docs, research question, reorg

documentation on accessing postgres data, research question, slight reorg ref #13 ref #10
carnival-data · Jan 27, 2022 · 125edd9 · 125edd9
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diff --git a/README.md b/README.md
@@ -120,3 +120,11 @@ Run tests with the following:
 docker-compose -f docker-compose-test.yml up
 ```
 This will run the unit tests. The test results will be printed in the docker log. An exit code of 0 will be returned if the tests pass, otherwise a non-zero code will be returned.
+
+## Viewing source data in Postgres
+
+Once docker has been started using `docker-compose up`, the database can be browsed using database GUI tool like DBeaver with the credentials:
+* Host: localhost
+* Database: EHR
+* Username: postgres
+* Password: postgres
diff --git a/db/careplans.csv → data/db/careplans.csv b/db/careplans.csv → data/db/careplans.csv
diff --git a/db/conditions.csv → data/db/conditions.csv b/db/conditions.csv → data/db/conditions.csv
diff --git a/db/encounters.csv → data/db/encounters.csv b/db/encounters.csv → data/db/encounters.csv
diff --git a/db/medications.csv → data/db/medications.csv b/db/medications.csv → data/db/medications.csv
diff --git a/db/organizations.csv → data/db/organizations.csv b/db/organizations.csv → data/db/organizations.csv
diff --git a/db/procedures.csv → data/db/procedures.csv b/db/procedures.csv → data/db/procedures.csv
diff --git a/db/providers.csv → data/db/providers.csv b/db/providers.csv → data/db/providers.csv
diff --git a/db/setup.sql → data/db/setup.sql b/db/setup.sql → data/db/setup.sql
diff --git a/data/survey/readme.md b/data/survey/readme.md
@@ -0,0 +1 @@
+Self-reported survey spreadsheets will go here
diff --git a/docs/walkthrough.md b/docs/walkthrough.md
@@ -16,13 +16,58 @@ This example will cover:
 > *Note: This demonstration is set up as Docker multi-container project, with one container holds the Carnival application and other containers that contain example databases. This walkthrough focuses excusively on the Carnival application. See [Running the Project](https://github.com/carnival-data/carnival-micronaut/blob/master/README.md#running-the-project) for instrucitons on running the entire project.*
 
 
-## Creating a new Carnival project
+# Research Problem
+For this example the researcher is looking for a case and control cohort of patients that meet certian criteria:
+
+*IN PROGRESS, pending info on EHR data*
+
+>Cases
+>* Age - between 18 and 55
+>* At least two healthcare encounters with indications of *DISEASE* via *CRITERIA*
+>* Has been perscribed medication *XXX*
+>* Self-reported social history of drinking or smoking
+>
+>Controls
+>* Age - between 18 and 55
+>* No indications of *DISEASE* via *CRITERIA*
+>* Has not been perscribes medication *XXX*
+>* Self-reported social history of drinking or smoking
+
+
+## Examining the Source Data
+There are two synthetic relational datasources:
+
+* **Electronic Heath Records(EHR) data** is stored in a Postgres database. The data is in **XXX** format.
+* **Self-reported patient survey data** is stored in csv spreadsheets
 
-## Defining the graph model
 
-## Connecting the data
 ### EHR Data in Postgres
-### CSV file data
+
+The EHR data is represented by synthetically-generated **XXX** formated dataset that contains information about patients and heathcare encounters. This data was generated using **XXX** (synthea?)
+
+
+For this example, we set up a Postgres database in a docker container using the default [Postgres docker image](https://hub.docker.com/_/postgres/). The raw data is located in `data/db`, and the image has been configured to automatically load the data when docker is started.
+
+
+Once docker has been started using `docker-compose up`, the database can be browsed using database GUI tool like DBeaver with the credentials:
+* Host: localhost
+* Database: EHR
+* Username: postgres
+* Password: postgres
+
+
+### Self-reported survey data in CSV file data
+
+CSV files that contain the results of self-reported surveys are located in `data/survey`.
+
+# Carnival
+This demonstration been set up as a Docker multi-container project, with a container that holds the Carnival/Micronaut server applications and other containers that have databases with test data. The source data for the carnival server is located in `/src`
+
+
+## Creating a new Carnival Project
+
+## Defining the graph model
+Now that we have examined the data and created an initial carnival project, we want to create a data model that harmonizes patient and encounter data and the survey data.
 
 ## Doing graph operations
 ### Drawing conclusions

diff --git a/postgres.Dockerfile b/postgres.Dockerfile
@@ -1,4 +1,4 @@
 FROM postgres
 
-COPY db/setup.sql 	/docker-entrypoint-initdb.d/setup.sql
-COPY db/*.csv		/db/
+COPY data/db/setup.sql 	/docker-entrypoint-initdb.d/setup.sql
+COPY data/db/*.csv		/db/