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Promote main script to RST run function

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Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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Thomas A. Christensen II 2022-01-05 16:43:44 -06:00
parent c09f664328
commit 5124acddc7
1 changed files with 66 additions and 63 deletions
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129
nfdocs-parser.py
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@ -1,10 +1,12 @@
#!/usr/bin/env python #!/usr/bin/env python
import sys
import yaml import yaml
from docutils import nodes from docutils import nodes
from docutils.parsers.rst import Directive from docutils.parsers.rst import Directive
from docutils.parsers.rst import directives
class NFDocs(Directive): class NFDocs(Directive):
# Class default overrides
required_arguments = 1
# Declare the docstring starting characters # Declare the docstring starting characters
DOC_STARTER = "/// " DOC_STARTER = "/// "
@ -37,7 +39,7 @@ class NFDocs(Directive):
tuple_item += nodes.paragraph(text="Tuple:") tuple_item += nodes.paragraph(text="Tuple:")
tuple_list = nodes.bullet_list() tuple_list = nodes.bullet_list()
for io in params["tuple"]: for io in params["tuple"]:
tuple_list += params_to_list(io) tuple_list += self.params_to_list(io)
tuple_item += tuple_list tuple_item += tuple_list
return tuple_item return tuple_item
else: else:
@ -48,75 +50,76 @@ class NFDocs(Directive):
io_item += nodes.paragraph(text=params["description"]) io_item += nodes.paragraph(text=params["description"])
return io_item return io_item
# Take path as single argument for now def run(self):
nextflow_path = sys.argv[1] # Take path as single argument for now
with open(nextflow_path) as nextflow_file: nextflow_path = self.arguments[0]
with open(nextflow_path) as nextflow_file:
# Split by lines # Split by lines
nextflow_lines = nextflow_file.readlines() nextflow_lines = nextflow_file.readlines()
# Declare some variables to keep track of where the docstrings begin and end # Declare some variables to keep track of where the docstrings begin and end
doc_start = 0 doc_start = 0
doc_end = 0 doc_end = 0
# Declare dictionaries to keep track of the docstrings # Declare dictionaries to keep track of the docstrings
docstring_positions = [] docstring_positions = []
# Calculate the start and end positions of each docstring # Calculate the start and end positions of each docstring
for i, line in enumerate(nextflow_lines): for i, line in enumerate(nextflow_lines):
# Check if this is a docstring # Check if this is a docstring
if line.startswith(DOC_STARTER): if line.startswith(self.DOC_STARTER):
# It is: check the next and previous lines to see if this is part of a block # It is: check the next and previous lines to see if this is part of a block
line_previous = nextflow_lines[i-1] line_previous = nextflow_lines[i-1]
line_next = nextflow_lines[i+1] line_next = nextflow_lines[i+1]
if not line_previous.startswith(DOC_STARTER): if not line_previous.startswith(self.DOC_STARTER):
doc_start = i doc_start = i
if not line_next.startswith(DOC_STARTER): if not line_next.startswith(self.DOC_STARTER):
doc_end = i doc_end = i
# Check if we've reached the end of a docstring block # Check if we've reached the end of a docstring block
if doc_end == i: if doc_end == i:
# Add this docstring position to the array # Add this docstring position to the array
docstring_positions.append(range(doc_start, doc_end+1)) docstring_positions.append(range(doc_start, doc_end+1))
# Create dictionaries for each of the block types # Create dictionaries for each of the block types
docstrings = { docstrings = {
"process": {}, "process": {},
"workflow": {}, "workflow": {},
"function": {} "function": {}
} }
# Parse out the docstrings and put them in the appropriate dictionary # Parse out the docstrings and put them in the appropriate dictionary
for pos in docstring_positions: for pos in docstring_positions:
proc_name, proc_type = definition_type(nextflow_lines[pos[-1]+1]) proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1])
doc_yaml = "" doc_yaml = ""
for i in pos: for i in pos:
doc_yaml = doc_yaml + nextflow_lines[i].replace(DOC_STARTER, "") doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "")
docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml) docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml)
# Create any array to return from the plugin # Create any array to return from the plugin
return_nodes = [] return_nodes = []
# Try to convert each definition to a node # Try to convert each definition to a node
for block_type, block_docs in docstrings.items(): for block_type, block_docs in docstrings.items():
block_section = nodes.section() block_section = nodes.section()
block_section += nodes.title(text=block_type) block_section += nodes.title(text=block_type)
for proc_name, proc_docs in block_docs.items(): for proc_name, proc_docs in block_docs.items():
proc_section = nodes.section() proc_section = nodes.section()
proc_section += nodes.title(text=proc_name) proc_section += nodes.title(text=proc_name)
proc_section += nodes.paragraph(text=proc_docs["summary"]) proc_section += nodes.paragraph(text=proc_docs["summary"])
io_methods = ["input", "output"] io_methods = ["input", "output"]
for met in io_methods: for met in io_methods:
if met in proc_docs.keys(): if met in proc_docs.keys():
io_section = nodes.section() io_section = nodes.section()
io_section += nodes.title(text=met) io_section += nodes.title(text=met)
io_list = nodes.bullet_list() io_list = nodes.bullet_list()
for io in proc_docs[met]: for io in proc_docs[met]:
io_list += params_to_list(io) io_list += self.params_to_list(io)
io_section += io_list io_section += io_list
proc_section += io_section proc_section += io_section
block_section += proc_section block_section += proc_section
return_nodes.append(block_section) return_nodes.append(block_section)
print(return_nodes) return return_nodes