holgi
/
s2rename
Archived
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
Browse Source

first working script

master
Holger Frey 6 years ago
parent
060994cb0a
commit
cb29c6d1c5
6 changed files with 264 additions and 146 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 49
      s2rename/cli.py
  2. 45
      s2rename/helpers.py
  3. 2
      setup.py
  4. 21
      tests/test_cli.py
  5. 182
      tests/test_helpers.py
  6. 111
      tests/test_s2rename.py

49
s2rename/cli.py
Unescape View File

@ -4,14 +4,55 @@ @@ -4,14 +4,55 @@
import sys
import click
from . import helpers
@click.command()
def main(args=None):
@click.argument(
"folder",
type=click.Path(
exists=True,
file_okay=False,
dir_okay=True,
writable=True,
readable=True,
allow_dash=False,
),
)
@click.option(
"--from",
"-f",
"from_",
type=click.Choice(["sensovation", "scienion"]),
required=True,
)
@click.option(
"--to", "-t", type=click.Choice(["sensovation", "scienion"]), required=True
)
@click.option("--digits", "-d", type=click.IntRange(1, 2), default=1)
@click.option("--ext", "-e", default=None)
@click.option("--verbose", "-v", count=True)
def main(folder, from_, to, digits, ext, verbose):
"""Console script for s2rename."""
click.echo("Replace this message by putting your code into " "s2rename.cli.main")
click.echo("See click documentation at http://click.pocoo.org/")
try:
if from_.startswith("sc"):
regex = helpers.RE_SCIENION
else:
regex = helpers.RE_SENSOVATION
if to.startswith("sc"):
template = helpers.template_scienion
else:
template = helpers.template_sensovation
file_list = helpers.get_source_list(folder, ext)
renamables = helpers.parse_source_list(file_list, regex)
helpers.rename_files(renamables, template, digits)
except IOError as e:
click.echo("could not rename files")
if verbose:
raise e
return 1
return 0
if __name__ == "__main__":
sys.exit(main()) # pragma: no cover
sys.exit(main())

45
s2rename/s2rename.py → s2rename/helpers.py
Unescape View File

@ -7,21 +7,29 @@ import re @@ -7,21 +7,29 @@ import re
from collections import namedtuple
from pathlib import Path
# on the complete regex '.*' is not used, since it would also capture
# double column definitions like "something_AB12"
REGEX_ID = r"(?P<row>[A-H])(?P<col>(0?[1-9]|1[0-2]))_(?P<channel>\d)"
REGEX_SENSOVATION = r"(?P<stem>(.+_|))" + REGEX_ID
REGEX_SCIENION = REGEX_ID + r"(?P<stem>(.+_|))"
REGEX_SCIENION = REGEX_ID + r"(?P<stem>(_.+|))"
RE_SENSOVATION = re.compile(REGEX_SENSOVATION)
RE_SCIENION = re.compile(REGEX_SENSOVATION)
RE_SCIENION = re.compile(REGEX_SCIENION)
TPL_ID = "{row}{col:0>{dec}d}_{channel}"
TPL_SENSOVATION = "{stem}" + TPL_ID
TPL_SCIENION = TPL_ID + "{stem}"
TPL_SENSOVATION = '{r.stem}_{r.row}{r.col:0>{dec}d}_{r.channel}'
class S2IOError(IOError):
""" custom IO Exception """
Renamable = namedtuple("Renamable", "path,stem,row,col,channel,ext")
FileNameTemplate = namedtuple("FileNameTemplate", "template,prefix,suffix")
template_sensovation = FileNameTemplate(template=TPL_SENSOVATION, prefix="", suffix="_")
template_scienion = FileNameTemplate(TPL_SCIENION, prefix="_", suffix="")
Renamable = namedtuple("Renamable", "path,stem,row,col,channel")
class S2IOError(IOError):
""" custom IO Exception """
def get_source_list(folder, suffix=None):
@ -49,16 +57,35 @@ def filter_source_list(source_list, suffix): @@ -49,16 +57,35 @@ def filter_source_list(source_list, suffix):
def parse_source_list(source_list, regex):
""" returns a list of items that can be renamed """
for path in source_list:
if path.name.startswith("."):
continue
groups = regex.match(path.stem)
if groups:
stem = groups["stem"]
if stem.endswith('_'):
stem = stem[:-1]
stem = groups["stem"].strip("_")
entry = Renamable(
path=path,
stem=stem,
row=groups["row"],
col=int(groups["col"]),
channel=groups["channel"],
ext=path.suffix,
)
yield entry
def get_new_name(item, name_template, digits):
stem = item.stem
if stem:
# only apply prefix and suffix if the name is not empty
stem = name_template.prefix + stem + name_template.suffix
new_name = name_template.template.format(
stem=stem, row=item.row, col=item.col, channel=item.channel, dec=digits
)
return new_name + item.ext
def rename_files(renamable_list, name_template, digits):
for item in renamable_list:
new_name = get_new_name(item, name_template, digits)
new_path = item.path.with_name(new_name)
item.path.replace(new_path)

2
setup.py
Unescape View File

@ -26,7 +26,7 @@ setup( @@ -26,7 +26,7 @@ setup(
"Programming Language :: Python :: 3.7",
],
description="Renaming files for SensoSpot and Scienion software",
entry_points={"console_scripts": ["s2rename=s2rename.cli:main"]},
entry_points={"console_scripts": ["s2renamecli=s2rename.cli:main"]},
install_requires=requirements,
long_description=readme,
include_package_data=True,

21
tests/test_cli.py
Unescape View File

@ -1,21 +0,0 @@ @@ -1,21 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tests for `s2rename` package."""
import pytest
from click.testing import CliRunner
from s2rename import cli
def test_command_line_interface():
"""Test the CLI."""
runner = CliRunner()
result = runner.invoke(cli.main)
assert result.exit_code == 0
assert "s2rename.cli.main" in result.output
help_result = runner.invoke(cli.main, ["--help"])
assert help_result.exit_code == 0
assert "--help Show this message and exit." in help_result.output

182
tests/test_helpers.py
Unescape View File

@ -0,0 +1,182 @@ @@ -0,0 +1,182 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tests for `s2rename` package."""
import pytest
from pathlib import Path
sensovation_source_list = [
Path("some thing_A1_1.tif"),
Path("some thing_A02_2.tif"),
Path("A03_3.tif"),
Path("some thing_A10_4"),
Path("some thing_A11_5.csv"),
Path("some thing_A12_6.xml"),
Path("some thing_B01_1.tif"),
Path("some thing_C01_1.tif"),
Path("some thing_D01_1.tif"),
Path("some thing_E01_1.tif"),
Path("some thing_F01_1.tif"),
Path("some thing_G01_1.tif"),
Path("some thing_H01_1.tif"),
Path("some thing_I01_1.tif"),
Path("some thing_FF01_1.tif"),
Path("some thing_F21_1.tif"),
Path("some thing_F00_1.tif"),
Path("some thing_F0_1.tif"),
Path("some thing_F13_1.tif"),
Path("some thing_F08.tif"),
Path(".some thing_F09_1.tif"),
]
scienion_source_list = [
Path("A1_1_some thing.tif"),
Path("A02_2_some thing.tif"),
Path("A03_3.tif"),
Path("A10_4_some thing"),
Path("A11_5_some thing.csv"),
Path("A12_6_some thing.xml"),
Path("B01_1_some thing.tif"),
Path("C01_1_some thing.tif"),
Path("D01_1_some thing.tif"),
Path("E01_1_some thing.tif"),
Path("F01_1_some thing.tif"),
Path("G01_1_some thing.tif"),
Path("H01_1_some thing.tif"),
Path("I01_1_some thing.tif"),
Path("FF01_1_some thing.tif"),
Path("F21_1_some thing.tif"),
Path("F00_1_some thing.tif"),
Path("F0_1_some thing.tif"),
Path("F13_1_some thing.tif"),
Path("F08_some thing.tif"),
Path(".F09_1_some thing.tif"),
]
@pytest.mark.parametrize("sources", [sensovation_source_list, scienion_source_list])
def test_parse_source_list_sensovation(sources):
from s2rename.helpers import RE_SENSOVATION, RE_SCIENION, parse_source_list
regex = RE_SENSOVATION if sources == sensovation_source_list else RE_SCIENION
result = list(parse_source_list(sources, regex))
assert len(result) == 13
assert {r.row for r in result} == set("ABCDEFGH")
assert {r.col for r in result} == {1, 2, 3, 10, 11, 12}
assert {r.channel for r in result} == set("123456")
assert {r.ext for r in result} == {".tif", ".csv", ".xml", ""}
assert {r.stem for r in result} == {"some thing", ""}
def test_get_source_list():
from s2rename.helpers import get_source_list
result = list(get_source_list("."))
assert {p.name for p in result} == {
"LICENSE",
"Pipfile",
"requirements_dev.txt",
"setup.cfg",
"Makefile",
"README.md",
"setup.py",
}
@pytest.mark.parametrize("path", ["/i/hope/this/doesnt/exist", "setup.py"])
def test_get_source_list_raises_error(path):
from s2rename.helpers import get_source_list, S2IOError
with pytest.raises(S2IOError):
get_source_list(path)
def test_get_source_list_with_type():
from s2rename.helpers import get_source_list
result = get_source_list(".", ".txt")
assert {p.name for p in result} == {"requirements_dev.txt"}
def test_filter_source_list_type():
from s2rename.helpers import filter_source_list
result = list(filter_source_list(sensovation_source_list, ".csv"))
assert len(result) == 1
assert result[0].name == "some thing_A11_5.csv"
def test_get_new_name_simple():
from s2rename.helpers import get_new_name, Renamable, template_sensovation
r = Renamable(
path=Path("x.csv"), stem="some_name", row="A", col=2, channel=3, ext=".csv"
)
result = get_new_name(r, template_sensovation, digits=2)
assert result == "some_name_A02_3.csv"
@pytest.mark.parametrize(
"tpl,stem,row,col,channel,digits,ext,expected",
[
("sen", "some_name", "A", 1, 2, 1, ".xls", "some_name_A1_2.xls"),
("sen", "some_name", "A", 1, 2, 2, ".xls", "some_name_A01_2.xls"),
("sen", "some_name", "A", 1, 2, 3, ".xls", "some_name_A001_2.xls"),
("sen", "some_name", "B", 1, 2, 2, ".xls", "some_name_B01_2.xls"),
("sen", "some_name", "A", 2, 2, 2, ".xls", "some_name_A02_2.xls"),
("sen", "some_name", "A", 1, 3, 2, ".xls", "some_name_A01_3.xls"),
("sen", "some_name", "A", 1, 3, 2, ".tif", "some_name_A01_3.tif"),
("sen", "", "A", 1, 3, 2, ".xls", "A01_3.xls"),
("sci", "some_name", "A", 1, 2, 1, ".xls", "A1_2_some_name.xls"),
("sci", "some_name", "A", 1, 2, 2, ".xls", "A01_2_some_name.xls"),
("sci", "some_name", "A", 1, 2, 3, ".xls", "A001_2_some_name.xls"),
("sci", "some_name", "B", 1, 2, 2, ".xls", "B01_2_some_name.xls"),
("sci", "some_name", "A", 2, 2, 2, ".xls", "A02_2_some_name.xls"),
("sci", "some_name", "A", 1, 3, 2, ".xls", "A01_3_some_name.xls"),
("sci", "some_name", "A", 1, 3, 2, ".tif", "A01_3_some_name.tif"),
("sci", "", "A", 1, 3, 2, ".xls", "A01_3.xls"),
],
)
def test_get_new_name(tpl, stem, row, col, channel, digits, ext, expected):
from s2rename.helpers import (
get_new_name,
Renamable,
template_sensovation,
template_scienion,
)
path = Path("x" + ext)
r = Renamable(path=path, stem=stem, row=row, col=col, channel=channel, ext=ext)
tpl = template_sensovation if tpl == "sen" else template_scienion
result = get_new_name(r, tpl, digits=digits)
assert result == expected
def test_rename_files():
from s2rename.helpers import rename_files, Renamable, template_sensovation
old_path = Path("old.txt")
new_path = Path("new_A001_2.xxx")
renamable_item = Renamable(
path=old_path, stem="new", row="A", col=1, channel=2, ext=".xxx"
)
with open(old_path, "w") as fh:
fh.write("\n")
assert old_path.is_file()
assert not new_path.is_file()
rename_files([renamable_item], template_sensovation, 3)
assert not old_path.is_file()
assert new_path.is_file()
new_path.unlink()

111
tests/test_s2rename.py
Unescape View File

@ -1,111 +0,0 @@ @@ -1,111 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tests for `s2rename` package."""
import pytest
from pathlib import Path
sensovation_source_list = [
Path("some prefix thing_A1_1.tif"),
Path("some prefix thing_A02_2.tif"),
Path("A03_3.tif"),
Path("some prefix thing_A10_4"),
Path("some prefix thing_A11_5.csv"),
Path("some prefix thing_A12_6.xml"),
Path("some prefix thing_B01_1.tif"),
Path("some prefix thing_C01_1.tif"),
Path("some prefix thing_D01_1.tif"),
Path("some prefix thing_E01_1.tif"),
Path("some prefix thing_F01_1.tif"),
Path("some prefix thing_G01_1.tif"),
Path("some prefix thing_H01_1.tif"),
Path("some prefix thing_I01_1.tif"),
Path("some prefix thing_FF01_1.tif"),
Path("some prefix thing_F21_1.tif"),
Path("some prefix thing_F00_1.tif"),
Path("some prefix thing_F0_1.tif"),
Path("some prefix thing_F13_1.tif"),
Path("some prefix thing_F08.tif"),
Path(".some prefix thing_F09_1.tif"),
]
scienion_source_list = [
Path("A1_1_some suffix thing.tif"),
Path("A02_2_some suffix thing.tif"),
Path("A03_3.tif"),
Path("A10_3_some suffix thing"),
Path("A11_4_some suffix thing.csv"),
Path("A12_5_some suffix thing.xml"),
Path("B01_1_some suffix thing.tif"),
Path("C01_1_some suffix thing.tif"),
Path("D01_1_some suffix thing.tif"),
Path("E01_1_some suffix thing.tif"),
Path("F01_1_some suffix thing.tif"),
Path("G01_1_some suffix thing.tif"),
Path("H01_1_some suffix thing.tif"),
Path("I01_1_some suffix thing.tif"),
Path("FF01_1_some suffix thing.tif"),
Path("F21_1_some suffix thing.tif"),
Path("F00_1_some suffix thing.tif"),
Path("F0_1_some suffix thing.tif"),
Path("F13_1_some suffix thing.tif"),
Path("F08_some suffix thing.tif"),
Path(".F09_1_some suffix thing.tif"),
]
@pytest.mark.parametrize("sources", [sensovation_source_list, scienion_source_list])
def test_parse_source_list_sensovation(sources):
from s2rename import s2rename
if sources == sensovation_source_list:
regex = s2rename.RE_SENSOVATION
else:
regex = s2rename.RE_SCIENION
result = list(s2rename.parse_source_list(sensovation_source_list, regex))
assert len(result) == 14
assert {r.row for r in result} == set("ABCDEFGH")
assert {r.col for r in result} == set([1, 2, 3, 9, 10, 11, 12])
def test_get_source_list():
from s2rename import s2rename
result = list(s2rename.get_source_list("."))
assert {p.name for p in result} == {
"LICENSE",
"Pipfile",
"requirements_dev.txt",
"setup.cfg",
"Makefile",
"README.md",
"setup.py",
}
@pytest.mark.parametrize("path", ["/i/hope/this/doesnt/exist", "setup.py"])
def test_get_source_list_raises_error(path):
from s2rename import s2rename
with pytest.raises(s2rename.S2IOError):
result = s2rename.get_source_list(path)
def test_get_source_list_with_type():
from s2rename import s2rename
result = s2rename.get_source_list(".", ".txt")
assert {p.name for p in result} == {"requirements_dev.txt"}
def test_filter_source_list_type():
from s2rename import s2rename
result = list(s2rename.filter_source_list(sensovation_source_list, ".csv"))
assert len(result) == 1
assert result[0].name == "some prefix thing_A11_5.csv"