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

def definition_type(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_table(type, params):
    # Create a table
    params_table = nodes.table()
    if type:
        params_table += nodes.title(text=type)

    # Make it two columns wide
    params_tgroup = nodes.tgroup(cols=2)
    for _ in range(2):
        colspec = nodes.colspec(colwidth=1)
        params_tgroup.append(colspec)

    # Create the row definitions
    params_rows = []

    for param in params:
        # Create a new row
        param_row = nodes.row()

        # If this parameter is a tuple, the new row takes on the form
        # +-------+------------------+
        # |       | +--------------+ |
        # | Tuple | | Params Table | |
        # |       | +--------------+ |
        # +-------+------------------+
        # via recursion
        if "tuple" in param.keys():
            # Tuple title
            param_name_entry = nodes.entry()
            param_name_entry += nodes.Text("Tuple")
            param_row += param_name_entry

            # Params table
            sub_params_entry = nodes.entry()
            sub_params_entry += params_to_table("Tuple", param["tuple"])
            param_row += sub_params_entry

        # If this is actually a parameter, the new row takes on the form
        # +------------+-------------+
        # | Name(Type) | Description |
        # +------------+-------------+
        # or
        # +------+-------------+
        # | Type | Description |
        # +------+-------------+
        else:
            # Parameter title
            param_name_entry = nodes.entry()
            if "name" in param.keys():
                param_name_entry += nodes.Text(f"{param['name']}({param['type']})")
            else:
                param_name_entry += nodes.Text(param["type"])
            param_row += param_name_entry

            # Parameter description
            param_description_entry = nodes.entry()
            param_description_entry += nodes.paragraph(text=param["description"])
            param_row += param_description_entry

        # Add this row to the vector
        params_rows.append(param_row)

    # Convert the rows to a table
    params_table_body = nodes.tbody()
    params_table_body.extend(params_rows)
    params_tgroup += params_table_body
    params_table += params_tgroup
    return params_table

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

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

    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 = 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_table = params_to_table(met, proc_docs[met])
                        proc_section += io_table
                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"
    }