diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1c2ca5eacd9a4eb429380c3f645237f2ec3fb69e..cb3cbaa424f9dad204ef996641aa02298873e9b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,17 @@
# `fsl_add_module` changelog
+## 0.5.0 (Monday 5th June 2023)
+
+ - New `fsl_generate_module_manifest` command, to generate a JSON manifest
+ for a set of files.
+ - Added ability to refer to 'built-in' manifests by aliases - the default
+ manifest is referred to as `fslcourse`, and the Graduate Programme manifest
+ as `gradcourse`, e.g. `fsl_add_module -m gradcourse`.
+ - Added support for a `size` field in manifest entries, specifying the file
+ size in bytes.
+
+
## 0.4.0 (Tuesday 24th January 2023)
- Changed the default behaviour so that only files in the `fsl_course_data`
diff --git a/fsl/add_module/__init__.py b/fsl/add_module/__init__.py
index 83da9f81721da6fa8bad53e6120e0ac6ea9c0de5..62c9a92f7ec757c1e831e5ce0d244524ed5050a9 100644
--- a/fsl/add_module/__init__.py
+++ b/fsl/add_module/__init__.py
@@ -9,5 +9,5 @@
"""
-__version__ = '0.4.0'
+__version__ = '0.5.0'
"""``fsl_add_module`` version number."""
diff --git a/fsl/add_module/plugin_manifest.py b/fsl/add_module/manifest.py
similarity index 76%
rename from fsl/add_module/plugin_manifest.py
rename to fsl/add_module/manifest.py
index 1da82cad645f2e314b0aa53765eabb84d098cd57..d32db16f9f20909cecdedb279236862ce28f3147 100644
--- a/fsl/add_module/plugin_manifest.py
+++ b/fsl/add_module/manifest.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
#
-# plugin_manifest.py - Classes and functions for working with FSL plugin
-# manifest files.
+# manifest.py - Classes and functions for working with FSL plugin
+# manifest files.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -15,6 +15,7 @@ list of FSL plugin definitions, e.g.::
"category" : "fsl_course_data",
"url" : "http://.../UnixIntro.zip",
"checksum" : "f8222...",
+ "size" : "15677939",
"description" : "Data for the unix introduction",
"version" : "1.2.3",
"destination" : "~/"
@@ -24,6 +25,7 @@ list of FSL plugin definitions, e.g.::
"category" : "fsl_atlases",
"url" : "http://localhost:8000/abcd123_mouse_atlas.tar.gz",
"checksum" : "658701ff9a49b06f0d0ee38bce36a1c370fdfd0751ab17c2fd7b7b561d3b92e0",
+ "size" : "123841532",
"description" : "ABCD123 FSL mouse atlas derived from hand segmentations of 3813 small chocolate mice.",
"terms_of_use" : "https://chocolate-mouse.com/terms-of-use",
"destination" : "$FSLDIR/data/atlases/"
@@ -39,6 +41,7 @@ optional but recommended:
- ``category``: The plugin category, used to organise plugins.
- ``checksum``: A SHA256 checksum of the plugin archive file, used to
verify that it has been successfully downloaded.
+ - ``size``: Size of the file in bytes
- ``description``: An extended description of the plugin
- ``version``: A version identifier for the plugin (used solely for
descriptive purposes)
@@ -98,12 +101,15 @@ class Plugin:
"""SHA256 checksum of the plugin archive file, used to verify downloads.
"""
+ size : Optional[int] = None
+ """Size of the archive file in bytes. """
+
version : Optional[str] = None
"""Version identifier for the plugin - displayed to the user, but not
used for any other purpose.
"""
- termsOfUse : Optional[str] = None
+ terms_of_use : Optional[str] = None
"""Terms of use for the plugin - displayed to the user during installation.
"""
@@ -137,13 +143,21 @@ class Plugin:
@property
def fileName(self):
"""Return a suitable name to use for the downloaded plugin file.
+ The file name may be prefixed with the plugin file category.
"""
- fname = op.basename(urlparse.urlparse(self.url).path)
+ fname = self.rawFileName
if self.category not in (None, UNCATEGORISED):
fname = f'{self.category}_{fname}'
return routines.sanitiseFileName(fname)
+ @property
+ def rawFileName(self):
+ """Return the file name of the plugin file as it appears in te URL.
+ """
+ return op.basename(urlparse.urlparse(self.url).path)
+
+
class Manifest(dict):
"""The ``Manifest``class simply a container for :class:`Plugin` instances.
A ``Manifest`` is a dict containing ``{name : Plugin}`` mappings.
@@ -154,27 +168,29 @@ class Manifest(dict):
def addPlugin(self,
- url : Union[str, pathlib.Path],
- name : Optional[str] = None,
- description : Optional[str] = None,
- category : Optional[str] = None,
- checksum : Optional[str] = None,
- version : Optional[str] = None,
- termsOfUse : Optional[str] = None,
- destination : Optional[str] = None) -> str:
+ url : Union[str, pathlib.Path],
+ name : Optional[str] = None,
+ description : Optional[str] = None,
+ category : Optional[str] = None,
+ checksum : Optional[str] = None,
+ size : Optional[int] = None,
+ version : Optional[str] = None,
+ terms_of_use : Optional[str] = None,
+ destination : Optional[str] = None) -> str:
"""Add a new :class:`Plugin` to the manifest.
- :arg url: URL of plugin archive file.
- :arg name: Plugin name. Defaults to filename component of
- ``url``.
- :arg description: Extended description of plugin
- :arg category: Plugin category
- :arg checksum: SHA256 checksum of archive file.
- :arg version: Version identifier for the plugin.
- :arg termsOfUse: Terms of use for the plugin.
- :arg destination: Default installation directory.
- :returns: The registered plugin name (equivalent to ``name``,
- if provided).
+ :arg url: URL of plugin archive file.
+ :arg name: Plugin name. Defaults to filename component of
+ ``url``.
+ :arg description: Extended description of plugin
+ :arg category: Plugin category
+ :arg checksum: SHA256 checksum of archive file.
+ :arg size: Size of archive file in bytes.
+ :arg version: Version identifier for the plugin.
+ :arg terms_of_use: Terms of use for the plugin.
+ :arg destination: Default installation directory.
+ :returns: The registered plugin name (equivalent to ``name``,
+ if provided).
"""
# support paths to local files
@@ -213,8 +229,9 @@ class Manifest(dict):
category=category,
description=description,
checksum=checksum,
+ size=size,
version=version,
- termsOfUse=termsOfUse,
+ terms_of_use=terms_of_use,
destination=destination,
origDestination=origDestination,
archiveFile=archiveFile,
@@ -264,7 +281,7 @@ def downloadManifest(url : Union[str, pathlib.Path]) -> Manifest:
with tempfile.TemporaryDirectory() as d:
dest = op.join(d, 'manifest.txt')
routines.downloadFile(url, dest, progress=False)
- rawmanifest = open(dest, 'rt').read()
+ rawmanifest = open(dest, 'rt', encoding='utf-8').read()
try:
rawmanifest = json.loads(rawmanifest)
@@ -276,14 +293,17 @@ def downloadManifest(url : Union[str, pathlib.Path]) -> Manifest:
# plugins must at least contain a URL
try:
+ try: size = int(plugin.get('size'))
+ except Exception: size = None
manifest.addPlugin(
url=plugin['url'],
name=plugin.get('name'),
description=plugin.get('description'),
category=plugin.get('category'),
checksum=plugin.get('checksum'),
+ size=size,
version=plugin.get('version'),
- termsOfUse=plugin.get('terms_of_use'),
+ terms_of_use=plugin.get('terms_of_use'),
destination=plugin.get('destination'))
except KeyError as e:
raise ManifestInvalid(f'The manifest file {url} '
@@ -291,3 +311,15 @@ def downloadManifest(url : Union[str, pathlib.Path]) -> Manifest:
'definition: {plugin}') from e
return manifest
+
+
+def genManifest(manifest : Manifest) -> str:
+ """Converts the given manifest to JSON. """
+
+ fields = ['name', 'url', 'category', 'checksum', 'size', 'description',
+ 'version', 'destination', 'terms_of_use']
+ plugins = list(manifest.values())
+ plugins = [dataclasses.asdict(p) for p in plugins]
+ plugins = [{f : p[f] for f in fields} for p in plugins]
+ plugins = [{k : v for k, v in p.items() if v is not None } for p in plugins]
+ return json.dumps(plugins, indent=4)
diff --git a/fsl/add_module/tests/test_fsl_add_module.py b/fsl/add_module/tests/test_fsl_add_module.py
index 66a45b3d8d2404afbe8ac0c3fc9c18709e80d4de..c8e68f084c66bf968a6f37f8c0d9fb1fd272a9a6 100644
--- a/fsl/add_module/tests/test_fsl_add_module.py
+++ b/fsl/add_module/tests/test_fsl_add_module.py
@@ -73,14 +73,14 @@ def test_loadManifest_different_sources():
with pytest.raises(RuntimeError):
fam.loadManifest(fam.parseArgs(['-m', 'nomanifest']))
- # otherwise should work ok
+ # Specify plugin URL
m, p = fam.loadManifest(
fam.parseArgs(['-m', 'nomanifest', 'http://abc.com/plugin.zip']))
assert p == ['plugin.zip']
assert list(m.keys()) == ['plugin.zip']
# default manifest
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL', url):
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST', url):
m, p = fam.loadManifest(fam.parseArgs([]))
assert len(p) == 0
assert list(m.keys()) == ['abc', 'def']
@@ -158,7 +158,7 @@ def test_loadManifest_destination_specified():
def test_selectPlugins_from_filepath_and_url():
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL', None):
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST', None):
args = fam.parseArgs('abc.zip def.zip -d dest'.split())
m, p = fam.loadManifest(args)
plugins = fam.selectPlugins(args, m, p)
@@ -188,7 +188,7 @@ def test_selectPlugins_name_from_manifest():
def test_selectPlugins_no_destination_specified():
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL', None):
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST', None):
args = fam.parseArgs('abc.zip def.zip'.split())
m, p = fam.loadManifest(args)
@@ -389,9 +389,9 @@ def test_main_noargs():
# patch os.environ in case FSLDIR is set
fammod = 'fsl.scripts.fsl_add_module'
- with mock.patch(f'{fammod}.DEFAULT_MANIFEST_URL', f'{cwd}/manifest.json'), \
- mock.patch(f'{fammod}.DEFAULT_CATEGORY', None), \
- mock.patch(f'{fammod}.ARCHIVE_DIR', f'{cwd}/archives'), \
+ with mock.patch(f'{fammod}.DEFAULT_MANIFEST', f'{cwd}/manifest.json'), \
+ mock.patch(f'{fammod}.DEFAULT_CATEGORY', None), \
+ mock.patch(f'{fammod}.ARCHIVE_DIR', f'{cwd}/archives'), \
mock.patch.dict(os.environ, clear=True):
# user will be asked what plugins they want,
@@ -414,7 +414,7 @@ def test_main_list():
with open('manifest.json', 'wt') as f:
f.write(json.dumps(manifest))
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL',
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST',
f'{cwd}/manifest.json'):
fam.main(['-l'])
fam.main('-l -v'.split())
@@ -511,8 +511,8 @@ def test_main_plugin_paths():
args = f'./abc.zip http://localhost:{srv.port}/def.zip'.split()
fammod = 'fsl.scripts.fsl_add_module'
- with mock.patch(f'{fammod}.DEFAULT_MANIFEST_URL', None), \
- mock.patch(f'{fammod}.ARCHIVE_DIR', f'{cwd}/archives'), \
+ with mock.patch(f'{fammod}.DEFAULT_MANIFEST', None), \
+ mock.patch(f'{fammod}.ARCHIVE_DIR', f'{cwd}/archives'), \
mock.patch.dict(os.environ, clear=True):
with mock_input(''):
@@ -615,7 +615,7 @@ def test_main_skip_already_downloaded():
# direct download - if file exists, it is
# assumed to be ok, and not re-downloaded.
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL', None):
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST', None):
fam.main(f'{url["abc"]} -a {archiveDir} -d {destDir} -f'.split())
assert os.stat(archivePath['abc']).st_mtime_ns == mtime['abc']
check_dir(destDir, ['a/b', 'c/d'])
@@ -652,7 +652,7 @@ def test_main_customise_plugin_dir():
os.mkdir(defdest)
os.mkdir(ghidest)
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL', None), \
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST', None), \
mock_input('c', abcdest, defdest, ghidest):
fam.main(f'abc.zip def.zip ghi.zip'.split())
@@ -743,7 +743,7 @@ def test_default_categories():
make_archive('d.zip', 'd/d.txt')
# default -> only fsl_course_data downloaded
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL',
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST',
f'{cwd}/manifest.json'):
fam.main('-f -a archives -d .'.split())
check_dir('.',
@@ -758,7 +758,7 @@ def test_default_categories():
shutil.rmtree('d')
# --category all -> all modules downloaded
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL',
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST',
f'{cwd}/manifest.json'):
fam.main('-f -a archives -d . -c all'.split())
check_dir('.',
@@ -775,7 +775,7 @@ def test_default_categories():
shutil.rmtree('d')
# --category <something> -> <something> modules downloaded
- with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST_URL',
+ with mock.patch('fsl.scripts.fsl_add_module.DEFAULT_MANIFEST',
f'{cwd}/manifest.json'):
fam.main('-f -a archives -d . -c patches'.split())
check_dir('.',
diff --git a/fsl/add_module/tests/test_fsl_generate_module_manifest.py b/fsl/add_module/tests/test_fsl_generate_module_manifest.py
new file mode 100644
index 0000000000000000000000000000000000000000..7752fc44963260650667ec6edc77953f334360fb
--- /dev/null
+++ b/fsl/add_module/tests/test_fsl_generate_module_manifest.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+#
+# test_fsl_generate_module_manifest.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os.path as op
+import json
+import shlex
+import textwrap as tw
+
+from . import tempdir, touch
+
+import fsl.add_module.routines as routines
+
+import fsl.scripts.fsl_generate_module_manifest as fgmm
+
+
+def test_fsl_generate_module_manifest():
+ plugins = ['1.zip', '2.zip', '3.zip']
+ existing = tw.dedent("""
+ [{
+ "name": "1.zip",
+ "url": "http://a.com/1.zip",
+ "category": "cat1",
+ "description": "desc1",
+ "checksum": "baba",
+ "size": 3
+ },
+ {
+ "name": "2.zip",
+ "url": "http://a.com/2.zip",
+ "category": "cat2",
+ "description": "desc2",
+ "checksum": "abcdf",
+ "size": 4
+ },
+ {
+ "name": "3.zip",
+ "url": "http://a.com/3.zip",
+ "category": "cat3",
+ "description": "desc3",
+ "checksum": "aew",
+ "size": 10
+ }]
+ """).strip()
+ with tempdir():
+ for p in plugins:
+ touch(p)
+
+ fgmm.main(shlex.split('-o manifest.json') + plugins)
+
+ with open('manifest.json', 'rt', encoding='utf-8') as f:
+ got = json.load(f)
+ assert len(got) == len(plugins)
+ for expp, gotp in zip(plugins, got):
+ assert gotp['name'] == expp
+ assert gotp['size'] == op.getsize(expp)
+ assert gotp['checksum'] == routines.calcChecksum(expp)
+
+ with open('existing.json', 'wt', encoding='utf-8') as f:
+ f.write(existing)
+
+ fgmm.main(shlex.split('-o manifest.json -m existing.json') + plugins)
+
+ with open('manifest.json', 'rt', encoding='utf-8') as f:
+ got = json.load(f)
+
+ assert len(got) == len(plugins)
+ for i, (expp, gotp) in enumerate(zip(plugins, got), 1):
+ assert gotp['name'] == expp
+ assert gotp['size'] == op.getsize(expp)
+ assert gotp['checksum'] == routines.calcChecksum(expp)
+ assert gotp['category'] == f'cat{i}'
+ assert gotp['description'] == f'desc{i}'
+ assert gotp['url'] == f'http://a.com/{i}.zip'
diff --git a/fsl/add_module/tests/test_plugin_manifest.py b/fsl/add_module/tests/test_manifest.py
similarity index 89%
rename from fsl/add_module/tests/test_plugin_manifest.py
rename to fsl/add_module/tests/test_manifest.py
index d04c96b4114fff6843433e9bd0bf0e003843a2d9..61aff61afb5c10f94325a782a52beb8d7c0b7cc6 100644
--- a/fsl/add_module/tests/test_plugin_manifest.py
+++ b/fsl/add_module/tests/test_manifest.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
#
-# test_plugin_manifest.py -
+# test_manifest.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
@@ -14,7 +14,7 @@ from unittest import mock
from . import tempdir, touch
-import fsl.add_module.plugin_manifest as plgman
+import fsl.add_module.manifest as plgman
def test_downloadManifest():
@@ -115,3 +115,17 @@ def test_addPlugin():
assert manifest['plugin13'].url == 'http://abc.com/plugin13'
manifest.addPlugin('http://abc.com/plugin14', name='plugin13')
assert manifest['plugin13'].url == 'http://abc.com/plugin14'
+
+
+def test_genManifest():
+ m = plgman.Manifest()
+ m['plugin1'] = plgman.Plugin(url='http://a.b.c.1', name='plugin1', category='abc')
+ m['plugin2'] = plgman.Plugin(url='http://a.b.c.2', name='plugin2', description='Second')
+
+ exp = [{'name' : 'plugin1', 'url' : 'http://a.b.c.1', 'category' : 'abc'},
+ {'name' : 'plugin2', 'url' : 'http://a.b.c.2', 'category' : 'uncategorised',
+ 'description' : 'Second'}]
+
+ got = plgman.genManifest(m)
+
+ assert exp == json.loads(got)
diff --git a/fsl/add_module/tests/test_ui.py b/fsl/add_module/tests/test_ui.py
index da7fdfc4f8134751d6fd15bdc7694585a1b6414a..f476aa4dcd4aa6ea089966496d3b52ad22198514 100644
--- a/fsl/add_module/tests/test_ui.py
+++ b/fsl/add_module/tests/test_ui.py
@@ -14,9 +14,9 @@ import pathlib as plib
import pytest
-import fsl.add_module.routines as routines
-import fsl.add_module.plugin_manifest as plgman
-import fsl.add_module.ui as ui
+import fsl.add_module.routines as routines
+import fsl.add_module.manifest as plgman
+import fsl.add_module.ui as ui
from . import tempdir, server, mock_input, make_archive, touch
diff --git a/fsl/add_module/ui.py b/fsl/add_module/ui.py
index d73af279d9654122f13af43fc29d7d176cf236d8..506648eed9b97fb4a58e79acbe8dca9ad97b24ad 100644
--- a/fsl/add_module/ui.py
+++ b/fsl/add_module/ui.py
@@ -14,22 +14,22 @@ import pathlib
from typing import Tuple, List, Union
-from fsl.add_module.routines import (expand,
- calcChecksum,
- downloadFile,
- CorruptArchive,
- extractArchive)
-from fsl.add_module.plugin_manifest import (Plugin,
- Manifest,
- downloadManifest)
-from fsl.add_module.messages import (info,
- important,
- question,
- warning,
- error,
- prompt,
- EMPHASIS,
- UNDERLINE)
+from fsl.add_module.routines import (expand,
+ calcChecksum,
+ downloadFile,
+ CorruptArchive,
+ extractArchive)
+from fsl.add_module.manifest import (Plugin,
+ Manifest,
+ downloadManifest)
+from fsl.add_module.messages import (info,
+ important,
+ question,
+ warning,
+ error,
+ prompt,
+ EMPHASIS,
+ UNDERLINE)
def downloadPluginManifest(url : Union[str, pathlib.Path]) -> Manifest:
@@ -62,10 +62,15 @@ def printPlugin(plugin : Plugin,
:arg verbose: If ``True``, more information is printed.
"""
- if index:
- info(f'{index:2d} {plugin.name:25s}', EMPHASIS, indent=2)
- else:
- info(f'{plugin.name:25s}', EMPHASIS, indent=2)
+ header = plugin.name
+
+ if index is not None:
+ header = f'{index:2d} {header}'
+ if plugin.size is not None:
+ mbytes = plugin.size / 1048576
+ header = f'{header} [{mbytes:0.2f} MB]'
+
+ info(header, EMPHASIS, indent=2)
if plugin.version is not None:
info(f'[version {plugin.version}]', indent=4)
@@ -73,11 +78,11 @@ def printPlugin(plugin : Plugin,
if plugin.description is not None:
info(plugin.description, indent=4, wrap=True)
- if plugin.termsOfUse is not None:
+ if plugin.terms_of_use is not None:
info('Installation of this plugin is subject '
'to the following terms of use:',
indent=4)
- info(plugin.termsOfUse, indent=6, wrap=True)
+ info(plugin.terms_of_use, indent=6, wrap=True)
if verbose:
for item in ('url', 'destination', 'checksum'):
diff --git a/fsl/scripts/fsl_add_module.py b/fsl/scripts/fsl_add_module.py
index edfb74450207a1c681c422ef658b9876874cffd2..787d3bb508b30801260ba5ecb604741008975066 100755
--- a/fsl/scripts/fsl_add_module.py
+++ b/fsl/scripts/fsl_add_module.py
@@ -35,9 +35,9 @@ Plugin manifest file
The plugin manifest file is a JSON file which contains information about all
plugins that are available. An official manifest file is hosted on the FSL
-website, but an alternative manifest file may be specified when this script
-is invoked. See the :mod:`.plugin_manifest` module for more details on the
-format of a plugin manifest file.
+website, but an alternative manifest file may be specified when this script is
+invoked. See the :mod:`.manifest` module for more details on the format of a
+plugin manifest file.
Usage examples
@@ -102,24 +102,32 @@ import argparse
from typing import List, Tuple
-import fsl.add_module.ui as ui
-import fsl.add_module.routines as routines
-import fsl.add_module.plugin_manifest as plgman
-from fsl.add_module import __version__
-from fsl.add_module.messages import (info,
- important,
- warning,
- error,
- EMPHASIS,
- UNDERLINE)
-
-
-DEFAULT_MANIFEST_URL = 'http://fsl.fmrib.ox.ac.uk/fslcourse/downloads/manifest.json'
-"""Location of the official FSL plugin manifest file, downloaded if an
-alternate manifest file is not specified.
+import fsl.add_module.ui as ui
+import fsl.add_module.routines as routines
+import fsl.add_module.manifest as plgman
+from fsl.add_module import __version__
+from fsl.add_module.messages import (info,
+ important,
+ warning,
+ error,
+ EMPHASIS,
+ UNDERLINE)
+
+
+OFFICIAL_MANIFEST_URLS = {
+ 'fslcourse' : 'http://fsl.fmrib.ox.ac.uk/fslcourse/downloads/manifest.json',
+ 'gradcourse' : 'https://fsl.fmrib.ox.ac.uk/fslcourse/graduate/downloads/manifest.json'
+}
+"""Locations of the official FSL plugin manifest files, downloaded if an
+alternate manifest file is not specified. These 'built-in' manifest URLs
+can be referred to by their aliases.
"""
+DEFAULT_MANIFEST = 'fslcourse'
+"""Default manifest to use, if one is not specified."""
+
+
DEFAULT_CATEGORY = 'fsl_course_data'
"""Default value for the ``--category`` command-line option, when the
user does not specify an alternative ``--manifest`` or ``--category``.
@@ -139,9 +147,12 @@ def parseArgs(argv : List[str]) -> argparse.Namespace:
'version' : 'Print version and exit.',
'verbose' : 'Output more information.',
'list' : 'Print all available modules and exit. All other '
- 'options, apart from --manifest, are ignored.',
+ 'options, apart from --manifest and --verbose, are '
+ 'ignored.',
'module' : 'Name or URL of FSL module to download.',
- 'manifest' : 'URL to module manifest file.',
+ 'manifest' : 'Name of official manifest file to download, or '
+ 'alternate URL to module manifest file (default: '
+ f'{DEFAULT_MANIFEST})',
'archiveDir' : 'Directory to cache downloaded files in.',
'category' : 'Only display available modules from the specified '
'category. Defaults to "fsl_course_data", unless '
@@ -187,12 +198,23 @@ def parseArgs(argv : List[str]) -> argparse.Namespace:
# course data. If we are using a custom manifest,
# we don't want to set a default category.
if args.manifest is None:
- args.manifest = DEFAULT_MANIFEST_URL
- if args.manifest == DEFAULT_MANIFEST_URL and args.category is None:
+ args.manifest = DEFAULT_MANIFEST
+ if args.manifest == DEFAULT_MANIFEST and args.category is None:
args.category = DEFAULT_CATEGORY
if args.category == 'all':
args.category = None
+ # Built-in manifest referred to by alias, e.g. "fslcourse"?
+ if not (args.manifest is None or
+ args.manifest.startswith('http') or
+ op.exists(args.manifest)):
+ try:
+ args.manifest = OFFICIAL_MANIFEST_URLS[args.manifest]
+ except KeyError:
+ warning(f'Unknown manifest: {args.manifest}. Known manifests: ' +
+ ", ".join(OFFICIAL_MANIFEST_URLS.keys()) + ' (or give a '
+ 'URL to an alternative manifest file)')
+
if args.archiveDir:
args.archiveDir = op.abspath(op.expanduser(args.archiveDir))
diff --git a/fsl/scripts/fsl_generate_module_manifest.py b/fsl/scripts/fsl_generate_module_manifest.py
new file mode 100644
index 0000000000000000000000000000000000000000..c4d89c1e9b5b85a14c0f79530f7f400565a9b2ee
--- /dev/null
+++ b/fsl/scripts/fsl_generate_module_manifest.py
@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+#
+# fsl_generate_module_manifest.py - Generate a template manifest.json file for
+# use by fsl_add_module.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""The ``fsl_generate_module_manifest`` script is intended for use by FSL
+dataset maintainers. It can be used to generate a JSON manifest file which
+describes a set of archive/plugin files that are to be made available for
+download.
+"""
+
+
+import sys
+import argparse
+import contextlib as ctxlib
+import os.path as op
+
+from typing import List
+
+import fsl.add_module.manifest as plgman
+import fsl.add_module.routines as routines
+
+
+def parseArgs(argv : List[str]) -> argparse.Namespace:
+ """Parse command-line arguments. The user is expected to provide a set of
+ input archive/plugin files and a destination file to save the JSON
+ manifest. An existing manifest file/URL can optionally be provided -
+ metadata will be copied over from this file for archive files with
+ matching names.
+ """
+
+ parser = argparse.ArgumentParser(
+ 'fsl_generate_module_manifest',
+ usage='fsl_generate_module_manifest [options] infile [infile ...]',
+ description='Generate a manifest.json file for use by fsl_add_module')
+
+ parser.add_argument('-m', '--manifest',
+ help='Previous version of manifest to copy metadata '
+ 'from. The name, category, url, description, and '
+ 'destination fields are all copied across for '
+ 'archive files with matching names.')
+ parser.add_argument('-o', '--outfile',
+ help='Location to save new manifest (default: stdout)')
+ parser.add_argument('infile', nargs='+',
+ help='Archive file to include in new manifest.')
+
+ return parser.parse_args(argv)
+
+
+def main(argv=None):
+ """Main routine. Generates a JSON manifest describing a set of files.
+ """
+ if argv is None:
+ argv = sys.argv[1:]
+
+ args = parseArgs(argv)
+
+ if args.manifest is not None:
+ oldmanifest = plgman.downloadManifest(args.manifest)
+ oldmanifest = {p.rawFileName : p for p in oldmanifest.values()}
+ else:
+ oldmanifest = plgman.Manifest()
+
+ newmanifest = plgman.Manifest()
+
+ for infile in args.infile:
+ basename = op.basename(infile)
+
+ if basename in oldmanifest:
+ plugin = oldmanifest[basename]
+ else:
+ plugin = plgman.Plugin(url='', name=basename)
+
+ plugin.size = op.getsize(infile)
+ plugin.checksum = routines.calcChecksum(infile)
+ newmanifest[plugin.name] = plugin
+
+ newmanifest = plgman.genManifest(newmanifest)
+
+ if args.outfile is None:
+ print(newmanifest)
+ else:
+ with open(args.outfile, 'wt', encoding='utf-8') as f:
+ f.write(newmanifest)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/setup.py b/setup.py
index 366f3113f82872901caceb69d97c7b2be4260e20..e35bd2053ae78c95df46debe6b5212c25a91dfda 100644
--- a/setup.py
+++ b/setup.py
@@ -52,7 +52,8 @@ setup(
entry_points={
'console_scripts' : [
- 'fsl_add_module = fsl.scripts.fsl_add_module:main',
+ 'fsl_add_module = fsl.scripts.fsl_add_module:main',
+ 'fsl_generate_module_manifest = fsl.scripts.fsl_generate_module_manifest:main',
]
}
)