clams-python 1.1.0__tar.gz → 1.1.2__tar.gz

{clams-python-1.1.0/clams_python.egg-info → clams-python-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.1.0
+Version: 1.1.2
 Summary: A collection of APIs to develop CLAMS app for python
 Home-page: https://clams.ai
 Author: Brandeis Lab for Linguistics and Computation
@@ -14,7 +14,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: mmif-python==1.0.8
+Requires-Dist: mmif-python==1.0.9
 Requires-Dist: Flask>=2
 Requires-Dist: Flask-RESTful>=0.3.9
 Requires-Dist: gunicorn>=20
@@ -33,9 +33,10 @@ Requires-Dist: jsonschema>=3
 1. a flask-based wrapper to run a Python CLAMS app as an HTTP web app
 1. cookie-cutter shell command that sets up everything and starts a new CLAMS app project
 
-### Start now from [Getting Started](introduction.html)!
+### Start now from [Getting Started](https://clamsproject.github.io/clams-python/introduction.html)!
 
 ## For more ...
-For user manuals and Python API documentation, take a look at [Python modules](https://clams.ai/clams-python/modules.html).
-
-For MMIF-specific Python API documentation, take a look at the [mmif-python website](https://clams.ai/mmif-python).
+* [Version history and patch notes](https://github.com/clamsproject/clams-python/blob/main/CHANGELOG.md)
+* [CLAMS Python API documentation](https://clamsproject.github.io/clams-python/modules.html)
+* [MMIF-specific Python API documentation](https://clamsproject.github.io/mmif-python)
+* [Public CLAMS App Directory](https://clamsproject.github.io/apps)

{clams-python-1.1.0 → clams-python-1.1.2}/README.md

@@ -9,9 +9,10 @@
 1. a flask-based wrapper to run a Python CLAMS app as an HTTP web app
 1. cookie-cutter shell command that sets up everything and starts a new CLAMS app project
 
-### Start now from [Getting Started](introduction.html)!
+### Start now from [Getting Started](https://clamsproject.github.io/clams-python/introduction.html)!
 
 ## For more ...
-For user manuals and Python API documentation, take a look at [Python modules](https://clams.ai/clams-python/modules.html).
-
-For MMIF-specific Python API documentation, take a look at the [mmif-python website](https://clams.ai/mmif-python).
+* [Version history and patch notes](https://github.com/clamsproject/clams-python/blob/main/CHANGELOG.md)
+* [CLAMS Python API documentation](https://clamsproject.github.io/clams-python/modules.html)
+* [MMIF-specific Python API documentation](https://clamsproject.github.io/mmif-python)
+* [Public CLAMS App Directory](https://clamsproject.github.io/apps)

clams-python-1.1.2/VERSION

@@ -0,0 +1 @@
+1.1.2

{clams-python-1.1.0 → clams-python-1.1.2}/clams/app/__init__.py

@@ -137,7 +137,6 @@ class ClamsApp(ABC):
         
         #. Create a new view (or views) by calling :meth:`~mmif.serialize.mmif.Mmif.new_view` on the input mmif object.
         #. Call :meth:`~clams.app.ClamsApp.sign_view` with the input runtime parameters for the record.
-        #. Call :meth:`~clams.app.ClamsApp.get_configuration` to get an "upgraded" runtime parameters with default values.
         #. Call :meth:`~mmif.serialize.view.View.new_contain` on the new view object with any annotation properties specified by the configuration.
         #. Process the data and create :class:`~mmif.serialize.annotation.Annotation` objects and add them to the new view. 
         #. While doing so, get help from :class:`~mmif.vocabulary.document_types.DocumentTypes`, :class:`~mmif.vocabulary.annotation_types.AnnotationTypes` classes to generate ``@type`` strings.
@@ -177,7 +176,7 @@ class ClamsApp(ABC):
     def get_configuration(self, **runtime_params):
         warnings.warn("ClamsApp.get_configuration() is deprecated. "
                       "If you are using this method in `_annotate()` method,"
-                      "it is no longer needed since `clams-python==1.0.10`.", 
+                      "it is no longer needed since `clams-python>1.0.9`.", 
                       DeprecationWarning, stacklevel=2)
         return self._refine_params(**runtime_params)
 
@@ -195,8 +194,8 @@ class ClamsApp(ABC):
         # TODO (krim @ 8/2/23): once all devs understood this change, make runtime_conf a required argument
         if runtime_conf is None:
             warnings.warn("`runtime_conf` argument for ClamsApp.sign_view() will "
-                          "no longer be optional in the future. Please just pass "
-                          "`runtime_params` from _annotate() method.",
+                          "no longer be optional in the future. Please pass `runtime_params` "
+                          "from _annotate() method.",
                           FutureWarning, stacklevel=2)
         view.metadata.app = self.metadata.identifier
         if runtime_conf is not None:
@@ -205,8 +204,6 @@ class ClamsApp(ABC):
             else:
                 conf = runtime_conf
             view.metadata.add_parameters(**{k: str(v) for k, v in conf.items()})
-            # TODO (krim @ 8/2/23): add "refined" parameters as well 
-            #  once https://github.com/clamsproject/mmif/issues/208 is resolved
         
     def set_error_view(self, mmif: Union[str, dict, Mmif], runtime_conf: Optional[dict] = None) -> Mmif:
         """

{clams-python-1.1.0 → clams-python-1.1.2}/clams/appmetadata/__init__.py

@@ -12,7 +12,7 @@ from mmif import vocabulary
 unresolved_app_version_num = 'unresolvable'
 app_version_envvar_key = 'CLAMS_APP_VERSION'
 # type aliases to use in app metadata and runtime parameter processing 
-primitives = Union[int, float, bool, str]
+real_valued_primitives = Union[int, float, bool, str]
 # these names are taken from the JSON schema data types
 param_value_types = Literal['integer', 'number', 'string', 'boolean']
 
@@ -69,7 +69,7 @@ class Output(_BaseModel):
         alias="@type", 
         description="The type of the object. Must be a IRI string."
     )
-    properties: Dict[str, str] = pydantic.Field(
+    properties: Dict[str, real_valued_primitives] = pydantic.Field(
         {}, 
         description="(optional) Specification for type properties, if any."
     )
@@ -126,11 +126,11 @@ class RuntimeParameter(_BaseModel):
         ...,
         description=f"Type of the parameter value the app expects. Must be one of {param_value_types_values}."
     ) 
-    choices: List[primitives] = pydantic.Field(
+    choices: List[real_valued_primitives] = pydantic.Field(
         None, 
         description="(optional) List of string values that can be accepted."
     )
-    default: primitives = pydantic.Field(
+    default: real_valued_primitives = pydantic.Field(
         None, 
         description="(optional) Default value for the parameter. Only valid for optional parameters. Namely, setting "
                     "a default value makes a parameter 'optional'."
@@ -344,9 +344,9 @@ class AppMetadata(pydantic.BaseModel):
             raise ValueError(f"Cannot add a duplicate output '{new}'.")
 
     def add_parameter(self, name: str, description: str, type: param_value_types,
-                      choices: Optional[List[primitives]] = None,
+                      choices: Optional[List[real_valued_primitives]] = None,
                       multivalued: bool = False,
-                      default: primitives = None):
+                      default: real_valued_primitives = None):
         """
         Helper method to add an element to the ``parameters`` list. 
         """

{clams-python-1.1.0 → clams-python-1.1.2}/clams/mmif_utils/rewind.py

@@ -6,44 +6,27 @@ from pathlib import Path as P
 import mmif
 
 
-def is_valid_choice(choice):
-    try:
-        ichoice = int(choice)
-        if 0 <= ichoice:
-            return ichoice
-        else:
-            raise ValueError(f"\nInvalid argument for -n. Please enter a positive integer.")
-    except ValueError:
-        raise argparse.ArgumentTypeError(f"\nInvalid argument for -n. Please enter a positive integer.")
-
-def user_choice(mmif_obj:mmif.Mmif) -> int:
+def prompt_user(mmif_obj: mmif.Mmif) -> int:
     """
     Function to ask user to choose the rewind range.
-
-    :param mmif_obj: mmif object
-    :return: int option number
     """
 
     ## Give a user options (#, "app", "timestamp") - time order
     n = len(mmif_obj.views)
     i = 0  # option number
+    aname = ""
+    a = 0
     # header
-    print("\n" + "{:<4} {:<30} {:<100}".format("num", "timestamp", "app"))
-    for view in mmif_obj.views:
-        option = "{:<4} {:<30} {:<100}".format(n-i, str(view.metadata.timestamp), str(view.metadata.app))
-        print(option)
+    print("\n" + "{:<8} {:<8} {:<30} {:<100}".format("view-num", "app-num", "timestamp", "app"))
+    for view in reversed(mmif_obj.views):
+        if view.metadata.app != aname:
+            aname = view.metadata.app
+            a += 1
         i += 1
+        print("{:<8} {:<8} {:<30} {:<100}".format(i, a, str(view.metadata.timestamp), str(view.metadata.app)))
 
     ## User input
-    while True:
-        choice = int(input("\nEnter the number to delete from that point by rewinding: "))
-        try:
-            if 0 <= choice <= n:
-                return choice
-            else:
-                print(f"\nInvalid choice. Please enter an integer in the range [0, {n}].")
-        except ValueError:
-            print("\nInvalid input. Please enter a valid number.")
+    return int(input("\nEnter the number to delete from that point by rewinding: "))
 
 
 def rewind_mmif(mmif_obj: mmif.Mmif, choice: int, choice_is_viewnum: bool = True) -> mmif.Mmif:
@@ -92,24 +75,32 @@ def describe_argparser():
 
 
 def prep_argparser(**kwargs):
-    parser = argparse.ArgumentParser(description=describe_argparser()[1], formatter_class=argparse.RawDescriptionHelpFormatter, **kwargs)
-    parser.add_argument("mmif_file", nargs=1, help="Path to the input MMIF file, or '-' to read from stdin.")
-    parser.add_argument("-o", '--output', default=None, metavar="PATH", help="Path to the rewound MMIF output file. When not given, the rewound MMIF is printed to stdout.")
-    parser.add_argument("-p", '--pretty', action='store_true', help="Pretty-print rewound MMIF. True by default")
-    parser.add_argument("-n", '--number', default="0", type=is_valid_choice, help="Number of views to rewind (default: interactive mode)")
-    parser.add_argument("-m", '--mode', choices=['app', 'view'], default='view', help="Number of views to rewind (default: interactive mode)")
+    parser = argparse.ArgumentParser(description=describe_argparser()[1], 
+                                     formatter_class=argparse.RawDescriptionHelpFormatter, **kwargs)
+    parser.add_argument("mmif_file", 
+                        help="Path to the input MMIF file, or '-' to read from stdin.")
+    parser.add_argument("-o", '--output', default=None, metavar="PATH", 
+                        help="Path to the rewound MMIF output file. When not given, the rewound is printed to stdout.")
+    parser.add_argument("-p", '--pretty', action='store_true', 
+                        help="Pretty-print rewound MMIF")
+    parser.add_argument("-n", '--number', default="0", type=int,
+                        help="Number of views or apps to rewind, must be a positive integer. "
+                             "If 0, the user will be prompted to choose. (default: 0)")
+    parser.add_argument("-m", '--mode', choices=['app', 'view'], default='view', 
+                        help="Choose to rewind by number of views or number of producer apps. (default: view)")
     return parser
 
 
 def main(args):
-    mmif_obj = mmif.Mmif(sys.stdin) if args.mmif_file[0] == '-' else mmif.Mmif(open(args.mmif_file[0]).read())
+    mmif_obj = mmif.Mmif(str(sys.stdin)) if args.mmif_file[0] == '-' else mmif.Mmif(open(args.mmif_file).read())
 
-    if args.number == 0: # If user doesn't know how many views to rewind, give them choices.
-        choice = user_choice(mmif_obj)
+    if args.number == 0:  # If user doesn't know how many views to rewind, give them choices.
+        choice = prompt_user(mmif_obj)
     else:
         choice = args.number
+    if not isinstance(choice, int) or choice <= 0:
+        raise ValueError(f"Only can rewind by a positive number of views. Got {choice}.")
 
-    
     if args.output:
         # Check if the same file name exist in the path and avoid overwriting.
         output_fp = P(args.output)
@@ -132,4 +123,3 @@ if __name__ == "__main__":
     parser = prep_argparser()
     args = parser.parse_args()
     main(args)
-

{clams-python-1.1.0 → clams-python-1.1.2}/clams/restify/__init__.py

@@ -6,7 +6,7 @@ from flask_restful import Resource, Api
 from mmif import Mmif
 
 from clams.app import ClamsApp
-from clams.appmetadata import primitives
+from clams.appmetadata import real_valued_primitives
 
 
 class Restifier(object):
@@ -160,10 +160,10 @@ class ParameterCaster(object):
 
     :param param_spec: A specification of a data types of parameters
     """
-    def __init__(self, param_spec: Dict[str, Tuple[primitives, bool]]):
+    def __init__(self, param_spec: Dict[str, Tuple[real_valued_primitives, bool]]):
         self.param_spec = param_spec
 
-    def cast(self, args: Dict[str, List[str]]) -> Dict[str, Union[primitives, List[primitives]]]:
+    def cast(self, args: Dict[str, List[str]]) -> Dict[str, Union[real_valued_primitives, List[real_valued_primitives]]]:
         """
         Given parameter specification, tries to cast values of args to specified Python data types.
         Note that this caster deals with query strings, thus all keys and values in the input args are plain strings. 
@@ -194,7 +194,10 @@ class ParameterCaster(object):
                         else: 
                             casted[k] = v
             else:
-                casted[k] = vs  
+                if len(vs) > 1:
+                    casted[k] = vs
+                else:
+                    casted[k] = vs[0]
                     
         return casted
 

clams-python-1.1.2/clams/ver/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.1.2"

{clams-python-1.1.0 → clams-python-1.1.2/clams_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.1.0
+Version: 1.1.2
 Summary: A collection of APIs to develop CLAMS app for python
 Home-page: https://clams.ai
 Author: Brandeis Lab for Linguistics and Computation
@@ -14,7 +14,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: mmif-python==1.0.8
+Requires-Dist: mmif-python==1.0.9
 Requires-Dist: Flask>=2
 Requires-Dist: Flask-RESTful>=0.3.9
 Requires-Dist: gunicorn>=20
@@ -33,9 +33,10 @@ Requires-Dist: jsonschema>=3
 1. a flask-based wrapper to run a Python CLAMS app as an HTTP web app
 1. cookie-cutter shell command that sets up everything and starts a new CLAMS app project
 
-### Start now from [Getting Started](introduction.html)!
+### Start now from [Getting Started](https://clamsproject.github.io/clams-python/introduction.html)!
 
 ## For more ...
-For user manuals and Python API documentation, take a look at [Python modules](https://clams.ai/clams-python/modules.html).
-
-For MMIF-specific Python API documentation, take a look at the [mmif-python website](https://clams.ai/mmif-python).
+* [Version history and patch notes](https://github.com/clamsproject/clams-python/blob/main/CHANGELOG.md)
+* [CLAMS Python API documentation](https://clamsproject.github.io/clams-python/modules.html)
+* [MMIF-specific Python API documentation](https://clamsproject.github.io/mmif-python)
+* [Public CLAMS App Directory](https://clamsproject.github.io/apps)

{clams-python-1.1.0 → clams-python-1.1.2}/clams_python.egg-info/requires.txt

@@ -1,4 +1,4 @@
-mmif-python==1.0.8
+mmif-python==1.0.9
 Flask>=2
 Flask-RESTful>=0.3.9
 gunicorn>=20

{clams-python-1.1.0 → clams-python-1.1.2}/requirements.txt

@@ -1,4 +1,4 @@
-mmif-python==1.0.8
+mmif-python==1.0.9
 
 Flask>=2
 Flask-RESTful>=0.3.9

{clams-python-1.1.0 → clams-python-1.1.2}/tests/test_clamsapp.py

@@ -127,7 +127,7 @@ class TestClamsApp(unittest.TestCase):
         self.app.metadata.add_output(AnnotationTypes.BoundingBox, boxType='text')
         metadata = json.loads(self.app.appmetadata())
         self.assertEqual(len(metadata['output']), 2)
-        # these should not be added as a duplicate
+        # these should not be added because they are duplicates
         with self.assertRaises(ValueError):
             self.app.metadata.add_input(at_type=DocumentTypes.TextDocument)
         with self.assertRaises(ValueError):
@@ -240,14 +240,19 @@ class TestClamsApp(unittest.TestCase):
         with self.app.open_document_location(mmif.documents['i1'], Image.open) as f:
             self.assertEqual(f.size, (200, 71))
             
-    def test_get_configuration(self):
+    def test_refine_parameters(self):
         self.app.metadata.parameters = []
         self.app.metadata.add_parameter('param1', 'first_param', 'string')
         self.app.metadata.add_parameter('param2', 'second_param', 'string', default='second_default')
         self.app.metadata.add_parameter('param3', 'third_param', 'boolean', default='f')
         self.app.metadata.add_parameter('param4', 'fourth_param', 'integer', default='1', choices="1 2 3".split())
         self.app.metadata.add_parameter('param5', 'fifth_param', 'number', default='0.5')
-        conf = self.app.get_configuration(param1='okay', non_parameter='should be ignored')
+        dummy_params = {'param1': 'okay', 'non_parameter': 'should be ignored'}
+        conf = self.app._refine_params(**dummy_params)
+        # should not refine what's already refined
+        double_refine = self.app._refine_params(**conf)
+        self.assertTrue(clams.ClamsApp._RAW_PARAMS_KEY in double_refine)
+        self.assertEqual(double_refine, conf)
         conf.pop(clams.ClamsApp._RAW_PARAMS_KEY, None)
         self.assertEqual(len(conf), 5)  # 1 from `param1`, 4 from default value
         self.assertFalse('non_parameter' in conf)
@@ -258,10 +263,10 @@ class TestClamsApp(unittest.TestCase):
         self.assertEqual(type(conf['param5']), float)
         with self.assertRaises(ValueError):
             # because param1 doesn't have a default value and thus a required param
-            self.app.get_configuration(param2='okay')
+            self.app._refine_params(param2='okay')
         with self.assertRaisesRegexp(ValueError, r'.+must be one of.+'):
             # because param4 can't be 4, note that param1 is "required" 
-            self.app.get_configuration(param1='p1', param4=4)
+            self.app._refine_params(param1='p1', param4=4)
             
     def test_error_handling(self):
         params = {'raise_error': True, 'pretty': True}
@@ -383,7 +388,9 @@ class TestParameterCaster(unittest.TestCase):
             'number_param': ["1.11"], 
             'int_param': [str(sys.maxsize)], 
             'bool_param': ['true'],
-            'str_multi_param': ['value1', 'value2']
+            'str_multi_param': ['value1', 'value2'],
+            'undefined_param_single': ['undefined_value1'],
+            'undefined_param_multi': ['undefined_value1', 'undefined_value2'],
         }
         self.assertTrue(all(map(lambda x: isinstance(x, str), itertools.chain.from_iterable(params.values()))))
         casted = caster.cast(params)
@@ -393,6 +400,10 @@ class TestParameterCaster(unittest.TestCase):
         self.assertTrue(isinstance(casted['int_param'], int))
         self.assertTrue(casted['bool_param'])
         self.assertEqual(set(casted['str_multi_param']), set(params['str_multi_param']))
+        self.assertTrue('undefined_param_single' in casted)
+        self.assertTrue('undefined_param_multi' in casted)
+        self.assertFalse(isinstance(casted['undefined_param_single'], list))
+        self.assertTrue(isinstance(casted['undefined_param_multi'], list))
         unknown_param_key = 'unknown'
         unknown_param_val = 'dunno'
         params[unknown_param_key] = [unknown_param_val]

clams-python-1.1.0/VERSION

@@ -1 +0,0 @@
-1.1.0

clams-python-1.1.0/clams/ver/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.1.0"