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Add org processor to generate compressed jsonl from org-mode files

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The corpus embeddings are generated from this compressed JSONL
using the specified transformer ML model
This commit is contained in:
Debanjum Singh Solanky 2021-08-15 22:49:09 -07:00
parent b74cb9a104
commit 354c541b62
3 changed files with 454 additions and 0 deletions
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0
processor/org-mode/__init__.py Normal file
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processor/org-mode/org-to-jsonl.py Normal file
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#!/usr/bin/env python3
# Import Modules
import orgnode
import json
import argparse
import pathlib
import glob
import gzip
# Define Functions
def dump_jsonl(jsonl_data, output_path, verbose=0):
"Write List of JSON objects to JSON line file"
with open(output_path, 'w', encoding='utf-8') as f:
f.write(jsonl_data)
if verbose > 0:
print(f'Wrote {len(jsonl_data)} records to jsonl at {output_path}')
def compress_jsonl_data(jsonl_data, output_path, verbose=0):
with gzip.open(f'{output_path}.gz', 'wt') as gzip_file:
gzip_file.write(jsonl_data)
if verbose > 0:
print(f'Wrote {len(jsonl_data)} records to gzip compressed jsonl at {output_path}.gz')
def load_jsonl(input_path, verbose=0):
"Read List of JSON objects from JSON line file"
data = []
with open(input_path, 'r', encoding='utf-8') as f:
for line in f:
data.append(json.loads(line.rstrip('\n|\r')))
if verbose > 0:
print(f'Loaded {len(data)} records from {input_path}')
return data
def get_org_files(org_directory, org_files=None, org_file_filter="*.org"):
"Get Org files to process"
expanded_org_directory = org_directory.expanduser()
filtered_org_files = {org_file
for org_file
in expanded_org_directory.glob(org_file_filter)
if not org_file.name.startswith('.')}
# Filter to User specified Org files when set by User
if org_files:
filtered_org_files = {str(org_file)
for org_file in filtered_org_files
if str(org_file.relative_to(expanded_org_directory)) in set(org_files)}
return filtered_org_files
def extract_org_entries(org_files):
"Extract entries from specified Org files"
entries = []
for org_file in org_files:
entries.extend(
orgnode.makelist(
str(org_file)))
return entries
def convert_org_entries_to_jsonl(entries, jsonl_file, verbose=0):
"Convert each org entries to json and write to jsonl file"
jsonl = ''
for entry in entries:
entry_dict = dict()
entry_dict["Title"] = entry.Heading()
if verbose > 1:
print(f"Title: {entry.Heading()}")
if entry.Tags():
tags_str = " ".join([tag for tag in entry.Tags()])
entry_dict["Tags"] = tags_str
if verbose > 1:
print(f"Tags: {tags_str}")
if entry.Body():
entry_dict["Body"] = entry.Body()
if verbose > 2:
print(f"Body: {entry.Body()}")
if entry_dict:
# Convert Dictionary to JSON and Append to JSONL string
jsonl += f'{json.dumps(entry_dict, ensure_ascii=False)}\n'
return jsonl
if __name__ == '__main__':
# Setup argument parser
parser = argparse.ArgumentParser(description="Map Org-Mode notes into JSONL format")
parser.add_argument('--jsonl-file', type=pathlib.Path, required=True, help="Output file for JSONL formatted notes")
parser.add_argument('--org-directory', default=pathlib.Path("./"), type=pathlib.Path, help="Input directory from which to retrieve Org-Mode files to convert. Default: Current directory.")
parser.add_argument('--org-files', '-f', nargs='+', help="List of org mode files to process. Requires file path relative to org_directory")
parser.add_argument('--org-file-filter', type=str, default="*.org", help="Regex filter org files in org_directory to process. Default: All org files in org_directory")
parser.add_argument('--compress', action='store_true', default=False, help="Compress output to gunzipped jsonl file")
parser.add_argument('--verbose', '-v', action='count', help="Show verbose conversion logs")
args = parser.parse_args()
# Get Org Files to Process
org_files = get_org_files(args.org_directory, args.org_files, args.org_file_filter)
# Extract Entries from specified Org files
entries = extract_org_entries(org_files)
# Process Each Entry from All Notes Files
jsonl_data = convert_org_entries_to_jsonl(entries, str(args.jsonl_file), verbose=args.verbose)
# Compress JSONL formatted Data
if args.compress:
compress_jsonl_data(jsonl_data, str(args.jsonl_file.expanduser()), verbose=args.verbose)
else:
dump_jsonl(jsonl_data, str(args.jsonl_file.expanduser()), verbose=args.verbose)

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processor/org-mode/orgnode.py Normal file
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# Copyright (c) 2010 Charles Cave
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use, copy,
# modify, merge, publish, distribute, sublicense, and/or sell copies
# of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# Program written by Charles Cave (charlesweb@optusnet.com.au)
# February - March 2009
# Version 2 - June 2009
# Added support for all tags, TODO priority and checking existence of a tag
# More information at
# http://members.optusnet.com.au/~charles57/GTD
"""
The Orgnode module consists of the Orgnode class for representing a
headline and associated text from an org-mode file, and routines for
constructing data structures of these classes.
"""
import re, sys
import datetime
def makelist(filename):
"""
Read an org-mode file and return a list of Orgnode objects
created from this file.
"""
ctr = 0
try:
f = open(filename, 'r')
except IOError:
print(f"Unable to open file {filename}")
print("Program terminating.")
sys.exit(1)
todos = { "TODO": "", "WAITING": "", "ACTIVE": "",
"DONE": "", "CANCELLED": "", "FAILED": ""} # populated from #+SEQ_TODO line
level = 0
heading = ""
bodytext = ""
tag1 = "" # The first tag enclosed in ::
alltags = [] # list of all tags in headline
sched_date = ''
deadline_date = ''
nodelist = []
propdict = dict()
in_properties_drawer = False
for line in f:
ctr += 1
hdng = re.search('^(\*+)\s(.*?)\s*$', line)
if hdng:
if heading: # we are processing a heading line
thisNode = Orgnode(level, heading, bodytext, tag1, alltags)
if sched_date:
thisNode.setScheduled(sched_date)
sched_date = ""
if deadline_date:
thisNode.setDeadline(deadline_date)
deadline_date = ''
thisNode.setProperties(propdict)
nodelist.append( thisNode )
propdict = dict()
level = hdng.group(1)
heading = hdng.group(2)
bodytext = ""
tag1 = ""
alltags = [] # list of all tags in headline
tagsrch = re.search('(.*?)\s*:([a-zA-Z0-9].*?):([a-zA-Z0-9].*?):$',heading)
if tagsrch:
heading = tagsrch.group(1)
tag1 = tagsrch.group(2)
alltags.append(tag1)
tag2 = tagsrch.group(3)
if tag2:
for t in tag2.split(':'):
if t != '': alltags.append(t)
else: # we are processing a non-heading line
if line[:10] == '#+SEQ_TODO':
kwlist = re.findall('([A-Z]+)\(', line)
for kw in kwlist: todos[kw] = ""
# Ignore Properties Drawers Completely
if re.search(':PROPERTIES:', line):
in_properties_drawer=True
continue
if in_properties_drawer and re.search(':END:', line):
in_properties_drawer=False
continue
# Ignore Clocking Lines
if re.search('CLOCK: \[[0-9]{4}-[0-9]{2}-[0-9]{2}', line):
continue
if not in_properties_drawer and line[:1] != '#':
bodytext = bodytext + line
prop_srch = re.search('^\s*:(.*?):\s*(.*?)\s*$', line)
if prop_srch:
propdict[prop_srch.group(1)] = prop_srch.group(2)
continue
sd_re = re.search('SCHEDULED:\s+<([0-9]+)\-([0-9]+)\-([0-9]+)', line)
if sd_re:
sched_date = datetime.date(int(sd_re.group(1)),
int(sd_re.group(2)),
int(sd_re.group(3)) )
dd_re = re.search('DEADLINE:\s*<(\d+)\-(\d+)\-(\d+)', line)
if dd_re:
deadline_date = datetime.date(int(dd_re.group(1)),
int(dd_re.group(2)),
int(dd_re.group(3)) )
# write out last node
thisNode = Orgnode(level, heading, bodytext, tag1, alltags)
thisNode.setProperties(propdict)
if sched_date:
thisNode.setScheduled(sched_date)
if deadline_date:
thisNode.setDeadline(deadline_date)
nodelist.append( thisNode )
# using the list of TODO keywords found in the file
# process the headings searching for TODO keywords
for n in nodelist:
h = n.Heading()
todoSrch = re.search('([A-Z]+)\s(.*?)$', h)
if todoSrch:
if todoSrch.group(1) in todos:
n.setHeading( todoSrch.group(2) )
n.setTodo ( todoSrch.group(1) )
prtysrch = re.search('^\[\#(A|B|C)\] (.*?)$', n.Heading())
if prtysrch:
n.setPriority(prtysrch.group(1))
n.setHeading(prtysrch.group(2))
return nodelist
######################
class Orgnode(object):
"""
Orgnode class represents a headline, tags and text associated
with the headline.
"""
def __init__(self, level, headline, body, tag, alltags):
"""
Create an Orgnode object given the parameters of level (as the
raw asterisks), headline text (including the TODO tag), and
first tag. The makelist routine postprocesses the list to
identify TODO tags and updates headline and todo fields.
"""
self.level = len(level)
self.headline = headline
self.body = body
self.tag = tag # The first tag in the list
self.tags = dict() # All tags in the headline
self.todo = ""
self.prty = "" # empty of A, B or C
self.scheduled = "" # Scheduled date
self.deadline = "" # Deadline date
self.properties = dict()
for t in alltags:
self.tags[t] = ''
# Look for priority in headline and transfer to prty field
def Heading(self):
"""
Return the Heading text of the node without the TODO tag
"""
return self.headline
def setHeading(self, newhdng):
"""
Change the heading to the supplied string
"""
self.headline = newhdng
def Body(self):
"""
Returns all lines of text of the body of this node except the
Property Drawer
"""
return self.body
def Level(self):
"""
Returns an integer corresponding to the level of the node.
Top level (one asterisk) has a level of 1.
"""
return self.level
def Priority(self):
"""
Returns the priority of this headline: 'A', 'B', 'C' or empty
string if priority has not been set.
"""
return self.prty
def setPriority(self, newprty):
"""
Change the value of the priority of this headline.
Values values are '', 'A', 'B', 'C'
"""
self.prty = newprty
def Tag(self):
"""
Returns the value of the first tag.
For example, :HOME:COMPUTER: would return HOME
"""
return self.tag
def Tags(self):
"""
Returns a list of all tags
For example, :HOME:COMPUTER: would return ['HOME', 'COMPUTER']
"""
return self.tags.keys()
def hasTag(self, srch):
"""
Returns True if the supplied tag is present in this headline
For example, hasTag('COMPUTER') on headling containing
:HOME:COMPUTER: would return True.
"""
return srch in self.tags
def setTag(self, newtag):
"""
Change the value of the first tag to the supplied string
"""
self.tag = newtag
def setTags(self, taglist):
"""
Store all the tags found in the headline. The first tag will
also be stored as if the setTag method was called.
"""
for t in taglist:
self.tags[t] = ''
def Todo(self):
"""
Return the value of the TODO tag
"""
return self.todo
def setTodo(self, value):
"""
Set the value of the TODO tag to the supplied string
"""
self.todo = value
def setProperties(self, dictval):
"""
Sets all properties using the supplied dictionary of
name/value pairs
"""
self.properties = dictval
def Property(self, keyval):
"""
Returns the value of the requested property or null if the
property does not exist.
"""
return self.properties.get(keyval, "")
def setScheduled(self, dateval):
"""
Set the scheduled date using the supplied date object
"""
self.scheduled = dateval
def Scheduled(self):
"""
Return the scheduled date object or null if nonexistent
"""
return self.scheduled
def setDeadline(self, dateval):
"""
Set the deadline (due) date using the supplied date object
"""
self.deadline = dateval
def Deadline(self):
"""
Return the deadline date object or null if nonexistent
"""
return self.deadline
def __repr__(self):
"""
Print the level, heading text and tag of a node and the body
text as used to construct the node.
"""
# This method is not completed yet.
n = ''
for i in range(0, self.level):
n = n + '*'
n = n + ' ' + self.todo + ' '
if self.prty:
n = n + '[#' + self.prty + '] '
n = n + self.headline
n = "%-60s " % n # hack - tags will start in column 62
closecolon = ''
for t in self.tags.keys():
n = n + ':' + t
closecolon = ':'
n = n + closecolon
# Need to output Scheduled Date, Deadline Date, property tags The
# following will output the text used to construct the object
n = n + "\n" + self.body
return n