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https://github.com/MillironX/nfdocs-parser.git
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Promote the parser script to a Directive class
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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1 changed files with 100 additions and 97 deletions
197
nfdocs-parser.py
197
nfdocs-parser.py
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@ -2,118 +2,121 @@
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import sys
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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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# Declare the docstring starting characters
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DOC_STARTER = "/// "
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class NFDocs(Directive):
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def definition_type(signature):
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# Returns "name", workflow|process|function
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def_type = "unknown"
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if "workflow" in signature:
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def_type = "workflow"
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elif "process" in signature:
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def_type = "process"
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elif "function" in signature:
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def_type = "function"
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# Declare the docstring starting characters
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DOC_STARTER = "/// "
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# Check if any signature was recognized
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if def_type == "unknown":
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return "unknown", "an error occurred"
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def definition_type(signature):
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# Returns "name", workflow|process|function
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def_type = "unknown"
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if "workflow" in signature:
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def_type = "workflow"
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elif "process" in signature:
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def_type = "process"
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elif "function" in signature:
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def_type = "function"
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# Parse out the definition name
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def_name = signature.replace(def_type, "").replace("{", "").strip()
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# Check if any signature was recognized
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if def_type == "unknown":
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return "unknown", "an error occurred"
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# Return the results
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return def_name, def_type
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# Parse out the definition name
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def_name = signature.replace(def_type, "").replace("{", "").strip()
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def params_to_list(params):
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if "tuple" in params.keys():
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tuple_item = nodes.list_item()
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if "name" in params.keys():
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tuple_item += nodes.paragraph(text=params["name"])
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tuple_item += nodes.paragraph(text="Tuple:")
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tuple_list = nodes.bullet_list()
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for io in params["tuple"]:
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tuple_list += params_to_list(io)
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tuple_item += tuple_list
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return tuple_item
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else:
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io_item = nodes.list_item()
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if "name" in params.keys():
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io_item += nodes.paragraph(text=params["name"])
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io_item += nodes.paragraph(text=f"Type: {params['type']}")
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io_item += nodes.paragraph(text=params["description"])
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return io_item
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# Return the results
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return def_name, def_type
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# Take path as single argument for now
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nextflow_path = sys.argv[1]
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with open(nextflow_path) as nextflow_file:
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def params_to_list(params):
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if "tuple" in params.keys():
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tuple_item = nodes.list_item()
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if "name" in params.keys():
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tuple_item += nodes.paragraph(text=params["name"])
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tuple_item += nodes.paragraph(text="Tuple:")
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tuple_list = nodes.bullet_list()
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for io in params["tuple"]:
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tuple_list += params_to_list(io)
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tuple_item += tuple_list
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return tuple_item
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else:
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io_item = nodes.list_item()
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if "name" in params.keys():
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io_item += nodes.paragraph(text=params["name"])
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io_item += nodes.paragraph(text=f"Type: {params['type']}")
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io_item += nodes.paragraph(text=params["description"])
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return io_item
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# Split by lines
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nextflow_lines = nextflow_file.readlines()
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# Take path as single argument for now
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nextflow_path = sys.argv[1]
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with open(nextflow_path) as nextflow_file:
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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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# Split by lines
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nextflow_lines = nextflow_file.readlines()
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# Declare dictionaries to keep track of the docstrings
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docstring_positions = []
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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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# 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(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(DOC_STARTER):
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doc_start = i
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if not line_next.startswith(DOC_STARTER):
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doc_end = i
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# Declare dictionaries to keep track of the docstrings
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docstring_positions = []
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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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# 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(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(DOC_STARTER):
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doc_start = i
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if not line_next.startswith(DOC_STARTER):
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doc_end = i
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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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# 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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# 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 = 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(DOC_STARTER, "")
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docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
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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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# Create any array to return from the plugin
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return_nodes = []
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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 = 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(DOC_STARTER, "")
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docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
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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 += params_to_list(io)
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io_section += io_list
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proc_section += io_section
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block_section += proc_section
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# Create any array to return from the plugin
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return_nodes = []
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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 += params_to_list(io)
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io_section += io_list
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proc_section += io_section
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block_section += proc_section
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print(return_nodes)
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return_nodes.append(block_section)
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print(return_nodes)
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