ensure housekeeping on the training result folder

CogStack · Nov 4, 2024 · e876992 · e876992
1 parent b5e1f40
commit e876992
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Showing 6 changed files with 22 additions and 25 deletions.
diff --git a/app/trainers/medcat_deid_trainer.py b/app/trainers/medcat_deid_trainer.py
@@ -110,6 +110,8 @@ def run(trainer: "MedcatDeIdentificationSupervisedTrainer",
                 examples = None
                 ner.training_arguments.num_train_epochs = 1
                 ner.training_arguments.logging_steps = 1
+                ner.training_arguments.overwrite_output_dir = False
+                ner.training_arguments.save_strategy = "no"
                 if training_params.get("lr_override") is not None:
                     ner.training_arguments.learning_rate = training_params["lr_override"]
                 if training_params.get("test_size") is not None:

diff --git a/docker/medcat-deid/Dockerfile b/docker/medcat-deid/Dockerfile
@@ -24,17 +24,16 @@ RUN addgroup --gid $CMS_GID cms || true && \
     adduser --uid $CMS_UID --gid $CMS_GID --disabled-password --gecos "" cms || true && \
     echo "cms ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 
-WORKDIR /app
-
-COPY --chown=$CMS_UID:$CMS_GID app /app
-COPY --chown=$CMS_UID:$CMS_GID docker/medcat-deid/requirements.txt .
+COPY app /app
+COPY docker/medcat-deid/requirements.txt /app/requirements.txt
 RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
-    chown -R $CMS_UID:$CMS_GID /app/model
+    chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
     pip install --no-cache-dir -r requirements.txt && \
     python -m spacy download en_core_web_md
 
+WORKDIR /app
 EXPOSE 8000
 USER cms:cms
 CMD ["sh", "-c", "python cli/cli.py serve --model-type medcat_deid --model-name \"${CMS_MODEL_NAME}\" --model-path /app/model/model.zip --host 0.0.0.0 --port 8000"]
diff --git a/docker/medcat-icd10/Dockerfile b/docker/medcat-icd10/Dockerfile
@@ -24,17 +24,16 @@ RUN addgroup --gid $CMS_GID cms || true && \
     adduser --uid $CMS_UID --gid $CMS_GID --disabled-password --gecos "" cms || true && \
     echo "cms ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 
-WORKDIR /app
-
-COPY --chown=$CMS_UID:$CMS_GID app /app
-COPY --chown=$CMS_UID:$CMS_GID docker/medcat-icd10/requirements.txt .
+COPY app /app
+COPY docker/medcat-icd10/requirements.txt /app/requirements.txt
 RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
-    chown -R $CMS_UID:$CMS_GID /app/model
+    chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
     pip install --no-cache-dir -r requirements.txt && \
     python -m spacy download en_core_web_md
 
+WORKDIR /app
 EXPOSE 8000
 USER cms:cms
 CMD ["sh", "-c", "python cli/cli.py serve --model-type medcat_icd10 --model-name \"${CMS_MODEL_NAME}\" --model-path /app/model/model.zip --host 0.0.0.0 --port 8000"]
diff --git a/docker/medcat-snomed/Dockerfile b/docker/medcat-snomed/Dockerfile
@@ -25,17 +25,16 @@ RUN addgroup --gid $CMS_GID cms || true && \
     adduser --uid $CMS_UID --gid $CMS_GID --disabled-password --gecos "" cms || true && \
     echo "cms ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 
-WORKDIR /app
-
-COPY --chown=$CMS_UID:$CMS_GID app /app
-COPY --chown=$CMS_UID:$CMS_GID docker/medcat-snomed/requirements.txt .
+COPY app /app
+COPY docker/medcat-snomed/requirements.txt /app/requirements.txt
 RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
-    chown -R $CMS_UID:$CMS_GID /app/model
+    chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
     pip install --no-cache-dir -r requirements.txt && \
     python -m spacy download en_core_web_md
 
+WORKDIR /app
 EXPOSE 8000
 USER cms:cms
 CMD ["sh", "-c", "python cli/cli.py serve --model-type medcat_snomed --model-name \"${CMS_MODEL_NAME}\" --model-path /app/model/model.zip --host 0.0.0.0 --port 8000"]
diff --git a/docker/medcat-umls/Dockerfile b/docker/medcat-umls/Dockerfile
@@ -24,17 +24,16 @@ RUN addgroup --gid $CMS_GID cms || true && \
     adduser --uid $CMS_UID --gid $CMS_GID --disabled-password --gecos "" cms || true && \
     echo "cms ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 
-WORKDIR /app
-
-COPY --chown=$CMS_UID:$CMS_GID app /app
-COPY --chown=$CMS_UID:$CMS_GID docker/medcat-umls/requirements.txt .
+COPY app /app
+COPY docker/medcat-umls/requirements.txt /app/requirements.txt
 RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
-    chown -R $CMS_UID:$CMS_GID /app/model
+    chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
     pip install --no-cache-dir -r requirements.txt && \
     python -m spacy download en_core_web_md
 
+WORKDIR /app
 EXPOSE 8000
 USER cms:cms
 CMD ["sh", "-c", "python cli/cli.py serve --model-type medcat_umls --model-name \"${CMS_MODEL_NAME}\" --model-path /app/model/model.zip --host 0.0.0.0 --port 8000"]
diff --git a/docker/trf-deid/Dockerfile b/docker/trf-deid/Dockerfile
@@ -24,17 +24,16 @@ RUN addgroup --gid $CMS_GID cms || true && \
     adduser --uid $CMS_UID --gid $CMS_GID --disabled-password --gecos "" cms || true && \
     echo "cms ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 
-WORKDIR /app
-
-COPY --chown=$CMS_UID:$CMS_GID app /app
-COPY --chown=$CMS_UID:$CMS_GID docker/trf-deid/requirements.txt .
+COPY app /app
+COPY docker/trf-deid/requirements.txt /app/requirements.txt
 RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
-    chown -R $CMS_UID:$CMS_GID /app/model
+    chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
     pip install --no-cache-dir -r requirements.txt && \
     python -m spacy download en_core_web_md
 
+WORKDIR /app
 EXPOSE 8000
 USER cms:cms
 CMD ["sh", "-c", "python cli/cli.py serve --model-type transformers_deid --model-name \"${CMS_MODEL_NAME}\" --model-path /app/model/model.zip --host 0.0.0.0 --port 8000"]