From f53ba968e10965ccf1ee777c6cac740ac523f696 Mon Sep 17 00:00:00 2001
From: Gregory Rushton <rushtong@users.noreply.github.com>
Date: Thu, 4 Apr 2024 14:17:09 -0400
Subject: [PATCH] [DUOS-2835][DUOS-2878][risk=no] Use the url dataset property
 instead of the dbGap version (#2278)

Co-authored-by: aarohinadkarni <68303030+aarohinadkarni@users.noreply.github.com>
---
 .../consent/http/service/DatasetService.java   |  3 ---
 src/main/resources/DataSetSample.tsv           |  2 --
 src/main/resources/changelog-master.xml        |  2 ++
 ...log-consent-2024-04-02-rm-old-dbgap-url.xml | 18 ++++++++++++++++++
 4 files changed, 20 insertions(+), 5 deletions(-)
 delete mode 100644 src/main/resources/DataSetSample.tsv
 create mode 100644 src/main/resources/changesets/changelog-consent-2024-04-02-rm-old-dbgap-url.xml

diff --git a/src/main/java/org/broadinstitute/consent/http/service/DatasetService.java b/src/main/java/org/broadinstitute/consent/http/service/DatasetService.java
index ac8cee8218..35db764c07 100644
--- a/src/main/java/org/broadinstitute/consent/http/service/DatasetService.java
+++ b/src/main/java/org/broadinstitute/consent/http/service/DatasetService.java
@@ -497,9 +497,6 @@ public Study convertDatasetToStudy(User user, Dataset dataset, StudyConversion s
       // Handle "URL"
       newPropConversion(dictionaries, dataset, "URL", "url", PropertyType.String,
           studyConversion.getUrl());
-      // Handle "dbGAP"
-      legacyPropConversion(dictionaries, dataset, "dbGAP", "url", PropertyType.String,
-          studyConversion.getUrl());
     }
 
     // Handle "Data Submitter User ID"
diff --git a/src/main/resources/DataSetSample.tsv b/src/main/resources/DataSetSample.tsv
deleted file mode 100644
index b50196782a..0000000000
--- a/src/main/resources/DataSetSample.tsv
+++ /dev/null
@@ -1,2 +0,0 @@
-Dataset Name	Data Type	Species	Phenotype/Indication	# of participants	Description	dbGAP	Data Depositor	Principal Investigator(PI)	Sample Collection ID	Consent ID
-(Bucienne Monco) - Muc-1 Kidney Disease	DNA, whole genome	human	muc-1, kidney disease	31	muc-1 patients that developed cancer , 5 weeks after treatment	http://....	John Doe	Mark Smith	SC-20658	1
\ No newline at end of file
diff --git a/src/main/resources/changelog-master.xml b/src/main/resources/changelog-master.xml
index 22d09c65f3..37a0dc86ec 100644
--- a/src/main/resources/changelog-master.xml
+++ b/src/main/resources/changelog-master.xml
@@ -146,4 +146,6 @@
     relativeToChangelogFile="true"/>
   <include file="changesets/changelog-consent-2024-04-01-rm-piname.xml"
     relativeToChangelogFile="true"/>
+  <include file="changesets/changelog-consent-2024-04-02-rm-old-dbgap-url.xml"
+    relativeToChangelogFile="true"/>
 </databaseChangeLog>
diff --git a/src/main/resources/changesets/changelog-consent-2024-04-02-rm-old-dbgap-url.xml b/src/main/resources/changesets/changelog-consent-2024-04-02-rm-old-dbgap-url.xml
new file mode 100644
index 0000000000..bd0d6d227c
--- /dev/null
+++ b/src/main/resources/changesets/changelog-consent-2024-04-02-rm-old-dbgap-url.xml
@@ -0,0 +1,18 @@
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
+  <changeSet id="changelog-consent-2024-03-28-dataset-dac-id-props.xml" author="grushton">
+    <sql>
+      -- Remove duplicate properties
+      DELETE
+      FROM dataset_property
+      WHERE property_key IN (SELECT key_id FROM dictionary d WHERE KEY = 'dbGAP')
+    </sql>
+    <sql>
+      -- Remove deprecated property key from dictionary
+      DELETE
+      FROM dictionary
+      WHERE key = 'dbGAP';
+    </sql>
+  </changeSet>
+</databaseChangeLog>