nfdocs-parser/nfdocs-parser.py

#!/usr/bin/env python
import os
import yaml
from docutils import nodes
from docutils.parsers.rst import Directive
from docutils.parsers.rst import directives

class NFDocs(Directive):
    # Class default overrides
    required_arguments = 1

    # Declare the docstring starting characters
    DOC_STARTER = "/// "

    def definition_type(self, signature):
        # Returns "name", workflow|process|function
        def_type = "unknown"
        if "workflow" in signature:
            def_type = "workflow"
        elif "process" in signature:
            def_type = "process"
        elif "function" in signature:
            def_type = "function"

        # Check if any signature was recognized
        if def_type == "unknown":
            return "unknown", "an error occurred"

        # Parse out the definition name
        def_name = signature.replace(def_type, "").replace("{", "").strip()

        # Return the results
        return def_name, def_type

    def params_to_list(self, params):
        if "tuple" in params.keys():
            tuple_item = nodes.list_item()
            if "name" in params.keys():
                tuple_item += nodes.paragraph(text=params["name"])
            tuple_item += nodes.paragraph(text="Tuple:")
            tuple_list = nodes.bullet_list()
            for io in params["tuple"]:
                tuple_list += self.params_to_list(io)
            tuple_item += tuple_list
            return tuple_item
        else:
            io_item = nodes.list_item()
            if "name" in params.keys():
                io_item += nodes.paragraph(text=params["name"])
            io_item += nodes.paragraph(text=f"Type: {params['type']}")
            io_item += nodes.paragraph(text=params["description"])
            return io_item

    def run(self):
        # Take path as single argument for now
        nextflow_path = self.arguments[0]
        print(nextflow_path)

        # Create dictionaries for each of the block types
        docstrings = {
            "process": {},
            "workflow": {},
            "function": {}
        }

        # Create any array to return from the plugin
        return_nodes = []

        for root, dirs, files in os.walk(nextflow_path):
            for f in files:
                if f.endswith(".nf"):
                    with open(os.path.join(root,f)) as nextflow_file:

                        # Split by lines
                        nextflow_lines = nextflow_file.readlines()

                        # Declare some variables to keep track of where the docstrings begin and end
                        doc_start = 0
                        doc_end = 0

                        # Declare dictionaries to keep track of the docstrings
                        docstring_positions = []

                        # Calculate the start and end positions of each docstring
                        for i, line in enumerate(nextflow_lines):
                            # Check if this is a docstring
                            if line.startswith(self.DOC_STARTER):
                                # It is: check the next and previous lines to see if this is part of a block
                                line_previous = nextflow_lines[i-1]
                                line_next = nextflow_lines[i+1]
                                if not line_previous.startswith(self.DOC_STARTER):
                                    doc_start = i
                                if not line_next.startswith(self.DOC_STARTER):
                                    doc_end = i

                                # Check if we've reached the end of a docstring block
                                if doc_end == i:
                                    # Add this docstring position to the array
                                    docstring_positions.append(range(doc_start, doc_end+1))

                        # Parse out the docstrings and put them in the appropriate dictionary
                        for pos in docstring_positions:
                            proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1])
                            doc_yaml = ""
                            for i in pos:
                                doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "")
                            docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)

        # Try to convert each definition to a node
        for block_type, block_docs in docstrings.items():
            block_section = nodes.section()
            block_section += nodes.title(text=block_type)
            for proc_name, proc_docs in block_docs.items():
                proc_section = nodes.section()
                proc_section += nodes.title(text=proc_name)
                proc_section += nodes.paragraph(text=proc_docs["summary"])
                io_methods = ["input", "output"]
                for met in io_methods:
                    if met in proc_docs.keys():
                        io_section = nodes.section()
                        io_section += nodes.title(text=met)
                        io_list = nodes.bullet_list()
                        for io in proc_docs[met]:
                            io_list += self.params_to_list(io)
                        io_section += io_list
                        proc_section += io_section
                        self.state_machine.document.note_implicit_target(io_section)
                self.state_machine.document.note_implicit_target(proc_section)
                block_section += proc_section

            self.state_machine.document.note_implicit_target(block_section)
            return_nodes.append(block_section)

        return return_nodes

def setup(app):
    app.add_directive('nfdocs', NFDocs)
    return {
        "version": "0.1.0"
    }