Merge branch 'develop' into 236-hwfetch

clams/mmif_utils/source.py

@@ -203,9 +203,10 @@ def generate_source_mmif_from_file(documents, prefix=None, scheme='file', **igno
                 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
+        location = str(location)
         doc = Document()
         doc.at_type = at_types[mime.split('/', maxsplit=1)[0]]
-        doc.properties.location = f"{location_uri.scheme}://{location}"
+        doc.properties.location = f"{location_uri.scheme}://{location if not location.startswith(location_uri.scheme) else location[len(location_uri.scheme)+3:]}"
         doc.properties.id = f'd{doc_id}'
         doc.properties.mime = mime
         pl.add_document(doc)
@@ -225,7 +226,14 @@ def describe_argparser():
 
 
 def prep_argparser(**kwargs):
-    parser = argparse.ArgumentParser(description=describe_argparser()[1], formatter_class=argparse.RawDescriptionHelpFormatter, **kwargs)
+    import pkgutil
+    import re
+    import importlib
+    discovered_docloc_plugins = {
+        name[len('mmif_docloc_'):]: importlib.import_module(name) for _, name, _ in pkgutil.iter_modules() if
+        re.match(r'mmif[-_]docloc[-_]', name)
+    }
+    parser = argparse.ArgumentParser(description=describe_argparser()[1], formatter_class=argparse.RawTextHelpFormatter, **kwargs)
     parser.add_argument(
         'documents',
         default=None,
@@ -255,12 +263,17 @@ def prep_argparser(**kwargs):
         nargs='?',
         help='A name of a file to capture a generated MMIF json. When not given, MMIF is printed to stdout.'
     )
+    scheme_help = 'A scheme to associate with the document location URI. When not given, the default scheme is `file://`.'
+    if len(discovered_docloc_plugins) > 0:
+        plugin_help = [f'"{scheme_name}" ({scheme_plugin.help() if "help" in dir(scheme_plugin) else "help msg not provided by developer"})' 
+                       for scheme_name, scheme_plugin in discovered_docloc_plugins.items()]
+        scheme_help += ' (AVAILABLE ADDITIONAL SCHEMES)  ' + ', '.join(plugin_help)
     parser.add_argument(
         '-s', '--scheme',
         default='file',
         action='store',
         nargs='?',
-        help='A scheme to associate with the document location URI. When not given, the default scheme is `file://`.'
+        help=scheme_help
     )
     return parser
 

documentation/appmetadata.rst

@@ -91,7 +91,7 @@ input specification can be as simple as the following:
       # and more app metadata fields, 
     }
     
-In the above example, the developer is declaring the app is expecting ``Token``annotation objects, with a ``posTagSet`` 
+In the above example, the developer is declaring the app is expecting ``Token`` annotation objects, with a ``posTagSet`` 
 property of which value is the URL of the Penn Treebank POS tag set, *verbatim*, in the input MMIF, and all other 
 existing annotation types in the input MMIF will be ignored during processing. There are some *grammar* of how this 
 ``input`` list can be written. 

documentation/autodoc/clams.appmetadata.rst

@@ -6,3 +6,15 @@ Module contents
 
 .. autoclass:: clams.appmetadata.AppMetadata
    :members:
+
+.. autoclass:: clams.appmetadata.Input
+   :members:
+   :inherited-members:
+
+.. autoclass:: clams.appmetadata.Output
+   :members:
+   :inherited-members:
+
+.. autoclass:: clams.appmetadata.RuntimeParameter
+   :members:
+   :inherited-members:

requirements.txt

@@ -1,4 +1,4 @@
-mmif-python==1.0.17
+mmif-python==1.0.18
 
 Flask>=2
 Flask-RESTful>=0.3.9