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https://github.com/MillironX/nfdocs-parser.git
synced 2024-11-21 16:46:05 +00:00
Refactor to parse multiple files from the directory
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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139C07724802BC5D
1 changed files with 68 additions and 62 deletions
130
nfdocs-parser.py
130
nfdocs-parser.py
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@ -1,4 +1,5 @@
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#!/usr/bin/env python
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import os
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import yaml
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from docutils import nodes
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from docutils.parsers.rst import Directive
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@ -53,79 +54,84 @@ class NFDocs(Directive):
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def run(self):
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# Take path as single argument for now
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nextflow_path = self.arguments[0]
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with open(nextflow_path) as nextflow_file:
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print(nextflow_path)
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# Split by lines
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nextflow_lines = nextflow_file.readlines()
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# Create dictionaries for each of the block types
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docstrings = {
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"process": {},
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"workflow": {},
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"function": {}
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}
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# Declare some variables to keep track of where the docstrings begin and end
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doc_start = 0
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doc_end = 0
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# Create any array to return from the plugin
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return_nodes = []
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# Declare dictionaries to keep track of the docstrings
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docstring_positions = []
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for root, dirs, files in os.walk(nextflow_path):
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for f in files:
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if f.endswith(".nf"):
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with open(os.path.join(root,f)) as nextflow_file:
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# Calculate the start and end positions of each docstring
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for i, line in enumerate(nextflow_lines):
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# Check if this is a docstring
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if line.startswith(self.DOC_STARTER):
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# It is: check the next and previous lines to see if this is part of a block
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line_previous = nextflow_lines[i-1]
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line_next = nextflow_lines[i+1]
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if not line_previous.startswith(self.DOC_STARTER):
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doc_start = i
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if not line_next.startswith(self.DOC_STARTER):
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doc_end = i
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# Split by lines
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nextflow_lines = nextflow_file.readlines()
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# Check if we've reached the end of a docstring block
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if doc_end == i:
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# Add this docstring position to the array
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docstring_positions.append(range(doc_start, doc_end+1))
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# Declare some variables to keep track of where the docstrings begin and end
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doc_start = 0
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doc_end = 0
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# Create dictionaries for each of the block types
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docstrings = {
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"process": {},
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"workflow": {},
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"function": {}
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}
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# Declare dictionaries to keep track of the docstrings
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docstring_positions = []
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# Parse out the docstrings and put them in the appropriate dictionary
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for pos in docstring_positions:
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proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1])
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doc_yaml = ""
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for i in pos:
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doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "")
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docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
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# Calculate the start and end positions of each docstring
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for i, line in enumerate(nextflow_lines):
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# Check if this is a docstring
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if line.startswith(self.DOC_STARTER):
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# It is: check the next and previous lines to see if this is part of a block
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line_previous = nextflow_lines[i-1]
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line_next = nextflow_lines[i+1]
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if not line_previous.startswith(self.DOC_STARTER):
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doc_start = i
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if not line_next.startswith(self.DOC_STARTER):
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doc_end = i
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# Create any array to return from the plugin
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return_nodes = []
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# Check if we've reached the end of a docstring block
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if doc_end == i:
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# Add this docstring position to the array
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docstring_positions.append(range(doc_start, doc_end+1))
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# Try to convert each definition to a node
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for block_type, block_docs in docstrings.items():
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block_section = nodes.section()
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block_section += nodes.title(text=block_type)
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for proc_name, proc_docs in block_docs.items():
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proc_section = nodes.section()
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proc_section += nodes.title(text=proc_name)
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proc_section += nodes.paragraph(text=proc_docs["summary"])
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io_methods = ["input", "output"]
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for met in io_methods:
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if met in proc_docs.keys():
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io_section = nodes.section()
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io_section += nodes.title(text=met)
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io_list = nodes.bullet_list()
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for io in proc_docs[met]:
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io_list += self.params_to_list(io)
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io_section += io_list
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proc_section += io_section
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self.state_machine.document.note_implicit_target(io_section)
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self.state_machine.document.note_implicit_target(proc_section)
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block_section += proc_section
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# Parse out the docstrings and put them in the appropriate dictionary
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for pos in docstring_positions:
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proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1])
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doc_yaml = ""
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for i in pos:
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doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "")
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docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
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self.state_machine.document.note_implicit_target(block_section)
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return_nodes.append(block_section)
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# Try to convert each definition to a node
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for block_type, block_docs in docstrings.items():
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block_section = nodes.section()
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block_section += nodes.title(text=block_type)
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for proc_name, proc_docs in block_docs.items():
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proc_section = nodes.section()
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proc_section += nodes.title(text=proc_name)
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proc_section += nodes.paragraph(text=proc_docs["summary"])
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io_methods = ["input", "output"]
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for met in io_methods:
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if met in proc_docs.keys():
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io_section = nodes.section()
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io_section += nodes.title(text=met)
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io_list = nodes.bullet_list()
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for io in proc_docs[met]:
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io_list += self.params_to_list(io)
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io_section += io_list
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proc_section += io_section
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self.state_machine.document.note_implicit_target(io_section)
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self.state_machine.document.note_implicit_target(proc_section)
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block_section += proc_section
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return return_nodes
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self.state_machine.document.note_implicit_target(block_section)
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return_nodes.append(block_section)
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return return_nodes
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def setup(app):
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app.add_directive('nfdocs', NFDocs)
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