From 811dd159680dabd5f732977dfce9ac3575a1ea50 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github@gulfdoctor.net>
Date: Thu, 20 May 2021 12:17:40 -0400
Subject: [PATCH 01/21] Add contributing.md

---
 CONTRIBUTING.md | 70 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..ea9dd48
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,70 @@
+# How to contribute
+
+## Please note:
+
+* (Optional) We adopt [Git Flow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow). Most feature branches are pushed to the repository and deleted when merged to *develop* branch.
+* (**Important**): Submit pull requests to the *develop* branch or *feature/* branches
+* Use *GitHub Issues* for feature requests and bug reports. Include as much information as possible while reporting bugs.
+
+
+## Contributing (Step-by-step)
+
+1. [Fork the repo](http://help.github.com/fork-a-repo) and clone it to your local computer, and set up the upstream remote:
+
+        git clone https://github.com/YourGithubUsername/ckblib.git
+        cd ckblib
+        git remote add upstream https://github.com/dermatologist/ckblib.git
+
+2. Checkout out a new local branch based on your master and update it to the latest (BRANCH-123 is the branch name, You can name it whatever you want. Try to give it a meaningful name. If you are fixing an issue, please include the issue #).
+
+        git checkout -b BRANCH-123 develop
+        git clean -df
+        git pull --rebase upstream develop
+
+ > Please keep your code clean. If you find another bug, you want to fix while being in a new branch, please fix it in a separated branch instead.
+
+3. Push the branch to your fork. Treat it as a backup.
+
+        git push origin BRANCH-123
+
+4. Code
+
+  * Adhere to common conventions you see in the existing code.
+  * Include tests as much as possible, and ensure they pass.
+
+5. Commit to your branch
+
+         git commit -m "BRANCH-123: Put change summary here (can be a ticket title)"
+
+  **NEVER leave the commit message blank!** Provide a detailed, clear, and complete description of your commit!
+
+6. Update your branch to the latest code.
+
+        git pull --rebase upstream develop
+
+7. **Important** If you have made many commits, please squash them into atomic units of work. (Most Git GUIs such as sourcetree and smartgit offer a squash option)
+
+
+        git checkout develop
+        git pull --rebase upstream develop
+        git merge --squash BRANCH-123
+        git commit -m "fix: 123"
+
+  Push changes to your fork:
+
+        git push
+
+8. Issue a Pull Request
+
+  In order to make a pull request:
+  * Click "Pull Request".
+  * Choose the develop branch
+  * Click 'Create pull request'
+  * Fill in some details about your potential patch including a meaningful title.
+  * Click "Create pull request".
+
+  Thanks for that -- we'll get to your pull request ASAP. We love pull requests!
+
+## Feedback
+
+   If you need to contact me, see my contact details on my profile page.

From 580afe4bc5589b92dd25acd8295c22133ca95f00 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 21 May 2021 21:02:02 -0400
Subject: [PATCH 02/21] Update README.md

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index b8a6dad..ed84a1e 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,8 @@
 
 ## About
 
-Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib consists of three modules.
+Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph™ (see above). ckblib consists of three modules:
+
 * The 'library' module wraps the NCBI's E-Utils API to harvest published article abstracts.
 * The 'qtakes' module provides a programmable interface to my quick-ctakes or the quarkus based apache ctakes, a fast clinical text annotation engine.
 * Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.
@@ -50,4 +51,4 @@ Providing clinical decision support requires some formal way of representing cli
 * [Bell Eapen](https://nuchange.ca) | [contact](https://nuchange.ca/contact) | [![Twitter Follow](https://img.shields.io/twitter/follow/beapen?style=social)](https://twitter.com/beapen)
 
 ## Contributors
-* PR welcome. Please see CONTRIBUTING.md for details.
\ No newline at end of file
+* PR welcome. Please see CONTRIBUTING.md for details.

From 83dc0c1bd06ffa8e58264930f541dca793b7195c Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Mon, 24 May 2021 08:27:01 -0400
Subject: [PATCH 03/21] update readme

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ed84a1e..0f7cf72 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,7 @@ Providing clinical decision support requires some formal way of representing cli
 
 * [Read how to install mvn packages from GitHub](https://docs.github.com/en/packages/guides/configuring-apache-maven-for-use-with-github-packages#installing-a-package)
 * Include dependencies in pom.xml
+* See an application [![forthebadge](https://forthebadge.com/images/badges/built-with-love.svg) using ckblib: [GulfDoctor](https://gulfdoctor.net)
 
 ```
 <dependency>
@@ -51,4 +52,5 @@ Providing clinical decision support requires some formal way of representing cli
 * [Bell Eapen](https://nuchange.ca) | [contact](https://nuchange.ca/contact) | [![Twitter Follow](https://img.shields.io/twitter/follow/beapen?style=social)](https://twitter.com/beapen)
 
 ## Contributors
-* PR welcome. Please see CONTRIBUTING.md for details.
+* PR welcome.
+* Please see CONTRIBUTING.md for details.

From 2f38d35a8729bd4180c4ac8910303197ffafe56f Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Mon, 24 May 2021 08:34:21 -0400
Subject: [PATCH 04/21] Update javadoc

---
 docs/apidocs/allclasses-index.html            |  6 +-
 docs/apidocs/allpackages-index.html           |  6 +-
 docs/apidocs/argfile                          | 41 ++++++++++
 .../ckblib/application/DemoApplication.html   |  6 +-
 .../application/Neo4jConfiguration.html       |  6 +-
 .../class-use/DemoApplication.html            |  6 +-
 .../class-use/Neo4jConfiguration.html         |  6 +-
 .../ckblib/application/package-summary.html   |  6 +-
 .../ckblib/application/package-tree.html      |  6 +-
 .../ckblib/application/package-use.html       |  6 +-
 .../graph/AnatomicalSiteRepository.html       |  6 +-
 .../ckblib/graph/AnatomicalSiteService.html   | 34 ++++++--
 .../ckblib/graph/BaseRelationRepository.html  |  6 +-
 .../ckblib/graph/BaseRelationService.html     | 19 ++++-
 .../ckblib/graph/D3Map.Builder.html           |  6 +-
 .../com/canehealth/ckblib/graph/D3Map.html    |  6 +-
 .../graph/DiseaseDisorderRepository.html      |  6 +-
 .../ckblib/graph/DiseaseDisorderService.html  | 79 +++++++++++++++++--
 .../graph/JournalArticleRepository.html       |  6 +-
 .../ckblib/graph/JournalArticleService.html   |  6 +-
 .../ckblib/graph/MedicationRepository.html    |  6 +-
 .../ckblib/graph/MedicationService.html       | 34 ++++++--
 .../ckblib/graph/Neo4jTestConfiguration.html  |  6 +-
 .../ckblib/graph/ProcedureRepository.html     |  6 +-
 .../ckblib/graph/ProcedureService.html        | 34 ++++++--
 .../ckblib/graph/SignSymptomRepository.html   |  6 +-
 .../ckblib/graph/SignSymptomService.html      | 34 ++++++--
 .../class-use/AnatomicalSiteRepository.html   |  6 +-
 .../class-use/AnatomicalSiteService.html      |  6 +-
 .../class-use/BaseRelationRepository.html     |  6 +-
 .../graph/class-use/BaseRelationService.html  |  6 +-
 .../ckblib/graph/class-use/D3Map.Builder.html |  6 +-
 .../ckblib/graph/class-use/D3Map.html         |  6 +-
 .../class-use/DiseaseDisorderRepository.html  |  6 +-
 .../class-use/DiseaseDisorderService.html     |  6 +-
 .../class-use/JournalArticleRepository.html   |  6 +-
 .../class-use/JournalArticleService.html      |  6 +-
 .../graph/class-use/MedicationRepository.html |  6 +-
 .../graph/class-use/MedicationService.html    |  6 +-
 .../class-use/Neo4jTestConfiguration.html     |  6 +-
 .../graph/class-use/ProcedureRepository.html  |  6 +-
 .../graph/class-use/ProcedureService.html     |  6 +-
 .../class-use/SignSymptomRepository.html      |  6 +-
 .../graph/class-use/SignSymptomService.html   |  6 +-
 .../graph/model/AnatomicalSiteMention.html    |  6 +-
 .../ckblib/graph/model/BaseRelation.html      |  6 +-
 .../ckblib/graph/model/ConceptAttributes.html |  6 +-
 .../graph/model/DiseaseDisorderMention.html   |  6 +-
 .../ckblib/graph/model/JournalArticle.html    |  6 +-
 .../ckblib/graph/model/MedicationMention.html |  6 +-
 .../ckblib/graph/model/ProcedureMention.html  |  6 +-
 .../graph/model/SignSymptomMention.html       |  6 +-
 .../class-use/AnatomicalSiteMention.html      | 19 +++--
 .../graph/model/class-use/BaseRelation.html   |  6 +-
 .../model/class-use/ConceptAttributes.html    |  6 +-
 .../class-use/DiseaseDisorderMention.html     | 24 ++++--
 .../graph/model/class-use/JournalArticle.html |  6 +-
 .../model/class-use/MedicationMention.html    | 19 +++--
 .../model/class-use/ProcedureMention.html     | 19 +++--
 .../model/class-use/SignSymptomMention.html   | 19 +++--
 .../ckblib/graph/model/package-summary.html   |  6 +-
 .../ckblib/graph/model/package-tree.html      |  6 +-
 .../ckblib/graph/model/package-use.html       |  6 +-
 .../ckblib/graph/package-summary.html         |  6 +-
 .../canehealth/ckblib/graph/package-tree.html |  6 +-
 .../canehealth/ckblib/graph/package-use.html  |  6 +-
 .../ckblib/library/model/BaseQuery.html       |  6 +-
 .../library/model/EsearchResultRoot.html      |  6 +-
 .../ckblib/library/model/Esearchresult.html   |  6 +-
 .../ckblib/library/model/Header.html          |  6 +-
 .../ckblib/library/model/Translationset.html  |  6 +-
 .../library/model/class-use/BaseQuery.html    |  6 +-
 .../model/class-use/EsearchResultRoot.html    |  6 +-
 .../model/class-use/Esearchresult.html        |  6 +-
 .../library/model/class-use/Header.html       |  6 +-
 .../model/class-use/Translationset.html       |  6 +-
 .../ckblib/library/model/package-summary.html |  6 +-
 .../ckblib/library/model/package-tree.html    |  6 +-
 .../ckblib/library/model/package-use.html     |  6 +-
 .../ckblib/library/service/CkbEfetch.html     |  6 +-
 .../ckblib/library/service/CkbEsearch.html    |  6 +-
 .../ckblib/library/service/MyService.html     |  6 +-
 .../library/service/ServiceProperties.html    |  6 +-
 .../library/service/class-use/CkbEfetch.html  |  6 +-
 .../library/service/class-use/CkbEsearch.html |  6 +-
 .../library/service/class-use/MyService.html  |  6 +-
 .../service/class-use/ServiceProperties.html  |  6 +-
 .../library/service/package-summary.html      |  6 +-
 .../ckblib/library/service/package-tree.html  |  6 +-
 .../ckblib/library/service/package-use.html   |  6 +-
 .../ckblib/library/util/CkbXpath.html         |  6 +-
 .../ckblib/library/util/CkblibConstants.html  |  6 +-
 .../library/util/class-use/CkbXpath.html      |  6 +-
 .../util/class-use/CkblibConstants.html       |  6 +-
 .../ckblib/library/util/package-summary.html  |  6 +-
 .../ckblib/library/util/package-tree.html     |  6 +-
 .../ckblib/library/util/package-use.html      |  6 +-
 .../ckblib/qtakes/model/ConceptAttribute.html |  6 +-
 .../ckblib/qtakes/model/ConceptMention.html   |  6 +-
 .../ckblib/qtakes/model/QtakesRoot.html       |  6 +-
 .../model/class-use/ConceptAttribute.html     |  6 +-
 .../model/class-use/ConceptMention.html       |  6 +-
 .../qtakes/model/class-use/QtakesRoot.html    |  6 +-
 .../ckblib/qtakes/model/package-summary.html  |  6 +-
 .../ckblib/qtakes/model/package-tree.html     |  6 +-
 .../ckblib/qtakes/model/package-use.html      |  6 +-
 .../ckblib/qtakes/service/QtakesService.html  |  6 +-
 .../service/class-use/QtakesService.html      |  6 +-
 .../qtakes/service/package-summary.html       |  6 +-
 .../ckblib/qtakes/service/package-tree.html   |  6 +-
 .../ckblib/qtakes/service/package-use.html    |  6 +-
 docs/apidocs/constant-values.html             |  6 +-
 docs/apidocs/deprecated-list.html             |  6 +-
 docs/apidocs/help-doc.html                    |  6 +-
 docs/apidocs/index-all.html                   | 37 ++++++++-
 docs/apidocs/index.html                       |  8 +-
 docs/apidocs/javadoc.sh                       |  1 +
 docs/apidocs/member-search-index.js           |  2 +-
 docs/apidocs/options                          | 24 ++++++
 docs/apidocs/overview-summary.html            |  6 +-
 docs/apidocs/overview-tree.html               |  6 +-
 121 files changed, 687 insertions(+), 384 deletions(-)
 create mode 100644 docs/apidocs/argfile
 create mode 100755 docs/apidocs/javadoc.sh
 create mode 100644 docs/apidocs/options

diff --git a/docs/apidocs/allclasses-index.html b/docs/apidocs/allclasses-index.html
index 95ad74f..b478d4f 100644
--- a/docs/apidocs/allclasses-index.html
+++ b/docs/apidocs/allclasses-index.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>All Classes (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>All Classes (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="class index">
 <meta name="generator" content="javadoc/AllClassesIndexWriter">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
diff --git a/docs/apidocs/allpackages-index.html b/docs/apidocs/allpackages-index.html
index 255bac4..26c4dcd 100644
--- a/docs/apidocs/allpackages-index.html
+++ b/docs/apidocs/allpackages-index.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>All Packages (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>All Packages (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="package index">
 <meta name="generator" content="javadoc/AllPackagesIndexWriter">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
diff --git a/docs/apidocs/argfile b/docs/apidocs/argfile
new file mode 100644
index 0000000..4500a29
--- /dev/null
+++ b/docs/apidocs/argfile
@@ -0,0 +1,41 @@
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/service/CkbEsearch.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/service/CkbEfetch.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/service/ServiceProperties.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/service/MyService.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/util/CkbXpath.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/util/CkblibConstants.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/model/BaseQuery.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/model/Header.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/model/EsearchResultRoot.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/model/Translationset.java'
+'/scratch/beapen/ckblib/library/src/main/java/com/canehealth/ckblib/library/model/Esearchresult.java'
+'/scratch/beapen/ckblib/qtakes/src/main/java/com/canehealth/ckblib/qtakes/service/QtakesService.java'
+'/scratch/beapen/ckblib/qtakes/src/main/java/com/canehealth/ckblib/qtakes/model/ConceptAttribute.java'
+'/scratch/beapen/ckblib/qtakes/src/main/java/com/canehealth/ckblib/qtakes/model/ConceptMention.java'
+'/scratch/beapen/ckblib/qtakes/src/main/java/com/canehealth/ckblib/qtakes/model/QtakesRoot.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/DiseaseDisorderService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/ProcedureRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/Neo4jTestConfiguration.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/BaseRelation.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/AnatomicalSiteMention.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/MedicationMention.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/JournalArticle.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/ProcedureMention.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/SignSymptomMention.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/ConceptAttributes.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/model/DiseaseDisorderMention.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/AnatomicalSiteService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/SignSymptomRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/SignSymptomService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/D3Map.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/BaseRelationRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/JournalArticleRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/ProcedureService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/AnatomicalSiteRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/MedicationRepository.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/BaseRelationService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/JournalArticleService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/MedicationService.java'
+'/scratch/beapen/ckblib/graph/src/main/java/com/canehealth/ckblib/graph/DiseaseDisorderRepository.java'
+'/scratch/beapen/ckblib/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java'
+'/scratch/beapen/ckblib/application/src/main/java/com/canehealth/ckblib/application/Neo4jConfiguration.java'
\ No newline at end of file
diff --git a/docs/apidocs/com/canehealth/ckblib/application/DemoApplication.html b/docs/apidocs/com/canehealth/ckblib/application/DemoApplication.html
index 1a61586..ff691d3 100644
--- a/docs/apidocs/com/canehealth/ckblib/application/DemoApplication.html
+++ b/docs/apidocs/com/canehealth/ckblib/application/DemoApplication.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>DemoApplication (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>DemoApplication (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="declaration: package: com.canehealth.ckblib.application, class: DemoApplication">
 <meta name="generator" content="javadoc/ClassWriterImpl">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
diff --git a/docs/apidocs/com/canehealth/ckblib/application/Neo4jConfiguration.html b/docs/apidocs/com/canehealth/ckblib/application/Neo4jConfiguration.html
index a9287ec..9517617 100644
--- a/docs/apidocs/com/canehealth/ckblib/application/Neo4jConfiguration.html
+++ b/docs/apidocs/com/canehealth/ckblib/application/Neo4jConfiguration.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Neo4jConfiguration (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Neo4jConfiguration (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="declaration: package: com.canehealth.ckblib.application, class: Neo4jConfiguration">
 <meta name="generator" content="javadoc/ClassWriterImpl">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
diff --git a/docs/apidocs/com/canehealth/ckblib/application/class-use/DemoApplication.html b/docs/apidocs/com/canehealth/ckblib/application/class-use/DemoApplication.html
index eb37c84..3acb058 100644
--- a/docs/apidocs/com/canehealth/ckblib/application/class-use/DemoApplication.html
+++ b/docs/apidocs/com/canehealth/ckblib/application/class-use/DemoApplication.html
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
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index 6b2349f..42045f9 100644
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.application.Neo4jConfiguration (cklib-core 0.15.0 API)</title>
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+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getAllAnatomies()">getAllAnatomies</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all anatomical sites in the graph</div>
+</td>
+</tr>
+<tr class="rowColor" id="i3">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
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+<div class="block">Returns all anatomical sites in the graph</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>All anatomy nodes in the graph</dd>
+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
+<dt><span class="seeLabel">See Also:</span></dt>
+<dd><a href="AnatomicalSiteRepository.html" title="interface in com.canehealth.ckblib.graph"><code>AnatomicalSiteRepository</code></a></dd>
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+<title>DiseaseDisorderRepository (cklib-core 0.15.0 API)</title>
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>DiseaseDisorderService (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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@@ -157,21 +157,43 @@ <h2>Method Summary</h2>
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="rowColor" id="i1">
+<td class="colFirst"><code>void</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#deleteDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">deleteDisease</a></span>&#8203;(<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</code></th>
+<td class="colLast">
+<div class="block">Deletes a disease node</div>
+</td>
+</tr>
+<tr class="altColor" id="i2">
+<td class="colFirst"><code>void</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#deleteDiseaseByCui(java.lang.String)">deleteDiseaseByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
+<td class="colLast">
+<div class="block">Finds a disease by CUI to which the
+ {@link #deleteDisease(DiseaseDisorderMention diseaseDisorderMention)) subscribes}</div>
+</td>
+</tr>
+<tr class="rowColor" id="i3">
 <td class="colFirst"><code><a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a></code></td>
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 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor" id="i2">
+<tr class="altColor" id="i4">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getAllDiseases()">getAllDiseases</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all diseases in the graph</div>
+</td>
+</tr>
+<tr class="rowColor" id="i5">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getDiseaseByCui(java.lang.String)">getDiseaseByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor" id="i3">
+<tr class="altColor" id="i6">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getDiseasesByName(java.lang.String)">getDiseasesByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor" id="i4">
+<tr class="rowColor" id="i7">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#saveDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">saveDisease</a></span>&#8203;(<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</code></th>
 <td class="colLast">&nbsp;</td>
@@ -216,6 +238,49 @@ <h2>Method Details</h2>
 <ul class="blockList">
 <li class="blockList">
 <section class="detail">
+<h3><a id="getAllDiseases()">getAllDiseases</a></h3>
+<div class="memberSignature"><span class="modifiers">public</span>&nbsp;<span class="returnType">reactor.core.publisher.Flux&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</span>&nbsp;<span class="memberName">getAllDiseases</span>()</div>
+<div class="block">Returns all diseases in the graph</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>All disease nodes in the graph</dd>
+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
+<dt><span class="seeLabel">See Also:</span></dt>
+<dd><a href="DiseaseDisorderRepository.html" title="interface in com.canehealth.ckblib.graph"><code>DiseaseDisorderRepository</code></a></dd>
+</dl>
+</section>
+</li>
+<li class="blockList">
+<section class="detail">
+<h3><a id="deleteDiseaseByCui(java.lang.String)">deleteDiseaseByCui</a></h3>
+<div class="memberSignature"><span class="modifiers">public</span>&nbsp;<span class="returnType">void</span>&nbsp;<span class="memberName">deleteDiseaseByCui</span>&#8203;(<span class="arguments"><a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</span></div>
+<div class="block">Finds a disease by CUI to which the
+ {@link #deleteDisease(DiseaseDisorderMention diseaseDisorderMention)) subscribes}</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>cui</code> - CUI</dd>
+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
+</dl>
+</section>
+</li>
+<li class="blockList">
+<section class="detail">
+<h3><a id="deleteDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">deleteDisease</a></h3>
+<div class="memberSignature"><span class="annotations">@Transactional
+</span><span class="modifiers">public</span>&nbsp;<span class="returnType">void</span>&nbsp;<span class="memberName">deleteDisease</span>&#8203;(<span class="arguments"><a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</span></div>
+<div class="block">Deletes a disease node</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>diseaseDisorderMention</code> - Disease NodeEntity to delete</dd>
+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
+</dl>
+</section>
+</li>
+<li class="blockList">
+<section class="detail">
 <h3><a id="getDiseaseByCui(java.lang.String)">getDiseaseByCui</a></h3>
 <div class="memberSignature"><span class="modifiers">public</span>&nbsp;<span class="returnType">reactor.core.publisher.Mono&lt;<a href="model/DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</span>&nbsp;<span class="memberName">getDiseaseByCui</span>&#8203;(<span class="arguments"><a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</span></div>
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+<title>JournalArticleRepository (cklib-core 0.15.0 API)</title>
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>JournalArticleService (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/MedicationRepository.html b/docs/apidocs/com/canehealth/ckblib/graph/MedicationRepository.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>MedicationRepository (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>MedicationRepository (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
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index 9ed7235..e44f848 100644
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 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>MedicationService (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>MedicationService (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
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@@ -20,7 +20,7 @@
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 <body class="class-declaration">
-<script type="text/javascript">var data = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10};
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@@ -162,16 +162,23 @@ <h2>Method Summary</h2>
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor" id="i2">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getAllMedications()">getAllMedications</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all medications in the graph</div>
+</td>
+</tr>
+<tr class="rowColor" id="i3">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor" id="i3">
+<tr class="altColor" id="i4">
 <td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor" id="i4">
+<tr class="rowColor" id="i5">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#saveSymptom(com.canehealth.ckblib.graph.model.MedicationMention)">saveSymptom</a></span>&#8203;(<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&nbsp;medicationMention)</code></th>
 <td class="colLast">&nbsp;</td>
@@ -216,6 +223,21 @@ <h2>Method Details</h2>
 <ul class="blockList">
 <li class="blockList">
 <section class="detail">
+<h3><a id="getAllMedications()">getAllMedications</a></h3>
+<div class="memberSignature"><span class="modifiers">public</span>&nbsp;<span class="returnType">reactor.core.publisher.Flux&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</span>&nbsp;<span class="memberName">getAllMedications</span>()</div>
+<div class="block">Returns all medications in the graph</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>All medication nodes in the graph</dd>
+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
+<dt><span class="seeLabel">See Also:</span></dt>
+<dd><a href="MedicationRepository.html" title="interface in com.canehealth.ckblib.graph"><code>MedicationRepository</code></a></dd>
+</dl>
+</section>
+</li>
+<li class="blockList">
+<section class="detail">
 <h3><a id="getSymptomByCui(java.lang.String)">getSymptomByCui</a></h3>
 <div class="memberSignature"><span class="modifiers">public</span>&nbsp;<span class="returnType">reactor.core.publisher.Mono&lt;<a href="model/MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</span>&nbsp;<span class="memberName">getSymptomByCui</span>&#8203;(<span class="arguments"><a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</span></div>
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Neo4jTestConfiguration (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Neo4jTestConfiguration (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/ProcedureRepository.html b/docs/apidocs/com/canehealth/ckblib/graph/ProcedureRepository.html
index 7d18141..88cc108 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/ProcedureRepository.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/ProcedureRepository.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>ProcedureRepository (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>ProcedureRepository (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/ProcedureService.html b/docs/apidocs/com/canehealth/ckblib/graph/ProcedureService.html
index 280644d..b727bea 100644
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 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>ProcedureService (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>ProcedureService (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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-<script type="text/javascript">var data = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10};
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@@ -162,16 +162,23 @@ <h2>Method Summary</h2>
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor" id="i2">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getAllProcedures()">getAllProcedures</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all procedures in the graph</div>
+</td>
+</tr>
+<tr class="rowColor" id="i3">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor" id="i3">
+<tr class="altColor" id="i4">
 <td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="model/ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor" id="i4">
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 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="model/ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
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+<dt><span class="simpleTagLabel">Since:</span></dt>
+<dd>0.14.0</dd>
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/class-use/ProcedureRepository.html b/docs/apidocs/com/canehealth/ckblib/graph/class-use/ProcedureRepository.html
index 521230b..dd9b2e9 100644
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Interface com.canehealth.ckblib.graph.ProcedureRepository (cklib-core 0.15.0 API)</title>
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index a21fd19..2994635 100644
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
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-<meta name="dc.created" content="2021-04-28">
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index b6e240f..d377587 100644
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Interface com.canehealth.ckblib.graph.SignSymptomRepository (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/class-use/SignSymptomService.html b/docs/apidocs/com/canehealth/ckblib/graph/class-use/SignSymptomService.html
index dd52402..0184ef4 100644
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.SignSymptomService (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/AnatomicalSiteMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/AnatomicalSiteMention.html
index a06bd53..5abf2f5 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/AnatomicalSiteMention.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>AnatomicalSiteMention (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/BaseRelation.html b/docs/apidocs/com/canehealth/ckblib/graph/model/BaseRelation.html
index 982a789..1ddc6b6 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/BaseRelation.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>BaseRelation (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/ConceptAttributes.html b/docs/apidocs/com/canehealth/ckblib/graph/model/ConceptAttributes.html
index 877ac70..2007ca7 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/ConceptAttributes.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>ConceptAttributes (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>ConceptAttributes (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/DiseaseDisorderMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/DiseaseDisorderMention.html
index 425cd9f..0f81b5c 100644
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
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+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>DiseaseDisorderMention (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/JournalArticle.html b/docs/apidocs/com/canehealth/ckblib/graph/model/JournalArticle.html
index 2a4361d..71c84a1 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/JournalArticle.html
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/MedicationMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/MedicationMention.html
index a4876b1..40e411f 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/MedicationMention.html
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 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>MedicationMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>MedicationMention (cklib-core 0.15.0 API)</title>
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/ProcedureMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/ProcedureMention.html
index c48d2e1..e1b820f 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/ProcedureMention.html
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 <!-- NewPage -->
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>ProcedureMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>ProcedureMention (cklib-core 0.15.0 API)</title>
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-<meta name="dc.created" content="2021-04-28">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/SignSymptomMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/SignSymptomMention.html
index a7cb01a..8dccc09 100644
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>SignSymptomMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>SignSymptomMention (cklib-core 0.15.0 API)</title>
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/AnatomicalSiteMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/AnatomicalSiteMention.html
index 7546d16..41e9feb 100644
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-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.AnatomicalSiteMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.AnatomicalSiteMention (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
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@@ -130,16 +130,23 @@ <h2>Uses of <a href="../AnatomicalSiteMention.html" title="class in com.caneheal
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">AnatomicalSiteService.</span><code><span class="memberNameLink"><a href="../../AnatomicalSiteService.html#getAllAnatomies()">getAllAnatomies</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all anatomical sites in the graph</div>
+</td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">AnatomicalSiteService.</span><code><span class="memberNameLink"><a href="../../AnatomicalSiteService.html#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">AnatomicalSiteService.</span><code><span class="memberNameLink"><a href="../../AnatomicalSiteService.html#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">AnatomicalSiteRepository.</span><code><span class="memberNameLink"><a href="../../AnatomicalSiteRepository.html#mergeDiseaseWithAnatomy(java.lang.String,java.lang.String,int,int,int)">mergeDiseaseWithAnatomy</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;dcui,
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@@ -148,7 +155,7 @@ <h2>Uses of <a href="../AnatomicalSiteMention.html" title="class in com.caneheal
 int&nbsp;d)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">AnatomicalSiteService.</span><code><span class="memberNameLink"><a href="../../AnatomicalSiteService.html#saveSymptom(com.canehealth.ckblib.graph.model.AnatomicalSiteMention)">saveSymptom</a></span>&#8203;(<a href="../AnatomicalSiteMention.html" title="class in com.canehealth.ckblib.graph.model">AnatomicalSiteMention</a>&nbsp;anatomicalSiteMention)</code></th>
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 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.BaseRelation (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.BaseRelation (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: BaseRelation">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ConceptAttributes.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ConceptAttributes.html
index c519b5a..8beb6d3 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ConceptAttributes.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ConceptAttributes.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.ConceptAttributes (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.ConceptAttributes (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: ConceptAttributes">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/DiseaseDisorderMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/DiseaseDisorderMention.html
index 5d25e77..8e4aded 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/DiseaseDisorderMention.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/DiseaseDisorderMention.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.DiseaseDisorderMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.DiseaseDisorderMention (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: DiseaseDisorderMention">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
@@ -126,16 +126,23 @@ <h2>Uses of <a href="../DiseaseDisorderMention.html" title="class in com.canehea
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#getAllDiseases()">getAllDiseases</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all diseases in the graph</div>
+</td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#getDiseaseByCui(java.lang.String)">getDiseaseByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#getDiseasesByName(java.lang.String)">getDiseasesByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#saveDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">saveDisease</a></span>&#8203;(<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</code></th>
 <td class="colLast">&nbsp;</td>
@@ -155,6 +162,13 @@ <h2>Uses of <a href="../DiseaseDisorderMention.html" title="class in com.canehea
 </thead>
 <tbody>
 <tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#deleteDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">deleteDisease</a></span>&#8203;(<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</code></th>
+<td class="colLast">
+<div class="block">Deletes a disease node</div>
+</td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">DiseaseDisorderService.</span><code><span class="memberNameLink"><a href="../../DiseaseDisorderService.html#saveDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">saveDisease</a></span>&#8203;(<a href="../DiseaseDisorderMention.html" title="class in com.canehealth.ckblib.graph.model">DiseaseDisorderMention</a>&nbsp;diseaseDisorderMention)</code></th>
 <td class="colLast">&nbsp;</td>
diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/JournalArticle.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/JournalArticle.html
index 131ef92..2f11cf5 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/JournalArticle.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/JournalArticle.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.JournalArticle (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.JournalArticle (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: JournalArticle">
 <meta name="generator" content="javadoc/ClassUseWriter">
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diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/MedicationMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/MedicationMention.html
index 66accf7..386885a 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/MedicationMention.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/MedicationMention.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.MedicationMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.MedicationMention (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: MedicationMention">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
@@ -130,16 +130,23 @@ <h2>Uses of <a href="../MedicationMention.html" title="class in com.canehealth.c
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">MedicationService.</span><code><span class="memberNameLink"><a href="../../MedicationService.html#getAllMedications()">getAllMedications</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all medications in the graph</div>
+</td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">MedicationService.</span><code><span class="memberNameLink"><a href="../../MedicationService.html#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">MedicationService.</span><code><span class="memberNameLink"><a href="../../MedicationService.html#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">MedicationRepository.</span><code><span class="memberNameLink"><a href="../../MedicationRepository.html#mergeDiseaseWithMedication(java.lang.String,java.lang.String,int,int,int)">mergeDiseaseWithMedication</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;dcui,
 <a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;scui,
@@ -148,7 +155,7 @@ <h2>Uses of <a href="../MedicationMention.html" title="class in com.canehealth.c
 int&nbsp;d)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">MedicationService.</span><code><span class="memberNameLink"><a href="../../MedicationService.html#saveSymptom(com.canehealth.ckblib.graph.model.MedicationMention)">saveSymptom</a></span>&#8203;(<a href="../MedicationMention.html" title="class in com.canehealth.ckblib.graph.model">MedicationMention</a>&nbsp;medicationMention)</code></th>
 <td class="colLast">&nbsp;</td>
diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ProcedureMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ProcedureMention.html
index 858a6f4..c5ba2e4 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ProcedureMention.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/ProcedureMention.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.ProcedureMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.ProcedureMention (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: ProcedureMention">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
@@ -130,16 +130,23 @@ <h2>Uses of <a href="../ProcedureMention.html" title="class in com.canehealth.ck
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">ProcedureService.</span><code><span class="memberNameLink"><a href="../../ProcedureService.html#getAllProcedures()">getAllProcedures</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all procedures in the graph</div>
+</td>
+</tr>
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">ProcedureService.</span><code><span class="memberNameLink"><a href="../../ProcedureService.html#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">ProcedureService.</span><code><span class="memberNameLink"><a href="../../ProcedureService.html#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">ProcedureRepository.</span><code><span class="memberNameLink"><a href="../../ProcedureRepository.html#mergeDiseaseWithProcedure(java.lang.String,java.lang.String,int,int,int)">mergeDiseaseWithProcedure</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;dcui,
 <a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;scui,
@@ -148,7 +155,7 @@ <h2>Uses of <a href="../ProcedureMention.html" title="class in com.canehealth.ck
 int&nbsp;d)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">ProcedureService.</span><code><span class="memberNameLink"><a href="../../ProcedureService.html#saveSymptom(com.canehealth.ckblib.graph.model.ProcedureMention)">saveSymptom</a></span>&#8203;(<a href="../ProcedureMention.html" title="class in com.canehealth.ckblib.graph.model">ProcedureMention</a>&nbsp;procedureMention)</code></th>
 <td class="colLast">&nbsp;</td>
diff --git a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/SignSymptomMention.html b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/SignSymptomMention.html
index fa17e52..c8096b6 100644
--- a/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/SignSymptomMention.html
+++ b/docs/apidocs/com/canehealth/ckblib/graph/model/class-use/SignSymptomMention.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Uses of Class com.canehealth.ckblib.graph.model.SignSymptomMention (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Uses of Class com.canehealth.ckblib.graph.model.SignSymptomMention (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="use: package: com.canehealth.ckblib.graph.model, class: SignSymptomMention">
 <meta name="generator" content="javadoc/ClassUseWriter">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
@@ -135,16 +135,23 @@ <h2>Uses of <a href="../SignSymptomMention.html" title="class in com.canehealth.
 <td class="colLast">&nbsp;</td>
 </tr>
 <tr class="rowColor">
+<td class="colFirst"><code>reactor.core.publisher.Flux&lt;<a href="../SignSymptomMention.html" title="class in com.canehealth.ckblib.graph.model">SignSymptomMention</a>&gt;</code></td>
+<th class="colSecond" scope="row"><span class="typeNameLabel">SignSymptomService.</span><code><span class="memberNameLink"><a href="../../SignSymptomService.html#getAllSignSymptoms()">getAllSignSymptoms</a></span>()</code></th>
+<td class="colLast">
+<div class="block">Returns all procedures in the graph</div>
+</td>
+</tr>
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../SignSymptomMention.html" title="class in com.canehealth.ckblib.graph.model">SignSymptomMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">SignSymptomService.</span><code><span class="memberNameLink"><a href="../../SignSymptomService.html#getSymptomByCui(java.lang.String)">getSymptomByCui</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;cui)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="altColor">
+<tr class="rowColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../SignSymptomMention.html" title="class in com.canehealth.ckblib.graph.model">SignSymptomMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">SignSymptomService.</span><code><span class="memberNameLink"><a href="../../SignSymptomService.html#getSymptomByName(java.lang.String)">getSymptomByName</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;name)</code></th>
 <td class="colLast">&nbsp;</td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>reactor.core.publisher.Mono&lt;<a href="../SignSymptomMention.html" title="class in com.canehealth.ckblib.graph.model">SignSymptomMention</a>&gt;</code></td>
 <th class="colSecond" scope="row"><span class="typeNameLabel">SignSymptomRepository.</span><code><span class="memberNameLink"><a href="../../SignSymptomRepository.html#mergeDiseaseWithSymptom(java.lang.String,java.lang.String,int,int,int)">mergeDiseaseWithSymptom</a></span>&#8203;(<a href="https://docs.oracle.com/en/java/javase/13/docs/api/java.base/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>&nbsp;dcui,
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@@ -208,6 +208,15 @@ <h2 class="title">D</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/qtakes/model/QtakesRoot.html#dateAnnotation">dateAnnotation</a></span> - Variable in class com.canehealth.ckblib.qtakes.model.<a href="com/canehealth/ckblib/qtakes/model/QtakesRoot.html" title="class in com.canehealth.ckblib.qtakes.model">QtakesRoot</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html#deleteDisease(com.canehealth.ckblib.graph.model.DiseaseDisorderMention)">deleteDisease(DiseaseDisorderMention)</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html" title="class in com.canehealth.ckblib.graph">DiseaseDisorderService</a></dt>
+<dd>
+<div class="block">Deletes a disease node</div>
+</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html#deleteDiseaseByCui(java.lang.String)">deleteDiseaseByCui(String)</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html" title="class in com.canehealth.ckblib.graph">DiseaseDisorderService</a></dt>
+<dd>
+<div class="block">Finds a disease by CUI to which the
+ {@link #deleteDisease(DiseaseDisorderMention diseaseDisorderMention)) subscribes}</div>
+</dd>
 <dt><a href="com/canehealth/ckblib/application/DemoApplication.html" title="class in com.canehealth.ckblib.application"><span class="typeNameLink">DemoApplication</span></a> - Class in <a href="com/canehealth/ckblib/application/package-summary.html">com.canehealth.ckblib.application</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/application/DemoApplication.html#%3Cinit%3E(com.canehealth.ckblib.library.service.MyService)">DemoApplication(MyService)</a></span> - Constructor for class com.canehealth.ckblib.application.<a href="com/canehealth/ckblib/application/DemoApplication.html" title="class in com.canehealth.ckblib.application">DemoApplication</a></dt>
@@ -326,6 +335,26 @@ <h2 class="title">G</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/library/service/CkbEsearch.html#get()">get()</a></span> - Method in class com.canehealth.ckblib.library.service.<a href="com/canehealth/ckblib/library/service/CkbEsearch.html" title="class in com.canehealth.ckblib.library.service">CkbEsearch</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/AnatomicalSiteService.html#getAllAnatomies()">getAllAnatomies()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/AnatomicalSiteService.html" title="class in com.canehealth.ckblib.graph">AnatomicalSiteService</a></dt>
+<dd>
+<div class="block">Returns all anatomical sites in the graph</div>
+</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html#getAllDiseases()">getAllDiseases()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html" title="class in com.canehealth.ckblib.graph">DiseaseDisorderService</a></dt>
+<dd>
+<div class="block">Returns all diseases in the graph</div>
+</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/MedicationService.html#getAllMedications()">getAllMedications()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/MedicationService.html" title="class in com.canehealth.ckblib.graph">MedicationService</a></dt>
+<dd>
+<div class="block">Returns all medications in the graph</div>
+</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/ProcedureService.html#getAllProcedures()">getAllProcedures()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/ProcedureService.html" title="class in com.canehealth.ckblib.graph">ProcedureService</a></dt>
+<dd>
+<div class="block">Returns all procedures in the graph</div>
+</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/SignSymptomService.html#getAllSignSymptoms()">getAllSignSymptoms()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/SignSymptomService.html" title="class in com.canehealth.ckblib.graph">SignSymptomService</a></dt>
+<dd>
+<div class="block">Returns all procedures in the graph</div>
+</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/library/service/CkbEfetch.html#getChain(com.canehealth.ckblib.library.model.BaseQuery)">getChain(BaseQuery)</a></span> - Method in class com.canehealth.ckblib.library.service.<a href="com/canehealth/ckblib/library/service/CkbEfetch.html" title="class in com.canehealth.ckblib.library.service">CkbEfetch</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html#getDiseaseByCui(java.lang.String)">getDiseaseByCui(String)</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/DiseaseDisorderService.html" title="class in com.canehealth.ckblib.graph">DiseaseDisorderService</a></dt>
@@ -334,6 +363,8 @@ <h2 class="title">G</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/library/model/BaseQuery.html#getFetchQuery(java.lang.String)">getFetchQuery(String)</a></span> - Method in class com.canehealth.ckblib.library.model.<a href="com/canehealth/ckblib/library/model/BaseQuery.html" title="class in com.canehealth.ckblib.library.model">BaseQuery</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/BaseRelationService.html#getLift(java.lang.String)">getLift(String)</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/BaseRelationService.html" title="class in com.canehealth.ckblib.graph">BaseRelationService</a></dt>
+<dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/application/Neo4jConfiguration.html#getMappingBasePackages()">getMappingBasePackages()</a></span> - Method in class com.canehealth.ckblib.application.<a href="com/canehealth/ckblib/application/Neo4jConfiguration.html" title="class in com.canehealth.ckblib.application">Neo4jConfiguration</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="com/canehealth/ckblib/graph/Neo4jTestConfiguration.html#getMappingBasePackages()">getMappingBasePackages()</a></span> - Method in class com.canehealth.ckblib.graph.<a href="com/canehealth/ckblib/graph/Neo4jTestConfiguration.html" title="class in com.canehealth.ckblib.graph">Neo4jTestConfiguration</a></dt>
diff --git a/docs/apidocs/index.html b/docs/apidocs/index.html
index 68afd17..c53b585 100644
--- a/docs/apidocs/index.html
+++ b/docs/apidocs/index.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Overview (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Overview (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="package index">
 <meta name="generator" content="javadoc/PackageIndexWriter">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
@@ -67,7 +67,7 @@
 </header>
 <main role="main">
 <div class="header">
-<h1 class="title">cklib-core 0.12.0 API</h1>
+<h1 class="title">cklib-core 0.15.0 API</h1>
 </div>
 <div class="contentContainer">
 <div class="overviewSummary">
diff --git a/docs/apidocs/javadoc.sh b/docs/apidocs/javadoc.sh
new file mode 100755
index 0000000..af9e6fd
--- /dev/null
+++ b/docs/apidocs/javadoc.sh
@@ -0,0 +1 @@
+/home/beapen/.jenv/versions/13/bin/javadoc @options @argfile
\ No newline at end of file
diff --git a/docs/apidocs/member-search-index.js b/docs/apidocs/member-search-index.js
index b5f7d5e..5f36e46 100644
--- a/docs/apidocs/member-search-index.js
+++ b/docs/apidocs/member-search-index.js
@@ -1 +1 @@
-memberSearchIndex = [{"p":"com.canehealth.ckblib.graph","c":"BaseRelationService","l":"addAttributes(String, String, int, int, int)","url":"addAttributes(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderService","l":"addDifferential(String, String, int, int, int)","url":"addDifferential(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleService","l":"addEvidence(String, String)","url":"addEvidence(java.lang.String,java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteService","l":"addRelation(String, String, int, int, int)","url":"addRelation(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationService","l":"addRelation(String, String, int, int, int)","url":"addRelation(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureService","l":"addRelation(String, String, int, int, int)","url":"addRelation(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomService","l":"addRelation(String, String, int, int, int)","url":"addRelation(java.lang.String,java.lang.String,int,int,int)"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"anatomicalSiteMention"},{"p":"com.canehealth.ckblib.graph.model","c":"AnatomicalSiteMention","l":"AnatomicalSiteMention()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteService","l":"AnatomicalSiteService()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.model","c":"BaseQuery","l":"BaseQuery()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph.model","c":"BaseRelation","l":"BaseRelation()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"BaseRelationService","l":"BaseRelationService()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptMention","l":"begin"},{"p":"com.canehealth.ckblib.graph","c":"D3Map.Builder","l":"build()"},{"p":"com.canehealth.ckblib.graph","c":"D3Map.Builder","l":"Builder(Driver)","url":"%3Cinit%3E(org.neo4j.driver.Driver)"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEfetch","l":"CkbEfetch()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEsearch","l":"CkbEsearch()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.util","c":"CkblibConstants","l":"CkblibConstants()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.util","c":"CkbXpath","l":"CkbXpath()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.qtakes.service","c":"QtakesService","l":"clearResults()"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptAttribute","l":"code"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptAttribute","l":"codingScheme"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptAttribute","l":"ConceptAttribute()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptMention","l":"conceptAttributes"},{"p":"com.canehealth.ckblib.graph.model","c":"ConceptAttributes","l":"ConceptAttributes()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptMention","l":"ConceptMention()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.util","c":"CkbXpath","l":"convertStringToXMLDocument(String)","url":"convertStringToXMLDocument(java.lang.String)"},{"p":"com.canehealth.ckblib.library.model","c":"Esearchresult","l":"count"},{"p":"com.canehealth.ckblib.graph","c":"D3Map","l":"createJson(String)","url":"createJson(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"D3Map","l":"createMap(String)","url":"createMap(java.lang.String)"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptAttribute","l":"cui"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"dateAnnotation"},{"p":"com.canehealth.ckblib.application","c":"DemoApplication","l":"DemoApplication(MyService)","url":"%3Cinit%3E(com.canehealth.ckblib.library.service.MyService)"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"diseaseDisorderMention"},{"p":"com.canehealth.ckblib.graph.model","c":"DiseaseDisorderMention","l":"DiseaseDisorderMention()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderService","l":"DiseaseDisorderService()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.application","c":"Neo4jConfiguration","l":"driver()"},{"p":"com.canehealth.ckblib.graph","c":"Neo4jTestConfiguration","l":"driver()"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"drugChangeStatusAnnotation"},{"p":"com.canehealth.ckblib.library.util","c":"CkblibConstants","l":"EFETCH_URL"},{"p":"com.canehealth.ckblib.qtakes.model","c":"ConceptMention","l":"end"},{"p":"com.canehealth.ckblib.library.util","c":"CkblibConstants","l":"ESEARCH_BASE"},{"p":"com.canehealth.ckblib.library.util","c":"CkblibConstants","l":"ESEARCH_URL"},{"p":"com.canehealth.ckblib.library.model","c":"EsearchResultRoot","l":"esearchresult"},{"p":"com.canehealth.ckblib.library.model","c":"Esearchresult","l":"Esearchresult()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.model","c":"EsearchResultRoot","l":"EsearchResultRoot()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"D3Map","l":"fetch()"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteRepository","l":"findAll()"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderRepository","l":"findAll()"},{"p":"com.canehealth.ckblib.graph","c":"MedicationRepository","l":"findAll()"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureRepository","l":"findAll()"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomRepository","l":"findAll()"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomRepository","l":"findAllByNameLikeIgnoreCase(String)","url":"findAllByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteRepository","l":"findOneByCui(String)","url":"findOneByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderRepository","l":"findOneByCui(String)","url":"findOneByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationRepository","l":"findOneByCui(String)","url":"findOneByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureRepository","l":"findOneByCui(String)","url":"findOneByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomRepository","l":"findOneByCui(String)","url":"findOneByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderRepository","l":"findOneByNameLikeIgnoreCase(String)","url":"findOneByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomRepository","l":"findOneByNameLikeIgnoreCase(String)","url":"findOneByNameLikeIgnoreCase(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleRepository","l":"findOneByPmid(String)","url":"findOneByPmid(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteService","l":"forD3(String)","url":"forD3(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderService","l":"forD3(String)","url":"forD3(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationService","l":"forD3(String)","url":"forD3(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureService","l":"forD3(String)","url":"forD3(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomService","l":"forD3(String)","url":"forD3(java.lang.String)"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"fractionStrengthAnnotation"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"frequencyUnitAnnotation"},{"p":"com.canehealth.ckblib.library.model","c":"Translationset","l":"from"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEfetch","l":"get()"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEsearch","l":"get()"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEfetch","l":"getChain(BaseQuery)","url":"getChain(com.canehealth.ckblib.library.model.BaseQuery)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderService","l":"getDiseaseByCui(String)","url":"getDiseaseByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"DiseaseDisorderService","l":"getDiseasesByName(String)","url":"getDiseasesByName(java.lang.String)"},{"p":"com.canehealth.ckblib.library.model","c":"BaseQuery","l":"getFetchQuery(String)","url":"getFetchQuery(java.lang.String)"},{"p":"com.canehealth.ckblib.application","c":"Neo4jConfiguration","l":"getMappingBasePackages()"},{"p":"com.canehealth.ckblib.graph","c":"Neo4jTestConfiguration","l":"getMappingBasePackages()"},{"p":"com.canehealth.ckblib.library.service","c":"ServiceProperties","l":"getMessage()"},{"p":"com.canehealth.ckblib.library.util","c":"CkbXpath","l":"getNodes(String)","url":"getNodes(java.lang.String)"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEfetch","l":"getPath(String)","url":"getPath(java.lang.String)"},{"p":"com.canehealth.ckblib.library.service","c":"CkbEfetch","l":"getPathFromString(String, 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String)","url":"getQueryWithAll(java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"BaseRelationRepository","l":"getRelationsByCui(String)","url":"getRelationsByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"BaseRelationService","l":"getRelationsByCui(String)","url":"getRelationsByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteService","l":"getSymptomByCui(String)","url":"getSymptomByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationService","l":"getSymptomByCui(String)","url":"getSymptomByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureService","l":"getSymptomByCui(String)","url":"getSymptomByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomService","l":"getSymptomByCui(String)","url":"getSymptomByCui(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"AnatomicalSiteService","l":"getSymptomByName(String)","url":"getSymptomByName(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleService","l":"getSymptomByName(String)","url":"getSymptomByName(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"MedicationService","l":"getSymptomByName(String)","url":"getSymptomByName(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"ProcedureService","l":"getSymptomByName(String)","url":"getSymptomByName(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"SignSymptomService","l":"getSymptomByName(String)","url":"getSymptomByName(java.lang.String)"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleService","l":"getSymptomByPmid(String)","url":"getSymptomByPmid(java.lang.String)"},{"p":"com.canehealth.ckblib.library.model","c":"EsearchResultRoot","l":"header"},{"p":"com.canehealth.ckblib.library.model","c":"Header","l":"Header()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.library.util","c":"CkblibConstants","l":"HELP_STRING"},{"p":"com.canehealth.ckblib.library.model","c":"Esearchresult","l":"idlist"},{"p":"com.canehealth.ckblib.library.model","c":"Esearchresult","l":"ids()"},{"p":"com.canehealth.ckblib.graph.model","c":"JournalArticle","l":"JournalArticle()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleService","l":"JournalArticleService()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.application","c":"DemoApplication","l":"main(String[])","url":"main(java.lang.String[])"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"measurementAnnotation"},{"p":"com.canehealth.ckblib.qtakes.model","c":"QtakesRoot","l":"medicationMention"},{"p":"com.canehealth.ckblib.graph.model","c":"MedicationMention","l":"MedicationMention()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"MedicationService","l":"MedicationService()","url":"%3Cinit%3E()"},{"p":"com.canehealth.ckblib.graph","c":"JournalArticleRepository","l":"mergeConceptWithEvidence(String, 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diff --git a/docs/apidocs/overview-summary.html b/docs/apidocs/overview-summary.html
index c6a422c..5a61870 100644
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 <link rel="canonical" href="index.html">
diff --git a/docs/apidocs/overview-tree.html b/docs/apidocs/overview-tree.html
index 9e7dce0..4e477cb 100644
--- a/docs/apidocs/overview-tree.html
+++ b/docs/apidocs/overview-tree.html
@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (13.0.2) on Wed Apr 28 07:56:32 EDT 2021 -->
-<title>Class Hierarchy (cklib-core 0.12.0 API)</title>
+<!-- Generated by javadoc (13.0.2) on Mon May 24 08:32:57 EDT 2021 -->
+<title>Class Hierarchy (cklib-core 0.15.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta name="dc.created" content="2021-04-28">
+<meta name="dc.created" content="2021-05-24">
 <meta name="description" content="class tree">
 <meta name="generator" content="javadoc/TreeWriter">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">

From c53f37b0506a471406594a5678d0107b00761606 Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Mon, 24 May 2021 08:38:18 -0400
Subject: [PATCH 05/21] fix: links in README

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 0f7cf72..c57a9ea 100644
--- a/README.md
+++ b/README.md
@@ -7,9 +7,9 @@
           \______  /____|__ \ |______  /          /_/
                  \/        \/        \/
 </pre>
-![omopfhirmap](https://forthebadge.com/images/badges/made-with-java.svg)
+[![ckblib](https://forthebadge.com/images/badges/made-with-java.svg)](https://dermatologist.co.in)
 
-[![ckblib](https://github.com/dermatologist/ckblib/blob/develop/notes/dermml.jpg)](https://nuchange.ca)
+[![ckblib](https://github.com/dermatologist/ckblib/blob/develop/notes/dermml.jpg)](https://gulfdoctor.net)
 
 ## About
 
@@ -23,7 +23,7 @@ Providing clinical decision support requires some formal way of representing cli
 
 * [Read how to install mvn packages from GitHub](https://docs.github.com/en/packages/guides/configuring-apache-maven-for-use-with-github-packages#installing-a-package)
 * Include dependencies in pom.xml
-* See an application [![forthebadge](https://forthebadge.com/images/badges/built-with-love.svg) using ckblib: [GulfDoctor](https://gulfdoctor.net)
+* See an application [![forthebadge](https://forthebadge.com/images/badges/built-with-love.svg)](https://gulfdoctor.net) using ckblib: [GulfDoctor](https://gulfdoctor.net)
 
 ```
 <dependency>

From af93a363a2c89e713e1b275c0d1d4a006a936beb Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Tue, 25 May 2021 20:57:49 -0400
Subject: [PATCH 06/21] refactor demo application

---
 README.md                                     |  2 +-
 .../ckblib/application/DemoApplication.java   | 24 +++----------------
 2 files changed, 4 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index c57a9ea..26d88f3 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ Providing clinical decision support requires some formal way of representing cli
 </dependency>
 ```
 * Read [javadoc](https://dermatologist.github.io/ckblib/index.html). Documentation is WIP.
-* Check the application module for an example end-to-end use.
+* Check the [application module](https://github.com/dermatologist/ckblib/blob/develop/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java) for an example end-to-end use.
 
 ## Author
 
diff --git a/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java b/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java
index bb9f90e..4a5491a 100644
--- a/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java
+++ b/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java
@@ -108,8 +108,7 @@ public void run(String... args) throws InterruptedException {
 
 			// Check and adjust for total count of articles
 			ckbEsearch.setBaseQuery(baseQuery);
-			ckbEsearch.get();
-			TimeUnit.SECONDS.sleep(1);
+			ckbEsearch.get().block();
 			EsearchResultRoot esearchResultRoot = ckbEsearch.getResults().get(0);
 			LOG.info("Count: " + esearchResultRoot.esearchresult.count);
 			int ct = Integer.parseInt(esearchResultRoot.esearchresult.count);
@@ -121,8 +120,7 @@ public void run(String... args) throws InterruptedException {
 
 			ckbEfetch.setBaseQuery(baseQuery);
 			TimeUnit.SECONDS.sleep(3);
-			ckbEfetch.get();
-			TimeUnit.SECONDS.sleep(5);
+			ckbEfetch.get().block();
 
 			// Fails if disease not known, Try again after adding concepts
 			try {
@@ -136,6 +134,7 @@ public void run(String... args) throws InterruptedException {
 			List<String> pmids = ckbEfetch.getPath("//PMID");
 			List<String> titles = ckbEfetch.getPath("//ArticleTitle");
 
+			// Visit https://github.com/dermatologist/quick-ctakes for details on using QTakes
 			qtakesService.setQtakesUrl("http://127.0.0.1:8093");
 
 			for (int i = 0; i < abstracts.size(); i++) {
@@ -275,28 +274,11 @@ public void run(String... args) throws InterruptedException {
 					procedureService.addRelation(mainCui, cui, polarity, 0, 0).block();
 					journalArticleService.addEvidence(cui, pmid).block();
 				}
-				//System.out.println(r);
 			}
 
 		} catch (Exception e) {
 			LOG.error(e.getLocalizedMessage());
 		}
-		// String myPublications = ckbEfetch.getPath("//Abstract").get(0);
-		// String myPMID = ckbEfetch.getPath("//PMID").get(0);
-		// System.out.print(myPublications);
-		// System.out.print(myPMID);
-
-		// qtakesService.setQtakesUrl("http://127.0.0.1:8093");
-		// qtakesService.post(myPublications);
-		// TimeUnit.SECONDS.sleep(3);
-		// QtakesRoot r = qtakesService.getQtakesResults();
-		// System.out.print(r.toString());
-		// String s = ckbEfetch.getChain(baseQuery).block();
-		// List<String> abstracts = ckbEfetch.getPathFromString("//Abstract", s);
-		// for (String abs : abstracts){
-		// 	System.out.println(abs);
-		// }
-
 	}
 
 }

From b15f0a97e150a4bf31109a821473120c6de2715d Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 28 May 2021 07:43:37 -0400
Subject: [PATCH 07/21] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 26d88f3..aceff4c 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@
 
 Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph™ (see above). ckblib consists of three modules:
 
-* The 'library' module wraps the NCBI's E-Utils API to harvest published article abstracts.
+* The 'library' module wraps the NCBI's E-Utils API for published article abstracts.
 * The 'qtakes' module provides a programmable interface to my quick-ctakes or the quarkus based apache ctakes, a fast clinical text annotation engine.
 * Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.
 

From ef6d5d1a543e3fd8d45dc96ddad34f5d6e454438 Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Fri, 28 May 2021 08:08:02 -0400
Subject: [PATCH 08/21] update README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index aceff4c..dfa9a7c 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph™ (see above). ckblib consists of three modules:
 
 * The 'library' module wraps the NCBI's E-Utils API for published article abstracts.
-* The 'qtakes' module provides a programmable interface to my quick-ctakes or the quarkus based apache ctakes, a fast clinical text annotation engine.
+* The 'qtakes' module provides a programmable interface to [quick-ctakes](https://github.com/dermatologist/quick-ctakes) or the quarkus based apache ctakes, a fast clinical text annotation engine.
 * Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.
 
 ## How to use

From f7d8d5e525165190284908c7a60db2c5a66eba46 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 28 May 2021 08:40:24 -0400
Subject: [PATCH 09/21] Create LICENSE

---
 LICENSE | 373 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 373 insertions(+)
 create mode 100644 LICENSE

diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..a612ad9
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

From f73941e6633d3b2ba6efe4e90a7dbe4b3e52497d Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Thu, 3 Jun 2021 18:08:03 -0400
Subject: [PATCH 10/21] Add umls models

---
 .gitignore                                    |  1 +
 pom-deploy.xml                                |  1 +
 pom.xml                                       |  1 +
 umls/pom.xml                                  | 69 +++++++++++++++++++
 .../ckblib/umls/model/AtomLite.java           | 22 ++++++
 .../ckblib/umls/model/ConceptLite.java        | 18 +++++
 .../ckblib/umls/model/SearchResult.java       | 11 +++
 .../umls/model/SourceAtomClusterLite.java     | 29 ++++++++
 .../canehealth/ckblib/umls/service/.gitkeep   |  0
 .../canehealth/ckblib/umls/service/.gitkeep   |  0
 10 files changed, 152 insertions(+)
 create mode 100644 umls/pom.xml
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SearchResult.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep
 create mode 100644 umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep

diff --git a/.gitignore b/.gitignore
index 3055737..b775340 100644
--- a/.gitignore
+++ b/.gitignore
@@ -44,3 +44,4 @@ application/.factorypath
 library/.factorypath
 qtakes/.factorypath
 graph/.factorypath
+umls/.factorypath
diff --git a/pom-deploy.xml b/pom-deploy.xml
index 1175ace..0ba6843 100644
--- a/pom-deploy.xml
+++ b/pom-deploy.xml
@@ -10,6 +10,7 @@
     <modules>
         <module>qtakes</module>
         <module>library</module>
+        <module>umls</module>
         <module>graph</module>
     </modules>
 
diff --git a/pom.xml b/pom.xml
index 84e2167..b06cb89 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,6 +11,7 @@
     <modules>
         <module>library</module>
         <module>qtakes</module>
+        <module>umls</module>
         <module>graph</module>
         <module>application</module>
     </modules>
diff --git a/umls/pom.xml b/umls/pom.xml
new file mode 100644
index 0000000..91ce144
--- /dev/null
+++ b/umls/pom.xml
@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>org.springframework.boot</groupId>
+		<artifactId>spring-boot-starter-parent</artifactId>
+		<version>2.4.3</version>
+		<relativePath/> <!-- lookup parent from repository -->
+	</parent>
+	<groupId>com.canehealth.ckblib</groupId>
+	<artifactId>umls</artifactId>
+	<version>0.15.0</version>
+	<name>ckblib-umls</name>
+	<description>Demo project for Spring Boot</description>
+
+	<properties>
+		<java.version>13</java.version>
+	</properties>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-webflux</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.mock-server</groupId>
+			<artifactId>mockserver-netty</artifactId>
+			<version>3.10.8</version>
+		</dependency>
+		<dependency>
+			<groupId>org.mock-server</groupId>
+			<artifactId>mockserver-client-java</artifactId>
+			<version>3.10.8</version>
+		</dependency>
+		<dependency>
+			<groupId>org.projectlombok</groupId>
+			<artifactId>lombok</artifactId>
+			<version>${lombok.version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.canehealth.ckblib</groupId>
+			<artifactId>library</artifactId>
+			<version>${project.version}</version>
+			<scope>provided</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+        <plugins>
+            <!-- javadocs -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-site-plugin</artifactId>
+                <version>3.9.1</version>
+            </plugin>
+        </plugins>
+	</build>
+</project>
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
new file mode 100644
index 0000000..85ea78a
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
@@ -0,0 +1,22 @@
+package com.canehealth.ckblib.umls.model;
+
+import lombok.Data;
+
+@Data
+public class AtomLite {
+	private String ui;
+	private String name;
+	private String termType;
+	private String language;
+	private boolean suppressible;
+	private boolean obsolete;
+	private String rootSource;
+	private String concept;
+	private String code;
+	private String sourceConcept;
+	private String sourceDescriptor;
+	private String parents;
+	private String children;
+	private String ancestors;
+	private String descendants;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
new file mode 100644
index 0000000..db783b1
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
@@ -0,0 +1,18 @@
+package com.canehealth.ckblib.umls.model;
+
+import java.util.HashMap;
+import java.util.List;
+
+import lombok.Data;
+
+@Data
+public class ConceptLite {
+    private String ui;
+    private String name;
+    private List<HashMap<String, Object>> semanticTypes;
+    private int atomCount;
+    private String atoms;
+    private String relations;
+    private String definitions;
+    private String defaultPreferredAtom;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchResult.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchResult.java
new file mode 100644
index 0000000..2b5dbaa
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchResult.java
@@ -0,0 +1,11 @@
+package com.canehealth.ckblib.umls.model;
+
+import lombok.Data;
+
+@Data
+public class SearchResult {
+    private String ui;
+    private String name;
+    private String uri;
+    private String rootSource;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
new file mode 100644
index 0000000..15d1b94
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
@@ -0,0 +1,29 @@
+package com.canehealth.ckblib.umls.model;
+
+import java.util.HashMap;
+import java.util.List;
+
+import lombok.Data;
+
+@Data
+public class SourceAtomClusterLite {
+    private String ui;
+    private String name;
+    private boolean obsolete;
+    private boolean suppressible;
+    private String rootSource;
+    private int cVMemberCount;
+    private int atomCount;
+    private String concepts;
+    private String atoms;
+    private String parents;
+    private String children;
+    private String descendants;
+    private String ancestors;
+    private String relations;
+    private String definitions;
+    private String attributes;
+    private String defaultPreferredAtom;
+    private List<HashMap<String, Object>> subsetMemberships;
+    private List<HashMap<String, Object>> contentViewMemberships;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep b/umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep b/umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep
new file mode 100644
index 0000000..e69de29

From 771ea2a64e9b41d503b1cc3c5d30eca9d672bb52 Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Thu, 3 Jun 2021 19:41:07 -0400
Subject: [PATCH 11/21] before test

---
 .../ckblib/library/util/CkblibConstants.java  |  3 ++
 .../ckblib/umls/model/PostModel.java          | 12 +++++
 .../umls/service/RestTicketService.java       | 53 +++++++++++++++++++
 3 files changed, 68 insertions(+)
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java

diff --git a/library/src/main/java/com/canehealth/ckblib/library/util/CkblibConstants.java b/library/src/main/java/com/canehealth/ckblib/library/util/CkblibConstants.java
index a75cf51..0ff6a13 100644
--- a/library/src/main/java/com/canehealth/ckblib/library/util/CkblibConstants.java
+++ b/library/src/main/java/com/canehealth/ckblib/library/util/CkblibConstants.java
@@ -11,4 +11,7 @@ public class CkblibConstants {
    public static final String ESEARCH_URL = ESEARCH_BASE + "esearch.fcgi";
    public static final String EFETCH_URL = ESEARCH_BASE + "efetch.fcgi";
 
+   public static final String UMLS_SERVICE_URL = "http://umlsks.nlm.nih.gov";
+   public static final String UMLS_AUTH_URL = "https://utslogin.nlm.nih.gov";
+
 }
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java
new file mode 100644
index 0000000..068a7ce
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java
@@ -0,0 +1,12 @@
+package com.canehealth.ckblib.umls.model;
+
+import org.springframework.stereotype.Component;
+
+import lombok.Data;
+
+@Data
+@Component
+public class PostModel {
+    private String apikey;
+    private String service = "http%3A%2F%2Fumlsks.nlm.nih.gov";
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
new file mode 100644
index 0000000..bcd30de
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
@@ -0,0 +1,53 @@
+package com.canehealth.ckblib.umls.service;
+
+import java.sql.Timestamp;
+import java.util.Date;
+import com.canehealth.ckblib.library.util.CkblibConstants;
+import com.canehealth.ckblib.umls.model.PostModel;
+import org.apache.commons.lang3.StringUtils;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.web.reactive.function.client.WebClient;
+
+import reactor.core.publisher.Mono;
+
+public class RestTicketService {
+    private String tgt = null;
+    private String st;
+    private PostModel postModel = new PostModel();
+    Timestamp timestamp;
+    private WebClient umlsServiceClient;
+    private WebClient umlsAuthClient;
+
+    public RestTicketService(String apikey){
+        this.postModel.setApikey(apikey);
+        this.umlsAuthClient = WebClient.create(CkblibConstants.UMLS_AUTH_URL);
+        this.umlsServiceClient = WebClient.create(CkblibConstants.UMLS_SERVICE_URL);
+    }
+
+    public Mono<String> getTgt() {
+        Mono<String> _tgt = this.umlsAuthClient.post().uri("/cas/v1/tickets")
+                .body(Mono.just(this.postModel), PostModel.class)
+                .retrieve()
+                .bodyToMono(String.class);
+
+        _tgt.subscribe(response -> processTgT(response));
+        return _tgt;
+    }
+
+    private void processTgT(String response){
+        this.tgt = StringUtils.substringBetween(response, "<form action=\"", "\" method=\"POST\">");
+        Date date = new Date();
+        this.timestamp = new Timestamp(date.getTime());
+    }
+
+    private int getElapsedTime(){
+        Date date = new Date();
+        Timestamp _now = new Timestamp(date.getTime());
+        long milliseconds = _now.getTime() - this.timestamp.getTime();
+        int seconds = (int) milliseconds / 1000;
+        int hours = seconds / 3600;
+        return hours;
+    }
+
+}

From 8935e5330c3489270832f5da3a1b689eb4980284 Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Thu, 3 Jun 2021 20:47:27 -0400
Subject: [PATCH 12/21] devcontainer in progress

---
 .devcontainer/Dockerfile        | 25 +++++++++++++++++++++
 .devcontainer/devcontainer.json | 40 +++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000..c67015b
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,25 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.137.0/containers/java/.devcontainer/base.Dockerfile
+ARG VARIANT="13"
+FROM mcr.microsoft.com/vscode/devcontainers/java:0-${VARIANT}
+
+# [Optional] Install Maven or Gradle
+ARG INSTALL_MAVEN="true"
+ARG MAVEN_VERSION=3.6.3
+ARG INSTALL_GRADLE="false"
+ARG GRADLE_VERSION=5.4.1
+RUN if [ "${INSTALL_MAVEN}" = "true" ]; then su vscode -c "source /usr/local/sdkman/bin/sdkman-init.sh && sdk install maven \"${MAVEN_VERSION}\""; fi \
+    && if [ "${INSTALL_GRADLE}" = "true" ]; then su vscode -c "source /usr/local/sdkman/bin/sdkman-init.sh && sdk install gradle \"${GRADLE_VERSION}\""; fi
+
+# [Optional] Install a version of Node.js using nvm for front end dev
+# ARG INSTALL_NODE="true"
+# ARG NODE_VERSION="lts/*"
+# RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "source /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# RUN mkdir /workspaces
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1
\ No newline at end of file
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..66d1a9d
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,40 @@
+{
+    "name": "ckblib",
+    "build": {
+        "dockerfile": "Dockerfile",
+    },
+    "containerEnv": {
+        "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
+        "GITHUB_USER": "${localEnv:GITHUB_USER}"
+    },
+    // Comment out the next line to run as root instead. Linux users,
+    // update Dockerfile with your user's UID/GID if not 1000.
+    // "runArgs": ["-u", "vscode"],
+    // In the container
+    // git clone into /workspaces by git clone https://github.com/dermatologist/dermml.git
+    // Increase password cache git config --global credential.helper 'cache --timeout=50600'
+    // "workspaceFolder": "/workspaces/dermml",
+    // "workspaceMount": "src=dermml,dst=/workspaces/dermml,type=volume,volume-driver=local",
+    // https://stackoverflow.com/questions/38520638/how-to-set-spring-profile-from-system-variable
+    // "runArgs": [ "-e", "SPRING_PROFILES_ACTIVE=dev"],
+    // Use 'settings' to set *default* container specific settings.json values on container create.
+    // You can edit these settings after create using File > Preferences > Settings > Remote.
+    "settings": {
+        "terminal.integrated.shell.linux": "/bin/bash"
+    },
+    // Uncomment the next line if you want to publish any ports.
+    // "appPort": [],
+    //"appPort": "8093:8080",
+    // Uncomment the next line to run commands after the container is created.
+    // "postCreateCommand": "java -version",
+    "shutdownAction": "none", // or stopContainer
+    "extensions": [
+        "vscjava.vscode-java-pack",
+        "redhat.vscode-xml",
+        "eamodio.gitlens",
+        "mhutchie.git-graph",
+        "humao.rest-client",
+        "Trinity.trinity",
+        "tht13.html-preview-vscode"
+    ]
+}
\ No newline at end of file

From 9e499652db1494d20150aa684489d284a2eb6439 Mon Sep 17 00:00:00 2001
From: beapen <github@gulfdoctor.net>
Date: Thu, 3 Jun 2021 20:51:49 -0400
Subject: [PATCH 13/21] update java version

---
 .devcontainer/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index c67015b..2d4c326 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,5 +1,6 @@
 # See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.137.0/containers/java/.devcontainer/base.Dockerfile
-ARG VARIANT="13"
+# 13 is not available
+ARG VARIANT="14"
 FROM mcr.microsoft.com/vscode/devcontainers/java:0-${VARIANT}
 
 # [Optional] Install Maven or Gradle

From 05408990244d83ff33712b88fc27cbbe39fc2650 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 02:04:51 +0000
Subject: [PATCH 14/21] feat: tgt in progress

---
 .../ckblib/umls/model/PostModel.java          | 12 -----------
 .../umls/service/RestTicketService.java       | 20 +++++++++++--------
 2 files changed, 12 insertions(+), 20 deletions(-)
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java

diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java
deleted file mode 100644
index 068a7ce..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/PostModel.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import org.springframework.stereotype.Component;
-
-import lombok.Data;
-
-@Data
-@Component
-public class PostModel {
-    private String apikey;
-    private String service = "http%3A%2F%2Fumlsks.nlm.nih.gov";
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
index bcd30de..e0da66a 100644
--- a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
@@ -3,10 +3,10 @@
 import java.sql.Timestamp;
 import java.util.Date;
 import com.canehealth.ckblib.library.util.CkblibConstants;
-import com.canehealth.ckblib.umls.model.PostModel;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
+import org.springframework.web.reactive.function.BodyInserters;
 import org.springframework.web.reactive.function.client.WebClient;
 
 import reactor.core.publisher.Mono;
@@ -14,20 +14,20 @@
 public class RestTicketService {
     private String tgt = null;
     private String st;
-    private PostModel postModel = new PostModel();
+    private String apikey;
+    private String service = "http%3A%2F%2Fumlsks.nlm.nih.gov";
     Timestamp timestamp;
-    private WebClient umlsServiceClient;
     private WebClient umlsAuthClient;
 
     public RestTicketService(String apikey){
-        this.postModel.setApikey(apikey);
-        this.umlsAuthClient = WebClient.create(CkblibConstants.UMLS_AUTH_URL);
-        this.umlsServiceClient = WebClient.create(CkblibConstants.UMLS_SERVICE_URL);
+        this.apikey = apikey;
     }
 
-    public Mono<String> getTgt() {
+    public Mono<String> getTgtAsync() {
+        this.umlsAuthClient = WebClient.create(CkblibConstants.UMLS_AUTH_URL);
         Mono<String> _tgt = this.umlsAuthClient.post().uri("/cas/v1/tickets")
-                .body(Mono.just(this.postModel), PostModel.class)
+                .header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE)
+                .body(BodyInserters.fromFormData("apikey", this.apikey))
                 .retrieve()
                 .bodyToMono(String.class);
 
@@ -50,4 +50,8 @@ private int getElapsedTime(){
         return hours;
     }
 
+    public String getTgt(){
+        return this.tgt;
+    }
+
 }

From 3fd6de99a70fcdc87583625cdbaceadfc00cd1ff Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 12:27:43 +0000
Subject: [PATCH 15/21] docs: add webclient notes

---
 notes/umls.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 notes/umls.md

diff --git a/notes/umls.md b/notes/umls.md
new file mode 100644
index 0000000..2a1d099
--- /dev/null
+++ b/notes/umls.md
@@ -0,0 +1,20 @@
+
+* https://stackoverflow.com/questions/59792224/how-to-post-request-with-spring-boot-web-client-for-form-data-for-content-type-a
+```
+webClient client = WebClient.builder()
+        .baseUrl("SOME-BASE-URL")
+        .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE)
+        .build();
+
+return client.post()
+        .uri("SOME-URI)
+        .body(BodyInserters.fromFormData("username", "SOME-USERNAME")
+                .with("password", "SONE-PASSWORD"))
+                .retrieve()
+                .bodyToFlux(SomeClass.class)
+                .onErrorMap(e -> new MyException("messahe",e))
+        .blockLast();
+```
+
+* https://howtodoinjava.com/spring-webflux/webclient-get-post-example/
+* https://www.baeldung.com/spring-5-webclient
\ No newline at end of file

From c6ce554f908dd1eff57708fb26df9a7070dd4cf6 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 15:09:36 +0000
Subject: [PATCH 16/21] Before removing unnecessary models

---
 notes/umls.md                                 | 13 ++++-
 .../umls/model/ContentViewMemberships.java    | 12 +++++
 .../ckblib/umls/model/ResultRoot.java         | 51 +++++++++++++++++++
 .../ckblib/umls/model/SearchRoot.java         | 14 +++++
 .../ckblib/umls/model/SingletonRoot.java      | 15 ++++++
 .../ckblib/umls/model/SubsetMemberships.java  | 12 +++++
 .../umls/service/RestTicketService.java       | 33 +++++++++---
 .../umls/service/RestTicketServiceTest.java   | 49 ++++++++++++++++++
 8 files changed, 190 insertions(+), 9 deletions(-)
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SearchRoot.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SingletonRoot.java
 create mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
 create mode 100644 umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java

diff --git a/notes/umls.md b/notes/umls.md
index 2a1d099..e7ccb7f 100644
--- a/notes/umls.md
+++ b/notes/umls.md
@@ -17,4 +17,15 @@ return client.post()
 ```
 
 * https://howtodoinjava.com/spring-webflux/webclient-get-post-example/
-* https://www.baeldung.com/spring-5-webclient
\ No newline at end of file
+* https://www.baeldung.com/spring-5-webclient
+
+* https://documentation.uts.nlm.nih.gov/rest/home.html
+
+* https://www.baeldung.com/webflux-webclient-parameters
+```
+this.webClient.get()
+  .uri(uriBuilder - > uriBuilder
+    .path("/products/{id}/attributes/{attributeId}")
+    .build(2, 13))
+  .retrieve();
+```
\ No newline at end of file
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
new file mode 100644
index 0000000..3f3fef6
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
@@ -0,0 +1,12 @@
+package com.canehealth.ckblib.umls.model;
+
+import lombok.Data;
+
+@Data
+public class ContentViewMemberships {
+    private String memberUri;
+
+    private String name;
+
+    private String uri;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
new file mode 100644
index 0000000..43f59ef
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
@@ -0,0 +1,51 @@
+package com.canehealth.ckblib.umls.model;
+
+import java.util.List;
+import lombok.Data;
+
+@Data
+public class ResultRoot {
+    private String classType;
+    private boolean sourceOriginated;
+    private String rootSource;
+    private String value;
+    private List<SearchResult> results;
+
+    private String ui;
+
+    private boolean suppressible;
+
+    private boolean obsolete;
+
+    private int atomCount;
+
+    private int cVMemberCount;
+
+    private String attributes;
+
+    private String atoms;
+
+    private String descendants;
+
+    private String ancestors;
+
+    private String parents;
+
+    private String children;
+
+    private String relations;
+
+    private String definitions;
+
+    private String concepts;
+
+    private String defaultPreferredAtom;
+
+    private List<SubsetMemberships> subsetMemberships;
+
+    private List<ContentViewMemberships> contentViewMemberships;
+
+    private String name;
+
+
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchRoot.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchRoot.java
new file mode 100644
index 0000000..f6a1c48
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/SearchRoot.java
@@ -0,0 +1,14 @@
+package com.canehealth.ckblib.umls.model;
+
+import lombok.Data;
+
+@Data
+public class SearchRoot {
+    private int pageSize;
+    private int pageNumber;
+    private int pageCount;
+    private ResultRoot result;
+}
+
+
+
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SingletonRoot.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SingletonRoot.java
new file mode 100644
index 0000000..4e55ba5
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/SingletonRoot.java
@@ -0,0 +1,15 @@
+package com.canehealth.ckblib.umls.model;
+
+import java.util.HashMap;
+import java.util.List;
+import lombok.Data;
+
+@Data
+public class SingletonRoot {
+    private int pageSize;
+    private int pageNumber;
+    private int pageCount;
+    private List<HashMap<String, Object>> result;
+}
+
+
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
new file mode 100644
index 0000000..8480b8b
--- /dev/null
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
@@ -0,0 +1,12 @@
+package com.canehealth.ckblib.umls.model;
+
+import lombok.Data;
+
+@Data
+public class SubsetMemberships {
+    private String memberUri;
+
+    private String name;
+
+    private String uri;
+}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
index e0da66a..39479ee 100644
--- a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
@@ -8,24 +8,22 @@
 import org.springframework.http.MediaType;
 import org.springframework.web.reactive.function.BodyInserters;
 import org.springframework.web.reactive.function.client.WebClient;
-
 import reactor.core.publisher.Mono;
 
 public class RestTicketService {
     private String tgt = null;
-    private String st;
     private String apikey;
-    private String service = "http%3A%2F%2Fumlsks.nlm.nih.gov";
+    private String service = "http://umlsks.nlm.nih.gov";
     Timestamp timestamp;
-    private WebClient umlsAuthClient;
 
     public RestTicketService(String apikey){
         this.apikey = apikey;
+        processTgT(getTgtAsync().block()); // Get a TGT on creation
     }
 
     public Mono<String> getTgtAsync() {
-        this.umlsAuthClient = WebClient.create(CkblibConstants.UMLS_AUTH_URL);
-        Mono<String> _tgt = this.umlsAuthClient.post().uri("/cas/v1/tickets")
+        WebClient client = WebClient.create(CkblibConstants.UMLS_AUTH_URL);
+        Mono<String> _tgt = client.post().uri("/cas/v1/tickets")
                 .header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE)
                 .body(BodyInserters.fromFormData("apikey", this.apikey))
                 .retrieve()
@@ -35,6 +33,25 @@ public Mono<String> getTgtAsync() {
         return _tgt;
     }
 
+    public Mono<String> getStAsync() {
+        if(this.getElapsedTime() > 6) // if token is older than 6 hours (valid till 8 hrs), get a new one
+            getTgtAsync();
+        WebClient client = WebClient.create(this.tgt);
+        Mono<String> _st = client.post()
+                .header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE)
+                .body(BodyInserters.fromFormData("service", this.service)).retrieve()
+                .bodyToMono(String.class);
+        return _st;
+    }
+
+    public WebClient webClient(){
+        WebClient client = WebClient.builder().baseUrl("https://uts-ws.nlm.nih.gov/rest")
+                .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
+                // .defaultUriVariables(Collections.singletonMap("ticket", getStAsync().block()))
+                .build();
+        return client;
+    }
+
     private void processTgT(String response){
         this.tgt = StringUtils.substringBetween(response, "<form action=\"", "\" method=\"POST\">");
         Date date = new Date();
@@ -50,8 +67,8 @@ private int getElapsedTime(){
         return hours;
     }
 
-    public String getTgt(){
-        return this.tgt;
+    public String getSt(){
+        return getStAsync().block();
     }
 
 }
diff --git a/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java b/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java
new file mode 100644
index 0000000..3d4d706
--- /dev/null
+++ b/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java
@@ -0,0 +1,49 @@
+package com.canehealth.ckblib.umls.service;
+
+import static org.junit.Assert.assertThrows;
+import static org.junit.Assert.assertTrue;
+import com.canehealth.ckblib.umls.model.SearchRoot;
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+import reactor.core.publisher.Mono;
+
+@SpringBootTest
+class RestTicketServiceTest {
+
+    @Test
+    void shouldRetrieveTgt() throws InterruptedException{
+
+        Exception exception = assertThrows(
+                org.springframework.web.reactive.function.client.WebClientResponseException.class, () -> {
+
+                    // * USAGE EXAMPLE with QueryParams
+                    RestTicketService restTicketService = new RestTicketService("YOURUMLSAPIKEY");
+                    Mono<SearchRoot> result = restTicketService.webClient().get()
+                            .uri(uriBuilder -> uriBuilder.path("/search/current")
+                                    .queryParam("ticket", restTicketService.getSt())
+                                    .queryParam("string", "diabetes")
+                                    .queryParam("searchType", "exact").build())
+                            .retrieve().bodyToMono(SearchRoot.class);
+                    /*
+                     * <-- WITH URL PARAMS --> this.webClient.get() .uri(uriBuilder - > uriBuilder
+                     * .path("/products/{id}/attributes/{attributeId}") .build(2, 13)) .retrieve();
+                     */
+                    System.out.println(result.block());
+        });
+        String expectedMessage = "401 Unauthorized from POST https://utslogin.nlm.nih.gov/cas/v1/tickets";
+        String actualMessage = exception.getMessage();
+        assertTrue(actualMessage.contains(expectedMessage));
+
+    }
+
+
+    @SpringBootApplication
+    @Configuration
+    @ComponentScan(basePackages = "com.canehealth.ckblib")
+    static class TestConfiguration {
+    }
+
+}
\ No newline at end of file

From ddc93819fa2b4ee628e521baa4454bdfe78d5c64 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 15:14:50 +0000
Subject: [PATCH 17/21] refactor: remove unwanted models

---
 .../ckblib/umls/model/AtomLite.java           | 22 --------------
 .../ckblib/umls/model/ConceptLite.java        | 18 ------------
 .../umls/model/ContentViewMemberships.java    | 12 --------
 .../ckblib/umls/model/ResultRoot.java         |  7 +++--
 .../umls/model/SourceAtomClusterLite.java     | 29 -------------------
 .../ckblib/umls/model/SubsetMemberships.java  | 12 --------
 .../canehealth/ckblib/umls/service/.gitkeep   |  0
 .../canehealth/ckblib/umls/service/.gitkeep   |  0
 8 files changed, 4 insertions(+), 96 deletions(-)
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
 delete mode 100644 umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep
 delete mode 100644 umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep

diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
deleted file mode 100644
index 85ea78a..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/AtomLite.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import lombok.Data;
-
-@Data
-public class AtomLite {
-	private String ui;
-	private String name;
-	private String termType;
-	private String language;
-	private boolean suppressible;
-	private boolean obsolete;
-	private String rootSource;
-	private String concept;
-	private String code;
-	private String sourceConcept;
-	private String sourceDescriptor;
-	private String parents;
-	private String children;
-	private String ancestors;
-	private String descendants;
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
deleted file mode 100644
index db783b1..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/ConceptLite.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import java.util.HashMap;
-import java.util.List;
-
-import lombok.Data;
-
-@Data
-public class ConceptLite {
-    private String ui;
-    private String name;
-    private List<HashMap<String, Object>> semanticTypes;
-    private int atomCount;
-    private String atoms;
-    private String relations;
-    private String definitions;
-    private String defaultPreferredAtom;
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
deleted file mode 100644
index 3f3fef6..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/ContentViewMemberships.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import lombok.Data;
-
-@Data
-public class ContentViewMemberships {
-    private String memberUri;
-
-    private String name;
-
-    private String uri;
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
index 43f59ef..9217acd 100644
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/model/ResultRoot.java
@@ -1,5 +1,6 @@
 package com.canehealth.ckblib.umls.model;
 
+import java.util.HashMap;
 import java.util.List;
 import lombok.Data;
 
@@ -41,9 +42,9 @@ public class ResultRoot {
 
     private String defaultPreferredAtom;
 
-    private List<SubsetMemberships> subsetMemberships;
-
-    private List<ContentViewMemberships> contentViewMemberships;
+    private List<HashMap<String, Object>> subsetMemberships;
+    
+    private List<HashMap<String, Object>> contentViewMemberships;
 
     private String name;
 
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
deleted file mode 100644
index 15d1b94..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/SourceAtomClusterLite.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import java.util.HashMap;
-import java.util.List;
-
-import lombok.Data;
-
-@Data
-public class SourceAtomClusterLite {
-    private String ui;
-    private String name;
-    private boolean obsolete;
-    private boolean suppressible;
-    private String rootSource;
-    private int cVMemberCount;
-    private int atomCount;
-    private String concepts;
-    private String atoms;
-    private String parents;
-    private String children;
-    private String descendants;
-    private String ancestors;
-    private String relations;
-    private String definitions;
-    private String attributes;
-    private String defaultPreferredAtom;
-    private List<HashMap<String, Object>> subsetMemberships;
-    private List<HashMap<String, Object>> contentViewMemberships;
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java b/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
deleted file mode 100644
index 8480b8b..0000000
--- a/umls/src/main/java/com/canehealth/ckblib/umls/model/SubsetMemberships.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package com.canehealth.ckblib.umls.model;
-
-import lombok.Data;
-
-@Data
-public class SubsetMemberships {
-    private String memberUri;
-
-    private String name;
-
-    private String uri;
-}
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep b/umls/src/main/java/com/canehealth/ckblib/umls/service/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep b/umls/src/test/java/com/canehealth/ckblib/umls/service/.gitkeep
deleted file mode 100644
index e69de29..0000000

From 1607e8f02a77dcff339329946e568b8f9b3cd85a Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 20:26:15 +0000
Subject: [PATCH 18/21] tests: cui test

---
 .../umls/service/RestTicketServiceTest.java   | 35 +++++++++++++++++--
 1 file changed, 33 insertions(+), 2 deletions(-)

diff --git a/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java b/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java
index 3d4d706..3f94887 100644
--- a/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java
+++ b/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java
@@ -3,6 +3,7 @@
 import static org.junit.Assert.assertThrows;
 import static org.junit.Assert.assertTrue;
 import com.canehealth.ckblib.umls.model.SearchRoot;
+import com.canehealth.ckblib.umls.model.SingletonRoot;
 import org.junit.jupiter.api.Test;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.test.context.SpringBootTest;
@@ -14,12 +15,16 @@
 class RestTicketServiceTest {
 
     @Test
-    void shouldRetrieveTgt() throws InterruptedException{
+    void shouldSearchAndReturnResults() throws InterruptedException{
 
         Exception exception = assertThrows(
                 org.springframework.web.reactive.function.client.WebClientResponseException.class, () -> {
 
-                    // * USAGE EXAMPLE with QueryParams
+                    /*
+                        USAGE EXAMPLE
+                        Constructor gets tgt refreshing token every 6 hours.
+                        So reuse the same object.
+                    */
                     RestTicketService restTicketService = new RestTicketService("YOURUMLSAPIKEY");
                     Mono<SearchRoot> result = restTicketService.webClient().get()
                             .uri(uriBuilder -> uriBuilder.path("/search/current")
@@ -39,6 +44,32 @@ void shouldRetrieveTgt() throws InterruptedException{
 
     }
 
+    @Test
+    void shouldRetrieveCui() throws InterruptedException {
+
+        Exception exception = assertThrows(
+                org.springframework.web.reactive.function.client.WebClientResponseException.class,
+                () -> {
+
+                    // * USAGE EXAMPLE with QueryParams
+                    RestTicketService restTicketService = new RestTicketService("YOURUMLSAPIKEY");
+                    Mono<SingletonRoot> result = restTicketService.webClient().get()
+                            .uri(uriBuilder -> uriBuilder.path("/content/current/CUI/{cui}/atoms")
+                                    .queryParam("ticket", restTicketService.getSt())
+                                    .queryParam("searchType", "exact").build("C0155502"))
+                            .retrieve().bodyToMono(SingletonRoot.class);
+                    /*
+                     * <-- WITH URL PARAMS --> this.webClient.get() .uri(uriBuilder - > uriBuilder
+                     * .path("/products/{id}/attributes/{attributeId}") .build(2, 13)) .retrieve();
+                     */
+                    System.out.println(result.block());
+                });
+        String expectedMessage =
+                "401 Unauthorized from POST https://utslogin.nlm.nih.gov/cas/v1/tickets";
+        String actualMessage = exception.getMessage();
+        assertTrue(actualMessage.contains(expectedMessage));
+
+    }
 
     @SpringBootApplication
     @Configuration

From 4584bf79de0a97643a920ce2a681dce436445847 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Fri, 4 Jun 2021 20:36:36 +0000
Subject: [PATCH 19/21] docs: Update README

---
 README.md | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index dfa9a7c..0060728 100644
--- a/README.md
+++ b/README.md
@@ -13,10 +13,11 @@
 
 ## About
 
-Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph™ (see above). ckblib consists of three modules:
+Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph™ (see above). ckblib consists of four modules:
 
 * The 'library' module wraps the NCBI's E-Utils API for published article abstracts.
 * The 'qtakes' module provides a programmable interface to [quick-ctakes](https://github.com/dermatologist/quick-ctakes) or the quarkus based apache ctakes, a fast clinical text annotation engine.
+* The 'umls' module is a wrapper for UMLS REST API managing the TGT and ST tokens using the reactive WebClient. See [RestTicketServiceTest.java](https://github.com/dermatologist/ckblib/blob/develop/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java) for example use.
 * Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.
 
 ## How to use
@@ -43,6 +44,12 @@ Providing clinical decision support requires some formal way of representing cli
   <artifactId>graph</artifactId>
   <version>${latest-version-from-releases-tab}</version>
 </dependency>
+
+<dependency>
+  <groupId>com.canehealth.ckblib</groupId>
+  <artifactId>umls</artifactId>
+  <version>${latest-version-from-releases-tab}</version>
+</dependency>
 ```
 * Read [javadoc](https://dermatologist.github.io/ckblib/index.html). Documentation is WIP.
 * Check the [application module](https://github.com/dermatologist/ckblib/blob/develop/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java) for an example end-to-end use.

From 1e5a26acbe8e8ec188562aada11b058fd4047109 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Sat, 5 Jun 2021 11:04:20 +0000
Subject: [PATCH 20/21] docs: Add javadoc and update README

---
 README.md                                     |  4 ++--
 .../umls/service/RestTicketService.java       | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 0060728..ebab98d 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
           \______  /____|__ \ |______  /          /_/
                  \/        \/        \/
 </pre>
-[![ckblib](https://forthebadge.com/images/badges/made-with-java.svg)](https://dermatologist.co.in)
+[![ckblib](https://forthebadge.com/images/badges/made-with-java.svg)](https://gulfdoctor.net)
 
 [![ckblib](https://github.com/dermatologist/ckblib/blob/develop/notes/dermml.jpg)](https://gulfdoctor.net)
 
@@ -17,7 +17,7 @@ Providing clinical decision support requires some formal way of representing cli
 
 * The 'library' module wraps the NCBI's E-Utils API for published article abstracts.
 * The 'qtakes' module provides a programmable interface to [quick-ctakes](https://github.com/dermatologist/quick-ctakes) or the quarkus based apache ctakes, a fast clinical text annotation engine.
-* The 'umls' module is a wrapper for UMLS REST API managing the TGT and ST tokens using the reactive WebClient. See [RestTicketServiceTest.java](https://github.com/dermatologist/ckblib/blob/develop/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java) for example use.
+* The 'umls' module is a wrapper for UMLS REST API managing the TGT and ST tokens using the reactive WebClient. See [RestTicketServiceTest.java](https://github.com/dermatologist/ckblib/blob/develop/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java) for example use. A list of available [UMLS REST APIs are here.](https://documentation.uts.nlm.nih.gov/rest/home.html)
 * Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.
 
 ## How to use
diff --git a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
index 39479ee..a3ad381 100644
--- a/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
+++ b/umls/src/main/java/com/canehealth/ckblib/umls/service/RestTicketService.java
@@ -1,3 +1,10 @@
+/**
+ * Copyright (c) 2021 Bell Eapen
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of
+ * the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
 package com.canehealth.ckblib.umls.service;
 
 import java.sql.Timestamp;
@@ -16,6 +23,10 @@ public class RestTicketService {
     private String service = "http://umlsks.nlm.nih.gov";
     Timestamp timestamp;
 
+    /** Constructor sets the TGT token
+     * @since 0.16.0
+     * @param apikey
+     */
     public RestTicketService(String apikey){
         this.apikey = apikey;
         processTgT(getTgtAsync().block()); // Get a TGT on creation
@@ -44,6 +55,10 @@ public Mono<String> getStAsync() {
         return _st;
     }
 
+    /** Returns WebClient with the default baseUrl and headers
+     * @since 0.16.0
+     * @return client
+     */
     public WebClient webClient(){
         WebClient client = WebClient.builder().baseUrl("https://uts-ws.nlm.nih.gov/rest")
                 .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)
@@ -67,6 +82,10 @@ private int getElapsedTime(){
         return hours;
     }
 
+    /**
+     * @since 0.16.0
+     * @return St token
+     */
     public String getSt(){
         return getStAsync().block();
     }

From 2d8ee3cd66334884c0352433b58ec877b8b10427 Mon Sep 17 00:00:00 2001
From: Bell Eapen <github_public@gulfdoctor.net>
Date: Sat, 5 Jun 2021 11:28:08 +0000
Subject: [PATCH 21/21] update version to 0.16.0

---
 application/pom.xml | 2 +-
 graph/pom.xml       | 2 +-
 library/pom.xml     | 2 +-
 pom-deploy.xml      | 2 +-
 pom.xml             | 2 +-
 qtakes/pom.xml      | 2 +-
 umls/pom.xml        | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/application/pom.xml b/application/pom.xml
index e8b4294..5a3a597 100644
--- a/application/pom.xml
+++ b/application/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>ckblib-application</artifactId>
-	<version>0.15.0</version>
+	<version>0.16.0</version>
 	<name>ckblib-application</name>
 	<description>Demo project for Spring Boot</description>
 	<properties>
diff --git a/graph/pom.xml b/graph/pom.xml
index 4e1c0b6..d6ba5f2 100644
--- a/graph/pom.xml
+++ b/graph/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>graph</artifactId>
-	<version>0.15.0</version>
+	<version>0.16.0</version>
 	<name>ckblib-graph</name>
 	<description>Demo project for Spring Boot</description>
 
diff --git a/library/pom.xml b/library/pom.xml
index 5f889d0..112f76c 100644
--- a/library/pom.xml
+++ b/library/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>library</artifactId>
-	<version>0.15.0</version>
+	<version>0.16.0</version>
 	<name>ckblib-library</name>
 	<description>Demo project for Spring Boot</description>
 
diff --git a/pom-deploy.xml b/pom-deploy.xml
index 0ba6843..c8b3b13 100644
--- a/pom-deploy.xml
+++ b/pom-deploy.xml
@@ -4,7 +4,7 @@
 
     <groupId>com.canehealth.ckblib</groupId>
     <artifactId>cklib-core</artifactId>
-    <version>0.15.0</version>
+    <version>0.16.0</version>
     <packaging>pom</packaging>
 
     <modules>
diff --git a/pom.xml b/pom.xml
index b06cb89..a99e7b5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>com.canehealth.ckblib</groupId>
     <artifactId>cklib-core</artifactId>
-    <version>0.15.0</version>
+    <version>0.16.0</version>
     <packaging>pom</packaging>
 
     <modules>
diff --git a/qtakes/pom.xml b/qtakes/pom.xml
index 964f774..f3a4b78 100644
--- a/qtakes/pom.xml
+++ b/qtakes/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>qtakes</artifactId>
-	<version>0.15.0</version>
+	<version>0.16.0</version>
 	<name>ckblib-qtakes</name>
 	<description>Demo project for Spring Boot</description>
 
diff --git a/umls/pom.xml b/umls/pom.xml
index 91ce144..032fa76 100644
--- a/umls/pom.xml
+++ b/umls/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>umls</artifactId>
-	<version>0.15.0</version>
+	<version>0.16.0</version>
 	<name>ckblib-umls</name>
 	<description>Demo project for Spring Boot</description>