variables to change in README

brabbit61 · brabbit61 · commit 7241d08ba04e · 2023-06-27T12:25:20.000-07:00
diff --git a/docker/data-review-tool/README.md b/docker/data-review-tool/README.md
@@ -2,7 +2,7 @@
 
 This docker image contains `Finding Fossils`, a data review tool built using Dash, Python. It is used to visualize the outputs of the models and verify the extracted entities for inclusion in the Neotoma Database. 
 
-The expected inputs are mounted onto the newly created container as volumes and can be dumped in the `data/data-review-tool` folder. It assumes the following:
+The expected inputs are mounted onto the newly created container as volumes and can be dumped in any folder. An environment variable is setup to provide the path to this folder. It assumes the following:
 1. A parquet file containing the outputs from the article relevance prediction component.
 2. A zipped file containing the outputs from the named entity extraction component.
 3. Once the articles have been verified we update the same parquet file referenced using the environment variable `ARTICLE_RELEVANCE_BATCH` with the entities verified by the steward and the status of review for the article.
@@ -15,13 +15,9 @@ The following environment variables can be set to change the behavior of the pip
 
 ## Sample Docker Compose Setup
 
-Update the environment variables defined under the `data-review-tool` 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 data-review-tool
-```
+Update the environment variables and the volume paths defined under the `data-review-tool` service in the `docker-compose.yml` file under the root directory. The volume paths are:
 
-This is the basic docker compose configuration for running the image.
+`INPUT_PATH`: The path to the directory where the data is dumped. eg. `./data/data-review-tool` (recommended)
 
 ```yaml
 version: "3.9"
@@ -32,5 +28,13 @@ services:
     ports:
       - "8050:8050"
     volumes:
-    - ./data/data-review-tool:/MetaExtractor/inputs
+    - {INPUT_PATH}:/MetaExtractor/inputs
+    environment:
+    - ARTICLE_RELEVANCE_BATCH=sample_parquet_output.parquet
+    - ENTITY_EXTRACTION_BATCH=sample_ner_output.zip
+```
+Then build and run the docker image to install the required dependencies using `docker-compose` as follows:
+```bash
+docker-compose build
+docker-compose up data-review-tool
 ```
diff --git a/docker/entity-extraction-pipeline/README.md b/docker/entity-extraction-pipeline/README.md
@@ -19,11 +19,10 @@ The following environment variables can be set to change the behavior of the pip
 
 ## 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
-```
+Update the environment variables defined under the `entity-extraction-pipeline` service in the `docker-compose.yml` file under the root directory. The volume paths are:
+
+- `INPUT_PATH`: The folder containing the raw text `nlp352` TSV file, eg. `./data/entity-extraction/raw/original_files/` (recommended)
+- `OUTPUT_PATH`: The folder to dump the final JSON files, eg. `./data/entity-extraction/processed/processed_articles/` (recommended)
 
 Below is a sample docker compose configuration for running the image:
 ```yaml
@@ -36,13 +35,19 @@ services:
     ports:
       - "5000:5000"
     volumes:
-    - ./data/raw/:/app/inputs/
-    - ./data/processed/:/app/outputs/
+    - {INPUT_PATH}:/app/inputs/
+    - {OUTPUT_PATH}:/app/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/
       - MAX_SENTENCES=20
       - MAX_ARTICLES=1
-```
+```
+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
+```
+
