Fix schema issues and parameter validation

Dockerfile.template

@@ -6,8 +6,6 @@ RUN apt-get update && apt-get install -y \
 libblas-dev liblapack-dev liblapacke-dev gfortran \
  && rm -rf /var/lib/apt/lists/*
 
-RUN pip install --no-cache-dir --upgrade numpy scipy scikit-learn
-
 RUN mkdir /cache/ /senpy-plugins /data/
 
 VOLUME /data/

requirements.txt

@@ -9,3 +9,6 @@ jsonref
 PyYAML
 rdflib
 rdflib-jsonld
+numpy
+scipy
+scikit-learn

senpy/api.py

@@ -147,7 +147,7 @@ def parse_params(indict, *specs):
         for param, options in iteritems(spec):
             for alias in options.get("aliases", []):
                 # Replace each alias with the correct name of the parameter
-                if alias in indict and alias is not param:
+                if alias in indict and alias != param:
                     outdict[param] = indict[alias]
                     del outdict[alias]
                     continue

senpy/blueprints.py

@@ -19,7 +19,7 @@ Blueprints for Senpy
 """
 from flask import (Blueprint, request, current_app, render_template, url_for,
                    jsonify)
-from .models import Error, Response, Help, Plugins, read_schema, Datasets
+from .models import Error, Response, Help, Plugins, read_schema, dump_schema, Datasets
 from . import api
 from .version import __version__
 from functools import wraps
@@ -67,9 +67,9 @@ def index():
 @api_blueprint.route('/schemas/<schema>')
 def schema(schema="definitions"):
     try:
-        return jsonify(read_schema(schema))
+        return dump_schema(read_schema(schema))
-    except Exception:  # Should be FileNotFoundError, but it's missing from py2
+    except Exception as ex:  # Should be FileNotFoundError, but it's missing from py2
-        return Error(message="Schema not found", status=404).flask()
+        return Error(message="Schema not found: {}".format(ex), status=404).flask()
 
 
 def basic_api(f):
@@ -133,6 +133,7 @@ def api_root():
     req = api.parse_call(request.parameters)
     return current_app.senpy.analyse(req)
 
+
 @api_blueprint.route('/evaluate/', methods=['POST', 'GET'])
 @basic_api
 def evaluate():
@@ -145,6 +146,7 @@ def evaluate():
         response = current_app.senpy.evaluate(params)
         return response
 
+
 @api_blueprint.route('/plugins/', methods=['POST', 'GET'])
 @basic_api
 def plugins():
@@ -163,10 +165,10 @@ def plugin(plugin=None):
     return sp.get_plugin(plugin)
 
 
-@api_blueprint.route('/datasets/', methods=['POST','GET'])
+@api_blueprint.route('/datasets/', methods=['POST', 'GET'])
 @basic_api
 def datasets():
     sp = current_app.senpy
     datasets = sp.datasets
-    dic = Datasets(datasets = list(datasets.values()))
+    dic = Datasets(datasets=list(datasets.values()))
-    return dic
+    return dic

senpy/models.py

@@ -51,6 +51,10 @@ def read_schema(schema_file, absolute=False):
         return jsonref.load(f, base_uri=schema_uri)
 
 
+def dump_schema(schema):
+    return jsonref.dumps(schema)
+
+
 def load_context(context):
     logging.debug('Loading context: {}'.format(context))
     if not context:

senpy/plugins/__init__.py

@@ -19,8 +19,6 @@ import importlib
 import yaml
 import threading
 
-import numpy as np
-
 from .. import models, utils
 from .. import api
 
@@ -49,11 +47,11 @@ class PluginMeta(models.BaseMeta):
         attrs['name'] = alias
         if 'description' not in attrs:
             doc = attrs.get('__doc__', None)
-            if not doc:
+            if doc:
-                raise Exception(('Please, add a description or '
+                attrs['description'] = doc
-                                 'documentation to class {}').format(name))
+            else:
-            attrs['description'] = doc
+                logger.warn(('Plugin {} does not have a description. '
-            attrs['name'] = alias
+                             'Please, add a short summary to help other developers').format(name))
         cls = super(PluginMeta, mcs).__new__(mcs, name, bases, attrs)
 
         if alias in mcs._classes:
@@ -291,7 +289,7 @@ class Box(AnalysisPlugin):
         return self
 
     def transform(self, X):
-        return np.array([self.predict_one(x) for x in X])
+        return [self.predict_one(x) for x in X]
 
     def predict(self, X):
         return self.transform(X)

senpy/schemas/evaluation.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-04/schema#",
-  "name": "Evalation",
+  "name": "Evaluation",
   "properties": {
     "@id": {
       "type": "string"

tests/test_api.py

@@ -32,7 +32,7 @@ class APITest(TestCase):
         query = {}
         plug_params = {
             'hello': {
-                'aliases': ['hello', 'hiya'],
+                'aliases': ['hiya', 'hello'],
                 'required': True
             }
         }
@@ -48,6 +48,26 @@ class APITest(TestCase):
         assert 'hello' in p
         assert p['hello'] == 'dlrow'
 
+    def test_parameters2(self):
+        in1 = {
+            'meaningcloud-key': 5
+        }
+        in2 = {
+            'apikey': 25
+        }
+        extra_params = {
+            "apikey": {
+                "aliases": [
+                    "apikey",
+                    "meaningcloud-key"
+                ],
+                "required": True
+            }
+        }
+        p1 = parse_params(in1, extra_params)
+        p2 = parse_params(in2, extra_params)
+        assert (p2['apikey'] / p1['apikey']) == 5
+
     def test_default(self):
         spec = {
             'hello': {

tests/test_schemas.py

@@ -8,6 +8,8 @@ from fnmatch import fnmatch
 
 from jsonschema import RefResolver, Draft4Validator, ValidationError
 
+from senpy.models import read_schema
+
 root_path = path.join(path.dirname(path.realpath(__file__)), '..')
 schema_folder = path.join(root_path, 'senpy', 'schemas')
 examples_path = path.join(root_path, 'docs', 'examples')
@@ -15,7 +17,8 @@ bad_examples_path = path.join(root_path, 'docs', 'bad-examples')
 
 
 class JSONSchemaTests(unittest.TestCase):
-    pass
+    def test_definitions(self):
+        read_schema('definitions.json')
 
 
 def do_create_(jsfile, success):