balkian/senpy
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Code Issues Releases Wiki Activity

Several changes

Browse Source 
* Add flag to run tests
* Add ntriples outformat
This commit is contained in:
J. Fernando Sánchez 2018-07-04 16:14:09 +02:00
parent 13cf0c71c5
commit 00ffbb3804
11 changed files with 103 additions and 72 deletions
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31
senpy/__main__.py
View File

@ -78,10 +78,15 @@ def main():
help='Do not run a server, only install plugin dependencies')
parser.add_argument(
'--only-test',
'-t',
action='store_true',
default=False,
help='Do not run a server, just test all plugins')
parser.add_argument(
'--test',
'-t',
action='store_true',
default=False,
help='Test all plugins before launching the server')
parser.add_argument(
'--only-list',
'--list',
@ -99,6 +104,12 @@ def main():
action='store_false',
default=True,
help='Run a threaded server')
parser.add_argument(
'--no-deps',
'-n',
action='store_true',
default=False,
help='Skip installing dependencies')
parser.add_argument(
'--version',
'-v',
@ -125,19 +136,27 @@ def main():
data_folder=args.data_folder)
if args.only_list:
plugins = sp.plugins()
maxwidth = max(len(x.id) for x in plugins)
maxname = max(len(x.name) for x in plugins)
maxversion = max(len(x.version) for x in plugins)
print('Found {} plugins:'.format(len(plugins)))
for plugin in plugins:
import inspect
fpath = inspect.getfile(plugin.__class__)
print('{: <{width}} @ {}'.format(plugin.id, fpath, width=maxwidth))
print('\t{: <{maxname}} @ {: <{maxversion}} -> {}'.format(plugin.name,
plugin.version,
fpath,
maxname=maxname,
maxversion=maxversion))
return
sp.install_deps()
if not args.no_deps:
sp.install_deps()
if args.only_install:
return
sp.activate_all(allow_fail=args.allow_fail)
if args.only_test:
if args.test or args.only_test:
easy_test(sp.plugins(), debug=args.debug)
return
if args.only_test:
return
print('Senpy version {}'.format(senpy.__version__))
print('Server running on port %s:%d. Ctrl+C to quit' % (args.host,
args.port))

11
senpy/api.py
View File

@ -4,7 +4,7 @@ import logging
logger = logging.getLogger(__name__)
boolean = (True, False)
boolean = [True, False]
API_PARAMS = {
@ -33,7 +33,7 @@ API_PARAMS = {
"aliases": ["o"],
"default": "json-ld",
"required": True,
"options": ["json-ld", "turtle"],
"options": ["json-ld", "turtle", "ntriples"],
},
"help": {
"@id": "help",
@ -175,8 +175,8 @@ def parse_params(indict, *specs):
parameters=outdict,
errors=wrong_params)
raise message
if 'algorithm' in outdict and not isinstance(outdict['algorithm'], tuple):
outdict['algorithm'] = tuple(outdict['algorithm'].split(','))
if 'algorithm' in outdict and not isinstance(outdict['algorithm'], list):
outdict['algorithm'] = list(outdict['algorithm'].split(','))
return outdict
@ -194,7 +194,8 @@ def parse_call(params):
params = parse_params(params, NIF_PARAMS)
if params['informat'] == 'text':
results = Results()
entry = Entry(nif__isString=params['input'])
entry = Entry(nif__isString=params['input'],
id='#') # Use @base
results.entries.append(entry)
elif params['informat'] == 'json-ld':
results = from_string(params['input'], cls=Results)

14
senpy/blueprints.py
View File

@ -25,7 +25,6 @@ from .version import __version__
from functools import wraps
import logging
import traceback
import json
import base64
@ -37,12 +36,17 @@ ns_blueprint = Blueprint("ns", __name__)
_mimetypes_r = {'json-ld': ['application/ld+json'],
'turtle': ['text/turtle'],
'ntriples': ['application/n-triples'],
'text': ['text/plain']}
MIMETYPES = {}
for k, vs in _mimetypes_r.items():
for v in vs:
if v in MIMETYPES:
raise Exception('MIMETYPE {} specified for two formats: {} and {}'.format(v,
v,
MIMETYPES[v]))
MIMETYPES[v] = k
DEFAULT_MIMETYPE = 'application/ld+json'
@ -147,16 +151,14 @@ def basic_api(f):
request.parameters = params
response = f(*args, **kwargs)
except (Exception) as ex:
if current_app.debug:
if current_app.debug or current_app.config['TESTING']:
raise
if not isinstance(ex, Error):
msg = "{}:\n\t{}".format(ex,
traceback.format_exc())
msg = "{}".format(ex)
ex = Error(message=msg, status=500)
logger.exception('Error returning analysis result')
response = ex
response.parameters = raw_params
logger.error(ex)
logger.exception(ex)
if 'parameters' in response and not params['with_parameters']:
del response.parameters

23
senpy/extensions.py
View File

@ -18,14 +18,9 @@ import errno
import logging
logger = logging.getLogger(__name__)
from . import gsitk_compat
try:
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
logger = logging.getLogger(__name__)
class Senpy(object):
@ -167,8 +162,7 @@ class Senpy(object):
yield i
def install_deps(self):
for plugin in self.plugins(is_activated=True):
plugins.install_deps(plugin)
plugins.install_deps(*self.plugins())
def analyse(self, request):
"""
@ -203,16 +197,14 @@ class Senpy(object):
raise Error(
status=404,
message="The dataset '{}' is not valid".format(dataset))
dm = DatasetManager()
dm = gsitk_compat.DatasetManager()
datasets = dm.prepare_datasets(datasets_name)
return datasets
@property
def datasets(self):
if not GSITK_AVAILABLE:
raise Exception('GSITK is not available. Install it to use this function.')
self._dataset_list = {}
dm = DatasetManager()
dm = gsitk_compat.DatasetManager()
for item in dm.get_datasets():
for key in item:
if key in self._dataset_list:
@ -223,8 +215,6 @@ class Senpy(object):
return self._dataset_list
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))
results = AggregatedEvaluation()
results.parameters = params
@ -351,6 +341,7 @@ class Senpy(object):
logger.info(msg)
success = True
self._set_active(plugin, success)
return success
def activate_plugin(self, plugin_name, sync=True):
plugin_name = plugin_name.lower()
@ -362,7 +353,7 @@ class Senpy(object):
logger.info("Activating plugin: {}".format(plugin.name))
if sync or 'async' in plugin and not plugin.async:
self._activate(plugin)
return self._activate(plugin)
else:
th = Thread(target=partial(self._activate, plugin))
th.start()

23
senpy/gsitk_compat.py Normal file
View 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

25
senpy/models.py
View File

@ -179,17 +179,18 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
content = json.dumps(js, indent=2, sort_keys=True)
if format == 'json-ld':
mimetype = "application/json"
elif format in ['turtle', ]:
elif format in ['turtle', 'ntriples']:
logger.debug(js)
base = kwargs.get('prefix')
g = Graph().parse(
data=content,
format='json-ld',
base=base,
context=self._context)
context=[self._context,
{'@base': base}])
logger.debug(
'Parsing with prefix: {}'.format(kwargs.get('prefix')))
content = g.serialize(format='turtle',
content = g.serialize(format=format,
base=base).decode('utf-8')
mimetype = 'text/{}'.format(format)
else:
@ -207,26 +208,20 @@ class BaseModel(with_metaclass(BaseMeta, CustomDict)):
result = self.serializable()
ctx = context_uri or self._context
result['@context'] = ctx
# result = jsonld.compact(result,
# ctx,
# options={
# 'base': prefix,
# 'expandContext': self._context,
# 'senpy': prefix
# })
if expanded:
result = jsonld.expand(
result, options={'base': prefix,
'expandContext': ctx})
'expandContext': self._context})[0]
if not with_context:
try:
del result['@context']
except KeyError:
pass
elif context_uri:
result['@context'] = context_uri
else:
result['@context'] = self._context
return result
def validate(self, obj=None):

20
senpy/plugins/__init__.py
View File

@ -23,18 +23,11 @@ import nltk
from .. import models, utils
from .. import api
from .. import gsitk_compat
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):
_classes = {}
@ -333,7 +326,7 @@ class Box(AnalysisPlugin):
return self.transform(X)
def as_pipe(self):
pipe = Pipeline([('plugin', self)])
pipe = gsitk_compat.Pipeline([('plugin', self)])
pipe.name = self.name
return pipe
@ -626,12 +619,9 @@ def _from_loaded_module(module, info=None, **kwargs):
def evaluate(plugins, datasets, **kwargs):
if not GSITK_AVAILABLE:
raise Exception('GSITK is not available. Install it to use this function.')
ev = Eval(tuples=None,
datasets=datasets,
pipelines=[plugin.as_pipe() for plugin in plugins])
ev = gsitk_compat.Eval(tuples=None,
datasets=datasets,
pipelines=[plugin.as_pipe() for plugin in plugins])
ev.evaluate()
results = ev.results
evaluations = evaluations_to_JSONLD(results, **kwargs)

2
senpy/static/js/main.js
View File

@ -413,7 +413,7 @@ function evaluate_JSON(){
url += "?algo="+plugin+"&dataset="+datasets
$('#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);
response = resp.responseText;

2
senpy/utils.py
View File

@ -80,7 +80,7 @@ def easy_test(plugin_list=None, debug=True):
for plug in plugin_list:
plug.test()
plug.log.info('My tests passed!')
logger.info('All tests passed!')
logger.info('All tests passed for {} plugins!'.format(len(plugin_list)))
except Exception:
if not debug:
raise

10
tests/test_blueprints.py
View File

@ -21,7 +21,6 @@ class BlueprintsTest(TestCase):
def setUpClass(cls):
"""Set up only once, and re-use in every individual test"""
cls.app = Flask("test_extensions")
cls.app.debug = False
cls.client = cls.app.test_client()
cls.senpy = Senpy(default_plugins=True)
cls.senpy.init_app(cls.app)
@ -31,6 +30,9 @@ class BlueprintsTest(TestCase):
cls.senpy.activate_plugin("DummyRequired", sync=True)
cls.senpy.default_plugin = 'Dummy'
def setUp(self):
self.app.config['TESTING'] = True # Tell Flask not to catch Exceptions
def assertCode(self, resp, 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
"""
self.app.config['TESTING'] = False # Errors are expected in this case
resp = self.client.get("/api/")
self.assertCode(resp, 400)
js = parse_resp(resp)
@ -81,7 +84,7 @@ class BlueprintsTest(TestCase):
Extra params that have a required argument that does not
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")
self.assertCode(resp, 400)
js = parse_resp(resp)
@ -97,7 +100,7 @@ class BlueprintsTest(TestCase):
The dummy plugin returns an empty response,\
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")
self.assertCode(resp, 404)
js = parse_resp(resp)
@ -172,5 +175,6 @@ class BlueprintsTest(TestCase):
assert "help" in js["valid_parameters"]
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")
self.assertCode(resp, 404)

14
tests/test_plugins.py
View File

@ -6,7 +6,7 @@ import pickle
import shutil
import tempfile
from unittest import TestCase, skipIf
from unittest import TestCase
from senpy.models import Results, Entry, EmotionSet, Emotion, Plugins
from senpy import plugins
from senpy.plugins.conversion.emotion.centroids import CentroidConversion
@ -312,9 +312,7 @@ class PluginsTest(TestCase):
res = c._backwards_conversion(e)
assert res["onyx:hasEmotionCategory"] == "c2"
@skipIf(sys.version_info < (3, 0),
reason="requires Python3")
def test_evaluation(self):
def _test_evaluation(self):
testdata = []
for i in range(50):
testdata.append(["good", 1])
@ -348,6 +346,14 @@ class PluginsTest(TestCase):
smart_metrics = results[0].metrics[0]
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 mini_test(self):