first working script

s2rename/cli.py

@@ -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())

s2rename/helpers.py

@@ -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):
 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)

setup.py

@@ -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,

tests/test_cli.py

@@ -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

tests/test_helpers.py

@@ -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()

tests/test_s2rename.py

@@ -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"
-