org-rw/org_rw/org_rw.py

from __future__ import annotations
from typing import Dict, Optional, TextIO
from datetime import timedelta
import collections
import difflib
import logging
import os
import re
import sys
from datetime import date, datetime, timedelta
from enum import Enum
from typing import cast, Iterator, List, Literal, Optional, Tuple, TypedDict, Union

from .types import HeadlineDict

from . import dom


DEBUG_DIFF_CONTEXT = 10

DEFAULT_TODO_KEYWORDS = ["TODO"]
DEFAULT_DONE_KEYWORDS = ["DONE"]

BASE_ENVIRONMENT = {
    "org-footnote-section": "Footnotes",
    "org-todo-keywords": " ".join(DEFAULT_TODO_KEYWORDS)
    + " | "
    + " ".join(DEFAULT_DONE_KEYWORDS),
    "org-options-keywords": (
        "ARCHIVE:",
        "AUTHOR:",
        "BIND:",
        "CATEGORY:",
        "COLUMNS:",
        "CREATOR:",
        "DATE:",
        "DESCRIPTION:",
        "DRAWERS:",
        "EMAIL:",
        "EXCLUDE_TAGS:",
        "FILETAGS:",
        "INCLUDE:",
        "INDEX:",
        "KEYWORDS:",
        "LANGUAGE:",
        "MACRO:",
        "OPTIONS:",
        "PROPERTY:",
        "PRIORITIES:",
        "SELECT_TAGS:",
        "SEQ_TODO:",
        "SETUPFILE:",
        "STARTUP:",
        "TAGS:" "TITLE:",
        "TODO:",
        "TYP_TODO:",
        "SELECT_TAGS:",
        "EXCLUDE_TAGS:",
    ),
}

HEADLINE_TAGS_RE = re.compile(r"((:(\w|[0-9_@#%])+)+:)\s*$")
HEADLINE_RE = re.compile(r"^(?P<stars>\*+)(?P<spacing>\s+)(?P<line>.*?)$")
KEYWORDS_RE = re.compile(
    r"^(?P<indentation>\s*)#\+(?P<key>[^:\[]+)(\[(?P<options>[^\]]*)\])?:(?P<spacing>\s*)(?P<value>.*)$"
)
DRAWER_START_RE = re.compile(r"^(?P<indentation>\s*):([^:]+):(?P<end_indentation>\s*)$")
DRAWER_END_RE = re.compile(r"^(?P<indentation>\s*):END:(?P<end_indentation>\s*)$", re.I)
NODE_PROPERTIES_RE = re.compile(
    r"^(?P<indentation>\s*):(?P<key>[^ ()+:]+)(?P<plus>\+)?:(?P<spacing>\s*)(?P<value>.+)$"
)
RAW_LINE_RE = re.compile(r"^\s*([^\s#:*|]|$)")
BASE_TIME_STAMP_RE = r"(?P<year>\d{4})-(?P<month>\d{2})-(?P<day>\d{2})( ?(?P<dow>[^ ]+))?( (?P<start_hour>\d{1,2}):(?P<start_minute>\d{1,2})(-+(?P<end_hour>\d{1,2}):(?P<end_minute>\d{1,2}))?)?(?P<repetition> (?P<rep_mark>(\+|\+\+|\.\+|-|--))(?P<rep_value>\d+)(?P<rep_unit>[hdwmy]))?"
CLEAN_TIME_STAMP_RE = r"\d{4}-\d{2}-\d{2}( ?([^ ]+))?( (\d{1,2}):(\d{1,2})(-+(\d{1,2}):(\d{1,2}))?)?( (\+|\+\+|\.\+|-|--)\d+[hdwmy])?"

ACTIVE_TIME_STAMP_RE = re.compile(r"<{}>".format(BASE_TIME_STAMP_RE))
INACTIVE_TIME_STAMP_RE = re.compile(r"\[{}\]".format(BASE_TIME_STAMP_RE))
PLANNING_RE = re.compile(
    r"(?P<indentation>\s*)"
    + r"(SCHEDULED:\s*(?P<scheduled>[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]](--[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]])?)\s*"
    + r"|CLOSED:\s*(?P<closed>[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]](--[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]])?)\s*"
    + r"|DEADLINE:\s*(?P<deadline>[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]](--[<\[]"
    + CLEAN_TIME_STAMP_RE
    + r"[>\]])?)\s*"
    r")+\s*"
)
LIST_ITEM_RE = re.compile(
    r"(?P<indentation>\s*)((?P<bullet>[*\-+])|((?P<counter>\d|[a-zA-Z])(?P<counter_sep>[.)]))) ((?P<checkbox_indentation>\s*)\[(?P<checkbox_value>[ Xx])\])?((?P<tag_indentation>\s*)(?P<tag>.*?)::)?(?P<content>.*)"
)

IMPLICIT_LINK_RE = re.compile(r"(https?:[^<> ]*[a-zA-Z0-9])")

# Org-Babel
BEGIN_BLOCK_RE = re.compile(r"^\s*#\+BEGIN_(?P<subtype>[^ ]+)(?P<arguments>.*)$", re.I)
END_BLOCK_RE = re.compile(r"^\s*#\+END_(?P<subtype>[^ ]+)\s*$", re.I)
RESULTS_DRAWER_RE = re.compile(r"^\s*:results:\s*$", re.I)
CodeSnippet = collections.namedtuple(
    "CodeSnippet", ("name", "content", "result", "arguments")
)

# Groupings
NON_FINISHED_GROUPS = (
    type(None),
    dom.ListGroupNode,
    dom.ResultsDrawerNode,
    dom.PropertyDrawerNode,
)
FREE_GROUPS = (dom.CodeBlock,)


# States
class HeadlineState(TypedDict):
    # To be extended to handle keyboard shortcuts
    name: str


class OrgDocDeclaredStates(TypedDict):
    not_completed: List[HeadlineState]
    completed: List[HeadlineState]


class NonReproducibleDocument(Exception):
    """
    Exception thrown when a document would be saved as different contents
    from what it's loaded from.
    """

    pass


def get_tokens(value):
    if isinstance(value, Text):
        return value.contents
    if isinstance(value, RawLine):
        return [value.line]
    if isinstance(value, list):
        return value
    raise Exception("Unknown how to get tokens from: {}".format(value))


class RangeInRaw:
    def __init__(self, content, start_token, end_token):
        self._content = content
        self._start_id = id(start_token)
        self._end_id = id(end_token)

    def update_range(self, new_contents):
        contents = self._content
        if isinstance(self._content, Text):
            contents = self._content.contents

        # Find start token
        for start_idx, tok in enumerate(contents):
            if id(tok) == self._start_id:
                break
        else:
            raise Exception("Start token not found")

        # Find end token
        for offset, tok in enumerate(contents[start_idx:]):
            if id(tok) == self._end_id:
                break
        else:
            raise Exception("End token not found")

        # Remove old contents
        for i in range(1, offset):
            contents.pop(start_idx + 1)

        # Add new ones
        for i, element in enumerate(new_contents):
            contents.insert(start_idx + i + 1, element)


def unescape_block_lines(block: str) -> str:
    """
    Remove leading ',' from block_lines if they escape `*` characters.
    """
    i = 0
    lines = block.split("\n")
    while i < len(lines):
        line = lines[i]
        if line.lstrip(" ").startswith(",") and line.lstrip(" ,").startswith("*"):
            # Remove leading ','
            lead_pos = line.index(",")
            line = line[:lead_pos] + line[lead_pos + 1 :]
            lines[i] = line

        i += 1

    return "\n".join(lines)


def get_links_from_content(content):
    in_link = False
    in_description = False
    link_value: List[str] = []
    link_description: List[str] = []

    for i, tok in enumerate(get_tokens(content)):
        if isinstance(tok, LinkToken):
            if tok.tok_type == LinkTokenType.OPEN_LINK:
                in_link = True
                open_link_token = tok
            elif tok.tok_type == LinkTokenType.OPEN_DESCRIPTION:
                in_description = True
            elif tok.tok_type == LinkTokenType.CLOSE:
                rng = RangeInRaw(content, open_link_token, tok)
                yield Link(
                    "".join(link_value),
                    "".join(link_description) if in_description else None,
                    rng,
                )
                in_link = False
                in_description = False
                link_value = []
                link_description = []
        elif isinstance(tok, str) and in_link:
            if in_description:
                link_description.append(tok)
            else:
                link_value.append(tok)
        elif isinstance(tok, str):
            implicit_links = IMPLICIT_LINK_RE.findall(tok)
            for link in implicit_links:
                yield Link(cast(str, link), cast(str, link), None)


def text_to_dom(tokens, item):
    if tokens is None:
        return None

    in_link = False
    in_description = False
    link_value: List[str] = []
    link_description: List[str] = []

    contents = []

    for tok in tokens:
        if isinstance(tok, LinkToken):
            if tok.tok_type == LinkTokenType.OPEN_LINK:
                in_link = True
                open_link_token = tok
            elif tok.tok_type == LinkTokenType.OPEN_DESCRIPTION:
                in_description = True
            elif tok.tok_type == LinkTokenType.CLOSE:
                rng = RangeInRaw(item, open_link_token, tok)
                contents.append(
                    Link(
                        "".join(link_value),
                        "".join(link_description) if in_description else None,
                        rng,
                    )
                )
                in_link = False
                in_description = False
                link_value = []
                link_description = []
        elif isinstance(tok, str) and in_link:
            if in_description:
                link_description.append(tok)
            else:
                link_value.append(tok)
        else:
            contents.append(tok)

    return contents


def get_line(item):
    if isinstance(item, Text):
        return item.linenum
    elif isinstance(item, ListItem):
        return item.linenum
    elif isinstance(item, Property):
        return item.linenum
    elif isinstance(item, tuple):
        return item[0]
    else:
        raise Exception("Unknown item type: {}".format(item))


class Headline:
    def __init__(
        self,
        start_line,
        depth,
        orig,
        properties,
        keywords,
        priority_start,
        priority,
        title_start,
        title,
        state,
        tags_start,
        tags,
        contents,
        children,
        structural,
        delimiters,
        list_items,
        table_rows,
        parent,
        is_todo: bool,
        is_done: bool,
        spacing,
        scheduled: Optional[Time] = None,
        deadline: Optional[Time] = None,
        closed: Optional[Time] = None,
    ):
        self.start_line = start_line
        self.depth = depth
        self.orig = orig
        self.properties = properties
        self.keywords = keywords
        self.priority_start = priority_start
        self.priority = priority
        self.title_start = title_start
        self.title = parse_content_block([RawLine(linenum=start_line, line=title)])
        self.state = state
        self.tags_start = tags_start
        self.shallow_tags = tags
        self.contents = contents
        self.children = children
        self.structural = structural
        self.delimiters = delimiters
        self.list_items = list_items
        self.table_rows = table_rows
        self.parent = parent
        self.is_todo = is_todo
        self.is_done = is_done
        self.scheduled = scheduled
        self.deadline = deadline
        self.closed = closed
        self.spacing = spacing

        # Read planning line
        planning_line = self.get_element_in_line(start_line + 1)

        # Ignore if not found or is a structural line
        if planning_line is None or isinstance(planning_line, tuple):
            return

        if m := PLANNING_RE.match(planning_line.get_raw()):
            self._planning_indendation = m.group("indentation")
            self._planning_order = []

            keywords = ["SCHEDULED", "CLOSED", "DEADLINE"]
            plan = planning_line.get_raw().split("\n")[0]
            indexes = [(kw, plan.find(kw)) for kw in keywords]

            self._planning_order = [
                kw
                for (kw, idx) in sorted(
                    filter(lambda v: v[1] >= 0, indexes), key=lambda v: v[1]
                )
            ]

            if scheduled_m := m.group("scheduled"):
                self.scheduled = parse_time(scheduled_m)
            if closed_m := m.group("closed"):
                self.closed = parse_time(closed_m)
            if deadline_m := m.group("deadline"):
                self.deadline = parse_time(deadline_m)

            # Remove from contents
            self._remove_element_in_line(start_line + 1)

    @property
    def doc(self):
        par = self.parent
        while isinstance(par, Headline):
            par = par.parent
        return par

    def as_dom(self):
        everything = (
            self.keywords
            + self.contents
            + self.list_items
            + self.table_rows
            + self.properties
            + self.structural
            + self.delimiters
        )

        tree: List[dom.DomNode] = []
        current_node: Optional[dom.DomNode] = None
        indentation_tree: List[dom.ContainerDomNode] = []
        contents: Optional[str] = None

        for line in sorted(everything, key=get_line):
            if isinstance(current_node, dom.CodeBlock):
                if (
                    isinstance(line, DelimiterLine)
                    and line.delimiter_type == DelimiterLineType.END_BLOCK
                ):

                    start = current_node.header.linenum
                    end = line.linenum

                    lines = self.get_lines_between(start + 1, end)
                    contents = unescape_block_lines("\n".join(lines))
                    if contents.endswith("\n"):
                        # This is not ideal, but to avoid having to do this maybe
                        # the content parsing must be re-thinked
                        contents = contents[:-1]

                    current_node.set_lines(contents)
                    tree.append(current_node)
                    current_node = None
                else:
                    pass  # Ignore

            elif isinstance(line, Property):
                if type(current_node) in NON_FINISHED_GROUPS:
                    current_node = dom.PropertyDrawerNode()
                    tree.append(current_node)
                assert isinstance(current_node, dom.PropertyDrawerNode)
                current_node.append(dom.PropertyNode(line.key, line.value))

            elif isinstance(line, Text):
                tree_up = list(indentation_tree)
                while len(tree_up) > 0:
                    node: dom.DomNode = tree_up[-1]
                    if isinstance(node, dom.BlockNode) or isinstance(
                        node, dom.DrawerNode
                    ):
                        node.append(dom.Text(line))
                        current_node = node
                        contents = None
                        break
                    elif (not isinstance(node, dom.TableNode)) and (
                        type(node) not in NON_FINISHED_GROUPS
                    ):
                        raise NotImplementedError(
                            "Not implemented node type: {} (headline_id={}, line={}, doc={})".format(
                                node,
                                self.id,
                                line.linenum,
                                self.doc.path,
                            )
                        )
                    else:
                        tree_up.pop(-1)
                else:
                    current_node = None
                    contents = None
                    tree.append(dom.Text(text_to_dom(line.contents, line)))
                indentation_tree = tree_up

            elif isinstance(line, ListItem):
                if (
                    current_node is None
                    or isinstance(current_node, dom.TableNode)
                    or isinstance(current_node, dom.BlockNode)
                    or isinstance(current_node, dom.DrawerNode)
                ):
                    was_node = current_node
                    current_node = dom.ListGroupNode()
                    if was_node is None:
                        tree.append(current_node)
                    else:
                        was_node.append(current_node)
                    indentation_tree.append(current_node)
                if not isinstance(current_node, dom.ListGroupNode):
                    if not isinstance(current_node, dom.ListGroupNode):
                        raise Exception(
                            "Expected a {}, found: {} on line {} on {}".format(
                                dom.ListGroupNode,
                                current_node,
                                line.linenum,
                                self.doc.path,
                            )
                        )
                        # This can happen. Frequently inside a LogDrawer

                if len(indentation_tree) > 0 and (
                    (len(indentation_tree[-1].children) > 0)
                    and len(
                        [
                            c
                            for c in indentation_tree[-1].children
                            if isinstance(c, dom.ListItem)
                        ][-1].orig.indentation
                    )
                    < len(line.indentation)
                ):
                    sublist = dom.ListGroupNode()
                    current_node.append(sublist)
                    current_node = sublist
                    indentation_tree.append(current_node)

                while len(indentation_tree) > 0:
                    list_children = [
                        c
                        for c in indentation_tree[-1].children
                        if isinstance(c, dom.ListItem)
                    ]

                    if len(list_children) == 0:
                        break
                    if len(list_children[-1].orig.indentation) <= len(line.indentation):
                        # No more breaking out of lists, it's indentation
                        # is less than ours
                        break

                    rem = indentation_tree.pop(-1)
                    if len(indentation_tree) == 0:
                        indentation_tree.append(rem)
                        current_node = rem
                        break
                    else:
                        current_node = indentation_tree[-1]

                node = dom.ListItem(
                    text_to_dom(line.tag, line),
                    text_to_dom(line.content, line),
                    orig=line,
                )
                current_node.append(node)

            elif isinstance(line, TableRow):
                if current_node is None:
                    current_node = dom.TableNode()
                    tree.append(current_node)
                    # TODO: Allow indentation of this element inside others
                    indentation_tree = [current_node]
                elif not isinstance(current_node, dom.TableNode):
                    if isinstance(current_node, dom.ListGroupNode):
                        # As an item inside a list
                        list_node = current_node
                        current_node = dom.TableNode()
                        list_node.append(current_node)
                        indentation_tree.append(current_node)
                    else:
                        logging.debug(
                            "Expected a {}, found: {} on line {}".format(
                                dom.TableNode, current_node, line.linenum
                            )
                        )
                        # This can happen. Frequently inside a LogDrawer

                if (
                    len(line.cells) > 0
                    and len(line.cells[0]) > 0
                    and line.cells[0][0] == "-"
                ):
                    node = dom.TableSeparatorRow(orig=line)
                else:
                    node = dom.TableRow(line.cells, orig=line)
                current_node = cast(dom.ContainerDomNode, current_node)
                current_node.append(node)

            elif (
                isinstance(line, DelimiterLine)
                and line.delimiter_type == DelimiterLineType.BEGIN_BLOCK
            ):
                assert type(current_node) in NON_FINISHED_GROUPS
                current_node = dom.CodeBlock(
                    line, line.type_data.subtype, line.arguments
                )

            elif isinstance(line, Keyword):
                logging.warning("Keywords not implemented on `as_dom()`")

            # elif (
            #     isinstance(line, DelimiterLine)
            #     and line.delimiter_type == DelimiterLineType.END_BLOCK
            # ):
            #     assert isinstance(current_node, dom.BlockNode)
            #     current_node = None

            elif (
                isinstance(line, tuple)
                and len(line) == 2
                and isinstance(line[0], int)
                and isinstance(line[1], str)
            ):
                # Structural
                (linenum, content) = line
                if content.strip().upper() == ":PROPERTIES:":
                    assert current_node is None
                    current_node = dom.PropertyDrawerNode()
                    tree.append(current_node)
                    # TODO: Check if this can be nested
                    indentation_tree = [current_node]
                elif content.strip().upper() == ":LOGBOOK:":
                    assert current_node is None
                    current_node = dom.LogbookDrawerNode()
                    tree.append(current_node)
                    # TODO: Check if this can be nested
                    indentation_tree = [current_node]
                elif content.strip().upper() == ":END:":
                    if current_node is None and len(indentation_tree) == 0:
                        logging.error("Finished node (:END:) with no known starter")
                    else:
                        tree_up = list(indentation_tree)
                        while len(tree_up) > 0:
                            node = tree_up[-1]
                            if isinstance(node, dom.DrawerNode):
                                indentation_tree = tree_up
                                current_node = node
                                tree_up.pop(-1)
                                break
                            else:
                                tree_up.pop(-1)
                        else:
                            raise Exception(
                                "Unexpected node ({}) on headline (id={}), line {}".format(
                                    current_node, self.id, linenum
                                )
                            )
                        current_node = None
                elif content.strip().upper() == ":RESULTS:":
                    assert current_node is None
                    current_node = dom.ResultsDrawerNode()

                    # TODO: Allow indentation of these blocks inside others
                    indentation_tree = [current_node]
                    tree.append(current_node)
                else:
                    raise Exception("Unknown structural line: {}".format(line))
            else:
                raise Exception("Unknown node type: {}".format(line))

        return tree

    def get_lists(self):
        lists = []
        last_line = None

        for li in self.list_items:
            if last_line is None:
                lists.append([li])
            else:
                num_lines = li.linenum - (last_line + 1)
                lines_between = "".join(
                    [
                        "\n" + l
                        for l in self.get_lines_between(last_line + 1, li.linenum)
                    ]
                )

                # Only empty lines
                if (num_lines == lines_between.count("\n")) and (
                    len(lines_between.strip()) == 0
                ):
                    lists[-1].append(li)
                else:
                    lists.append([li])

            last_line = li.linenum + sum(c.count("\n") for c in li.content)
        return lists

    # @DEPRECATED: use `get_lists`
    def getLists(self):
        return self.get_lists()

    def get_tables(self):
        tables: List[List] = []  # TableRow[][]
        last_line = None

        for row in self.table_rows:
            if last_line == row.linenum - 1:
                tables[-1].append(row)
            else:
                tables.append([row])

            last_line = row.linenum
        return tables

    def get_planning_line(self):
        if self.scheduled is None and self.closed is None and self.deadline is None:
            return None

        contents = [self._planning_indendation]

        for el in self._planning_order:
            if el == "SCHEDULED" and self.scheduled is not None:
                contents.append("SCHEDULED: {} ".format(self.scheduled.to_raw()))

            elif el == "CLOSED" and self.closed is not None:
                contents.append("CLOSED: {} ".format(self.closed.to_raw()))

            elif el == "DEADLINE" and self.deadline is not None:
                contents.append("DEADLINE: {} ".format(self.deadline.to_raw()))

        # Consider elements added (not present on planning order)
        if ("SCHEDULED" not in self._planning_order) and (self.scheduled is not None):
            contents.append("SCHEDULED: {} ".format(self.scheduled.to_raw()))

        if ("CLOSED" not in self._planning_order) and (self.closed is not None):
            contents.append("CLOSED: {} ".format(self.closed.to_raw()))

        if ("DEADLINE" not in self._planning_order) and (self.deadline is not None):
            contents.append("DEADLINE: {} ".format(self.deadline.to_raw()))

        return "".join(contents).rstrip()

    @property
    def id(self):
        return self.get_property("ID")

    @id.setter
    def id(self, value):
        self.set_property("ID", value)

    @property
    def clock(self):
        times = []
        for chunk in self.contents:
            for line in chunk.get_raw().split("\n"):
                content = line.strip()
                if not content.startswith("CLOCK:"):
                    continue

                time_seg = content[len("CLOCK:") :].strip()

                parsed: Optional[Time] = None
                if "--" in time_seg:
                    # TODO: Consider duration
                    start, end = time_seg.split("=")[0].split("--")
                    as_time_range = parse_org_time_range(start, end)
                    parsed = as_time_range
                else:
                    parsed = OrgTime.parse(time_seg)

                if parsed is not None:
                    times.append(parsed)

        return times

    @property
    def tags(self):
        if isinstance(self.parent, OrgDoc):
            return list(self.shallow_tags)
        else:
            return list(self.shallow_tags) + self.parent.tags

    def add_tag(self, tag: str):
        self.shallow_tags.append(tag)

    def get_property(self, name: str, default=None):
        for prop in self.properties:
            if prop.key == name:
                return prop.value

        return default

    def set_property(self, name: str, value: str):
        for prop in self.properties:

            # A matching property is found, update it
            if prop.key == name:
                prop.value = value
                return

        # No matching property found, add it
        else:
            if len(self.properties) > 0:
                last_prop = self.properties[-1]
                last_line = last_prop.linenum
                last_match = last_prop.match
            else:
                self.structural.append(
                    (
                        -2,  # Linenum
                        ":PROPERTIES:",
                    )
                )
                self.structural.append(
                    (
                        0,  # Linenum
                        ":END:",
                    )
                )

                last_line = -1
                last_match = None
            self.properties.append(
                Property(
                    linenum=last_line,
                    match=last_match,
                    key=name,
                    value=value,
                    options=None,
                )
            )

    def get_links(self):
        for content in self.contents:
            yield from get_links_from_content(content)

        for lst in self.get_lists():
            for item in lst:
                if item.tag:
                    yield from get_links_from_content(item.tag)
                yield from get_links_from_content(item.content)

    def get_lines_between(self, start, end):
        for line in self.contents:
            if start <= line.linenum < end:
                yield "".join(line.get_raw())

    def get_contents(self, format):
        if format == "raw":
            yield from map(
                lambda x: token_list_to_raw(x.contents),
                sorted(self.contents, key=lambda x: x.linenum),
            )
        else:
            raise NotImplementedError()

    def get_element_in_line(self, linenum):
        for line in self.contents:
            if linenum == line.linenum:
                return line

        for s_lnum, struc in self.structural:
            if linenum == s_lnum:
                return ("structural", struc)

    def _remove_element_in_line(self, linenum):
        found = None
        for i, line in enumerate(self.contents):
            if linenum == line.linenum:
                found = i
                break

        assert found is not None
        el = self.contents[found]
        assert isinstance(el, Text)

        raw = el.get_raw()
        if "\n" not in raw:
            # Remove the element found
            self.contents.pop(found)
        else:
            # Remove the first line
            self.contents[found] = parse_content_block(
                [RawLine(self.contents[found].linenum + 1, raw.split("\n", 1)[1])]
            )

    def get_structural_end_after(self, linenum):
        for s_lnum, struc in self.structural:
            if s_lnum > linenum and struc.strip().upper() == ":END:":
                return (s_lnum, struc)

    def get_code_snippets(self):
        inside_code = False

        sections = []
        arguments = None

        for delimiter in self.delimiters:
            if (
                delimiter.delimiter_type == DelimiterLineType.BEGIN_BLOCK
                and delimiter.type_data.subtype.lower() == "src"
            ):
                line_start = delimiter.linenum
                inside_code = True
                arguments = delimiter.arguments
            elif (
                delimiter.delimiter_type == DelimiterLineType.END_BLOCK
                and delimiter.type_data.subtype.lower() == "src"
            ):
                inside_code = False
                start, end = line_start, delimiter.linenum

                lines = self.get_lines_between(start + 1, end)
                contents = unescape_block_lines("\n".join(lines))
                if contents.endswith("\n"):
                    # This is not ideal, but to avoid having to do this maybe
                    # the content parsing must be re-thinked
                    contents = contents[:-1]

                sections.append(
                    {
                        "line_first": start + 1,
                        "line_last": end - 1,
                        "content": contents,
                        "arguments": arguments,
                    }
                )
                arguments = None
                line_start = None

        for kword in self.keywords:
            if kword.key.upper() == "RESULTS":
                for snippet in sections:
                    if kword.linenum > snippet["line_last"]:
                        result_first = self.get_element_in_line(kword.linenum + 1)

                        if isinstance(result_first, Text):
                            result = "\n".join(result_first.contents)
                            snippet["result"] = result

                            if result.strip().startswith(": "):
                                # Split lines and remove ':'
                                lines = result.split("\n")
                                s_result = []
                                for line in lines:
                                    if ": " not in line:
                                        break
                                    s_result.append(line.lstrip(" ")[2:])
                                snippet["result"] = "\n".join(s_result)
                        elif (
                            isinstance(result_first, tuple)
                            and len(result_first) == 2
                            and result_first[0] == "structural"
                            and result_first[1].strip().upper() == ":RESULTS:"
                        ):

                            (end_line, _) = self.get_structural_end_after(
                                kword.linenum + 1
                            )
                            contents = "\n".join(
                                self.get_lines_between(kword.linenum + 1, end_line)
                            )
                            indentation = result_first[1].index(":")
                            dedented = "\n".join(
                                [line[indentation:] for line in contents.split("\n")]
                            )
                            if dedented.endswith("\n"):
                                dedented = dedented[:-1]

                            snippet["result"] = dedented

                        break

        results = []
        for section in sections:
            name = None
            content = section["content"]
            code_result = section.get("result", None)
            arguments = section.get("arguments", None)
            results.append(
                CodeSnippet(
                    name=name, content=content, result=code_result, arguments=arguments
                )
            )

        return results

    def create_headline_at_end(self) -> Headline:
        headline = Headline(
            start_line=1,
            depth=self.depth + 1,
            orig=None,
            properties=[],
            keywords=[],
            priority_start=None,
            priority=None,
            title_start=None,
            title="",
            state="",
            tags_start=None,
            tags=[],
            contents=[],
            children=[],
            structural=[],
            delimiters=[],
            list_items=[],
            table_rows=[],
            parent=self,
            is_todo=False,
            is_done=False,
            spacing=" ",
        )

        self.children.append(headline)
        return headline


RawLine = collections.namedtuple("RawLine", ("linenum", "line"))
Keyword = collections.namedtuple(
    "Keyword", ("linenum", "match", "key", "value", "options")
)
Property = collections.namedtuple(
    "Property", ("linenum", "match", "key", "value", "options")
)


class ListItem:
    def __init__(
        self,
        linenum,
        match,
        indentation,
        bullet,
        counter,
        counter_sep,
        checkbox_indentation,
        checkbox_value,
        tag_indentation,
        tag,
        content,
    ):
        self.linenum = linenum
        self.match = match
        self.indentation = indentation
        self.bullet = bullet
        self.counter = counter
        self.counter_sep = counter_sep
        self.checkbox_indentation = checkbox_indentation
        self.checkbox_value = checkbox_value
        self.tag_indentation = tag_indentation
        self.tag = tag
        self.content = content

    @property
    def text_start_pos(self):
        return len(self.indentation) + 1  # Indentation + bullet

    def append_line(self, line):
        self.content += parse_content_block("\n" + line).contents


TableRow = collections.namedtuple(
    "TableRow",
    (
        "linenum",
        "indentation",
        "suffix",
        "last_cell_closed",
        "cells",
    ),
)


# @TODO How are [YYYY-MM-DD HH:mm--HH:mm] and ([... HH:mm]--[... HH:mm]) differentiated ?
# @TODO Consider recurrence annotations
class Timestamp:
    def __init__(
        self,
        active: bool = True,
        year: Optional[int] = None,
        month: Optional[int] = None,
        day: Optional[int] = None,
        dow: Optional[str] = None,
        hour: Optional[int] = None,
        minute: Optional[int] = None,
        repetition: Optional[str] = None,
        datetime_: Optional[Union[date, datetime]] = None,
    ):
        """
        Initializes a Timestamp instance.

        Args:
            active (bool): Whether the timestamp is active.
            year (Optional[int]): The year of the timestamp.
            month (Optional[int]): The month of the timestamp.
            day (Optional[int]): The day of the timestamp.
            dow (Optional[str]): The day of the week, if any.
            hour (Optional[int]): The hour of the timestamp, if any.
            minute (Optional[int]): The minute of the timestamp, if any.
            repetition (Optional[str]): The repetition pattern, if any.
            datetime_ (Optional[Union[date, datetime]]): A date or datetime object.

        Raises:
            ValueError: If neither datetime_ nor the combination of year, month, and day are provided.
        """
        self.active = active

        if datetime_ is not None:
            self.from_datetime(datetime_)
        elif year is not None and month is not None and day is not None:
            self._year = year
            self._month = month
            self._day = day
            self.dow = dow
            self.hour = hour
            self.minute = minute
        else:
            raise ValueError(
                "Either datetime_ or year, month, and day must be provided."
            )
        self.repetition = repetition

    def to_datetime(self) -> datetime:
        """
        Converts the Timestamp to a datetime object.

        Returns:
            datetime: The corresponding datetime object.
        """
        if self.hour is not None:
            return datetime(
                self.year, self.month, self.day, self.hour, self.minute or 0
            )
        else:
            return datetime(self.year, self.month, self.day, 0, 0)

    def from_datetime(self, dt: Union[datetime, date]) -> None:
        """
        Updates the current Timestamp instance based on a datetime or date object.

        Args:
            dt (Union[datetime, date]): The datetime or date object to use for updating the instance.
        """
        if isinstance(dt, datetime):
            self._year = dt.year
            self._month = dt.month
            self._day = dt.day
            self.hour = dt.hour
            self.minute = dt.minute
        elif isinstance(dt, date):
            self._year = dt.year
            self._month = dt.month
            self._day = dt.day
            self.hour = None
            self.minute = None
        else:
            raise TypeError("Expected datetime or date object")

        self.dow = None  # Day of the week can be set to None

    def __add__(self, delta: timedelta) -> "Timestamp":
        """
        Adds a timedelta to the Timestamp.

        Args:
            delta (timedelta): The time difference to add.

        Returns:
            Timestamp: The resulting Timestamp instance.
        """
        as_dt = self.to_datetime()
        to_dt = as_dt + delta

        return Timestamp(
            self.active,
            year=to_dt.year,
            month=to_dt.month,
            day=to_dt.day,
            dow=None,
            hour=to_dt.hour if self.hour is not None or to_dt.hour != 0 else None,
            minute=(
                to_dt.minute if self.minute is not None or to_dt.minute != 0 else None
            ),
            repetition=self.repetition,
        )

    def __eq__(self, other: object) -> bool:
        """
        Checks if two Timestamp instances are equal.

        Args:
            other (object): The other object to compare with.

        Returns:
            bool: True if the instances are equal, False otherwise.
        """
        if not isinstance(other, Timestamp):
            return False
        return (
            self.active == other.active
            and self.year == other.year
            and self.month == other.month
            and self.day == other.day
            and self.dow == other.dow
            and self.hour == other.hour
            and self.minute == other.minute
            and self.repetition == other.repetition
        )

    def __lt__(self, other: object) -> bool:
        """
        Checks if the Timestamp is less than another Timestamp.

        Args:
            other (object): The other object to compare with.

        Returns:
            bool: True if this Timestamp is less than the other, False otherwise.
        """
        if not isinstance(other, Timestamp):
            return False
        return self.to_datetime() < other.to_datetime()

    def __gt__(self, other: object) -> bool:
        """
        Checks if the Timestamp is greater than another Timestamp.

        Args:
            other (object): The other object to compare with.

        Returns:
            bool: True if this Timestamp is greater than the other, False otherwise.
        """
        if not isinstance(other, Timestamp):
            return False
        return self.to_datetime() > other.to_datetime()

    def __repr__(self) -> str:
        """
        Returns a string representation of the Timestamp.

        Returns:
            str: The string representation of the Timestamp.
        """
        return timestamp_to_string(self)

    @property
    def year(self) -> int:
        """Returns the year of the timestamp."""
        return self._year

    @year.setter
    def year(self, value: int) -> None:
        """Sets the year of the timestamp and resets the day of the week."""
        self._year = value
        self.dow = None

    @property
    def month(self) -> int:
        """Returns the month of the timestamp."""
        return self._month

    @month.setter
    def month(self, value: int) -> None:
        """Sets the month of the timestamp and resets the day of the week."""
        self._month = value
        self.dow = None

    @property
    def day(self) -> int:
        """Returns the day of the timestamp."""
        return self._day

    @day.setter
    def day(self, value: int) -> None:
        """Sets the day of the timestamp and resets the day of the week."""
        self._day = value
        self.dow = None


class DelimiterLineType(Enum):
    BEGIN_BLOCK = 1
    END_BLOCK = 2


BlockDelimiterTypeData = collections.namedtuple("BlockDelimiterTypeData", ("subtype"))

DelimiterLine = collections.namedtuple(
    "DelimiterLine", ("linenum", "line", "delimiter_type", "type_data", "arguments")
)


class MarkerType(Enum):
    NO_MODE = 0b0
    BOLD_MODE = 0b1
    CODE_MODE = 0b10
    ITALIC_MODE = 0b100
    STRIKE_MODE = 0b1000
    UNDERLINED_MODE = 0b10000
    VERBATIM_MODE = 0b100000


MARKERS = {
    "*": MarkerType.BOLD_MODE,
    "~": MarkerType.CODE_MODE,
    "/": MarkerType.ITALIC_MODE,
    "+": MarkerType.STRIKE_MODE,
    "_": MarkerType.UNDERLINED_MODE,
    "=": MarkerType.VERBATIM_MODE,
}

ModeToMarker = {}

for tok, mode in MARKERS.items():
    ModeToMarker[mode] = tok

MarkerToken = collections.namedtuple("MarkerToken", ("closing", "tok_type"))
LinkToken = collections.namedtuple("LinkToken", ("tok_type"))


class LinkTokenType(Enum):
    OPEN_LINK = 3
    OPEN_DESCRIPTION = 5
    CLOSE = 4


BEGIN_PROPERTIES = "OPEN_PROPERTIES"
END_PROPERTIES = "CLOSE_PROPERTIES"


def token_from_type(tok_type):
    return ModeToMarker[tok_type]


class TimeRange:
    """Represents a range of time with a start and end time.

    Attributes:
        start_time (OrgTime): The start time of the range.
        end_time (OrgTime): The end time of the range.
    """

    def __init__(self, start_time: OrgTime, end_time: OrgTime) -> None:
        """Initializes a TimeRange with a start time and an end time.

        Args:
            start_time (OrgTime): The start time of the range.
            end_time (OrgTime): The end time of the range.

        Raises:
            AssertionError: If start_time or end_time is None.
        """
        if start_time is None or end_time is None:
            raise ValueError("start_time and end_time must not be None.")
        self.start_time = start_time
        self.end_time = end_time

    def to_raw(self) -> str:
        """Converts the TimeRange to its raw string representation.

        Returns:
            str: The raw string representation of the TimeRange.
        """
        return timerange_to_string(self)

    @property
    def duration(self) -> timedelta:
        """Calculates the duration of the TimeRange.

        Returns:
            timedelta: The duration between start_time and end_time.
        """
        delta = self.end - self.start
        return delta

    @property
    def start(self) -> datetime:
        """Gets the start time as a datetime object.

        Returns:
            datetime: The start time of the TimeRange.
        """
        return self.start_time.time.to_datetime()

    @property
    def end(self) -> datetime:
        """Gets the end time as a datetime object.

        Returns:
            datetime: The end time of the TimeRange.
        """
        return self.end_time.time.to_datetime()

    def activate(self) -> None:
        """
        Sets the active state for the times.
        """
        self.start_time.active = True
        self.end_time.active = True

    def deactivate(self) -> None:
        """
        Sets the inactive state for the times.
        """
        self.start_time.active = False
        self.end_time.active = False


class OrgTime:
    """Represents a point in time with optional end time and repetition.

    Attributes:
        time (Timestamp): The start time of the OrgTime instance.
        end_time (Optional[Timestamp]): The end time of the OrgTime instance, if any.
    """

    def __init__(self, ts: Timestamp, end_time: Optional[Timestamp] = None) -> None:
        """Initializes an OrgTime with a start time and an optional end time.

        Args:
            ts (Timestamp): The start time of the OrgTime instance.
            end_time (Optional[Timestamp], optional): The end time of the OrgTime instance. Defaults to None.

        Raises:
            ValueError: If ts is None.
        """
        if ts is None:
            raise ValueError("Timestamp (ts) must not be None.")
        self.time = ts
        self.end_time = end_time

    @property
    def repetition(self) -> Optional[str]:
        """Gets the repetition information from the start time.

        Returns:
            Optional[str]: The repetition information, or None if not present.
        """
        return self.time.repetition

    @property
    def duration(self) -> timedelta:
        """Calculates the duration between the start and end times.

        Returns:
            timedelta: The duration between the start and end times. If no end time is present, returns zero timedelta.
        """
        if self.end_time is None:
            return timedelta()  # No duration
        return self.end_time.to_datetime() - self.time.to_datetime()

    def to_raw(self) -> str:
        """Converts the OrgTime to its raw string representation.

        Returns:
            str: The raw string representation of the OrgTime.
        """
        return timestamp_to_string(self.time, self.end_time)

    def __repr__(self) -> str:
        """Provides a string representation of the OrgTime instance.

        Returns:
            str: The string representation of the OrgTime.
        """
        return f"OrgTime({self.to_raw()})"

    @classmethod
    def parse(cls, value: str) -> Optional["OrgTime"]:
        """Parses a string into an OrgTime object.

        Args:
            value (str): The string representation of the OrgTime.

        Returns:
            Optional[OrgTime]: The parsed OrgTime instance, or None if parsing fails.
        """
        if m := ACTIVE_TIME_STAMP_RE.match(value):
            active = True
        elif m := INACTIVE_TIME_STAMP_RE.match(value):
            active = False
        else:
            return None

        repetition = None
        if m.group("repetition"):
            repetition = m.group("repetition").strip()

        if m.group("end_hour"):
            return cls(
                Timestamp(
                    active,
                    int(m.group("year")),
                    int(m.group("month")),
                    int(m.group("day")),
                    m.group("dow"),
                    int(m.group("start_hour")),
                    int(m.group("start_minute")),
                    repetition=repetition,
                ),
                Timestamp(
                    active,
                    int(m.group("year")),
                    int(m.group("month")),
                    int(m.group("day")),
                    m.group("dow"),
                    int(m.group("end_hour")),
                    int(m.group("end_minute")),
                ),
            )

        return cls(
            Timestamp(
                active,
                int(m.group("year")),
                int(m.group("month")),
                int(m.group("day")),
                m.group("dow"),
                int(m.group("start_hour")) if m.group("start_hour") else None,
                int(m.group("start_minute")) if m.group("start_minute") else None,
                repetition=repetition,
            )
        )

    @property
    def active(self) -> bool:
        """
        Checks if the time is set as active.
        """
        return self.time.active

    @active.setter
    def active(self, value: bool) -> None:
        """
        Sets the active state for the timestamp.
        """
        self.time.active = value

    def activate(self) -> None:
        """
        Sets the active state for the timestamp.
        """
        self.active = True

    def deactivate(self) -> None:
        """
        Sets the inactive state for the timestamp.
        """
        self.active = False

    def from_datetime(self, dt: datetime) -> None:
        """
        Updates the timestamp to use the given datetime.

        Args:
            dt (datetime): The datetime to update the timestamp with.
        """
        self.time.from_datetime(dt)
        if self.end_time:
            self.end_time.from_datetime(dt)


def time_from_str(s: str) -> Optional[OrgTime]:
    return OrgTime.parse(s)


def timerange_to_string(tr: TimeRange):
    return tr.start_time.to_raw() + "--" + tr.end_time.to_raw()


def timestamp_to_string(ts: Timestamp, end_time: Optional[Timestamp] = None) -> str:
    date = "{year}-{month:02d}-{day:02d}".format(
        year=ts.year, month=ts.month, day=ts.day
    )
    if ts.dow:
        date = date + " " + ts.dow

    if ts.hour is not None:
        base = "{date} {hour:02}:{minute:02d}".format(
            date=date, hour=ts.hour, minute=ts.minute or 0
        )
    else:
        base = date

    if end_time is not None:
        assert end_time.hour is not None
        assert end_time.minute is not None
        base = "{base}-{hour:02}:{minute:02d}".format(
            base=base, hour=end_time.hour, minute=end_time.minute
        )

    if ts.repetition is not None:
        base = base + " " + ts.repetition

    if ts.active:
        return "<{}>".format(base)
    else:
        return "[{}]".format(base)


Time = Union[TimeRange, OrgTime]


def parse_time(value: str) -> Optional[Time]:
    if (value.count(">--<") == 1) or (value.count("]--[") == 1):
        # Time ranges with two different dates
        # @TODO properly consider "=> DURATION" section
        start, end = value.split("=")[0].split("--")
        as_time_range = parse_org_time_range(start, end)
        if as_time_range is None:
            return None

        if (as_time_range.start_time is not None) and (
            as_time_range.end_time is not None
        ):
            return as_time_range
        else:
            raise Exception("Unknown time range format: {}".format(value))
    elif as_time := OrgTime.parse(value):
        return as_time
    else:
        return None


def parse_org_time_range(start, end) -> Optional[TimeRange]:
    start_time = OrgTime.parse(start)
    end_time = OrgTime.parse(end)

    if start_time is None or end_time is None:
        return None
    return TimeRange(start_time, end_time)


def get_raw(doc):
    if isinstance(doc, str):
        return doc
    else:
        return doc.get_raw()


class Line:
    def __init__(self, linenum, contents):
        self.linenum = linenum
        self.contents = contents

    def get_raw(self):
        rawchunks = []
        for chunk in self.contents:
            if isinstance(chunk, str):
                rawchunks.append(chunk)
            else:
                rawchunks.append(chunk.get_raw())
        return "".join(rawchunks) + "\n"


class Link:
    def __init__(
        self, value: str, description: Optional[str], origin: Optional[RangeInRaw]
    ):
        self._value = value
        self._description = description
        self._origin = origin

    def get_raw(self):
        if self.description:
            return "[[{}][{}]]".format(self.value, self.description)
        else:
            return "[[{}]]".format(self.value)

    def _update_content(self):
        new_contents: List[Union[str, LinkToken]] = []
        new_contents.append(self._value)
        if self._description:
            new_contents.append(LinkToken(LinkTokenType.OPEN_DESCRIPTION))
            new_contents.append(self._description)
        if self._origin is not None:
            self._origin.update_range(new_contents)

    @property
    def value(self):
        return self._value

    @value.setter
    def value(self, new_value):
        self._value = new_value
        self._update_content()

    @property
    def description(self):
        return self._description

    @description.setter
    def description(self, new_description):
        self._description = new_description
        self._update_content()


class Text:
    def __init__(self, contents, line):
        self.contents = contents
        self.linenum = line

    def __repr__(self):
        return "{{Text line: {}; content: {} }}".format(self.linenum, self.contents)

    def get_text(self) -> str:
        return token_list_to_plaintext(self.contents)

    def get_raw(self):
        return token_list_to_raw(self.contents)


def token_list_to_plaintext(tok_list) -> str:
    contents = []
    in_link = False
    in_description = False
    link_description = []
    link_url = []
    for chunk in tok_list:
        if isinstance(chunk, str):
            if not in_link:
                contents.append(chunk)
            elif in_description:
                link_description.append(chunk)
            else:
                link_url.append(chunk)
        elif isinstance(chunk, LinkToken):
            if chunk.tok_type == LinkTokenType.OPEN_LINK:
                in_link = True
            elif chunk.tok_type == LinkTokenType.OPEN_DESCRIPTION:
                in_description = True
            else:
                assert chunk.tok_type == LinkTokenType.CLOSE
                if not in_description:
                    # This might happen when link doesn't have a separate description
                    link_description = link_url
                contents.append("".join(link_description))

                in_link = False
                in_description = False
                link_description = []
                link_url = []
        else:
            assert isinstance(chunk, MarkerToken)

    return "".join(contents)


def token_list_to_raw(tok_list):
    contents = []
    for chunk in tok_list:
        if isinstance(chunk, str):
            contents.append(chunk)
        elif isinstance(chunk, LinkToken):
            if chunk.tok_type == LinkTokenType.OPEN_LINK:
                contents.append("[[")
            elif chunk.tok_type == LinkTokenType.OPEN_DESCRIPTION:
                contents.append("][")
            else:
                assert chunk.tok_type == LinkTokenType.CLOSE
                contents.append("]]")
        else:
            assert isinstance(chunk, MarkerToken)
            contents.append(token_from_type(chunk.tok_type))
    return "".join(contents)


class Bold:
    Marker = "*"

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


class Code:
    Marker = "~"

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


class Italic:
    Marker = "/"

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


class Strike:
    Marker = "+"

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


class Underlined:
    Marker = "_"

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


class Verbatim:
    Marker = "="

    def __init__(self, contents, line):
        self.contents = contents

    def get_raw(self):
        raw = "".join(map(get_raw, self.contents))
        return f"{self.Marker}{raw}{self.Marker}"


def is_pre(char: Optional[str]) -> bool:
    if isinstance(char, str):
        return char in "\n\r\t -({'\""
    else:
        return True


def is_marker(char: str) -> bool:
    if isinstance(char, str):
        return char in "*=/+_~"
    else:
        return False


def is_border(char: str) -> bool:
    if isinstance(char, str):
        return char not in "\n\r\t "
    else:
        return False


def is_body(char: str) -> bool:
    if isinstance(char, str):
        return True
    else:
        return False


def is_post(char: str) -> bool:
    if isinstance(char, str):
        return char in "-.,;:!?')}[\""
    else:
        return False


TOKEN_TYPE_TEXT = 0
TOKEN_TYPE_OPEN_MARKER = 1
TOKEN_TYPE_CLOSE_MARKER = 2
TOKEN_TYPE_OPEN_LINK = 3
TOKEN_TYPE_CLOSE_LINK = 4
TOKEN_TYPE_OPEN_DESCRIPTION = 5

TokenItems = Union[Tuple[int, Union[None, str, MarkerToken]],]


def tokenize_contents(contents: str) -> List[TokenItems]:
    tokens: List[TokenItems] = []
    last_char = None

    text: List[str] = []
    closes = set()
    in_link = False
    in_link_description = False
    last_link_start = 0

    def cut_string():
        nonlocal text
        nonlocal tokens

        if len(text) > 0:
            tokens.append((TOKEN_TYPE_TEXT, "".join(text)))
            text = []

    cursor = enumerate(contents)
    for i, char in cursor:
        has_changed = False

        # Possible link opening
        if char == "[":
            if (
                len(contents) > i + 3
                # At least 3 characters more to open and close a link
                and contents[i + 1] == "["
                # TODO: Generalize this to a backtracking, don't just fix the test case...
                and contents[i + 2] != "["
            ):
                close = contents.find("]]", i)

                if close != -1:
                    # Link with no description
                    cut_string()

                    in_link = True
                    tokens.append((TOKEN_TYPE_OPEN_LINK, None))
                    assert "[" == (next(cursor)[1])
                    last_link_start = i
                    continue
                if close != -1 and contents[close + 1] == "[":
                    # Link with description?

                    close = contents.find("]", close + 1)
                    if close != -1 and contents[close + 1] == "]":
                        # No match here means this is not an Org link
                        cut_string()

                        in_link = True
                        tokens.append((TOKEN_TYPE_OPEN_LINK, None))
                        assert "[" == (next(cursor)[1])
                        last_link_start = i
                        continue

        # Possible link close or open of description
        if char == "]" and len(contents) > i + 1 and in_link:
            if contents[i + 1] == "]":
                cut_string()

                tokens.append((TOKEN_TYPE_CLOSE_LINK, None))
                assert "]" == (next(cursor)[1])
                in_link = False
                in_link_description = False
                continue

            elif contents[i + 1] == "[":
                cut_string()

                tokens.append((TOKEN_TYPE_OPEN_DESCRIPTION, None))
                assert "[" == (next(cursor)[1])
                continue

        if in_link and not in_link_description:
            # Link's pointer have no formatting
            pass

        elif (
            (i not in closes)
            and is_marker(char)
            and is_pre(last_char)
            and ((i + 1 < len(contents)) and is_border(contents[i + 1]))
        ):

            is_valid_mark = False
            # Check that is closed later
            text_in_line = True
            for j in range(i, len(contents) - 1):
                if contents[j] == "\n":
                    if not text_in_line:
                        break
                    text_in_line = False
                elif is_border(contents[j]) and contents[j + 1] == char:
                    is_valid_mark = True
                    closes.add(j + 1)
                    break
                else:
                    text_in_line |= is_body(contents[j])

            if is_valid_mark:
                cut_string()
                tokens.append((TOKEN_TYPE_OPEN_MARKER, char))
                has_changed = True
        elif i in closes:
            cut_string()
            tokens.append((TOKEN_TYPE_CLOSE_MARKER, char))
            has_changed = True

        if not has_changed:
            text.append(char)
        last_char = char

    if len(text) > 0:
        tokens.append((TOKEN_TYPE_TEXT, "".join(text)))

    return tokens


def parse_contents(raw_contents: List[RawLine]):
    if len(raw_contents) == 0:
        return []

    blocks = []
    current_block: List[RawLine] = []

    for line in raw_contents:
        if len(current_block) == 0:
            # Seed the first block
            current_line = line.linenum
            current_block.append(line)
        else:
            current_line = cast(int, current_line)
            if line.linenum == current_line + 1:
                # Continue with the current block
                current_line = line.linenum
                current_block.append(line)
            else:
                # Split the blocks
                blocks.append(current_block)
                current_line = line.linenum
                current_block = [line]

    # Check that the current block is not left behind
    if len(current_block) > 0:
        blocks.append(current_block)

    return [parse_content_block(block) for block in blocks]


def parse_content_block(raw_contents: Union[List[RawLine], str]) -> Text:
    contents_buff = []
    if isinstance(raw_contents, str):
        contents_buff.append(raw_contents)
    else:
        for line in raw_contents:
            contents_buff.append(line.line)

    contents_buff_text = "\n".join(contents_buff)
    tokens = tokenize_contents(contents_buff_text)
    if isinstance(raw_contents, str):
        current_line = None
    else:
        current_line = raw_contents[0].linenum

    contents: List[Union[str, MarkerToken, LinkToken]] = []
    # Use tokens to tag chunks of text with it's container type
    for tok_type, tok_val in tokens:
        if tok_type == TOKEN_TYPE_TEXT:
            assert isinstance(tok_val, str)
            contents.append(tok_val)
        elif tok_type == TOKEN_TYPE_OPEN_MARKER:
            assert isinstance(tok_val, str)
            contents.append(MarkerToken(False, MARKERS[tok_val]))
        elif tok_type == TOKEN_TYPE_CLOSE_MARKER:
            assert isinstance(tok_val, str)
            contents.append(MarkerToken(True, MARKERS[tok_val]))
        elif tok_type == TOKEN_TYPE_OPEN_LINK:
            contents.append(LinkToken(LinkTokenType.OPEN_LINK))
        elif tok_type == TOKEN_TYPE_OPEN_DESCRIPTION:
            contents.append(LinkToken(LinkTokenType.OPEN_DESCRIPTION))
        elif tok_type == TOKEN_TYPE_CLOSE_LINK:
            contents.append(LinkToken(LinkTokenType.CLOSE))

    return Text(contents, current_line)


def dump_contents(raw):
    if isinstance(raw, RawLine):
        return (raw.linenum, raw.line)

    elif isinstance(raw, ListItem):
        bullet = raw.bullet if raw.bullet else raw.counter + raw.counter_sep
        content_full = token_list_to_raw(raw.content)
        content_lines = content_full.split("\n")
        content = "\n".join(content_lines)
        checkbox = f"[{raw.checkbox_value}]" if raw.checkbox_value else ""
        tag = (
            f"{raw.tag_indentation}{token_list_to_raw(raw.tag or '')}::"
            if raw.tag or raw.tag_indentation
            else ""
        )
        return (
            raw.linenum,
            f"{raw.indentation}{bullet} {checkbox}{tag}{content}",
        )

    elif isinstance(raw, TableRow):
        closed = "|" if raw.last_cell_closed else ""
        return (
            raw.linenum,
            f"{' ' * raw.indentation}|{'|'.join(raw.cells)}{closed}{raw.suffix}",
        )

    return (raw.linenum, raw.get_raw())


def parse_headline(hl, doc, parent) -> Headline:
    stars = hl["orig"].group("stars")
    depth = len(stars)
    spacing = hl["orig"].group("spacing")

    # TODO: Parse line for priority, cookies and tags
    line = hl["orig"].group("line")
    hl_tags = HEADLINE_TAGS_RE.search(line)

    if hl_tags is None:
        tags = []
    else:
        tags = hl_tags.group(0)[1:-1].split(":")
        line = HEADLINE_TAGS_RE.sub("", line)

    hl_state = None
    title = line
    is_done = is_todo = False
    for state in doc.todo_keywords or []:
        if title.startswith(state["name"] + " "):
            hl_state = state
            title = title[len(state["name"] + " ") :]
            is_todo = True
            break
    else:
        for state in doc.done_keywords or []:
            if title.startswith(state["name"] + " "):
                hl_state = state
                title = title[len(state["name"] + " ") :]
                is_done = True
                break

    contents = parse_contents(hl["contents"])

    if not (isinstance(parent, OrgDoc) or depth > parent.depth):
        raise AssertionError(
            "Incorrectly parsed parent on `{}' > `{}'".format(parent.title, title)
        )

    headline = Headline(
        start_line=hl["linenum"],
        depth=depth,
        orig=hl["orig"],
        title=title,
        state=hl_state,
        contents=contents,
        children=None,
        keywords=hl["keywords"],
        properties=hl["properties"],
        structural=hl["structural"],
        delimiters=hl["delimiters"],
        list_items=hl["list_items"],
        table_rows=hl["table_rows"],
        title_start=None,
        priority=None,
        priority_start=None,
        tags_start=None,
        tags=tags,
        parent=parent,
        is_todo=is_todo,
        is_done=is_done,
        spacing=spacing,
    )

    headline.children = [
        parse_headline(child, doc, headline) for child in hl["children"]
    ]
    return headline


def dump_kw(kw):
    options = kw.match.group("options")
    if not options:
        options = ""

    return (
        kw.linenum,
        "{indentation}#+{key}{options}:{spacing}{value}".format(
            indentation=kw.match.group("indentation"),
            key=kw.key,
            options=kw.options,
            spacing=kw.match.group("spacing"),
            value=kw.value,
        ),
    )


def dump_property(prop: Property):
    plus = ""
    indentation = ""
    spacing = " "
    if prop.match is not None:
        plus = prop.match.group("plus")
        if plus is None:
            plus = ""
        indentation = prop.match.group("indentation")
        spacing = prop.match.group("spacing")

    if isinstance(prop.value, TimeRange):
        value = timerange_to_string(prop.value)
    elif isinstance(prop.value, OrgTime):
        value = prop.value.to_raw()
    else:
        value = prop.value

    return (
        prop.linenum,
        "{indentation}:{key}{plus}:{spacing}{value}".format(
            indentation=indentation,
            key=prop.key,
            plus=plus,
            spacing=spacing,
            value=value,
        ),
    )


def dump_structural(structural: Tuple):
    return (structural[0], structural[1])


def dump_delimiters(line: DelimiterLine):
    return (line.linenum, line.line)


def parse_todo_done_keywords(line: str) -> OrgDocDeclaredStates:
    clean_line = re.sub(r"\([^)]+\)", "", line)
    if "|" in clean_line:
        todo_kws, done_kws = clean_line.split("|", 1)
        has_split = True
    else:
        # Standard behavior in this case is: the last state is the one considered as DONE
        todo_kws = clean_line

    todo_keywords = re.sub(r"\s{2,}", " ", todo_kws.strip()).split()
    if has_split:
        done_keywords = re.sub(r"\s{2,}", " ", done_kws.strip()).split()
    else:
        done_keywods = [todo_keywords[-1]]
        todo_keywords = todo_keywords[:-1]

    return {
        "not_completed": [HeadlineState(name=keyword) for keyword in todo_keywords],
        "completed": [HeadlineState(name=keyword) for keyword in done_keywords],
    }


class OrgDoc:
    def __init__(
        self,
        headlines,
        keywords,
        contents,
        list_items,
        structural,
        properties,
        environment=BASE_ENVIRONMENT,
    ):
        self.todo_keywords = [HeadlineState(name=kw) for kw in DEFAULT_TODO_KEYWORDS]
        self.done_keywords = [HeadlineState(name=kw) for kw in DEFAULT_DONE_KEYWORDS]

        keywords_set_in_file = False
        for keyword in keywords:
            if keyword.key in ("TODO", "SEQ_TODO"):
                states = parse_todo_done_keywords(keyword.value)
                self.todo_keywords, self.done_keywords = (
                    states["not_completed"],
                    states["completed"],
                )
                keywords_set_in_file = True

        if not keywords_set_in_file and "org-todo-keywords" in environment:
            # Read keywords from environment
            states = parse_todo_done_keywords(environment["org-todo-keywords"])
            self.todo_keywords, self.done_keywords = (
                states["not_completed"],
                states["completed"],
            )

        self.keywords: List[Property] = keywords
        self.contents: List[RawLine] = contents
        self.list_items: List[ListItem] = list_items
        self.structural: List = structural
        self.properties: List = properties
        self._path = None
        self.headlines: List[Headline] = list(
            map(lambda hl: parse_headline(hl, self, self), headlines)
        )

    @property
    def id(self):
        """
        Created by org-roam v2.
        """
        for p in self.properties:
            if p.key == "ID":
                return p.value
        return None

    @property
    def path(self):
        return self._path

    ## Querying
    def get_links(self):
        for headline in self.headlines:
            yield from headline.get_links()

        for content in self.contents:
            yield from get_links_from_content(content)

    def get_keywords(self, name: str, default=None):
        for prop in self.keywords:
            if prop.key == name:
                return prop.value

        return default

    def get_property(self, name: str, default=None):
        for prop in self.properties:
            if prop.key == name:
                return prop.value

        return default

    def getProperties(self):
        return self.keywords

    def getTopHeadlines(self):
        return self.headlines

    def getAllHeadlines(self) -> Iterator[Headline]:
        todo = self.headlines[::-1]  # We go backwards, to pop/append and go depth-first
        while len(todo) != 0:
            hl = todo.pop()
            todo.extend(hl.children[::-1])

            yield hl

    def get_code_snippets(self):
        for headline in self.headlines:
            yield from headline.get_code_snippets()

    # Writing
    def dump_headline(self, headline, recursive=True):

        tags = ""
        if len(headline.shallow_tags) > 0:
            tags = ":" + ":".join(headline.shallow_tags) + ":"

        state = ""
        if headline.state:
            state = headline.state["name"] + " "

        raw_title = token_list_to_raw(headline.title.contents)
        tags_padding = ""
        if not (raw_title.endswith(" ") or raw_title.endswith("\t")) and tags:
            tags_padding = " "

        yield "*" * headline.depth + headline.spacing + state + raw_title + tags_padding + tags

        planning = headline.get_planning_line()
        if planning is not None:
            yield planning

        lines = []
        KW_T = 0
        CONTENT_T = 1
        PROPERTIES_T = 2
        STRUCTURAL_T = 3
        for keyword in headline.keywords:
            lines.append((KW_T, dump_kw(keyword)))

        for content in headline.contents:
            lines.append((CONTENT_T, dump_contents(content)))

        for li in headline.list_items:
            lines.append((CONTENT_T, dump_contents(li)))

        for row in headline.table_rows:
            lines.append((CONTENT_T, dump_contents(row)))

        for prop in headline.properties:
            lines.append((PROPERTIES_T, dump_property(prop)))

        for struct in headline.structural:
            lines.append((STRUCTURAL_T, dump_structural(struct)))

        for content in headline.delimiters:
            lines.append((STRUCTURAL_T, dump_delimiters(content)))

        lines = sorted(lines, key=lambda x: x[1][0])

        structured_lines = []
        last_type = None
        for i, line in enumerate(lines):
            ltype = line[0]
            content = line[1][1]

            content = content + "\n"
            last_type = ltype
            structured_lines.append(content)

        if last_type == PROPERTIES_T:
            # No structural closing

            indentation = 0
            if len(lines) > 0:
                last_line = lines[i - 1][1][1]
                indentation = last_line.index(":")
            structured_lines.append(" " * indentation + ":END:\n")
            logging.warning(
                "Added structural:{}: {}".format(
                    line[1][0], structured_lines[-1].strip()
                )
            )

        if len(structured_lines) > 0:
            content = "".join(structured_lines)

            # Remove the last line jump, which will be accounted for by the "yield operation"
            assert content.endswith("\n")
            content = content[:-1]
            yield content

        if recursive:
            for child in headline.children:
                yield from self.dump_headline(child, recursive=recursive)

    def dump(self):
        lines = []
        for prop in self.properties:
            lines.append(dump_property(prop))

        for struct in self.structural:
            lines.append(dump_structural(struct))

        for kw in self.keywords:
            lines.append(dump_kw(kw))

        for line in self.contents:
            lines.append(dump_contents(line))

        for li in self.list_items:
            lines.append(dump_contents(li))

        yield from map(lambda x: x[1], sorted(lines, key=lambda x: x[0]))

        for headline in self.headlines:
            yield from self.dump_headline(headline)


class OrgDocReader:
    def __init__(self, environment=BASE_ENVIRONMENT):
        self.headlines: List[HeadlineDict] = []
        self.keywords: List[Keyword] = []
        self.headline_hierarchy: List[Optional[HeadlineDict]] = []
        self.contents: List[RawLine] = []
        self.delimiters: List[DelimiterLine] = []
        self.list_items: List[ListItem] = []
        self.table_rows: List[TableRow] = []
        self.structural: List = []
        self.properties: List = []
        self.current_drawer: Optional[List] = None
        self.environment = environment

    def finalize(self) -> OrgDoc:
        return OrgDoc(
            self.headlines,
            self.keywords,
            self.contents,
            self.list_items,
            self.structural,
            self.properties,
            self.environment,
        )

    ## Construction
    def add_headline(self, linenum: int, match: re.Match):
        # Position reader on the proper headline
        stars = match.group("stars")
        depth = len(stars)

        headline: HeadlineDict = {
            "linenum": linenum,
            "orig": match,
            "title": match.group("line"),
            "contents": [],
            "children": [],
            "keywords": [],
            "properties": [],
            "logbook": [],
            "structural": [],
            "delimiters": [],
            "results": [],  # TODO: Move to each specific code block?
            "list_items": [],
            "table_rows": [],
        }

        while (depth - 1) > len(self.headline_hierarchy):
            # Introduce structural headlines
            self.headline_hierarchy.append(None)
        while depth <= len(self.headline_hierarchy):
            self.headline_hierarchy.pop()

        if depth == 1:
            self.headlines.append(headline)
        else:
            parent_idx = len(self.headline_hierarchy) - 1
            while self.headline_hierarchy[parent_idx] is None:
                parent_idx -= 1
            parent_headline = self.headline_hierarchy[parent_idx]
            assert parent_headline is not None
            parent_headline["children"].append(headline)
        self.headline_hierarchy.append(headline)

        if all([hl is not None for hl in self.headline_hierarchy]):
            if not (
                [
                    len(cast(HeadlineDict, hl)["orig"].group("stars"))
                    for hl in self.headline_hierarchy
                ]
                == list(range(1, len(self.headline_hierarchy) + 1))
            ):
                raise AssertionError("Error on Headline Hierarchy")
        else:
            # This might happen if headlines with more that 1 level deeper are found
            pass

        # We can safely assert this as all the `None`s are there to
        #  support the addition of a `HeadlineDict` at the correct
        #  depth but not more
        assert self.headline_hierarchy[-1] is not None

    def add_list_item_line(self, linenum: int, match: re.Match) -> ListItem:
        li = ListItem(
            linenum=linenum,
            match=match,
            indentation=match.group("indentation"),
            bullet=match.group("bullet"),
            counter=match.group("counter"),
            counter_sep=match.group("counter_sep"),
            checkbox_indentation=match.group("checkbox_indentation"),
            checkbox_value=match.group("checkbox_value"),
            tag_indentation=match.group("tag_indentation"),
            tag=(
                parse_content_block(
                    [RawLine(linenum=linenum, line=match.group("tag"))]
                ).contents
                if match.group("tag")
                else None
            ),
            content=parse_content_block(
                [RawLine(linenum=linenum, line=match.group("content"))]
            ).contents,
        )

        if len(self.headline_hierarchy) == 0:
            self.list_items.append(li)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["list_items"].append(li)
        return li

    def add_table_line(self, linenum: int, line: str):
        chunks = line.split("|")
        indentation = len(chunks[0])
        if chunks[-1].strip() == "":
            suffix = chunks[-1]
            cells = chunks[1:-1]
            last_cell_closed = True
        else:
            suffix = ""
            cells = chunks[1:]
            last_cell_closed = False

        row = TableRow(
            linenum,
            indentation,
            suffix,
            last_cell_closed,
            cells,
        )

        if len(self.headline_hierarchy) == 0:
            self.table_rows.append(row)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["table_rows"].append(row)

    def add_keyword_line(self, linenum: int, match: re.Match):
        options = match.group("options")
        kw = Keyword(
            linenum,
            match,
            match.group("key"),
            match.group("value"),
            options if options is not None else "",
        )
        if len(self.headline_hierarchy) == 0:
            self.keywords.append(kw)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["keywords"].append(kw)

    def add_raw_line(self, linenum: int, line: str):
        raw = RawLine(linenum, line)
        if len(self.headline_hierarchy) == 0:
            self.contents.append(raw)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["contents"].append(raw)

    def add_begin_block_line(self, linenum: int, match: re.Match):
        line = DelimiterLine(
            linenum,
            match.group(0),
            DelimiterLineType.BEGIN_BLOCK,
            BlockDelimiterTypeData(match.group("subtype")),
            match.group("arguments"),
        )
        if len(self.headline_hierarchy) == 0:
            self.delimiters.append(line)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["delimiters"].append(line)

    def add_end_block_line(self, linenum: int, match: re.Match):
        line = DelimiterLine(
            linenum,
            match.group(0),
            DelimiterLineType.END_BLOCK,
            BlockDelimiterTypeData(match.group("subtype")),
            None,
        )
        if len(self.headline_hierarchy) == 0:
            self.delimiters.append(line)
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["delimiters"].append(line)

    def add_property_drawer_line(self, linenum: int, line: str, match: re.Match):
        if len(self.headline_hierarchy) == 0:
            self.current_drawer = self.properties
            self.structural.append((linenum, line))
        else:
            assert self.headline_hierarchy[-1] is not None
            self.current_drawer = self.headline_hierarchy[-1]["properties"]
            self.headline_hierarchy[-1]["structural"].append((linenum, line))

    def add_results_drawer_line(self, linenum: int, line: str, match: re.Match):
        assert self.headline_hierarchy[-1] is not None
        self.current_drawer = self.headline_hierarchy[-1]["results"]
        self.headline_hierarchy[-1]["structural"].append((linenum, line))

    def add_logbook_drawer_line(self, linenum: int, line: str, match: re.Match):
        assert self.headline_hierarchy[-1] is not None
        self.current_drawer = self.headline_hierarchy[-1]["logbook"]
        self.headline_hierarchy[-1]["structural"].append((linenum, line))

    def add_drawer_end_line(self, linenum: int, line: str, match: re.Match):
        self.current_drawer = None
        if len(self.headline_hierarchy) == 0:
            self.structural.append((linenum, line))
        else:
            assert self.headline_hierarchy[-1] is not None
            self.headline_hierarchy[-1]["structural"].append((linenum, line))

    def add_node_properties_line(self, linenum: int, match: re.Match):
        key = match.group("key")
        value = match.group("value").strip()

        if as_time := parse_time(value):
            value = as_time

        if self.current_drawer is None:  # Throw a better error on this case
            raise Exception(
                "Found properties before :PROPERTIES: line. Error on Org file?"
            )

        self.current_drawer.append(Property(linenum, match, key, value, None))

    def read(self, s):
        lines = s.split("\n")
        line_count = len(lines)
        reader = enumerate(lines)
        in_drawer = False
        in_block = False
        list_item_indentation = None
        list_item = None

        def add_raw_line_with_possible_indentation(linenum, line):
            added = False
            nonlocal list_item
            nonlocal list_item_indentation
            if list_item:
                if (line[: list_item.text_start_pos].strip() == "") or (
                    len(line.strip()) == 0
                ):
                    list_item.append_line(line)
                    added = True
                else:
                    list_item = None
                    list_item_indentation = None

            if not added:
                self.add_raw_line(linenum, line)

        for lnum, line in reader:
            linenum = lnum + 1
            try:
                if in_block:
                    if m := END_BLOCK_RE.match(line):
                        self.add_end_block_line(linenum, m)
                        in_block = False
                        list_item_indentation = None
                        list_item = None
                    else:
                        add_raw_line_with_possible_indentation(linenum, line)

                elif m := HEADLINE_RE.match(line):
                    list_item_indentation = None
                    list_item = None
                    self.add_headline(linenum, m)
                elif m := LIST_ITEM_RE.match(line):
                    list_item = self.add_list_item_line(linenum, m)
                    list_item_indentation = m.group("indentation")
                elif m := RAW_LINE_RE.match(line):
                    add_raw_line_with_possible_indentation(linenum, line)
                # Org-babel
                elif m := BEGIN_BLOCK_RE.match(line):
                    self.add_begin_block_line(linenum, m)
                    in_block = True
                    list_item_indentation = None
                    list_item = None
                elif m := END_BLOCK_RE.match(line):
                    self.add_end_block_line(linenum, m)
                    in_block = False
                    list_item_indentation = None
                    list_item = None
                # Generic properties
                elif m := KEYWORDS_RE.match(line):
                    self.add_keyword_line(linenum, m)
                elif m := DRAWER_END_RE.match(line):
                    self.add_drawer_end_line(linenum, line, m)
                    in_drawer = False
                    list_item_indentation = None
                    list_item = None
                elif (not in_drawer) and (m := DRAWER_START_RE.match(line)):
                    self.add_property_drawer_line(linenum, line, m)
                    in_drawer = True
                    list_item_indentation = None
                    list_item = None
                elif (not in_drawer) and (m := RESULTS_DRAWER_RE.match(line)):
                    self.add_results_drawer_line(linenum, line, m)
                    in_drawer = True
                    list_item_indentation = None
                    list_item = None
                elif m := NODE_PROPERTIES_RE.match(line):
                    self.add_node_properties_line(linenum, m)
                elif line.strip().startswith("|"):
                    self.add_table_line(linenum, line)
                    list_item_indentation = None
                    list_item = None
                # Not captured
                else:
                    add_raw_line_with_possible_indentation(linenum, line)
            except:
                logging.error("Error line {}: {}".format(linenum + 1, line))
                raise


def loads(
    s: str, environment: Optional[Dict] = BASE_ENVIRONMENT, extra_cautious: bool = True
) -> OrgDoc:
    """
    Load an Org-mode document from a string.

    Args:
        s (str): The string representation of the Org-mode document.
        environment (Optional[dict]): The environment for parsing. Defaults to
            `BASE_ENVIRONMENT`.
        extra_cautious (bool): If True, perform an extra check to ensure that
            the document can be re-serialized to the original string. Defaults to True.

    Returns:
        OrgDoc: The loaded Org-mode document.

    Raises:
        NonReproducibleDocument: If `extra_cautious` is True and there is a
            difference between the original string and the re-serialized document.
    """
    reader = OrgDocReader(environment)
    reader.read(s)
    doc = reader.finalize()
    if extra_cautious:  # Check that all options can be properly re-serialized
        after_dump = dumps(doc)
        if after_dump != s:
            diff = list(
                difflib.Differ().compare(
                    s.splitlines(keepends=True), after_dump.splitlines(keepends=True)
                )
            )

            context_start = None
            context_last_line = None
            for i, line in enumerate(diff):
                if not line.startswith(" "):
                    if context_start is None:
                        context_start = i
                    context_last_line = i
                elif context_start:
                    assert context_last_line is not None
                    if i > (context_last_line + DEBUG_DIFF_CONTEXT):
                        start = max(0, context_start - DEBUG_DIFF_CONTEXT)
                        end = min(len(diff), context_last_line + DEBUG_DIFF_CONTEXT)
                        print(
                            "## Lines {} to {}".format(start + 1, end + 1),
                            file=sys.stderr,
                        )
                        sys.stderr.writelines(diff[start:end])
                        context_start = None
                        context_last_line = None
            # print("---\n" + after_dump + "\n---")

            raise NonReproducibleDocument(
                "Difference found between existing version and dumped"
            )
    return doc


def load(
    f: TextIO,
    environment: Optional[dict] = BASE_ENVIRONMENT,
    extra_cautious: bool = False,
) -> OrgDoc:
    """
    Load an Org-mode document from a file object.

    Args:
        f (TextIO): The file object containing the Org-mode document.
        environment (Optional[dict]): The environment for parsing. Defaults to
            `BASE_ENVIRONMENT`.
        extra_cautious (bool): If True, perform an extra check to ensure that
            the document can be re-serialized to the original string. Defaults to False.

    Returns:
        OrgDoc: The loaded Org-mode document.
    """
    doc = loads(f.read(), environment, extra_cautious)
    doc._path = os.path.abspath(f.name)
    return doc


def dumps(doc: OrgDoc) -> str:
    """
    Serialize an OrgDoc object to a string.

    Args:
        doc (OrgDoc): The OrgDoc object to serialize.

    Returns:
        str: The serialized string representation of the OrgDoc object.
    """
    dump = list(doc.dump())
    result = "\n".join(dump)
    return result


def dump(doc: OrgDoc, fp: TextIO) -> None:
    """
    Serialize an OrgDoc object to a file.

    Args:
        doc (OrgDoc): The OrgDoc object to serialize.
        fp (TextIO): The file-like object to write the serialized data to.

    Returns:
        None
    """
    it = doc.dump()

    # Write first line separately
    line = next(it)
    fp.write(line)

    # Write following ones preceded by line jump
    for line in it:
        fp.write("\n" + line)