Fix missing docker image tag (#30)

* Fix tag instruction

* Small refactor

* Fix tag

* Fix ci workflow

* Fix CI workflow

* Fix model name in Dockerfile

* Fix style

* Fix remaining model name occurrences

* Fix config name

* Remove save_bert.py

* Fix ci

.env.bert-base-ner

@@ -1 +1,2 @@
+CONFIG_NAME=bert-base-ner
 MODEL_NAME=dslim/bert-base-NER

.env.bert-base-ner-uncased

@@ -1 +1,2 @@
+CONFIG_NAME=bert-base-ner-uncased
 MODEL_NAME=dslim/bert-base-NER-uncased

.env.bert-large-ner

@@ -1 +1,2 @@
+CONFIG_NAME=bert-large-ner
 MODEL_NAME=dslim/bert-large-NER

.github/workflows/ci.yml

@@ -131,7 +131,7 @@ jobs:
       run: |
         IMAGE=${{ env.docker_repository_base }}-${{ matrix.config-name }}
         TAGS=${{ env.tags }}
-        NEW_TAGS="$(echo $TAGS | tr "," "\n" ":" | awk -v image="$IMAGE" '{print image ":" $1}' | paste -sd "," -)"
+        NEW_TAGS="$(echo $TAGS | tr "," "\n" | awk -v image="$IMAGE" '{print image ":" $1}' | paste -sd "," -)"
         echo tags=$NEW_TAGS >> $GITHUB_ENV
 
     - name: Set up QEMU
@@ -158,7 +158,7 @@ jobs:
         push: ${{ env.push }}
         tags: ${{ env.tags }}
         build-args: |
-          HUGGINGFACE_MODEL=${{ env.MODEL_NAME }}
+          MODEL_NAME=${{ env.MODEL_NAME }}
         labels: |
           org.opencontainers.image.created=${{ env.created }}
           org.opencontainers.image.source=${{ github.repositoryUrl }}

docker-compose.yml

@@ -6,7 +6,7 @@ services:
     build:
       context: server
       # args:
-        # HUGGINGFACE_MODEL: "dslim/bert-base-NER"
+        # MODEL_NAME: "dslim/bert-base-NER"
     container_name: phi-annotator
     networks:
       - nlpsandbox-internal

server/Dockerfile

@@ -1,5 +1,6 @@
 FROM python:3.9.6-slim-buster
-ARG HUGGINGFACE_MODEL="dslim/bert-base-NER"
+
+ARG MODEL_NAME="dslim/bert-base-NER"
 
 ENV APP_DIR=/opt/app
 
@@ -27,14 +28,13 @@ RUN pip install --no-cache-dir \
     && useradd --create-home --shell /bin/bash nlp
 
 # Download model from HuggingFace:
-ENV HUGGINGFACE_MODEL=${HUGGINGFACE_MODEL}
+ENV MODEL_NAME=${MODEL_NAME}
 COPY save_model.py ./
 RUN python save_model.py
 
 # Copy source code
 COPY openapi_server openapi_server/
 
-
 WORKDIR /
 COPY docker-entrypoint.sh .
 RUN chmod +x docker-entrypoint.sh

server/openapi_server/config.py

@@ -0,0 +1,50 @@
+import os
+from enum import Enum
+
+defaultValues = {
+    "CONFIG_NAME": "",
+    "MODEL_NAME": ""
+}
+
+
+class ConfigName(Enum):
+    BERT_BASE_NER = "bert-base-ner"
+    BERT_BASE_NER_UNCASED = "bert-base-ner-uncased"
+    BERT_LARGE_NER = "bert-large-ner"
+
+
+class AbstractConfig(object):
+    """
+    Parent class containing get_property to return the environment variable or
+    default value if not found.
+    """
+    def __init__(self):
+        self._defaultValues = defaultValues
+
+    def get_property(self, property_name):
+        if os.getenv(property_name) is not None:
+            return os.getenv(property_name)
+        # we don't want KeyError?
+        if property_name not in self._defaultValues.keys():
+            return None  # No default value found
+        # return default value
+        return self._defaultValues[property_name]
+
+
+class Config(AbstractConfig):
+    """
+    This class is used to provide coniguration values to the application, first
+    using environment variables and if not found, defaulting to those values
+    provided in the defaultValues dictionary above.
+    """
+
+    @property
+    def config_name(self):
+        return self.get_property('CONFIG_NAME')
+
+    @property
+    def model_name(self):
+        return self.get_property('MODEL_NAME')
+
+
+config = Config()

server/openapi_server/controllers/text_location_annotation_controller.py

@@ -3,7 +3,7 @@
 from openapi_server.models.text_location_annotation import TextLocationAnnotation  # noqa: E501
 from openapi_server.models.text_location_annotation_request import TextLocationAnnotationRequest  # noqa: E501
 from openapi_server.models.text_location_annotation_response import TextLocationAnnotationResponse  # noqa: E501
-from openapi_server.nlp_config import bert
+from openapi_server.huggingface import huggingFace
 
 
 def create_text_location_annotations():  # noqa: E501
@@ -23,7 +23,7 @@ def create_text_location_annotations():  # noqa: E501
             annotation_request = TextLocationAnnotationRequest.from_dict(connexion.request.get_json())  # noqa: E501
             note = annotation_request._note
             annotations = []
-            location_annotations = bert.get_entities(note.text, 'LOC')
+            location_annotations = huggingFace.get_entities(note.text, 'LOC')
             add_location_annotation(annotations, location_annotations)
             res = TextLocationAnnotationResponse(annotations)
             status = 200

server/openapi_server/controllers/text_person_name_annotation_controller.py

@@ -3,7 +3,7 @@
 from openapi_server.models.text_person_name_annotation import TextPersonNameAnnotation
 from openapi_server.models.text_person_name_annotation_request import TextPersonNameAnnotationRequest  # noqa: E501
 from openapi_server.models.text_person_name_annotation_response import TextPersonNameAnnotationResponse  # noqa: E501
-from openapi_server.nlp_config import bert
+from openapi_server.huggingface import huggingFace
 
 
 def create_text_person_name_annotations():  # noqa: E501
@@ -20,7 +20,7 @@ def create_text_person_name_annotations():  # noqa: E501
             annotation_request = TextPersonNameAnnotationRequest.from_dict(connexion.request.get_json())  # noqa: E501
             note = annotation_request._note  # noqa: E501
             annotations = []
-            name_annotations = bert.get_entities(note.text, "PER")
+            name_annotations = huggingFace.get_entities(note.text, "PER")
             add_name_annotation(annotations, name_annotations)
             res = TextPersonNameAnnotationResponse(annotations)
             status = 200

server/openapi_server/controllers/tool_controller.py

@@ -2,7 +2,7 @@
 from openapi_server.models.tool_dependencies import ToolDependencies  # noqa: E501
 from openapi_server.models.tool_type import ToolType  # noqa: E501
 from openapi_server.models.license import License
-from openapi_server.nlp_config import bert
+from openapi_server.config import config
 
 
 def get_tool():  # noqa: E501
@@ -14,15 +14,14 @@ def get_tool():  # noqa: E501
     :rtype: Tool
     """
     tool = Tool(
-        name="phi-annotator-example",
-        version="1.2.1",
+        name=f"phi-annotator-huggingface-{config.config_name}",
+        version="1.0.0",
         license=License.APACHE_2_0,
-        repository="github:nlpsandbox/phi-annotator-example",
-        description="Implementation of the NLP Sandbox PHI Annotator using "
-                    "HuggingFace Model: '%s'" % (bert.get_name()),
+        repository="github:nlpsandbox/phi-annotator-huggingface",
+        description="Hugging Face PHI annotator ({config.model_name})",
         author="NLP Sandbox Team",
         author_email="[email protected]",
-        url="https://github.com/nlpsandbox/phi-annotator-example",
+        url="https://github.com/nlpsandbox/phi-annotator-huggingface",
         type=ToolType.PHI_ANNOTATOR,
         api_version="1.2.0"
     )

server/openapi_server/nlp_config.py → server/openapi_server/huggingface.py

@@ -130,7 +130,7 @@ def __call__(self, inputs: Union[str, List[str]], **kwargs):
         return answers
 
 
-class Bert:
+class HuggingFace:
     def __init__(self):
         self.tokenizer = at.from_pretrained("hf")
         self.model = amc.from_pretrained("hf")
@@ -148,4 +148,4 @@ def get_name(self):
         return self.name
 
 
-bert = Bert()
+huggingFace = HuggingFace()

server/save_model.py

@@ -2,7 +2,7 @@
 from transformers import AutoModelForTokenClassification as amc, AutoTokenizer as at
 
 
-MODEL_NAME = os.getenv('HUGGINGFACE_MODEL', 'dslim/bert-base-NER')
+MODEL_NAME = os.getenv('MODEL_NAME', 'dslim/bert-base-NER')
 LOCAL_DIRECTORY = 'hf'
 
 # Save tokenizer