compute a check digit for a noid

* new option `-d/--check-digit`
* reassigned `-v` for verbose; now `-V` for validate
* better test coverage
* extended documentation

Author: Paul K. Korir, PhD

README.md

@@ -25,9 +25,9 @@ noid
 There are various options available using `-h/--help`:
 ```shell
 noid -h
-usage: noid [-h] [-c CONFIG_FILE] [-v] [-s SCHEME] [-N NAA] [-t TEMPLATE] [-n INDEX] [--verbose] [noid]
+usage: noid [-h] [-c CONFIG_FILE] [-V | -d] [-s SCHEME] [-N NAA] [-t TEMPLATE] [-n INDEX] [-v] [noid]
 
-generate nice and opaque identifiers (noids)
+generate nice and opaque identifiers
 
 positional arguments:
   noid                  a noid
@@ -36,15 +36,16 @@ optional arguments:
   -h, --help            show this help message and exit
   -c CONFIG_FILE, --config-file CONFIG_FILE
                         path to a config file with a noid section
-  -v, --validate        validate the given noid [default: False]
+  -V, --validate        validate the given noid [default: False]
+  -d, --check-digit     compute and print the corresponding check digit for the given noid [default: False]
   -s SCHEME, --scheme SCHEME
                         the noid scheme [default: 'ark:/']
   -N NAA, --naa NAA     the name assigning authority (NAA) number [default: ]
   -t TEMPLATE, --template TEMPLATE
                         the template by which to generate noids [default: 'zeeddk']
   -n INDEX, --index INDEX
                         a number for which to generate a valid noid [default: random positive integer]
-  --verbose             turn on verbose text [default: False]
+  -v, --verbose         turn on verbose text [default: False]
 
 ```
 
@@ -54,6 +55,13 @@ Validate a noid using the `-v/--validate` flag and pass a noid.
 noid -v $(noid) # self-validation
 ```
 
+### Compute the check digit for a noid
+Compute the check digit using `-d/--check-digit` flag and pass a noid.
+```shell
+noid -d $(noid -t zeee -n 1234) && noid -t zeee -n 1234 && noid -t zeeek -n 1234
+```
+The example above prints out the check digit, the full noid without a check digit and the full noid with a check digit. 
+
 ### Options
 #### Specify the NAA
 Use the `-N/--naa` option.

noid/cli.py

@@ -22,12 +22,19 @@
     '-c', '--config-file',
     help="path to a config file with a noid section"
 )
-parser.add_argument(
-    '-v', '--validate',
+noid_action = parser.add_mutually_exclusive_group()
+noid_action.add_argument(
+    '-V', '--validate',
     action='store_true',
     default=False,
     help="validate the given noid [default: False]"
 )
+noid_action.add_argument(
+    '-d', '--check-digit',
+    action='store_true',
+    default=False,
+    help="compute and print the corresponding check digit for the given noid [default: False]"
+)
 parser.add_argument(
     '-s', '--scheme',
     default=DEFAULT_SCHEME,
@@ -50,7 +57,7 @@
     help="a number for which to generate a valid noid [default: random positive integer]"
 )
 parser.add_argument(
-    '--verbose',
+    '-v', '--verbose',
     action='store_true',
     default=False,
     help="turn on verbose text [default: False]"
@@ -94,12 +101,13 @@ def parse_args():
                 if o in configs['noid']:
                     setattr(args, o, configs.get('noid', o))
                 else:
-                    print(f"warning: configs missing option '{o}'; using default value ({getattr(args, o)})", file=sys.stderr)
+                    print(f"warning: configs missing option '{o}'; using default value ({getattr(args, o)})",
+                          file=sys.stderr)
         else:
             print(f"warning: config file '{args.config_file}' lacks 'noid' section; ignoring config file",
                   file=sys.stderr)
     # argument validation
-    if args.validate and args.noid is None:
+    if (args.validate or args.check_digit) and args.noid is None:
         print("error: missing noid to validate", file=sys.stderr)
         return None
     return args

noid/pynoid.py

@@ -5,7 +5,7 @@
 from noid import utils, cli
 
 
-def mint(template='zek', n=-1, scheme='', naa='') -> str:
+def mint(template: str = 'zek', n: int = -1, scheme: str = '', naa: str = '') -> str:
     """ Mint identifiers according to template with a prefix of scheme + naa.
 
     :param str template: a string consisting of GENTYPE + (DIGTYPE)+ [+ CHECKDIGIT]
@@ -52,7 +52,7 @@ def mint(template='zek', n=-1, scheme='', naa='') -> str:
     return noid
 
 
-def generate_noid(mask:str, n:int) -> str:
+def generate_noid(mask: str, n: int) -> str:
     """The actual noid generation
 
     :param str mask: the mask string
@@ -134,6 +134,7 @@ def index_of(x):
         try:
             return utils.XDIGIT.index(x)
         except:
+            print(f"error: invalid character '{x}'; digits should be in '{''.join(utils.XDIGIT)}'", file=sys.stderr)
             return 0
 
     total = list()
@@ -152,6 +153,11 @@ def main():
         if args.verbose:
             print(f"info: validating '{args.noid}'...", file=sys.stderr)
         print(f"'{args.noid}' valid? {validate(args.noid)}")
+    elif args.check_digit:
+        if args.verbose:
+            print(f"info: computing check digit for '{args.noid}'...", file=sys.stderr)
+        check_digit = calculate_check_digit(args.noid)
+        print(check_digit)
     else:
         if args.verbose:
             print(f"info: generating noid using template={args.template}, n={args.index}, "

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="noid",
-    version="1.0.1",
+    version="1.1.0",
     author="Paul K. Korir",
     author_email="pkorir@ebi.ac.uk, paulkorir@gmail.com",
     description="Mint NOIDs using a CLI or API",

test/test.py

@@ -27,14 +27,17 @@
 noid -n/--index
 
 """
+import io
+import os
+import pathlib
 import random
 import re
+import sys
+import tempfile
 import unittest
 
 from noid import cli, pynoid, utils
 
-import pathlib
-
 BASE_DIR = pathlib.Path(__file__).parent.parent
 CONFIG_FILE = BASE_DIR / 'noid' / 'noid.cfg'
 
@@ -53,7 +56,16 @@ def test_default(self):
 
     def test_validate(self):
         """Validation requires noid positional argument"""
-        self.assertIsNone(cli.cli(f"noid -v"))
+        self.assertIsNone(cli.cli(f"noid -V"))
+
+    def test_check_digit(self):
+        """Show the check digit for the given string"""
+        args = cli.cli(f"noid -d 123456")
+        self.assertEqual('123456', args.noid)
+        self.assertTrue(args.check_digit)
+        # you cannot validate and check at the same time
+        with self.assertRaises(SystemExit):
+            cli.cli(f"noid -d -V 123456")
 
     def test_config(self):
         """Using a config file"""
@@ -66,6 +78,37 @@ def test_config(self):
         self.assertEqual('zeeeeddddk', args.template)
         self.assertEqual(-1, args.index)
         self.assertFalse(args.verbose)
+        sys.stdout = io.StringIO()
+        configs = cli.read_configs(args)
+        print(configs)
+        self.assertRegex(sys.stdout.getvalue(), r"(?ms:.*[[]noid[]].*template.*scheme.*naa.*)")
+
+    def test_missing_noid_validate(self):
+        """Print error for validating a blank noid"""
+        args = cli.cli(f"noid -V")
+        self.assertIsNone(args)
+
+    def test_invalid_configs(self):
+        """Use defaults when configs invalid"""
+        # case 1: no 'noid' section
+        _configs = """[noids]\ntemplate = zeedddeeek\nscheme = doi:\nnaa = 1234\n"""
+        temp_configs = tempfile.NamedTemporaryFile()
+        with open(temp_configs.name, 'w') as f:
+            print(_configs, file=f)
+        sys.stdout = sys.stderr = io.StringIO()
+        cli.cli(f"noid -c {temp_configs.name}")
+        self.assertRegex(sys.stderr.getvalue(), r"(?ms:^warning: config file .* lacks 'noid' section.*ignoring.*)")
+        # case 2: some sections missing
+        _configs = """[noid]\ntemplates = zeedddeeek\nschemes = doi:\nnaat = 1234\n"""
+        temp_configs = tempfile.NamedTemporaryFile()
+        with open(temp_configs.name, 'w') as f:
+            print(_configs, file=f)
+        sys.stderr = io.StringIO()
+        cli.cli(f"noid -c {temp_configs.name}")
+        self.assertRegex(
+            sys.stderr.getvalue(),
+            r"(?ms:^warning: configs missing option 'template'.*missing option 'scheme'.*missing option 'naa'.*)"
+        )
 
 
 class PynoidAPI(unittest.TestCase):
@@ -125,6 +168,68 @@ def test_mint_invalid_template(self):
         self.assertEqual('', noid)
 
 
+class PynoidNoid(unittest.TestCase):
+    """Tests for the entry point"""
+
+    def test_default(self):
+        """The result of simply calling 'noid'"""
+        cli.cli(f"noid -v")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(sys.stdout.getvalue(), r"(?ms:^info: generating noid.*template=.*scheme=.*ark[:][/][\w\d]+)")
+
+    def test_error(self):
+        """Exit status on *nix is os.EX_USAGE"""
+        cli.cli(f"noid -V")
+        ex = pynoid.main()
+        self.assertEqual(os.EX_USAGE, ex)
+
+    def test_config(self):
+        """Using config"""
+        cli.cli(f"noid -v -c {CONFIG_FILE}")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(
+            sys.stdout.getvalue(),
+            r"(?ms:^info: generating noid.*template=zeeeeddddk.*scheme="
+            r"http[:][/][/].*naa=83812.*http[:][/][/]83812[/][\w\d]+)"
+        )
+
+    def test_validate(self):
+        """Using check digit"""
+        noid = 'xg64G'
+        cli.cli(f"noid -v -V {noid}")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(sys.stdout.getvalue(), rf"(?ms:^info: validating '{noid}'.*'{noid}' valid[?] True)")
+
+    def test_check_digit(self):
+        """Using check digit"""
+        noid = '123456'
+        check_digit = pynoid.calculate_check_digit(noid)
+        cli.cli(f"noid -v -d {noid}")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(sys.stdout.getvalue(), rf"(?ms:^info: computing check digit for '{noid}'.*{check_digit})")
+
+    def test_scheme_naa_template(self):
+        """Minting options"""
+        cli.cli(f"noid -v -t zeeddk -s https:// -N 54321")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(sys.stdout.getvalue(),
+                         r"(?ms:^info: generating noid.*template=zeeddk.*scheme=https[:][/][/].*naa=54321.*https[:][/][/]54321[/][\w\d]+)")
+
+    def test_index(self):
+        """Set index"""
+        index = random.randint(1000, 2000)
+        cli.cli(f"noid -v -n {index}")
+        sys.stdout = sys.stderr = io.StringIO()
+        pynoid.main()
+        self.assertRegex(sys.stdout.getvalue(),
+                         rf"(?ms:^info: generating noid.*template=zeeddk.*n={index}.*scheme=ark[:][/].*naa=.*ark[:][/][\w\d]+)")
+
+
 class PynoidUtils(unittest.TestCase):
     def test_validate_mask(self):
         """Validate a mask"""