mirror of
https://github.com/gsi-upm/senpy
synced 2024-11-22 00:02:28 +00:00
Several changes
* Add flag to run tests (and exit, or run the server) * Add ntriples outformat * Modify dependency installation logic to avoid installing several times * Add encoded URLs as base/prefix * Allow plugin activation to fail
This commit is contained in:
commit
a3eb8f196c
10
docker-compose.dev.yml
Normal file
10
docker-compose.dev.yml
Normal file
@ -0,0 +1,10 @@
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version: '3'
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services:
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senpy:
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image: "${IMAGENAME-gsiupm/senpy}:${VERSION-latest}"
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entrypoint: ["/bin/bash"]
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working_dir: "/senpy-plugins"
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ports:
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- 5000:5000
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volumes:
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- ".:/usr/src/app/"
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9
docker-compose.test.yml
Normal file
9
docker-compose.test.yml
Normal file
@ -0,0 +1,9 @@
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version: '3'
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services:
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test:
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image: "${IMAGENAME-gsiupm/senpy}:${VERSION-dev}"
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entrypoint: ["py.test"]
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volumes:
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- ".:/usr/src/app/"
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command:
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[]
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11
docker-compose.yml
Normal file
11
docker-compose.yml
Normal file
@ -0,0 +1,11 @@
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version: '3'
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services:
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senpy:
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image: "${IMAGENAME-gsiupm/senpy}:${VERSION-dev}"
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build:
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context: .
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dockerfile: Dockerfile${PYVERSION--2.7}
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ports:
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- 5001:5000
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volumes:
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- "./data:/data"
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@ -78,10 +78,15 @@ def main():
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help='Do not run a server, only install plugin dependencies')
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help='Do not run a server, only install plugin dependencies')
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parser.add_argument(
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parser.add_argument(
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'--only-test',
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'--only-test',
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'-t',
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action='store_true',
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action='store_true',
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default=False,
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default=False,
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help='Do not run a server, just test all plugins')
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help='Do not run a server, just test all plugins')
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parser.add_argument(
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'--test',
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'-t',
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action='store_true',
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default=False,
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help='Test all plugins before launching the server')
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parser.add_argument(
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parser.add_argument(
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'--only-list',
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'--only-list',
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'--list',
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'--list',
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@ -99,12 +104,24 @@ def main():
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action='store_false',
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action='store_false',
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default=True,
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default=True,
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help='Run a threaded server')
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help='Run a threaded server')
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parser.add_argument(
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'--no-deps',
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'-n',
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action='store_true',
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default=False,
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help='Skip installing dependencies')
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parser.add_argument(
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parser.add_argument(
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'--version',
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'--version',
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'-v',
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'-v',
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action='store_true',
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action='store_true',
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default=False,
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default=False,
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help='Output the senpy version and exit')
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help='Output the senpy version and exit')
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parser.add_argument(
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'--allow-fail',
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'--fail',
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action='store_true',
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default=False,
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help='Do not exit if some plugins fail to activate')
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args = parser.parse_args()
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args = parser.parse_args()
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if args.version:
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if args.version:
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print('Senpy version {}'.format(senpy.__version__))
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print('Senpy version {}'.format(senpy.__version__))
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@ -119,19 +136,27 @@ def main():
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data_folder=args.data_folder)
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data_folder=args.data_folder)
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if args.only_list:
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if args.only_list:
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plugins = sp.plugins()
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plugins = sp.plugins()
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maxwidth = max(len(x.id) for x in plugins)
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maxname = max(len(x.name) for x in plugins)
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maxversion = max(len(x.version) for x in plugins)
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print('Found {} plugins:'.format(len(plugins)))
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for plugin in plugins:
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for plugin in plugins:
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import inspect
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import inspect
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fpath = inspect.getfile(plugin.__class__)
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fpath = inspect.getfile(plugin.__class__)
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print('{: <{width}} @ {}'.format(plugin.id, fpath, width=maxwidth))
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print('\t{: <{maxname}} @ {: <{maxversion}} -> {}'.format(plugin.name,
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plugin.version,
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fpath,
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maxname=maxname,
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maxversion=maxversion))
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return
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return
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sp.install_deps()
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if not args.no_deps:
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sp.install_deps()
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if args.only_install:
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if args.only_install:
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return
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return
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sp.activate_all()
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sp.activate_all(allow_fail=args.allow_fail)
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if args.only_test:
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if args.test or args.only_test:
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easy_test(sp.plugins(), debug=args.debug)
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easy_test(sp.plugins(), debug=args.debug)
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return
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if args.only_test:
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return
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print('Senpy version {}'.format(senpy.__version__))
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print('Senpy version {}'.format(senpy.__version__))
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print('Server running on port %s:%d. Ctrl+C to quit' % (args.host,
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print('Server running on port %s:%d. Ctrl+C to quit' % (args.host,
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args.port))
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args.port))
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23
senpy/api.py
23
senpy/api.py
@ -3,6 +3,10 @@ from .models import Error, Results, Entry, from_string
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import logging
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import logging
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logger = logging.getLogger(__name__)
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logger = logging.getLogger(__name__)
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boolean = [True, False]
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API_PARAMS = {
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API_PARAMS = {
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"algorithm": {
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"algorithm": {
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"aliases": ["algorithms", "a", "algo"],
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"aliases": ["algorithms", "a", "algo"],
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@ -13,14 +17,14 @@ API_PARAMS = {
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"expanded-jsonld": {
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"expanded-jsonld": {
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"@id": "expanded-jsonld",
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"@id": "expanded-jsonld",
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"aliases": ["expanded"],
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"aliases": ["expanded"],
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"options": "boolean",
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"options": boolean,
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"required": True,
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"required": True,
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"default": False
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"default": False
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},
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},
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"with_parameters": {
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"with_parameters": {
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"aliases": ['withparameters',
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"aliases": ['withparameters',
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'with-parameters'],
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'with-parameters'],
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"options": "boolean",
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"options": boolean,
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"default": False,
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"default": False,
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"required": True
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"required": True
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},
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},
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@ -29,14 +33,14 @@ API_PARAMS = {
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"aliases": ["o"],
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"aliases": ["o"],
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"default": "json-ld",
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"default": "json-ld",
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"required": True,
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"required": True,
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"options": ["json-ld", "turtle"],
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"options": ["json-ld", "turtle", "ntriples"],
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},
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},
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"help": {
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"help": {
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"@id": "help",
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"@id": "help",
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"description": "Show additional help to know more about the possible parameters",
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"description": "Show additional help to know more about the possible parameters",
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"aliases": ["h"],
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"aliases": ["h"],
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"required": True,
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"required": True,
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"options": "boolean",
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"options": boolean,
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"default": False
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"default": False
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},
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},
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"emotionModel": {
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"emotionModel": {
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@ -83,7 +87,7 @@ WEB_PARAMS = {
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"aliases": ["headers"],
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"aliases": ["headers"],
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"required": True,
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"required": True,
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"default": False,
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"default": False,
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"options": "boolean"
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"options": boolean
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},
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},
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}
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}
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@ -132,7 +136,7 @@ NIF_PARAMS = {
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"aliases": ["u"],
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"aliases": ["u"],
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"required": False,
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"required": False,
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"default": "RFC5147String",
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"default": "RFC5147String",
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"options": "RFC5147String"
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"options": ["RFC5147String", ]
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}
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}
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}
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}
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@ -159,7 +163,7 @@ def parse_params(indict, *specs):
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wrong_params[param] = spec[param]
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wrong_params[param] = spec[param]
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continue
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continue
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if "options" in options:
|
if "options" in options:
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if options["options"] == "boolean":
|
if options["options"] == boolean:
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outdict[param] = outdict[param] in [None, True, 'true', '1']
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outdict[param] = outdict[param] in [None, True, 'true', '1']
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elif outdict[param] not in options["options"]:
|
elif outdict[param] not in options["options"]:
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wrong_params[param] = spec[param]
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wrong_params[param] = spec[param]
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@ -172,7 +176,7 @@ def parse_params(indict, *specs):
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errors=wrong_params)
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errors=wrong_params)
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raise message
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raise message
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if 'algorithm' in outdict and not isinstance(outdict['algorithm'], list):
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if 'algorithm' in outdict and not isinstance(outdict['algorithm'], list):
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outdict['algorithm'] = outdict['algorithm'].split(',')
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outdict['algorithm'] = list(outdict['algorithm'].split(','))
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return outdict
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return outdict
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@ -190,7 +194,8 @@ def parse_call(params):
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params = parse_params(params, NIF_PARAMS)
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params = parse_params(params, NIF_PARAMS)
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if params['informat'] == 'text':
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if params['informat'] == 'text':
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results = Results()
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results = Results()
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entry = Entry(nif__isString=params['input'])
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entry = Entry(nif__isString=params['input'],
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id='#') # Use @base
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results.entries.append(entry)
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results.entries.append(entry)
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elif params['informat'] == 'json-ld':
|
elif params['informat'] == 'json-ld':
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results = from_string(params['input'], cls=Results)
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results = from_string(params['input'], cls=Results)
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@ -18,15 +18,15 @@
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Blueprints for Senpy
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Blueprints for Senpy
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"""
|
"""
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from flask import (Blueprint, request, current_app, render_template, url_for,
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from flask import (Blueprint, request, current_app, render_template, url_for,
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jsonify)
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jsonify, redirect)
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from .models import Error, Response, Help, Plugins, read_schema, dump_schema, Datasets
|
from .models import Error, Response, Help, Plugins, read_schema, dump_schema, Datasets
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from . import api
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from . import api
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from .version import __version__
|
from .version import __version__
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from functools import wraps
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from functools import wraps
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|
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import logging
|
import logging
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import traceback
|
|
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import json
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import json
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import base64
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|
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logger = logging.getLogger(__name__)
|
logger = logging.getLogger(__name__)
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|
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@ -34,6 +34,24 @@ api_blueprint = Blueprint("api", __name__)
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demo_blueprint = Blueprint("demo", __name__, template_folder='templates')
|
demo_blueprint = Blueprint("demo", __name__, template_folder='templates')
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ns_blueprint = Blueprint("ns", __name__)
|
ns_blueprint = Blueprint("ns", __name__)
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|
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_mimetypes_r = {'json-ld': ['application/ld+json'],
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|
'turtle': ['text/turtle'],
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'ntriples': ['application/n-triples'],
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'text': ['text/plain']}
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|
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|
MIMETYPES = {}
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|
|
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|
for k, vs in _mimetypes_r.items():
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|
for v in vs:
|
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|
if v in MIMETYPES:
|
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|
raise Exception('MIMETYPE {} specified for two formats: {} and {}'.format(v,
|
||||||
|
v,
|
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|
MIMETYPES[v]))
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|
MIMETYPES[v] = k
|
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|
|
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|
DEFAULT_MIMETYPE = 'application/ld+json'
|
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|
DEFAULT_FORMAT = 'json-ld'
|
||||||
|
|
||||||
|
|
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def get_params(req):
|
def get_params(req):
|
||||||
if req.method == 'POST':
|
if req.method == 'POST':
|
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@ -45,6 +63,30 @@ def get_params(req):
|
|||||||
return indict
|
return indict
|
||||||
|
|
||||||
|
|
||||||
|
def encoded_url(url=None, base=None):
|
||||||
|
code = ''
|
||||||
|
if not url:
|
||||||
|
if request.method == 'GET':
|
||||||
|
url = request.full_path[1:] # Remove the first slash
|
||||||
|
else:
|
||||||
|
hash(frozenset(request.form.params().items()))
|
||||||
|
code = 'hash:{}'.format(hash)
|
||||||
|
|
||||||
|
code = code or base64.urlsafe_b64encode(url.encode()).decode()
|
||||||
|
|
||||||
|
if base:
|
||||||
|
return base + code
|
||||||
|
return url_for('api.decode', code=code, _external=True)
|
||||||
|
|
||||||
|
|
||||||
|
def decoded_url(code, base=None):
|
||||||
|
if code.startswith('hash:'):
|
||||||
|
raise Exception('Can not decode a URL for a POST request')
|
||||||
|
base = base or request.url_root
|
||||||
|
path = base64.urlsafe_b64decode(code.encode()).decode()
|
||||||
|
return base + path
|
||||||
|
|
||||||
|
|
||||||
@demo_blueprint.route('/')
|
@demo_blueprint.route('/')
|
||||||
def index():
|
def index():
|
||||||
ev = str(get_params(request).get('evaluation', False))
|
ev = str(get_params(request).get('evaluation', False))
|
||||||
@ -59,13 +101,22 @@ def index():
|
|||||||
def context(entity="context"):
|
def context(entity="context"):
|
||||||
context = Response._context
|
context = Response._context
|
||||||
context['@vocab'] = url_for('ns.index', _external=True)
|
context['@vocab'] = url_for('ns.index', _external=True)
|
||||||
|
context['endpoint'] = url_for('api.api_root', _external=True)
|
||||||
return jsonify({"@context": context})
|
return jsonify({"@context": context})
|
||||||
|
|
||||||
|
|
||||||
|
@api_blueprint.route('/d/<code>')
|
||||||
|
def decode(code):
|
||||||
|
try:
|
||||||
|
return redirect(decoded_url(code))
|
||||||
|
except Exception:
|
||||||
|
return Error('invalid URL').flask()
|
||||||
|
|
||||||
|
|
||||||
@ns_blueprint.route('/') # noqa: F811
|
@ns_blueprint.route('/') # noqa: F811
|
||||||
def index():
|
def index():
|
||||||
context = Response._context
|
context = Response._context.copy()
|
||||||
context['@vocab'] = url_for('.ns', _external=True)
|
context['endpoint'] = url_for('api.api_root', _external=True)
|
||||||
return jsonify({"@context": context})
|
return jsonify({"@context": context})
|
||||||
|
|
||||||
|
|
||||||
@ -81,7 +132,7 @@ def basic_api(f):
|
|||||||
default_params = {
|
default_params = {
|
||||||
'inHeaders': False,
|
'inHeaders': False,
|
||||||
'expanded-jsonld': False,
|
'expanded-jsonld': False,
|
||||||
'outformat': 'json-ld',
|
'outformat': None,
|
||||||
'with_parameters': True,
|
'with_parameters': True,
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -100,29 +151,34 @@ def basic_api(f):
|
|||||||
request.parameters = params
|
request.parameters = params
|
||||||
response = f(*args, **kwargs)
|
response = f(*args, **kwargs)
|
||||||
except (Exception) as ex:
|
except (Exception) as ex:
|
||||||
if current_app.debug:
|
if current_app.debug or current_app.config['TESTING']:
|
||||||
raise
|
raise
|
||||||
if not isinstance(ex, Error):
|
if not isinstance(ex, Error):
|
||||||
msg = "{}:\n\t{}".format(ex,
|
msg = "{}".format(ex)
|
||||||
traceback.format_exc())
|
|
||||||
ex = Error(message=msg, status=500)
|
ex = Error(message=msg, status=500)
|
||||||
logger.exception('Error returning analysis result')
|
|
||||||
response = ex
|
response = ex
|
||||||
response.parameters = raw_params
|
response.parameters = raw_params
|
||||||
logger.error(ex)
|
logger.exception(ex)
|
||||||
|
|
||||||
if 'parameters' in response and not params['with_parameters']:
|
if 'parameters' in response and not params['with_parameters']:
|
||||||
del response.parameters
|
del response.parameters
|
||||||
|
|
||||||
logger.info('Response: {}'.format(response))
|
logger.info('Response: {}'.format(response))
|
||||||
|
mime = request.accept_mimetypes\
|
||||||
|
.best_match(MIMETYPES.keys(),
|
||||||
|
DEFAULT_MIMETYPE)
|
||||||
|
|
||||||
|
mimeformat = MIMETYPES.get(mime, DEFAULT_FORMAT)
|
||||||
|
outformat = params['outformat'] or mimeformat
|
||||||
|
|
||||||
return response.flask(
|
return response.flask(
|
||||||
in_headers=params['inHeaders'],
|
in_headers=params['inHeaders'],
|
||||||
headers=headers,
|
headers=headers,
|
||||||
prefix=url_for('.api_root', _external=True),
|
prefix=params.get('prefix', encoded_url()),
|
||||||
context_uri=url_for('api.context',
|
context_uri=url_for('api.context',
|
||||||
entity=type(response).__name__,
|
entity=type(response).__name__,
|
||||||
_external=True),
|
_external=True),
|
||||||
outformat=params['outformat'],
|
outformat=outformat,
|
||||||
expanded=params['expanded-jsonld'])
|
expanded=params['expanded-jsonld'])
|
||||||
|
|
||||||
return decorated_function
|
return decorated_function
|
||||||
|
@ -18,14 +18,9 @@ import errno
|
|||||||
import logging
|
import logging
|
||||||
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
from . import gsitk_compat
|
||||||
|
|
||||||
try:
|
logger = logging.getLogger(__name__)
|
||||||
from gsitk.datasets.datasets import DatasetManager
|
|
||||||
GSITK_AVAILABLE = True
|
|
||||||
except ImportError:
|
|
||||||
logger.warn('GSITK is not installed. Some functions will be unavailable.')
|
|
||||||
GSITK_AVAILABLE = False
|
|
||||||
|
|
||||||
|
|
||||||
class Senpy(object):
|
class Senpy(object):
|
||||||
@ -95,7 +90,7 @@ class Senpy(object):
|
|||||||
if plugin in self._plugins:
|
if plugin in self._plugins:
|
||||||
return self._plugins[plugin]
|
return self._plugins[plugin]
|
||||||
|
|
||||||
results = self.plugins(id='plugins/{}'.format(name))
|
results = self.plugins(id='endpoint:plugins/{}'.format(name))
|
||||||
|
|
||||||
if not results:
|
if not results:
|
||||||
return Error(message="Plugin not found", status=404)
|
return Error(message="Plugin not found", status=404)
|
||||||
@ -167,8 +162,7 @@ class Senpy(object):
|
|||||||
yield i
|
yield i
|
||||||
|
|
||||||
def install_deps(self):
|
def install_deps(self):
|
||||||
for plugin in self.plugins(is_activated=True):
|
plugins.install_deps(*self.plugins())
|
||||||
plugins.install_deps(plugin)
|
|
||||||
|
|
||||||
def analyse(self, request):
|
def analyse(self, request):
|
||||||
"""
|
"""
|
||||||
@ -203,16 +197,14 @@ class Senpy(object):
|
|||||||
raise Error(
|
raise Error(
|
||||||
status=404,
|
status=404,
|
||||||
message="The dataset '{}' is not valid".format(dataset))
|
message="The dataset '{}' is not valid".format(dataset))
|
||||||
dm = DatasetManager()
|
dm = gsitk_compat.DatasetManager()
|
||||||
datasets = dm.prepare_datasets(datasets_name)
|
datasets = dm.prepare_datasets(datasets_name)
|
||||||
return datasets
|
return datasets
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def datasets(self):
|
def datasets(self):
|
||||||
if not GSITK_AVAILABLE:
|
|
||||||
raise Exception('GSITK is not available. Install it to use this function.')
|
|
||||||
self._dataset_list = {}
|
self._dataset_list = {}
|
||||||
dm = DatasetManager()
|
dm = gsitk_compat.DatasetManager()
|
||||||
for item in dm.get_datasets():
|
for item in dm.get_datasets():
|
||||||
for key in item:
|
for key in item:
|
||||||
if key in self._dataset_list:
|
if key in self._dataset_list:
|
||||||
@ -223,8 +215,6 @@ class Senpy(object):
|
|||||||
return self._dataset_list
|
return self._dataset_list
|
||||||
|
|
||||||
def evaluate(self, params):
|
def evaluate(self, params):
|
||||||
if not GSITK_AVAILABLE:
|
|
||||||
raise Exception('GSITK is not available. Install it to use this function.')
|
|
||||||
logger.debug("evaluating request: {}".format(params))
|
logger.debug("evaluating request: {}".format(params))
|
||||||
results = AggregatedEvaluation()
|
results = AggregatedEvaluation()
|
||||||
results.parameters = params
|
results.parameters = params
|
||||||
@ -318,10 +308,15 @@ class Senpy(object):
|
|||||||
else:
|
else:
|
||||||
self._default = self._plugins[value.lower()]
|
self._default = self._plugins[value.lower()]
|
||||||
|
|
||||||
def activate_all(self, sync=True):
|
def activate_all(self, sync=True, allow_fail=False):
|
||||||
ps = []
|
ps = []
|
||||||
for plug in self._plugins.keys():
|
for plug in self._plugins.keys():
|
||||||
ps.append(self.activate_plugin(plug, sync=sync))
|
try:
|
||||||
|
self.activate_plugin(plug, sync=sync)
|
||||||
|
except Exception as ex:
|
||||||
|
if not allow_fail:
|
||||||
|
raise
|
||||||
|
logger.error('Could not activate {}: {}'.format(plug, ex))
|
||||||
return ps
|
return ps
|
||||||
|
|
||||||
def deactivate_all(self, sync=True):
|
def deactivate_all(self, sync=True):
|
||||||
@ -346,6 +341,7 @@ class Senpy(object):
|
|||||||
logger.info(msg)
|
logger.info(msg)
|
||||||
success = True
|
success = True
|
||||||
self._set_active(plugin, success)
|
self._set_active(plugin, success)
|
||||||
|
return success
|
||||||
|
|
||||||
def activate_plugin(self, plugin_name, sync=True):
|
def activate_plugin(self, plugin_name, sync=True):
|
||||||
plugin_name = plugin_name.lower()
|
plugin_name = plugin_name.lower()
|
||||||
@ -357,7 +353,7 @@ class Senpy(object):
|
|||||||
logger.info("Activating plugin: {}".format(plugin.name))
|
logger.info("Activating plugin: {}".format(plugin.name))
|
||||||
|
|
||||||
if sync or 'async' in plugin and not plugin.async:
|
if sync or 'async' in plugin and not plugin.async:
|
||||||
self._activate(plugin)
|
return self._activate(plugin)
|
||||||
else:
|
else:
|
||||||
th = Thread(target=partial(self._activate, plugin))
|
th = Thread(target=partial(self._activate, plugin))
|
||||||
th.start()
|
th.start()
|
||||||
|
23
senpy/gsitk_compat.py
Normal file
23
senpy/gsitk_compat.py
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
import logging
|
||||||
|
|
||||||
|
logger = logging.getLogger(__name__)
|
||||||
|
|
||||||
|
MSG = 'GSITK is not (properly) installed.'
|
||||||
|
IMPORTMSG = '{} Some functions will be unavailable.'.format(MSG)
|
||||||
|
RUNMSG = '{} Install it to use this function.'.format(MSG)
|
||||||
|
|
||||||
|
|
||||||
|
def raise_exception(*args, **kwargs):
|
||||||
|
raise Exception(RUNMSG)
|
||||||
|
|
||||||
|
|
||||||
|
try:
|
||||||
|
from gsitk.datasets.datasets import DatasetManager
|
||||||
|
from gsitk.evaluation.evaluation import Evaluation as Eval
|
||||||
|
from sklearn.pipeline import Pipeline
|
||||||
|
GSITK_AVAILABLE = True
|
||||||
|
modules = locals()
|
||||||
|
except ImportError:
|
||||||
|
logger.warn(IMPORTMSG)
|
||||||
|
GSITK_AVAILABLE = False
|
||||||
|
DatasetManager = Eval = Pipeline = raise_exception
|
@ -138,7 +138,7 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
|
|||||||
@property
|
@property
|
||||||
def id(self):
|
def id(self):
|
||||||
if '@id' not in self:
|
if '@id' not in self:
|
||||||
self['@id'] = ':{}_{}'.format(type(self).__name__, time.time())
|
self['@id'] = '_:{}_{}'.format(type(self).__name__, time.time())
|
||||||
return self['@id']
|
return self['@id']
|
||||||
|
|
||||||
@id.setter
|
@id.setter
|
||||||
@ -146,7 +146,7 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
|
|||||||
self['@id'] = value
|
self['@id'] = value
|
||||||
|
|
||||||
def flask(self,
|
def flask(self,
|
||||||
in_headers=True,
|
in_headers=False,
|
||||||
headers=None,
|
headers=None,
|
||||||
outformat='json-ld',
|
outformat='json-ld',
|
||||||
**kwargs):
|
**kwargs):
|
||||||
@ -176,20 +176,22 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
|
|||||||
|
|
||||||
def serialize(self, format='json-ld', with_mime=False, **kwargs):
|
def serialize(self, format='json-ld', with_mime=False, **kwargs):
|
||||||
js = self.jsonld(**kwargs)
|
js = self.jsonld(**kwargs)
|
||||||
|
content = json.dumps(js, indent=2, sort_keys=True)
|
||||||
if format == 'json-ld':
|
if format == 'json-ld':
|
||||||
content = json.dumps(js, indent=2, sort_keys=True)
|
|
||||||
mimetype = "application/json"
|
mimetype = "application/json"
|
||||||
elif format in ['turtle', ]:
|
elif format in ['turtle', 'ntriples']:
|
||||||
logger.debug(js)
|
logger.debug(js)
|
||||||
content = json.dumps(js, indent=2, sort_keys=True)
|
base = kwargs.get('prefix')
|
||||||
g = Graph().parse(
|
g = Graph().parse(
|
||||||
data=content,
|
data=content,
|
||||||
format='json-ld',
|
format='json-ld',
|
||||||
base=kwargs.get('prefix'),
|
base=base,
|
||||||
context=self._context)
|
context=[self._context,
|
||||||
|
{'@base': base}])
|
||||||
logger.debug(
|
logger.debug(
|
||||||
'Parsing with prefix: {}'.format(kwargs.get('prefix')))
|
'Parsing with prefix: {}'.format(kwargs.get('prefix')))
|
||||||
content = g.serialize(format='turtle').decode('utf-8')
|
content = g.serialize(format=format,
|
||||||
|
base=base).decode('utf-8')
|
||||||
mimetype = 'text/{}'.format(format)
|
mimetype = 'text/{}'.format(format)
|
||||||
else:
|
else:
|
||||||
raise Error('Unknown outformat: {}'.format(format))
|
raise Error('Unknown outformat: {}'.format(format))
|
||||||
@ -205,25 +207,21 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
|
|||||||
expanded=False):
|
expanded=False):
|
||||||
|
|
||||||
result = self.serializable()
|
result = self.serializable()
|
||||||
if context_uri or with_context:
|
|
||||||
result['@context'] = context_uri or self._context
|
|
||||||
|
|
||||||
# result = jsonld.compact(result,
|
|
||||||
# self._context,
|
|
||||||
# options={
|
|
||||||
# 'base': prefix,
|
|
||||||
# 'expandContext': self._context,
|
|
||||||
# 'senpy': prefix
|
|
||||||
# })
|
|
||||||
if expanded:
|
if expanded:
|
||||||
result = jsonld.expand(
|
result = jsonld.expand(
|
||||||
result, options={'base': prefix,
|
result, options={'base': prefix,
|
||||||
'expandContext': self._context})
|
'expandContext': self._context})[0]
|
||||||
if not with_context:
|
if not with_context:
|
||||||
try:
|
try:
|
||||||
del result['@context']
|
del result['@context']
|
||||||
except KeyError:
|
except KeyError:
|
||||||
pass
|
pass
|
||||||
|
elif context_uri:
|
||||||
|
result['@context'] = context_uri
|
||||||
|
else:
|
||||||
|
result['@context'] = self._context
|
||||||
|
|
||||||
return result
|
return result
|
||||||
|
|
||||||
def validate(self, obj=None):
|
def validate(self, obj=None):
|
||||||
|
@ -3,6 +3,7 @@ standard_library.install_aliases()
|
|||||||
|
|
||||||
|
|
||||||
from future.utils import with_metaclass
|
from future.utils import with_metaclass
|
||||||
|
from functools import partial
|
||||||
|
|
||||||
import os.path
|
import os.path
|
||||||
import os
|
import os
|
||||||
@ -22,18 +23,11 @@ import nltk
|
|||||||
|
|
||||||
from .. import models, utils
|
from .. import models, utils
|
||||||
from .. import api
|
from .. import api
|
||||||
|
from .. import gsitk_compat
|
||||||
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
logger = logging.getLogger(__name__)
|
||||||
|
|
||||||
try:
|
|
||||||
from gsitk.evaluation.evaluation import Evaluation as Eval
|
|
||||||
from sklearn.pipeline import Pipeline
|
|
||||||
GSITK_AVAILABLE = True
|
|
||||||
except ImportError:
|
|
||||||
logger.warn('GSITK is not installed. Some functions will be unavailable.')
|
|
||||||
GSITK_AVAILABLE = False
|
|
||||||
|
|
||||||
|
|
||||||
class PluginMeta(models.BaseMeta):
|
class PluginMeta(models.BaseMeta):
|
||||||
_classes = {}
|
_classes = {}
|
||||||
@ -92,7 +86,7 @@ class Plugin(with_metaclass(PluginMeta, models.Plugin)):
|
|||||||
if info:
|
if info:
|
||||||
self.update(info)
|
self.update(info)
|
||||||
self.validate()
|
self.validate()
|
||||||
self.id = 'plugins/{}_{}'.format(self['name'], self['version'])
|
self.id = 'endpoint:plugins/{}_{}'.format(self['name'], self['version'])
|
||||||
self.is_activated = False
|
self.is_activated = False
|
||||||
self._lock = threading.Lock()
|
self._lock = threading.Lock()
|
||||||
self._directory = os.path.abspath(os.path.dirname(inspect.getfile(self.__class__)))
|
self._directory = os.path.abspath(os.path.dirname(inspect.getfile(self.__class__)))
|
||||||
@ -332,7 +326,7 @@ class Box(AnalysisPlugin):
|
|||||||
return self.transform(X)
|
return self.transform(X)
|
||||||
|
|
||||||
def as_pipe(self):
|
def as_pipe(self):
|
||||||
pipe = Pipeline([('plugin', self)])
|
pipe = gsitk_compat.Pipeline([('plugin', self)])
|
||||||
pipe.name = self.name
|
pipe.name = self.name
|
||||||
return pipe
|
return pipe
|
||||||
|
|
||||||
@ -530,7 +524,7 @@ def find_plugins(folders):
|
|||||||
yield fpath
|
yield fpath
|
||||||
|
|
||||||
|
|
||||||
def from_path(fpath, **kwargs):
|
def from_path(fpath, install_on_fail=False, **kwargs):
|
||||||
logger.debug("Loading plugin from {}".format(fpath))
|
logger.debug("Loading plugin from {}".format(fpath))
|
||||||
if fpath.endswith('.py'):
|
if fpath.endswith('.py'):
|
||||||
# We asume root is the dir of the file, and module is the name of the file
|
# We asume root is the dir of the file, and module is the name of the file
|
||||||
@ -540,7 +534,7 @@ def from_path(fpath, **kwargs):
|
|||||||
yield instance
|
yield instance
|
||||||
else:
|
else:
|
||||||
info = parse_plugin_info(fpath)
|
info = parse_plugin_info(fpath)
|
||||||
yield from_info(info, **kwargs)
|
yield from_info(info, install_on_fail=install_on_fail, **kwargs)
|
||||||
|
|
||||||
|
|
||||||
def from_folder(folders, loader=from_path, **kwargs):
|
def from_folder(folders, loader=from_path, **kwargs):
|
||||||
@ -551,7 +545,7 @@ def from_folder(folders, loader=from_path, **kwargs):
|
|||||||
return plugins
|
return plugins
|
||||||
|
|
||||||
|
|
||||||
def from_info(info, root=None, **kwargs):
|
def from_info(info, root=None, install_on_fail=True, **kwargs):
|
||||||
if any(x not in info for x in ('module',)):
|
if any(x not in info for x in ('module',)):
|
||||||
raise ValueError('Plugin info is not valid: {}'.format(info))
|
raise ValueError('Plugin info is not valid: {}'.format(info))
|
||||||
module = info["module"]
|
module = info["module"]
|
||||||
@ -559,7 +553,12 @@ def from_info(info, root=None, **kwargs):
|
|||||||
if not root and '_path' in info:
|
if not root and '_path' in info:
|
||||||
root = os.path.dirname(info['_path'])
|
root = os.path.dirname(info['_path'])
|
||||||
|
|
||||||
return one_from_module(module, root=root, info=info, **kwargs)
|
fun = partial(one_from_module, module, root=root, info=info, **kwargs)
|
||||||
|
try:
|
||||||
|
return fun()
|
||||||
|
except (ImportError, LookupError):
|
||||||
|
install_deps(info)
|
||||||
|
return fun()
|
||||||
|
|
||||||
|
|
||||||
def parse_plugin_info(fpath):
|
def parse_plugin_info(fpath):
|
||||||
@ -606,17 +605,9 @@ def _instances_in_module(module):
|
|||||||
yield obj
|
yield obj
|
||||||
|
|
||||||
|
|
||||||
def _from_module_name(module, root, info=None, install=True, **kwargs):
|
def _from_module_name(module, root, info=None, **kwargs):
|
||||||
try:
|
module = load_module(module, root)
|
||||||
module = load_module(module, root)
|
|
||||||
except (ImportError, LookupError):
|
|
||||||
if not install or not info:
|
|
||||||
raise
|
|
||||||
install_deps(info)
|
|
||||||
module = load_module(module, root)
|
|
||||||
for plugin in _from_loaded_module(module=module, root=root, info=info, **kwargs):
|
for plugin in _from_loaded_module(module=module, root=root, info=info, **kwargs):
|
||||||
if install:
|
|
||||||
install_deps(plugin)
|
|
||||||
yield plugin
|
yield plugin
|
||||||
|
|
||||||
|
|
||||||
@ -628,12 +619,9 @@ def _from_loaded_module(module, info=None, **kwargs):
|
|||||||
|
|
||||||
|
|
||||||
def evaluate(plugins, datasets, **kwargs):
|
def evaluate(plugins, datasets, **kwargs):
|
||||||
if not GSITK_AVAILABLE:
|
ev = gsitk_compat.Eval(tuples=None,
|
||||||
raise Exception('GSITK is not available. Install it to use this function.')
|
datasets=datasets,
|
||||||
|
pipelines=[plugin.as_pipe() for plugin in plugins])
|
||||||
ev = Eval(tuples=None,
|
|
||||||
datasets=datasets,
|
|
||||||
pipelines=[plugin.as_pipe() for plugin in plugins])
|
|
||||||
ev.evaluate()
|
ev.evaluate()
|
||||||
results = ev.results
|
results = ev.results
|
||||||
evaluations = evaluations_to_JSONLD(results, **kwargs)
|
evaluations = evaluations_to_JSONLD(results, **kwargs)
|
||||||
|
@ -413,7 +413,7 @@ function evaluate_JSON(){
|
|||||||
url += "?algo="+plugin+"&dataset="+datasets
|
url += "?algo="+plugin+"&dataset="+datasets
|
||||||
|
|
||||||
$('#doevaluate').attr("disabled", true);
|
$('#doevaluate').attr("disabled", true);
|
||||||
$.ajax({type: "GET", url: url, dataType: 'json'}).done(function(resp) {
|
$.ajax({type: "GET", url: url, dataType: 'json'}).always(function(resp) {
|
||||||
$('#doevaluate').attr("disabled", false);
|
$('#doevaluate').attr("disabled", false);
|
||||||
response = resp.responseText;
|
response = resp.responseText;
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@ def easy_test(plugin_list=None, debug=True):
|
|||||||
for plug in plugin_list:
|
for plug in plugin_list:
|
||||||
plug.test()
|
plug.test()
|
||||||
plug.log.info('My tests passed!')
|
plug.log.info('My tests passed!')
|
||||||
logger.info('All tests passed!')
|
logger.info('All tests passed for {} plugins!'.format(len(plugin_list)))
|
||||||
except Exception:
|
except Exception:
|
||||||
if not debug:
|
if not debug:
|
||||||
raise
|
raise
|
||||||
|
@ -21,7 +21,6 @@ class BlueprintsTest(TestCase):
|
|||||||
def setUpClass(cls):
|
def setUpClass(cls):
|
||||||
"""Set up only once, and re-use in every individual test"""
|
"""Set up only once, and re-use in every individual test"""
|
||||||
cls.app = Flask("test_extensions")
|
cls.app = Flask("test_extensions")
|
||||||
cls.app.debug = False
|
|
||||||
cls.client = cls.app.test_client()
|
cls.client = cls.app.test_client()
|
||||||
cls.senpy = Senpy(default_plugins=True)
|
cls.senpy = Senpy(default_plugins=True)
|
||||||
cls.senpy.init_app(cls.app)
|
cls.senpy.init_app(cls.app)
|
||||||
@ -31,6 +30,9 @@ class BlueprintsTest(TestCase):
|
|||||||
cls.senpy.activate_plugin("DummyRequired", sync=True)
|
cls.senpy.activate_plugin("DummyRequired", sync=True)
|
||||||
cls.senpy.default_plugin = 'Dummy'
|
cls.senpy.default_plugin = 'Dummy'
|
||||||
|
|
||||||
|
def setUp(self):
|
||||||
|
self.app.config['TESTING'] = True # Tell Flask not to catch Exceptions
|
||||||
|
|
||||||
def assertCode(self, resp, code):
|
def assertCode(self, resp, code):
|
||||||
self.assertEqual(resp.status_code, code)
|
self.assertEqual(resp.status_code, code)
|
||||||
|
|
||||||
@ -42,6 +44,7 @@ class BlueprintsTest(TestCase):
|
|||||||
"""
|
"""
|
||||||
Calling with no arguments should ask the user for more arguments
|
Calling with no arguments should ask the user for more arguments
|
||||||
"""
|
"""
|
||||||
|
self.app.config['TESTING'] = False # Errors are expected in this case
|
||||||
resp = self.client.get("/api/")
|
resp = self.client.get("/api/")
|
||||||
self.assertCode(resp, 400)
|
self.assertCode(resp, 400)
|
||||||
js = parse_resp(resp)
|
js = parse_resp(resp)
|
||||||
@ -81,7 +84,7 @@ class BlueprintsTest(TestCase):
|
|||||||
Extra params that have a required argument that does not
|
Extra params that have a required argument that does not
|
||||||
have a default should raise an error.
|
have a default should raise an error.
|
||||||
"""
|
"""
|
||||||
self.app.debug = False
|
self.app.config['TESTING'] = False # Errors are expected in this case
|
||||||
resp = self.client.get("/api/?i=My aloha mohame&algo=DummyRequired")
|
resp = self.client.get("/api/?i=My aloha mohame&algo=DummyRequired")
|
||||||
self.assertCode(resp, 400)
|
self.assertCode(resp, 400)
|
||||||
js = parse_resp(resp)
|
js = parse_resp(resp)
|
||||||
@ -97,7 +100,7 @@ class BlueprintsTest(TestCase):
|
|||||||
The dummy plugin returns an empty response,\
|
The dummy plugin returns an empty response,\
|
||||||
it should contain the context
|
it should contain the context
|
||||||
"""
|
"""
|
||||||
self.app.debug = False
|
self.app.config['TESTING'] = False # Errors are expected in this case
|
||||||
resp = self.client.get("/api/?i=My aloha mohame&algo=DOESNOTEXIST")
|
resp = self.client.get("/api/?i=My aloha mohame&algo=DOESNOTEXIST")
|
||||||
self.assertCode(resp, 404)
|
self.assertCode(resp, 404)
|
||||||
js = parse_resp(resp)
|
js = parse_resp(resp)
|
||||||
@ -139,7 +142,7 @@ class BlueprintsTest(TestCase):
|
|||||||
js = parse_resp(resp)
|
js = parse_resp(resp)
|
||||||
logging.debug(js)
|
logging.debug(js)
|
||||||
assert "@id" in js
|
assert "@id" in js
|
||||||
assert js["@id"] == "plugins/Dummy_0.1"
|
assert js["@id"] == "endpoint:plugins/Dummy_0.1"
|
||||||
|
|
||||||
def test_default(self):
|
def test_default(self):
|
||||||
""" Show only one plugin"""
|
""" Show only one plugin"""
|
||||||
@ -148,7 +151,7 @@ class BlueprintsTest(TestCase):
|
|||||||
js = parse_resp(resp)
|
js = parse_resp(resp)
|
||||||
logging.debug(js)
|
logging.debug(js)
|
||||||
assert "@id" in js
|
assert "@id" in js
|
||||||
assert js["@id"] == "plugins/Dummy_0.1"
|
assert js["@id"] == "endpoint:plugins/Dummy_0.1"
|
||||||
|
|
||||||
def test_context(self):
|
def test_context(self):
|
||||||
resp = self.client.get("/api/contexts/context.jsonld")
|
resp = self.client.get("/api/contexts/context.jsonld")
|
||||||
@ -172,5 +175,6 @@ class BlueprintsTest(TestCase):
|
|||||||
assert "help" in js["valid_parameters"]
|
assert "help" in js["valid_parameters"]
|
||||||
|
|
||||||
def test_conversion(self):
|
def test_conversion(self):
|
||||||
|
self.app.config['TESTING'] = False # Errors are expected in this case
|
||||||
resp = self.client.get("/api/?input=hello&algo=emoRand&emotionModel=DOES NOT EXIST")
|
resp = self.client.get("/api/?input=hello&algo=emoRand&emotionModel=DOES NOT EXIST")
|
||||||
self.assertCode(resp, 404)
|
self.assertCode(resp, 404)
|
||||||
|
@ -121,8 +121,8 @@ class ExtensionsTest(TestCase):
|
|||||||
# Leaf (defaultdict with __setattr__ and __getattr__.
|
# Leaf (defaultdict with __setattr__ and __getattr__.
|
||||||
r1 = analyse(self.senpy, algorithm="Dummy", input="tupni", output="tuptuo")
|
r1 = analyse(self.senpy, algorithm="Dummy", input="tupni", output="tuptuo")
|
||||||
r2 = analyse(self.senpy, input="tupni", output="tuptuo")
|
r2 = analyse(self.senpy, input="tupni", output="tuptuo")
|
||||||
assert r1.analysis[0] == "plugins/Dummy_0.1"
|
assert r1.analysis[0] == "endpoint:plugins/Dummy_0.1"
|
||||||
assert r2.analysis[0] == "plugins/Dummy_0.1"
|
assert r2.analysis[0] == "endpoint:plugins/Dummy_0.1"
|
||||||
assert r1.entries[0]['nif:isString'] == 'input'
|
assert r1.entries[0]['nif:isString'] == 'input'
|
||||||
|
|
||||||
def test_analyse_empty(self):
|
def test_analyse_empty(self):
|
||||||
@ -156,8 +156,8 @@ class ExtensionsTest(TestCase):
|
|||||||
r2 = analyse(self.senpy,
|
r2 = analyse(self.senpy,
|
||||||
input="tupni",
|
input="tupni",
|
||||||
output="tuptuo")
|
output="tuptuo")
|
||||||
assert r1.analysis[0] == "plugins/Dummy_0.1"
|
assert r1.analysis[0] == "endpoint:plugins/Dummy_0.1"
|
||||||
assert r2.analysis[0] == "plugins/Dummy_0.1"
|
assert r2.analysis[0] == "endpoint:plugins/Dummy_0.1"
|
||||||
assert r1.entries[0]['nif:isString'] == 'input'
|
assert r1.entries[0]['nif:isString'] == 'input'
|
||||||
|
|
||||||
def test_analyse_error(self):
|
def test_analyse_error(self):
|
||||||
|
@ -6,7 +6,7 @@ import pickle
|
|||||||
import shutil
|
import shutil
|
||||||
import tempfile
|
import tempfile
|
||||||
|
|
||||||
from unittest import TestCase, skipIf
|
from unittest import TestCase
|
||||||
from senpy.models import Results, Entry, EmotionSet, Emotion, Plugins
|
from senpy.models import Results, Entry, EmotionSet, Emotion, Plugins
|
||||||
from senpy import plugins
|
from senpy import plugins
|
||||||
from senpy.plugins.conversion.emotion.centroids import CentroidConversion
|
from senpy.plugins.conversion.emotion.centroids import CentroidConversion
|
||||||
@ -312,9 +312,7 @@ class PluginsTest(TestCase):
|
|||||||
res = c._backwards_conversion(e)
|
res = c._backwards_conversion(e)
|
||||||
assert res["onyx:hasEmotionCategory"] == "c2"
|
assert res["onyx:hasEmotionCategory"] == "c2"
|
||||||
|
|
||||||
@skipIf(sys.version_info < (3, 0),
|
def _test_evaluation(self):
|
||||||
reason="requires Python3")
|
|
||||||
def test_evaluation(self):
|
|
||||||
testdata = []
|
testdata = []
|
||||||
for i in range(50):
|
for i in range(50):
|
||||||
testdata.append(["good", 1])
|
testdata.append(["good", 1])
|
||||||
@ -348,6 +346,14 @@ class PluginsTest(TestCase):
|
|||||||
smart_metrics = results[0].metrics[0]
|
smart_metrics = results[0].metrics[0]
|
||||||
assert abs(smart_metrics['accuracy'] - 1) < 0.01
|
assert abs(smart_metrics['accuracy'] - 1) < 0.01
|
||||||
|
|
||||||
|
def test_evaluation(self):
|
||||||
|
if sys.version_info < (3, 0):
|
||||||
|
with self.assertRaises(Exception) as context:
|
||||||
|
self._test_evaluation()
|
||||||
|
self.assertTrue('GSITK ' in str(context.exception))
|
||||||
|
else:
|
||||||
|
self._test_evaluation()
|
||||||
|
|
||||||
|
|
||||||
def make_mini_test(fpath):
|
def make_mini_test(fpath):
|
||||||
def mini_test(self):
|
def mini_test(self):
|
||||||
|
Loading…
Reference in New Issue
Block a user