CRIOPS-252 Documentation Refinements

Author: heathharrelson

README.md

@@ -23,13 +23,13 @@ Copy `env.sample` to `.env` and update as needed. At a minimum, you should updat
 * `OMOP_DATASOURCE_USERNAME`
 * `OMOP_DATASOURCE_PASSWORD`
 
-You should also configure the authentication system properties as needed. See the "LDAP authentication" and "table-based authentication" sections.
+You should also configure the authentication system properties as needed. See the "LDAP authentication" and "table-based authentication" sections of `env.sample`.
 
 ## Application Startup
 
 ### Running with Docker
 
-Build the project,
+Build the project.
 
 ```
 mvn clean package -DskipTests
@@ -80,9 +80,8 @@ mkdir src/main/resources/db/migration/0.0.1
 
 Now add your migrations in this directory. For example, `V19700101000042__my_first_migration.sql` which follows the format: `V`, followed by the year, month, day, hours, minutes, seconds (YYYYMMDDhhmmss), two underscores, a short description, and finally `.sql`.
 
-
 ## Search Indexing
 
-The Judging interface for OMOP Annotator provides judges with the ability to perform full text searches on VisitOccurrences as well as all related visit data. To do this efficiently, the application uses the Hibernate Search library, which provides a consistent API over full text search engines such as Apache Lucene and Elasticsearch. See the `application.properties` file to view the configuration options.
+The Judging interface for OMOP Annotator provides judges with the ability to perform full text searches on VisitOccurrences as well as all related visit data. To do this efficiently, the application uses the [Hibernate Search](https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/) library, which provides a consistent API over full text search engines such as Apache Lucene and Elasticsearch. See the `application.properties` file to view the configuration options.
 
 The default search engine is Lucene, which stores index data to disk. An index schema is created on application startup, but the index is not populated until the Indexer has been run. The easiest way to do this is to login as an admin and navigate to the url: `/admin/search/init_index`. Note that this operation will index all visit occurrences associated with a Patient record that has been assigned to a Pool. This operation can take a long time so it should be performed when the application is not in use.

RUNNING.md

@@ -1,10 +1,10 @@
 # Running the OMOP Annotator
 
-In addition to running the OMOP Annotator with [Docker Compose](https://docs.docker.com/compose/) as described in [README.md](./README.md), you can also run the jar file attached to each release, or using an IDE.
+In addition to running the OMOP Annotator with [Docker Compose](https://docs.docker.com/compose/) as described in [README.md](./README.md), you can also run the jar file attached to the [GitHub release](https://github.com/OHSU-OCTRI/omop-annotator/releases).
 
 ## Prerequisites
 
-The Annotator is a Java application and requires the Java 17 Runtime Environment for running the provided application.
+The Annotator is a Java application and requires the Java 17 Runtime Environment to execute.
 
 The application requires two data sources - the read-only [OMOP](https://www.ohdsi.org/data-standardization/) database and a writable database to store application users and their annotations. Both data sources are configurable, but the writable data source has only been tested with MySQL, and the OMOP data source has been tested with Oracle and PostgreSQL.
 
@@ -140,7 +140,7 @@ VALUES ('LDAP', 0, 0, '<org_email>', 1, '<first_name>', '<last_name>', '<usernam
 SET @userid = (SELECT last_insert_id());
 SET @admin = (SELECT id FROM user_role WHERE role_name = 'ROLE_ADMIN' limit 1);
 INSERT INTO user_user_role (user, user_role)
-VALUES (@suserid, @admin);
+VALUES (@userid, @admin);
 ````
 
 If your organization will have table-based users only, start by creating the first user and role, setting the credentials to expired, and providing an email that will be used for confirmation of password reset: