptions=_nw_align_input_descriptions, + parameter_descriptions=_nw_align_parameter_descriptions, output_descriptions=_align_and_summarize_output_descriptions, name="Pairwise global alignment and summarization.", description=("Perform global pairwise sequence alignment using a slow " "Needleman-Wunsch (NW) implementation, and generate a " "visual summary of the alignment."), - citations=_align_and_summarize_output_citations, - examples={'Align two sequences and summarize the alignment.': - align_and_summarize_example_1} + # Only citations new to this Pipeline need to be defined. Citations for + # the Actions called from the Pipeline are automatically included. + citations=[], + examples={} +) ``` As a **required exercise** after adding this code to your `plugin_setup.py` file, define the variables used in this code block in such a way that it avoids the DRY violation mentioned above.