clams-python 1.2.2__tar.gz → 1.2.4__tar.gz

{clams_python-1.2.2/clams_python.egg-info → clams_python-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.2.2
+Version: 1.2.4
 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==1.0.14
+Requires-Dist: mmif-python==1.0.16
 Requires-Dist: Flask>=2
 Requires-Dist: Flask-RESTful>=0.3.9
 Requires-Dist: gunicorn>=20

clams_python-1.2.4/VERSION

@@ -0,0 +1 @@
+1.2.4

{clams_python-1.2.2 → clams_python-1.2.4}/clams/app/__init__.py

@@ -20,6 +20,16 @@ logging.basicConfig(
     datefmt="%Y-%m-%d %H:%M:%S")
 
 
+falsy_values = [
+    'False', 
+    'false', 
+    'F',
+    'f',
+    '0',
+    0, 
+    False
+]
+
 class ClamsApp(ABC):
     """
     An abstract class to define API's for ClamsApps. A CLAMS app should inherit
@@ -388,7 +398,7 @@ class ParameterCaster(object):
         """
         Helper function to convert string values to bool type.
         """
-        return False if value in (False, 0, 'False', 'false', '0') else True
+        return False if value in falsy_values else True
 
     @staticmethod
     def float_param(value) -> float:

{clams_python-1.2.2 → clams_python-1.2.4}/clams/appmetadata/__init__.py

@@ -162,7 +162,8 @@ class RuntimeParameter(_BaseModel):
     type: param_value_types = pydantic.Field(
         ...,
         description=f"Type of the parameter value the app expects. Must be one of {param_value_types_values}. When "
-                    "type is ``map``, ``multivalued=true`` is automatically forced. \n\n"
+                    "type is ``map``, ``multivalued=true`` is forced, and when ``boolean``, ``multivalued=false`` is "
+                    "forced. \n\n"
                     "Notes for developers: \n\n"
                     "When the type is ``map``, the parameter value (still a single string from the users' perspective) "
                     "must be formatted as a ``KEY:VALUE`` pair, namely a colon-separated string. To pass multiple "
@@ -186,7 +187,7 @@ class RuntimeParameter(_BaseModel):
         description="(optional) Default value for the parameter.\n\n"
                     "Notes for developers: \n\n"
                     "Setting a default value makes a parameter `optional`. \n\n"
-                    "When ``multivalued=True``, the default value should be a list of values. \n\n"
+                    "When ``multivalued=true``, the default value should be a list of values. \n\n"
                     "When ``type=map``, the default value should be a list of colon-separated strings. \n\n"
     )
     multivalued: bool = pydantic.Field(
@@ -420,8 +421,10 @@ class AppMetadata(pydantic.BaseModel):
         # see https://docs.pydantic.dev/1.10/usage/types/#unions
         # e.g. casting 0.1 using the `primitives` dict will result in  0 (int)
         # while casting "0.1" using the `primitives` dict will result in  0.1 (float)
-        if type == 'map' and multivalued is False:
+        if type == 'map':
             multivalued = True
+        if type == 'boolean':
+            multivalued = False
         if default is not None:
             if isinstance(default, list):
                 default = [str(d) for d in default]

{clams_python-1.2.2 → clams_python-1.2.4}/clams/develop/__init__.py

@@ -7,6 +7,7 @@ from typing import List
 
 import clams
 
+update_tmp_suffix = '.tmp'
 available_recipes = {
     'app': {
         'description': 'Skeleton code for a CLAMS app',
@@ -26,7 +27,7 @@ class CookieCutter(object):
     def __init__(self, name: str, outdir: str, recipes: List[str]):
         self.rawname = name 
         self.name_tokens = self.tokenize_rawname()
-        self.ourdir = pathlib.Path(outdir)
+        self.outdir = pathlib.Path(outdir)
         if recipes:
             self.recipes = recipes
         else:
@@ -42,24 +43,30 @@ class CookieCutter(object):
                 words.pop()
         return words
     
-    def bake(self):
+    def bake(self, update_level=0):
         print(f"Baking {self.recipes}")
         for recipe in self.recipes:
             src_dir = pathlib.Path(__file__).parent / 'templates' / available_recipes[recipe]['sourcedir']
-            dst_dir = self.ourdir / self.rawname / available_recipes[recipe]['targetdir']
+            dst_dir = self.outdir / self.rawname / available_recipes[recipe]['targetdir']
             if recipe == 'app':
-                self.bake_app(src_dir, dst_dir)
+                caps = [t.capitalize() for t in self.name_tokens]
+                app_vars = {
+                    'CLAMS_VERSION': clams.__version__,
+                    'APP_CLASS_NAME': "".join(caps),
+                    'APP_NAME': " ".join(caps),
+                    'APP_IDENTIFIER': '-'.join(self.name_tokens)
+                }
+                if update_level > 0:
+                    self.reheat_app(src_dir, dst_dir, app_vars, reheat_level=update_level)
+                else:
+                    if dst_dir.exists():
+                        raise FileExistsError(f"  {dst_dir} already exists. Did you mean `--update`? ")
+                    self.bake_app(src_dir, dst_dir, app_vars)
             if recipe == 'gha':
+                # There's nothing for devs to tweak GHA template, so first generation and updating are the same.
                 self.bake_gha(src_dir, dst_dir)
             
-    def bake_app(self, src_dir, dst_dir):
-        caps = [t.capitalize() for t in self.name_tokens]
-        templating_vars = {
-            'CLAMS_VERSION': clams.__version__,
-            'APP_CLASS_NAME': "".join(caps),
-            'APP_NAME': " ".join(caps),
-            'APP_IDENTIFIER': '-'.join(self.name_tokens)
-        }
+    def bake_app(self, src_dir, dst_dir, templating_vars):
         for g in src_dir.glob("**/*.template"):
             r = g.relative_to(src_dir).parent
             f = g.with_suffix('').name
@@ -71,7 +78,40 @@ class CookieCutter(object):
                 out_f.write(compiled)
         print(f"App skeleton code is copied to {self.rawname}")
         print(f"  Checkout {self.rawname}/README.md for the next steps!")
-                
+
+    def reheat_app(self, src_dir, dst_dir, templating_vars, reheat_level=1):
+        essentials = ['app.py', 'metadata.py', 'cli.py', 'Containerfile', 'requirements.txt']
+        for template in src_dir.glob("**/*.template"):
+            dirname = template.relative_to(src_dir).parent
+            basename = template.with_suffix('').name
+            if basename not in essentials:
+                # if non-essential, just skip when updating
+                continue
+            in_f = open(template, 'r')
+            tmpl_to_compile = Template(in_f.read())
+            compiled = tmpl_to_compile.safe_substitute(templating_vars)
+            in_f.close()
+            ori_fpath = dst_dir / dirname / basename
+            if not ori_fpath.exists():
+                # this file is new in this version of cookiecutter 
+                with open(ori_fpath, 'w') as out_f:
+                    out_f.write(compiled)
+            else:
+                ori_f = open(ori_fpath, 'r')
+                ori_content = ori_f.read()
+                if ori_content != compiled:
+                    # when the target file already exists, we need to do diff & patch 
+                    # TODO (krim @ 5/5/24): add update level 2 and 3 code here
+                    out_fpath = f'{ori_fpath}{update_tmp_suffix}'
+                    print(f'    {dst_dir / dirname / basename} already exists, generating a tmp file: {out_fpath}')
+                    with open(out_fpath, 'w') as out_f:
+                        out_f.write(compiled)
+                else:
+                    print(f'    {dst_dir / dirname / basename} already exists, but the content is unchanged from the '
+                          f'template, skipping re-generating')
+        print(f"App skeleton code is updated in {self.rawname}")
+        print(f"  Checkout {self.rawname}/README.md for the next steps!")
+
     def bake_gha(self, src_dir, dst_dir):
         self.simple_recursive_copy_minus_template_suffix(src_dir, dst_dir)
         print(f"GitHub Actions workflow files are copied to {self.rawname}/.github")
@@ -128,12 +168,23 @@ def prep_argparser(**kwargs):
         nargs='?',
         help='The name of the parent directory where the app skeleton directory is placed. (default: current directory)'
     )
+    parser.add_argument(
+        '-u', '--update',
+        action='count',
+        default=0,  #  > Note, the default will be None unless explicitly set to 0. (https://docs.python.org/3/library/argparse.html#action)
+        help=f'Set update level by passing this flag multiple times. This is EXPERIMENTAL, and developers MUST NOT'
+             f'rely on the update results, and should conduct manual checks afterward. LEVEL 0: does not update and '
+             f'raise an error when existing directory found. LEVEL 1: generate non-existing files and generate '
+             f'`{update_tmp_suffix}`-suffixed files for existing one. LEVEL 2 (WIP): generate non-existing files and '
+             f'automatically generate patch files for existing files. LEVEL 3 (WIP): generate non-existing files and '
+             f'apply patches to existing files. (default: 0)'
+    )
     return parser
 
 
 def main(args):
     cutter = CookieCutter(name=args.name, outdir=args.parent_dir, recipes=args.recipes)
-    cutter.bake()
+    cutter.bake(args.update)
 
 if __name__ == '__main__':
     parser = prep_argparser()

{clams_python-1.2.2 → clams_python-1.2.4}/clams/develop/templates/app/Containerfile.template

@@ -1,11 +1,11 @@
 # Use the same base image version as the clams-python python library version
 FROM ghcr.io/clamsproject/clams-python:$CLAMS_VERSION
 # See https://github.com/orgs/clamsproject/packages?tab=packages&q=clams-python for more base images
-# IF you want to automatically publish this image to the clamsproject organization, 
+# IF you want to automatically publish this image to the clamsproject organization,
 # 1. you should have generated this template without --no-github-actions flag
-# 1. to add arm64 support, change relevant line in .github/workflows/container.yml 
-#     * NOTE that a lots of software doesn't install/compile or run on arm64 architecture out of the box 
-#     * make sure you locally test the compatibility of all software dependencies before using arm64 support 
+# 1. to add arm64 support, change relevant line in .github/workflows/container.yml
+#     * NOTE that a lots of software doesn't install/compile or run on arm64 architecture out of the box
+#     * make sure you locally test the compatibility of all software dependencies before using arm64 support
 # 1. use a git tag to trigger the github action. You need to use git tag to properly set app version anyway
 
 ################################################################################
@@ -14,6 +14,20 @@ ARG CLAMS_APP_VERSION
 ENV CLAMS_APP_VERSION ${CLAMS_APP_VERSION}
 ################################################################################
 
+################################################################################
+# This is duplicate from the base image Containerfile
+# but makes sure the cache directories are consistent across all CLAMS apps
+
+# https://github.com/openai/whisper/blob/ba3f3cd54b0e5b8ce1ab3de13e32122d0d5f98ab/whisper/__init__.py#L130
+ENV XDG_CACHE_HOME='/cache'
+# https://huggingface.co/docs/huggingface_hub/main/en/package_reference/environment_variables#hfhome
+ENV HF_HOME="/cache/huggingface"
+# https://pytorch.org/docs/stable/hub.html#where-are-my-downloaded-models-saved
+ENV TORCH_HOME="/cache/torch"
+
+RUN mkdir /cache && rm -rf /root/.cache && ln -s /cache /root/.cache
+################################################################################
+
 ################################################################################
 # clams-python base images are based on debian distro
 # install more system packages as needed using the apt manager
@@ -23,8 +37,8 @@ ENV CLAMS_APP_VERSION ${CLAMS_APP_VERSION}
 # main app installation
 COPY ./ /app
 WORKDIR /app
-RUN pip3 install -r requirements.txt
+RUN pip3 install --no-cache-dir -r requirements.txt
 
-# default command to run the CLAMS app in a production server 
+# default command to run the CLAMS app in a production server
 CMD ["python3", "app.py", "--production"]
 ################################################################################

{clams_python-1.2.2 → clams_python-1.2.4}/clams/develop/templates/app/README.md.template

@@ -1,33 +1,33 @@
 # TO_DEVS: BURN AFTER READING
 
-Delete this section of the document once the app development is done, before publishing the repository. 
+Delete this section of the document once the app development is done, before publishing the repository.
 
 ---
-This skeleton code is a scaffolding for Python-based CLAMS app development. Specifically, it contains 
+This skeleton code is a scaffolding for Python-based CLAMS app development. Specifically, it contains
 
-1. `app.py` and `metadata.py` to write the app 
+1. `app.py` and `metadata.py` to write the app
 1. `requirements.txt` to specify python dependencies
 1. `Containerfile` to containerize the app and specify system dependencies
 1. `.gitignore` and `.dockerignore` files listing commonly ignored files
 1. an empty `LICENSE` file to replace with an actual license information of the app
 1. This `README.md` file for additional information not specified in the general user manual at https://apps.clams.ai/clamsapp
-1. A number of GitHub Actions workflows for issue/bug-report management 
+1. A number of GitHub Actions workflows for issue/bugreport management
 1. A GHA workflow to publish app images upon any push of a git tag
    * **NOTE**: All GHA workflows included are designed to only work in repositories under `clamsproject` organization.
 
 Before pushing your first commit, please make sure to delete this section of the document.
 
-Then use the following section to document any additional information specific to this app. If your app works significantly different from what's described in the generic readme file, be as specific as possible. 
+Then use the following section to document any additional information specific to this app. If your app works significantly different from what's described in the generic readme file, be as specific as possible.
 
 
-> **warning** 
+> **warning**
 > TO_DEVS: Delete these `TO_DEVS` notes and warnings before publishing the repository.
 
 ---
 
 # $APP_NAME
 
-> **warning** 
+> **warning**
 > TO_DEVS: Again, delete these `TO_DEVS` notes and warnings before publishing the repository.
 
 ## Description
@@ -37,11 +37,11 @@ Then use the following section to document any additional information specific t
 
 ## User instruction
 
-General user instructions for CLAMS apps is available at [CLAMS Apps documentation](https://apps.clams.ai/clamsapp).
+General user instructions for CLAMS apps are available at [CLAMS Apps documentation](https://apps.clams.ai/clamsapp).
 
 Below is a list of additional information specific to this app.
 
-> **note** 
+> **note**
 > TO_DEVS: Below is a list of additional information specific to this app.
 
 
@@ -57,7 +57,7 @@ Below is a list of additional information specific to this app.
 
 ### Configurable runtime parameter
 
-For the full list of parameters, please refer to the app metadata from [CLAMS App Directory](https://apps.clams.ai) or [`metadata.py`](metadata.py) file in this repository.
+For the full list of parameters, please refer to the app metadata from the [CLAMS App Directory](https://apps.clams.ai) or the [`metadata.py`](metadata.py) file in this repository.
 
 > **warning**
 > TO_DEVS: If you're not developing this app for publishing on the CLAMS App Directory, the above paragraph is not applicable. Feel free to delete or change it.

{clams_python-1.2.2 → clams_python-1.2.4}/clams/develop/templates/app/app.py.template

@@ -6,7 +6,7 @@ app.py Template
 The app.py script does several things:
 - import the necessary code
 - create a subclass of ClamsApp that defines the metadata and provides a method to run the wrapped NLP tool
-- provide a way to run the code as a RESTful Flask service 
+- provide a way to run the code as a RESTful Flask service
 
 
 """
@@ -31,14 +31,24 @@ class $APP_CLASS_NAME(ClamsApp):
 
     def _appmetadata(self):
         # see https://sdk.clams.ai/autodoc/clams.app.html#clams.app.ClamsApp._load_appmetadata
-        # Also check out ``metadata.py`` in this directory. 
-        # When using the ``metadata.py`` leave this do-nothing "pass" method here. 
+        # Also check out ``metadata.py`` in this directory.
+        # When using the ``metadata.py`` leave this do-nothing "pass" method here.
         pass
 
     def _annotate(self, mmif: Mmif, **parameters) -> Mmif:
         # see https://sdk.clams.ai/autodoc/clams.app.html#clams.app.ClamsApp._annotate
         raise NotImplementedError
 
+def get_app():
+    """
+    This function effectively creates an instance of the app class, without any arguments passed in, meaning, any
+    external information such as initial app configuration should be set without using function arguments. The easiest
+    way to do this is to set global variables before calling this.
+    """
+    # for example:
+    # return $APP_CLASS_NAME(create, from, global, params)
+    raise NotImplementedError
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
@@ -50,7 +60,9 @@ if __name__ == "__main__":
     parsed_args = parser.parse_args()
 
     # create the app instance
-    app = $APP_CLASS_NAME()
+    # if get_app() call requires any "configurations", they should be set now as global variables
+    # and referenced in the get_app() function. NOTE THAT you should not change the signature of get_app()
+    app = get_app()
 
     http_app = Restifier(app, port=int(parsed_args.port))
     # for running the application in production mode

clams_python-1.2.4/clams/develop/templates/app/cli.py.template

@@ -0,0 +1,92 @@
+#!/usr/bin/env python3
+"""
+The purpose of this file is to define a thin CLI interface for your app
+
+DO NOT CHANGE the name of the file
+"""
+
+import argparse
+import sys
+from contextlib import redirect_stdout
+
+import app
+
+import clams.app
+from clams import AppMetadata
+
+
+def metadata_to_argparser(app_metadata: AppMetadata) -> argparse.ArgumentParser:
+    """
+    Automatically generate an argparse.ArgumentParser from parameters specified in the app metadata (metadata.py).
+    """
+
+    parser = argparse.ArgumentParser(
+        description=f"{app_metadata.name}: {app_metadata.description} (visit {app_metadata.url} for more info)",
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    # parse cli args from app parameters
+    for parameter in app_metadata.parameters:
+        if parameter.multivalued:
+            a = parser.add_argument(
+                f"--{parameter.name}",
+                help=parameter.description,
+                nargs='+',
+                action='extend',
+                type=str
+            )
+        else:
+            a = parser.add_argument(
+                f"--{parameter.name}",
+                help=parameter.description,
+                nargs=1,
+                action="store",
+                type=str)
+        if parameter.choices is not None:
+            a.choices = parameter.choices
+        if parameter.default is not None:
+            a.help += f" (default: {parameter.default}"
+            if parameter.type == "boolean":
+                a.help += (f", any value except for {[v for v in clams.app.falsy_values if isinstance(v, str)]} "
+                           f"will be interpreted as True")
+            a.help += ')'
+            # then we don't have to add default values to the arg_parser
+            # since that's handled by the app._refined_params() method.
+    parser.add_argument('IN_MMIF_FILE', nargs='?', type=argparse.FileType('r'),
+                        help='input MMIF file path, or STDIN if `-` or not provided. NOTE: When running this cli.py in '
+                             'a containerized environment, make sure the container is run with `-i` flag to keep stdin '
+                             'open.',
+                        # will check if stdin is a keyboard, and return None if it is
+                        default=None if sys.stdin.isatty() else sys.stdin)
+    parser.add_argument('OUT_MMIF_FILE', nargs='?', type=argparse.FileType('w'),
+                        help='output MMIF file path, or STDOUT if `-` or not provided. NOTE: When this is set to '
+                             'STDOUT, any print statements in the app code will be redirected to stderr.',
+                        default=sys.stdout)
+    return parser
+
+
+if __name__ == "__main__":
+    clamsapp = app.get_app()
+    arg_parser = metadata_to_argparser(app_metadata=clamsapp.metadata)
+    args = arg_parser.parse_args()
+    if args.IN_MMIF_FILE:
+        in_data = args.IN_MMIF_FILE.read()
+        # since flask webapp interface will pass parameters as "unflattened" dict to handle multivalued parameters
+        # (https://werkzeug.palletsprojects.com/en/latest/datastructures/#werkzeug.datastructures.MultiDict.to_dict)
+        # we need to convert arg_parsers results into a similar structure, which is the dict values are wrapped in lists
+        params = {}
+        for pname, pvalue in vars(args).items():
+            if pvalue is None or pname in ['IN_MMIF_FILE', 'OUT_MMIF_FILE']:
+                continue
+            elif isinstance(pvalue, list):
+                params[pname] = pvalue
+            else:
+                params[pname] = [pvalue]
+        if args.OUT_MMIF_FILE.name == '<stdout>':
+            with redirect_stdout(sys.stderr):
+                out_mmif = clamsapp.annotate(in_data, **params)
+        else:
+            out_mmif = clamsapp.annotate(in_data, **params)
+        args.OUT_MMIF_FILE.write(out_mmif)
+    else:
+        arg_parser.print_help()
+        sys.exit(1)

{clams_python-1.2.2 → clams_python-1.2.4}/clams/develop/templates/app/metadata.py.template

@@ -1,5 +1,5 @@
 """
-The purpose of this file is to define the metadata of the app with minimal imports. 
+The purpose of this file is to define the metadata of the app with minimal imports.
 
 DO NOT CHANGE the name of the file
 """
@@ -10,12 +10,12 @@ from clams.app import ClamsApp
 from clams.appmetadata import AppMetadata
 
 
-# DO NOT CHANGE the function name 
+# DO NOT CHANGE the function name
 def appmetadata() -> AppMetadata:
     """
     Function to set app-metadata values and return it as an ``AppMetadata`` obj.
     Read these documentations before changing the code below
-    - https://sdk.clams.ai/appmetadata.html metadata specification. 
+    - https://sdk.clams.ai/appmetadata.html metadata specification.
     - https://sdk.clams.ai/autodoc/clams.appmetadata.html python API
     
     :return: AppMetadata object holding all necessary information.
@@ -26,7 +26,7 @@ def appmetadata() -> AppMetadata:
         name="$APP_NAME",
         description="",  # briefly describe what the purpose and features of the app
         app_license="",  # short name for a software license like MIT, Apache2, GPL, etc.
-        identifier="$APP_IDENTIFIER",  # should be a single string without whitespaces. If you don't intent to publish this app to the CLAMS app-directory, please use a full IRI format. 
+        identifier="$APP_IDENTIFIER",  # should be a single string without whitespaces. If you don't intent to publish this app to the CLAMS app-directory, please use a full IRI format.
         url="https://fakegithub.com/some/repository",  # a website where the source code and full documentation of the app is hosted
         # (if you are on the CLAMS team, this MUST be "https://github.com/clamsproject/app-$APP_IDENTIFIER"
         # (see ``.github/README.md`` file in this directory for the reason)

{clams_python-1.2.2 → clams_python-1.2.4}/clams/mmif_utils/rewind.py

@@ -77,10 +77,14 @@ def describe_argparser():
 def prep_argparser(**kwargs):
     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("IN_MMIF_FILE",
+                        nargs="?", type=argparse.FileType("r"),
+                        default=None if sys.stdin.isatty() else sys.stdin,
+                        help='input MMIF file path, or STDIN if `-` or not provided.')
+    parser.add_argument("OUT_MMIF_FILE",
+                        nargs="?", type=argparse.FileType("w"),
+                        default=sys.stdout,
+                        help='output MMIF file path, or STDOUT if `-` or not provided.')
     parser.add_argument("-p", '--pretty', action='store_true', 
                         help="Pretty-print rewound MMIF")
     parser.add_argument("-n", '--number', default="0", type=int,
@@ -92,7 +96,7 @@ def prep_argparser(**kwargs):
 
 
 def main(args):
-    mmif_obj = mmif.Mmif(str(sys.stdin)) if args.mmif_file[0] == '-' else mmif.Mmif(open(args.mmif_file).read())
+    mmif_obj = mmif.Mmif(args.IN_MMIF_FILE.read())
 
     if args.number == 0:  # If user doesn't know how many views to rewind, give them choices.
         choice = prompt_user(mmif_obj)
@@ -101,22 +105,7 @@ def main(args):
     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)
-        if output_fp.is_file():
-            parent = output_fp.parent
-            stem = output_fp.stem
-            suffix = output_fp.suffix
-            count = 1
-            while (parent / f"{stem}_{count}{suffix}").is_file():
-                count += 1
-            output_fp = parent / f"{stem}_{count}{suffix}"
-        
-        out_f = open(output_fp, 'w')
-    else:
-        out_f = sys.stdout
-    out_f.write(rewind_mmif(mmif_obj, choice, args.mode == 'view').serialize(pretty=args.pretty))
+    args.OUT_MMIF_FILE.write(rewind_mmif(mmif_obj, choice, args.mode == 'view').serialize(pretty=args.pretty))
 
 
 if __name__ == "__main__":

{clams_python-1.2.2 → clams_python-1.2.4}/clams/restify/__init__.py

@@ -145,6 +145,7 @@ class ClamsHTTPApi(Resource):
         try:
             return self.json_to_response(self.cla.annotate(raw_data, **raw_params))
         except Exception:
+            self.cla.logger.exception("Error in annotation")
             return self.json_to_response(self.cla.record_error(raw_data, **raw_params).serialize(pretty=True), status=500)
 
     put = post

clams_python-1.2.4/clams/ver/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.4"

{clams_python-1.2.2 → clams_python-1.2.4/clams_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clams-python
-Version: 1.2.2
+Version: 1.2.4
 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==1.0.14
+Requires-Dist: mmif-python==1.0.16
 Requires-Dist: Flask>=2
 Requires-Dist: Flask-RESTful>=0.3.9
 Requires-Dist: gunicorn>=20

{clams_python-1.2.2 → clams_python-1.2.4}/clams_python.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ clams/develop/templates/app/Containerfile.template
 clams/develop/templates/app/LICENSE.template
 clams/develop/templates/app/README.md.template
 clams/develop/templates/app/app.py.template
+clams/develop/templates/app/cli.py.template
 clams/develop/templates/app/metadata.py.template
 clams/develop/templates/app/requirements.txt.template
 clams/develop/templates/gha/for-clams-team.md.template

{clams_python-1.2.2 → clams_python-1.2.4}/clams_python.egg-info/requires.txt

@@ -1,4 +1,4 @@
-mmif-python==1.0.14
+mmif-python==1.0.16
 Flask>=2
 Flask-RESTful>=0.3.9
 gunicorn>=20

{clams_python-1.2.2 → clams_python-1.2.4}/requirements.txt

@@ -1,4 +1,4 @@
-mmif-python==1.0.14
+mmif-python==1.0.16
 
 Flask>=2
 Flask-RESTful>=0.3.9

clams_python-1.2.2/VERSION

@@ -1 +0,0 @@
-1.2.2

clams_python-1.2.2/clams/ver/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.2"