clams-python 1.1.6__tar.gz → 1.2.1__tar.gz

{clams-python-1.1.6/clams_python.egg-info → clams_python-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.1.6
+Version: 1.2.1
 Summary: A collection of APIs to develop CLAMS app for python
 Home-page: https://clams.ai
 Author: Brandeis Lab for Linguistics and Computation

clams_python-1.2.1/VERSION

@@ -0,0 +1 @@
+1.2.1

{clams-python-1.1.6 → clams_python-1.2.1}/clams/app/__init__.py

@@ -122,7 +122,9 @@ class ClamsApp(ABC):
             if key not in self.annotate_param_spec:
                 issued_warnings.append(UserWarning(f'An undefined parameter "{key}" (value: "{runtime_params[key]}") is passed'))
         # this will do casting + refinement altogether
+        self.logger.debug(f"User parameters: {runtime_params}")
         refined = self._refine_params(**runtime_params)
+        self.logger.debug(f"Refined parameters: {refined}")
         pretty = refined.get('pretty', False)
         with warnings.catch_warnings(record=True) as ws:
             annotated = self._annotate(mmif, **refined)
@@ -190,7 +192,7 @@ class ClamsApp(ABC):
                       DeprecationWarning, stacklevel=2)
         return self._refine_params(**runtime_params)
 
-    def sign_view(self, view: View, runtime_conf: Optional[dict] = None) -> None:
+    def sign_view(self, view: View, runtime_conf: dict) -> None:
         """
         A method to "sign" a new view that this app creates at the beginning of annotation.
         Signing will populate the view metadata with information and configuration of this app.
@@ -201,27 +203,22 @@ class ClamsApp(ABC):
         :param view: a view to sign
         :param runtime_conf: runtime configuration of the app as k-v pairs
         """
-        # 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 pass `runtime_params` "
-                          "from _annotate() method.",
-                          FutureWarning, stacklevel=2)
-            return
         view.metadata.app = self.metadata.identifier
+        params_map = {p.name: p for p in self.metadata.parameters}
         if self._RAW_PARAMS_KEY in runtime_conf:
             for k, v in runtime_conf.items():
                 if k == self._RAW_PARAMS_KEY:
                     for orik, oriv in v.items():
-                        if orik in self.metadata.parameters and self.metadata.parameters[orik].multivalued:
+                        if orik in params_map and params_map[orik].multivalued:
                             view.metadata.add_parameter(orik, str(oriv))
                         else:
                             view.metadata.add_parameter(orik, oriv[0])
-                view.metadata.add_app_configuration(k, v)
+                else:
+                    view.metadata.add_app_configuration(k, v)
         else:
             # meaning the parameters directly from flask or argparser and values are in lists
             for k, v in runtime_conf.items():
-                if k in self.metadata.parameters and self.metadata.parameters[k].multivalued:
+                if k in params_map and params_map[k].multivalued:
                     view.metadata.add_parameter(k, str(v))
                 else:
                     view.metadata.add_parameter(k, v[0])

{clams-python-1.1.6 → clams_python-1.2.1}/clams/develop/templates/app/app.py.template

@@ -13,7 +13,6 @@ The app.py script does several things:
 
 import argparse
 import logging
-from typing import Union
 
 # Imports needed for Clams and MMIF.
 # Non-NLP Clams applications will require AnnotationTypes
@@ -36,7 +35,7 @@ class $APP_CLASS_NAME(ClamsApp):
         # When using the ``metadata.py`` leave this do-nothing "pass" method here. 
         pass
 
-    def _annotate(self, mmif: Union[str, dict, Mmif], **parameters) -> Mmif:
+    def _annotate(self, mmif: Mmif, **parameters) -> Mmif:
         # see https://sdk.clams.ai/autodoc/clams.app.html#clams.app.ClamsApp._annotate
         raise NotImplementedError
 

{clams-python-1.1.6 → clams_python-1.2.1}/clams/mmif_utils/source.py

@@ -1,9 +1,9 @@
 import argparse
 import itertools
 import json
+import pathlib
 import sys
 import textwrap
-from os import path
 from typing import Union, Generator, List, Optional, Iterable
 from urllib.parse import urlparse
 
@@ -171,24 +171,18 @@ class WorkflowSource:
             yield self.produce()
 
 
-def generate_source_mmif_from_file(documents, prefix=None, **ignored):
-    from string import Template
+def generate_source_mmif_from_file(documents, prefix=None, scheme='file', **ignored):
     at_types = {
         'video': DocumentTypes.VideoDocument,
         'audio': DocumentTypes.AudioDocument,
         'text': DocumentTypes.TextDocument,
         'image': DocumentTypes.ImageDocument
     }
-    template = Template('''{
-          "@type": "${at_type}",
-          "properties": {
-            "id": "${aid}",
-            "mime": "${mime}",
-            "location": "${location}" }
-        }''')
     pl = WorkflowSource()
-    if prefix and not path.isabs(prefix):
-        raise ValueError(f"prefix must be an absolute path; given \"{prefix}\".")
+    if prefix:
+        prefix = pathlib.PurePosixPath(prefix)
+        if not prefix.is_absolute():
+            raise ValueError(f"prefix must be an absolute path; given \"{prefix}\".")
     for doc_id, arg in enumerate(documents, start=1):
         arg = arg.strip()
         if len(arg) < 1:
@@ -200,57 +194,20 @@ def generate_source_mmif_from_file(documents, prefix=None, **ignored):
             raise ValueError(
                 f'Invalid MIME types, or no MIME type and/or path provided, in argument {doc_id-1} to source'
             )
-        if prefix and path.isabs(location):
-            raise ValueError(f"when prefix is used, file location must not be an absolute path; given \"{location}\".")
-        elif not prefix and not path.isabs(location):
-            raise ValueError(f'file location must be an absolute path, or --prefix must be used; given \"{location}\".')
-        elif prefix and not path.isabs(location):
-            location = path.join(prefix, location)
-        doc = template.substitute(
-            at_type=str(at_types[mime.split('/', maxsplit=1)[0]]),
-            aid=f'd{doc_id}',
-            mime=mime,
-            location=location
-        )
-        pl.add_document(doc)
-    return pl.produce().serialize(pretty=True)
-
-
-def generate_source_mmif_from_customscheme(documents, scheme, **ignored):
-    from string import Template
-    at_types = {
-        'video': DocumentTypes.VideoDocument,
-        'audio': DocumentTypes.AudioDocument,
-        'text': DocumentTypes.TextDocument,
-        'image': DocumentTypes.ImageDocument
-    }
-    template = Template('''{
-          "@type": "${at_type}",
-          "properties": {
-            "id": "${aid}",
-            "mime": "${mime}",
-            "location": "${location}" }
-        }''')
-    pl = WorkflowSource()
-    for doc_id, arg in enumerate(documents, start=1):
-        arg = arg.strip()
-        if len(arg) < 1:
-            continue
-        result = arg.split(':', maxsplit=1)
-        if len(result) == 2 and result[0].split('/', maxsplit=1)[0] in at_types:
-            mime, location = result
-        else:
-            raise ValueError(
-                f'Invalid MIME types, or no MIME type and/or path provided, in argument {doc_id-1} to source'
-            )
-        if urlparse(location).scheme == '':
-            location = scheme + '://' + location
-        doc = template.substitute(
-            at_type=str(at_types[mime.split('/', maxsplit=1)[0]]),
-            aid=f'd{doc_id}',
-            mime=mime,
-            location=location
-        )
+        location_uri = urlparse(location, scheme=scheme)
+        if location_uri.scheme == 'file':
+            location = pathlib.PurePosixPath(location_uri.path)
+            if prefix and location.is_absolute():
+                raise ValueError(f"when prefix is used, file location must not be an absolute path; given \"{location}\".")
+            elif not prefix and not location.is_absolute():
+                raise ValueError(f'file location must be an absolute path, or --prefix must be used; given \"{location}\".')
+            elif prefix and not location.is_absolute():
+                location = prefix / location
+        doc = Document()
+        doc.at_type = at_types[mime.split('/', maxsplit=1)[0]]
+        doc.properties.location = f"{location_uri.scheme}://{location}"
+        doc.properties.id = f'd{doc_id}'
+        doc.properties.mime = mime
         pl.add_document(doc)
     return pl.produce().serialize(pretty=True)
 
@@ -274,19 +231,22 @@ def prep_argparser(**kwargs):
         default=None,
         action='store',
         nargs='+',
-        help="This list of documents should be colon-joined pairs of document types and file paths. A document type "
-             "can be one of ``audio``, ``video``, ``text``, ``image``, or a MIME type string (such as video/mp4). The "
-             "output will be a MMIF file containing a document for each of those file paths, with the appropriate "
-             "``@type`` and MIME type (if given), printed to the standard output. "
+        help='This list of documents MUST be colon-delimited pairs of document types and file locations. A document '
+             'type can be one of `audio`, `video`, `text`, `image`, or a MIME type string (such as video/mp4). The '
+             'file locations MUST be valid URI strings (e.g. `file:///path/to/file.mp4`, or URI scheme part can be '
+             'omitted, when `--scheme` flag is used). Note that when `file://` scheme is used (default), locations '
+             'MUST BE POSIX forms (Windows forms are not supported). The output will be a MMIF file containing a '
+             'document for each of those file paths, with the appropriate ``@type`` and MIME type (if given).'
     )
     parser.add_argument(
         '-p', '--prefix',
         default=None,
         metavar='PATH',
         nargs='?',
-        help='An absolute path to use as prefix for file paths (ONLY WORKS with `file` scheme, ignored otherwise). If '
-             'prefix is set, document file paths MUST be relative. Useful when creating source MMIF files from a '
-             'system that\'s different from the system that actually runs the workflow (e.g. in a container).'
+        help='An absolute path to use as prefix for file paths (ONLY WORKS with the default `file://` scheme, ignored '
+             'otherwise. MUST BE a POSIX form, Windows form is not supported). If prefix is set, document file paths '
+             'MUST be relative. Useful when creating source MMIF files from a system that\'s different from the '
+             'environment that actually runs the workflow (e.g. in a container).'
     )
     parser.add_argument(
         '-o', '--output',
@@ -300,7 +260,7 @@ def prep_argparser(**kwargs):
         default='file',
         action='store',
         nargs='?',
-        help='A scheme to associate with the document location URI. When not given, the default scheme is `file`.'
+        help='A scheme to associate with the document location URI. When not given, the default scheme is `file://`.'
     )
     return parser
 
@@ -310,10 +270,7 @@ def main(args):
         out_f = open(args.output, 'w')
     else:
         out_f = sys.stdout
-    if args.scheme == 'file':
-        mmif = generate_source_mmif_from_file(**vars(args))
-    else:
-        mmif = generate_source_mmif_from_customscheme(**vars(args))
+    mmif = generate_source_mmif_from_file(windows_path=False, **vars(args))
     out_f.write(mmif)
     return mmif
 

clams_python-1.2.1/clams/ver/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.1"

{clams-python-1.1.6 → clams_python-1.2.1/clams_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.1.6
+Version: 1.2.1
 Summary: A collection of APIs to develop CLAMS app for python
 Home-page: https://clams.ai
 Author: Brandeis Lab for Linguistics and Computation

{clams-python-1.1.6 → clams_python-1.2.1}/tests/test_clamsapp.py

@@ -228,7 +228,26 @@ class TestClamsApp(unittest.TestCase):
         in_mmif.metadata.mmif = f"http://mmif.clams.ai/{incompat_ver}"
         with pytest.raises(ValueError):
             self.app.annotate(in_mmif)
-        
+
+    def test_sign_view(self):
+        m = Mmif(self.in_mmif)
+        v1 = m.new_view()
+        self.app.sign_view(v1, {})
+        self.assertEqual(v1.metadata.app, self.app.metadata.identifier)
+        self.assertEqual(len(v1.metadata.parameters), 0)
+        v2 = m.new_view()
+        raw_query_string_arguments = {'undefined_param1': ['value1']}  # values are lists as our restifier uses `to_dict(flat=False)`
+        self.app.sign_view(v2, self.app._refine_params(**raw_query_string_arguments))
+        self.assertEqual(v2.metadata.app, self.app.metadata.identifier)
+        self.assertEqual(len(v2.metadata.parameters), 1)
+        self.assertFalse(clams.ClamsApp._RAW_PARAMS_KEY in v2.metadata.appConfiguration)
+        for param in self.app.metadata.parameters:
+            # any parameter with defaults should be recorded
+            if param.default is not None:
+                self.assertTrue(param.name in v2.metadata.appConfiguration)
+            elif param.name not in raw_query_string_arguments:
+                self.assertFalse(param.name in v2.metadata.appConfiguration)
+
     def test_annotate(self):
         # The example app is hard-coded to **always** emit version mismatch warning
         out_mmif = self.app.annotate(self.in_mmif)

{clams-python-1.1.6 → clams_python-1.2.1}/tests/test_clamscli.py

@@ -3,6 +3,7 @@ import copy
 import io
 import os
 import unittest
+import unittest.mock
 
 from mmif.serialize import Mmif
 from mmif.vocabulary import DocumentTypes, AnnotationTypes
@@ -63,6 +64,10 @@ class TestSource(unittest.TestCase):
         with self.assertRaises(ValueError):
             self.generate_source_mmif()
 
+    @unittest.mock.patch('os.name', 'nt')
+    def test_on_windows(self):
+        self.test_accept_file_paths()
+
     def test_accept_prefixed_file_paths(self):
         self.prefix = '/a/b'
         self.docs.append("video:c.mp4")

clams-python-1.1.6/VERSION

@@ -1 +0,0 @@
-1.1.6

clams-python-1.1.6/clams/ver/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.1.6"