docs: updated calls and examples

tieandrews · tieandrews · commit 2ffc78f598cd · 2023-06-27T12:54:35.000-07:00
diff --git a/docker/entity-extraction-pipeline/README.md b/docker/entity-extraction-pipeline/README.md
@@ -17,9 +17,23 @@ The following environment variables can be set to change the behavior of the pip
 - `MAX_ARTICLES`: This variable can be set to a number to limit the number of articles processed. This is useful for testing and debugging. The default is `-1` which means no limit.
 - `LOG_OUTPUT_DIR`: This variable is set to the path of the output folder to write the log file. Default is the directory from which the docker container is run.
 
+## Testing the Docker Image to Run on xDD
+
+The docker image must be able to be run without root permissions. To test that this is correctly setup, run the following command and ensure it completes without error.
+
+```bash
+docker run -u $(id -u) -p 5000:5000 -v /${PWD}/data/entity-extraction/raw/original_files/:/inputs/ -v /${PWD}/data/entity-extraction/processed/processed_articles/:/outputs/ --env LOG_OUTPUT_DIR="../outputs/" metaextractor-entity-extraction-pipeline:v0.0.3
+```
+
+**Details**:  
+- the $(id -u) is used to run the docker container as the current user so that the output files are not owned by root  
+- the LOG_OUTPUT_DIR="../outputs/" is different from the docker compose as it is relative to the current directory which from Docker run starts in app folder
+- for git bash on windows the /${PWD} is used to get the current directory and the forward slash is important to get the correct path
+
 ## Sample Docker Compose Setup
 
 Update the environment variables defined under the `entity-extraction-pipeline` service in the `docker-compose.yml` file under the root directory. Then build and run the docker image to install the required dependencies using `docker-compose` as follows:
+
 ```bash
 docker-compose build
 docker-compose up entity-extraction-pipeline
@@ -30,19 +44,40 @@ Below is a sample docker compose configuration for running the image:
 version: "0.0.1"
 services:
   entity-extraction-pipeline:
-    image: metaextractor-entity-extraction-pipeline:v0.0.1
+    image: metaextractor-entity-extraction-pipeline:v0.0.3
     build: 
         ...
     ports:
       - "5000:5000"
     volumes:
-    - ./data/raw/:/app/inputs/
-    - ./data/processed/:/app/outputs/
+    - ./data/raw/:/inputs/
+    - ./data/processed/:/outputs/
     environment:
-      - HF_NER_MODEL_NAME=finding-fossils/metaextractor
-      - SPACY_NER_MODEL_NAME=en_metaextractor_spacy
       - USE_NER_MODEL_TYPE=huggingface
-      - LOG_OUTPUT_DIR=/app/outputs/
+      - LOG_OUTPUT_DIR=/outputs/
       - MAX_SENTENCES=20
       - MAX_ARTICLES=1
+```
+
+## Pushing the Docker Image to Docker Hub
+
+To push the docker image to docker hub, first login to docker hub using the following command:
+
+```bash
+docker login
+```
+
+Then tag the docker image with the following two commands:
+
+```bash
+# to update the "latest" tag image
+docker tag metaextractor-entity-extraction-pipeline:v<VERSION NUMBER> <DOCKER HUB USER ID>/metaextractor-entity-extraction-pipeline
+# to upload a specific version tagged image
+docker tag metaextractor-entity-extraction-pipeline:v<VERSION NUMBER> <DOCKER HUB USER ID>/metaextractor-entity-extraction-pipeline:v<VERSION NUMBER>
+```
+
+Finally, push the docker image to docker hub using the following command:
+
+```bash
+docker push <DOCKER HUB USER ID>/metaextractor-entity-extraction-pipeline
 ```
