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get rid of porg dependency, use orgparse directly

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Dima Gerasimov 2020-11-06 04:04:05 +00:00 • committed by karlicoss
parent 62e1bdc39a
commit a6e5908e6d
8 changed files with 101 additions and 54 deletions
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21
my/body/blood.py
View file

@ -7,11 +7,11 @@ from typing import Iterable, NamedTuple, Optional
from ..core.common import listify
from ..core.error import Res, echain
from ..core.orgmode import parse_org_datetime
from ..core.orgmode import parse_org_datetime, one_table
import pandas as pd # type: ignore
import porg
import orgparse
from my.config import blood as config
@ -47,14 +47,13 @@ def try_float(s: str) -> Optional[float]:
return None
return float(x)
def glucose_ketones_data() -> Iterable[Result]:
o = porg.Org.from_file(str(config.blood_log))
tbl = o.xpath('//table')
o = orgparse.load(config.blood_log)
tbl = one_table(o)
# todo some sort of sql-like interface for org tables might be ideal?
for l in tbl.lines:
kets = l['ket'].strip()
glus = l['glu'].strip()
for l in tbl.as_dicts:
kets = l['ket']
glus = l['glu']
extra = l['notes']
dt = parse_org_datetime(l['datetime'])
try:
@ -75,9 +74,9 @@ def glucose_ketones_data() -> Iterable[Result]:
def blood_tests_data() -> Iterable[Result]:
o = porg.Org.from_file(str(config.blood_tests_log))
tbl = o.xpath('//table')
for d in tbl.lines:
o = orgparse.load(config.blood_tests_log)
tbl = one_table(o)
for d in tbl.as_dicts:
try:
dt = parse_org_datetime(d['datetime'])
assert isinstance(dt, datetime), dt

16
my/body/exercise/cross_trainer.py
View file

@ -9,6 +9,7 @@ from datetime import datetime, timedelta
from typing import Optional
from ...core.pandas import DataFrameT, check_dataframe as cdf
from ...core.orgmode import collect, Table, parse_org_datetime, TypedTable
from my.config import exercise as config
@ -26,11 +27,15 @@ def tzify(d: datetime) -> datetime:
def cross_trainer_data():
# FIXME some manual entries in python
# I guess just convert them to org
import orgparse
# todo should use all org notes and just query from them?
wlog = orgparse.load(config.workout_log)
from porg import Org
# FIXME should use all org notes and just query from them?
wlog = Org.from_file(config.workout_log)
cross_table = wlog.xpath('//org[heading="Cross training"]//table')
[table] = collect(
wlog,
lambda n: [] if n.heading != 'Cross training' else [x for x in n.body_rich if isinstance(x, Table)]
)
cross_table = TypedTable(table)
def maybe(f):
def parse(s):
@ -46,13 +51,12 @@ def cross_trainer_data():
# todo eh. not sure if there is a way of getting around writing code...
# I guess would be nice to have a means of specifying type in the column? maybe multirow column names??
# need to look up org-mode standard..
from ...core.orgmode import parse_org_datetime
mappers = {
'duration': lambda s: parse_mm_ss(s),
'date' : lambda s: tzify(parse_org_datetime(s)),
'comment' : str,
}
for row in cross_table.lines:
for row in cross_table.as_dicts:
# todo make more defensive, fallback on nan for individual fields??
try:
d = {}

2
my/body/weight.py
View file

@ -45,7 +45,7 @@ def from_orgmode() -> Iterator[Result]:
log.exception(e)
yield e
continue
# todo perhaps, better to use timezone provider
# FIXME use timezone provider
created = config.default_timezone.localize(created)
yield Entry(
dt=created,

35
my/core/orgmode.py
View file

@ -2,8 +2,6 @@
Various helpers for reading org-mode data
"""
from datetime import datetime
def parse_org_datetime(s: str) -> datetime:
s = s.strip('[]')
for fmt, cl in [
@ -19,3 +17,36 @@ def parse_org_datetime(s: str) -> datetime:
continue
else:
raise RuntimeError(f"Bad datetime string {s}")
from orgparse import OrgNode
from typing import Iterable, TypeVar, Callable
V = TypeVar('V')
def collect(n: OrgNode, cfun: Callable[[OrgNode], Iterable[V]]) -> Iterable[V]:
yield from cfun(n)
for c in n.children:
yield from collect(c, cfun)
from more_itertools import one
from orgparse.extra import Table
def one_table(o: OrgNode) -> Table:
return one(collect(o, lambda n: (x for x in n.body_rich if isinstance(x, Table))))
from typing import Iterator, Dict, Any
class TypedTable(Table):
def __new__(cls, orig: Table) -> 'TypedTable':
tt = super().__new__(TypedTable)
tt.__dict__ = orig.__dict__
blocks = list(orig.blocks)
header = blocks[0] # fist block is schema
if len(header) == 2:
# TODO later interpret first line as types
header = header[1:]
tt._blocks = [header, *blocks[1:]]
return tt
@property
def blocks(self):
return getattr(self, '_blocks')

59
my/orgmode.py
View file

@ -5,14 +5,14 @@ from datetime import datetime, date
from pathlib import Path
from typing import List, Sequence, Iterable, NamedTuple, Optional
from .core import PathIsh
from .core import PathIsh, get_files
from .core.common import mcachew
from .core.cachew import cache_dir
from .core.orgmode import collect
from my.config import orgmode as user_config
from porg import Org
import orgparse
# temporary? hack to cache org-mode notes
@ -28,12 +28,33 @@ def _sanitize(p: Path) -> str:
return re.sub(r'\W', '_', str(p))
def to_note(x: Org) -> OrgNote:
from typing import Tuple
_rgx = re.compile(orgparse.date.gene_timestamp_regex(brtype='inactive'), re.VERBOSE)
def _created(n: orgparse.OrgNode) -> Tuple[Optional[datetime], str]:
heading = n.heading
# meh.. support in orgparse?
pp = {} if n.is_root() else n.properties # type: ignore
createds = pp.get('CREATED', None)
if createds is None:
# try to guess from heading
m = _rgx.search(heading)
if m is not None:
createds = m.group(0) # could be None
if createds is None:
return (None, heading)
[odt] = orgparse.date.OrgDate.list_from_str(createds)
dt = odt.start
# todo a bit hacky..
heading = heading.replace(createds + ' ', '')
return (dt, heading)
def to_note(x: orgparse.OrgNode) -> OrgNote:
# ugh. hack to merely make it cacheable
heading = x.heading
created: Optional[datetime]
try:
# TODO(porg) not sure if created should ever throw... maybe warning/log?
c = x.created
c, heading = _created(x)
if isinstance(c, datetime):
created = c
else:
@ -43,12 +64,11 @@ def to_note(x: Org) -> OrgNote:
created = None
return OrgNote(
created=created,
heading=x.heading, # todo include the rest?
heading=heading, # todo include the body?
tags=list(x.tags),
)
# todo move to porg?
class Query:
def __init__(self, files: Sequence[Path]) -> None:
self.files = files
@ -59,27 +79,20 @@ class Query:
depends_on=lambda _, f: (f, f.stat().st_mtime),
)
def _iterate(self, f: Path) -> Iterable[OrgNote]:
o = Org.from_file(f)
for x in o.iterate():
o = orgparse.load(f)
for x in o:
yield to_note(x)
def all(self) -> Iterable[OrgNote]:
# TODO build a virtual hierarchy from it?
for f in self.files:
yield from self._iterate(f)
# TODO very confusing names...
# TODO careful... maybe use orgparse iterate instead?? ugh.
def get_all(self):
return self._xpath_all('//org')
def query_all(self, query):
for of in self.files:
org = Org.from_file(str(of))
yield from query(org)
def _xpath_all(self, query: str):
return self.query_all(lambda x: x.xpath_all(query))
def collect_all(self, collector) -> Iterable[orgparse.OrgNode]:
for f in self.files:
o = orgparse.load(f)
yield from collect(o, collector)
def query() -> Query:
return Query(files=list(user_config.files))
return Query(files=get_files(user_config.paths))

4
tests/config.py
View file

@ -6,9 +6,9 @@ def setup_notes_path(notes: Path) -> None:
from my.cfg import config
class user_config:
roots = [notes]
paths = [notes]
config.orgmode = user_config # type: ignore[misc,assignment]
# TODO FIXME ugh. this belongs to tz provider or global config or someting
# TODO ugh. this belongs to tz provider or global config or someting
import pytz
class user_config_2:
default_timezone = pytz.timezone('Europe/London')

4
tests/orgmode.py
View file

@ -1,7 +1,7 @@
from my import orgmode
from my.core.orgmode import collect
def test() -> None:
# meh
results = list(orgmode.query().query_all(lambda x: x.with_tag('python')))
results = list(orgmode.query().collect_all(lambda n: [n] if 'python' in n.tags else []))
assert len(results) > 5

14
tox.ini
View file

@ -20,6 +20,9 @@ commands =
# my.calendar.holidays dep
pip install workalendar
# my.body.weight dep
pip install orgparse
python3 -m pytest \
tests/core.py \
tests/misc.py \
@ -29,10 +32,8 @@ commands =
tests/bluemaestro.py \
tests/location.py \
tests/tz.py \
tests/calendar.py
# TODO add; once I figure out porg depdencency?? tests/config.py
# TODO run demo.py? just make sure with_my is a bit cleverer?
# TODO e.g. under CI, rely on installing
tests/calendar.py \
tests/config.py
hpi modules
@ -45,6 +46,7 @@ commands = ./demo.py
whitelist_externals = bash
commands =
pip install -e .[testing] .[optional]
pip install orgparse
pip install git+https://github.com/karlicoss/ghexport
pip install git+https://github.com/karlicoss/hypexport
pip install git+https://github.com/karlicoss/instapexport
@ -52,8 +54,6 @@ commands =
pip install git+https://github.com/karlicoss/rexport
pip install git+https://github.com/karlicoss/endoexport
pip install git+https://github.com/karlicoss/porg
# ugh fuck. soo... need to reset HOME, otherwise user's site-packages are somehow leaking into mypy's path...
# see https://github.com/python/mypy/blob/f6fb60ef69738cbfe2dfe56c747eca8f03735d8e/mypy/modulefinder.py#L487
# this is particularly annoying when user's config is leaking and mypy isn't running against the repository config
@ -82,5 +82,5 @@ commands =
[testenv:mypy]
skip_install = true
commands =
pip install -e .[testing] .[optional]
pip install -e .[testing] .[optional] orgparse
./lint